DETAILED ACTION
Status of claim rejection
The objection to the abstract has been withdrawn in view of Applicant’s filing of a substitute abstract in the response filed 12/04/2025.
The rejections under 35 USC 112(b) are withdrawn in view of Applicant’s amendments/cancellation of the claims in the response filed 12/04/2025.
The rejection under 35 USC 112(a) is withdrawn in view of Applicant’s amendments to the claims in the response filed 12/04/2025.
The rejections under 35 USC 101 are withdrawn in view of Applicant’s cancellation of the claim in the response filed 12/04/2025.
The rejection under 35 USC 102 is withdrawn in view of Applicant’s amendments to the claims in the response filed 12/04/2025.
The rejection under 35 USC 103 is modified in view of Applicant’s amendments to the claims in the response filed 12/04/2025.
This Action is Final, as necessitated by Applicant’s amendments.
Information Disclosure Statement
The information disclosure statement(s) (IDS) submitted on 12/04/2025 and 12/05/2025 were filed after the mailing date of the Non-Final Office Action on 09/04/2025. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
New Claim Rejections - 35 USC § 112(a)
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claim 18 is rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the enablement requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
While determining whether a specification is enabling, one considered whether the claimed invention provides sufficient guidance to make and use the claimed invention, if not, whether an artisan would have required undue experimentation to make and use the claimed invention and whether working examples have been provided. There are many factors to be considered when determining whether there is sufficient evidence to support a determination that a disclosure does not satisfy the enablement requirement and whether any necessary experimentation is “undue.” These factors include, but are not limited to:
(A) The breadth of the claims;
(B) The nature of the invention;
(C) The state of the prior art;
(D) The level of one of ordinary skill;
(E) The level of predictability in the art;
(F) The amount of direction provided by the inventor;
(G) The existence of working examples; and
(H) The quantity of experimentation needed to make or use the invention based on the content of the disclosure.
In re Wands, 858 F.2d 731, 737, 8 USPQ2d 1400, 1404 (Fed. Cir. 1988).
All Wands factors listed above have been considered with regard to the instant claims, with the relevant factors discussed below.
Furthermore, the USPTO does not have laboratory facilities to test if an invention with function as claimed when working examples are not disclosed in the specification, therefore, enablement issues are raised and discussed based on the state of knowledge pertinent to an art at the time of the invention, therefore, skepticism raised in the enablement rejection are those raised in the art by artisans of expertise.
Nature of the inventions: Independent claim 5 is drawn to “A host cell for producing hydroxyproline, wherein the expression level of a polypeptide having an L-proline efflux function in the host cell is decreased, wherein the polypeptide having the activity of the L-proline efflux function is: A) a polypeptide having an amino acid sequence consisting of SEQ ID NO: 1 or SEQ ID NO: 2; or B) a variant polypeptide comprising an amino acid sequence having at least 99% sequence identity to the polypeptide of (A), wherein the variant polypeptide retains an L-proline efflux function wherein the expression level of a proline hydroxylase is increased.”
Moreover, claim 18 recites “the host cell for producing hydroxyproline as claimed in claim 6, wherein a glutamate kinase in the bacterium comprises a G149K mutation” (emphasis added).
The breadth of the claims: The claim at issue encompasses, under broadest reasonable interpretation, a host cell having decreased L-proline efflux protein expression for the production of hydroxyproline (see claim 5), while also having a glutamate kinase within the host cell that comprises a G149K mutation.
The level of skill in the art: The level of skill is high, including, e.g., a researcher with a PhD degree.
The working examples and guidance provided: The specification fails to provide any working examples in which the G149K mutation is used for the production of hydroxyproline. Indeed, the specification only evidences that the G149K mutation is responsible for increasing L-proline production and increasing the activity of the L-proline efflux protein (CITE TO SPEC), and not production of hydroxyproline. Further, the specification evidences that only knockout of the thrE L-proline efflux protein is used to increase yield of hydroxyproline (CITE TO SPEC).
The state and unpredictable nature of the prior art: The state of the prior art for having a host cell containing a G149K mutation in a glutamate kinase for decreased L-proline efflux function in the host cell was unpredictable before the effective filing date of the claimed invention.
Zhang et al (cited in previous Office Action) evidences de novo engineering of C. glutamicum for L-proline production (see abstract; title). Specifically, Zhang teaches mutagenesis of C. glutamicum to create an industrial hyper-L-proline-producing strain (i.e., enhancing the production of proline in the strain) by including various mutations: 1) overexpression of a feedback inhibition resistant gamma-glutamate kinase proB G149K mutant, 2) deletion of proline dehydrogenase to block L-proline degradation, 3) overexpression of glutamate dehydrogenase to increase glutamate synthesis flux, 4) the mutation of 6-phosphate gluconate dehydrogenase and glucose-6-phosphate-dehydrogenase in the pentose phosphate pathway to enhance NADPH supply, 5) the deletion of pyruvate aminotransferase to decrease the byproduct L-alanine synthesis, and 6) weakening of α-ketoglutarate dehydrogenase to regulate the TCA cycle (see abstract; see also Fig 2-3; pg. 1900, col 1-2; Fig. 5; pg. 1902, col 1-2). Zhang teaches that the L-proline titer of the final strain ZQJY-9 (the C. glutamicum strain containing all 6 mutations including G149K mutation see abstract and Fig. 6) reached 120.18 g/L at 76 h with the highest productivity of 1.581 g/L/h in the bioreactor (see Fig. 6; see pg. 1903, col 1).
As evidenced above, the art available at the time of filing fails to exemplify the use of the glutamate kinase harboring the G149K mutation for decreased L-proline efflux and production of hydroxyproline. The art as cited above demonstrates that the glutamate kinase G149K mutation does the exact opposite function (i.e., increases L-proline efflux function in host cells).
Consequently, the state of the art, when combined with the lack of any disclosed direct experimental test of Applicant’s hypothesis, shows that one of ordinary skill would have no basis to reasonably predict or conclude that a glutamate kinase harboring the claimed mutation as instantly claimed would be capable of decreasing L-proline efflux. Furthermore, the lack of working examples is a factor to be considered in a case involving both physiological activity and an underdeveloped art. When a patent applicant chooses to forego exemplification and bases utility on broad terminology and general allegations, they run the risk that unless one of ordinary skill in the art would accept the allegations as obviously valid and correct, the PTO may, properly, ask for evidence to substantiate them. Ex parte Sudilosky, 21 USPQ2d 1702, 1705 (BPAI 1991); In re Novak, 134 USPA 335 (CCPA 1962); In re Fouche, 169 USPQ 429 (CCPA 1971). Tossing out the germ of an idea does not constitute an enabling disclosure. While every aspect of a generic claim need not have been carried out by an inventor or exemplified in the specification, reasonable detail must be provided in order to enable one of ordinary skill to understand and carry out the invention. It is true that a specification need not disclose what is well known in the art. However, that general, oft-repeated statement is merely a rule of supplementation, not a substitute for a basic enabling disclosure. It means that the omission of minor details does not cause a specification to fail to meet the enablement requirement under 35 U.S.C. 112(a) or 35 U.S.C. 112, first paragraph.
Absent specific guidance, one skilled in the art before the effective filing date of the claimed invention would not know how to practice the claimed invention and would require undue experimentation to practice over the full scope of the invention claimed.
The amount of experimentation necessary: The specification merely contains a speculative embodiments of the potential of G149K mutation for the production of L-proline, NOT hydroxyproline. The specification offers no working examples or direction for the use of the G149K mutant for production of hydroxyproline and decreasing L-proline efflux function in the host cell. Nothing in the specification remotely demonstrates or suggests that the mutation would have the claimed efficacy or desired effect on proline efflux, because the specification does not have any data suggesting that the mutation would lead to such a function as encompassed by the instant claims. In sum, there is no nexus between the claimed mutation and the ability to be used for decreasing L-proline efflux as claimed.
For the reasons set forth above, one skilled in the art before the effective filing date of the claimed invention would not be able to make and/or use the invention as claimed. This is particularly true given the nature of the invention, the state of the prior art, the breadth of the claims, the amount of experimentation necessary, the level of skill which is high, the working examples provided and scarcity of guidance in the specification, and the unpredictable nature of the art. Thus, claim 18 is rejected under 35 U.S.C. 112(a) for failure to meet the enablement requirement.
New Claim Rejections - 35 USC § 112(b)
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.
Claim 2 and 18 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 2 recites, inter alia, "A strain for producing L-proline, wherein the strain over-expresses the following polypeptide. . .” . The claim requires an “overexpression” of the polypeptide of A) or B) but it is unclear what the overexpression is being compared to (a wildtype strain? A strain containing another mutated polypeptide?). Thus, the claim is indefinite. For the purposes of compact patent prosecution, the examiner is interpreting the overexpression to be in comparison to a wildtype strain.
Claim 18 recites “a glutamate kinase in the bacterium. . .”. There is insufficient antecedent basis for this limitation in the claim, as there is no previous recitation of any bacterium earlier in the claim, or in claim 5 or 6, from which this claim depends. Thus, the claim is indefinite.
Claim Interpretations
The claims recite “for producing L-proline” (claim 2), or “for producing hydroxyproline” (see claim 5-6). The limitations of “for producing L-proline” and “for producing hydroxyproline” have been interpreted to be intended uses of the polypeptide, strain, and host cell. If the body of a claim fully and intrinsically sets forth all of the limitations of the claimed invention, and the preamble merely states, for example, the purpose or intended use of the invention, rather than any distinct definition of any of the claimed invention’s limitations, then the preamble is not considered a limitation and is of no significance to claim construction. Shoes by Firebug LLC v. Stride Rite Children’s Grp., LLC, 962 F.3d 1362, 2020 USPQ2d 10701 (Fed. Cir. 2020) (The court found that the preamble in one patent’s claim is limiting but is not in a related patent); Pitney Bowes, Inc. v. Hewlett-Packard Co., 182 F.3d 1298, 1305, 51 USPQ2d 1161, 1165 (Fed. Cir. 1999). See also Rowe v. Dror, 112 F.3d 473, 478, 42 USPQ2d 1550, 1553 (Fed. Cir. 1997) ("where a patentee defines a structurally complete invention in the claim body and uses the preamble only to state a purpose or intended use for the invention, the preamble is not a claim limitation") (see MPEP 2111.02).
Modified Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
First rejection
Claims 2 and 10-12 are rejected under 35 U.S.C. 103 as being unpatentable over Yang (see also IDS 08/15/2023; prior art of record). Note a copy of the Yang article is also furnished with this rejection.
Yang teaches an amino acid export carrier protein (i.e., a polypeptide of A) as in claim 2) that has 100% sequence identity to SEQ ID NO: 1 (see alignment below). Yang also teaches that the protein is produced by (i.e., expressed by) C. glutamicum strain ATCC 13869 derived from soil (see pg. 2, col 1, of Yang and portion of Yang reproduced below; a strain expresses the polypeptide of A as in claim 2). Yang also teaches C. glutamicum can be modified in various ways to make it more useful for humans through classical strain breeding methods have been used to introduce mutations into the C. glutamicum genome based on random mutation and screening/selection techniques, and can be used to generate glutamate (as well as other amino acids, such as lysine) hyper producing strains (see pg. 2, col 1, paragraph 2). Yang further teaches that because C. glutamicum strains are widely used for the industrial production of amino acids, and C. glutamicum strains could be useful for the industrial production of glutamate, arginine, or proline (see pg. 10, col 2).
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Therefore, it would have been prima facie obvious to one of ordinary skill at the time of filing to make a strain of C. glutamicum that hyper-produces (i.e., over-expresses) L-proline as taught by Yang to arrive at the claimed invention. One of ordinary skill would have been motivated to do so because Yang explicitly teaches a strain capable of producing the claimed polypeptide and that metabolic engineering of the strain can advantageously be used to generate proline hyper-producing strains.
Regarding claims 10-12, Yang teaches using C. glutamicum (i.e., a bacterium in claim 10, Corynebcterium in claim 11, and C. glutamicum in claim 12).
Second rejection
Claim 3 and 20 are rejected under 35 U.S.C. 103 as being unpatentable over Yang in view of Nakanishi et al (US4444885A; published 04/24/1984; hereinafter “Nakanishi”).
As discussed above, Yang teaches production of a polypeptide of SEQ ID NO: 1 (i.e., expression of the polypeptide) by C. glutamicum strain ATCC 13869 derived from soil (see Yang reproduced below; a strain expresses the polypeptide of A).
Yang does not explicitly teach culturing the strain to produce L-proline.
However, Nakanishi teaches a method for producing L-proline from, for example, Corynebacterium, using fermentation (see claim 1; abstract). Nakanishi specifically teaches improved production of the yield of L-proline during fermentation without addition of any surfactant to the mediums (see Example 1; Table 1, Example 3-4). The mediums contained sodium L-glutamate, pyrrolidonecarboxylic acid, peptone, meat extract, yeast extract, sodium chloride, molasses, soybean meal hydrolysate, etc. (see Example 1; Table 1, Example 3-4).
Therefore, it would have been prima facie obvious to one of ordinary skill at the time of filing to modify the strain of Yang by using the culturing method of Nakanishi and arrive at the claimed invention. As Yang teaches a strain of Corynebacterium capable of producing an amino acid export carrier polypeptide (i.e., for producing L-proline) and Nakanishi teaches successful production of L-proline using culturing/fermentation conditions, one of ordinary skill would have been motivated to use the method of Nakanishi with a reasonable expectation of success. One of ordinary skill would have been motivated to make the modification because Nakanishi explicitly teaches that the culturing method advantageously improves yield of L-proline during fermentation without addition of any surfactant to the mediums.
Regarding claim 20, Nakanishi teaches recovery of L-proline from the fermented broths (see col 3, lines 33-36).
Accordingly, the claimed inventions were prima facie obvious to one of ordinary skill at the time of filing, especially in the absence of evidence to the contrary.
Third rejection
Claim 13 and 14 are rejected under 35 U.S.C. 103 as being unpatentable over Yang in view of Zhang et al (De Novo Engineering of Corynebacterium glutamicum for L-Proline Production. ACS Synth Biol. 2020 Jul 17;9(7):1897-1906. doi: 10.1021/acssynbio.0c00249. Epub 2020 Jul 6. Erratum in: ACS Synth Biol. 2020 Oct 16;9(10):2856; hereinafter “Zhang”; prior art of record).
As discussed above, Yang teaches production of a polypeptide of SEQ ID NO: 1 (i.e., expression of the polypeptide) by C. glutamicum strain ATCC 13869 derived from soil (see portion of Yang reproduced above; a strain expressing the polypeptide of A as in claim 2).
Yang does not explicitly teach a glutamate kinase in the bacterium comprises a G149K mutation (as in claim 13) or the expression of a glutamate kinase and/or a glutamate-semialdehyde dehydrogenase and/or a pyrroline-5- carboxylate reductase in the bacterium is increased (as in claim 14).
However, Zhang teaches de novo engineering of C. glutamicum for L-proline production (see abstract; title). Specifically, Zhang teaches mutagenesis of C. glutamicum to create an industrial hyper-L-proline-producing strain (i.e., enhance the production of proline in the strain) by including various mutations: 1) overexpression of a feedback inhibition resistant gamma-glutamate kinase proB G149K mutant (as in claim 13; increased expression of glutamate kinase as in claim 14), 2) deletion of proline dehydrogenase to block L-proline degradation, 3) overexpression of glutamate dehydrogenase to increase glutamate synthesis flux, 4) the mutation of 6-phosphate gluconate dehydrogenase and glucose-6-phosphate-dehydrogenase in the pentose phosphate pathway to enhance NADPH supply, 5) the deletion of pyruvate aminotransferase to decrease the byproduct L-alanine synthesis, and 6) weakening of α-ketoglutarate dehydrogenase to regulate the TCA cycle (see abstract; see also Fig 2-3; pg. 1900, col 1-2; Fig. 5; pg. 1902, col 1-2). Zhang teaches that the L-proline titer of the final strain ZQJY-9 (the C. glutamicum strain containing all 6 mutations including G149K mutation see abstract and Fig. 6) reached 120.18 g/L at 76 h with the highest productivity of 1.581 g/L/h in the bioreactor (see Fig. 6; see pg. 1903, col 1).
Therefore, it would have been prima facie obvious to one of ordinary skill at the time of filing to modify the strain of Yang by using the de novo mutagenesis protocol of Zhang to create an industrial hyper-L-proline-producing strain of C. glutamicum and arrive at the claimed invention. As Yang teaches a strain of Corynebacterium capable of producing an amino acid export carrier polypeptide (i.e., for producing L-proline) and Zhang teaches de novo engineering of C. glutamicum for L-proline production, one of ordinary skill would have been motivated to use the engineering strategy of Zhang with a reasonable expectation of success. One of ordinary skill would have been motivated to make the modification because Zhang teaches that mutation strategies, such as overexpression of a feedback inhibition resistant gamma-glutamate kinase mutant containing the G149K mutation is advantageously capable of creating industrial hyper-L-proline-producing strain of Corynebacterium.
Accordingly, the claimed inventions were prima facie obvious to one of ordinary skill at the time of filing, especially in the absence of evidence to the contrary.
Fourth rejection
Claim 5, 7, and 21 are rejected under 35 U.S.C. 103 as being unpatentable over Yang in view of Shibasaki et al (Construction of a novel hydroxyproline-producing recombinant Escherichia coli by introducing a proline 4-hydroxylase gene. J Biosci Bioeng. 2000, 90 (5): 522-525; hereinafter “Shibasaki”; prior art of record).
Yang teaches a polypeptide of SEQ ID NO: 1 from C. glutamicum strain ATCC 13869 derived from soil (see portion of Yang reproduced above).
Yang does not explicitly teach a host cell to produce hydroxyproline wherein the expression level of the polypeptide having L-proline efflux function is decreased in the host cell and wherein the expression level of a proline hydroxylase is increased.
However, Shibasaki teaches construction of a novel hydroxyproline-producing recombinant E. coli (a host cell for producing hydroxyproline as in claim 5; see title; abstract). Shibasaki explicitly teaches that the strain was created by introducing a proline-4-hydoxylase gene (i.e., increasing expression level of a proline hydroxylase as in claim 5) into an L-proline producing E. coli (see abstract; see pg. 522, col 1). Shibasaki teaches that the recombinant E. coli expresses a mutated proB gene that encodes a feedback-resistant glutamate kinase that causes overexpression of L-proline (see pg. 522, col 1; Fig. 1). Shibasaki teaches that the W1485 mutant carrying either the pPF1+pWFH1 or pPF2+pWFH1 plasmids (each carrying the proB mutant and proline-4-hydroxylase gene, respectively) produced little to no L-proline but was capable of producing hydroxyproline (see pg. 523, Table 1; pg. 524, col 1, paragraph 1-2). Shibasaki teaches reduction or elimination of L-proline production in the host cell (i.e., decreased L-proline efflux as in claim 8, step 1; see pg. 523, Table 1; pg. 524, col 1, paragraph 1-2),
Therefore, it would have been prima facie obvious to one of ordinary skill at the time of filing to modify the polypeptide of Yang by using the host cell and the mutagenesis protocol of Shibasaki to arrive at the claimed invention. As Yang teaches an amino acid export carrier polypeptide (i.e., for producing L-proline) and Shibasaki teaches an E. coli host cell for production of hydroxyproline via introducing a proline-4-hydoxylase gene into the cell, one of ordinary skill would have been motivated to make the modification with a reasonable expectation of success. One of ordinary skill would have been motivated to make the modification because Shibasaki explicitly teaches that L-proline can be advantageously reduced or eliminated to increase hydroxyproline production in a recombinant host cell via metabolic pathway engineering.
Regarding independent claim 7 and claim 21, Shibasaki teaches culturing of the E. coli host cell to produce hydroxyproline as well as accumulation of the hydroxyproline in the fermentation broth (see pg. 523, col 2, paragraph 2; pg. 524, col 1-2).
Fifth rejection
Claim 6, 15-17, and 19 are rejected under 35 U.S.C. 103 as being unpatentable over Yang and Shibasaki as applied to claim 5 above, and further in view of Sun et al (CN107674863A; published 02/09/2018; hereinafter “Sun”; prior art of record). Please note that the Sun reference is originally in Chinese. The rejection set forth below is based on the English translation, which has been furnished with the rejection.
As discussed above, claim 5 was rendered prima facie obvious by the combined teachings of Yang and Shibasaki.
The difference between Yang, Shibasaki, and the instant claims is that neither reference explicitly teaches the proline hydroxylase is trans-4-proline hydroxylase having a nucleotide sequence as set forth in SEQ ID NO: 5 (as in claim 6).
However, Sun teaches the use of trans-4-proline hydroxylase to produce trans-4-hydroxyproline (i.e., hydroxyproline) (see abstract; claim 1-10). Specifically, Sun teaches that proline 4-hydroxylase can be expressed in L-proline producing bacteria and has high catalytic activity, which allows for industrial production of trans-4-hydroxy-L-proline (see pg. 2, paragraph 4). Sun teaches the cloning and expression of a nucleotide sequence of trans-4-proline hydroxylase (see pg. 6, Example/Embodiment 1) in E. coli before subsequent production and purification of hydroxyproline (see Example 4 and Table 4). The nucleotide sequence of Sun, SEQ ID NO: 2, has 100% identity to instant SEQ ID NO: 5 (see alignment below):
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Therefore, it would have been prima facie obvious to one of ordinary skill to modify the hydroxyproline producing strain of Yang and Shibasaki by including the trans-4-proline hydroxylase of Sun to arrive at the claimed invention. As Yang and Shibasaki teach (in combination) increased hydroxyproline production in a recombinant host cell expressing proline-4-hydroxylase and Sun teaches a sequence of trans-4-proline hydroxylase capable of being expressed in recombinant cells to produce hydroxyproline, one of ordinary skill would have been motivated to use the trans-4-proline hydroxylase of Sun with a reasonable expectation of success. One of ordinary skill would have been motivated to make the modification because Sun explicitly teaches that the proline 4-hydroxylase can be expressed in L-proline producing bacteria, has high catalytic activity, and allows for industrial production of trans-4-hydroxy-L-proline.
Regarding claim 15-17, Yang teaches using C. glutamicum bacterium (see above). It would have been prima facie obvious to one of ordinary skill at the time of filing to use the C. glutamicum strain as a host cell as a simple substitution of one known element (the E. coli of Shibasaki or Sun) for another (the C. glutamicum of Yang) with a reasonable expectation of success. One of ordinary skill would have been motivated to make the modification because the references teach that host cells such as E. coli and C. glutamicum are both useful for the production of amino acids, such as proline and hydroxyproline.
Regarding claim 19, Shibasaki teaches that the recombinant E. coli expresses a mutated proB gene that encodes a feedback-resistant glutamate kinase (i.e., increased expression of glutamate kinase; see above).
Accordingly, the claimed invention was prima facie obvious to one of ordinary skill at the time of filing, especially in the absence of evidence to the contrary.
Response to Arguments
Applicant's arguments filed 12/04/2025 have been fully considered but they are not persuasive.
On pg. 10-13 of the remarks, Applicant argues the Yang reference discloses the amino acid sequence of the thrE protein but fails to disclose or suggest the specific utility of the protein. Applicant argues that Yang is silent on the role of thrE in L-proline transport or utility in regulating proline/hydroxyproline biosynthesis. Applicant argues that the invention is based on identification of L-proline efflux activity of the protein, not described in the prior art and points to Examples 1-2 of the specification, as well as Example 3 (for L-proline production) and Example 4 (for hydroxyproline production). Applicant urges that a PHOSITA would not have expected the genetic mutations are not known in the prior art as the thrE protein’s role in L-proline efflux was not known or suggested.
In response, the examiner disagrees. First, as discussed above “for producing L-proline/hydroxyproline” have been interpreted to be intended uses of the polypeptide, strain, and host cell. If the body of a claim fully and intrinsically sets forth all of the limitations of the claimed invention, and the preamble merely states, for example, the purpose or intended use of the invention, rather than any distinct definition of any of the claimed invention’s limitations, then the preamble is not considered a limitation and is of no significance to claim construction. Shoes by Firebug LLC v. Stride Rite Children’s Grp., LLC, 962 F.3d 1362, 2020 USPQ2d 10701 (Fed. Cir. 2020) (The court found that the preamble in one patent’s claim is limiting but is not in a related patent); Pitney Bowes, Inc. v. Hewlett-Packard Co., 182 F.3d 1298, 1305, 51 USPQ2d 1161, 1165 (Fed. Cir. 1999). See also Rowe v. Dror, 112 F.3d 473, 478, 42 USPQ2d 1550, 1553 (Fed. Cir. 1997) ("where a patentee defines a structurally complete invention in the claim body and uses the preamble only to state a purpose or intended use for the invention, the preamble is not a claim limitation") (see MPEP 2111.02). A recitation of the intended use of the claimed invention must result in a structural difference between the claimed invention and the prior art in order to patentably distinguish the claimed invention from the prior art. If the prior art structure is capable of performing the intended use, then it meets the claim.
In response to applicant's argument that “Yang is silent on the role of thrE in L-proline transport or utility in regulating proline/hydroxyproline biosynthesis, and . . . [the invention is] based on identification of L-proline efflux activity of the protein not described in the prior art”, the fact that the inventor has recognized another advantage which would flow naturally from following the suggestion of the prior art cannot be the basis for patentability when the differences would otherwise be obvious. See Ex parte Obiaya, 227 USPQ 58, 60 (Bd. Pat. App. & Inter. 1985). The claimed strain only requires the expression of the polypeptide of A or B, which is taught by Yang (see above). Yang also provides a PHOSITA the teaching, suggestion, and motivation to hyper-produce amino acids using C. glutamicum via genetic/metabolic engineering (see above). The prior art provides a PHOSITA various teachings to create strains that produce both L-proline and hydroxyproline through culturing methods that advantageously improves yield of L-proline during fermentation without addition of any surfactant to the mediums (see Nakanishi above), 1) overexpression of a feedback inhibition resistant gamma-glutamate kinase proB G149K mutant, 2) deletion of proline dehydrogenase to block L-proline degradation, 3) overexpression of glutamate dehydrogenase to increase glutamate synthesis flux, 4) the mutation of 6-phosphate gluconate dehydrogenase and glucose-6-phosphate-dehydrogenase in the pentose phosphate pathway to enhance NADPH supply, 5) the deletion of pyruvate aminotransferase to decrease the byproduct L-alanine synthesis, and 6) weakening of α-ketoglutarate dehydrogenase to regulate the TCA cycle (see Zhang above), reducing or eliminating L-proline production to increase hydroxyproline production in a recombinant host cell via metabolic pathway engineering (see Shibasaki above), and a sequence of trans-4-proline hydroxylase capable of being expressed in recombinant cells to produce hydroxyproline (see Sun above). Thus, the rejections are maintained as set forth above.
Conclusion
NO CLAIMS ALLOWED.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). 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.
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/G.C.R./Examiner, Art Unit 1651
/THOMAS J. VISONE/Supervisory Patent Examiner, Art Unit 1672