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 .
DETAILED ACTION
1. Preliminary amendment filed 5/13/24 is acknowledged. Claims 1-3, 5, 7, 9-11, 13, 15, 17, 19, 21, 23, 25, 27, 32, 39, 42 & 44 are present and under consideration in this Office Action.
2. Drawings
The drawings filed on 8/14/23 are acknowledged.
3. Priority
Applicant’s claim for domestic priority under 35 U.S.C. 119(e), filed 2/15/21, is acknowledged.
4. Specification
The specification has not been checked to the extent necessary to determine the presence of all possible minor errors. Applicant's cooperation is requested in correcting any errors of which applicant may become aware in the specification.
5. 35 U.S.C. § 112, first paragraph (Written Description)
Claims 1-3, 5, 7, 9-11, 13, 15, 17, 19, 21, 23, 25, 27, 32, 39, 42 & 44 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claims 1-3, 5, 7, 9-11, 13, 15, 17, 19, 21, 23, 25, 27, 32, 39, 42 & 44 are directed to the following genus claims.
1. An engineered microbial host cell capable of producing ergothioneine, wherein the host cell comprises a) a first exogenous nucleic acid sequence coding for an Egt1 enzyme capable of converting L-histidine and/or L-cysteine to hercynylcysteine sulfoxide; b) a second exogenous nucleic acid sequence coding for an Egt2 enzyme capable of converting hercynylcystenie sulfoxide to 2-sulfenohercynine; and c) a third exogenous nucleic acid sequence coding for a methionine transporter having at least 70% amino acid sequence identity to SEQ ID NO: 96.
2. The engineered microbial host cell of claim 1, wherein the methionine transporter is a YjeH protein comprising the amino acid sequence set forth in SEQ ID NO: 96.
3. The engineered microbial host cell for claim 1, wherein: (i) the third exogenous nucleic acid sequence has at least 70% sequence identity to SEQ ID NO: 95; and/or (ii) the third exogenous nucleic acid sequence comprises the nucleic acid sequence of SEQ ID NO: 95.
4. (canceled)
5. The engineered microbial host cell for claim 1, wherein the first exogenous nucleic acid sequence encodes a heterologous enzyme Egt1 comprising: (i) an amino acid sequence having at least 70% sequence identity to SEQ ID NO: 18; or (ii) the amino acid sequence of SEQ ID NO: 18.
6. (canceled)
7. The engineered microbial host cell of claim 1, wherein the second exogenous nucleic acid sequence encodes a heterologous enzyme Egt2 comprising: (i) an amino acid sequence having at least 70% identity to SEQ ID NO: 90; or (ii) the amino acid sequence of SEQ ID NO: 90.
8. (canceled)
9. The engineered microbial host cell of claim 1, wherein the first exogenous nucleic acid sequence encodes a heterologous enzyme Egt1 comprising the amino acid sequence of SEQ ID NO: 18 and the second exogenous nucleic acid sequence encodes a heterologous enzyme Egt2 comprising the amino acid sequence of SEQ ID NO: 90.
10. The engineered microbial host cell of claim 9, wherein the first exogenous nucleic acid sequence comprises the nucleic acid sequence of SEQ ID NO: 17 and the second exogenous nucleic acid sequence comprises the nucleic acid sequence of SEQ ID NO: 89.
11. The engineered microbial host cell for claim 1, wherein the first exogenous nucleic acid sequence encodes a heterologous enzyme Egt1 comprising: (i) an amino acid sequence having at least 70% sequence identity to SEQ ID NO: 20; or (ii) the amino acid sequence of SEQ ID NO: 20.
12. (canceled)
13. The engineered microbial host cell of claim 1, wherein the second exogenous nucleic acid sequence encodes a heterologous enzyme Egt2 comprising: (i) an amino acid sequence having at least 70% identity to SEQ ID NO: 90; or (ii) the amino acid sequence of SEQ ID NO: 90.
14. (canceled)
15. The engineered microbial host cell of claim 1, wherein: (i) the first exogenous nucleic acid sequence encodes a heterologous enzyme Egt1 comprising the amino acid sequence of SEQ ID NO: 20 and the second exogenous nucleic acid sequence encodes a heterologous enzyme Egt2 comprising the amino acid sequence of SEQ ID NO: 90; and/or (ii) the first exogenous nucleic acid sequence comprises the nucleic acid sequence of SEQ ID NO: 19 and the second exogenous nucleic acid sequence comprises the nucleic acid sequence of SEQ ID NO: 89.
16. (canceled)
17. The engineered microbial host cell for claim 1, wherein the first exogenous nucleic acid sequence encodes a heterologous enzyme Egt1 comprising: (i) an amino acid sequence having at least 70% sequence identity to SEQ ID NO: 138; or (ii) the amino acid sequence of SEQ ID NO: 138.
18. (canceled)
19. The engineered microbial host cell of claim 1, wherein the second exogenous nucleic acid sequence encodes a heterologous enzyme Egt2 comprising: (i) an amino acid sequence having at least 70% identity to SEQ ID NO: 4; or (ii) the amino acid sequence of SEQ ID NO: 4.
20. (canceled)
21. The engineered microbial host cell of claim 1, wherein: (i) the first exogenous nucleic acid sequence encodes a heterologous enzyme Egt1 comprising the amino acid sequence of SEQ ID NO: 138 and the second exogenous nucleic acid sequence encodes a heterologous enzyme Egt2 comprising the amino acid sequence of SEQ ID NO: 4; and/or (ii) the first exogenous nucleic acid sequence comprises the nucleic acid sequence of SEQ ID NO: 137 and the second exogenous nucleic acid sequence comprises the nucleic acid sequence of SEQ ID NO: 3.
22. (canceled)
23. The engineered microbial host cell of claim 1, wherein: (i) the first exogenous nucleic acid sequence and the second exogenous nucleic acid sequence are on a self-replicating plasmid; or (ii) the first exogenous nucleic acid sequence and the second exogenous nucleic acid sequence are integrated into the host chromosomal DNA.
24. (canceled)
25. The engineered microbial host cell of claim 1, wherein: (i) the first exogenous nucleic acid sequence and the second exogenous nucleic acid sequence are under a constitutive promoter; or (ii) the first exogenous nucleic acid sequence and the second exogenous nucleic acid sequence are under an inducible promoter.
26. (canceled)
27. The engineered host cell of claim 1, wherein the host cell is; (i) a bacterial cell selected from a group consisting of Escherichia, Salmonella, Bacillus, Acinetobacter, Streptomyces, Corynebacterium, Methylosinus, Methylomona, Rhodococcus, Pseudomonas, Rhodobacter, Synechocystis, Arthrobotlys, Brevibacteria, Microbacterium, Arthrobacter, Citrobacter, Klebsiella, Pantoea, and Clostridium; (ii) a fungal cell selected from the group consisting of Saccharomyces; Zygosaccharomyces, Kluyveromyces, Candida, Hansenula, Debaryomyces, Mucor, Pichia, Torulopsis, and Aspergillus; (iii) an Escherichia coli cell; (iv) a Saccharomyces cerevisiae cell; and/or (v) a Pichia pastoris cell.
28.-31. (canceled)
32. The engineered microbial host cell of claim 1, further comprising: (i) a mutation in tnaA gene, wherein the mutation is deletion, frameshift or point mutation and wherein such mutation leads to decrease or elimination of tryptophanase activity, and wherein the tnaA gene comprises a nucleic acid sequence having at least 70% sequence identity to SEQ ID NO: 97; (ii) a mutation in sdaA gene, wherein the mutation is deletion, frameshift or point mutation and wherein the sdaA gene comprises a nucleic acid sequence having at least 70% sequence identity to SEQ ID NO: 99; (iii) a mutation in yhaM gene, wherein the mutation is deletion, frameshift or point mutation and wherein the yhaM gene comprises a nucleic acid sequence having at least 70% sequence identity to SEQ ID NO: 115; (iv) a mutation in one or more of genes associated with serine biosynthesis selected from the group consisting of serA gene with a nucleic acid sequence having at least 70% sequence identity to SEQ ID NO: 101; serB gene with a nucleic acid sequence having at least 70% sequence identity to SEQ ID NO: 102; and serC gene with a nucleic acid sequence having at least 70% sequence identity to SEQ ID NO: 105; wherein the mutation involves the use of a constitutively active promoter to upregulate the gene expression; (v) a mutation in cysM gene coding for cysteine synthase A with an amino acid sequence having at least 70% sequence identity to SEQ ID NO: 108, wherein the mutation involves the use of a constitutively active promoter to upregulate the gene expression; (vi) a mutation in nrdH gene having an amino acid sequence having at least 70% sequence identity to SEQ ID NO: 110, wherein the mutation involves the use of a constitutively active promoter to upregulate the gene expression; and/or (vii) an exogenous cysE gene, wherein the cysE gene comprises an amino acid sequence having at least 70% sequence identity to SEQ ID NO: 112.
33.-38. (canceled)
39. The engineered host cell of claim 2, further comprising: (i) an exogenous ydeE gene, wherein the ydeE gene comprises an amino acid sequence having at least 70% sequence identity to SEQ ID NO: 114; (ii) comprising an exogenous cysB gene on a plasmid vector under an inducible promoter, wherein the cysB gene comprise an amino acid sequence having at least 70% identity SEQ ID NO: 118; and/or (iii) an exogenous gene encoding for a protein selected from a group consisting of CysA, CysP, CysT and CysW and wherein the transporter proteins CysA, CysP, CysT and CysW comprise amino acid sequence having at least 70% identity to SEQ ID NOS: 122, 124, 126 and 128 respectively.
40.-41. (canceled)
42. The engineered microbial host cell of claim 1, further comprising a mutation in metJ gene wherein the mutation is deletion, frameshift or point mutation and wherein: (i) the metJ gene comprises a nucleic acid sequence having at least 70% sequence identity to SEQ ID NO: 143; or (ii) the metJ gene comprises a nucleic acid sequence as in SEQ ID NO: 143.
43. (canceled)
44. A method for producing ergothioneine comprising: (a) culturing an engineered microbial host cell capable of producing ergothioneine, wherein the host cell comprises a) a first exogenous nucleic acid sequence coding for an Egt1 enzyme capable of converting L-histidine and/or L-cysteine to hercynylcysteine sulfoxide; b) a second exogenous nucleic acid sequence coding for an Egt2 enzyme capable of converting hercynylcystenie sulfoxide to 2-sulfenohercynine; and c) a third exogenous nucleic acid sequence coding for a methionine transporter having at least 70% amino acid sequence identity to SEQ ID NO: 96; (b) expressing the Egt1 enzyme, the Egt2 enzyme, and the methionine transporter; (c) feeding the engineered microbial host cell at least one substrate selected from the group consisting of histidine, methionine, cysteine and combinations thereof; and (d) collecting ergothioneine, or a method thereof.
In University of California v. Eli Lilly & Co., 43 USPQ2d 1938, the Court of Appeals for the Federal Circuit has held that “A written description of an invention involving a chemical genus, like a description of a chemical species, ‘requires a precise definition, such as by structure, formula, [or] chemical name,’ of the claimed subject matter sufficient to distinguish it from other materials”. As indicated in MPEP § 2163, the written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice, reduction to drawings, or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show that Applicant was in possession of the claimed genus. In addition, MPEP § 2163 states that a representative number of species means that the species which are adequately described are representative of the entire genus. Thus, when there is substantial variation within the genus, one must describe a sufficient variety of species to reflect the variation within the genus.
The specification, however, only provides description of – “An engineered Schizosaccharomyces pompe host cell capable of producing ergothioneine, wherein the host cell comprises a) a first exogenous nucleic acid sequence coding for an ergothioneine biosynthesis protein Egt1 enzyme of SEQ ID NO: 18 capable of converting L-histidine and/or L-cysteine to hercynylcysteine sulfoxide; b) a second exogenous nucleic acid sequence coding for an Egt2 enzyme of SEQ ID NO: 90 capable of converting hercynylcystenie sulfoxide to 2-sulfenohercynine; and c) a third exogenous nucleic acid sequence coding for a methionine transporter of the amino acid sequence identity to SEQ ID NO: 96.
The specification does not contain any disclosure or description of any engineered microbial host cell capable of producing ergothioneine, wherein the host cell comprises a) a first exogenous nucleic acid sequence coding for an Egt1 enzyme capable of converting L-histidine and/or L-cysteine to hercynylcysteine sulfoxide from any source; b) a second exogenous nucleic acid sequence coding for an Egt2 enzyme capable of converting hercynylcystenie sulfoxide to 2-sulfenohercynine from any source; and c) a third exogenous nucleic acid sequence coding for a methionine transporter having at least 70% amino acid sequence identity to SEQ ID NO: 96, and wherein the sequence is modified by 30%.
The single Schizosaccharomyces pompe cell construct or method thereof for producing ergothioneine, consisting of the specific sequences of SEQ ID NO: 18, 90 & 96 is not representative of the genus claimed. According to MPEP 2163, to satisfy the written description requirement, a patent specification must describe the claimed invention in sufficient detail that one skilled in the art can reasonably conclude that the inventor had possession of the claimed invention. See, e.g., Moba, B.V. v.Diamond Automation, Inc., 325 F.3d 1306, 1319, 66 USPQ2d 1429, 1438 (Fed.Cir. 2003); Vas-Cath, Inc. v. Mahurkar, 935 F.2d at 1563, 19 USPQ2d at 1116.
The scope of each genus includes many members of Egt1, Egt2 enzymes and methionine transporter from any source with widely differing structural, chemical, and physical characteristics. As evidence from [§0019 of the published application] as well as (FIG. 1) which illustrates the ergothioneine biosynthetic pathway. In the bacterial system, a set of five genes (egtABCDE) are involved in the biosynthesis of ergothioneine from L-histidine. In the fungal system, only two enzymes namely Egt1 and Egt2 enzymes are involved in the biosynthesis of ergothioneine from L-histidine. Similarly, in the anoxygenic bacterium Chlorobium lumicola, only two enzymes namely EanA and EanB are involved in the biosynthesis of ergothioneine from L-histidine. Hence the system to operate in any system is not feasible.
Furthermore, each genus is highly variable because a significant number of structural differences between genus members exit as shown in Figures 4 & 5 of instant application. The specification does not describe and define any structural features and amino acid sequences commonly possessed by each genus. There is no art-recognized correlation between any structure of a Egt1, Egt2 enzymes and methionine transporter and sequences having varying sequence homology, for example i.e., 70% of SEQ ID NO: 96. Those of ordinary skill in the art would not be able to identify without further testing what specific DNA sequences would encode a protein having Egt1, Egt2 enzymes and methionine transporter activity.
An important consideration is that structure is not necessarily a reliable indicator of function. The instant specification provides no disclosure relating similarity or identity of structure to conservation of function. General knowledge in the art provides guidance to modification of some amino acids that are tolerated without losing a protein’s tertiary structure.
The claim includes a genus that can be analyzed at several levels sequentially for the purpose of focusing the issue. First, the disclosure (for example) of the amino acid sequences of SEQ ID NO: 18, 90 and 96 (or the encoding DNA) combined with pre-existing knowledge in the art regarding the genetic code and its redundancies would have put one in possession of the genus of nucleic acids that encode SEQ ID NO: 18, 90 and 96 (the encoding protein) that are 95% identical. With the aid of a computer, one of skill in the art could identify all of the amino acid sequences with at least 95% sequence identity to the claimed sequences.
However, there is no teaching regarding which 30% of the amino acids can vary from SEQ ID NO: 96 (for example) and still result in a protein that that function like the transporter. The same is true of the varying homology claimed for other sequences. An important consideration is that structure is not necessarily a reliable indicator of function. In this example, there is no disclosure relating similarity of structure to conservation of function. General knowledge in the art included the knowledge that some amino acid variations are tolerated without losing a protein’s tertiary structure. The results of amino acid substitutions have been studied so extensively that amino acids are grouped in so-called “exchange groups” of similar properties because substituting within the exchange group is expected to conserve the overall structure. For example, the expectation from replacing leucine with isoleucine would be that the protein would likely retain its tertiary structure. On the other hand, when non-exchange group members are substituted, e.g., proline for tryptophan, the expectation would be that the substitution would not likely conserve the protein’s tertiary structure. Given what is known in the art about the likely outcome of substitutions on structure, those in the art would have likely expected the applicant to have been in possession of a genus of proteins having a tertiary structure similar to specific sequences although the claim is not so limited. However, conservation of structure is not necessarily a surrogate for conservation of function. In this case, there is no disclosed correlation between structure and function. There is no disclosure of the active site amino acid residues responsible for the catalytic activity. While general knowledge in the art may have allowed one of skill in the art to identify other proteins expected to have the same or similar tertiary structure, in this case there is no general knowledge in the art about similar proteins to the claimed sequence employed in the host cell construction or method thereof to suggest that general similarity of structure confers the activity. Accordingly, one of skill in the art would not accept the limited disclosure in an unpredictable art as representative of other proteins having the desired activity. The specification, taken with the pre-existing knowledge in the art of amino acid substitution and the genetic code, fails to satisfy the written description requirement of 35 U.S.C. 112, first paragraph.
6. Claim Rejections - 35 USC § 112 (second paragraph)
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 1-3, 5, 7, 9-11, 13, 15, 17, 19, 21, 23, 25, 27, 32, 39, 42 & 44 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 pre-AIA the applicant regards as the invention.
Claims 1, 5, 9, 11, 15, 17, 21 & 44 recite – abbreviations such as Egt1 & Egt2. The claims are not clear about the full name of the abbreviation. At least the first occurrence of these abbreviations must be spelled out.
Claims 2-3, 7, 10, 13, 19, 23, 25, 27, 32, 39 & 42 are included in the rejection for failing to correct the defect present in the base claim(s).
7. The closest prior art of record is – Borodina, Irina et al. (2020), Vol. 22, pages 190-217. The Biology of ergothioneine, an antioxidant nutraceutical. The reference however, does not teach the claimed invention.
Borodina et al discloses an engineered microbial host cell capable of producing ergothioneine, wherein the host cell comprises a first exogenous nucleic acid sequence coding for an Egt1 enzyme capable of converting L-histidine and/or L-cysteine to hercynylcysteine sulfoxide and a second exogenous nucleic acid sequence coding for an Egt2 enzyme capable of converting hercynylcystenie sulfoxide to 2-sulfenohercynine.
The subject-matter of claim 1 therefore differs from this known microbial host cell and related method in that it comprises a third exogenous nucleic acid sequence coding for a methionine transporter of SEQ ID NO: 96.
8. No claim is allowed.
9. Any inquiry concerning this communication or earlier communications from the examiner should be directed to TEKCHAND SAIDHA whose telephone number is (571)272-0940. The examiner can normally be reached on M-F 8.00-5.30. 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.
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/TEKCHAND SAIDHA/
Primary Examiner, Art Unit 1652
Recombinant Enzymes, Hoteling
Telephone: (571) 272-0940
Fax: (571) 273-0940