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 .
Status of the Claims
Claims 1-14 are pending in the application.
Claim for Domestic Benefit
This application claims the benefit of and priority to U.S. Provisional Application No., 63/385234 filed Nov. 29, 2022, is acknowledged.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 11/15/2023 was filed prior to the mailing of the instant first Office action on the merits. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statements are being considered by the examiner. A copy of Form PTO/SB/08 is attached to the instant Office action.
Drawings
The presented drawings (Figure 1 and Figure 2) have been considered by the examiner.
Claim Rejections - 35 USC § 112
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.
Claims 1 and claims 2-14 dependent therefrom 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 adequately 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 applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention, i.e. a bioengineered beta-lactone synthetase(s).
MPEP 2163.1I.A.2.(a).i) states, “Whether the specification shows that applicant was in possession of the claimed invention is not a single, simple determination, but rather is a factual determination reached by considering a number of factors. Factors to be considered in determining whether there is sufficient evidence of possession include the level of skill and knowledge in the art, partial structure, physical and/or chemical properties, functional characteristics alone or coupled with a known or disclosed correlation between structure and function, and the method of making the claimed invention”.
For claims drawn to a genus, MPEP § 2168 states 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 the applicant was in possession of the claimed genus. See Elf Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406.
According to MPEP 2163.II.A.3.(a).ii), [s]atisfactory disclosure of a ‘representative number depends on whether one of skill in the art would recognize that the applicant was in possession of the necessary common attributes or features possessed by the members of the genus in view of the species disclosed. For inventions in an unpredictable art, adequate written description of a genus which embraces widely variant species cannot be achieved by disclosing only one species within the genus. Instead, the disclosure must adequately reflect the structural diversity of the claimed genus, either through the disclosure of sufficient species that are ‘representative of the full variety or scope of the genus,’ or by the establishment of ‘a reasonable structure-function correlation.”
The factors considered in the Written Description requirement are (1) Actual reduction to practice; (2) Disclosure of drawings, structural characterization, and sequence data; (3) Sufficient relevant identifying characteristics; (4) Detailed method of making the claimed invention; (5) Level of skill and knowledge in the art; and (6) Predictability in the art. Disclosure of any combination of such identifying characteristics that distinguish the claimed invention from other materials and would lead one of skill in the art to the conclusion that the applicant was in possession of the claimed species is sufficient.
Claims 1 and 2-14 dependent therefrom recite a genus of bioengineered beta-lactone synthetases. In view of the recitation of bioengineered beta-lactone synthetases, the structure (i.e., amino acid sequences) of the genus of bioengineered beta-lactone synthetase is extremely large. As such, the genus of bioengineered beta-lactone synthetases is considered to be widely variant with respect to structure.
The specification does not teach the structure/function relationship of the proposed bioengineered beta-lactone synthetases and there is also a lack of straightforward information for one of ordinary skill in the art to make a functional bioengineered beta-lactone synthetase(s). The disclosure also does not demonstrate possession of the full scope of the claimed subject matter.
As noted above, the structures of the genus of recited “bioengineered beta-lactone synthetases” is extremely large. The reference of Singh et al. (Protein Engineering Approaches in the Post-Genomic Era, Curr. Protein Pept. Sci.,vol. 18, 1-11, 2017; cited on Form PTO-892) reviews various protein engineering methods and discloses that despite the availability of an ever-growing database of protein structures and highly sophisticated computational algorithms, protein engineering is still limited by the incomplete understanding of protein functions, folding, flexibility, and conformational changes (see p. 7, column 1, top).
The unpredictability of structure and function associated with amino acid modifications of an enzyme/protein is exemplified by the reference of Zhang et al. (Propagated Perturbations from a Peripheral Mutation Show Interactions Supporting WW Domain Thermostability, Structure, vol. 26, issue 11:1474-1485, 2018; cited on Form PTO-892), which discloses that even a mutation that was predicted to be benign caused significant structural changes and unexpected effects on the function of a polypeptide (p. 1475, column 1).The level of knowledge and skill in the art does not allow those skilled in the art to structurally envisage or recognize those structures of the genus of recited “bioengineered beta-lactone synthetases” as claimed herein. The specification fails to describe an extremely large number of mutations to a bioengineered beta-lactone synthetase and beta-lactone synthesis as recited in claim 1. Given that the genus of recited bioengineered beta-lactone synthetases is widely variant with respect to structure, in view of the high level of unpredictability in the art of amino acid modification, the specification fails to adequately describe the claimed invention. One of skill in the art would reasonably conclude that the disclosure fails to provide a representative number of species to describe the genus, and thus, that the applicant was not in possession of the recited genus. The claimed subject matter is not supported by an adequate written description because a representative number of species has not been described.
.
Therefore, claims 1-14 are rejected for failing to satisfy the written description requirement.
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, 7, 10-11 are rejected under 35 U.S.C. 112(b).
Claim 3 is rejected under 35 U.S.C. 112(b) and is drawn to the components of the microorganism’s feedstock which includes the phrase "and the like". The inclusion of “and the like” renders the claim(s) indefinite because the claim(s) include(s) elements not actually disclosed (those encompassed by "and the like"), thereby rendering the scope of the claim(s) unascertainable. See MPEP § 2173.05(d).Claim 7 is rejected under 35 U.S.C. 112(b). Claim 7 recites the limitation "enzymes are selected from the group…" from the method of Claim 1 in the first line of the claim. There is insufficient antecedent basis for this limitation in the claim. It is not stated clearly which of the enzymes in claim 1 are being referred to as Claim 1 recites two different enzymes or enzyme groupings
Claims 10 and 11 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, for lack of internal antecedence. The chemical structures as written are indistinguishable and it is not clear which of the R-groups referred to in the legend applies to which R groups in the formula. Proper designation of R-groups (R1 and R2, for example) would clarify the chemical structures as drawn.
The R-groups are also currently infinitely undefined as being -CnH2n+1. Please state the exact chain lengths of the R-groups in which the beta-lactone synthetase has successfully acted upon the substrates (instant claim 10) to make the corresponding beta-lactones (instant claim 11).
Claim Rejections - 35 USC § 103
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.
Claims 1-14 are rejected under 35 U.S.C. 103 as being unpatentable over (Robinson, et. al, Mechanism of a Standalone b-Lactone Synthetase: New Continuous Assay for a Widespread ANL Superfamily Enzyme, ChemBioChem 2019, 20, 1701 – 1711) (examiner cited), (Perez-Zabaleta, et. a;, Increasing the production of (R)‑3‑hydroxybutyrate in recombinant Escherichia coli by improved cofactor supply, Microb Cell Fact (2016) 15:91) (applicant IDS) and (Xie, et.al., Ring-Opening Polymerization of beta-butyrolactone by Thermophilic Lipases, Macromolecules, 30, 6997-6998, 1997) (examiner cited), (Chen, et.al., Advanced Strategies for Production of Natural Prodcuts in Yeast, iScience, 23, 100879, 2020) (examiner cited), and (Pommier, et.al., Recent Advances in beta-lactone chemistry, Synthesis, May 1993, 441-459) (examiner cited).
Claim 1 is drawn to a method reacting a feedstock and a recombinant microorganism harboring the biosynthetic pathway for 3-hydroxycarboxylic acid synthesis having C1-C10 alkyl groups and allowed to form said carboxylic acid. These 3-hydroxycarboxylic acids produced are then reacted upon by a bioengineered beta-lactone synthetase to produce the corresponding beta-lactones. Claim 2 is drawn to synthesizing a polyhydroxyalkanote (PHA) through ring opening biocatalysis of the produced beta-lactones. Claim 3 is drawn a feedstock from the group consisting of sugar, vegetable oil, crude oil, methane, syngas, lignocellulosic biomass, algae biomass, municipal solid waste. Claim 4 is drawn to a microorganism selected from the group consisting of a prokaryotic organism, a eukaryotic organism, and any combination thereof. Claim 5 states that the prokaryotic organism is selected from the group consisting of E. coli, B. subtilis, Corynebacterium sp., Pseudomonas sp., and any combination thereof. Claim 6 is drawn to the microorganism being a eukaryotic organism selected from the group consisting of yeast, filamentous fungi, or any combination thereof. Claim 7 is drawn to wherein the enzyme in the method of claim 1 are selected from the group consisting of 3-ketothiolase (PhaA), P-ketoacyl-CoA thiolase, NADPH-dependent acetoacetyl-CoA reductase (PhaB), acetoacetyl-CoA reductase, PHA synthase (PhaC), PHA polymerase, poly(3-hydroxyalkanoate) depolymerase (Pha), PHA depolymerase, acyl-CoA thioesterase II (TesB), acyl-CoA thioesterase II, phosphotransbutyrylase-butyrate kinase (Ptb-Buk), and any combination thereof. Claim 8 is drawn to the bioengineered beta-lactone synthetase is engineered based on rational or random mutagenesis. Claim 9 is drawn to the reacting of the 3-hydroxycarboxilic acid with a bioengineered natural P-lactone synthetase to produce the P-lactone is fueled by an energy source selected from the group consisting of adenosine triphosphate (ATP), adenosine diphosphate (ADP), pyrophosphate (PPi), thioester bonds, and any combination thereof. Claim 10 is drawn to the structure of a 3-hydroxycarboxylic acid. Claim 11 is drawn to the structure of a beta-lactone. Claim 12 is drawn to a reaction where (R)-3-hydroxybutanoic acid and the produced beta-lactone is (R)-3-methyloxetan-2-one. Claim 13 is drawn to a reaction where (2R,3S)-3-hydroxy-2-methylbutanoic acid and the produced beta-lactone is (2R,3S)-3-4-dimethyloxetan-2-one. Claim 14 is drawn to a reaction where (R)-3- hydroxypentanoic acid and the produced beta-lactone is (R)-4-ethyloxetan-2-one.
The reference of Robinson teaches the overexpression, purification, site-directed mutagenesis, and the biochemical and bioinformatical characterization of the long-chain beta-lactone synthetase, OleC, from Xanthomonas campestris.
The generation of a bioengineered natural beta-lactone synthetase (instant claim 1, 8) is taught by Robinson (page 1709, second column, third paragraph). Robinson utilizes the OleC enzyme (beta-lactone synthetase) from X. campestris and it was recombinantly expressed with a C-terminal hexahistidine tag in Escherichia coli. The reaction of the beta-lactone synthetase with 3-hydroxycarboxylic acids having alkyl side chains of C1-C10 length (instant claim 1, 10-11) is taught by Robinson (page 1706, Figure 4). Here Robinson measured the substrate preference of OleC (beta-lactone synthetase) by monitoring both ATP consumption (instant claim 9) and AMP release which was quantified by HPLC (figure 4, page 1706).
What Robinson does not teach that is applicable to the claims of the application is the generation of a recombinant microorganism for the production of 3-hydroxycarboxylic acids having alkyl side chains of C1-C10.
These deficits in the teachings of Robinson are remedied by the teachings of Perez-Zabaleta.
The bioengineering of a microorganism encoding the metabolic pathway for a C1 – C10 containing 3-hydroxycarboxylic acids (instant claim 1) is taught by Perez-Zabaleta (page 7 Figure 5). Perez-Zabaleta teaches the production of (R)-3-hydroxybutyrate in a recombinant E. coli strain (instant claims 4-5) (page 7, column 2, Strains and Plasmids) harboring the gene for the production of (NADPH-dependent) acetoacetyl-CoA reductase (instant claim 7) from H. boliviensis (page 3, Figure 2 and Table1). The recombinant E. coli strain was grown via fermentation and cultivation of the microorganism’s feedstock containing glucose (sugar) (instant claim 3) (page 7, column 2, last paragraph).
The teachings of Robinson and Perez-Zabaleta are set forth above, what they do not teach is synthesizing a polyhydroxyalkanoate (PHA) through ring-opening biocatalysis of the produce beta-lactone. This is remedied by the teachings of Xie.
The ring opening polymerization of beta-butyrolactone by thermophilic lipases is taught by Xie. Herein the enzyme-catalyzed ring-opening biocatalysis of beta-lactones (instant claim 2) is carried out to form polyhydroxyalkanoates (page 6997, second column, Polymerization section).
What the above teachings of Robinson, Perez-Zabaleta, and Xie do not teach regarding the applicant’s claims is the utilization of yeast or filamentous fungi and the production of beta-lactones given specific starting materials.
The use of yeast (instant claim 6) in biosynthesis and in strategies for the production of natural products is taught by Chen (page 1, last paragraph and subsections).
The above teachings of Robinson, Perez-Zabaleta, Xie, and Chen do not teach the ring closure reaction of 3-hydroxycarboxylic acids to make beta-lactones. This is remedied by the teachings of Pommier .
The ring closure of simple 3-hydroxycarboxylic acids to produce the corresponding beta-lactones is known within the literature to be a difficult and challenging process due to ring strain and the potential for competing side reactions (i.e., dehydration or oligomerization). General synthetic strategies include activation of the carboxylic acid to an acid chloride, use of mixed anhydrides, tosylation, and thiol ester cyclization methods. Some additional methods of beta-lactone ring closure are taught by Pommier (schemes 5-9, pages 443-444).
One of ordinary skill in the art would find that it would be obvious to explore other methods of making beta-lactones including the utilization of enzymatic methods (instant claims 12-14). The role of the beta-lactone synthetase enzyme(s) are to catalyze the formation of the four-membered ring beta-lactones from the appropriate 3-hydroxycarboxylic acids starting material. It would be obvious to employ such a strategy to facilitate making this class of four-membered ring compounds.
At the time of the applicant’s invention, it would have been obvious to one of ordinary skill in the art to combine the teachings of Robinson, Perez-Zabaleta,Xie, Chen, and Pommier to develop an engineered microorganism that produces 3-hydroxycarboxylic acids and couple that with a bioengineered beta-lactone synthetase to produce the corresponding beta-lactones which are further biocatalyzed to produce polyhydroxyalkanoates (PHA). One would have been motivated to couple the reactions of a recombinant microorganism producing 3-hydroxycarboxylic acids having alkyl side chains of C1-C10 with a bioengineered beta-lactone synthetase in order to produce the corresponding beta-lactones and further reacting them to make PHA. One would have had a reasonable expectation of success of making beta-lactones, and by extension, PHAs by combining the teachings of Robinson, Perez-Zabaleta, Xie, Chen, and Pommier. Therefore, claims 1-14 would have been obvious to one of ordinary skill in the art at the time of invention.
Status of the claims
• Claims 1-14 are pending.
• Claims 1-14 are rejected.
• No claim is in condition for allowance.
Conclusion
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/A.S./Examiner, Art Unit 1656
/MANJUNATH N RAO/Supervisory Patent Examiner, Art Unit 1656