DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claim Objections
Claims 1-17 are objected to because of the following informalities:
Claims 1 recites a gene encoding a fucosyltransferase and a gene encoding a protein tag is connected to the gene encoding fucosyltransferase. A gene can encode one or more polypeptides. A single polypeptide cannot be encoded by two different connected gene. Claims 1 and 7 are understood as reciting “a gene encoding α-1,2-fucosyltransferase fused to a protein tag,” and the claims are required to be amended to similar claim language of a gene encoding a single polypeptide fusion protein.
In claims 1 and 7, the abbreviations TrxA and MBP should be defined upon first usage.
In claims 1 and 7, “the amino acid sequence of the MBP is” and “the amino acid sequence of TrxA is” are understood to have inherent antecedent basis in MBP and TrxA since every protein necessary has an amino acid sequence. However, since additional sequence may also be present, it is recommended that the claims be presented in better form as ““an amino acid sequence of the MBP comprises SEQ ID NO: 2” and “an amino acid sequence of TrxA comprises SEQ ID NO: 5.”
Claims 9 and 13, last two lines, similarly recites “the amino acid sequences encoded” that should be “amino acid sequences encoded” without a definite article “the.”
In claims 2-5, 10-12 and 14-15, consistent claim terminology should be used throughout the claims. Claim 1 recites “engineered bacterium” that is a singular noun. “Bacteria” as recited in claims 2-5 and 9-15 is a plural noun. Applicant may consider amending all claims to consistently recite bacterium or bacteria in a manner consistent with claim 1 (although this is not a basis of rejection).
Claims 2, 7 and 8 reference “the nucleotide of the gene encoding” multiple time. Such feature is considered to have antecedent basis in the prior recitation of corresponding genes, where any gene has a nucleotide sequence. However, claims should be placed in better form by reciting “a nucleotide sequence of the gene encoding” upon first recitation of the same in the claims.
In claims 16 and 17, recitation of “the” in “the preparation of fucosyllactose” is unnecessary and should be removed. “The” in this usage is considered to have self-antecedent basis in the concept of preparation, but is nevertheless grammatically inappropriate.
In claim 6, multiple recitations of “the concentration” should preferably be “a concentration.”
Appropriate correction is required.
Claim Interpretation
Claim 7 recites “A recombinant expression vector comprising a gene encoding a protein tag and a gene encoding α-1,2-fucosyltransferase.” The claim does not recite any connection or fusion between the protein tag and α-1,2-fucosyltransferase such that the claim recites one gene encoding a fucosyltransferase as one polypeptide and a second gene encoding a protein tag as a second polypeptide that is not a fusion protein. If recitation of a fusion protein is intended, the claims should be amended to reflect the same.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 10 and 14-17 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter. The claim(s) does/do not fall within at least one of the four categories of patent eligible subject matter because the claims recite a “use.” "Use" claims that do not purport to claim a process, machine, manufacture, or composition of matter fail to comply with 35 U.S.C. 101. MPEP 2173.05(q).
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 3-17 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 3 recites the limitation "the GDP-fucose degradation pathway," “the GDP-mannose degradation pathway, and ” “the lactose operon β-galactosidase,” in lines 3, 5 and 9. There is insufficient antecedent basis for this limitation in the claim. There are no literal antecedent basis for these claim terms nor can a generic engineered bacterium provide inherent antecedent basis for specific pathways and enzymes even if the same are common pathways or enzymes found in bacteria. For these reasons, it is unclear as to what claim features “the GDP-fucose degradation pathway," “the GDP-mannose degradation pathway, and ” “the lactose operon β-galactosidase” reference. As such, it is unclear as to what claim limitations are referenced.
Claim 9 recites the limitation "the genetically engineered bacteria" in line 1. There is insufficient antecedent basis for this limitation in the claim. There is no prior recitation of prior claim features that provide a literal nor any reasonable antecedent basis for "the genetically engineered bacteria" wherein claim 7 only recites an expression vector. As such it is unclear as to what claim limitation “the genetically engineered bacteria” references.
Claims 4 and 11-12 recites the limitation “the fermentation medium” in last line and last two lines, respectively. There is insufficient antecedent basis for this limitation in the claim. There is no literal antecedent basis for the fermentation medium nor a prior recited claim element that provides a reasonable antecedent basis for “the fermentation medium.” As such, it is unclear as to what claim feature is referenced.
Claim 13 recites the limitation "the genetically engineered bacteria" in line 1. There is insufficient antecedent basis for this limitation in the claim. There is no prior recitation of prior claim features that provide a literal nor any reasonable antecedent basis for "the genetically engineered bacteria" wherein claims 7 and 8 only recites an expression vector. As such it is unclear as to what claim limitation “the genetically engineered bacteria” references.
Claim 5 recites the limitation "the reaction system" in line 3. There is insufficient antecedent basis for this limitation in the claim. There is no literal antecedent basis for “the reaction system” in the claims. Further, as far as claim 4 recites a method, there is no prior recited claim features that can be considered to provide a necessarily inherent antecedent basis for “the reaction system.” As such, it is unclear as to what claim element is referenced.
Claim 6 recites the limitation "the fermentation" in line 3. There is insufficient antecedent basis for this limitation in the claim. Claim 4 has an optional fermentation medium, which as indicated above has no antecedent basis. As far as the such a fermentation medium is the antecedent basis for “the fermentation,” the same also lacks antecedent basis for at least this reason. Further, it is unclear if “the fermentation” is a reference to “the fermentation medium” of claim 4. Consistent claim terminology should be used.
Claim 13 recites the limitation "the genetically engineered bacteria" in line 1. There is insufficient antecedent basis for this limitation in the claim. There is no prior recitation of prior claim features that provide a literal nor any reasonable antecedent basis for "the genetically engineered bacteria" wherein claims 7 and only recites an expression vector. As such it is unclear as to what claim limitation “the genetically engineered bacteria” references.
Claims 9 and 13 recite the limitation " the LacZ, wcaJ, nudD and/or nukK genes" in line 4. There is insufficient antecedent basis for this limitation in the claim. There are no literal antecedent basis for these claim terms nor can a generic engineered bacterium or E. coli provide inherent antecedent basis for specific genes even if the same are common in bacteria. As such, it is unclear as to what claim limitations are referenced.
Regarding claims 3, 4, and 7-17, the phrase "preferably” renders the claims indefinite because it is unclear whether the limitations following the phrase are part of the claimed invention. See MPEP § 2173.05(d). All of these claims recite “preferably” wherein it is unclear if the claim features following are or are not required. As such, an ordinarily skilled artisan cannot determine how to avoid infringement.
Further regarding claims 10 and 14-17, “It is appropriate to reject a claim that recites a use but fails to recite steps under 35 U.S.C. 101 and 35 U.S.C. 112(b) if the facts support both rejections.” MPEP 2173.05(q). Here, just as claims 10 and 14-17 fil to recite steps of a method under 35 U.S.C. 101, it is unclear how these claims are infringed or not infringed such that an ordinarily skilled artisan cannot determine how to avoid infringement.
Examiner’s comment regarding prior art
Closest identified prior art is CN 112322565 A (published 02/05/2021). A machine translation of CN’565 is provided and cited herein.
The invention claims a method for improving yield of 2'-fucosyllactose in recombinant Escherichia coli, belonging to the technical field of gene engineering. The invention uses flexible Linker to respectively fuse four different protein labels on the N end of α -1, 2-fucosyltransferase FutC, the constructed fusion protein FP-futC can improve the yield of α -1, 2-fucosyltransferase catalytic synthesis of2'-FL. wherein, using TrxA-futC fusion protein synthesis 2' -FL, the 2.94g/L of the substrate lactose reaches 3.55g/L, lactose conversion is 0.58mol/mol and in the control group, the yield of recombinant Escherichia coli synthesized 2' the recombinant Escherichia coli obtained by the plasmid pMA09-futC constructed by the non-protein tag is only 1.71g/L, the lactose consumption is 2.88g/L, the lactose conversion rate is only 0.42mol/mol further integrating the TrxA-futC fusion protein gene to the yjiP site on the Escherichia coli MG1655genome, obtaining a plasmid-free 2'-FL gene engineering strain MG-26 △yjiP: trxA-futC; The yield of the 2'-FL after shake flask fermentation reaches 3.85g/L, lactose conversion is 0.68mol/mol.
In the claims of CN’565:
1. A method for improving yield of 2'-fucosyllactose in recombinant Escherichia coli, wherein the method is α-1, 2-fucosyltransferase of heterologous expression N-terminal fusion protein label in Escherichia coli host.
2. The method according to claim 1, wherein: the Escherichia coli host is Escherichia coli MG1655 Δ fliR: futC, △fuck: fkp, △lacI, △wcaJ,△lacZ, △flgA: futC, △flgG: futC.
3. The method according to claim 1, wherein said protein label is maltose binding protein, thioredoxin A, transcription termination anti-termination factor or ubiquitin-like protein modification molecule.
4. The method according to claim 3, wherein the amino acid sequence of the thioredoxin A is shown as SEQ ID NO.2; the amino acid sequence of the ubiquitin protein modified molecule is shown as SEQ ID NO.3; the amino acid sequence of the maltose binding protein is shown as SEQ ID NO.2. NO.4, transcription termination anti-stop factor amino acid sequence is shown as SEQ ID NO.5.
An alignment between SEQ ID NO: 2 (109 amino acid residues) of CN’565 and recited SEQ ID NO: 5 (189 amino acid residues) is as follows:
PNG
media_image1.png
192
605
media_image1.png
Greyscale
Regardless of a match over the first 109 residues, SEQ ID NO: 2 of CN’565 is missing amino acid residues 110-189 of recited SEQ ID NO: 5 and therefore does not meet the limitations of “the amino acid sequence of the TrxA as shown in SEQ ID NO: 5” as recited in claim 1.
A sequence search of patent, Genbank and Uniprot databases did not yield any search hits for the full and complete sequence of recited SEQ ID NO: 5. The closest sequence match in Genbank database is Uniprot, Accession No. A0A369HXL4, 2021, www.uniprot.org, having 160 amino acid residues matching wherein the database protein has 221 amino acid residues:
PNG
media_image2.png
302
747
media_image2.png
Greyscale
The closes patent database hit of SEQ ID NO: 5 is represented by EQ ID NO: 6 of Kalum et al. (U.S. 2014/0274882 A1) with the following alignment:
PNG
media_image3.png
307
746
media_image3.png
Greyscale
Sequence search further revealed the following non-prior art reference being SEQ ID NO: 2 of CN116143936 A:
PNG
media_image4.png
389
729
media_image4.png
Greyscale
CN’936 describes a thioredoxin protein from a type of mussel.
Similar, a search of recited SEQ ID NO: 2 did not find any exact sequence matches as required by claim 1. The closest prior art match in the Uniprot database is Uniprot, Accession No. A0A0F8NYV9, 2015, www.uniprot.org, as follows:
PNG
media_image5.png
596
746
media_image5.png
Greyscale
The same sequence has been identified in patent documents including SEQ ID NO: 113 of U.S. 2006/0247416 A1; however, no exact sequence match of SEQ ID NO: 2 has been identified after through search.
The Written Opinion of the ISA for PCT/CN2022/124826 (priority application) has been studies; however, the same provides for no explanation for how SEQ ID NO: 2 or 5 is met by the prior art. Further, SUMO1 and SUMO2 has been removed from the Markush group of claim 1.
In summary, the claims require a sequence 100% identical to SEQ ID NO: 2 or 5, wherein neither sequence is identifiable in the prior art. Further, it is noted that a specific motivation would be required to replace the thioredoxin or TrxA sequence as taught by CN’565 with a different sequence. For these reasons, the features of the claims are not suggested by the prior art.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to TODD M EPSTEIN whose telephone number is (571)272-5141. The examiner can normally be reached Mon-Fri 9:00a-5:30p.
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, Robert Mondesi can be reached at (408) 918-7584. 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.
/TODD M EPSTEIN/Primary Examiner, Art Unit 1652