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 .
Applicants' arguments filed on 9/15/2025, have been fully considered and are not deemed to be persuasive to overcome the rejections previously applied. Rejections and/or objections not reiterated from previous office actions are hereby withdrawn. Claims 19, 20, 22, 24, 26, 27, 29, 31, 34 and 36 are pending and at issue for examination.
Claim Rejections - 35 USC § 102
The rejection of claims 18, 20-23, 25, 27-30, are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Patel and Archana (Applied Soil Ecology, Vol 124, pp 34-44, 2018) is withdrawn based upon applicants amendment of the claims and arguments presented in the paper of 2/6/2025.
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.
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.
The rejection of claims 18-24, 25-31, 32-36 are rejected under 35 U.S.C. 103 as being unpatentable over Frost (US 2007/0178571), Almario et al. (Frontiers in Microbiology, Vol 8, Article 1218, June 2017) and Patel and Archana (Applied Soil Ecology, Vol 124, pp 34-44, 2018) and Gasser et al. (WO 2008/128701) is withdrawn based upon applicants amendment of the claims and arguments presented in the paper of 2/6/2025.
The rejection of claim(s) 19, 20, 22, 24, 26, 27, 29, 31, 34, 36 under 35 U.S.C. 103 as being unpatentable over Frost et al. (US 2007/0178571), Gasser et al. (WO 2008/128701) and DeGroot et al., Uniprot Accession No. A0A1H1FBR5, June 7, 2017) is withdrawn based upon applicants amendment of the claims and arguments and Declaration presented in the paper of 5/19/2025. The rejection is withdrawn based upon applicants argument and Declaration of Vincent Lafaquiere under 37 CFR 1.132.
Claim(s) 19, 20, 22, 24, 26, 27, 29, 31, 34, 36 is/are rejected under 35 U.S.C. 103 as being unpatentable over FRANDSEN RASMUS JOHN NORMAND (WO 2016/198623), Gasser et al. (WO 2008/128701) and DeGroot et al., Uniprot Accession No. A0A1H1FBR5, June 7, 2017.
This rejection was stated in the previous office action as it applied to previous claims 19, 20, 22, 24, 26, 27 29, 31, 34, 36. In response to the rejection applicants have not amended the claims but merely traverse the rejection as it applies to the previous and current claims.
FRANDSEN RASMUS JOHN NORMAND (WO 2016/198623) teach that small molecules, of biological origin, often include aromatic or cyclic groups that impact their physiochemical and biological properties. Although nature is rich in aromatic compounds with different carbon skeletons, there is an urgent need for biosynthetic systems capable of producing both natural and new-to-nature aromatic compounds. FRANDSEN RASMUS JOHN NORMAND (WO 2016/198623), teach one of the most versatile biosynthetic schemes for producing aromatic compounds is via the non-reducing polyketide pathways, wherein two-carbon units (-CH.sub.2-CO-), referred to as ketides or 'ketide units', are polymerized into linear chains called polyketides, which subsequently can fold into aromatic structures. FRANDSEN RASMUS JOHN NORMAND (WO 2016/198623), teach methods for producing individual or libraries of tri- to pentadecaketide-derived aromatic compounds of interest by heterologous expression of polyketide synthase and aromatase/cyclase in a recombinant host cell.
FRANDSEN RASMUS JOHN NORMAND (WO 2016/198623), disclose that their invention is based on experimental results disclosed, which demonstrate that in vivo heterologous co-expression of a Type III polyketide synthase (PKSIII) from plants/bacteria/fungi and one or more 'small molecule foldases' from fungi/bacteria, wherein the aromatase/cyclase is from a different genus than the PKSIII, in a recombinant host cell (e.g. a yeast cell or bacterial cell), provides a suitable biosynthetic pathway for the production of aromatic compounds. The in vivo heterologously-expressed PKSIII produces a non-reduced polyketide which is converted in vivo into cyclic or/and aromatic compounds of interest by the action of the one or more heterologously-expressed 'small molecule foldases'. FRANDSEN RASMUS JOHN NORMAND (WO 2016/198623) teach recombinant host cells expressing the PKSIII and one or more 'small molecule foldases' collectively form a programmable system for the formation of aromatic compounds, of any desirable length and fold.
FRANDSEN RASMUS JOHN NORMAND (WO 2016/198623) disclose methods of producing a polyketide-derived aromatic polyaromatic, cyclic or polycyclic compound comprising providing a recombinant yeast host cell comprising a nucleic acid encoding a heterologous type III polyketide synthase from various bacterial species, wherein said
DeGroot et al., Uniprot Accession No. A0A1H1FBR5 teach a polypeptide and its encoding nucleic acid isolated from Tsukamurella pulmonis which has polyketide synthase type-III activity. The polypeptide having polyketide synthase type-III activity taught by Uniprot Accession No. A0A1H1FBR5 is 390 amino acids in length and has 100% sequence identity to instant SEQ ID NO:4.
Gasser et al. (WO 2008/128701) teach a number of eukaryotic expression vectors comprising a yeast promoter and a yeast transcription terminator for integration into the yeast host cell genome for expressing a protein of interest.
One of skill in the art before the effective filing date would have been motivated to substitute the protein and encoding nucleic acid taught by DeGroot et al., Uniprot Accession No. A0A1H1FBR5 in the methods taught by FRANDSEN RASMUS JOHN NORMAND to confirm the enzymatic activity of the protein identified from Tsukamurella pulmonis as a polyketide synthase III activity. The obvious method would be contacting a suitable substrate, malonyl-CoA, with a yeast host cell expressing the nucleic acid encoding the polypeptide taught by DeGroot et al., Uniprot Accession No. A0A1H1FBR5 under control of an exogenous regulatable yeast promoter and comprising a yeast transcription terminator and growing the yeast host cell under conditions to allow growth and expression of the encoding nucleic acid, so as to produce a polyketide such as phloroglucinol. In order to practice the obvious methods above, one of skill in the art before the effective filing date would have been motivated to transform a yeast host cell so as to comprise a nucleic acid encoding the protein and encoding nucleic acid taught by DeGroot et al., Uniprot Accession No. A0A1H1FBR5 in a yeast vector under control of an exogenous promoter and comprising a transcription terminator as taught by Gasser et al. One of skill in the art would have been further motivated to integrate the above obvious nucleic acid under control of an exogenous regulatable promoter into the yeast host genome so that the nucleic acid construct will be more stable and not need to be continually transformed into the bacteria. The expectation of success is high as the level of recombinant protein expression in the art is high as exemplified by FRANDSEN RASMUS JOHN NORMAND, DeGroot et al., Uniprot Accession No. A0A1H1FBR5 and Gasser et al. who teach all that is required to practice the obvious methods.
Applicants Response
Applicants submit that though the Examiner states that the invention of Normand is based on experimental results demonstrating in vivo heterologous co-expression of a PKSIII from plants/bacteria/fungi and a small molecule foldase from bacteria/fungi in a recombinant host cell, applicants submit that the only type III polyketide synthases specifically used in the Examples in Normand are derived from plants, i.e., eukaryotic cells, rather than bacteria. Applicants submit that while Normand generally states that the PKSIII can be of bacterial origin, it fails exemplify a single specific use of a bacterial type III polyketide synthase. Applicants submit that in contrast to Normand, the type III PKSs expressed by the host cells according to the present invention are derived from bacteria, i.e., prokaryotic cells. Applicants submit that Normand generally discloses (but does not exemplify) that even if the encoded enzyme of its invention is of bacterial origin, it is preferably selected from Pseudomonas or Streptomyces. submit that in contrast, none of SEQ ID. Nos 1-10 of the present invention are derived from bacteria belonging to the Pseudomonas or Streptomyces genera, and in fact, the present invention specifically excludes Pseudomonas fluorescens phlD.
Applicants submit that the fact that proteins derived from eukaryotic cells, as in Normand, can be produced efficiently in eukaryotic cells would not lead a person of skill in the art to conclude that proteins derived from prokaryotic cells can be produced efficiently in eukaryotic cells. This point is confirmed by the Examples in the present application, as further detailed below, which show that PHLD from P. fluorescens is not active when expressed in a yeast model (Example 2, Figures 4-7).
Applicants submit that DeGroot fails to remedy the deficiencies of Normand. Applicants submit that the Examiner alleges that a skilled artisan would be motivated to substitute the protein and encoding nucleic acid of DeGroot in the methods taught by Normand to confirm the enzymatic activity of the protein identified from Tsukamurella pulmonis. Applicants submit that however, as previously explained in prior responses and in the previously submitted Declaration, a person of ordinary skill in the art would in fact not have considered that the polypeptide sequence of DeGroot would have possessed phloroglucinol synthase activity.
Applicants submit that DeGroot, teaches that its disclosed polypeptide is "a long-chain alpha-pyrone synthase"(DeGroot, line 6, item "DE SubName") and not a type III polyketide synthase, let alone a "phloroglucinol synthase" (PHLD). Notably, long-chain alpha-pyrone synthases do not have phloroglucinol synthase activity. Other mentioned activities (Chalcone/stilbene synthase, thiolase-like, or Polyketide synthase type-III) are putative and not experimentally demonstrated. Importantly, all these activities are very different from phloroglucinol synthase activity. See Declaration at paragraph 9 and 13-20.
Applicants submit that A POSA would have no reason to consider the polypeptide of De Groot as a putative phloroglucinol synthase, and in fact would have concluded that the polypeptide in DeGroot is a long-chain alpha-pyrone synthase, which is not worth testing for PHLD activity. See Declaration at paragraph 9 and 21. As detailed in the Declaration, a POSA would reach such a conclusion based on the state of the knowledge in the art at the time of the invention.
Applicants submit that in addition, even if a POSA could identify the A0A1H1FBR5 sequence as a potential member of type III polyketide synthase family (which Applicant explicitly disagrees with), there is no basis (and the Examiner did not point out any) for predicting that this particular polypeptide could catalyze phloroglucinol synthesis.
Applicants submit that as explained in the Declaration, type III polyketide synthases are known to be highly specialized in the production of many secondary metabolites, and thus different members of the superfamily utilize a great variety of substrates to produce a variety of products with varying efficiency. Applicants submit that given the very large size and functional diversity of the PKS III enzyme superfamily, a POSA would have no expectation of success in achieving phloroglucinol synthesis when applying DeGroot's polypeptide to methods disclosed in Normand. Therefore, a POSA would not have been motivated to select the polypeptide in DeGroot for testing phloroglucinol synthase activity from among the many other possible candidates available.
Applicant respectfully points out that, even if a prima facie case of obviousness has been made (and Applicant does not concede that it has been made), it may be rebutted based on "unexpected results" by demonstrating "that the claimed invention exhibits some superior property or advantage that a person of ordinary skill in the relevant art would have found surprising or unexpected." In re Soni, 54 F.3d 746, 750 (Fed.Cir. 1995).
Applicants submit that The present application demonstrates that all ten polypeptides as defined in the claims (comprising an amino acid sequence SEQ ID NOs: 1-10) surprisingly and unexpectedly display phloroglucinol synthase activity that is superior to that of PHLDs of the prior art (PHLD.Pf and PHDL.Es) and that the PHLDs of the invention are all active when expressed by a yeast model widely used in industrial processes for enzyme production.
Applicants submit that The In other words, even if a skilled artisan applied Normand's method to the AOA1H1FBR5 polypeptide of DeGroot, it is unclear that phloroglucinol synthesis would have been observed. Nothing in the cited prior art teaches or suggests that PHLDs from bacteria other than Pseudomonas fluorescens could be expressed and that functional and efficient phloroglucinol synthases could be produced by yeast host cells, belonging to the Fungi kingdom, a kingdom far removed from that of bacteria (to which actinomycetes bacteria belong).
Gasser fails to remedy the deficiencies of Normand and DeGroot. Notably, Gasser fails to address type III polyketide synthases at all. Rather, the Examiner relies on Gasser only for a general teaching of eukaryotic expression vectors.
In sum, nothing in the prior art indicates that PHLDs from bacteria other than P. fluorescens can be expressed and that functional and efficient phloroglucinol synthases can be produced by a yeast host cell. In fact, it is well known to a person of skill in the art that cellular mechanisms (such as those involved in protein production) are very different between actinomycetes bacteria and more complex eukaryotic organisms such as yeasts. This is further corroborated by the experimental data described in the application as detailed above. Indeed, Example 2 of the application shows that the only bacterial phloroglucinol synthase known from the prior art, the PHLD from Pseudomonas fluorescens, is not functional when expressed in yeast, unlike the PHLDs according to the invention. Consequently, a person of ordinary skill in the art would have had no reasonable expectation of success in improving phloroglucinol production by generating yeast host cells, transformed with a sequence encoding a PHLD from bacteria other than Pseudomonas fluorescens as defined in the claims.
For all the reasons above, Applicant respectfully submits that there is nothing in the cited references that would have motivated a person of ordinary skill to combine the cited prior art references and then to further modify them to arrive at the present invention. And, there is nothing in the combination of cited references that would provide any indication that the presently claimed host cells would provide the benefits of the present invention as explained above.
Applicants complete argument is acknowledged andhas been carefully considered, however is found nonpersuasive for the reasons previously made of record and for those reasons repeated herein,
In response to applicants submission that only type III polyketide synthases specifically used in the Examples in Normand are derived from plants, i.e., eukaryotic cells, rather than bacteria, this is not found persuasive because as stated previously, Normand states that the PKSIII can be of bacterial origin. This is the basis of the obviousness and Normand need not “exemplify” expression of a bacterial species for the motivation to substitute a bacterial species for that applicants submit is “exemplified”.
In response to applicants submission that the fact that proteins derived from eukaryotic cells, as in Normand, can be produced efficiently in eukaryotic cells would not lead a person of skill in the art to conclude that proteins derived from prokaryotic cells can be produced efficiently in eukaryotic cells, this is not found persuasive on the basis that the origin such as prokaryotic or eukaryotic is not related to the previously stated motivation or expectation of success. Further as stated previously, NORMAND disclose that their invention is based on experimental results disclosed, which demonstrate that in vivo heterologous co-expression of a Type III polyketide synthase (PKSIII) from plants/bacteria/fungi and one or more 'small molecule foldases' from fungi/bacteria, wherein the aromatase/cyclase is from a different genus than the PKSIII, in a recombinant host cell (e.g. a yeast cell or bacterial cell), provides a suitable biosynthetic pathway for the production of aromatic compounds.
In response to applicants submission that DeGroot fails to remedy the deficiencies of Normand and that as previously explained in prior responses and in the previously submitted Declaration, a person of ordinary skill in the art would in fact not have considered that the polypeptide sequence of DeGroot would have possessed phloroglucinol synthase activity, this is not found persuasive because the possession of phloroglucinol synthase activity or knowledged of such is unrelated to the current rejection based upon obviousness. As stated previously, one of skill in the art before the effective filing date would have been motivated to substitute the protein and encoding nucleic acid taught by DeGroot et al., Uniprot Accession No. A0A1H1FBR5 identified as having polyketide synthase type-III activity in the methods taught by FRANDSEN RASMUS JOHN NORMAND to confirm the enzymatic activity of the protein identified from Tsukamurella pulmonis as a polyketide synthase III protein.
In response to applicants submission that DeGroot, teaches that its disclosed polypeptide is "a long-chain alpha-pyrone synthase"(DeGroot, line 6, item "DE SubName") and not a type III polyketide synthase, let alone a "phloroglucinol synthase" (PHLD), this is not found persuasive for the reasons stated previously that Degroot disclose that the protein Uniprot Accession No. A0A1H1FBR5 isolated from Tsukamurella pulmonis identifies as has polyketide synthase type-III activity
In response to applicants submission that a POSA would have no reason to consider the polypeptide of De Groot as a putative phloroglucinol synthase, and in fact would have concluded that the polypeptide in DeGroot is a long-chain alpha-pyrone synthase, which is not worth testing for PHLD activity, as stated previously and repeated above, the motivation for one of skill in the art to substitute the protein and encoding nucleic acid taught by DeGroot et al., Uniprot Accession No. A0A1H1FBR5 in the methods taught by FRANDSEN RASMUS JOHN NORMAND is to confirm the enzymatic activity of the protein identified from Tsukamurella pulmonis as a polyketide synthase III protein, not as a phloroglucinol synthase.
In response to applicants submission that the present application demonstrates that all ten polypeptides as defined in the claims (comprising an amino acid sequence SEQ ID NOs: 1-10) surprisingly and unexpectedly display phloroglucinol synthase activity that is superior to that of PHLDs of the prior art (PHLD.Pf and PHDL.Es) and that the PHLDs of the invention are all active when expressed by a yeast model widely used in industrial processes for enzyme production, this is not found persuasive on the basis that the current motivation is not related to phloroglucinol synthase activity but rather polyketide synthase III activity. As previously stated and repeated above, one of skill in the art to substitute the protein and encoding nucleic acid taught by DeGroot et al., Uniprot Accession No. A0A1H1FBR5 in the methods taught by FRANDSEN RASMUS JOHN NORMAND is to confirm the enzymatic activity of the protein identified from Tsukamurella pulmonis as a polyketide synthase III protein, not as a phloroglucinol synthase.
In response to applicants submission that even if a skilled artisan applied Normand's method to the AOA1H1FBR5 polypeptide of DeGroot, it is unclear that phloroglucinol synthesis would have been observed, this is not found persuasive on the basis that the current motivation is not related to phloroglucinol synthase activity but rather polyketide synthase III activity. As previously stated and repeated above, one of skill in the art to substitute the protein and encoding nucleic acid taught by DeGroot et al., Uniprot Accession No. A0A1H1FBR5 in the methods taught by FRANDSEN RASMUS JOHN NORMAND is to confirm the enzymatic activity of the protein identified from Tsukamurella pulmonis as a polyketide synthase III protein, not as a phloroglucinol synthase.
Claim(s) 19, 20, 22, 24, 26, 27, 29, 31, 34, 36 is/are rejected under 35 U.S.C. 103 as being unpatentable over FRANDSEN RASMUS JOHN NORMAND (WO 2016/198623), Gasser et al. (WO 2008/128701) and DeGroot et al., Uniprot Accession No. A0A1H1FBR5, June 7, 2017.
Remarks
No claim is allowed.
Conclusion
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to RICHARD G HUTSON whose telephone number is (571)272-0930. The examiner can normally be reached 6-3 EST Mon-Fri.
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rgh
11/3/2025
/RICHARD G HUTSON/Primary Examiner, Art Unit 1652