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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 04/27/2026 has been entered.
Priority
This application is a 371 of PCT/EP2020/086342 filed 12/16/2020 which claims benefit of provisional application 62/950,167 filed 12/19/2019. Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged.
Acknowledgment is made of applicant’s claim for foreign priority under 35 U.S.C. 119 (a)-(d). based on EPO 19217809.3 filed 12/19/2019. Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Status of the Claims
Claims 16, 18-29, 32 and 33 are pending. Claims 25-28 are withdrawn. Claims 16, 24 and 29 are amended. Claim 17 is cancelled. Claims 32 and 33 are new.
Claims 16, 18-24, 29, 32 and 33 (claim set filed 04/27/2026) are examined on the merits herein.
Withdrawal of Rejections
The response and amendment filed on 04/27/2026 are acknowledged. All of the amendment and arguments have been thoroughly reviewed and considered.
For the purposes of clarity of the record, the reasons for the Examiner's withdrawal and/or maintaining if applicable, of the substantive or essential claim rejections are detailed directly below and/or in the Examiner's response to arguments section.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 19-22, 24 and 33 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.
Claims 19 and 20 are directed to “Method according to claim 17” and claim 17 is cancelled. Thus, there is insufficient antecedent basis for this limitation in the claims. The scope and boundaries of claims 19 and 20 are not certain making claims 19 and 20 indefinite.
Claims 21, 22 and 33, dependent on claim 20, do not resolve the issue mentioned above and are rejected.
In the interest on compact prosecution claims 19 and 20 are interpreted and examined as dependent on claim 16.
Claim 24 has two issues:
A broad range or limitation together with a narrow range or limitation that falls within
the broad range or limitation (in the same claim) may be considered indefinite if the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c). In the present instance, claim 24 recites the broad recitation “the one or more of fine chemical”, and the claim also recites “preferably … one or more oligosaccharide” which is the narrower statement of the limitation. The claim 24 is considered indefinite because there is a question or doubt as to whether the feature introduced by such narrower language is (a) merely exemplary of the remainder of the claim, and therefore not required, or (b) a required feature of the claims.
Claim 24 recites: “corresponding to Crr protein in E. coli (SEQ ID NO: 26)”. Since SEQ ID
NO: 26 is in the parenthesis, it is not clear whether SEQ ID NO:26 is limiting to the claim or the narrower scope claimed. The scope and boundaries of claim 24 are not certain making claim 24 indefinite.
For examination SEQ ID NO: 26 is not considered to be claim 24 limitation. If applicant is claiming an E. coli with the claimed sequence, the examiner suggests amending the phrase to ‘E. coli with a SEQ ID NO: 26.’
Claim 33 has several issues: (i) the issue of the absence of antecedent basis of the claim, claim
33 depends upon as describes above; (ii) since SEQ ID NOS: 19 and 20 are sequences of complete cyaA proteins from E. coli (specification, p. 6, lines 5 and 7), it is not clear what part of these sequences is considered C-terminal part; (iii) it is not clear whether 80% sequence identity and positions 1 to 412 refer to SEQ ID NOS: 19 or 20. The scope and boundaries of the claim are not certain making claim indefinite.
For examination claim 33 is interpreted as directed to the method to increase the carbon substrate flexibility (elected species) of the production of fine chemicals by the host organism having increased cAMP levels by deletion of the C-terminal part of adenylate cyclase with sequence provided in SEQ ID NOS 19 or 20 or with sequence having 80% identity to positions 1 to 412 of SEQ ID NO: 19 or 20.
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 33 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 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 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.
Claim 33, dependent on claim 20, recites the limitation for the adenylate cyclase protein to have at least 80% sequence identity to positions 1 to 412. Claim 33 is interpreted as the method to increase the carbon substrate flexibility of the production of fine chemicals by the host organism having increased cAMP levels by deletion of the C-terminal part of adenylate cyclase having the limitation for the adenylate cyclase protein to have at least 80% sequence identity to positions 1 to 412 of SEQ ID NO: 19 or 20. Thus, the adenylate cyclase has the sequence 20% or less of which vary from the sequence of positions 1 to 412 of SEQ ID NO: 19 or 20.
Therefore, claim 33 broadly encompasses a genus of adenylate cyclase, retaining functional activity to produce cAMP and having 80% or more sequence identity to positions 1 to 412 of SEQ ID NO: 19 or 20. This would represent a large pool of variant protein sequences for adenylate cyclase that are functional. At the same time adenylate cyclase can have 20% or less of sequences that can differ from positions 1 to 412 of SEQ ID NO: 19 or 20. The Specification does not provide structure function correlation for adenylate cyclase and does not describe domains and/or amino acid residues essential for adenylate cyclase function and domain and/or amino acid residues which can be modified without loss of adenylate cyclase function. The Specification provides examples of adenylate cyclase with SEQ ID NO 20 and variants having different deletions of the C-terminal part but having 100% of the same sequence for positions 1 to 412 (Tables 2A, 2B). Examples of the variants of positions 1 to 412 and examples of the domains or amino acid residues within 1-412 sequence modification of which results in the loss of adenylate cyclase function are not described. The prior art of Linder (Linder Biochem. J., 2008, 415, 449-454 on record in IDS) teaches mutagenesis of E. coli adenylate cyclase (AC) (Abstract). Linder determined that among conserved amino acid residues substitution of several residues resulted in decreased catalytic activity of AC (p. 452, Table 2) and other residues were either non-essential (p. 452, Table 1) or involved in protein folding rather than activity and mutant AC were not soluble (p. 453, left column, 2nd paragraph). Therefore, the prior art does not predict result of modification of 20% of SEQ ID NOS: 19 or 20 at positions 1 to 412 that represents 82 amino acid residues.
Thus, one of ordinary skill in the art would not be able to identify which amino acid sequences that have at least 80% identity to positions 1 to 412 of SEQ ID NOS: 19 or 20 encode for functional adenylate cyclase. One of ordinary skill in the art would conclude based on the lack of representative number of species and the lack of describing the domains or amino acid residues of SEQ ID NO: 19 or 20 critical for the function of adenylate cyclase that the Applicant was not in possession of the claimed genus and the specification fails to satisfy the requirements of written description under 35 U.S.C. 112 (a).
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.
Claims 16, 18-23, 29 , 32 and 33 are rejected under 35 U.S.C. 103 as being unpatentable over Lee (Lee at al., Microbial cell Factories, 2012, 11, 48, 1-9) in view of Pastan (Pastan and Perlman, Science, 1970, 169, 339-344) and Crasnier (Crasnier et al. Mol. Gen. Genet., 1994, 243, 409-416 on record in IDS) as evidenced by UniProt (UniProt, P00936 CYAA_ECOLI [retrieved on 03/28/2025]. Retrieved from the Internet: <https://www.uniprot.org/uniprotkb/P00936/entry>).
Regarding claim 16, Lee teaches whole cell biosynthesis of a functional oligosaccharide, 2’-fucosyllactose (2-FL) in engineered Escherichia coli (Abstract). Lee describes fermentation of E.coli in the presence of substrates including growing of bacterial cells and production of 2-FL (p. 3, left column, last paragraph, right column, 1st paragraph, Figure 3). Fine chemical is defined in the specification as: “Fine chemical according to the invention is a biochemical substance comprising two or more sugar units.” (p. 9, lines 11-12). Thus, Lee teaches production of a fine chemical in a host organism.
Lee does not teach increasing cAMP levels in the host organism by introduction into the host organism of a mutated adenylate cyclase (AC) lacking the regulatory activity found in the wild-type AC.
Pastan teaches that cAMP stimulates enzyme synthesis in cultures repressed by glucose (p. 340, left column, 1st paragraph). Pastan describes that the E. coli mutant strain deficient in adenyl cyclase activity and having undetectable level of cAMP synthesized by adenylate cyclase was unable to grow on lactose, maltose, arabinose, mannitol or glycerol and grew slowly on glucose, fructose and galactose. The addition of cAMP permitted normal utilization of all of these carbon sources (p. 340, right column, 1st paragraph, p. 341, Table 3) and hence increased substrate flexibility.
Crasnier teaches the presence of catalytic and regulatory domains in E. coli adenylate cyclase (AC) (Abstract). Crasnier mentions that the junction between the two domains is located on proline 412 (p. 414, right column, last paragraph). Crasnier describes spontaneous mutants producing large amounts of cAMP in strains deficient in EnzymeIIA (interacting with the regulatory domain) (Abstract). These mutations were deletions generating truncated at the C-terminal AC (Abstract). Crasnier discloses that mutant 48 kDa AC protein that has the last retained residue of P412 and deletion of the regulatory domain (p. 414, right column, last paragraph) produced 10 time more cAMP relative to the wild-type adenylate cyclase. Crasnier concludes that the regulatory domain is inhibitory to the activity of the catalytic domain (Abstract).
First, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to follow Pastan teaching and increase the level of cAMP during production of fine chemicals based on Lee teaching. One would have been motivated to do so since Pastan teaches that addition of cAMP increases substrate flexibility and allows cultures to grow on different carbon sources including lactose necessary for synthesis of 2-FL in Lee teaching. A skilled artisan would have reasonably expected success in this combination because Lee describes synthesis of fine chemical and Pastan provides method to support fermentation with the necessary substrate.
Second, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine teachings of Crasnier, Lee and Pastan and introduce into the host organism of Lee teaching the mutated adenylate cyclase having truncated or deleted C-terminal regulatory part of adenylate cyclase without disruption of the catalytic part and apply it for production of fine chemicals based on Lee and Pastan teachings. One would have been motivated to do so since Crasnier teaches that regulatory domain is inhibitory to adenylate cyclase action and that deletion of the C-terminal domain increases the cAMP level and Pastan teaches that cAMP stimulates of enzyme synthesis and utilization of various carbon sources increasing substrate flexibility. A skilled artisan would have reasonably expected success in this combination because Lee teaches production of fine chemicals by microbial system, Pastan teaches necessity of cAMP for efficient production and Crasnier describes genetic modification to increase in cAMP level in microbial host cells. Thus, teachings of Lee, Pastan and Crasnier render claim 16 obvious.
Regarding claim 18, Crasnier teaches introduction of mutated adenylate cyclase gene lacking the regulatory domain into the microbial cell that increases cAMP level as described above. Crasnier discloses that the high level of production of cAMP is toxic to E. coli (p. 413, right column) pointing to necessity to control adenylate cyclase expression and hence the cAMP level.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to introduce into the host organism of Lee teaching the mutated adenylate cyclase having deleted C-terminal regulatory part and express it in the inducible manner and apply it for production of fine chemicals based on Lee and Pastan teachings. One would have been motivated to do so since Crasnier teaches that high level of cAMP is toxic to E. coli cells and inducible expression of adenylate cyclase will allow to increase cAMP level only for the period of production of fine chemicals preventing toxicity during microbial growth. A skilled artisan would have reasonably expected success in this combination because Pastan teaches necessity of cAMP for efficient production of fine chemical of Lee teaching and Crasnier describes introduction of adenylate cyclase providing increased cAMP level necessary during production and induced expression of introduced gene is routine and conventional. Thus, teachings of Lee, Pastan and Crasnier render claim 18 obvious.
Regarding claims 19-22 and 33, Crasnier teaches introduction of mutated cya gene into different strains of E. coli (as introduction of a transgene) (p. 411, left column, 2nd paragraph). Please note that cya gene is synonym of claimed CyaA gene of E.coli as evidenced by UniProt (p. 3). Mutations provide inactivation of regulatory activity pf AC by truncation or deletion of the C-terminal regulatory domain of AC without disruption of the catalytic part producing cAMP. Crasnier discloses that 48-kDa protein produces increased intracellular amount of cAMP compared to the wild-type AC (p. 414, right column, 1st paragraph). The genetic analysis of the genes encoding 48-kDa protein revealed that the last retained amino acid residue of AC sequence is proline 412. Crasnier describes P412 to be localized at the junction between catalytic and regulatory domains. Crasnier confirms that by additional deletion of 15 C-terminal amino acid residues (from P412) leading to reduction in AC activity (p. 414, right column, 2nd paragraph). Crasnier concludes that the regulatory domain is inhibitory to the activity of the catalytic domain (Abstract). Crasnier teaches adenylate cyclase of Escherichia coli K12. The sequence of AC of E. coli K-12 strain is 100% identical to instant SEQ ID NO: 19 as evidenced by UniProt.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to follow teaching of Crasnier and introduce mutated AC as a transgene and reduce regulatory activity of AC by deletion of the C-terminal regulatory domain of AC with sequence 100% identical to instant SEQ ID NO: 19 without disrupting the catalytic domain and use that modification for production of fine chemical based on Lee and Pastan teachings. One would have been motivated to do so since Crasnier teaches that regulatory domain is inhibitory to adenylate cyclase action and that deletion of the C-terminal domain increases the cAMP level and Pastan teaches that cAMP stimulates of enzyme synthesis and utilization of various carbon sources increasing substrate flexibility. A skilled artisan would have reasonably expected success in this combination because Lee teaches production of fine chemicals by microbial system, Pastan teaches necessity of cAMP for efficient production and Crasnier describes genetic modification to increase in cAMP level in microbial host cells. Thus, teachings of Lee, Pastan and Crasnier as evidenced by UniProt render claims 19-22 and 33 obvious.
Regarding claim 23, Lee teaches addition of a substrate, lactose, during fermentation as a carbon source (p. 3, right column, 1st paragraph). Thus, Lee, Pastan and Crasnier teachings render claim 23 obvious.
Regarding claim 29, Lee teaches production of 2FL and mentions that 2-FL is the most abundant fucosyloligosaccharide in human milk and accounts for more than 30% of total human milk oligosaccharides (p. 1, right column). Thus, Lee, Pastan and Crasnier teachings render claim 29 obvious.
Regarding claim 32, the recited in the “wherein” clause, i.e. 20% increase of the recited parameter compared to control is interpreted as intended use. The intended use is given weight to the extent that it imparts a structural limitation and the prior art needs to be capable of performing the intended use. See MPEP 2111.02, section II. MPEP 2111.04 states: “ … the court noted that a "whereby clause in a method claim is not given weight when it simply expresses the intended result of a process step positively recited.’" Id. (quoting Minton v. Nat’l Ass’n of Securities Dealers, Inc., 336 F.3d 1373, 1381, 67 USPQ2d 1614, 1620 (Fed. Cir. 2003))”. In instant case, the combination of prior art of Lee, Pastan and Crasnier renders the instantly claimed method steps obvious and the prior art of Pastan teaches increase in carbon substrate flexibility (elected species) and therefore the method of production of fine chemicals taught by prior art of Lee, Pastan and Crasnier is capable to have 20% increase in carbon flexibility of the production compared to control. Thus, Lee, Pastan and Crasnier teachings render claim 32 obvious.
Claim 24 is rejected under 35 U.S.C. 103 as being unpatentable over Lee (Lee at al., Microbial cell Factories, 2012, 11, 48, 1-9) in view of Pastan (Pastan and Perlman, Science, 1970, 169, 339-344) and Crasnier (Crasnier et al. Mol. Gen. Genet., 1994, 243, 409-416 on record in IDS) as applied to claim 16 above, and further in view of Deutscher (Deutscher et al. Microbiol. Molec. Biol. Reviews, 2014, 231-256).
The teachings of Lee, Pastan and Crasnier have been set forth above.
Lee, Pastan and Crasnier do not teach inactivation or removal of Crr protein.
Deutscher teaches regulation of the bacterial phosphoenolpyruvate: carbohydrate phosphotransferase system (PTS) (Abstract). EIIAGlc protein, also called Crr, the component of PTS was found to be central regulator of carbon metabolism (p. 232, left column, 2nd paragraph and p. 233, left column, 2nd paragraph). Deutscher discloses that Crr from E. coli was shown to interact with non-PST proteins (p. 242, left column) and describes that interaction leads to: “inhibition of the non-PTS proteins, which are usually transporters or transporter associated components. Their inhibition prevents the uptake of the corresponding carbon source and consequently the formation of the necessary inducer; this regulation mechanism was therefore called inducer exclusion.” (p. 242, left column). Deutscher demonstrates on Figure 5 that the inducer exclusion is prevented when the EIIAGlc-encoding crr gene is deleted allowing the uptake of the other four carbohydrates, L-arabinose, D-galactose, melibiose, and raffinose (p. 242, Figure 5 legend). Thus, deletion or inactivation of Crr protein results in the uptake of various carbon substrates increasing substrate flexibility.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to follow Deutscher teachings and add inactivation or deletion of Crr protein to the host organism genetically modified to produce fine chemicals based on Lee, Pastan and Crasnier teachings. One would have been motivated to do so since Deutscher teaches that Crr inhibits transporters or transporter associated components and that deletion or inactivation of Crr leads to uptake of various carbon substrates and hence would increase substrate flexibility. A skilled artisan would have reasonably expected success in this combination because Lee provides method of production of fine chemicals by microbial system, Pastan and Deutscher teach increase in substrate flexibility and Crasnier and Deutscher teach genetic modifications leading to increase in the substrate flexibility. Thus, teachings of Lee, Pastan, Crasnier and Deutscher render claim 24 obvious.
Response to Arguments
Applicant's arguments filed 04/27/2026 have been fully considered but they are not persuasive.
Applicant’s arguments with respect to prior art of Bhadra and Hara have been considered but are moot because the new ground of rejection does not rely on prior art of Bhadra and Hara applied in the prior rejection of record for any teaching or matter specifically challenged in the argument. Arguments regarding prior art of Crasnier are addressed below.
Applicant argues (addressing p. 7 of the Remarks) that Crasnier discloses that a 48kDa protein half the size of the wild type protein produces the effect of increased cAMP level. Applicant further argues that reading Crasnier it is not possible to elucidate what this 48 kDa protein is and the skilled person would not able to repeat any of the work in Crasnier. These arguments are not persuasive because:
Crasnier teaches sequencing of genes encoding 48 kDa proteins (p. 414, right column, last paragraph). Analysis showed that the last amino acid residue retained from the original sequence was proline 412. Figure 1 shows that for pDIA1920 proline 412 is the last residue of original sequence followed by 6 residues not present in AC sequence since mutated gene was obtained by deletion of 5 nucleotides. Crasnier further describes that P412 is a conserved residue in all AC of class I and is located at the junction between two domains based on primary and secondary structure of AC. Crasnier confirmed that 412 residue is the last residue of the catalytic domain by deletion of additional 15 residues from C-terminus starting from P412 that led to reduction in AC activity (p. 414, right column, last paragraph). Additionally, Crasnier mentions that removal of 305 C-terminal amino acid residues (about two-thirds of the regulatory domain) from AC generated protein with 65 kDa producing 5 times more cAMP that the wild-type AC, while removal of complete regulatory domain results in 10-fold increase in cAMP level. That confirms Crasnier conclusion that regulatory domain is inhibitory to the activity of catalytic domain of AC (p. 415, left column, 2nd paragraph). Since the sequence of E. coli AC is known and Crasnier points to P412 at the junction of catalytic and regulatory domains and teaches inhibitory function of regulatory domain, one of ordinary skill in the art would be able to construct expression vector to express AC retaining the catalytic domain and with deletion or truncation of the regulatory domain and to use that vector to increase level of cAMP produced in the host cell.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to LIOUBOV G KOROTCHKINA whose telephone number is (571)270-0911. The examiner can normally be reached Monday-Friday: 8:00-5:30.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Sharmila G Landau can be reached at (571)272-0614. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/L.G.K./Examiner, Art Unit 1653
/SHARMILA G LANDAU/Supervisory Patent Examiner, Art Unit 1653
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