DETAILED CORRESPONDENCE
Status of the Application
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant’s submission filed on 02/17/2026 has been entered.
Claims 40 and 43-81 are pending in this application.
Applicant’s amendment to the claims filed 02/17/2026 is acknowledged. This listing of the claims replaces all prior versions and listings of the claims.
Applicant’s remarks filed on 02/17/2026 in response to the final rejection mailed on 11/24/2025 are acknowledged and have been fully considered.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Election
The elected subject matter is:
Invention II, corresponding to claims 51-53, 55-57, 59-60 and 76-81 drawn to the technical feature of a cell comprising a polynucleotide encoding a polypeptide with α-(1,3)-fucosyltransferase activity with the specified regions of conserved amino acid sequence, and
Species (A3), wherein the polypeptide is SEQ ID NO: 6,
elected in the response filed 12/18/2023.
New claims 76-78 and 80 are dependent from claim 51 and are considered drawn to the elected Invention II.
New claims 79 and 81 are drawn to a cell that produces α-fucosyllactose comprising a polynucleotide encoding a polypeptide consisting of SEQ ID NO: 6 and are therefore drawn to the elected Invention II.
Claims 40, 43-50, 54, 58 and 61-75 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 12/18/2023.
Claims 51-53, 55-57, 59-60 and 76-81 are being examined on the merits only to the extent the claims read on the elected subject matter as set forth above.
Information Disclosure Statement
The Information Disclosure Statement (IDS) submitted on 02/17/2026 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the IDS has been considered by the examiner.
Non-Patent Literature Document 6 on the IDS submitted 02/17/2026 has been lined through because there is no copy of a document that is a 144 page Response to Australian Patent Examination Report No. 1 for Australian Application No. 2019409833 dated June 18, 2025 in the application file.
Claim Rejections - 35 USC § 103
Claims 51-53, 55, 57, 59-60 and 76-81 are rejected under 35 U.S.C. 103 as being unpatentable over Heidtman et al. (WO 2016/040531; cited on the Form PTO-892 mailed 1/12/2024; herein referred to as Heidtman) in view of Whiteson (BMC Genomics, 2014, 15:169; cited on Form PTO-892 mailed 01/12/2024; herein referred to as Whiteson) and evidentiary reference NCBI GenPept Database Accession Number AIL2582 (08/27/2014, 2 pages; cited on the form PTO-892 mailed 01/12/2024; herein referred to as NCBI).
The instant rejection is maintained from the previous Office Action and any newly recited portions are necessitated by claim amendment.
Claim 51 (claims 52-53, 55, 57, 59-60, 76-78 and 80 dependent therefrom) is drawn to a cell that produces α-1,3-fucosyllactose, the cell comprising at least one polynucleotide encoding a polypeptide with α-1,3-fucosyltransferase activity and with the ability to use lactose as an acceptor substrate to produce α-1,3-fucosyllactose, wherein the polypeptide with α-1,3-fucosyltransferase activity and with the ability to use lactose as an acceptor substrate is exogenous to the cell, and wherein the polypeptide with α-1,3-fucosyltransferase activity and with the ability to use lactose as an acceptor substrate comprises:
i) an amino acid sequence comprising a conserved GDP-fucose binding domain with SEQ ID NO: 33,
ii) an amino acid sequence comprising SEQ ID NO: 34, and
iii) if ii) is SEQ ID NO: 36, then a conserved motif SEQ ID NO: 35 present at the N- terminal region of the polypeptide with a-1,3-fucosyltransferase activity and with the ability to use lactose as an acceptor substrate,
and wherein the C-terminus of the polypeptide with a-1,3-fucosyltransferase activity and with the ability to use lactose as an acceptor substrate has no more than 100 amino acids starting from the first amino acid of the GDP-fucose binding domain.
Claim 79 is drawn to a recombinant Escherichia coli K12 cell that produces a-1,3-fucosyllactose, wherein the cell comprises a chromosomally integrated polynucleotide encoding a polypeptide consisting of SEQ ID NO:6, and wherein the polypeptide comprises: (i) a conserved GDP-fucose binding domain corresponding to residues 233-237 of SEQ IDNO:6; and (ii) an amino acid sequence comprising SEQ ID NO:34; wherein the C-terminus of the polypeptide has no more than 100 amino acids from the first amino acid of the GDP-fucose binding domain.
Claim 81 is drawn to a recombinant Escherichia coli K12 cell that produces a-1,3-fucosyllactose, wherein the cell is transformed with a vector comprising a polynucleotide encoding a polypeptide consisting of SEQ ID NO:6, and wherein the polypeptide comprises: (i) a conserved GDP-fucose binding domain corresponding to residues 233-237 of SEQ IDNO:6; and (ii) an amino acid sequence comprising SEQ ID NO:34; wherein the C-terminus of the polypeptide has no more than 100 amino acids from the first amino acid of the GDP-fucose binding domain.
Regarding the limitation “the ability to use lactose as an acceptor substrate to produce a-1,3-fucosyllactose” in claim 51, the limitation is considered to be a functional limitation, wherein the limitation recites a feature of the claimed polypeptide “by what it does rather than by what it is”, and does not impose any structural limitations on the recited polypeptide according to MPEP 2173.05(g).
Heidtman teaches methods for producing purified fucosylated oligosaccharides in milk [para 3], involving the use of engineered bacteria with heterologously expressed enzymes in order to optimize production efficiency [para 6]. Heidtman discloses methods that include production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25].
Regarding claims 51-52, Heidtman teaches “methods for producing α-(1,3)-fucosylated oligosaccharides utilizing a bacterial strain harbouring an expression plasmid containing two different α-(1,3)-fucosyltransferases in ‘tandem’ arrangement. These tandem α-(1,3)-fucosyltransferases may be under the control of the PL promoter” [para 18], and that the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49]. Furthermore, Heidtman states “a preferred α-(1,3)-fucosyltransferase utilizes GDP-fucose as a donor, and lactose is the acceptor for that donor [para 98]. As such, Heidtman satisfies the limitations of claim 52, as well as the limitations of claim 51 regarding a cell that produces α-1,3-fucosyllactose, the cell comprising at least one polynucleotide encoding an exogenous polypeptide with α-1,3-fucosyltransferase activity and able to use lactose as an acceptor substrate to produce α-1,3-fucosyllactose.
Heidtman further discusses methods of identifying α-(1,3)-fucosyltransferases enzymes capable of synthesizing fucosylated oligosaccharides such as 3-FL [para 47] and fucosyltransferase enzymes capable of using lactose as an acceptor comprising performing a computational search to define a broad group of simple sequence homologs of any known, lactose-utilizing fucosyltransferase, searching that group for common sequence and/or structural motifs shared by members of that group, searching sequence databases for said common sequence and/or structural motifs to identify candidate sequences, and expressing candidate enzymes to test for lactose utilization [para 99].
Heidtman does not teach the limitations of claim 51 regarding the sequence of the polypeptide with α-1,3-fucosyltransferase activity and able to use lactose as an acceptor substrate as recited in i), ii), and iii).
Whiteson describes the genomic analysis of the bacteria Basilea psittacipulmonis [title], wherein the genome was deposited and the encoded polypeptides were annotated by NCBI, namely the polypeptide AIL32582.1. This polypeptide is identified as an α-(1,3)-fucosyltransferase domain-containing polypeptide as evidenced by NCBI. This polypeptide further contains a GDP-fucose binding domain of YITEK (residues 233-237) that corresponds to SEQ ID NO: 33 specified in i) of claim 51, as well as the sequence DLYLGF (residues 107-112) that corresponds to SEQ ID NO: 34 specified in ii) of claim 51. As the polypeptide of Whiteson is 329 amino acids in length, the starting amino acid of the GDP-fucose binding domain (residue 233) is less than 100 amino acids from the C-terminus of the polypeptide. Therefore, the polypeptide AIL32582.1 as evidenced by NCBI is considered to contain the “α-1,3-fucosyltransferase activity and the ability to use lactose as an acceptor substrate” as recited in claim 51, as the activity is considered to be inherent to the structure of the polypeptide (see MPEP 2112.01(I)).
It would have been prima facie obvious for one of ordinary skill in the art before the effective filing date of the claimed invention to combine Heidtman and Whiteson to modify the cell of Heidtman, by using the polynucleotide encoding the polypeptide of Whiteson, to arrive at the claimed invention. One of ordinary skill in the art would have recognized that both the polypeptide of Heidtman and the polypeptide encoded by the polynucleotide of Whiteson as evidenced by NCBI of Whiteson are α-(1,3)-fucosyltransferases, and as such both are capable of being incorporated into a cell as described by Heidtman. It would have been obvious to one of ordinary skill in the art to replace the enzyme of Heidtman with the enzyme of Whiteson, as one of ordinary skill in the art would have been able to carry out such a substitution with a reasonable expectation of success because Heidtman discusses the engineering of bacteria with heterologously expressed enzymes in order to optimize production efficiency of human milk oligosaccharides such as α-(1,3)-fucosyllactose, because Heidtman discloses a method to screen sequence databases for novel enzymes capable of carrying out target fucosyltransferase activity, and because both Whiteson and Heidtman discuss cells that contain polynucleotides which encode polypeptides with α-(1,3)-fucosyltransferase activity.
Regarding claim 53 and the elected species of SEQ ID NO: 6, the polypeptide AIL32582.1 of Whiteson is 100% identical to SEQ ID NO: 6 as evidenced by the attached sequence search results [see Appendix A].
Regarding claim 55, Heidtman teaches methods that include production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25].
Regarding claim 57, Heidtman teaches synthetic genes of α-(1-3)-fucosyltransferase genes are designed using standard methods known in the art, and include sequences that are codon-optimized for expression in a host bacterial strain [para 117].
Regarding claim 59, Heidtman teaches methods that include production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1-3)-fucosyltransferase gene” [para 25], and Whiteson teaches the polypeptide AIL32582.1 that contains the GDP-fucose binding domain specified by SEQ ID NO: 33, the amino acid sequence specified by SEQ ID NO: 34, and less than 100 amino acids between the beginning of the GDP-fucose binding domain and the C-terminus of the peptide as discussed above.
Regarding claim 60, Whiteson teaches the polypeptide AIL32582.1 that is 100% identical to SEQ ID NO: 6 as evidenced by the attached sequence search results [see Appendix A] as discussed above.
Regarding claim 76, the combined cell of Heidtman and Whiteson as described above produces the polypeptide of Whiteson which is 100% identical to SEQ ID NO: 6 as discussed above [see Appendix A].
Regarding claim 77, Heidtman teaches the nucleic acid can be integrated into the genome of the host cell [para 23].
Regarding claim 78, the combined cell of Heidtman and Whiteson as described above produces the polypeptide of Whiteson which is 100% identical to SEQ ID NO: 6 as discussed above [see Appendix A], and therefore it is considered to have a conserved GDP-fucose binding domain corresponding to residues 233-237 of SEQ ID NO: 6.
Regarding claim 79, Heidtman teaches “methods for producing α-(1,3)-fucosylated oligosaccharides utilizing a bacterial strain harbouring an expression plasmid containing two different α-(1,3)-fucosyltransferases in ‘tandem’ arrangement. These tandem α-(1,3)-fucosyltransferases may be under the control of the PL promoter” [para 18], and that the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49], and that the nucleic acid can be integrated into the genome of the host cell [para 23]. Heidtman further teaches the method includes production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25], wherein the E. coli is typically Escherichia coli K12 [para 27]. Furthermore, Heidtman states “a preferred α-(1,3)-fucosyltransferase utilizes GDP-fucose as a donor, and lactose is the acceptor for that donor [para 98]. As such, Heidtman satisfies the limitations of claim 52, as well as the limitations of claim 51 regarding a cell that produces α-1,3-fucosyllactose, the cell comprising at least one polynucleotide encoding an exogenous polypeptide with α-1,3-fucosyltransferase activity and able to use lactose as an acceptor substrate to produce α-1,3-fucosyllactose. Heidtman further discusses methods of identifying α-(1,3)-fucosyltransferases enzymes capable of synthesizing fucosylated oligosaccharides such as 3-FL [para 47] and fucosyltransferase enzymes capable of using lactose as an acceptor comprising performing a computational search to define a broad group of simple sequence homologs of any known, lactose-utilizing fucosyltransferase, searching that group for common sequence and/or structural motifs shared by members of that group, searching sequence databases for said common sequence and/or structural motifs to identify candidate sequences, and expressing candidate enzymes to test for lactose utilization [para 99].
Regarding claim 79, Whiteson describes the genomic analysis of the bacteria Basilea psittacipulmonis [title], wherein the genome was deposited and the encoded polypeptides were annotated by NCBI, namely the polypeptide AIL32582.1. This polypeptide is identified as an α-(1,3)-fucosyltransferase domain-containing polypeptide as evidenced by NCBI. This polypeptide further contains a GDP-fucose binding domain of YITEK (residues 233-237) that corresponds to SEQ ID NO: 33 specified in i) of claim 51, as well as the sequence DLYLGF (residues 107-112) that corresponds to SEQ ID NO: 34 specified in ii) of claim 51. As the polypeptide of Whiteson is 329 amino acids in length, the starting amino acid of the GDP-fucose binding domain (residue 233) is less than 100 amino acids from the C-terminus of the polypeptide. Therefore, the polypeptide AIL32582.1 as evidenced by NCBI is considered to contain the “α-1,3-fucosyltransferase activity and the ability to use lactose as an acceptor substrate” as recited in claim 51, as the activity is considered to be inherent to the structure of the polypeptide (see MPEP 2112.01(I)). As the polypeptide of Whiteson shares 100% identity with SEQ ID NO: 6, it is considered to have the GDP-fucose binding domain corresponding to residues 233-237 of SEQ ID NO: 6.
It would have been prima facie obvious for one of ordinary skill in the art before the effective filing date of the claimed invention to combine Heidtman and Whiteson to modify the cell of Heidtman, by using the polynucleotide encoding the polypeptide of Whiteson, to arrive at the claimed invention. One of ordinary skill in the art would have recognized that both the polypeptide of Heidtman and the polypeptide encoded by the polynucleotide of Whiteson as evidenced by NCBI of Whiteson are α-(1,3)-fucosyltransferases, and as such both are capable of being incorporated into a cell as described by Heidtman. It would have been obvious to one of ordinary skill in the art to replace the enzyme of Heidtman with the enzyme of Whiteson, as one of ordinary skill in the art would have been able to carry out such a substitution with a reasonable expectation of success because Heidtman discusses the engineering of bacteria with heterologously expressed enzymes in order to optimize production efficiency of human milk oligosaccharides such as α-(1,3)-fucosyllactose, because Heidtman discloses a method to screen sequence databases for novel enzymes capable of carrying out target fucosyltransferase activity, and because both Whiteson and Heidtman discuss cells that contain polynucleotides which encode polypeptides with α-(1,3)-fucosyltransferase activity.
Regarding claim 80 (dependent from claim 51), Heidtman teaches the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49] as discussed in the rejection of claim 51 above, and the recombinant DNA constructs are supplied on a plasmid expression vector [para 36].
Regarding claim 81, Heidtman teaches “methods for producing α-(1,3)-fucosylated oligosaccharides utilizing a bacterial strain harbouring an expression plasmid containing two different α-(1,3)-fucosyltransferases in ‘tandem’ arrangement. These tandem α-(1,3)-fucosyltransferases may be under the control of the PL promoter” [para 18], and that the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49], and that the recombinant DNA constructs are supplied on a plasmid expression vector [para 36]. Heidtman further teaches the method includes production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25], wherein the E. coli is typically Escherichia coli K12 [para 27]. Furthermore, Heidtman states “a preferred α-(1,3)-fucosyltransferase utilizes GDP-fucose as a donor, and lactose is the acceptor for that donor [para 98]. As such, Heidtman satisfies the limitations of claim 52, as well as the limitations of claim 51 regarding a cell that produces α-1,3-fucosyllactose, the cell comprising at least one polynucleotide encoding an exogenous polypeptide with α-1,3-fucosyltransferase activity and able to use lactose as an acceptor substrate to produce α-1,3-fucosyllactose. Heidtman further discusses methods of identifying α-(1,3)-fucosyltransferases enzymes capable of synthesizing fucosylated oligosaccharides such as 3-FL [para 47] and fucosyltransferase enzymes capable of using lactose as an acceptor comprising performing a computational search to define a broad group of simple sequence homologs of any known, lactose-utilizing fucosyltransferase, searching that group for common sequence and/or structural motifs shared by members of that group, searching sequence databases for said common sequence and/or structural motifs to identify candidate sequences, and expressing candidate enzymes to test for lactose utilization [para 99].
Regarding claim 81, Whiteson describes the genomic analysis of the bacteria Basilea psittacipulmonis [title], wherein the genome was deposited and the encoded polypeptides were annotated by NCBI, namely the polypeptide AIL32582.1. This polypeptide is identified as an α-(1,3)-fucosyltransferase domain-containing polypeptide as evidenced by NCBI. This polypeptide further contains a GDP-fucose binding domain of YITEK (residues 233-237) that corresponds to SEQ ID NO: 33 specified in i) of claim 51, as well as the sequence DLYLGF (residues 107-112) that corresponds to SEQ ID NO: 34 specified in ii) of claim 51. As the polypeptide of Whiteson is 329 amino acids in length, the starting amino acid of the GDP-fucose binding domain (residue 233) is less than 100 amino acids from the C-terminus of the polypeptide. Therefore, the polypeptide AIL32582.1 as evidenced by NCBI is considered to contain the “α-1,3-fucosyltransferase activity and the ability to use lactose as an acceptor substrate” as recited in claim 51, as the activity is considered to be inherent to the structure of the polypeptide (see MPEP 2112.01(I)). As the polypeptide of Whiteson shares 100% identity with SEQ ID NO: 6, it is considered to have the GDP-fucose binding domain corresponding to residues 233-237 of SEQ ID NO: 6.
It would have been prima facie obvious for one of ordinary skill in the art before the effective filing date of the claimed invention to combine Heidtman and Whiteson to modify the cell of Heidtman, by using the polynucleotide encoding the polypeptide of Whiteson, to arrive at the claimed invention. One of ordinary skill in the art would have recognized that both the polypeptide of Heidtman and the polypeptide encoded by the polynucleotide of Whiteson as evidenced by NCBI of Whiteson are α-(1,3)-fucosyltransferases, and as such both are capable of being incorporated into a cell as described by Heidtman. It would have been obvious to one of ordinary skill in the art to replace the enzyme of Heidtman with the enzyme of Whiteson, as one of ordinary skill in the art would have been able to carry out such a substitution with a reasonable expectation of success because Heidtman discusses the engineering of bacteria with heterologously expressed enzymes in order to optimize production efficiency of human milk oligosaccharides such as α-(1,3)-fucosyllactose, because Heidtman discloses a method to screen sequence databases for novel enzymes capable of carrying out target fucosyltransferase activity, and because both Whiteson and Heidtman discuss cells that contain polynucleotides which encode polypeptides with α-(1,3)-fucosyltransferase activity.
Therefore, the invention of claims 51-53, 55, 57, 59-60 and 76-81 would have been obvious to one of skill in the art before the effective filing date.
Claim 56 is rejected under 35 U.S.C. 103 as being unpatentable over Heidtman and Whiteson and evidentiary reference NCBI as applied to claims 51-53, 55, 57, 59-60 and 76-81 above, and further in view of Ahmad et al. (Appl Microbiol Technol, 2014, 98:5301-5317; cited on the Form PTO-892 mailed 1/12/2024; herein referred to as Ahmad).
The instant rejection is maintained from the previous Office Action and any newly recited portions are necessitated by claim amendment.
Claim 56 is drawn to the cell of claim 51, wherein the cell is a yeast cell.
The teachings of Heidtman and Whiteson and evidentiary reference NCBI as applied to claims 51-53, 55, 57, 59-60 and 76-81 are discussed above. These references do not teach that the cell is a yeast cell.
Ahmad reviews protein expression in the yeast Pichia pastoris [title], wherein it is taught that “P. pastoris is an established protein expression host for the production of biopharmaceuticals and industrial enzymes” [abstract].
Regarding claim 56, Ahmad teaches “this methyltrophic yeast is a distinguished production system for its growth to very high cell densities, for the available strong and tightly regulated promoters, and for the options to produce gram amounts of recombinant protein per litre of culture broth both intracellularly and in secretory fashion” [abstract].
In view of Ahmad, it would have been prima facie obvious for one of ordinary skill in the art before the effective filing date of the claimed invention to modify the combined cell of Heidtman and Whiteson by using a Pichia pastoris cell, as taught by Ahmad, to arrive at the claimed invention. One of ordinary skill in the art would have been motivated to modify the combined cell of Heidtman and Whiteson by using the yeast cell of Ahmad, because Ahmad teaches that P. pastoris is an established protein expression host for the production of biopharmaceuticals and industrial enzymes. One of ordinary skill in the art would have had a reasonable expectation of success because Heidtman discloses a cellular system for the production of α-(1,3)-fucosyllactose that is considered a biopharmaceutical, and Ahmad discusses cellular systems for the production of biopharmaceuticals.
Therefore, the invention of claim 56 would have been obvious to one of skill in the art before the effective filing date.
Response to Remarks: Beginning on page 11 of Applicant’s response to rejections under 35 USC 103; Applicant in summary contends the Examiner misused the Functional Limitation Doctrine of MPEP 2173.05(g) the express structural and positional limitations of the claim were disregarded; Applicant further contends one of ordinary skill in the art would not select a particular peptide for substitution into the cell of Heidtman as opposed to selecting other peptides; Applicant further contends there is no structural criterion that would make it obvious to substitute the polypeptide of Whiteson into the cell of Heidtman rather than other polypeptides; Applicant further contends there is no rationale that would make the combination of Heidtman and Whiteson obvious to try; Applicant further contends that establishing a substitution could be made does not satisfy the requirement to explain why the specific modification would have been made according to MPEP 2143; Applicant further contends the substitution is not obvious as Heidtman does not explicitly state to use the particular polypeptide of Whiteson, and that the polypeptide of Whiteson was not known to possess lactose-acceptor activity at the time of invention; Applicant further contends the substitution would not have yielded a predictable result because Heidtman teaches the experimental validation for lactose-utilizing activity; Applicant further contends the Examiner improperly used inherency to supply motivation and expectation of success, as inherency does not provide a motivation to justify selection of a particular protein; Applicant further contends Heidtman teaches away from routine substitution and toward screening and testing, which does not amount to routine interchangeability of annotated enzymes; Applicant further contends newly added claims illustrate the absence of a reasoned selection rationale.
Applicants remarks are considered and found not convincing.
Regarding the assertion that the functional limitation doctrine was misused: the rejection above addresses each limitation recited in the claims, including the structural limitations. The limitation of “the ability to use lactose as an acceptor substrate to produce a-1,3-fucosyllactose” is a functional limitation, and contrary to Applicants remarks does not structurally limit the claimed polypeptide, but instead limits its function. As such, no structural limitations are disregarded.
Regarding the assertion that one of ordinary skill in the art would not select a particular peptide for substitution into the cell of Heidtman as opposed to selecting other peptides, and that there is no structural criterion to make the substitution obvious:
Heidtman teaches a cell which can produce α-(1,3)-fucosylated oligosaccharides by the activity of α-(1,3)-fucosyltransferases. Heidtman states that it is preferred for the α-(1,3)-fucosyltransferase to have the ability to use lactose as the acceptor. Heidtman further teaches how to screen for enzymes that generate fucosylated oligosaccharides and confirm that they use lactose as an acceptor, which includes replacing the enzyme of the cell with candidates identified from broad groups of simple sequence homologs. Whiteson teaches a polypeptide that is annotated as α-(1,3)-fucosyltransferase. It would have been obvious to replace the enzyme of Heidtman with the enzyme of Whiteson, because one of ordinary skill in the art would have recognized both enzymes are annotated as α-(1,3)-fucosyltransferases, and as such both are capable of being incorporated into the cell of Heidtman. One of ordinary skill in the art would have had a reasonable expectation of success that the substitution would have resulted in a cell capable of producing α-(1,3)-fucosylated oligosaccharides, because Heidtman and White both describe α-(1,3)-fucosyltransferase enzymes, and Heidtman teaches to identify annotated enzymes and use them. Put another way, there does not need to be an express teaching of selecting the particular polypeptide of Whiteson, the fact that the polypeptide of Whiteson was known in the art before the effective filing date and would have been a recognized as an annotated α-(1,3)-fucosyltransferase such as what Heidtman suggests using would have made this substitution obvious.
Regarding the assertion that there is no rationale that would make the combination of Heidtman and Whiteson obvious to try, the rejection does not rely on this rationale for obviousness.
Regarding the assertion that establishing a substitution could be made does not satisfy the requirement to explain why the specific modification would have been made according to MPEP 2143:
MPEP 2143.I.B outlines the criteria for a simple substitution as (1) a finding that the prior art contained a product which differed from the claimed device by the substitution of some components with other components, (2) a finding that the substituted components and their functions were known in the art, (3) a finding that one of ordinary skill in the art could have substituted one known element for another, and (4) the results of the substitution would have been predictable, and whatever additional findings based on the Graham factual inquiries may be necessary. Each of these requirements have been addressed in the rejection above as well as the response to remarks above.
Regarding the assertion that the substitution is not obvious as Heidtman does not explicitly state to use the particular polypeptide of Whiteson, and that the polypeptide of Whiteson was not known to possess lactose-acceptor activity at the time of invention:
There is no requirement for Heidtman to expressly teach the use of a particular polypeptide. Heidtman describes the cell and its capabilities to produce α-(1,3)-fucosylated oligosaccharides, and describes the enzyme class required to produce the cell, and even states preferences for a sub-class of enzyme to use. It is therefore obvious to replace the enzyme of the cell of Heidtman with any enzyme of the disclosed class of α-(1,3)-fucosyltransferases in order to successfully produce the cell of Heidtman. One of ordinary skill in the art in searching protein databanks would see the polypeptide of Whiteson, note that it falls within the criteria for generating the cell of Heidtman, and in making the substitution arrive at the claimed invention. Regarding what was known about the specific lactose-acceptor activity of the polypeptide of Whiteson at the time of the invention, MPEP 2112.I states that something which is old does not become patentable upon the discovery of a new property, indicating that the knowledge of lactose-acceptor activity need not be known at the time of the invention in order for the substitution to be obvious, especially considering the annotation of the polypeptide as a α-(1,3)-fucosyltransferase is the criteria suggested for the generation of the cell of Heidtman, and therefore the rationale for substitution.
Regarding the assertion that the substitution would not have yielded a predictable result because Heidtman teaches the experimental validation for lactose-utilizing activity:
Heidtman teaches a cell with α-(1,3)-fucosyltransferase activity, which preferably has the ability to utilize lactose as an acceptor. Heidtman teaches a method to validate candidate substitutes for having this lactose-utilization activity, but this activity is not a requirement for the generation of the cell of Heidtman. The simple substitution rationale is based on replacement of the enzyme of Heidtman with the polypeptide of Whiteson due to both being recognized having α-(1,3)-fucosyltransferase activity, and therefore both being capable of being incorporated into a cell as described by Heidtman with a reasonable expectation of success.
Regarding the assertion that the Examiner improperly used inherency to supply motivation and expectation of success, as inherency does not provide a motivation to justify selection of a particular protein: The rejection above does not use inherency as a motivating factor for substitution or expectation of success. The details of the rejection are stated above.
Regarding the assertion that Heidtman teaches away from routine substitution and toward screening and testing, which does not amount to routine interchangeability of annotated enzymes: There is no teaching away of substitution by Heidtman, as Heidtman does not criticize, discredit, or otherwise discourage carrying out substitution according to MPEP 2143.01.I. Furthermore, the rejection does not pertain to “routine substitution”.
Regarding the assertion that the newly added claims illustrate the absence of a reasoned selection rationale, the new claims are addressed above and rejected as unpatentable over Heidtman in view of Whiteson.
Double Patenting
The provisional double patenting rejections over co-pending Application No. 17/904,196 from the previous office action (Rejection E) are withdrawn in view of the abandonment of co-pending Application No. 17/904,196.
A. Claims 51-53, 55-57, 59-60 and 76-81 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 12 and 23 of U.S. Patent No. 10,570,430 (cited in the Form PTO-892 mailed 01/12/2024; hereafter “patent”) in view of Heidtman, Whiteson and NCBI.
The instant rejection is maintained from the previous Office Action and any newly recited portions are necessitated by claim amendment.
Regarding instant claim 51 and the limitation of “a cell comprising at least one polynucleotide encoding a polypeptide with α-(1,3)-fucosyltransferase activity”, claim 1 of the patent recites a metabolically engineered bacterium or yeast for the production of a fucosyllactose, wherein the comprising enzymes include a fucosyltransferase. Claim 12 of the patent further recites that the fucosyllactose generated is a 1,3-fucosyllactose, which is known as 3-fucosyllactose in the art.
The claims of the patent do not recite a fucosyltransferase enzyme that contains a GDP-fucose binding domain described by SEQ ID NO: 33, an amino acid region described by SEQ ID NO: 34, or that the C-terminus of the peptide is 100 amino acids or less from the first residue of the GDP-fucose binding domain.
Heidtman discloses methods for producing purified fucosylated oligosaccharides in milk [para 3], involving the use of engineered bacteria with heterologously expressed enzymes in order to optimize production efficiency [para 6]. Heidtman discloses methods that include production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25].
Regarding instant claims 51-52, Heidtman discloses “methods for producing α-(1,3)-fucosylated oligosaccharides utilizing a bacterial strain harbouring an expression plasmid containing two different α-(1,3)-fucosyltransferases in ‘tandem’ arrangement. These tandem α-(1,3)-fucosyltransferases may be under the control of the PL promoter” [para 18], and that the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49]. Furthermore, Heidtman states “a preferred α-(1,3)-fucosyltransferase utilizes GDP-fucose as a donor, and lactose is the acceptor for that donor [para 98]. As such, Heidtman satisfies the limitations of instant claim 52, as well as the limitations of instant claim 51 regarding a cell that produces α-1,3-fucosyllactose, the cell comprising at least one polynucleotide encoding an exogenous polypeptide with α-1,3-fucosyltransferase activity and able to use lactose as an acceptor substrate.
Heidtman further discusses methods of identifying α-(1,3)-fucosyltransferases enzymes capable of synthesizing fucosylated oligosaccharides such as 3-FL [para 47] and fucosyltransferase enzymes capable of using lactose as an acceptor comprising performing a computational search to define a broad group of simple sequence homologs of any known, lactose-utilizing fucosyltransferase, searching that group for common sequence and/or structural motifs shared by members of that group, searching sequence databases for said common sequence and/or structural motifs to identify candidate sequences, and expressing candidate enzymes to test for lactose utilization [para 99].
Whiteson describes the genomic analysis of the bacteria Basilea psittacipulmonis [title], wherein the genome was deposited and the encoded polypeptides were annotated by NCBI, namely the polypeptide AIL32582.1. This polypeptide is identified as an α-(1,3)-fucosyltransferase domain containing polypeptide as evidenced by NCBI. This polypeptide further contains a GDP-fucose binding domain of YITEK (residues 233-237) that corresponds to SEQ ID NO: 33 specified in i) of claim 51, as well as the sequence DLYLGF (residues 107-112) that corresponds to SEQ ID NO: 34 specified in ii) of instant claim 51. As the polypeptide of Whiteson is 329 amino acids in length, the starting amino acid of the GDP-fucose binding domain (residue 233) is less than 100 amino acids from the C-terminus of the polypeptide. Therefore, the polypeptide AIL32582.1 as evidenced by NCBI is considered to contain the “α-1,3-fucosyltransferase activity and the ability to use lactose as an acceptor substrate” as recited in instant claim 51, as the activity is considered to be inherent to the structure of the polypeptide (see MPEP 2112.01(I)).
In view of Heidtman and Whiteson, it would have been obvious to one of ordinary skill in the art before the effective filing date to modify the cell of the patent to use the polypeptide of Whiteson as identified by NCBI, since the simple substitution of one known element for another results in a predictable result. One of ordinary skill in the art would have recognized that the both the enzyme by the patent and the polypeptide of Whiteson are fucosyltransferases, and as such both are capable of being incorporated into such cells as described by both the patent and Whiteson. One of ordinary skill in the art would have been motivated to replace the fucosyltransferase of the patent with the fucosyltransferase of Whiteson, because Heidtman discloses the engineering of bacteria with heterologously expressed enzymes in order to optimize production efficiency of human milk oligosaccharides such as α-(1,3)-fucosyllactose, and because Heidtman discusses a method to screen sequence databases for novel enzymes capable of carrying out target fucosyltransferase activity. Thus it would have been obvious to one of ordinary skill in the art to replace the fucosyltransferase of the patent with the polypeptide of Whiteson, as one of ordinary skill in the art would have been able to carry out such a substitution with a reasonable expectation of success because both the patent and Whiteson discuss cells capable of producing fucosyltransferase enzymes.
Regarding instant claim 53 and the elected species of SEQ ID NO: 6, the polypeptide AIL32582.1 of Whiteson is 100% identical to SEQ ID NO: 6 as evidenced by the attached sequence search results [see Appendix A].
Regarding instant claim 55, Heidtman discloses methods that include production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25].
Regarding instant claim 56, claim 1 of the patent discloses a metabolically engineered yeast for the production of fucosyllactose.
Regarding instant claim 57, Heidtman discloses synthetic genes of α-(1-3)-fucosyltransferase genes are designed using standard methods known in the art, and include sequences that are codon-optimized for expression in a host bacterial strain [para 117].
Regarding instant claim 59, Heidtman discloses methods that include production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1-3)-fucosyltransferase gene” [para 25], and Whiteson discloses the polypeptide AIL32582.1 that contains the GDP-fucose binding domain specified by SEQ ID NO: 33, the amino acid sequence specified by SEQ ID NO: 34, and less than 100 amino acids between the beginning of the GDP-fucose binding domain and the C-terminus of the peptide as discussed above.
Regarding instant claim 60, Whiteson discloses the polypeptide AIL32582.1 that is 100% identical to SEQ ID NO: 6 as evidenced by the attached sequence search results [see Appendix A] as discussed above.
Regarding instant claim 76, the polypeptide of Whiteson as described above is 100% identical to SEQ ID NO: 6 as discussed above [see Appendix A].
Regarding instant claim 77, Heidtman discloses the nucleic acid can be integrated into the genome of the host cell [para 23].
Regarding instant claim 78, the polypeptide of Whiteson as described above is 100% identical to SEQ ID NO: 6 as discussed above [see Appendix A], and therefore it is considered to have a conserved GDP-fucose binding domain corresponding to residues 233-237 of SEQ ID NO: 6.
Regarding instant claim 79, Heidtman discloses “methods for producing α-(1,3)-fucosylated oligosaccharides utilizing a bacterial strain harbouring an expression plasmid containing two different α-(1,3)-fucosyltransferases in ‘tandem’ arrangement. These tandem α-(1,3)-fucosyltransferases may be under the control of the PL promoter” [para 18], and that the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49], and that the nucleic acid can be integrated into the genome of the host cell [para 23]. Heidtman further discloses the method includes production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25], wherein the E. coli is typically Escherichia coli K12 [para 27]. Furthermore, Heidtman states “a preferred α-(1,3)-fucosyltransferase utilizes GDP-fucose as a donor, and lactose is the acceptor for that donor [para 98]. As such, Heidtman satisfies the limitations of claim 52, as well as the limitations of claim 51 regarding a cell that produces α-1,3-fucosyllactose, the cell comprising at least one polynucleotide encoding an exogenous polypeptide with α-1,3-fucosyltransferase activity and able to use lactose as an acceptor substrate to produce α-1,3-fucosyllactose. Heidtman further discusses methods of identifying α-(1,3)-fucosyltransferases enzymes capable of synthesizing fucosylated oligosaccharides such as 3-FL [para 47] and fucosyltransferase enzymes capable of using lactose as an acceptor comprising performing a computational search to define a broad group of simple sequence homologs of any known, lactose-utilizing fucosyltransferase, searching that group for common sequence and/or structural motifs shared by members of that group, searching sequence databases for said common sequence and/or structural motifs to identify candidate sequences, and expressing candidate enzymes to test for lactose utilization [para 99].
Regarding instant claim 79, Whiteson describes the genomic analysis of the bacteria Basilea psittacipulmonis [title], wherein the genome was deposited and the encoded polypeptides were annotated by NCBI, namely the polypeptide AIL32582.1. This polypeptide is identified as an α-(1,3)-fucosyltransferase domain-containing polypeptide as evidenced by NCBI. This polypeptide further contains a GDP-fucose binding domain of YITEK (residues 233-237) that corresponds to SEQ ID NO: 33 specified in i) of claim 51, as well as the sequence DLYLGF (residues 107-112) that corresponds to SEQ ID NO: 34 specified in ii) of claim 51. As the polypeptide of Whiteson is 329 amino acids in length, the starting amino acid of the GDP-fucose binding domain (residue 233) is less than 100 amino acids from the C-terminus of the polypeptide. Therefore, the polypeptide AIL32582.1 as evidenced by NCBI is considered to contain the “α-1,3-fucosyltransferase activity and the ability to use lactose as an acceptor substrate” as recited in claim 51, as the activity is considered to be inherent to the structure of the polypeptide (see MPEP 2112.01(I)). As the polypeptide of Whiteson shares 100% identity with SEQ ID NO: 6, it is considered to have the GDP-fucose binding domain corresponding to residues 233-237 of SEQ ID NO: 6.
In view of Heidtman and Whiteson, it would have been obvious to one of ordinary skill in the art before the effective filing date to modify the cell of the patent to use the polypeptide of Whiteson as identified by NCBI, since the simple substitution of one known element for another results in a predictable result. One of ordinary skill in the art would have recognized that the enzyme by the patent and the polypeptide of Whiteson are fucosyltransferases, and as such both are capable of being incorporated into such cells as described by both the patent and Whiteson. One of ordinary skill in the art would have been motivated to replace the fucosyltransferase of the patent with the fucosyltransferase of Whiteson, because Heidtman discloses the engineering of bacteria with heterologously expressed enzymes in order to optimize production efficiency of human milk oligosaccharides such as α-(1,3)-fucosyllactose, and because Heidtman discusses a method to screen sequence databases for novel enzymes capable of carrying out target fucosyltransferase activity. Thus it would have been obvious to one of ordinary skill in the art to replace the fucosyltransferase of the patent with the polypeptide of Whiteson, as one of ordinary skill in the art would have been able to carry out such a substitution with a reasonable expectation of success because both the patent and Whiteson discuss cells capable of producing fucosyltransferase enzymes.
Regarding instant claim 80 (dependent from instant claim 51), Heidtman discloses the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49] as discussed in the rejection of claim 51 above, and the recombinant DNA constructs are supplied on a plasmid expression vector [para 36].
Regarding instant claim 81, Heidtman discloses “methods for producing α-(1,3)-fucosylated oligosaccharides utilizing a bacterial strain harbouring an expression plasmid containing two different α-(1,3)-fucosyltransferases in ‘tandem’ arrangement. These tandem α-(1,3)-fucosyltransferases may be under the control of the PL promoter” [para 18], and that the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49], and that the recombinant DNA constructs are supplied on a plasmid expression vector [para 36]. Heidtman further discloses the method includes production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25], wherein the E. coli is typically Escherichia coli K12 [para 27]. Furthermore, Heidtman states “a preferred α-(1,3)-fucosyltransferase utilizes GDP-fucose as a donor, and lactose is the acceptor for that donor [para 98]. As such, Heidtman satisfies the limitations of claim 52, as well as the limitations of claim 51 regarding a cell that produces α-1,3-fucosyllactose, the cell comprising at least one polynucleotide encoding an exogenous polypeptide with α-1,3-fucosyltransferase activity and able to use lactose as an acceptor substrate to produce α-1,3-fucosyllactose. Heidtman further discusses methods of identifying α-(1,3)-fucosyltransferases enzymes capable of synthesizing fucosylated oligosaccharides such as 3-FL [para 47] and fucosyltransferase enzymes capable of using lactose as an acceptor comprising performing a computational search to define a broad group of simple sequence homologs of any known, lactose-utilizing fucosyltransferase, searching that group for common sequence and/or structural motifs shared by members of that group, searching sequence databases for said common sequence and/or structural motifs to identify candidate sequences, and expressing candidate enzymes to test for lactose utilization [para 99].
Regarding instant claim 81, Whiteson describes the genomic analysis of the bacteria Basilea psittacipulmonis [title], wherein the genome was deposited and the encoded polypeptides were annotated by NCBI, namely the polypeptide AIL32582.1. This polypeptide is identified as an α-(1,3)-fucosyltransferase domain-containing polypeptide as evidenced by NCBI. This polypeptide further contains a GDP-fucose binding domain of YITEK (residues 233-237) that corresponds to SEQ ID NO: 33 specified in i) of claim 51, as well as the sequence DLYLGF (residues 107-112) that corresponds to SEQ ID NO: 34 specified in ii) of claim 51. As the polypeptide of Whiteson is 329 amino acids in length, the starting amino acid of the GDP-fucose binding domain (residue 233) is less than 100 amino acids from the C-terminus of the polypeptide. Therefore, the polypeptide AIL32582.1 as evidenced by NCBI is considered to contain the “α-1,3-fucosyltransferase activity and the ability to use lactose as an acceptor substrate” as recited in claim 51, as the activity is considered to be inherent to the structure of the polypeptide (see MPEP 2112.01(I)). As the polypeptide of Whiteson shares 100% identity with SEQ ID NO: 6, it is considered to have the GDP-fucose binding domain corresponding to residues 233-237 of SEQ ID NO: 6.
In view of Heidtman and Whiteson, it would have been obvious to one of ordinary skill in the art before the effective filing date to modify the cell of the patent to use the polypeptide of Whiteson as identified by NCBI, since the simple substitution of one known element for another results in a predictable result. One of ordinary skill in the art would have recognized that the enzyme by the patent and the polypeptide of Whiteson are fucosyltransferases, and as such both are capable of being incorporated into such cells as described by both the patent and Whiteson. One of ordinary skill in the art would have been motivated to replace the fucosyltransferase of the patent with the fucosyltransferase of Whiteson, because Heidtman discloses the engineering of bacteria with heterologously expressed enzymes in order to optimize production efficiency of human milk oligosaccharides such as α-(1,3)-fucosyllactose, and because Heidtman discusses a method to screen sequence databases for novel enzymes capable of carrying out target fucosyltransferase activity. Thus it would have been obvious to one of ordinary skill in the art to replace the fucosyltransferase of the patent with the polypeptide of Whiteson, as one of ordinary skill in the art would have been able to carry out such a substitution with a reasonable expectation of success because both the patent and Whiteson discuss cells capable of producing fucosyltransferase enzymes.
B. Claims 51-53, 55-57, 59-60 and 76-81 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 9-13 and 16 of U.S. Patent No. 10,858,684 (cited in the Form PTO-892 mailed 01/12/2024; hereafter “patent”) in view of Heidtman, Whiteson and NCBI.
The instant rejection is maintained from the previous Office Action and any newly recited portions are necessitated by claim amendment.
Regarding instant claim 51 and the limitation of “a cell comprising at least one polynucleotide encoding a polypeptide with α-(1,3)-fucosyltransferase activity”, claim 1 of the patent recites a method for producing microorganisms that resist lactose killing comprising mutating a lactose transporter gene. Claim 9 of the patent further limits the mutation to the introduction of a lactose transporter cassette comprising a heterologous sequence of a lactose transporter gene. Claim 10 of the patent further limits this gene to at least one enzyme from the lactose degradation pathway being knocked out. Claim 11 of the patent further limits this method to culturing selected microorganisms for production of lactose-based specialty products. Claim 12 of the patent further limits the lactose-based specialty products to be carbohydrates. Claim 13 of the patent further limits the carbohydrates to include 3-fucosyllactose.
The claims of the patent do not recite a fucosyltransferase enzyme that contains a GDP-fucose binding domain described by SEQ ID NO: 33, an amino acid region described by SEQ ID NO: 34, or that the C-terminus of the peptide is 100 amino acids or less from the first residue of the GDP-fucose binding domain.
Heidtman discloses methods for producing purified fucosylated oligosaccharides in milk [para 3], involving the use of engineered bacteria with heterologously expressed enzymes in order to optimize production efficiency [para 6]. Heidtman discloses methods that include production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25].
Regarding instant claims 51-52, Heidtman discloses “methods for producing α-(1,3)-fucosylated oligosaccharides utilizing a bacterial strain harbouring an expression plasmid containing two different α-(1,3)-fucosyltransferases in ‘tandem’ arrangement. These tandem α-(1,3)-fucosyltransferases may be under the control of the PL promoter” [para 18], and that the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49]. Furthermore, Heidtman states “a preferred α-(1,3)-fucosyltransferase utilizes GDP-fucose as a donor, and lactose is the acceptor for that donor [para 98]. As such, Heidtman satisfies the limitations of instant claim 52, as well as the limitations of instant claim 51 regarding a cell that produces α-1,3-fucosyllactose, the cell comprising at least one polynucleotide encoding an exogenous polypeptide with α-1,3-fucosyltransferase activity and able to use lactose as an acceptor substrate.
Heidtman further discusses methods of identifying α-(1,3)-fucosyltransferases enzymes capable of synthesizing fucosylated oligosaccharides such as 3-FL [para 47] and fucosyltransferase enzymes capable of using lactose as an acceptor comprising performing a computational search to define a broad group of simple sequence homologs of any known, lactose-utilizing fucosyltransferase, searching that group for common sequence and/or structural motifs shared by members of that group, searching sequence databases for said common sequence and/or structural motifs to identify candidate sequences, and expressing candidate enzymes to test for lactose utilization [para 99].
Whiteson describes the genomic analysis of the bacteria Basilea psittacipulmonis [title], wherein the genome was deposited and the encoded polypeptides were annotated by NCBI, namely the polypeptide AIL32582.1. This polypeptide is identified as an α-(1,3)-fucosyltransferase domain containing polypeptide as evidenced by NCBI. This polypeptide further contains a GDP-fucose binding domain of YITEK (residues 233-237) that corresponds to SEQ ID NO: 33 specified in i) of claim 51, as well as the sequence DLYLGF (residues 107-112) that corresponds to SEQ ID NO: 34 specified in ii) of instant claim 51. As the polypeptide of Whiteson is 329 amino acids in length, the starting amino acid of the GDP-fucose binding domain (residue 233) is less than 100 amino acids from the C-terminus of the polypeptide. Therefore, the polypeptide AIL32582.1 as evidenced by NCBI is considered to contain the “α-1,3-fucosyltransferase activity and the ability to use lactose as an acceptor substrate” as recited in instant claim 51, as the activity is considered to be inherent to the structure of the polypeptide (see MPEP 2112.01(I)).
In view of Heidtman and Whiteson, it would have been obvious to one of ordinary skill in the art before the effective filing date to modify the cell of the patent to use the polypeptide of Whiteson as identified by NCBI, since the simple substitution of one known element for another results in a predictable result. One of ordinary skill in the art would have recognized that the both the enzyme by the patent and the polypeptide of Whiteson are fucosyltransferases, and as such both are capable of being incorporated into such cells as described by both the patent and Whiteson. One of ordinary skill in the art would have been motivated to replace the fucosyltransferase of the patent with the fucosyltransferase of Whiteson, because Heidtman discloses the engineering of bacteria with heterologously expressed enzymes in order to optimize production efficiency of human milk oligosaccharides such as α-(1,3)-fucosyllactose, and because Heidtman discusses a method to screen sequence databases for novel enzymes capable of carrying out target fucosyltransferase activity. Thus it would have been obvious to one of ordinary skill in the art to replace the fucosyltransferase of the patent with the polypeptide of Whiteson, as one of ordinary skill in the art would have been able to carry out such a substitution with a reasonable expectation of success because both the patent and Whiteson discuss cells capable of producing fucosyltransferase enzymes.
Regarding instant claim 53 and the elected species of SEQ ID NO: 6, the polypeptide AIL32582.1 of Whiteson is 100% identical to SEQ ID NO: 6 as evidenced by the attached sequence search results [see Appendix A].
Regarding instant claim 55, Heidtman discloses methods that include production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25].
Regarding instant claim 56, claim 16 of the patent discloses the engineered microorganism to be a yeast.
Regarding instant claim 57, Heidtman discloses synthetic genes of α-(1-3)-fucosyltransferase genes are designed using standard methods known in the art, and include sequences that are codon-optimized for expression in a host bacterial strain [para 117].
Regarding instant claim 59, Heidtman discloses methods that include production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1-3)-fucosyltransferase gene” [para 25], and Whiteson discloses the polypeptide AIL32582.1 that contains the GDP-fucose binding domain specified by SEQ ID NO: 33, the amino acid sequence specified by SEQ ID NO: 34, and less than 100 amino acids between the beginning of the GDP-fucose binding domain and the C-terminus of the peptide as discussed above.
Regarding instant claim 60, Whiteson discloses the polypeptide AIL32582.1 that is 100% identical to SEQ ID NO: 6 as evidenced by the attached sequence search results [see Appendix A] as discussed above.
Regarding instant claim 76, the polypeptide of Whiteson as described above is 100% identical to SEQ ID NO: 6 as discussed above [see Appendix A].
Regarding instant claim 77, Heidtman discloses the nucleic acid can be integrated into the genome of the host cell [para 23].
Regarding instant claim 78, the polypeptide of Whiteson as described above is 100% identical to SEQ ID NO: 6 as discussed above [see Appendix A], and therefore it is considered to have a conserved GDP-fucose binding domain corresponding to residues 233-237 of SEQ ID NO: 6.
Regarding instant claim 79, Heidtman discloses “methods for producing α-(1,3)-fucosylated oligosaccharides utilizing a bacterial strain harbouring an expression plasmid containing two different α-(1,3)-fucosyltransferases in ‘tandem’ arrangement. These tandem α-(1,3)-fucosyltransferases may be under the control of the PL promoter” [para 18], and that the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49], and that the nucleic acid can be integrated into the genome of the host cell [para 23]. Heidtman further discloses the method includes production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25], wherein the E. coli is typically Escherichia coli K12 [para 27]. Furthermore, Heidtman states “a preferred α-(1,3)-fucosyltransferase utilizes GDP-fucose as a donor, and lactose is the acceptor for that donor [para 98]. As such, Heidtman satisfies the limitations of claim 52, as well as the limitations of claim 51 regarding a cell that produces α-1,3-fucosyllactose, the cell comprising at least one polynucleotide encoding an exogenous polypeptide with α-1,3-fucosyltransferase activity and able to use lactose as an acceptor substrate to produce α-1,3-fucosyllactose. Heidtman further discusses methods of identifying α-(1,3)-fucosyltransferases enzymes capable of synthesizing fucosylated oligosaccharides such as 3-FL [para 47] and fucosyltransferase enzymes capable of using lactose as an acceptor comprising performing a computational search to define a broad group of simple sequence homologs of any known, lactose-utilizing fucosyltransferase, searching that group for common sequence and/or structural motifs shared by members of that group, searching sequence databases for said common sequence and/or structural motifs to identify candidate sequences, and expressing candidate enzymes to test for lactose utilization [para 99].
Regarding instant claim 79, Whiteson describes the genomic analysis of the bacteria Basilea psittacipulmonis [title], wherein the genome was deposited and the encoded polypeptides were annotated by NCBI, namely the polypeptide AIL32582.1. This polypeptide is identified as an α-(1,3)-fucosyltransferase domain-containing polypeptide as evidenced by NCBI. This polypeptide further contains a GDP-fucose binding domain of YITEK (residues 233-237) that corresponds to SEQ ID NO: 33 specified in i) of claim 51, as well as the sequence DLYLGF (residues 107-112) that corresponds to SEQ ID NO: 34 specified in ii) of claim 51. As the polypeptide of Whiteson is 329 amino acids in length, the starting amino acid of the GDP-fucose binding domain (residue 233) is less than 100 amino acids from the C-terminus of the polypeptide. Therefore, the polypeptide AIL32582.1 as evidenced by NCBI is considered to contain the “α-1,3-fucosyltransferase activity and the ability to use lactose as an acceptor substrate” as recited in claim 51, as the activity is considered to be inherent to the structure of the polypeptide (see MPEP 2112.01(I)). As the polypeptide of Whiteson shares 100% identity with SEQ ID NO: 6, it is considered to have the GDP-fucose binding domain corresponding to residues 233-237 of SEQ ID NO: 6.
In view of Heidtman and Whiteson, it would have been obvious to one of ordinary skill in the art before the effective filing date to modify the cell of the patent to use the polypeptide of Whiteson as identified by NCBI, since the simple substitution of one known element for another results in a predictable result. One of ordinary skill in the art would have recognized that the enzyme by the patent and the polypeptide of Whiteson are fucosyltransferases, and as such both are capable of being incorporated into such cells as described by both the patent and Whiteson. One of ordinary skill in the art would have been motivated to replace the fucosyltransferase of the patent with the fucosyltransferase of Whiteson, because Heidtman discloses the engineering of bacteria with heterologously expressed enzymes in order to optimize production efficiency of human milk oligosaccharides such as α-(1,3)-fucosyllactose, and because Heidtman discusses a method to screen sequence databases for novel enzymes capable of carrying out target fucosyltransferase activity. Thus it would have been obvious to one of ordinary skill in the art to replace the fucosyltransferase of the patent with the polypeptide of Whiteson, as one of ordinary skill in the art would have been able to carry out such a substitution with a reasonable expectation of success because both the patent and Whiteson discuss cells capable of producing fucosyltransferase enzymes.
Regarding instant claim 80 (dependent from claim 51), Heidtman discloses the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49] as discussed in the rejection of claim 51 above, and the recombinant DNA constructs are supplied on a plasmid expression vector [para 36].
Regarding instant claim 81, Heidtman discloses “methods for producing α-(1,3)-fucosylated oligosaccharides utilizing a bacterial strain harbouring an expression plasmid containing two different α-(1,3)-fucosyltransferases in ‘tandem’ arrangement. These tandem α-(1,3)-fucosyltransferases may be under the control of the PL promoter” [para 18], and that the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49], and that the recombinant DNA constructs are supplied on a plasmid expression vector [para 36]. Heidtman further discloses the method includes production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25], wherein the E. coli is typically Escherichia coli K12 [para 27]. Furthermore, Heidtman states “a preferred α-(1,3)-fucosyltransferase utilizes GDP-fucose as a donor, and lactose is the acceptor for that donor [para 98]. As such, Heidtman satisfies the limitations of claim 52, as well as the limitations of claim 51 regarding a cell that produces α-1,3-fucosyllactose, the cell comprising at least one polynucleotide encoding an exogenous polypeptide with α-1,3-fucosyltransferase activity and able to use lactose as an acceptor substrate to produce α-1,3-fucosyllactose. Heidtman further discusses methods of identifying α-(1,3)-fucosyltransferases enzymes capable of synthesizing fucosylated oligosaccharides such as 3-FL [para 47] and fucosyltransferase enzymes capable of using lactose as an acceptor comprising performing a computational search to define a broad group of simple sequence homologs of any known, lactose-utilizing fucosyltransferase, searching that group for common sequence and/or structural motifs shared by members of that group, searching sequence databases for said common sequence and/or structural motifs to identify candidate sequences, and expressing candidate enzymes to test for lactose utilization [para 99].
Regarding instant claim 81, Whiteson describes the genomic analysis of the bacteria Basilea psittacipulmonis [title], wherein the genome was deposited and the encoded polypeptides were annotated by NCBI, namely the polypeptide AIL32582.1. This polypeptide is identified as an α-(1,3)-fucosyltransferase domain-containing polypeptide as evidenced by NCBI. This polypeptide further contains a GDP-fucose binding domain of YITEK (residues 233-237) that corresponds to SEQ ID NO: 33 specified in i) of claim 51, as well as the sequence DLYLGF (residues 107-112) that corresponds to SEQ ID NO: 34 specified in ii) of claim 51. As the polypeptide of Whiteson is 329 amino acids in length, the starting amino acid of the GDP-fucose binding domain (residue 233) is less than 100 amino acids from the C-terminus of the polypeptide. Therefore, the polypeptide AIL32582.1 as evidenced by NCBI is considered to contain the “α-1,3-fucosyltransferase activity and the ability to use lactose as an acceptor substrate” as recited in claim 51, as the activity is considered to be inherent to the structure of the polypeptide (see MPEP 2112.01(I)). As the polypeptide of Whiteson shares 100% identity with SEQ ID NO: 6, it is considered to have the GDP-fucose binding domain corresponding to residues 233-237 of SEQ ID NO: 6.
In view of Heidtman and Whiteson, it would have been obvious to one of ordinary skill in the art before the effective filing date to modify the cell of the patent to use the polypeptide of Whiteson as identified by NCBI, since the simple substitution of one known element for another results in a predictable result. One of ordinary skill in the art would have recognized that the enzyme by the patent and the polypeptide of Whiteson are fucosyltransferases, and as such both are capable of being incorporated into such cells as described by both the patent and Whiteson. One of ordinary skill in the art would have been motivated to replace the fucosyltransferase of the patent with the fucosyltransferase of Whiteson, because Heidtman discloses the engineering of bacteria with heterologously expressed enzymes in order to optimize production efficiency of human milk oligosaccharides such as α-(1,3)-fucosyllactose, and because Heidtman discusses a method to screen sequence databases for novel enzymes capable of carrying out target fucosyltransferase activity. Thus it would have been obvious to one of ordinary skill in the art to replace the fucosyltransferase of the patent with the polypeptide of Whiteson, as one of ordinary skill in the art would have been able to carry out such a substitution with a reasonable expectation of success because both the patent and Whiteson discuss cells capable of producing fucosyltransferase enzymes.
C. Claims 51-53, 55, 57, 59-60 and 76-81 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 51 and 67-68 of copending Application No. 17/627088 (hereafter “reference application”) in view of Heidtman, Whiteson and NCBI.
The instant rejection is maintained from the previous Office Action and any newly recited portions are necessitated by claim amendment.
Regarding instant claim 51 and the limitation of “a cell comprising at least one polynucleotide encoding a polypeptide with α-(1,3)-fucosyltransferase activity”, claim 51 of the reference application recites a host cell modified for the production of a fucosyllactose comprising a nucleic acid encoding a fucosyltransferase, claim 67 recites a method for producing fucosyllactose comprising cultivating the host cell of claim 51, and claim 68 of the reference application recites the fucosyllactose is 3-fucosyllactose
The claims of the reference application do not recite that the fucosyltransferase has the domains specified in SEQ ID NOs: 33 and 34 of instant claim 51, nor that the C-terminus is 100 amino acids or less from the GDP-fucose binding domain (SEQ ID NO: 33).
Heidtman discloses methods for producing purified fucosylated oligosaccharides in milk [para 3], involving the use of engineered bacteria with heterologously expressed enzymes in order to optimize production efficiency [para 6]. Heidtman discloses methods that include production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25].
Regarding instant claims 51-52, Heidtman discloses “methods for producing α-(1,3)-fucosylated oligosaccharides utilizing a bacterial strain harbouring an expression plasmid containing two different α-(1,3)-fucosyltransferases in ‘tandem’ arrangement. These tandem α-(1,3)-fucosyltransferases may be under the control of the PL promoter” [para 18], and that the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49]. Furthermore, Heidtman states “a preferred α-(1,3)-fucosyltransferase utilizes GDP-fucose as a donor, and lactose is the acceptor for that donor [para 98]. As such, Heidtman satisfies the limitations of instant claim 52, as well as the limitations of instant claim 51 regarding a cell that produces α-1,3-fucosyllactose, the cell comprising at least one polynucleotide encoding an exogenous polypeptide with α-1,3-fucosyltransferase activity and able to use lactose as an acceptor substrate.
Heidtman further discusses methods of identifying α-(1,3)-fucosyltransferases enzymes capable of synthesizing fucosylated oligosaccharides such as 3-FL [para 47] and fucosyltransferase enzymes capable of using lactose as an acceptor comprising performing a computational search to define a broad group of simple sequence homologs of any known, lactose-utilizing fucosyltransferase, searching that group for common sequence and/or structural motifs shared by members of that group, searching sequence databases for said common sequence and/or structural motifs to identify candidate sequences, and expressing candidate enzymes to test for lactose utilization [para 99].
Whiteson describes the genomic analysis of the bacteria Basilea psittacipulmonis [title], wherein the genome was deposited and the encoded polypeptides were annotated by NCBI, namely the polypeptide AIL32582.1. This polypeptide is identified as an α-(1,3)-fucosyltransferase domain containing polypeptide as evidenced by NCBI. This polypeptide further contains a GDP-fucose binding domain of YITEK (residues 233-237) that corresponds to SEQ ID NO: 33 specified in i) of claim 51, as well as the sequence DLYLGF (residues 107-112) that corresponds to SEQ ID NO: 34 specified in ii) of instant claim 51. As the polypeptide of Whiteson is 329 amino acids in length, the starting amino acid of the GDP-fucose binding domain (residue 233) is less than 100 amino acids from the C-terminus of the polypeptide. Therefore, the polypeptide AIL32582.1 as evidenced by NCBI is considered to contain the “α-1,3-fucosyltransferase activity and the ability to use lactose as an acceptor substrate” as recited in instant claim 51, as the activity is considered to be inherent to the structure of the polypeptide (see MPEP 2112.01(I)).
In view of Heidtman and Whiteson, it would have been obvious to one of ordinary skill in the art before the effective filing date to modify the cell of the reference application to use the polypeptide of Whiteson as identified by NCBI, since the simple substitution of one known element for another results in a predictable result. One of ordinary skill in the art would have recognized that the enzyme by the reference application and the polypeptide of Whiteson are fucosyltransferases, and as such both are capable of being incorporated into such cells as described by both the reference application and Whiteson. One of ordinary skill in the art would have been motivated to replace the fucosyltransferase of the reference application with the fucosyltransferase of Whiteson, because Heidtman discloses the engineering of bacteria with heterologously expressed enzymes in order to optimize production efficiency of human milk oligosaccharides such as α-(1,3)-fucosyllactose, and because Heidtman discusses a method to screen sequence databases for novel enzymes capable of carrying out target fucosyltransferase activity. Thus it would have been obvious to one of ordinary skill in the art to replace the fucosyltransferase of the reference application with the polypeptide of Whiteson, as one of ordinary skill in the art would have been able to carry out such a substitution with a reasonable expectation of success because both the reference application and Whiteson discuss cells capable of producing fucosyltransferase enzymes.
Regarding instant claim 53 and the elected species of SEQ ID NO: 6, the polypeptide AIL32582.1 of Whiteson is 100% identical to SEQ ID NO: 6 as evidenced by the attached sequence search results [see Appendix A].
Regarding instant claim 55, Heidtman discloses methods that include production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25].
Regarding instant claim 56, claim 16 of the patent discloses the engineered microorganism to be a yeast.
Regarding instant claim 57, Heidtman discloses synthetic genes of α-(1-3)-fucosyltransferase genes are designed using standard methods known in the art, and include sequences that are codon-optimized for expression in a host bacterial strain [para 117].
Regarding instant claim 59, Heidtman discloses methods that include production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1-3)-fucosyltransferase gene” [para 25], and Whiteson discloses the polypeptide AIL32582.1 that contains the GDP-fucose binding domain specified by SEQ ID NO: 33, the amino acid sequence specified by SEQ ID NO: 34, and less than 100 amino acids between the beginning of the GDP-fucose binding domain and the C-terminus of the peptide as discussed above.
Regarding instant claim 60, Whiteson discloses the polypeptide AIL32582.1 that is 100% identical to SEQ ID NO: 6 as evidenced by the attached sequence search results [see Appendix A] as discussed above.
Regarding instant claim 76, the polypeptide of Whiteson as described above is 100% identical to SEQ ID NO: 6 as discussed above [see Appendix A].
Regarding instant claim 77, Heidtman discloses the nucleic acid can be integrated into the genome of the host cell [para 23].
Regarding instant claim 78, the polypeptide of Whiteson as described above is 100% identical to SEQ ID NO: 6 as discussed above [see Appendix A], and therefore it is considered to have a conserved GDP-fucose binding domain corresponding to residues 233-237 of SEQ ID NO: 6.
Regarding instant claim 79, Heidtman discloses “methods for producing α-(1,3)-fucosylated oligosaccharides utilizing a bacterial strain harbouring an expression plasmid containing two different α-(1,3)-fucosyltransferases in ‘tandem’ arrangement. These tandem α-(1,3)-fucosyltransferases may be under the control of the PL promoter” [para 18], and that the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49], and that the nucleic acid can be integrated into the genome of the host cell [para 23]. Heidtman further discloses the method includes production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25], wherein the E. coli is typically Escherichia coli K12 [para 27]. Furthermore, Heidtman states “a preferred α-(1,3)-fucosyltransferase utilizes GDP-fucose as a donor, and lactose is the acceptor for that donor [para 98]. As such, Heidtman satisfies the limitations of claim 52, as well as the limitations of claim 51 regarding a cell that produces α-1,3-fucosyllactose, the cell comprising at least one polynucleotide encoding an exogenous polypeptide with α-1,3-fucosyltransferase activity and able to use lactose as an acceptor substrate to produce α-1,3-fucosyllactose. Heidtman further discusses methods of identifying α-(1,3)-fucosyltransferases enzymes capable of synthesizing fucosylated oligosaccharides such as 3-FL [para 47] and fucosyltransferase enzymes capable of using lactose as an acceptor comprising performing a computational search to define a broad group of simple sequence homologs of any known, lactose-utilizing fucosyltransferase, searching that group for common sequence and/or structural motifs shared by members of that group, searching sequence databases for said common sequence and/or structural motifs to identify candidate sequences, and expressing candidate enzymes to test for lactose utilization [para 99].
Regarding instant claim 79, Whiteson describes the genomic analysis of the bacteria Basilea psittacipulmonis [title], wherein the genome was deposited and the encoded polypeptides were annotated by NCBI, namely the polypeptide AIL32582.1. This polypeptide is identified as an α-(1,3)-fucosyltransferase domain-containing polypeptide as evidenced by NCBI. This polypeptide further contains a GDP-fucose binding domain of YITEK (residues 233-237) that corresponds to SEQ ID NO: 33 specified in i) of claim 51, as well as the sequence DLYLGF (residues 107-112) that corresponds to SEQ ID NO: 34 specified in ii) of claim 51. As the polypeptide of Whiteson is 329 amino acids in length, the starting amino acid of the GDP-fucose binding domain (residue 233) is less than 100 amino acids from the C-terminus of the polypeptide. Therefore, the polypeptide AIL32582.1 as evidenced by NCBI is considered to contain the “α-1,3-fucosyltransferase activity and the ability to use lactose as an acceptor substrate” as recited in claim 51, as the activity is considered to be inherent to the structure of the polypeptide (see MPEP 2112.01(I)). As the polypeptide of Whiteson shares 100% identity with SEQ ID NO: 6, it is considered to have the GDP-fucose binding domain corresponding to residues 233-237 of SEQ ID NO: 6.
In view of Heidtman and Whiteson, it would have been obvious to one of ordinary skill in the art before the effective filing date to modify the cell of the reference application to use the polypeptide of Whiteson as identified by NCBI, since the simple substitution of one known element for another results in a predictable result. One of ordinary skill in the art would have recognized that the enzyme by the reference application and the polypeptide of Whiteson are fucosyltransferases, and as such both are capable of being incorporated into such cells as described by both the reference application and Whiteson. One of ordinary skill in the art would have been motivated to replace the fucosyltransferase of the reference application with the fucosyltransferase of Whiteson, because Heidtman discloses the engineering of bacteria with heterologously expressed enzymes in order to optimize production efficiency of human milk oligosaccharides such as α-(1,3)-fucosyllactose, and because Heidtman discusses a method to screen sequence databases for novel enzymes capable of carrying out target fucosyltransferase activity. Thus it would have been obvious to one of ordinary skill in the art to replace the fucosyltransferase of the reference application with the polypeptide of Whiteson, as one of ordinary skill in the art would have been able to carry out such a substitution with a reasonable expectation of success because both the reference application and Whiteson discuss cells capable of producing fucosyltransferase enzymes.
Regarding instant claim 80 (dependent from claim 51), Heidtman discloses the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49] as discussed in the rejection of claim 51 above, and the recombinant DNA constructs are supplied on a plasmid expression vector [para 36].
Regarding instant claim 81, Heidtman discloses “methods for producing α-(1,3)-fucosylated oligosaccharides utilizing a bacterial strain harbouring an expression plasmid containing two different α-(1,3)-fucosyltransferases in ‘tandem’ arrangement. These tandem α-(1,3)-fucosyltransferases may be under the control of the PL promoter” [para 18], and that the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49], and that the recombinant DNA constructs are supplied on a plasmid expression vector [para 36]. Heidtman further discloses the method includes production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25], wherein the E. coli is typically Escherichia coli K12 [para 27]. Furthermore, Heidtman states “a preferred α-(1,3)-fucosyltransferase utilizes GDP-fucose as a donor, and lactose is the acceptor for that donor [para 98]. As such, Heidtman satisfies the limitations of claim 52, as well as the limitations of claim 51 regarding a cell that produces α-1,3-fucosyllactose, the cell comprising at least one polynucleotide encoding an exogenous polypeptide with α-1,3-fucosyltransferase activity and able to use lactose as an acceptor substrate to produce α-1,3-fucosyllactose. Heidtman further discusses methods of identifying α-(1,3)-fucosyltransferases enzymes capable of synthesizing fucosylated oligosaccharides such as 3-FL [para 47] and fucosyltransferase enzymes capable of using lactose as an acceptor comprising performing a computational search to define a broad group of simple sequence homologs of any known, lactose-utilizing fucosyltransferase, searching that group for common sequence and/or structural motifs shared by members of that group, searching sequence databases for said common sequence and/or structural motifs to identify candidate sequences, and expressing candidate enzymes to test for lactose utilization [para 99].
Regarding instant claim 81, Whiteson describes the genomic analysis of the bacteria Basilea psittacipulmonis [title], wherein the genome was deposited and the encoded polypeptides were annotated by NCBI, namely the polypeptide AIL32582.1. This polypeptide is identified as an α-(1,3)-fucosyltransferase domain-containing polypeptide as evidenced by NCBI. This polypeptide further contains a GDP-fucose binding domain of YITEK (residues 233-237) that corresponds to SEQ ID NO: 33 specified in i) of claim 51, as well as the sequence DLYLGF (residues 107-112) that corresponds to SEQ ID NO: 34 specified in ii) of claim 51. As the polypeptide of Whiteson is 329 amino acids in length, the starting amino acid of the GDP-fucose binding domain (residue 233) is less than 100 amino acids from the C-terminus of the polypeptide. Therefore, the polypeptide AIL32582.1 as evidenced by NCBI is considered to contain the “α-1,3-fucosyltransferase activity and the ability to use lactose as an acceptor substrate” as recited in claim 51, as the activity is considered to be inherent to the structure of the polypeptide (see MPEP 2112.01(I)). As the polypeptide of Whiteson shares 100% identity with SEQ ID NO: 6, it is considered to have the GDP-fucose binding domain corresponding to residues 233-237 of SEQ ID NO: 6.
In view of Heidtman and Whiteson, it would have been obvious to one of ordinary skill in the art before the effective filing date to modify the cell of the reference application to use the polypeptide of Whiteson as identified by NCBI, since the simple substitution of one known element for another results in a predictable result. One of ordinary skill in the art would have recognized that the enzyme by the reference application and the polypeptide of Whiteson are fucosyltransferases, and as such both are capable of being incorporated into such cells as described by both the reference application and Whiteson. One of ordinary skill in the art would have been motivated to replace the fucosyltransferase of the reference application with the fucosyltransferase of Whiteson, because Heidtman discloses the engineering of bacteria with heterologously expressed enzymes in order to optimize production efficiency of human milk oligosaccharides such as α-(1,3)-fucosyllactose, and because Heidtman discusses a method to screen sequence databases for novel enzymes capable of carrying out target fucosyltransferase activity. Thus it would have been obvious to one of ordinary skill in the art to replace the fucosyltransferase of the reference application with the polypeptide of Whiteson, as one of ordinary skill in the art would have been able to carry out such a substitution with a reasonable expectation of success because both the reference application and Whiteson discuss cells capable of producing fucosyltransferase enzymes.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claim 56 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 51 and 67-68 of copending Application No. 17/627088 in view of Heidtman, Whiteson and NCBI, and further in view of Ahmad.
The instant rejection is maintained from the previous Office Action and any newly recited portions are necessitated by claim amendment.
Claim 56 is drawn to the cell of claim 51, wherein the cell is a yeast cell.
The claims of the reference application and disclosures of Heidtman, Whiteson and NCBI as applied to claims 51-53, 55, 57, 59-60 and 76-81 are discussed above. The claims of the reference application do not recite the cell is a yeast cell.
Ahmad reviews protein expression in the yeast Pichia pastoris [title], wherein it is disclosed that “P. pastoris is an established protein expression host for the production of biopharmaceuticals and industrial enzymes” [abstract].
Regarding instant claim 56, Ahmad discloses “this methyltrophic yeast is a distinguished production system for its growth to very high cell densities, for the available strong and tightly regulated promoters, and for the options to produce gram amounts of recombinant protein per litre of culture broth both intracellularly and in secretory fashion” [abstract].
In view of Ahmad, it would have been obvious for one of ordinary skill in the art before the effective filing date of the claimed invention to modify the combined cell of the reference application, Heidtman and Whiteson by using a Pichia pastoris cell, as disclosed by Ahmad, to arrive at the claimed invention. One of ordinary skill in the art would have been motivated to modify the combined cell of the reference application, Heidtman and Whiteson by using the yeast cell of Ahmad, because Ahmad discloses that P. pastoris is an established protein expression host for the production of biopharmaceuticals and industrial enzymes. One of ordinary skill in the art would have had a reasonable expectation of success because the reference application and Heidtman disclose cellular systems for the production of α-(1,3)-fucosyllactose that is considered a biopharmaceutical, and Ahmad discuss cellular systems for the production of biopharmaceuticals.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
D. Claims 51-53, 55-57, 59-60 and 76-81 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 94-95 and 97-98 of copending Application No. 17/904189 (hereafter “reference application”) in view of Heidtman, Whiteson and NCBI.
The instant rejection is maintained from the previous Office Action and any newly recited portions are necessitated by claim amendment.
Regarding instant claim 51 and the limitation of “a cell comprising at least one polynucleotide encoding a polypeptide with α-(1,3)-fucosyltransferase activity”, claims 95 and 98 of the reference application recite a method of producing 3-fucosyllactose by a cell genetically modified to encode an enzyme for glycosylated product synthesis, which is considered to encompass fucosyltransferase enzymes.
The claims of the reference application do not recite a fucosyltransferase with the domains specified in SEQ ID NOs: 33 and 34 of instant claim 51, nor that the C-terminus is 100 amino acids or less from the GDP-fucose binding domain (SEQ ID NO: 33).
Heidtman discloses methods for producing purified fucosylated oligosaccharides in milk [para 3], involving the use of engineered bacteria with heterologously expressed enzymes in order to optimize production efficiency [para 6]. Heidtman discloses methods that include production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25].
Regarding instant claims 51-52, Heidtman discloses “methods for producing α-(1,3)-fucosylated oligosaccharides utilizing a bacterial strain harbouring an expression plasmid containing two different α-(1,3)-fucosyltransferases in ‘tandem’ arrangement. These tandem α-(1,3)-fucosyltransferases may be under the control of the PL promoter” [para 18], and that the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49]. Furthermore, Heidtman states “a preferred α-(1,3)-fucosyltransferase utilizes GDP-fucose as a donor, and lactose is the acceptor for that donor [para 98]. As such, Heidtman satisfies the limitations of instant claim 52, as well as the limitations of instant claim 51 regarding a cell that produces α-1,3-fucosyllactose, the cell comprising at least one polynucleotide encoding an exogenous polypeptide with α-1,3-fucosyltransferase activity and able to use lactose as an acceptor substrate.
Heidtman further discusses methods of identifying α-(1,3)-fucosyltransferases enzymes capable of synthesizing fucosylated oligosaccharides such as 3-FL [para 47] and fucosyltransferase enzymes capable of using lactose as an acceptor comprising performing a computational search to define a broad group of simple sequence homologs of any known, lactose-utilizing fucosyltransferase, searching that group for common sequence and/or structural motifs shared by members of that group, searching sequence databases for said common sequence and/or structural motifs to identify candidate sequences, and expressing candidate enzymes to test for lactose utilization [para 99].
Whiteson describes the genomic analysis of the bacteria Basilea psittacipulmonis [title], wherein the genome was deposited and the encoded polypeptides were annotated by NCBI, namely the polypeptide AIL32582.1. This polypeptide is identified as an α-(1,3)-fucosyltransferase domain containing polypeptide as evidenced by NCBI. This polypeptide further contains a GDP-fucose binding domain of YITEK (residues 233-237) that corresponds to SEQ ID NO: 33 specified in i) of claim 51, as well as the sequence DLYLGF (residues 107-112) that corresponds to SEQ ID NO: 34 specified in ii) of instant claim 51. As the polypeptide of Whiteson is 329 amino acids in length, the starting amino acid of the GDP-fucose binding domain (residue 233) is less than 100 amino acids from the C-terminus of the polypeptide. Therefore, the polypeptide AIL32582.1 as evidenced by NCBI is considered to contain the “α-1,3-fucosyltransferase activity and the ability to use lactose as an acceptor substrate” as recited in instant claim 51, as the activity is considered to be inherent to the structure of the polypeptide (see MPEP 2112.01(I)).
In view of Heidtman and Whiteson, it would have been obvious to one of ordinary skill in the art before the effective filing date to modify the cell of the reference application to use the polypeptide of Whiteson as identified by NCBI, since the simple substitution of one known element for another results in a predictable result. One of ordinary skill in the art would have recognized that the enzyme for glycosylated product synthesis disclosed by the reference application and the polypeptide of Whiteson are both capable of generating glycosylated products, and as such both are capable of being incorporated into such cells as described by both the reference application and Whiteson. One of ordinary skill in the art would have been motivated to replace the fucosyltransferase of the reference application with the polypeptide of Whiteson, because Heidtman discloses the engineering of bacteria with heterologously expressed enzymes in order to optimize production efficiency of human milk oligosaccharides such as α-(1,3)-fucosyllactose, and because Heidtman discusses a method to screen sequence databases for novel enzymes capable of carrying out target fucosyltransferase activity. Thus it would have been obvious to one of ordinary skill in the art to replace the enzyme for glycosylated product synthesis of the reference application with the polypeptide of Whiteson, as one of ordinary skill in the art would have been able to carry out such a substitution with a reasonable expectation of success because both the reference application and Whiteson discuss cells capable of producing glycosylated products.
Regarding instant claim 53 and the elected species of SEQ ID NO: 6, the polypeptide AIL32582.1 of Whiteson is 100% identical to SEQ ID NO: 6 as evidenced by the attached sequence search results [see Appendix A].
Regarding instant claim 55, claim 94 of the reference application discloses that the cell is an Escherichia coli cell.
Regarding instant claim 56, claim 97 of the reference application discloses that the cell is a bacterium or a yeast.
Regarding instant claim 57, Heidtman discloses synthetic genes of α-(1-3)-fucosyltransferase genes are designed using standard methods known in the art, and include sequences that are codon-optimized for expression in a host bacterial strain [para 117].
Regarding instant claim 59, claim 95 discloses a genetically modified cell producing a glycosylated product, and Whiteson discloses the polypeptide AIL32582.1 that contains the domains in SEQ ID NOs: 33 and 34 as described in the double patenting rejection on instant claim 51 above.
Regarding instant claim 60, Whiteson discloses the polypeptide AIL32582.1 that is 100% identical to SEQ ID NO: 6 as evidenced by the attached sequence search results [see Appendix A] as discussed above.
Regarding instant claim 76, the polypeptide of Whiteson as described above is 100% identical to SEQ ID NO: 6 as discussed above [see Appendix A].
Regarding instant claim 77, Heidtman discloses the nucleic acid can be integrated into the genome of the host cell [para 23].
Regarding instant claim 78, the polypeptide of Whiteson as described above is 100% identical to SEQ ID NO: 6 as discussed above [see Appendix A], and therefore it is considered to have a conserved GDP-fucose binding domain corresponding to residues 233-237 of SEQ ID NO: 6.
Regarding instant claim 79, Heidtman discloses “methods for producing α-(1,3)-fucosylated oligosaccharides utilizing a bacterial strain harbouring an expression plasmid containing two different α-(1,3)-fucosyltransferases in ‘tandem’ arrangement. These tandem α-(1,3)-fucosyltransferases may be under the control of the PL promoter” [para 18], and that the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49], and that the nucleic acid can be integrated into the genome of the host cell [para 23]. Heidtman further discloses the method includes production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25], wherein the E. coli is typically Escherichia coli K12 [para 27]. Furthermore, Heidtman states “a preferred α-(1,3)-fucosyltransferase utilizes GDP-fucose as a donor, and lactose is the acceptor for that donor [para 98]. As such, Heidtman satisfies the limitations of claim 52, as well as the limitations of claim 51 regarding a cell that produces α-1,3-fucosyllactose, the cell comprising at least one polynucleotide encoding an exogenous polypeptide with α-1,3-fucosyltransferase activity and able to use lactose as an acceptor substrate to produce α-1,3-fucosyllactose. Heidtman further discusses methods of identifying α-(1,3)-fucosyltransferases enzymes capable of synthesizing fucosylated oligosaccharides such as 3-FL [para 47] and fucosyltransferase enzymes capable of using lactose as an acceptor comprising performing a computational search to define a broad group of simple sequence homologs of any known, lactose-utilizing fucosyltransferase, searching that group for common sequence and/or structural motifs shared by members of that group, searching sequence databases for said common sequence and/or structural motifs to identify candidate sequences, and expressing candidate enzymes to test for lactose utilization [para 99].
Regarding instant claim 79, Whiteson describes the genomic analysis of the bacteria Basilea psittacipulmonis [title], wherein the genome was deposited and the encoded polypeptides were annotated by NCBI, namely the polypeptide AIL32582.1. This polypeptide is identified as an α-(1,3)-fucosyltransferase domain-containing polypeptide as evidenced by NCBI. This polypeptide further contains a GDP-fucose binding domain of YITEK (residues 233-237) that corresponds to SEQ ID NO: 33 specified in i) of claim 51, as well as the sequence DLYLGF (residues 107-112) that corresponds to SEQ ID NO: 34 specified in ii) of claim 51. As the polypeptide of Whiteson is 329 amino acids in length, the starting amino acid of the GDP-fucose binding domain (residue 233) is less than 100 amino acids from the C-terminus of the polypeptide. Therefore, the polypeptide AIL32582.1 as evidenced by NCBI is considered to contain the “α-1,3-fucosyltransferase activity and the ability to use lactose as an acceptor substrate” as recited in claim 51, as the activity is considered to be inherent to the structure of the polypeptide (see MPEP 2112.01(I)). As the polypeptide of Whiteson shares 100% identity with SEQ ID NO: 6, it is considered to have the GDP-fucose binding domain corresponding to residues 233-237 of SEQ ID NO: 6.
In view of Heidtman and Whiteson, it would have been obvious to one of ordinary skill in the art before the effective filing date to modify the cell of the reference application to use the polypeptide of Whiteson as identified by NCBI, since the simple substitution of one known element for another results in a predictable result. One of ordinary skill in the art would have recognized that the enzyme by the reference application and the polypeptide of Whiteson are fucosyltransferases, and as such both are capable of being incorporated into such cells as described by both the reference application and Whiteson. One of ordinary skill in the art would have been motivated to replace the fucosyltransferase of the reference application with the fucosyltransferase of Whiteson, because Heidtman discloses the engineering of bacteria with heterologously expressed enzymes in order to optimize production efficiency of human milk oligosaccharides such as α-(1,3)-fucosyllactose, and because Heidtman discusses a method to screen sequence databases for novel enzymes capable of carrying out target fucosyltransferase activity. Thus it would have been obvious to one of ordinary skill in the art to replace the fucosyltransferase of the reference application with the polypeptide of Whiteson, as one of ordinary skill in the art would have been able to carry out such a substitution with a reasonable expectation of success because both the reference application and Whiteson discuss cells capable of producing fucosyltransferase enzymes.
Regarding instant claim 80 (dependent from claim 51), Heidtman discloses the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49] as discussed in the rejection of claim 51 above, and the recombinant DNA constructs are supplied on a plasmid expression vector [para 36].
Regarding instant claim 81, Heidtman discloses “methods for producing α-(1,3)-fucosylated oligosaccharides utilizing a bacterial strain harbouring an expression plasmid containing two different α-(1,3)-fucosyltransferases in ‘tandem’ arrangement. These tandem α-(1,3)-fucosyltransferases may be under the control of the PL promoter” [para 18], and that the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49], and that the recombinant DNA constructs are supplied on a plasmid expression vector [para 36]. Heidtman further discloses the method includes production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25], wherein the E. coli is typically Escherichia coli K12 [para 27]. Furthermore, Heidtman states “a preferred α-(1,3)-fucosyltransferase utilizes GDP-fucose as a donor, and lactose is the acceptor for that donor [para 98]. As such, Heidtman satisfies the limitations of claim 52, as well as the limitations of claim 51 regarding a cell that produces α-1,3-fucosyllactose, the cell comprising at least one polynucleotide encoding an exogenous polypeptide with α-1,3-fucosyltransferase activity and able to use lactose as an acceptor substrate to produce α-1,3-fucosyllactose. Heidtman further discusses methods of identifying α-(1,3)-fucosyltransferases enzymes capable of synthesizing fucosylated oligosaccharides such as 3-FL [para 47] and fucosyltransferase enzymes capable of using lactose as an acceptor comprising performing a computational search to define a broad group of simple sequence homologs of any known, lactose-utilizing fucosyltransferase, searching that group for common sequence and/or structural motifs shared by members of that group, searching sequence databases for said common sequence and/or structural motifs to identify candidate sequences, and expressing candidate enzymes to test for lactose utilization [para 99].
Regarding instant claim 81, Whiteson describes the genomic analysis of the bacteria Basilea psittacipulmonis [title], wherein the genome was deposited and the encoded polypeptides were annotated by NCBI, namely the polypeptide AIL32582.1. This polypeptide is identified as an α-(1,3)-fucosyltransferase domain-containing polypeptide as evidenced by NCBI. This polypeptide further contains a GDP-fucose binding domain of YITEK (residues 233-237) that corresponds to SEQ ID NO: 33 specified in i) of claim 51, as well as the sequence DLYLGF (residues 107-112) that corresponds to SEQ ID NO: 34 specified in ii) of claim 51. As the polypeptide of Whiteson is 329 amino acids in length, the starting amino acid of the GDP-fucose binding domain (residue 233) is less than 100 amino acids from the C-terminus of the polypeptide. Therefore, the polypeptide AIL32582.1 as evidenced by NCBI is considered to contain the “α-1,3-fucosyltransferase activity and the ability to use lactose as an acceptor substrate” as recited in claim 51, as the activity is considered to be inherent to the structure of the polypeptide (see MPEP 2112.01(I)). As the polypeptide of Whiteson shares 100% identity with SEQ ID NO: 6, it is considered to have the GDP-fucose binding domain corresponding to residues 233-237 of SEQ ID NO: 6.
In view of Heidtman and Whiteson, it would have been obvious to one of ordinary skill in the art before the effective filing date to modify the cell of the reference application to use the polypeptide of Whiteson as identified by NCBI, since the simple substitution of one known element for another results in a predictable result. One of ordinary skill in the art would have recognized that the enzyme by the reference application and the polypeptide of Whiteson are fucosyltransferases, and as such both are capable of being incorporated into such cells as described by both the reference application and Whiteson. One of ordinary skill in the art would have been motivated to replace the fucosyltransferase of the reference application with the fucosyltransferase of Whiteson, because Heidtman discloses the engineering of bacteria with heterologously expressed enzymes in order to optimize production efficiency of human milk oligosaccharides such as α-(1,3)-fucosyllactose, and because Heidtman discusses a method to screen sequence databases for novel enzymes capable of carrying out target fucosyltransferase activity. Thus it would have been obvious to one of ordinary skill in the art to replace the fucosyltransferase of the reference application with the polypeptide of Whiteson, as one of ordinary skill in the art would have been able to carry out such a substitution with a reasonable expectation of success because both the reference application and Whiteson discuss cells capable of producing fucosyltransferase enzymes.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
F. Claims 51-53, 55-57, 59-60 and 76-81 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 60 and 75 of copending Application No. 18/041137 (hereafter “reference application”) in view of Heidtman, Whiteson and NCBI.
The instant rejection is maintained from the previous Office Action and any newly recited portions are necessitated by claim amendment.
Regarding instant claim 51 and the limitation of “a cell comprising at least one polynucleotide encoding a polypeptide with α-(1,3)-fucosyltransferase activity”, claim 60 of the reference application recites a genetically modified cell that expresses a fucosyltransferase.
The claims of the reference application do not recite that a fucosyltransferase with the domains specified in SEQ ID NOs: 33 and 34 of instant claim 51, nor that the C-terminus is 100 amino acids or less from the GDP-fucose binding domain (SEQ ID NO: 33).
Heidtman discloses methods for producing purified fucosylated oligosaccharides in milk [para 3], involving the use of engineered bacteria with heterologously expressed enzymes in order to optimize production efficiency [para 6]. Heidtman discloses methods that include production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25].
Regarding instant claims 51-52, Heidtman discloses “methods for producing α-(1,3)-fucosylated oligosaccharides utilizing a bacterial strain harbouring an expression plasmid containing two different α-(1,3)-fucosyltransferases in ‘tandem’ arrangement. These tandem α-(1,3)-fucosyltransferases may be under the control of the PL promoter” [para 18], and that the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49]. Furthermore, Heidtman states “a preferred α-(1,3)-fucosyltransferase utilizes GDP-fucose as a donor, and lactose is the acceptor for that donor [para 98]. As such, Heidtman satisfies the limitations of instant claim 52, as well as the limitations of instant claim 51 regarding a cell that produces α-1,3-fucosyllactose, the cell comprising at least one polynucleotide encoding an exogenous polypeptide with α-1,3-fucosyltransferase activity and able to use lactose as an acceptor substrate.
Heidtman further discusses methods of identifying α-(1,3)-fucosyltransferases enzymes capable of synthesizing fucosylated oligosaccharides such as 3-FL [para 47] and fucosyltransferase enzymes capable of using lactose as an acceptor comprising performing a computational search to define a broad group of simple sequence homologs of any known, lactose-utilizing fucosyltransferase, searching that group for common sequence and/or structural motifs shared by members of that group, searching sequence databases for said common sequence and/or structural motifs to identify candidate sequences, and expressing candidate enzymes to test for lactose utilization [para 99].
Whiteson describes the genomic analysis of the bacteria Basilea psittacipulmonis [title], wherein the genome was deposited and the encoded polypeptides were annotated by NCBI, namely the polypeptide AIL32582.1. This polypeptide is identified as an α-(1,3)-fucosyltransferase domain containing polypeptide as evidenced by NCBI. This polypeptide further contains a GDP-fucose binding domain of YITEK (residues 233-237) that corresponds to SEQ ID NO: 33 specified in i) of claim 51, as well as the sequence DLYLGF (residues 107-112) that corresponds to SEQ ID NO: 34 specified in ii) of instant claim 51. As the polypeptide of Whiteson is 329 amino acids in length, the starting amino acid of the GDP-fucose binding domain (residue 233) is less than 100 amino acids from the C-terminus of the polypeptide. Therefore, the polypeptide AIL32582.1 as evidenced by NCBI is considered to contain the “α-1,3-fucosyltransferase activity and the ability to use lactose as an acceptor substrate” as recited in instant claim 51, as the activity is considered to be inherent to the structure of the polypeptide (see MPEP 2112.01(I)).
In view of Heidtman and Whiteson, it would have been obvious to one of ordinary skill in the art before the effective filing date to modify the cell of the reference application to use the polypeptide of Whiteson as identified by NCBI, since the simple substitution of one known element for another results in a predictable result. One of ordinary skill in the art would have recognized that both the enzyme disclosed by the reference application and the polypeptide of Whiteson are fucosyltransferases, and as such both are capable of being incorporated into such cells as described by both the reference application and Whiteson. One of ordinary skill in the art would have been motivated to replace the fucosyltransferase of the reference application with the polypeptide of Whiteson, because Heidtman discloses the engineering of bacteria with heterologously expressed enzymes in order to optimize production efficiency of human milk oligosaccharides such as α-(1,3)-fucosyllactose, and because Heidtman discusses a method to screen sequence databases for novel enzymes capable of carrying out target fucosyltransferase activity. Thus it would have been obvious to one of ordinary skill in the art to replace the fucosyltransferase of the reference application with the polypeptide of Whiteson, as one of ordinary skill in the art would have been able to carry out such a substitution with a reasonable expectation of success because both the reference application and Whiteson discuss cells capable of producing fucosyltransferase enzymes.
Regarding instant claim 53 and the elected species of SEQ ID NO: 6, the polypeptide AIL32582.1 of Whiteson is 100% identical to SEQ ID NO: 6 as evidenced by the attached sequence search results [see Appendix A].
Regarding instant claim 55, Heidtman discloses methods that include production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25].
Regarding instant claim 56, claim 75 of the reference application discloses that the cell is a bacterium or a yeast.
Regarding instant claim 57, Heidtman discloses synthetic genes of α-(1-3)-fucosyltransferase genes are designed using standard methods known in the art, and include sequences that are codon-optimized for expression in a host bacterial strain [para 117].
Regarding instant claim 59, Heidtman discloses methods that include production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1-3)-fucosyltransferase gene” [para 25], and Whiteson discloses the polypeptide AIL32582.1 that contains the GDP-fucose binding domain specified by SEQ ID NO: 33, the amino acid sequence specified by SEQ ID NO: 34, and less than 100 amino acids between the beginning of the GDP-fucose binding domain and the C-terminus of the peptide as discussed above.
Regarding instant claim 60, Whiteson discloses the polypeptide AIL32582.1 that is 100% identical to SEQ ID NO: 6 as evidenced by the attached sequence search results [see Appendix A] as discussed above.
Regarding instant claim 76, the polypeptide of Whiteson as described above is 100% identical to SEQ ID NO: 6 as discussed above [see Appendix A].
Regarding instant claim 77, Heidtman discloses the nucleic acid can be integrated into the genome of the host cell [para 23].
Regarding instant claim 78, the polypeptide of Whiteson as described above is 100% identical to SEQ ID NO: 6 as discussed above [see Appendix A], and therefore it is considered to have a conserved GDP-fucose binding domain corresponding to residues 233-237 of SEQ ID NO: 6.
Regarding instant claim 79, Heidtman discloses “methods for producing α-(1,3)-fucosylated oligosaccharides utilizing a bacterial strain harbouring an expression plasmid containing two different α-(1,3)-fucosyltransferases in ‘tandem’ arrangement. These tandem α-(1,3)-fucosyltransferases may be under the control of the PL promoter” [para 18], and that the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49], and that the nucleic acid can be integrated into the genome of the host cell [para 23]. Heidtman further discloses the method includes production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25], wherein the E. coli is typically Escherichia coli K12 [para 27]. Furthermore, Heidtman states “a preferred α-(1,3)-fucosyltransferase utilizes GDP-fucose as a donor, and lactose is the acceptor for that donor [para 98]. As such, Heidtman satisfies the limitations of claim 52, as well as the limitations of claim 51 regarding a cell that produces α-1,3-fucosyllactose, the cell comprising at least one polynucleotide encoding an exogenous polypeptide with α-1,3-fucosyltransferase activity and able to use lactose as an acceptor substrate to produce α-1,3-fucosyllactose. Heidtman further discusses methods of identifying α-(1,3)-fucosyltransferases enzymes capable of synthesizing fucosylated oligosaccharides such as 3-FL [para 47] and fucosyltransferase enzymes capable of using lactose as an acceptor comprising performing a computational search to define a broad group of simple sequence homologs of any known, lactose-utilizing fucosyltransferase, searching that group for common sequence and/or structural motifs shared by members of that group, searching sequence databases for said common sequence and/or structural motifs to identify candidate sequences, and expressing candidate enzymes to test for lactose utilization [para 99].
Regarding instant claim 79, Whiteson describes the genomic analysis of the bacteria Basilea psittacipulmonis [title], wherein the genome was deposited and the encoded polypeptides were annotated by NCBI, namely the polypeptide AIL32582.1. This polypeptide is identified as an α-(1,3)-fucosyltransferase domain-containing polypeptide as evidenced by NCBI. This polypeptide further contains a GDP-fucose binding domain of YITEK (residues 233-237) that corresponds to SEQ ID NO: 33 specified in i) of claim 51, as well as the sequence DLYLGF (residues 107-112) that corresponds to SEQ ID NO: 34 specified in ii) of claim 51. As the polypeptide of Whiteson is 329 amino acids in length, the starting amino acid of the GDP-fucose binding domain (residue 233) is less than 100 amino acids from the C-terminus of the polypeptide. Therefore, the polypeptide AIL32582.1 as evidenced by NCBI is considered to contain the “α-1,3-fucosyltransferase activity and the ability to use lactose as an acceptor substrate” as recited in claim 51, as the activity is considered to be inherent to the structure of the polypeptide (see MPEP 2112.01(I)). As the polypeptide of Whiteson shares 100% identity with SEQ ID NO: 6, it is considered to have the GDP-fucose binding domain corresponding to residues 233-237 of SEQ ID NO: 6.
In view of Heidtman and Whiteson, it would have been obvious to one of ordinary skill in the art before the effective filing date to modify the cell of the reference application to use the polypeptide of Whiteson as identified by NCBI, since the simple substitution of one known element for another results in a predictable result. One of ordinary skill in the art would have recognized that the enzyme by the reference application and the polypeptide of Whiteson are fucosyltransferases, and as such both are capable of being incorporated into such cells as described by both the reference application and Whiteson. One of ordinary skill in the art would have been motivated to replace the fucosyltransferase of the reference application with the fucosyltransferase of Whiteson, because Heidtman discloses the engineering of bacteria with heterologously expressed enzymes in order to optimize production efficiency of human milk oligosaccharides such as α-(1,3)-fucosyllactose, and because Heidtman discusses a method to screen sequence databases for novel enzymes capable of carrying out target fucosyltransferase activity. Thus it would have been obvious to one of ordinary skill in the art to replace the fucosyltransferase of the reference application with the polypeptide of Whiteson, as one of ordinary skill in the art would have been able to carry out such a substitution with a reasonable expectation of success because both the reference application and Whiteson discuss cells capable of producing fucosyltransferase enzymes.
Regarding instant claim 80 (dependent from claim 51), Heidtman discloses the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49] as discussed in the rejection of claim 51 above, and the recombinant DNA constructs are supplied on a plasmid expression vector [para 36].
Regarding instant claim 81, Heidtman discloses “methods for producing α-(1,3)-fucosylated oligosaccharides utilizing a bacterial strain harbouring an expression plasmid containing two different α-(1,3)-fucosyltransferases in ‘tandem’ arrangement. These tandem α-(1,3)-fucosyltransferases may be under the control of the PL promoter” [para 18], and that the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49], and that the recombinant DNA constructs are supplied on a plasmid expression vector [para 36]. Heidtman further discloses the method includes production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25], wherein the E. coli is typically Escherichia coli K12 [para 27]. Furthermore, Heidtman states “a preferred α-(1,3)-fucosyltransferase utilizes GDP-fucose as a donor, and lactose is the acceptor for that donor [para 98]. As such, Heidtman satisfies the limitations of claim 52, as well as the limitations of claim 51 regarding a cell that produces α-1,3-fucosyllactose, the cell comprising at least one polynucleotide encoding an exogenous polypeptide with α-1,3-fucosyltransferase activity and able to use lactose as an acceptor substrate to produce α-1,3-fucosyllactose. Heidtman further discusses methods of identifying α-(1,3)-fucosyltransferases enzymes capable of synthesizing fucosylated oligosaccharides such as 3-FL [para 47] and fucosyltransferase enzymes capable of using lactose as an acceptor comprising performing a computational search to define a broad group of simple sequence homologs of any known, lactose-utilizing fucosyltransferase, searching that group for common sequence and/or structural motifs shared by members of that group, searching sequence databases for said common sequence and/or structural motifs to identify candidate sequences, and expressing candidate enzymes to test for lactose utilization [para 99].
Regarding instant claim 81, Whiteson describes the genomic analysis of the bacteria Basilea psittacipulmonis [title], wherein the genome was deposited and the encoded polypeptides were annotated by NCBI, namely the polypeptide AIL32582.1. This polypeptide is identified as an α-(1,3)-fucosyltransferase domain-containing polypeptide as evidenced by NCBI. This polypeptide further contains a GDP-fucose binding domain of YITEK (residues 233-237) that corresponds to SEQ ID NO: 33 specified in i) of claim 51, as well as the sequence DLYLGF (residues 107-112) that corresponds to SEQ ID NO: 34 specified in ii) of claim 51. As the polypeptide of Whiteson is 329 amino acids in length, the starting amino acid of the GDP-fucose binding domain (residue 233) is less than 100 amino acids from the C-terminus of the polypeptide. Therefore, the polypeptide AIL32582.1 as evidenced by NCBI is considered to contain the “α-1,3-fucosyltransferase activity and the ability to use lactose as an acceptor substrate” as recited in claim 51, as the activity is considered to be inherent to the structure of the polypeptide (see MPEP 2112.01(I)). As the polypeptide of Whiteson shares 100% identity with SEQ ID NO: 6, it is considered to have the GDP-fucose binding domain corresponding to residues 233-237 of SEQ ID NO: 6.
In view of Heidtman and Whiteson, it would have been obvious to one of ordinary skill in the art before the effective filing date to modify the cell of the reference application to use the polypeptide of Whiteson as identified by NCBI, since the simple substitution of one known element for another results in a predictable result. One of ordinary skill in the art would have recognized that the enzyme by the reference application and the polypeptide of Whiteson are fucosyltransferases, and as such both are capable of being incorporated into such cells as described by both the reference application and Whiteson. One of ordinary skill in the art would have been motivated to replace the fucosyltransferase of the reference application with the fucosyltransferase of Whiteson, because Heidtman discloses the engineering of bacteria with heterologously expressed enzymes in order to optimize production efficiency of human milk oligosaccharides such as α-(1,3)-fucosyllactose, and because Heidtman discusses a method to screen sequence databases for novel enzymes capable of carrying out target fucosyltransferase activity. Thus it would have been obvious to one of ordinary skill in the art to replace the fucosyltransferase of the reference application with the polypeptide of Whiteson, as one of ordinary skill in the art would have been able to carry out such a substitution with a reasonable expectation of success because both the reference application and Whiteson discuss cells capable of producing fucosyltransferase enzymes.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
G. Claims 51-53, 55-57, 59-60 and 76-81 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 35, 37 and 52 of copending Application No. 18/167687 (hereafter “reference application”) in view of Heidtman, Whiteson and NCBI.
The instant rejection is maintained from the previous Office Action and any newly recited portions are necessitated by claim amendment.
Regarding instant claim 51 and the limitation of “a cell comprising at least one polynucleotide encoding a polypeptide with α-(1,3)-fucosyltransferase activity”, claim 35 of the reference application recites a genetically modified cell that synthesizes a galactosylated disaccharide or oligosaccharide, and claim 37 of the reference application limits that cell to express enzymes that include fucosyltransferases.
The claims of the reference application do not recite a fucosyltransferase with the domains specified in SEQ ID NOs: 33 and 34 of instant claim 51, nor that the C-terminus is 100 amino acids or less from the GDP-fucose binding domain (SEQ ID NO: 33).
Heidtman discloses methods for producing purified fucosylated oligosaccharides in milk [para 3], involving the use of engineered bacteria with heterologously expressed enzymes in order to optimize production efficiency [para 6]. Heidtman discloses methods that include production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25].
Regarding instant claims 51-52, Heidtman discloses “methods for producing α-(1,3)-fucosylated oligosaccharides utilizing a bacterial strain harbouring an expression plasmid containing two different α-(1,3)-fucosyltransferases in ‘tandem’ arrangement. These tandem α-(1,3)-fucosyltransferases may be under the control of the PL promoter” [para 18], and that the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49]. Furthermore, Heidtman states “a preferred α-(1,3)-fucosyltransferase utilizes GDP-fucose as a donor, and lactose is the acceptor for that donor [para 98]. As such, Heidtman satisfies the limitations of instant claim 52, as well as the limitations of instant claim 51 regarding a cell that produces α-1,3-fucosyllactose, the cell comprising at least one polynucleotide encoding an exogenous polypeptide with α-1,3-fucosyltransferase activity and able to use lactose as an acceptor substrate.
Heidtman further discusses methods of identifying α-(1,3)-fucosyltransferases enzymes capable of synthesizing fucosylated oligosaccharides such as 3-FL [para 47] and fucosyltransferase enzymes capable of using lactose as an acceptor comprising performing a computational search to define a broad group of simple sequence homologs of any known, lactose-utilizing fucosyltransferase, searching that group for common sequence and/or structural motifs shared by members of that group, searching sequence databases for said common sequence and/or structural motifs to identify candidate sequences, and expressing candidate enzymes to test for lactose utilization [para 99].
Whiteson describes the genomic analysis of the bacteria Basilea psittacipulmonis [title], wherein the genome was deposited and the encoded polypeptides were annotated by NCBI, namely the polypeptide AIL32582.1. This polypeptide is identified as an α-(1,3)-fucosyltransferase domain containing polypeptide as evidenced by NCBI. This polypeptide further contains a GDP-fucose binding domain of YITEK (residues 233-237) that corresponds to SEQ ID NO: 33 specified in i) of claim 51, as well as the sequence DLYLGF (residues 107-112) that corresponds to SEQ ID NO: 34 specified in ii) of instant claim 51. As the polypeptide of Whiteson is 329 amino acids in length, the starting amino acid of the GDP-fucose binding domain (residue 233) is less than 100 amino acids from the C-terminus of the polypeptide. Therefore, the polypeptide AIL32582.1 as evidenced by NCBI is considered to contain the “α-1,3-fucosyltransferase activity and the ability to use lactose as an acceptor substrate” as recited in instant claim 51, as the activity is considered to be inherent to the structure of the polypeptide (see MPEP 2112.01(I)).
In view of Heidtman and Whiteson, it would have been obvious to one of ordinary skill in the art before the effective filing date to modify the cell of the reference application to use the polypeptide of Whiteson as identified by NCBI, since the simple substitution of one known element for another results in a predictable result. One of ordinary skill in the art would have recognized that fucosyltransferase disclosed by the reference application and the polypeptide of Whiteson are fucosyltransferases, and as such both are capable of being incorporated into such cells as described by both the reference application and Whiteson. One of ordinary skill in the art would have been motivated to replace the fucosyltransferase of the reference application with the polypeptide of Whiteson, because Heidtman discloses the engineering of bacteria with heterologously expressed enzymes in order to optimize production efficiency of human milk oligosaccharides such as α-(1,3)-fucosyllactose, and because Heidtman discusses a method to screen sequence databases for novel enzymes capable of carrying out target fucosyltransferase activity. Thus it would have been obvious to one of ordinary skill in the art to replace the fucosyltransferase of the reference application with the polypeptide of Whiteson, as one of ordinary skill in the art would have been able to carry out such a substitution with a reasonable expectation of success because both the reference application and Whiteson discuss cells capable of producing fucosyltransferase enzymes.
Regarding instant claim 53 and the elected species of SEQ ID NO: 6, the polypeptide AIL32582.1 of Whiteson is 100% identical to SEQ ID NO: 6 as evidenced by the attached sequence search results [see Appendix A].
Regarding instant claim 55, Heidtman discloses methods that include production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25].
Regarding instant claim 56, claim 52 of the reference application recites the cell is a bacterium or yeast cell.
Regarding instant claim 57, Heidtman discloses synthetic genes of α-(1-3)-fucosyltransferase genes are designed using standard methods known in the art, and include sequences that are codon-optimized for expression in a host bacterial strain [para 117].
Regarding instant claim 59, Heidtman discloses methods that include production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1-3)-fucosyltransferase gene” [para 25], and Whiteson discloses the polypeptide AIL32582.1 that contains the GDP-fucose binding domain specified by SEQ ID NO: 33, the amino acid sequence specified by SEQ ID NO: 34, and less than 100 amino acids between the beginning of the GDP-fucose binding domain and the C-terminus of the peptide as discussed above.
Regarding instant claim 60, Whiteson discloses the polypeptide AIL32582.1 that is 100% identical to SEQ ID NO: 6 as evidenced by the attached sequence search results [see Appendix A] as discussed above.
Regarding instant claim 76, the polypeptide of Whiteson as described above is 100% identical to SEQ ID NO: 6 as discussed above [see Appendix A].
Regarding instant claim 77, Heidtman discloses the nucleic acid can be integrated into the genome of the host cell [para 23].
Regarding instant claim 78, the polypeptide of Whiteson as described above is 100% identical to SEQ ID NO: 6 as discussed above [see Appendix A], and therefore it is considered to have a conserved GDP-fucose binding domain corresponding to residues 233-237 of SEQ ID NO: 6.
Regarding instant claim 79, Heidtman discloses “methods for producing α-(1,3)-fucosylated oligosaccharides utilizing a bacterial strain harbouring an expression plasmid containing two different α-(1,3)-fucosyltransferases in ‘tandem’ arrangement. These tandem α-(1,3)-fucosyltransferases may be under the control of the PL promoter” [para 18], and that the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49], and that the nucleic acid can be integrated into the genome of the host cell [para 23]. Heidtman further discloses the method includes production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25], wherein the E. coli is typically Escherichia coli K12 [para 27]. Furthermore, Heidtman states “a preferred α-(1,3)-fucosyltransferase utilizes GDP-fucose as a donor, and lactose is the acceptor for that donor [para 98]. As such, Heidtman satisfies the limitations of claim 52, as well as the limitations of claim 51 regarding a cell that produces α-1,3-fucosyllactose, the cell comprising at least one polynucleotide encoding an exogenous polypeptide with α-1,3-fucosyltransferase activity and able to use lactose as an acceptor substrate to produce α-1,3-fucosyllactose. Heidtman further discusses methods of identifying α-(1,3)-fucosyltransferases enzymes capable of synthesizing fucosylated oligosaccharides such as 3-FL [para 47] and fucosyltransferase enzymes capable of using lactose as an acceptor comprising performing a computational search to define a broad group of simple sequence homologs of any known, lactose-utilizing fucosyltransferase, searching that group for common sequence and/or structural motifs shared by members of that group, searching sequence databases for said common sequence and/or structural motifs to identify candidate sequences, and expressing candidate enzymes to test for lactose utilization [para 99].
Regarding instant claim 79, Whiteson describes the genomic analysis of the bacteria Basilea psittacipulmonis [title], wherein the genome was deposited and the encoded polypeptides were annotated by NCBI, namely the polypeptide AIL32582.1. This polypeptide is identified as an α-(1,3)-fucosyltransferase domain-containing polypeptide as evidenced by NCBI. This polypeptide further contains a GDP-fucose binding domain of YITEK (residues 233-237) that corresponds to SEQ ID NO: 33 specified in i) of claim 51, as well as the sequence DLYLGF (residues 107-112) that corresponds to SEQ ID NO: 34 specified in ii) of claim 51. As the polypeptide of Whiteson is 329 amino acids in length, the starting amino acid of the GDP-fucose binding domain (residue 233) is less than 100 amino acids from the C-terminus of the polypeptide. Therefore, the polypeptide AIL32582.1 as evidenced by NCBI is considered to contain the “α-1,3-fucosyltransferase activity and the ability to use lactose as an acceptor substrate” as recited in claim 51, as the activity is considered to be inherent to the structure of the polypeptide (see MPEP 2112.01(I)). As the polypeptide of Whiteson shares 100% identity with SEQ ID NO: 6, it is considered to have the GDP-fucose binding domain corresponding to residues 233-237 of SEQ ID NO: 6.
In view of Heidtman and Whiteson, it would have been obvious to one of ordinary skill in the art before the effective filing date to modify the cell of the reference application to use the polypeptide of Whiteson as identified by NCBI, since the simple substitution of one known element for another results in a predictable result. One of ordinary skill in the art would have recognized that the enzyme by the reference application and the polypeptide of Whiteson are fucosyltransferases, and as such both are capable of being incorporated into such cells as described by both the reference application and Whiteson. One of ordinary skill in the art would have been motivated to replace the fucosyltransferase of the reference application with the fucosyltransferase of Whiteson, because Heidtman discloses the engineering of bacteria with heterologously expressed enzymes in order to optimize production efficiency of human milk oligosaccharides such as α-(1,3)-fucosyllactose, and because Heidtman discusses a method to screen sequence databases for novel enzymes capable of carrying out target fucosyltransferase activity. Thus it would have been obvious to one of ordinary skill in the art to replace the fucosyltransferase of the reference application with the polypeptide of Whiteson, as one of ordinary skill in the art would have been able to carry out such a substitution with a reasonable expectation of success because both the reference application and Whiteson discuss cells capable of producing fucosyltransferase enzymes.
Regarding instant claim 80 (dependent from claim 51), Heidtman discloses the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49] as discussed in the rejection of claim 51 above, and the recombinant DNA constructs are supplied on a plasmid expression vector [para 36].
Regarding instant claim 81, Heidtman discloses “methods for producing α-(1,3)-fucosylated oligosaccharides utilizing a bacterial strain harbouring an expression plasmid containing two different α-(1,3)-fucosyltransferases in ‘tandem’ arrangement. These tandem α-(1,3)-fucosyltransferases may be under the control of the PL promoter” [para 18], and that the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49], and that the recombinant DNA constructs are supplied on a plasmid expression vector [para 36]. Heidtman further discloses the method includes production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25], wherein the E. coli is typically Escherichia coli K12 [para 27]. Furthermore, Heidtman states “a preferred α-(1,3)-fucosyltransferase utilizes GDP-fucose as a donor, and lactose is the acceptor for that donor [para 98]. As such, Heidtman satisfies the limitations of claim 52, as well as the limitations of claim 51 regarding a cell that produces α-1,3-fucosyllactose, the cell comprising at least one polynucleotide encoding an exogenous polypeptide with α-1,3-fucosyltransferase activity and able to use lactose as an acceptor substrate to produce α-1,3-fucosyllactose. Heidtman further discusses methods of identifying α-(1,3)-fucosyltransferases enzymes capable of synthesizing fucosylated oligosaccharides such as 3-FL [para 47] and fucosyltransferase enzymes capable of using lactose as an acceptor comprising performing a computational search to define a broad group of simple sequence homologs of any known, lactose-utilizing fucosyltransferase, searching that group for common sequence and/or structural motifs shared by members of that group, searching sequence databases for said common sequence and/or structural motifs to identify candidate sequences, and expressing candidate enzymes to test for lactose utilization [para 99].
Regarding instant claim 81, Whiteson describes the genomic analysis of the bacteria Basilea psittacipulmonis [title], wherein the genome was deposited and the encoded polypeptides were annotated by NCBI, namely the polypeptide AIL32582.1. This polypeptide is identified as an α-(1,3)-fucosyltransferase domain-containing polypeptide as evidenced by NCBI. This polypeptide further contains a GDP-fucose binding domain of YITEK (residues 233-237) that corresponds to SEQ ID NO: 33 specified in i) of claim 51, as well as the sequence DLYLGF (residues 107-112) that corresponds to SEQ ID NO: 34 specified in ii) of claim 51. As the polypeptide of Whiteson is 329 amino acids in length, the starting amino acid of the GDP-fucose binding domain (residue 233) is less than 100 amino acids from the C-terminus of the polypeptide. Therefore, the polypeptide AIL32582.1 as evidenced by NCBI is considered to contain the “α-1,3-fucosyltransferase activity and the ability to use lactose as an acceptor substrate” as recited in claim 51, as the activity is considered to be inherent to the structure of the polypeptide (see MPEP 2112.01(I)). As the polypeptide of Whiteson shares 100% identity with SEQ ID NO: 6, it is considered to have the GDP-fucose binding domain corresponding to residues 233-237 of SEQ ID NO: 6.
In view of Heidtman and Whiteson, it would have been obvious to one of ordinary skill in the art before the effective filing date to modify the cell of the reference application to use the polypeptide of Whiteson as identified by NCBI, since the simple substitution of one known element for another results in a predictable result. One of ordinary skill in the art would have recognized that the enzyme by the reference application and the polypeptide of Whiteson are fucosyltransferases, and as such both are capable of being incorporated into such cells as described by both the reference application and Whiteson. One of ordinary skill in the art would have been motivated to replace the fucosyltransferase of the reference application with the fucosyltransferase of Whiteson, because Heidtman discloses the engineering of bacteria with heterologously expressed enzymes in order to optimize production efficiency of human milk oligosaccharides such as α-(1,3)-fucosyllactose, and because Heidtman discusses a method to screen sequence databases for novel enzymes capable of carrying out target fucosyltransferase activity. Thus it would have been obvious to one of ordinary skill in the art to replace the fucosyltransferase of the reference application with the polypeptide of Whiteson, as one of ordinary skill in the art would have been able to carry out such a substitution with a reasonable expectation of success because both the reference application and Whiteson discuss cells capable of producing fucosyltransferase enzymes.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
I. Claims 51-53, 55-57, 59-60 and 76-81 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 128 and 185 of copending Application No. 18/041167 (hereafter “reference application”) in view of Heidtman, Whiteson and NCBI.
The instant rejection is maintained from the previous Office Action and any newly recited portions are necessitated by claim amendment.
Regarding instant claim 51 and the limitation of “a cell comprising at least one polynucleotide encoding a polypeptide with α-(1,3)-fucosyltransferase activity”, claim 128 of the reference application recites a method of producing an oligosaccharide comprising the expression of a fucosyltransferase in a cell.
The claims of the reference application do not recite a fucosyltransferase with the domains specified in SEQ ID NOs: 33 and 34 of instant claim 51, nor that the C-terminus is 100 amino acids or less from the GDP-fucose binding domain (SEQ ID NO: 33).
Heidtman discloses methods for producing purified fucosylated oligosaccharides in milk [para 3], involving the use of engineered bacteria with heterologously expressed enzymes in order to optimize production efficiency [para 6]. Heidtman discloses methods that include production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25].
Regarding instant claims 51-52, Heidtman discloses “methods for producing α-(1,3)-fucosylated oligosaccharides utilizing a bacterial strain harbouring an expression plasmid containing two different α-(1,3)-fucosyltransferases in ‘tandem’ arrangement. These tandem α-(1,3)-fucosyltransferases may be under the control of the PL promoter” [para 18], and that the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49]. Furthermore, Heidtman states “a preferred α-(1,3)-fucosyltransferase utilizes GDP-fucose as a donor, and lactose is the acceptor for that donor [para 98]. As such, Heidtman satisfies the limitations of instant claim 52, as well as the limitations of instant claim 51 regarding a cell that produces α-1,3-fucosyllactose, the cell comprising at least one polynucleotide encoding an exogenous polypeptide with α-1,3-fucosyltransferase activity and able to use lactose as an acceptor substrate.
Heidtman further discusses methods of identifying α-(1,3)-fucosyltransferases enzymes capable of synthesizing fucosylated oligosaccharides such as 3-FL [para 47] and fucosyltransferase enzymes capable of using lactose as an acceptor comprising performing a computational search to define a broad group of simple sequence homologs of any known, lactose-utilizing fucosyltransferase, searching that group for common sequence and/or structural motifs shared by members of that group, searching sequence databases for said common sequence and/or structural motifs to identify candidate sequences, and expressing candidate enzymes to test for lactose utilization [para 99].
Whiteson describes the genomic analysis of the bacteria Basilea psittacipulmonis [title], wherein the genome was deposited and the encoded polypeptides were annotated by NCBI, namely the polypeptide AIL32582.1. This polypeptide is identified as an α-(1,3)-fucosyltransferase domain containing polypeptide as evidenced by NCBI. This polypeptide further contains a GDP-fucose binding domain of YITEK (residues 233-237) that corresponds to SEQ ID NO: 33 specified in i) of claim 51, as well as the sequence DLYLGF (residues 107-112) that corresponds to SEQ ID NO: 34 specified in ii) of instant claim 51. As the polypeptide of Whiteson is 329 amino acids in length, the starting amino acid of the GDP-fucose binding domain (residue 233) is less than 100 amino acids from the C-terminus of the polypeptide. Therefore, the polypeptide AIL32582.1 as evidenced by NCBI is considered to contain the “α-1,3-fucosyltransferase activity and the ability to use lactose as an acceptor substrate” as recited in instant claim 51, as the activity is considered to be inherent to the structure of the polypeptide (see MPEP 2112.01(I)).
In view of Heidtman and Whiteson, it would have been obvious to one of ordinary skill in the art before the effective filing date to modify the cell of the reference application to use the polypeptide of Whiteson as identified by NCBI, since the simple substitution of one known element for another results in a predictable result. One of ordinary skill in the art would have recognized that both the fucosyltransferase disclosed by the reference application and the polypeptide of Whiteson are fucosyltransferases, and as such both are capable of being incorporated into such cells as described by both the reference application and Whiteson. One of ordinary skill in the art would have been motivated to replace the fucosyltransferase of the reference application with the polypeptide of Whiteson, because Heidtman discloses the engineering of bacteria with heterologously expressed enzymes in order to optimize production efficiency of human milk oligosaccharides such as α-(1,3)-fucosyllactose, and because Heidtman discusses a method to screen sequence databases for novel enzymes capable of carrying out target fucosyltransferase activity. Thus it would have been obvious to one of ordinary skill in the art to replace the fucosyltransferase of the reference application with the polypeptide of Whiteson, as one of ordinary skill in the art would have been able to carry out such a substitution with a reasonable expectation of success because both the reference application and Whiteson discuss cells capable of producing fucosyltransferase enzymes.
Regarding instant claim 53 and the elected species of SEQ ID NO: 6, the polypeptide AIL32582.1 of Whiteson is 100% identical to SEQ ID NO: 6 as evidenced by the attached sequence search results [see Appendix A].
Regarding instant claim 55, Heidtman discloses methods that include production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25].
Regarding instant claim 56, claim 185 of the reference application recites the cell is a bacterium or yeast cell.
Regarding instant claim 57, Heidtman discloses synthetic genes of α-(1-3)-fucosyltransferase genes are designed using standard methods known in the art, and include sequences that are codon-optimized for expression in a host bacterial strain [para 117].
Regarding instant claim 59, Heidtman discloses methods that include production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1-3)-fucosyltransferase gene” [para 25], and Whiteson discloses the polypeptide AIL32582.1 that contains the GDP-fucose binding domain specified by SEQ ID NO: 33, the amino acid sequence specified by SEQ ID NO: 34, and less than 100 amino acids between the beginning of the GDP-fucose binding domain and the C-terminus of the peptide as discussed above.
Regarding instant claim 60, Whiteson discloses the polypeptide AIL32582.1 that is 100% identical to SEQ ID NO: 6 as evidenced by the attached sequence search results [see Appendix A] as discussed above.
Regarding instant claim 76, the polypeptide of Whiteson as described above is 100% identical to SEQ ID NO: 6 as discussed above [see Appendix A].
Regarding instant claim 77, Heidtman discloses the nucleic acid can be integrated into the genome of the host cell [para 23].
Regarding instant claim 78, the polypeptide of Whiteson as described above is 100% identical to SEQ ID NO: 6 as discussed above [see Appendix A], and therefore it is considered to have a conserved GDP-fucose binding domain corresponding to residues 233-237 of SEQ ID NO: 6.
Regarding instant claim 79, Heidtman discloses “methods for producing α-(1,3)-fucosylated oligosaccharides utilizing a bacterial strain harbouring an expression plasmid containing two different α-(1,3)-fucosyltransferases in ‘tandem’ arrangement. These tandem α-(1,3)-fucosyltransferases may be under the control of the PL promoter” [para 18], and that the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49], and that the nucleic acid can be integrated into the genome of the host cell [para 23]. Heidtman further discloses the method includes production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25], wherein the E. coli is typically Escherichia coli K12 [para 27]. Furthermore, Heidtman states “a preferred α-(1,3)-fucosyltransferase utilizes GDP-fucose as a donor, and lactose is the acceptor for that donor [para 98]. As such, Heidtman satisfies the limitations of claim 52, as well as the limitations of claim 51 regarding a cell that produces α-1,3-fucosyllactose, the cell comprising at least one polynucleotide encoding an exogenous polypeptide with α-1,3-fucosyltransferase activity and able to use lactose as an acceptor substrate to produce α-1,3-fucosyllactose. Heidtman further discusses methods of identifying α-(1,3)-fucosyltransferases enzymes capable of synthesizing fucosylated oligosaccharides such as 3-FL [para 47] and fucosyltransferase enzymes capable of using lactose as an acceptor comprising performing a computational search to define a broad group of simple sequence homologs of any known, lactose-utilizing fucosyltransferase, searching that group for common sequence and/or structural motifs shared by members of that group, searching sequence databases for said common sequence and/or structural motifs to identify candidate sequences, and expressing candidate enzymes to test for lactose utilization [para 99].
Regarding instant claim 79, Whiteson describes the genomic analysis of the bacteria Basilea psittacipulmonis [title], wherein the genome was deposited and the encoded polypeptides were annotated by NCBI, namely the polypeptide AIL32582.1. This polypeptide is identified as an α-(1,3)-fucosyltransferase domain-containing polypeptide as evidenced by NCBI. This polypeptide further contains a GDP-fucose binding domain of YITEK (residues 233-237) that corresponds to SEQ ID NO: 33 specified in i) of claim 51, as well as the sequence DLYLGF (residues 107-112) that corresponds to SEQ ID NO: 34 specified in ii) of claim 51. As the polypeptide of Whiteson is 329 amino acids in length, the starting amino acid of the GDP-fucose binding domain (residue 233) is less than 100 amino acids from the C-terminus of the polypeptide. Therefore, the polypeptide AIL32582.1 as evidenced by NCBI is considered to contain the “α-1,3-fucosyltransferase activity and the ability to use lactose as an acceptor substrate” as recited in claim 51, as the activity is considered to be inherent to the structure of the polypeptide (see MPEP 2112.01(I)). As the polypeptide of Whiteson shares 100% identity with SEQ ID NO: 6, it is considered to have the GDP-fucose binding domain corresponding to residues 233-237 of SEQ ID NO: 6.
In view of Heidtman and Whiteson, it would have been obvious to one of ordinary skill in the art before the effective filing date to modify the cell of the reference application to use the polypeptide of Whiteson as identified by NCBI, since the simple substitution of one known element for another results in a predictable result. One of ordinary skill in the art would have recognized that the enzyme by the reference application and the polypeptide of Whiteson are fucosyltransferases, and as such both are capable of being incorporated into such cells as described by both the reference application and Whiteson. One of ordinary skill in the art would have been motivated to replace the fucosyltransferase of the reference application with the fucosyltransferase of Whiteson, because Heidtman discloses the engineering of bacteria with heterologously expressed enzymes in order to optimize production efficiency of human milk oligosaccharides such as α-(1,3)-fucosyllactose, and because Heidtman discusses a method to screen sequence databases for novel enzymes capable of carrying out target fucosyltransferase activity. Thus it would have been obvious to one of ordinary skill in the art to replace the fucosyltransferase of the reference application with the polypeptide of Whiteson, as one of ordinary skill in the art would have been able to carry out such a substitution with a reasonable expectation of success because both the reference application and Whiteson discuss cells capable of producing fucosyltransferase enzymes.
Regarding instant claim 80 (dependent from claim 51), Heidtman discloses the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49] as discussed in the rejection of claim 51 above, and the recombinant DNA constructs are supplied on a plasmid expression vector [para 36].
Regarding instant claim 81, Heidtman discloses “methods for producing α-(1,3)-fucosylated oligosaccharides utilizing a bacterial strain harbouring an expression plasmid containing two different α-(1,3)-fucosyltransferases in ‘tandem’ arrangement. These tandem α-(1,3)-fucosyltransferases may be under the control of the PL promoter” [para 18], and that the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49], and that the recombinant DNA constructs are supplied on a plasmid expression vector [para 36]. Heidtman further discloses the method includes production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25], wherein the E. coli is typically Escherichia coli K12 [para 27]. Furthermore, Heidtman states “a preferred α-(1,3)-fucosyltransferase utilizes GDP-fucose as a donor, and lactose is the acceptor for that donor [para 98]. As such, Heidtman satisfies the limitations of claim 52, as well as the limitations of claim 51 regarding a cell that produces α-1,3-fucosyllactose, the cell comprising at least one polynucleotide encoding an exogenous polypeptide with α-1,3-fucosyltransferase activity and able to use lactose as an acceptor substrate to produce α-1,3-fucosyllactose. Heidtman further discusses methods of identifying α-(1,3)-fucosyltransferases enzymes capable of synthesizing fucosylated oligosaccharides such as 3-FL [para 47] and fucosyltransferase enzymes capable of using lactose as an acceptor comprising performing a computational search to define a broad group of simple sequence homologs of any known, lactose-utilizing fucosyltransferase, searching that group for common sequence and/or structural motifs shared by members of that group, searching sequence databases for said common sequence and/or structural motifs to identify candidate sequences, and expressing candidate enzymes to test for lactose utilization [para 99].
Regarding instant claim 81, Whiteson describes the genomic analysis of the bacteria Basilea psittacipulmonis [title], wherein the genome was deposited and the encoded polypeptides were annotated by NCBI, namely the polypeptide AIL32582.1. This polypeptide is identified as an α-(1,3)-fucosyltransferase domain-containing polypeptide as evidenced by NCBI. This polypeptide further contains a GDP-fucose binding domain of YITEK (residues 233-237) that corresponds to SEQ ID NO: 33 specified in i) of claim 51, as well as the sequence DLYLGF (residues 107-112) that corresponds to SEQ ID NO: 34 specified in ii) of claim 51. As the polypeptide of Whiteson is 329 amino acids in length, the starting amino acid of the GDP-fucose binding domain (residue 233) is less than 100 amino acids from the C-terminus of the polypeptide. Therefore, the polypeptide AIL32582.1 as evidenced by NCBI is considered to contain the “α-1,3-fucosyltransferase activity and the ability to use lactose as an acceptor substrate” as recited in claim 51, as the activity is considered to be inherent to the structure of the polypeptide (see MPEP 2112.01(I)). As the polypeptide of Whiteson shares 100% identity with SEQ ID NO: 6, it is considered to have the GDP-fucose binding domain corresponding to residues 233-237 of SEQ ID NO: 6.
In view of Heidtman and Whiteson, it would have been obvious to one of ordinary skill in the art before the effective filing date to modify the cell of the reference application to use the polypeptide of Whiteson as identified by NCBI, since the simple substitution of one known element for another results in a predictable result. One of ordinary skill in the art would have recognized that the enzyme by the reference application and the polypeptide of Whiteson are fucosyltransferases, and as such both are capable of being incorporated into such cells as described by both the reference application and Whiteson. One of ordinary skill in the art would have been motivated to replace the fucosyltransferase of the reference application with the fucosyltransferase of Whiteson, because Heidtman discloses the engineering of bacteria with heterologously expressed enzymes in order to optimize production efficiency of human milk oligosaccharides such as α-(1,3)-fucosyllactose, and because Heidtman discusses a method to screen sequence databases for novel enzymes capable of carrying out target fucosyltransferase activity. Thus it would have been obvious to one of ordinary skill in the art to replace the fucosyltransferase of the reference application with the polypeptide of Whiteson, as one of ordinary skill in the art would have been able to carry out such a substitution with a reasonable expectation of success because both the reference application and Whiteson discuss cells capable of producing fucosyltransferase enzymes.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
J. Claims 51-53, 55, 57, 59-60 and 76-81 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 49 of copending Application No. 17/767400 (hereafter “reference application”) in view of Heidtman, Whiteson and NCBI.
The instant rejection is maintained from the previous Office Action and any newly recited portions are necessitated by claim amendment.
Regarding instant claim 51 and the limitation of “a cell comprising at least one polynucleotide encoding a polypeptide with α-(1,3)-fucosyltransferase activity”, claim 49 of the reference application recites a cell producing an oligosaccharide bioproduct selected from the group consisting of fucosyllactoses.
The claims of the reference application do not recite a fucosyltransferase with the domains specified in SEQ ID NOs: 33 and 34 of instant claim 51, nor that the C-terminus is 100 amino acids or less from the GDP-fucose binding domain (SEQ ID NO: 33).
Heidtman discloses methods for producing purified fucosylated oligosaccharides in milk [para 3], involving the use of engineered bacteria with heterologously expressed enzymes in order to optimize production efficiency [para 6]. Heidtman discloses methods that include production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25], and discusses methods of including exogenous α-(1,3)-fucosyltransferases in engineered cells can offer a biological alternative to expensive chemical synthesis of human milk oligosaccharides [para 6] such as 3FL [para 5].
Regarding instant claims 51-52, Heidtman discloses “methods for producing α-(1,3)-fucosylated oligosaccharides utilizing a bacterial strain harbouring an expression plasmid containing two different α-(1,3)-fucosyltransferases in ‘tandem’ arrangement. These tandem α-(1,3)-fucosyltransferases may be under the control of the PL promoter” [para 18], and that the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49]. Furthermore, Heidtman states “a preferred α-(1,3)-fucosyltransferase utilizes GDP-fucose as a donor, and lactose is the acceptor for that donor [para 98]. As such, Heidtman satisfies the limitations of instant claim 52, as well as the limitations of instant claim 51 regarding a cell that produces α-1,3-fucosyllactose, the cell comprising at least one polynucleotide encoding an exogenous polypeptide with α-1,3-fucosyltransferase activity and able to use lactose as an acceptor substrate.
Heidtman further discusses methods of identifying α-(1,3)-fucosyltransferases enzymes capable of synthesizing fucosylated oligosaccharides such as 3-FL [para 47] and fucosyltransferase enzymes capable of using lactose as an acceptor comprising performing a computational search to define a broad group of simple sequence homologs of any known, lactose-utilizing fucosyltransferase, searching that group for common sequence and/or structural motifs shared by members of that group, searching sequence databases for said common sequence and/or structural motifs to identify candidate sequences, and expressing candidate enzymes to test for lactose utilization [para 99].
Whiteson describes the genomic analysis of the bacteria Basilea psittacipulmonis [title], wherein the genome was deposited and the encoded polypeptides were annotated by NCBI, namely the polypeptide AIL32582.1. This polypeptide is identified as an α-(1,3)-fucosyltransferase domain containing polypeptide as evidenced by NCBI. This polypeptide further contains a GDP-fucose binding domain of YITEK (residues 233-237) that corresponds to SEQ ID NO: 33 specified in i) of claim 51, as well as the sequence DLYLGF (residues 107-112) that corresponds to SEQ ID NO: 34 specified in ii) of instant claim 51. As the polypeptide of Whiteson is 329 amino acids in length, the starting amino acid of the GDP-fucose binding domain (residue 233) is less than 100 amino acids from the C-terminus of the polypeptide. Therefore, the polypeptide AIL32582.1 as evidenced by NCBI is considered to contain the “α-1,3-fucosyltransferase activity and the ability to use lactose as an acceptor substrate” as recited in instant claim 51, as the activity is considered to be inherent to the structure of the polypeptide (see MPEP 2112.01(I)).
In view of Heidtman, it would have been obvious to one of ordinary skill in the art before the effective filing date to modify the cell of the patent by expressing the exogenous enzyme of Heidtman. One of ordinary skill in the art would have been motivated to modify the claims of the patent by using the enzyme of Heidtman because Heidtman discusses methods of including exogenous α-(1,3)-fucosyltransferases in engineered cells can offer a biological alternative to expensive chemical synthesis of human milk oligosaccharides such as 3FL. One of ordinary skill in the art would have had a reasonable expectation of success because both the patent and Heidtman relate to cells comprising enzymes for the production of 3FL.
In view of Whiteson, it would have been obvious to one of ordinary skill in the art before the effective filing date to modify the combined cell of the patent and Heidtman by replacing the polypeptide of Heidtman with the polypeptide of Whiteson. One of ordinary skill in the art would have recognized that the both the polypeptide of Heidtman and the polypeptide of Whiteson are a-1,3-fucosyltransferases, and as such both are capable of being incorporated into such cells as described by the patent and Heidtman. One of ordinary skill in the art would have been motivated to replace the fucosyltransferase of the Heidtman with the polypeptide of Whiteson, because Heidtman discloses the engineering of bacteria with heterologously expressed enzymes in order to optimize production efficiency of human milk oligosaccharides such as α-(1,3)-fucosyllactose, and because Heidtman discusses a method to screen sequence databases for novel enzymes capable of carrying out target fucosyltransferase activity. Thus it would have been obvious to one of ordinary skill in the art to replace the polypeptide of the Heidtman with the polypeptide of Whiteson, as one of ordinary skill in the art would have been able to carry out such a substitution with a reasonable expectation of success because Heidtman and Whiteson discuss cells capable of producing fucosyltransferase enzymes.
Regarding instant claim 53 and the elected species of SEQ ID NO: 6, the polypeptide AIL32582.1 of Whiteson is 100% identical to SEQ ID NO: 6 as evidenced by the attached sequence search results [see Appendix A].
Regarding instant claim 55, Heidtman discloses methods that include production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25].
Regarding instant claim 57, Heidtman discloses synthetic genes of α-(1-3)-fucosyltransferase genes are designed using standard methods known in the art, and include sequences that are codon-optimized for expression in a host bacterial strain [para 117].
Regarding instant claim 59, Heidtman discloses methods that include production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1-3)-fucosyltransferase gene” [para 25], and Whiteson discloses the polypeptide AIL32582.1 that contains the GDP-fucose binding domain specified by SEQ ID NO: 33, the amino acid sequence specified by SEQ ID NO: 34, and less than 100 amino acids between the beginning of the GDP-fucose binding domain and the C-terminus of the peptide as discussed above.
Regarding instant claim 60, Whiteson discloses the polypeptide AIL32582.1 that is 100% identical to SEQ ID NO: 6 as evidenced by the attached sequence search results [see Appendix A] as discussed above.
Regarding instant claim 76, the polypeptide of Whiteson as described above is 100% identical to SEQ ID NO: 6 as discussed above [see Appendix A].
Regarding instant claim 77, Heidtman discloses the nucleic acid can be integrated into the genome of the host cell [para 23].
Regarding instant claim 78, the polypeptide of Whiteson as described above is 100% identical to SEQ ID NO: 6 as discussed above [see Appendix A], and therefore it is considered to have a conserved GDP-fucose binding domain corresponding to residues 233-237 of SEQ ID NO: 6.
Regarding instant claim 79, Heidtman discloses “methods for producing α-(1,3)-fucosylated oligosaccharides utilizing a bacterial strain harbouring an expression plasmid containing two different α-(1,3)-fucosyltransferases in ‘tandem’ arrangement. These tandem α-(1,3)-fucosyltransferases may be under the control of the PL promoter” [para 18], and that the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49], and that the nucleic acid can be integrated into the genome of the host cell [para 23]. Heidtman further discloses the method includes production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25], wherein the E. coli is typically Escherichia coli K12 [para 27]. Furthermore, Heidtman states “a preferred α-(1,3)-fucosyltransferase utilizes GDP-fucose as a donor, and lactose is the acceptor for that donor [para 98]. As such, Heidtman satisfies the limitations of claim 52, as well as the limitations of claim 51 regarding a cell that produces α-1,3-fucosyllactose, the cell comprising at least one polynucleotide encoding an exogenous polypeptide with α-1,3-fucosyltransferase activity and able to use lactose as an acceptor substrate to produce α-1,3-fucosyllactose. Heidtman further discusses methods of identifying α-(1,3)-fucosyltransferases enzymes capable of synthesizing fucosylated oligosaccharides such as 3-FL [para 47] and fucosyltransferase enzymes capable of using lactose as an acceptor comprising performing a computational search to define a broad group of simple sequence homologs of any known, lactose-utilizing fucosyltransferase, searching that group for common sequence and/or structural motifs shared by members of that group, searching sequence databases for said common sequence and/or structural motifs to identify candidate sequences, and expressing candidate enzymes to test for lactose utilization [para 99].
Regarding instant claim 79, Whiteson describes the genomic analysis of the bacteria Basilea psittacipulmonis [title], wherein the genome was deposited and the encoded polypeptides were annotated by NCBI, namely the polypeptide AIL32582.1. This polypeptide is identified as an α-(1,3)-fucosyltransferase domain-containing polypeptide as evidenced by NCBI. This polypeptide further contains a GDP-fucose binding domain of YITEK (residues 233-237) that corresponds to SEQ ID NO: 33 specified in i) of claim 51, as well as the sequence DLYLGF (residues 107-112) that corresponds to SEQ ID NO: 34 specified in ii) of claim 51. As the polypeptide of Whiteson is 329 amino acids in length, the starting amino acid of the GDP-fucose binding domain (residue 233) is less than 100 amino acids from the C-terminus of the polypeptide. Therefore, the polypeptide AIL32582.1 as evidenced by NCBI is considered to contain the “α-1,3-fucosyltransferase activity and the ability to use lactose as an acceptor substrate” as recited in claim 51, as the activity is considered to be inherent to the structure of the polypeptide (see MPEP 2112.01(I)). As the polypeptide of Whiteson shares 100% identity with SEQ ID NO: 6, it is considered to have the GDP-fucose binding domain corresponding to residues 233-237 of SEQ ID NO: 6.
In view of Heidtman and Whiteson, it would have been obvious to one of ordinary skill in the art before the effective filing date to modify the cell of the reference application to use the polypeptide of Whiteson as identified by NCBI, since the simple substitution of one known element for another results in a predictable result. One of ordinary skill in the art would have recognized that the enzyme by the reference application and the polypeptide of Whiteson are fucosyltransferases, and as such both are capable of being incorporated into such cells as described by both the reference application and Whiteson. One of ordinary skill in the art would have been motivated to replace the fucosyltransferase of the reference application with the fucosyltransferase of Whiteson, because Heidtman discloses the engineering of bacteria with heterologously expressed enzymes in order to optimize production efficiency of human milk oligosaccharides such as α-(1,3)-fucosyllactose, and because Heidtman discusses a method to screen sequence databases for novel enzymes capable of carrying out target fucosyltransferase activity. Thus it would have been obvious to one of ordinary skill in the art to replace the fucosyltransferase of the reference application with the polypeptide of Whiteson, as one of ordinary skill in the art would have been able to carry out such a substitution with a reasonable expectation of success because both the reference application and Whiteson discuss cells capable of producing fucosyltransferase enzymes.
Regarding instant claim 80 (dependent from claim 51), Heidtman discloses the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49] as discussed in the rejection of claim 51 above, and the recombinant DNA constructs are supplied on a plasmid expression vector [para 36].
Regarding instant claim 81, Heidtman discloses “methods for producing α-(1,3)-fucosylated oligosaccharides utilizing a bacterial strain harbouring an expression plasmid containing two different α-(1,3)-fucosyltransferases in ‘tandem’ arrangement. These tandem α-(1,3)-fucosyltransferases may be under the control of the PL promoter” [para 18], and that the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49], and that the recombinant DNA constructs are supplied on a plasmid expression vector [para 36]. Heidtman further discloses the method includes production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25], wherein the E. coli is typically Escherichia coli K12 [para 27]. Furthermore, Heidtman states “a preferred α-(1,3)-fucosyltransferase utilizes GDP-fucose as a donor, and lactose is the acceptor for that donor [para 98]. As such, Heidtman satisfies the limitations of claim 52, as well as the limitations of claim 51 regarding a cell that produces α-1,3-fucosyllactose, the cell comprising at least one polynucleotide encoding an exogenous polypeptide with α-1,3-fucosyltransferase activity and able to use lactose as an acceptor substrate to produce α-1,3-fucosyllactose. Heidtman further discusses methods of identifying α-(1,3)-fucosyltransferases enzymes capable of synthesizing fucosylated oligosaccharides such as 3-FL [para 47] and fucosyltransferase enzymes capable of using lactose as an acceptor comprising performing a computational search to define a broad group of simple sequence homologs of any known, lactose-utilizing fucosyltransferase, searching that group for common sequence and/or structural motifs shared by members of that group, searching sequence databases for said common sequence and/or structural motifs to identify candidate sequences, and expressing candidate enzymes to test for lactose utilization [para 99].
Regarding instant claim 81, Whiteson describes the genomic analysis of the bacteria Basilea psittacipulmonis [title], wherein the genome was deposited and the encoded polypeptides were annotated by NCBI, namely the polypeptide AIL32582.1. This polypeptide is identified as an α-(1,3)-fucosyltransferase domain-containing polypeptide as evidenced by NCBI. This polypeptide further contains a GDP-fucose binding domain of YITEK (residues 233-237) that corresponds to SEQ ID NO: 33 specified in i) of claim 51, as well as the sequence DLYLGF (residues 107-112) that corresponds to SEQ ID NO: 34 specified in ii) of claim 51. As the polypeptide of Whiteson is 329 amino acids in length, the starting amino acid of the GDP-fucose binding domain (residue 233) is less than 100 amino acids from the C-terminus of the polypeptide. Therefore, the polypeptide AIL32582.1 as evidenced by NCBI is considered to contain the “α-1,3-fucosyltransferase activity and the ability to use lactose as an acceptor substrate” as recited in claim 51, as the activity is considered to be inherent to the structure of the polypeptide (see MPEP 2112.01(I)). As the polypeptide of Whiteson shares 100% identity with SEQ ID NO: 6, it is considered to have the GDP-fucose binding domain corresponding to residues 233-237 of SEQ ID NO: 6.
In view of Heidtman and Whiteson, it would have been obvious to one of ordinary skill in the art before the effective filing date to modify the cell of the reference application to use the polypeptide of Whiteson as identified by NCBI, since the simple substitution of one known element for another results in a predictable result. One of ordinary skill in the art would have recognized that the enzyme by the reference application and the polypeptide of Whiteson are fucosyltransferases, and as such both are capable of being incorporated into such cells as described by both the reference application and Whiteson. One of ordinary skill in the art would have been motivated to replace the fucosyltransferase of the reference application with the fucosyltransferase of Whiteson, because Heidtman discloses the engineering of bacteria with heterologously expressed enzymes in order to optimize production efficiency of human milk oligosaccharides such as α-(1,3)-fucosyllactose, and because Heidtman discusses a method to screen sequence databases for novel enzymes capable of carrying out target fucosyltransferase activity. Thus it would have been obvious to one of ordinary skill in the art to replace the fucosyltransferase of the reference application with the polypeptide of Whiteson, as one of ordinary skill in the art would have been able to carry out such a substitution with a reasonable expectation of success because both the reference application and Whiteson discuss cells capable of producing fucosyltransferase enzymes.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claim 56 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 49 of copending Application No. 17/767400 in view of Heidtman, Whiteson and NCBI, and further in view of Ahmad.
The instant rejection is maintained from the previous Office Action and any newly recited portions are necessitated by claim amendment.
Claim 56 is drawn to the cell of claim 51, wherein the cell is a yeast cell.
The claims of the reference application and disclosures of Heidtman, Whiteson and NCBI as applied to claims 51-53, 55, 57, 59-60 and 76-81 are discussed above. The claims of the reference application do not recite the cell is a yeast cell.
Ahmad reviews protein expression in the yeast Pichia pastoris [title], wherein it is disclosed that “P. pastoris is an established protein expression host for the production of biopharmaceuticals and industrial enzymes” [abstract].
Regarding instant claim 56, Ahmad discloses “this methyltrophic yeast is a distinguished production system for its growth to very high cell densities, for the available strong and tightly regulated promoters, and for the options to produce gram amounts of recombinant protein per litre of culture broth both intracellularly and in secretory fashion” [abstract].
In view of Ahmad, it would have been obvious for one of ordinary skill in the art before the effective filing date of the claimed invention to modify the combined cell of the reference application, Heidtman and Whiteson by using a Pichia pastoris cell, as disclosed by Ahmad, to arrive at the claimed invention. One of ordinary skill in the art would have been motivated to modify the combined cell of the reference application, Heidtman and Whiteson by using the yeast cell of Ahmad, because Ahmad discloses that P. pastoris is an established protein expression host for the production of biopharmaceuticals and industrial enzymes. One of ordinary skill in the art would have had a reasonable expectation of success because the reference application and Heidtman disclose cellular systems for the production of α-(1,3)-fucosyllactose that is considered a biopharmaceutical, and Ahmad discuss cellular systems for the production of biopharmaceuticals.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
K. Claims 51-53, 55-57, 59-60 and 76-81 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 75, 78 and 95 of copending Application No. 18/555611 (hereafter “reference application”) in view of Heidtman, Whiteson and NCBI.
The instant rejection is maintained from the previous Office Action and any newly recited portions are necessitated by claim amendment.
Regarding instant claim 51 and the limitation of “a cell comprising at least one polynucleotide encoding a polypeptide with α-(1,3)-fucosyltransferase activity”, claim 75 of the reference application recites a cell producing an oligosaccharide bioproduct selected from the group containing 3-fucosyllactose, and claim 78 of the reference application limits the cell to further expressing a fucosyltransferase.
The claims of the reference application do not recite a fucosyltransferase with the domains specified in SEQ ID NOs: 33 and 34 of instant claim 51, nor that the C-terminus is 100 amino acids or less from the GDP-fucose binding domain (SEQ ID NO: 33).
Heidtman discloses methods for producing purified fucosylated oligosaccharides in milk [para 3], involving the use of engineered bacteria with heterologously expressed enzymes in order to optimize production efficiency [para 6]. Heidtman discloses methods that include production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25].
Regarding instant claims 51-52, Heidtman discloses “methods for producing α-(1,3)-fucosylated oligosaccharides utilizing a bacterial strain harbouring an expression plasmid containing two different α-(1,3)-fucosyltransferases in ‘tandem’ arrangement. These tandem α-(1,3)-fucosyltransferases may be under the control of the PL promoter” [para 18], and that the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49]. Furthermore, Heidtman states “a preferred α-(1,3)-fucosyltransferase utilizes GDP-fucose as a donor, and lactose is the acceptor for that donor [para 98]. As such, Heidtman satisfies the limitations of instant claim 52, as well as the limitations of instant claim 51 regarding a cell that produces α-1,3-fucosyllactose, the cell comprising at least one polynucleotide encoding an exogenous polypeptide with α-1,3-fucosyltransferase activity and able to use lactose as an acceptor substrate.
Heidtman further discusses methods of identifying α-(1,3)-fucosyltransferases enzymes capable of synthesizing fucosylated oligosaccharides such as 3-FL [para 47] and fucosyltransferase enzymes capable of using lactose as an acceptor comprising performing a computational search to define a broad group of simple sequence homologs of any known, lactose-utilizing fucosyltransferase, searching that group for common sequence and/or structural motifs shared by members of that group, searching sequence databases for said common sequence and/or structural motifs to identify candidate sequences, and expressing candidate enzymes to test for lactose utilization [para 99].
Whiteson describes the genomic analysis of the bacteria Basilea psittacipulmonis [title], wherein the genome was deposited and the encoded polypeptides were annotated by NCBI, namely the polypeptide AIL32582.1. This polypeptide is identified as an α-(1,3)-fucosyltransferase domain containing polypeptide as evidenced by NCBI. This polypeptide further contains a GDP-fucose binding domain of YITEK (residues 233-237) that corresponds to SEQ ID NO: 33 specified in i) of claim 51, as well as the sequence DLYLGF (residues 107-112) that corresponds to SEQ ID NO: 34 specified in ii) of instant claim 51. As the polypeptide of Whiteson is 329 amino acids in length, the starting amino acid of the GDP-fucose binding domain (residue 233) is less than 100 amino acids from the C-terminus of the polypeptide. Therefore, the polypeptide AIL32582.1 as evidenced by NCBI is considered to contain the “α-1,3-fucosyltransferase activity and the ability to use lactose as an acceptor substrate” as recited in instant claim 51, as the activity is considered to be inherent to the structure of the polypeptide (see MPEP 2112.01(I)).
In view of Heidtman and Whiteson, it would have been obvious to one of ordinary skill in the art before the effective filing date to modify the cell of the reference application to use the polypeptide of Whiteson as identified by NCBI, since the simple substitution of one known element for another results in a predictable result. One of ordinary skill in the art would have recognized that both the fucosyltransferase disclosed by the reference application and the polypeptide of Whiteson are fucosyltransferases, and as such both are capable of being incorporated into such cells as described by both the reference application and Whiteson. One of ordinary skill in the art would have been motivated to replace the fucosyltransferase of the reference application with the polypeptide of Whiteson, because Heidtman discloses the engineering of bacteria with heterologously expressed enzymes in order to optimize production efficiency of human milk oligosaccharides such as α-(1,3)-fucosyllactose, and because Heidtman discusses a method to screen sequence databases for novel enzymes capable of carrying out target fucosyltransferase activity. Thus it would have been obvious to one of ordinary skill in the art to replace the fucosyltransferase of the reference application with the polypeptide of Whiteson, as one of ordinary skill in the art would have been able to carry out such a substitution with a reasonable expectation of success because both the reference application and Whiteson discuss cells capable of producing fucosyltransferase enzymes.
Regarding instant claim 53 and the elected species of SEQ ID NO: 6, the polypeptide AIL32582.1 of Whiteson is 100% identical to SEQ ID NO: 6 as evidenced by the attached sequence search results [see Appendix A].
Regarding instant claim 55, Heidtman discloses methods that include production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25].
Regarding instant claim 56, claim 95 of the reference application limits the cell to be a bacterium or yeast.
Regarding instant claim 57, Heidtman discloses synthetic genes of α-(1-3)-fucosyltransferase genes are designed using standard methods known in the art, and include sequences that are codon-optimized for expression in a host bacterial strain [para 117].
Regarding instant claim 59, Heidtman discloses methods that include production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1-3)-fucosyltransferase gene” [para 25], and Whiteson discloses the polypeptide AIL32582.1 that contains the GDP-fucose binding domain specified by SEQ ID NO: 33, the amino acid sequence specified by SEQ ID NO: 34, and less than 100 amino acids between the beginning of the GDP-fucose binding domain and the C-terminus of the peptide as discussed above.
Regarding instant claim 60, Whiteson discloses the polypeptide AIL32582.1 that is 100% identical to SEQ ID NO: 6 as evidenced by the attached sequence search results [see Appendix A] as discussed above.
Regarding instant claim 76, the polypeptide of Whiteson as described above is 100% identical to SEQ ID NO: 6 as discussed above [see Appendix A].
Regarding instant claim 77, Heidtman discloses the nucleic acid can be integrated into the genome of the host cell [para 23].
Regarding instant claim 78, the polypeptide of Whiteson as described above is 100% identical to SEQ ID NO: 6 as discussed above [see Appendix A], and therefore it is considered to have a conserved GDP-fucose binding domain corresponding to residues 233-237 of SEQ ID NO: 6.
Regarding instant claim 79, Heidtman discloses “methods for producing α-(1,3)-fucosylated oligosaccharides utilizing a bacterial strain harbouring an expression plasmid containing two different α-(1,3)-fucosyltransferases in ‘tandem’ arrangement. These tandem α-(1,3)-fucosyltransferases may be under the control of the PL promoter” [para 18], and that the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49], and that the nucleic acid can be integrated into the genome of the host cell [para 23]. Heidtman further discloses the method includes production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25], wherein the E. coli is typically Escherichia coli K12 [para 27]. Furthermore, Heidtman states “a preferred α-(1,3)-fucosyltransferase utilizes GDP-fucose as a donor, and lactose is the acceptor for that donor [para 98]. As such, Heidtman satisfies the limitations of claim 52, as well as the limitations of claim 51 regarding a cell that produces α-1,3-fucosyllactose, the cell comprising at least one polynucleotide encoding an exogenous polypeptide with α-1,3-fucosyltransferase activity and able to use lactose as an acceptor substrate to produce α-1,3-fucosyllactose. Heidtman further discusses methods of identifying α-(1,3)-fucosyltransferases enzymes capable of synthesizing fucosylated oligosaccharides such as 3-FL [para 47] and fucosyltransferase enzymes capable of using lactose as an acceptor comprising performing a computational search to define a broad group of simple sequence homologs of any known, lactose-utilizing fucosyltransferase, searching that group for common sequence and/or structural motifs shared by members of that group, searching sequence databases for said common sequence and/or structural motifs to identify candidate sequences, and expressing candidate enzymes to test for lactose utilization [para 99].
Regarding instant claim 79, Whiteson describes the genomic analysis of the bacteria Basilea psittacipulmonis [title], wherein the genome was deposited and the encoded polypeptides were annotated by NCBI, namely the polypeptide AIL32582.1. This polypeptide is identified as an α-(1,3)-fucosyltransferase domain-containing polypeptide as evidenced by NCBI. This polypeptide further contains a GDP-fucose binding domain of YITEK (residues 233-237) that corresponds to SEQ ID NO: 33 specified in i) of claim 51, as well as the sequence DLYLGF (residues 107-112) that corresponds to SEQ ID NO: 34 specified in ii) of claim 51. As the polypeptide of Whiteson is 329 amino acids in length, the starting amino acid of the GDP-fucose binding domain (residue 233) is less than 100 amino acids from the C-terminus of the polypeptide. Therefore, the polypeptide AIL32582.1 as evidenced by NCBI is considered to contain the “α-1,3-fucosyltransferase activity and the ability to use lactose as an acceptor substrate” as recited in claim 51, as the activity is considered to be inherent to the structure of the polypeptide (see MPEP 2112.01(I)). As the polypeptide of Whiteson shares 100% identity with SEQ ID NO: 6, it is considered to have the GDP-fucose binding domain corresponding to residues 233-237 of SEQ ID NO: 6.
In view of Heidtman and Whiteson, it would have been obvious to one of ordinary skill in the art before the effective filing date to modify the cell of the reference application to use the polypeptide of Whiteson as identified by NCBI, since the simple substitution of one known element for another results in a predictable result. One of ordinary skill in the art would have recognized that the enzyme by the reference application and the polypeptide of Whiteson are fucosyltransferases, and as such both are capable of being incorporated into such cells as described by both the reference application and Whiteson. One of ordinary skill in the art would have been motivated to replace the fucosyltransferase of the reference application with the fucosyltransferase of Whiteson, because Heidtman discloses the engineering of bacteria with heterologously expressed enzymes in order to optimize production efficiency of human milk oligosaccharides such as α-(1,3)-fucosyllactose, and because Heidtman discusses a method to screen sequence databases for novel enzymes capable of carrying out target fucosyltransferase activity. Thus it would have been obvious to one of ordinary skill in the art to replace the fucosyltransferase of the reference application with the polypeptide of Whiteson, as one of ordinary skill in the art would have been able to carry out such a substitution with a reasonable expectation of success because both the reference application and Whiteson discuss cells capable of producing fucosyltransferase enzymes.
Regarding instant claim 80 (dependent from claim 51), Heidtman discloses the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49] as discussed in the rejection of claim 51 above, and the recombinant DNA constructs are supplied on a plasmid expression vector [para 36].
Regarding instant claim 81, Heidtman discloses “methods for producing α-(1,3)-fucosylated oligosaccharides utilizing a bacterial strain harbouring an expression plasmid containing two different α-(1,3)-fucosyltransferases in ‘tandem’ arrangement. These tandem α-(1,3)-fucosyltransferases may be under the control of the PL promoter” [para 18], and that the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49], and that the recombinant DNA constructs are supplied on a plasmid expression vector [para 36]. Heidtman further discloses the method includes production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25], wherein the E. coli is typically Escherichia coli K12 [para 27]. Furthermore, Heidtman states “a preferred α-(1,3)-fucosyltransferase utilizes GDP-fucose as a donor, and lactose is the acceptor for that donor [para 98]. As such, Heidtman satisfies the limitations of claim 52, as well as the limitations of claim 51 regarding a cell that produces α-1,3-fucosyllactose, the cell comprising at least one polynucleotide encoding an exogenous polypeptide with α-1,3-fucosyltransferase activity and able to use lactose as an acceptor substrate to produce α-1,3-fucosyllactose. Heidtman further discusses methods of identifying α-(1,3)-fucosyltransferases enzymes capable of synthesizing fucosylated oligosaccharides such as 3-FL [para 47] and fucosyltransferase enzymes capable of using lactose as an acceptor comprising performing a computational search to define a broad group of simple sequence homologs of any known, lactose-utilizing fucosyltransferase, searching that group for common sequence and/or structural motifs shared by members of that group, searching sequence databases for said common sequence and/or structural motifs to identify candidate sequences, and expressing candidate enzymes to test for lactose utilization [para 99].
Regarding instant claim 81, Whiteson describes the genomic analysis of the bacteria Basilea psittacipulmonis [title], wherein the genome was deposited and the encoded polypeptides were annotated by NCBI, namely the polypeptide AIL32582.1. This polypeptide is identified as an α-(1,3)-fucosyltransferase domain-containing polypeptide as evidenced by NCBI. This polypeptide further contains a GDP-fucose binding domain of YITEK (residues 233-237) that corresponds to SEQ ID NO: 33 specified in i) of claim 51, as well as the sequence DLYLGF (residues 107-112) that corresponds to SEQ ID NO: 34 specified in ii) of claim 51. As the polypeptide of Whiteson is 329 amino acids in length, the starting amino acid of the GDP-fucose binding domain (residue 233) is less than 100 amino acids from the C-terminus of the polypeptide. Therefore, the polypeptide AIL32582.1 as evidenced by NCBI is considered to contain the “α-1,3-fucosyltransferase activity and the ability to use lactose as an acceptor substrate” as recited in claim 51, as the activity is considered to be inherent to the structure of the polypeptide (see MPEP 2112.01(I)). As the polypeptide of Whiteson shares 100% identity with SEQ ID NO: 6, it is considered to have the GDP-fucose binding domain corresponding to residues 233-237 of SEQ ID NO: 6.
In view of Heidtman and Whiteson, it would have been obvious to one of ordinary skill in the art before the effective filing date to modify the cell of the reference application to use the polypeptide of Whiteson as identified by NCBI, since the simple substitution of one known element for another results in a predictable result. One of ordinary skill in the art would have recognized that the enzyme by the reference application and the polypeptide of Whiteson are fucosyltransferases, and as such both are capable of being incorporated into such cells as described by both the reference application and Whiteson. One of ordinary skill in the art would have been motivated to replace the fucosyltransferase of the reference application with the fucosyltransferase of Whiteson, because Heidtman discloses the engineering of bacteria with heterologously expressed enzymes in order to optimize production efficiency of human milk oligosaccharides such as α-(1,3)-fucosyllactose, and because Heidtman discusses a method to screen sequence databases for novel enzymes capable of carrying out target fucosyltransferase activity. Thus it would have been obvious to one of ordinary skill in the art to replace the fucosyltransferase of the reference application with the polypeptide of Whiteson, as one of ordinary skill in the art would have been able to carry out such a substitution with a reasonable expectation of success because both the reference application and Whiteson discuss cells capable of producing fucosyltransferase enzymes.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
L. Claims 51-53, 55-57, 59-60 and 76-81 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 103 and 110 of copending Application No. 18/040356 (hereafter “reference application”) in view of Heidtman, Whiteson and NCBI.
The instant rejection is maintained from the previous Office Action and any newly recited portions are necessitated by claim amendment.
Regarding instant claim 51 and the limitation of “a cell comprising at least one polynucleotide encoding a polypeptide with α-(1,3)-fucosyltransferase activity”, claim 103 of the reference application recites a metabolically engineered cell producing oligosaccharides that expresses fucosyltransferases.
The claims of the reference application do not recite a fucosyltransferase with the domains specified in SEQ ID NOs: 33 and 34 of instant claim 51, nor that the C-terminus is 100 amino acids or less from the GDP-fucose binding domain (SEQ ID NO: 33).
Heidtman discloses methods for producing purified fucosylated oligosaccharides in milk [para 3], involving the use of engineered bacteria with heterologously expressed enzymes in order to optimize production efficiency [para 6]. Heidtman discloses methods that include production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25].
Regarding instant claims 51-52, Heidtman discloses “methods for producing α-(1,3)-fucosylated oligosaccharides utilizing a bacterial strain harbouring an expression plasmid containing two different α-(1,3)-fucosyltransferases in ‘tandem’ arrangement. These tandem α-(1,3)-fucosyltransferases may be under the control of the PL promoter” [para 18], and that the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49]. Furthermore, Heidtman states “a preferred α-(1,3)-fucosyltransferase utilizes GDP-fucose as a donor, and lactose is the acceptor for that donor [para 98]. As such, Heidtman satisfies the limitations of instant claim 52, as well as the limitations of instant claim 51 regarding a cell that produces α-1,3-fucosyllactose, the cell comprising at least one polynucleotide encoding an exogenous polypeptide with α-1,3-fucosyltransferase activity and able to use lactose as an acceptor substrate.
Heidtman further discusses methods of identifying α-(1,3)-fucosyltransferases enzymes capable of synthesizing fucosylated oligosaccharides such as 3-FL [para 47] and fucosyltransferase enzymes capable of using lactose as an acceptor comprising performing a computational search to define a broad group of simple sequence homologs of any known, lactose-utilizing fucosyltransferase, searching that group for common sequence and/or structural motifs shared by members of that group, searching sequence databases for said common sequence and/or structural motifs to identify candidate sequences, and expressing candidate enzymes to test for lactose utilization [para 99].
Whiteson describes the genomic analysis of the bacteria Basilea psittacipulmonis [title], wherein the genome was deposited and the encoded polypeptides were annotated by NCBI, namely the polypeptide AIL32582.1. This polypeptide is identified as an α-(1,3)-fucosyltransferase domain containing polypeptide as evidenced by NCBI. This polypeptide further contains a GDP-fucose binding domain of YITEK (residues 233-237) that corresponds to SEQ ID NO: 33 specified in i) of claim 51, as well as the sequence DLYLGF (residues 107-112) that corresponds to SEQ ID NO: 34 specified in ii) of instant claim 51. As the polypeptide of Whiteson is 329 amino acids in length, the starting amino acid of the GDP-fucose binding domain (residue 233) is less than 100 amino acids from the C-terminus of the polypeptide. Therefore, the polypeptide AIL32582.1 as evidenced by NCBI is considered to contain the “α-1,3-fucosyltransferase activity and the ability to use lactose as an acceptor substrate” as recited in instant claim 51, as the activity is considered to be inherent to the structure of the polypeptide (see MPEP 2112.01(I)).
In view of Heidtman and Whiteson, it would have been obvious to one of ordinary skill in the art before the effective filing date to modify the cell of the reference application to use the polypeptide of Whiteson as identified by NCBI, since the simple substitution of one known element for another results in a predictable result. One of ordinary skill in the art would have recognized that both fucosyltransferase disclosed by the reference application and the polypeptide of Whiteson are fucosyltransferases, and as such both are capable of being incorporated into such cells as described by both the reference application and Whiteson. One of ordinary skill in the art would have been motivated to replace the fucosyltransferase of the reference application with the polypeptide of Whiteson, because Heidtman discloses the engineering of bacteria with heterologously expressed enzymes in order to optimize production efficiency of human milk oligosaccharides such as α-(1,3)-fucosyllactose, and because Heidtman discusses a method to screen sequence databases for novel enzymes capable of carrying out target fucosyltransferase activity. Thus it would have been obvious to one of ordinary skill in the art to replace the fucosyltransferase of the reference application with the polypeptide of Whiteson, as one of ordinary skill in the art would have been able to carry out such a substitution with a reasonable expectation of success because both the reference application and Whiteson discuss cells capable of producing fucosyltransferase enzymes.
Regarding instant claim 53 and the elected species of SEQ ID NO: 6, the polypeptide AIL32582.1 of Whiteson is 100% identical to SEQ ID NO: 6 as evidenced by the attached sequence search results [see Appendix A].
Regarding instant claim 55, Heidtman discloses methods that include production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25].
Regarding instant claim 56, claim 110 of the reference application limits the cell to be a bacterium or yeast.
Regarding instant claim 57, Heidtman discloses synthetic genes of α-(1-3)-fucosyltransferase genes are designed using standard methods known in the art, and include sequences that are codon-optimized for expression in a host bacterial strain [para 117].
Regarding instant claim 59, Heidtman discloses methods that include production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1-3)-fucosyltransferase gene” [para 25], and Whiteson discloses the polypeptide AIL32582.1 that contains the GDP-fucose binding domain specified by SEQ ID NO: 33, the amino acid sequence specified by SEQ ID NO: 34, and less than 100 amino acids between the beginning of the GDP-fucose binding domain and the C-terminus of the peptide as discussed above.
Regarding instant claim 60, Whiteson discloses the polypeptide AIL32582.1 that is 100% identical to SEQ ID NO: 6 as evidenced by the attached sequence search results [see Appendix A] as discussed above.
Regarding instant claim 76, the polypeptide of Whiteson as described above is 100% identical to SEQ ID NO: 6 as discussed above [see Appendix A].
Regarding instant claim 77, Heidtman discloses the nucleic acid can be integrated into the genome of the host cell [para 23].
Regarding instant claim 78, the polypeptide of Whiteson as described above is 100% identical to SEQ ID NO: 6 as discussed above [see Appendix A], and therefore it is considered to have a conserved GDP-fucose binding domain corresponding to residues 233-237 of SEQ ID NO: 6.
Regarding instant claim 79, Heidtman discloses “methods for producing α-(1,3)-fucosylated oligosaccharides utilizing a bacterial strain harbouring an expression plasmid containing two different α-(1,3)-fucosyltransferases in ‘tandem’ arrangement. These tandem α-(1,3)-fucosyltransferases may be under the control of the PL promoter” [para 18], and that the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49], and that the nucleic acid can be integrated into the genome of the host cell [para 23]. Heidtman further discloses the method includes production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25], wherein the E. coli is typically Escherichia coli K12 [para 27]. Furthermore, Heidtman states “a preferred α-(1,3)-fucosyltransferase utilizes GDP-fucose as a donor, and lactose is the acceptor for that donor [para 98]. As such, Heidtman satisfies the limitations of claim 52, as well as the limitations of claim 51 regarding a cell that produces α-1,3-fucosyllactose, the cell comprising at least one polynucleotide encoding an exogenous polypeptide with α-1,3-fucosyltransferase activity and able to use lactose as an acceptor substrate to produce α-1,3-fucosyllactose. Heidtman further discusses methods of identifying α-(1,3)-fucosyltransferases enzymes capable of synthesizing fucosylated oligosaccharides such as 3-FL [para 47] and fucosyltransferase enzymes capable of using lactose as an acceptor comprising performing a computational search to define a broad group of simple sequence homologs of any known, lactose-utilizing fucosyltransferase, searching that group for common sequence and/or structural motifs shared by members of that group, searching sequence databases for said common sequence and/or structural motifs to identify candidate sequences, and expressing candidate enzymes to test for lactose utilization [para 99].
Regarding instant claim 79, Whiteson describes the genomic analysis of the bacteria Basilea psittacipulmonis [title], wherein the genome was deposited and the encoded polypeptides were annotated by NCBI, namely the polypeptide AIL32582.1. This polypeptide is identified as an α-(1,3)-fucosyltransferase domain-containing polypeptide as evidenced by NCBI. This polypeptide further contains a GDP-fucose binding domain of YITEK (residues 233-237) that corresponds to SEQ ID NO: 33 specified in i) of claim 51, as well as the sequence DLYLGF (residues 107-112) that corresponds to SEQ ID NO: 34 specified in ii) of claim 51. As the polypeptide of Whiteson is 329 amino acids in length, the starting amino acid of the GDP-fucose binding domain (residue 233) is less than 100 amino acids from the C-terminus of the polypeptide. Therefore, the polypeptide AIL32582.1 as evidenced by NCBI is considered to contain the “α-1,3-fucosyltransferase activity and the ability to use lactose as an acceptor substrate” as recited in claim 51, as the activity is considered to be inherent to the structure of the polypeptide (see MPEP 2112.01(I)). As the polypeptide of Whiteson shares 100% identity with SEQ ID NO: 6, it is considered to have the GDP-fucose binding domain corresponding to residues 233-237 of SEQ ID NO: 6.
In view of Heidtman and Whiteson, it would have been obvious to one of ordinary skill in the art before the effective filing date to modify the cell of the reference application to use the polypeptide of Whiteson as identified by NCBI, since the simple substitution of one known element for another results in a predictable result. One of ordinary skill in the art would have recognized that the enzyme by the reference application and the polypeptide of Whiteson are fucosyltransferases, and as such both are capable of being incorporated into such cells as described by both the reference application and Whiteson. One of ordinary skill in the art would have been motivated to replace the fucosyltransferase of the reference application with the fucosyltransferase of Whiteson, because Heidtman discloses the engineering of bacteria with heterologously expressed enzymes in order to optimize production efficiency of human milk oligosaccharides such as α-(1,3)-fucosyllactose, and because Heidtman discusses a method to screen sequence databases for novel enzymes capable of carrying out target fucosyltransferase activity. Thus it would have been obvious to one of ordinary skill in the art to replace the fucosyltransferase of the reference application with the polypeptide of Whiteson, as one of ordinary skill in the art would have been able to carry out such a substitution with a reasonable expectation of success because both the reference application and Whiteson discuss cells capable of producing fucosyltransferase enzymes.
Regarding instant claim 80 (dependent from claim 51), Heidtman discloses the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49] as discussed in the rejection of claim 51 above, and the recombinant DNA constructs are supplied on a plasmid expression vector [para 36].
Regarding instant claim 81, Heidtman discloses “methods for producing α-(1,3)-fucosylated oligosaccharides utilizing a bacterial strain harbouring an expression plasmid containing two different α-(1,3)-fucosyltransferases in ‘tandem’ arrangement. These tandem α-(1,3)-fucosyltransferases may be under the control of the PL promoter” [para 18], and that the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49], and that the recombinant DNA constructs are supplied on a plasmid expression vector [para 36]. Heidtman further discloses the method includes production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25], wherein the E. coli is typically Escherichia coli K12 [para 27]. Furthermore, Heidtman states “a preferred α-(1,3)-fucosyltransferase utilizes GDP-fucose as a donor, and lactose is the acceptor for that donor [para 98]. As such, Heidtman satisfies the limitations of claim 52, as well as the limitations of claim 51 regarding a cell that produces α-1,3-fucosyllactose, the cell comprising at least one polynucleotide encoding an exogenous polypeptide with α-1,3-fucosyltransferase activity and able to use lactose as an acceptor substrate to produce α-1,3-fucosyllactose. Heidtman further discusses methods of identifying α-(1,3)-fucosyltransferases enzymes capable of synthesizing fucosylated oligosaccharides such as 3-FL [para 47] and fucosyltransferase enzymes capable of using lactose as an acceptor comprising performing a computational search to define a broad group of simple sequence homologs of any known, lactose-utilizing fucosyltransferase, searching that group for common sequence and/or structural motifs shared by members of that group, searching sequence databases for said common sequence and/or structural motifs to identify candidate sequences, and expressing candidate enzymes to test for lactose utilization [para 99].
Regarding instant claim 81, Whiteson describes the genomic analysis of the bacteria Basilea psittacipulmonis [title], wherein the genome was deposited and the encoded polypeptides were annotated by NCBI, namely the polypeptide AIL32582.1. This polypeptide is identified as an α-(1,3)-fucosyltransferase domain-containing polypeptide as evidenced by NCBI. This polypeptide further contains a GDP-fucose binding domain of YITEK (residues 233-237) that corresponds to SEQ ID NO: 33 specified in i) of claim 51, as well as the sequence DLYLGF (residues 107-112) that corresponds to SEQ ID NO: 34 specified in ii) of claim 51. As the polypeptide of Whiteson is 329 amino acids in length, the starting amino acid of the GDP-fucose binding domain (residue 233) is less than 100 amino acids from the C-terminus of the polypeptide. Therefore, the polypeptide AIL32582.1 as evidenced by NCBI is considered to contain the “α-1,3-fucosyltransferase activity and the ability to use lactose as an acceptor substrate” as recited in claim 51, as the activity is considered to be inherent to the structure of the polypeptide (see MPEP 2112.01(I)). As the polypeptide of Whiteson shares 100% identity with SEQ ID NO: 6, it is considered to have the GDP-fucose binding domain corresponding to residues 233-237 of SEQ ID NO: 6.
In view of Heidtman and Whiteson, it would have been obvious to one of ordinary skill in the art before the effective filing date to modify the cell of the reference application to use the polypeptide of Whiteson as identified by NCBI, since the simple substitution of one known element for another results in a predictable result. One of ordinary skill in the art would have recognized that the enzyme by the reference application and the polypeptide of Whiteson are fucosyltransferases, and as such both are capable of being incorporated into such cells as described by both the reference application and Whiteson. One of ordinary skill in the art would have been motivated to replace the fucosyltransferase of the reference application with the fucosyltransferase of Whiteson, because Heidtman discloses the engineering of bacteria with heterologously expressed enzymes in order to optimize production efficiency of human milk oligosaccharides such as α-(1,3)-fucosyllactose, and because Heidtman discusses a method to screen sequence databases for novel enzymes capable of carrying out target fucosyltransferase activity. Thus it would have been obvious to one of ordinary skill in the art to replace the fucosyltransferase of the reference application with the polypeptide of Whiteson, as one of ordinary skill in the art would have been able to carry out such a substitution with a reasonable expectation of success because both the reference application and Whiteson discuss cells capable of producing fucosyltransferase enzymes.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
M. Claims 51-53, 55-57, 59-60 and 76-81 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 6, 10 and 28 of copending Application No. 18/718677 (hereafter “reference application”) in view of Heidtman, Whiteson and NCBI.
The instant rejection is maintained from the previous Office Action and any newly recited portions are necessitated by claim amendment.
Regarding instant claim 51 and the limitation of “a cell comprising at least one polynucleotide encoding a polypeptide with α-(1,3)-fucosyltransferase activity”, claim 6 of the reference application recites a method of producing a fucosylated compound with an alpha-1,3-fucosyltranserase and claim 10 of the reference application limits the method to occur in a cell.
The claims of the reference application do not recite a fucosyltransferase with the domains specified in SEQ ID NOs: 33 and 34 of instant claim 51, nor that the C-terminus is 100 amino acids or less from the GDP-fucose binding domain (SEQ ID NO: 33).
Heidtman discloses methods for producing purified fucosylated oligosaccharides in milk [para 3], involving the use of engineered bacteria with heterologously expressed enzymes in order to optimize production efficiency [para 6]. Heidtman discloses methods that include production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25].
Regarding instant claims 51-52, Heidtman discloses “methods for producing α-(1,3)-fucosylated oligosaccharides utilizing a bacterial strain harbouring an expression plasmid containing two different α-(1,3)-fucosyltransferases in ‘tandem’ arrangement. These tandem α-(1,3)-fucosyltransferases may be under the control of the PL promoter” [para 18], and that the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49]. Furthermore, Heidtman states “a preferred α-(1,3)-fucosyltransferase utilizes GDP-fucose as a donor, and lactose is the acceptor for that donor [para 98]. As such, Heidtman satisfies the limitations of instant claim 52, as well as the limitations of instant claim 51 regarding a cell that produces α-1,3-fucosyllactose, the cell comprising at least one polynucleotide encoding an exogenous polypeptide with α-1,3-fucosyltransferase activity and able to use lactose as an acceptor substrate.
Heidtman further discusses methods of identifying α-(1,3)-fucosyltransferases enzymes capable of synthesizing fucosylated oligosaccharides such as 3-FL [para 47] and fucosyltransferase enzymes capable of using lactose as an acceptor comprising performing a computational search to define a broad group of simple sequence homologs of any known, lactose-utilizing fucosyltransferase, searching that group for common sequence and/or structural motifs shared by members of that group, searching sequence databases for said common sequence and/or structural motifs to identify candidate sequences, and expressing candidate enzymes to test for lactose utilization [para 99].
Whiteson describes the genomic analysis of the bacteria Basilea psittacipulmonis [title], wherein the genome was deposited and the encoded polypeptides were annotated by NCBI, namely the polypeptide AIL32582.1. This polypeptide is identified as an α-(1,3)-fucosyltransferase domain containing polypeptide as evidenced by NCBI. This polypeptide further contains a GDP-fucose binding domain of YITEK (residues 233-237) that corresponds to SEQ ID NO: 33 specified in i) of claim 51, as well as the sequence DLYLGF (residues 107-112) that corresponds to SEQ ID NO: 34 specified in ii) of instant claim 51. As the polypeptide of Whiteson is 329 amino acids in length, the starting amino acid of the GDP-fucose binding domain (residue 233) is less than 100 amino acids from the C-terminus of the polypeptide. Therefore, the polypeptide AIL32582.1 as evidenced by NCBI is considered to contain the “α-1,3-fucosyltransferase activity and the ability to use lactose as an acceptor substrate” as recited in instant claim 51, as the activity is considered to be inherent to the structure of the polypeptide (see MPEP 2112.01(I)).
In view of Heidtman and Whiteson, it would have been obvious to one of ordinary skill in the art before the effective filing date to modify the cell of the reference application to use the polypeptide of Whiteson as identified by NCBI, since the simple substitution of one known element for another results in a predictable result. One of ordinary skill in the art would have recognized that the both the means for alpha-1,3-fucosyltranserase activity disclosed by the reference application and the polypeptide of Whiteson are means for alpha-1,3-fucosyltranserase activity, and as such both are capable of being incorporated into such cells as described by both the reference application and Whiteson. One of ordinary skill in the art would have been motivated to replace the means for alpha-1,3-fucosyltranserase activity of the reference application with the polypeptide of Whiteson, because Heidtman discloses the engineering of bacteria with heterologously expressed enzymes in order to optimize production efficiency of human milk oligosaccharides such as α-(1,3)-fucosyllactose, and because Heidtman discusses a method to screen sequence databases for novel enzymes capable of carrying out target fucosyltransferase activity. Thus it would have been obvious to one of ordinary skill in the art to replace the fucosyltransferase of the reference application with the polypeptide of Whiteson, as one of ordinary skill in the art would have been able to carry out such a substitution with a reasonable expectation of success because both the reference application and Whiteson discuss cells capable of producing fucosyltransferase enzymes.
Regarding instant claim 53 and the elected species of SEQ ID NO: 6, the polypeptide AIL32582.1 of Whiteson is 100% identical to SEQ ID NO: 6 as evidenced by the attached sequence search results [see Appendix A].
Regarding instant claim 55, Heidtman discloses methods that include production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25].
Regarding instant claim 56, claim 28 of the reference application limits the cell to be a bacterium or yeast.
Regarding instant claim 57, Heidtman discloses synthetic genes of α-(1-3)-fucosyltransferase genes are designed using standard methods known in the art, and include sequences that are codon-optimized for expression in a host bacterial strain [para 117].
Regarding instant claim 59, Heidtman discloses methods that include production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1-3)-fucosyltransferase gene” [para 25], and Whiteson discloses the polypeptide AIL32582.1 that contains the GDP-fucose binding domain specified by SEQ ID NO: 33, the amino acid sequence specified by SEQ ID NO: 34, and less than 100 amino acids between the beginning of the GDP-fucose binding domain and the C-terminus of the peptide as discussed above.
Regarding instant claim 60, Whiteson discloses the polypeptide AIL32582.1 that is 100% identical to SEQ ID NO: 6 as evidenced by the attached sequence search results [see Appendix A] as discussed above.
Regarding instant claim 76, the polypeptide of Whiteson as described above is 100% identical to SEQ ID NO: 6 as discussed above [see Appendix A].
Regarding instant claim 77, Heidtman discloses the nucleic acid can be integrated into the genome of the host cell [para 23].
Regarding instant claim 78, the polypeptide of Whiteson as described above is 100% identical to SEQ ID NO: 6 as discussed above [see Appendix A], and therefore it is considered to have a conserved GDP-fucose binding domain corresponding to residues 233-237 of SEQ ID NO: 6.
Regarding instant claim 79, Heidtman discloses “methods for producing α-(1,3)-fucosylated oligosaccharides utilizing a bacterial strain harbouring an expression plasmid containing two different α-(1,3)-fucosyltransferases in ‘tandem’ arrangement. These tandem α-(1,3)-fucosyltransferases may be under the control of the PL promoter” [para 18], and that the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49], and that the nucleic acid can be integrated into the genome of the host cell [para 23]. Heidtman further discloses the method includes production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25], wherein the E. coli is typically Escherichia coli K12 [para 27]. Furthermore, Heidtman states “a preferred α-(1,3)-fucosyltransferase utilizes GDP-fucose as a donor, and lactose is the acceptor for that donor [para 98]. As such, Heidtman satisfies the limitations of claim 52, as well as the limitations of claim 51 regarding a cell that produces α-1,3-fucosyllactose, the cell comprising at least one polynucleotide encoding an exogenous polypeptide with α-1,3-fucosyltransferase activity and able to use lactose as an acceptor substrate to produce α-1,3-fucosyllactose. Heidtman further discusses methods of identifying α-(1,3)-fucosyltransferases enzymes capable of synthesizing fucosylated oligosaccharides such as 3-FL [para 47] and fucosyltransferase enzymes capable of using lactose as an acceptor comprising performing a computational search to define a broad group of simple sequence homologs of any known, lactose-utilizing fucosyltransferase, searching that group for common sequence and/or structural motifs shared by members of that group, searching sequence databases for said common sequence and/or structural motifs to identify candidate sequences, and expressing candidate enzymes to test for lactose utilization [para 99].
Regarding instant claim 79, Whiteson describes the genomic analysis of the bacteria Basilea psittacipulmonis [title], wherein the genome was deposited and the encoded polypeptides were annotated by NCBI, namely the polypeptide AIL32582.1. This polypeptide is identified as an α-(1,3)-fucosyltransferase domain-containing polypeptide as evidenced by NCBI. This polypeptide further contains a GDP-fucose binding domain of YITEK (residues 233-237) that corresponds to SEQ ID NO: 33 specified in i) of claim 51, as well as the sequence DLYLGF (residues 107-112) that corresponds to SEQ ID NO: 34 specified in ii) of claim 51. As the polypeptide of Whiteson is 329 amino acids in length, the starting amino acid of the GDP-fucose binding domain (residue 233) is less than 100 amino acids from the C-terminus of the polypeptide. Therefore, the polypeptide AIL32582.1 as evidenced by NCBI is considered to contain the “α-1,3-fucosyltransferase activity and the ability to use lactose as an acceptor substrate” as recited in claim 51, as the activity is considered to be inherent to the structure of the polypeptide (see MPEP 2112.01(I)). As the polypeptide of Whiteson shares 100% identity with SEQ ID NO: 6, it is considered to have the GDP-fucose binding domain corresponding to residues 233-237 of SEQ ID NO: 6.
In view of Heidtman and Whiteson, it would have been obvious to one of ordinary skill in the art before the effective filing date to modify the cell of the reference application to use the polypeptide of Whiteson as identified by NCBI, since the simple substitution of one known element for another results in a predictable result. One of ordinary skill in the art would have recognized that the enzyme by the reference application and the polypeptide of Whiteson are fucosyltransferases, and as such both are capable of being incorporated into such cells as described by both the reference application and Whiteson. One of ordinary skill in the art would have been motivated to replace the fucosyltransferase of the reference application with the fucosyltransferase of Whiteson, because Heidtman discloses the engineering of bacteria with heterologously expressed enzymes in order to optimize production efficiency of human milk oligosaccharides such as α-(1,3)-fucosyllactose, and because Heidtman discusses a method to screen sequence databases for novel enzymes capable of carrying out target fucosyltransferase activity. Thus it would have been obvious to one of ordinary skill in the art to replace the fucosyltransferase of the reference application with the polypeptide of Whiteson, as one of ordinary skill in the art would have been able to carry out such a substitution with a reasonable expectation of success because both the reference application and Whiteson discuss cells capable of producing fucosyltransferase enzymes.
Regarding instant claim 80 (dependent from claim 51), Heidtman discloses the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49] as discussed in the rejection of claim 51 above, and the recombinant DNA constructs are supplied on a plasmid expression vector [para 36].
Regarding instant claim 81, Heidtman discloses “methods for producing α-(1,3)-fucosylated oligosaccharides utilizing a bacterial strain harbouring an expression plasmid containing two different α-(1,3)-fucosyltransferases in ‘tandem’ arrangement. These tandem α-(1,3)-fucosyltransferases may be under the control of the PL promoter” [para 18], and that the nucleic acid is “operably linked to one or more heterologous control sequences that direct the production of said enzyme in said production strain” [claim 49], and that the recombinant DNA constructs are supplied on a plasmid expression vector [para 36]. Heidtman further discloses the method includes production “in a bacterial host, e.g. an E. coli bacterium comprising an exogenous α-(1,3)-fucosyltransferase gene” [para 25], wherein the E. coli is typically Escherichia coli K12 [para 27]. Furthermore, Heidtman states “a preferred α-(1,3)-fucosyltransferase utilizes GDP-fucose as a donor, and lactose is the acceptor for that donor [para 98]. As such, Heidtman satisfies the limitations of claim 52, as well as the limitations of claim 51 regarding a cell that produces α-1,3-fucosyllactose, the cell comprising at least one polynucleotide encoding an exogenous polypeptide with α-1,3-fucosyltransferase activity and able to use lactose as an acceptor substrate to produce α-1,3-fucosyllactose. Heidtman further discusses methods of identifying α-(1,3)-fucosyltransferases enzymes capable of synthesizing fucosylated oligosaccharides such as 3-FL [para 47] and fucosyltransferase enzymes capable of using lactose as an acceptor comprising performing a computational search to define a broad group of simple sequence homologs of any known, lactose-utilizing fucosyltransferase, searching that group for common sequence and/or structural motifs shared by members of that group, searching sequence databases for said common sequence and/or structural motifs to identify candidate sequences, and expressing candidate enzymes to test for lactose utilization [para 99].
Regarding instant claim 81, Whiteson describes the genomic analysis of the bacteria Basilea psittacipulmonis [title], wherein the genome was deposited and the encoded polypeptides were annotated by NCBI, namely the polypeptide AIL32582.1. This polypeptide is identified as an α-(1,3)-fucosyltransferase domain-containing polypeptide as evidenced by NCBI. This polypeptide further contains a GDP-fucose binding domain of YITEK (residues 233-237) that corresponds to SEQ ID NO: 33 specified in i) of claim 51, as well as the sequence DLYLGF (residues 107-112) that corresponds to SEQ ID NO: 34 specified in ii) of claim 51. As the polypeptide of Whiteson is 329 amino acids in length, the starting amino acid of the GDP-fucose binding domain (residue 233) is less than 100 amino acids from the C-terminus of the polypeptide. Therefore, the polypeptide AIL32582.1 as evidenced by NCBI is considered to contain the “α-1,3-fucosyltransferase activity and the ability to use lactose as an acceptor substrate” as recited in claim 51, as the activity is considered to be inherent to the structure of the polypeptide (see MPEP 2112.01(I)). As the polypeptide of Whiteson shares 100% identity with SEQ ID NO: 6, it is considered to have the GDP-fucose binding domain corresponding to residues 233-237 of SEQ ID NO: 6.
In view of Heidtman and Whiteson, it would have been obvious to one of ordinary skill in the art before the effective filing date to modify the cell of the reference application to use the polypeptide of Whiteson as identified by NCBI, since the simple substitution of one known element for another results in a predictable result. One of ordinary skill in the art would have recognized that the enzyme by the reference application and the polypeptide of Whiteson are fucosyltransferases, and as such both are capable of being incorporated into such cells as described by both the reference application and Whiteson. One of ordinary skill in the art would have been motivated to replace the fucosyltransferase of the reference application with the fucosyltransferase of Whiteson, because Heidtman discloses the engineering of bacteria with heterologously expressed enzymes in order to optimize production efficiency of human milk oligosaccharides such as α-(1,3)-fucosyllactose, and because Heidtman discusses a method to screen sequence databases for novel enzymes capable of carrying out target fucosyltransferase activity. Thus it would have been obvious to one of ordinary skill in the art to replace the fucosyltransferase of the reference application with the polypeptide of Whiteson, as one of ordinary skill in the art would have been able to carry out such a substitution with a reasonable expectation of success because both the reference application and Whiteson discuss cells capable of producing fucosyltransferase enzymes.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Response to Remarks: beginning on page 17 of Applicant’s response to double patenting rejections; Applicant in summary contends the ‘430 and ‘684 patents do not recite the enzyme of the instant application, that here is no motivation to use the enzyme of SEQ ID NO: 6, there is no predictable result rationale in view of the art, inherency cannot supply motivation, and the instant claims are patentably distinct; Applicant contends a Terminal Disclaimer has been submitted over the cited applications in the provisional double patenting rejections.
Applicant’s remarks are considered and found not convincing.
While the ‘430 and ‘684 patents do not recite the specific enzyme of the instant application, the ‘430 patent broadly recites a cell comprising a fucosyltransferase enzyme for the production of a fucosyllated oligosaccharide, and the ‘684 patent broadly recites a cell capable of producing 3-fucosyllactose, which is considered to correspond to the production of a fucosyllated oligosaccharide by a fucosyltransferase enzyme. This subject matter overlaps with the instantly claimed cell is outlined in the rejection above, as well as the rationales for why it would have been obvious in view of the prior art to modify the claims of the patent to arrive at the instantly claimed invention. T
The obviousness rationales used in the double patenting rejections are that of simple substitution, which does not require a motivation, as MPEP 2143.I.B states criteria for simple substitution are (1) a finding that the prior art contained a product which differed from the claimed device by the substitution of some components with other components, (2) a finding that the substituted components and their functions were known in the art, (3) a finding that one of ordinary skill in the art could have substituted one known element for another, and (4) the results of the substitution would have been predictable, and whatever additional findings based on the Graham factual inquiries may be necessary. Each of these requirements have been addressed in the rejection above as well as the response to remarks above.
Regarding predictable results, Heidtman discloses a cell with α-(1,3)-fucosyltransferase activity, which preferably has the ability to utilize lactose as an acceptor. Heidtman discloses a method to validate candidate substitutes for having this lactose-utilization activity, but this activity is not a requirement for the generation of the cell of the patent or of Heidtman. The simple substitution rationale is based on replacement of the enzyme of the respective with the polypeptide of Whiteson due to both being recognized having fucosyltransferase activity, and therefore both being capable of being incorporated into a cell as described by both the patent and Heidtman with a reasonable expectation of success.
Regarding inherency, inherency was not used in the rejections to supply motivation or expectation of success.
For these reasons and those outlined in the rejections above, the pending claims are rejected on the ground of nonstatutory double patenting as stated above and are not patentably distinct in view of the broad scope of the claims of the patents.
Regarding the provisional double patenting rejections, as of 03/14/2026 the Office has disapproved the Terminal Disclaimer, and therefore the provisional double patenting rejections are maintained.
Conclusion
Status of the Claims:
Claims 40 and 43-81 are pending.
Claims 40, 43-50, 54, 58 and 61-75 are withdrawn.
Claims 51-53, 55-57, 59-60 and 76-81 are rejected.
No claim is in condition for allowance.
All claims are identical to or patentably indistinct from, or have unity of invention with claims in the application prior to the entry of the submission under 37 CFR 1.114 (that is, restriction (including a lack of unity of invention) would not be proper) and all claims could have been finally rejected on the grounds and art of record in the next Office action if they had been entered in the application prior to entry under 37 CFR 1.114. Accordingly, THIS ACTION IS MADE FINAL even though it is a first action after the filing of a request for continued examination and the submission under 37 CFR 1.114. See MPEP § 706.07(b). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JOSEPH SPANGLER whose telephone number is (571)270-0314. The examiner can normally be reached M-F 7:30 am - 4:30 pm.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Manjunath Rao can be reached at (571) 272-0939. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/JOSEPH R SPANGLER/
Examiner
Art Unit 1656
/David Steadman/Primary Examiner, Art Unit 1656
Appendix A
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Appendix A. Sequence Search Results of SEQ ID NO: 6
Prosecution Insights