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 .
Reopening of Prosecution After Appeal Brief
In view of the Appeal Brief filed on 07/13/2026, PROSECUTION IS HEREBY REOPENED. A new grounds of rejections are set forth below.
To avoid abandonment of the application, appellant must exercise one of the following two options:
(1) file a reply under 37 CFR 1.111 (if this Office action is non-final) or a reply under 37 CFR 1.113 (if this Office action is final); or,
(2) initiate a new appeal by filing a notice of appeal under 37 CFR 41.31 followed by an appeal brief under 37 CFR 41.37. The previously paid notice of appeal fee and appeal brief fee can be applied to the new appeal. If, however, the appeal fees set forth in 37 CFR 41.20 have been increased since they were previously paid, then appellant must pay the difference between the increased fees and the amount previously paid.
A Supervisory Patent Examiner (SPE) has approved of reopening prosecution by signing below:
/SHARMILA G LANDAU/Supervisory Patent Examiner, Art Unit 1653
Priority
This application is a 371 of PCT/EP2020/054172 filed 02/18/2020. 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 EP19215651.l, filed on 12/12/2019 and EP19158372.3 filed on 02/20/2019. Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Status of the Claims
Claims 1, 10-23 and 25-30 are pending. Claims 21 and 22 are withdrawn.
Claims 1, 10-20, 23 and 25-30 (claim set as filed on 11/06/2025) are examined of the merits herein.
Withdrawal of Rejections
The Appeal Brief and the Declarations under 37 C.F.R. 1.132 of Dr. Daub filed on 07/13/2026 are acknowledged. All of the 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.
The previous claims 1, 10-20, 23 and 25-30 rejections under 35 U.S.C. 103 have been withdrawn necessitated by Applicant’s arguments which are persuasive.
The previous claims 1, 10-19 and 25-30 double patenting rejection over application 17/432,203 has been withdrawn necessitated by abandonment of application 17/432,203.
Claim Rejections - 35 USC § 102
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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1, 10-12, 14-16, 18, 20, 26, 28 and 29 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Martinez (Martinez et al. Enzyme Microbiol. Technol., 1998, 22, 520-526) as evidenced by Park (Park et al. J. Bacter., 1989, 171, 2657-2665).
Regarding claim 1, Martinez teaches production of Escherichia coli β-galactosidase in Bacillus subtilis using fed-batch cultures (Abstract). Martinez describes providing chemically defined minimal medium containing glucose at 0.4-0.6 g/l and mineral salts (K2HPO4, 5.32 g; (NH4)2SO4, 4 g; KH2PO4, 6.4 g; MgSO4 x 7H2O, 0.4 g; MnCl2, 5 mg; CaCl2, 40 mg; FeSO4 x 7H2O, 30 mg) (p. 521, left column, last paragraph). Martinez discloses inoculation of the fermentation medium with Bacillus subtilis with lacZ gene encoding β-glucosidase under the control of aprE promoter (p. 521, left column, last paragraph). Martinez applies glucose-limited exponentially fed-batch cultures for fermentation (Abstract). Martinez describes feeding the glucose solution of 40-500 g/l and addition of mineral salt solution containing 6.4 g/l MgSO4 (p. 521, left column, last paragraph). The fed operation is initiated 2h after initial batch phase and implemented using computer controlled feeding profile to maintain specific growth rate (p. 521, right column, 1st paragraph). Martinez mentions that the maximum β-galactosidase activity was achieved at the maximal growth rate (Abstract). Martinez suggested that preventing glucose limitation is important to obtain production of β-galactosidase in defined glucose-mineral media (p. 524, right column, 2nd paragraph). Martinez does not teach Bacillus cell to be genetically modified in its ability to take up or metabolize an inducer molecule.
Thus, Martinez teaches all the steps and limitations of the claimed process and hence Martinez teaching anticipates claim 1.
Regarding claims 10 and 11, Martinez teaches addition of mineral salts including 0.4 g/l MgSO4 x 7H2O (p. 521, left column, last paragraph) that reads on claims 10 and 11 limitations. Thus, Martinez teaching anticipates claims 10 and 11.
Regarding claim 12, Martinez teaches addition of mineral salts including 40 mg/l FeSO4 x 7H2O (elected species) that corresponds to 108 µM (p. 521, left column, last paragraph) and reads on claim 12 limitation. Thus, Martinez teaching anticipates claim 12.
Regarding claim 14, Martinez teaches glucose as a carbon source (p. 521, left column, last paragraph). Thus, Martinez teaching anticipates claim 14.
Regarding claim 15, Martinez teaches addition of nitrogen source and nutrients mixture, i.e. K2HPO4, 5.32 g; (NH4)2SO4, 4 g; KH2PO4, 6.4 g; MgSO4 x 7H2O, 0.4 g; MnCl2, 5 mg; CaCl2, 40 mg; FeSO4 x 7H2O, 30 mg (p. 521, left column, last paragraph) that includes chemically defined nitrogen and sulfur source, (NH4)2SO4, and chemically defined potassium source, KH2PO4. Thus, Martinez teaching anticipates claim 15.
Regarding claim 16, Martinez teaches fermentation at pH 7.0 (p. 521, right column, 1st paragraph). Thus, Martinez teaching anticipates claim 16.
Regarding claim 17, the recited in the “wherein” clause, i.e. “the fermentation process provides a titer of at least 5 g/l of protein of interest” 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, Martinez teaching anticipates the instantly claimed method steps and therefore the fermentation process taught by Martinez is capable to provide a titer of at least 5 g/l of protein of interest. Thus, Martinez teaching anticipates claim 17.
Regarding claims 18 and 20, Martinez teaches production of β-galactosidase which is an enzyme (Abstract). Thus, Martinez teaching anticipates claims 18 and 20.
Regarding claim 23, the recitation in the preamble: “A method for increasing a titer of a protein of interest above 5 g/l” is interpreted as recitation of 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. In instant case, Martinez teaching anticipates the instantly claimed method steps and therefore the fermentation process taught by Martinez is capable to increase a titer of protein of interest above 5 g/l. Thus, Martinez teaching anticipates claim 23.
Regarding claim 26, Martinez teaches production of β-galactosidase in Bacillus subtilis (Abstract). Thus, Martinez teaching anticipates claim 26.
Regarding claim 28, Martinez teaches production of β-glucosidase under the control of aprE promoter of Bacillus subtilis (Abstract). aprE promoter is a sigma factor A core promoter as evidenced by Park (Title) teaching that subtilisin gene with aprE promoter can be transcribed by the σA form of RNA polymerase in vitro (Abstract). Thus, Martinez teaching as evidenced by Park anticipates claim 28.
Regarding claim 29, Martinez teaches production of β-glucosidase under the control of aprE promoter of Bacillus subtilis (Abstract). aprE promoter is regulated by several regulatory genes including sacU gene (elected species) as evidenced by Park (p. 2657, left column, 1st paragraph). Thus, Martinez teaching as evidenced by Park anticipates claim 29.
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.
Claim 13 is rejected under 35 U.S.C. 103 as being unpatentable over Martinez (Martinez et al. Enzyme Microbiol. Technol., 1998, 22, 520-526) as applied to claim 1 above, and further in view of Korneli (Korneli et al. Biotechnol. Bioengin, 2012, 109, 1538-1550).
Martinez teaching has been set forth above.
Martinez does not teach presence of the trace elements recited in claim 13 added to the fermentation medium.
Regarding claim 13, Korneli teaches production of recombinant protein (GFP) in Bacillus megaterium (Abstract). Korneli performs fermentation in minimal chemically defined medium comprising fructose as sole carbon source and a mixture of salts. Korneli describes feeding solution for fed-batch fermentation: “The feed solution, applied in fed-batch, contained 150 g L-1 fructose, 5 g L-1 xylose, 10 mg L-1 tetracycline. 9.9 g L-1 KH2PO4, 14.98 g L-1 Na2HPO4, 0.3 g L-1 MgSO4 x 7 H2O, 25 g L-1 (NH4)2SO4, 40 mgL-1 MnCl2 x 2 H2O, 53 mg L-1 CaCl2 x 2 H2O, 2.5 mg L-1 FeSO4 x 7 H2O, 2 mg L-1 (NH4)6Mo7O24 x 4 H2O and 1.1 mg L-1 CoCl2 ( p. 1539, right column, 1st paragraph). The composition of the salt mixture in Korneli teaching has the same components as in the salt mixture of Martinez, e.g. KH2PO4, MgSO4 x 7 H2O, (NH4)2SO4, MnCl2, CaCl2 and FeSO4 x 7 H2O and similar concentrations of several components. For instance, 0.4 g/l of MgSO4 x 7 H2O in Martinez versus 0.3 g/l in Korneli. At the same time Korneli feeding solution has additional trace elements, such as 2 mg L-1 (NH4)6Mo7O24 x 4 H2O and 1.1 mg L-1 CoCl2. That corresponds to 1.6 µmol per liter of (NH4)6Mo7O24 x 4 H2O and 8.5 µmol per liter of CoCl2 that reads on claim 13 limitations. Korneli discloses that the fed-batch fermentation resulted in steady increase in produced GFP yield reaching 5% of total cell dry weight (p. 1540, right column, last paragraph).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to add additional trace elements, i.e. cobalt and molybdenum as taught by Korneli for the feeding solution during production of GFP in fed-batch fermentation to the method of production of protein of interest in chemically defined medium under control of aprE promoter described by Martinez. One would have been motivated to do so because Korneli and Martinez use the same components in the feeding solution for fermentation in Bacillus cells with similar concentrations and Korneli showed the fermentation including feeding with additional trace elements provides steady increase in produced GFP yield reaching 5% of total cell dry weight. A skilled artisan would have reasonably expected success in that since Martinez and Korneli describe production of protein of interest in Bacillus cells using chemically defined fermentation medium in fed-batch fermentation. Thus, Martinez and Korneli teachings render claim 13 obvious.
Claim 19 is rejected under 35 U.S.C. 103 as being unpatentable over Martinez (Martinez et al. Enzyme Microbiol. Technol., 1998, 22, 520-526) as applied to claim 1 above, and further in view of Pierce (Pierce and Robertson Biotechnol. Progress, 1992, 8, 211-218).
Martinez teaching has been set forth above.
Martinez does not teach secretion of the fermentation product into the fermentation broth.
Regarding claim 19, Pierce teaches strategies to enhance production of subtilisin in Bacillus subtilis (Abstract). Pierce describes expression of subtilisin gene (aprE) monitored with aprE:lacZ gene fusion. Pierce mentions that subtilisin is secreted into fermentation broth and the fusion construct integrated in tandem with the subtilisin gene provides direct comparison between the transcriptional activity of aprE gene and the level of secreted subtilisin (p. 211, right column, 2nd paragraph). Pierce discloses application of the fed-batch technique to further extend subtilisin production (Abstract).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to add Pierce teaching of production of secreted subtilisin to the method of production of protein of interest in chemically defined medium under control of aprE promoter described by Martinez. One would have been motivated to do so because Pierce teaches that subtilisin encoded by subtilisin (aprE) gene is secreted into medium and Martinez describes conditions including medium and controlled feeding profile to achieve specific growth rate for increased production of protein under control of the same promoter and hence Martinez method can be applied to increased production of secreted subtilisin. A skilled artisan would have reasonably expected success in that since Martinez and Pierce describe production of protein of interest under the control of aprE promoter in Bacillus subtilis using chemically defined fermentation medium in fed-batch fermentation. Thus, Martinez and Pierce teachings render claim 19 obvious.
Claim 25 is rejected under 35 U.S.C. 103 as being unpatentable over Martinez (Martinez et al. Enzyme Microbiol. Technol., 1998, 22, 520-526) as applied to claim 1 above, and further in view of Jarmer (Jarmer Microbiology, 2001, 147, 2417- 2424) as evidenced by Park (Park et al. J. Bacter., 1989, 171, 2657-2665).
Martinez teaching has been set forth above.
Matrinez does not teach the aprE promoter sequence with HMM-score above 50.
Jarmer teaches a hidden Markov model of crA RNA polymerase cofactor recognition sites in Bacillus subtilis: "We have used hidden Markov models (HM Ms) and trained them to recognize σA - binding sites in B. subtilis from existing experimentally generated data." (p. 2418, left column, 3rd paragraph). Jarmer discloses that: "The central idea of an HMM is to embed the statistics of a motif in a set of states with transitions between them." (p. 2418, left column, 4th paragraph). The training of a model is performed based on the prior knowledge of signal associated with the sequence motif (p. 2418, left column, 5th paragraph). Jarmer teaches that the developed trained model can be used to search for new sequences: "The trained model is then used to analyze sequences not included in the training set." (p. 2418, right column, 3rd paragraph). By using HMM-based prediction tool Jarmer predicted Bacillus subtilis genome to have 2538 σA- binding sites, from which 1127 binding sites were located within the 400 bp sequences upstream of predicted genes. Jarmer confirmed the HMM predictions on the example of response regulator aspartate phosphatase (rap) promoter since site-directed mutagenesis of the predicted σA- binding sites resulted in the decrease in expression of rap genes. (p. 2423, left column, 3rd paragraph). Jarmer teaches that the probability score in HMM model depends on the motif and signals associated with the motif: "The better the motif and its contextual signals fit the model, the higher the probability score, and the more confidence will be placed in the prediction." (p. 2418, right column, 6th paragraph).
Jarmer does not explicitly teach an HMM-score above 50 for the aprE promoter, however, Jarmer teaches that the predictability score of HMM model depends on the motif itself and its training based on prior knowledge about signals associated with the motif. Thus, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention that the HMM score is the result effective variable that can be determined by motif of interest. One would have been motivated to determine the HMM score with reasonably expected success for the application to aprE promoter based on set of corresponding sequences used to train HMM.
Additionally, aprE promoter is a sigma factor A (σA) core promoter as evidenced by Park (Title) teaching that subtilisin gene with aprE promoter can be transcribed by the σA form of RNA polymerase in vitro (Abstract)
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to add HMM prediction model for aprE promoter as described by Jarmer for σA - binding sites in B. subtilis promoters to the method of production of protein of interest in chemically defined medium under control of aprE promoter described by Martinez. One would have been motivated to do so because Jarmer described development of HMM model used to identify 2538 σA- binding sites in Bacillus subtilis cells and HMM model trained on aprE promoter sequence can be applied for search of new genes regulated by aprE promoter. A skilled artisan would have reasonably expected success in the modification since Martinez provided method of production of protein of interest under the control of aprE promoter in Bacillus subtilis using chemically defined fermentation medium, aprE promoter includes σA – binding site as evidenced by Park and Jarmer provided method of developing HMM model for σA - binding region in Bacillus subtilis promoters. Thus, Martinez and Jarmer teachings as evidenced by Park render claim 25 obvious.
Claim 27 is rejected under 35 U.S.C. 103 as being unpatentable over Martinez (Martinez et al. Enzyme Microbiol. Technol., 1998, 22, 520-526) as applied to claim 1 above, and further in view of Wieland (US 7510859 B2).
Martinez teaching has been set forth above.
Martinez does not teach the sequence of subtilisin Carlsberg protease.
Wieland teaches novel perhydrolases, subtilisin variants, derived from Carlsberg protease and methods of production of novel perhydrolases (Abstract). The subtilisin Carlsberg protease in Wieland teaching with SEQ ID NO: 23 has 100% identity to instant subtilisin Carlsberg protease with SEQ ID NO:2 (elected species). Wieland discloses that expression of protease can be regulated either by natural or genetically modified promoter: "Thus expression can be carried out by the natural promoter originally located outside this gene, and also via genetically engineered fusion both by a host cell promoter on the expression vector and also by a modified or completely different promoter from another organism." (column 9, lines 22- 27). Wieland teaches host cells for perhydrolases fermentation to preferably be Bacillus cells, including Bacillus licheniformis from which subtilisin Carlsberg protease originates (column 10, lines 37-43). Wieland discloses that modification of subtilisin Carlsberg protease can generate perhydrolases with improved properties for bleaching as washing and cleaning agents (column 2, lines 8- 16).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine method of production of protein of interest in chemically defined medium under control of aprE promoter described by Martinez with the method of production of subtilisin protease with improved efficiency based on modified Carlsberg protease as described by Wieland. One would have been motivated to do so because Wieland teaches modification of subtilisin Carlsberg protease which can be produced in Bacillus cells and which has better bleaching properties to serve as perhydrolase in washing and cleaning agents. A skilled artisan would have reasonably expected success in the modification since Martinez and Wieland provide methods of production of protein of interest in Bacillus fermentation. Thus, combination of Martinez and Wieland teachings renders claim 27 obvious.
Claim 30 is rejected under 35 U.S.C. 103 as being unpatentable over Martinez (Martinez et al. Enzyme Microbiol. Technol., 1998, 22, 520-526) as applied to claim 1 above, and further in view of Henner (Henner et al. J. Bacter., 1988, 170, 296-300).
Martinez teaching has been set forth above.
Martinez does not teach the sequence of aprE promoter.
Henner teaches analysis of aprE (subtilisin) promoter of Bacillus subtilis (Abstract). Henner reports determination of up-to 500 base pairs upstream of the initiation codon (p. 297, left column, 2nd paragraph). Henner performed deletion analysis of aprE promoter to identify the regulatory regions of the promoter by production of β-galactosidase under aprE promoter variants (p. 297, left column, last paragraph, Table 1). Henner determined the regions of aprE promoter stimulated by mutation of sacU32 and hpr-97 genes of Bacillus subtilis, leading to increase in the level of aprE mRNA and predicted location of the targeted sites in aprE promoter sequence (Abstract). These mutations resulted in 10-fold increased β-galactosidase synthesis (p. 297, left column, last paragraph). The nucleotide sequence of aprE promoter in Henner teaching presented on Fig. 1 (p. 297) comprises instant aprE promoter sequence of SEQ ID NO: 8 with 100 % identity.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to produce recombinant protein in fed-batch fermentation in chemically defined medium as described by Martinez under control of aprE promoter from Bacillus subtilis taught by Henner and identical to instant SEQ ID NO: 8. One would have been motivated to do so because Henner teaches complete sequence of natural aprE promoter of Bacillus subtilis, predicts regulatory regions of the promoter and suggests mutations of Bacillus subtilis genes to stimulate aprE regulated expression of protein of interest. A skilled artisan would have reasonably expected success in the that since both Martinez and Henner teach production of β-galactosidase under aprE promoter in Bacillus subtilis. Thus, Martinez and Henner teachings render claim 30 obvious.
Response to Arguments
Applicant’s arguments, see p. 2-10 of the Appeal Brief and Declarations under 37 C.F.R. 1.132 of Dr. Daub, filed 07/13/2026, with respect to the rejections of claims 1, 10-20, 23, 26 and 28-30 over Wenzel in view of Bongiorni, claim 25 over Wenzel, Bongiorni and Jarmer and claim 27 over Wenzel, Bongiorni and Wieland under 35 U.S.C. 103 have been fully considered and are persuasive. Therefore, the rejections have been withdrawn. However, upon further consideration, a new ground(s) of rejection is made in view of newly found prior art references.
Applicant’s arguments with respect to prior art of Wenzel and Bongiorni have been considered but are moot because the new ground of rejection does not rely on any references applied in the prior rejection of record for any teaching or matter specifically challenged in the argument.
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
