The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
This office action is in response to Applicants’ amendments/remarks received December 22, 2025.
Rejections and/or objections not reiterated from previous office actions are hereby withdrawn.
Claims 3, 7, 11 are canceled. Claims 1-2, 4-6, 8-10, 12-17 are under consideration.
Priority: This application is a 371 of PCT/EP2021/070662, filed July 23, 2021, which claims benefit to foreign applications EP 20187745.3, filed July 24, 2020, and EP 20187746.1, filed July 24, 2020. Copies of the foreign priority documents have been received in the instant application on January 23, 2023 and are in the English language.
Objections and Rejections
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claim 4 is rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 4 is indefinite because it is dependent on a canceled claim. Claim 3 is currently indicated as a canceled claim. Further correction and/or clarification is requested.
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.
Claims 1-2, 4-6, 8-10, 12-17 are rejected under 35 U.S.C. 103 as being unpatentable over Rij et al. (WO 2015055558; IDS 06.07.23, previously cited). Rij et al. disclose that it has been surprisingly found that a host cell deficient in an essential gene coding for an essential polypeptide comprising a vector (or plasmid) carrying a mutated essential gene complementing at least in part said deficiency can be used for the production of a compound of interest with high yield (at least p. 4 lines 10-13). Rij et al. disclose the essential gene is a gene encoding for an alanine racemase (dal or alr gene) of Bacillus (Bacillus subtilis or Bacillus licheniformis) (at least p. 16-17), and the host cell is Bacillus selected from among others Bacillus licheniformis cell, a Bacillus pumilus cell (at least p. 35-36). Rij et al. disclose the host cell deficient in the essential gene coding for an essential polypeptide comprises a vector, where the vector comprises at least an autonomous replication sequence (at least p. 20-22), a nucleotide sequence encoding the essential polypeptide where the nucleotide sequence has at least 60%, at least 99%, sequence identity to the sequence identity of the essential gene (at least p. 12-13, p. 20-22) operably linked to a promoter (p. 20-22), and a nucleotide sequence encoding a compound of interest operably linked to a promoter, where the compound of interest is a biopolymer (at least p. 26-30). Rij et al. disclose a Bacillus host cell, where the essential gene codes for an alanine racemase not native to the host cell has at least 60%, at least 99%, sequence identity to the sequence identity of the essential polypeptide (alr) having the amino acid sequence of SEQ ID NO: 45 (at least p. 12-13, 16-17), where SEQ ID NO: 45 has 100% sequence identity to instant SEQ ID NO: 4.
The working examples of Rij et al. disclose a Bacillus subtilis having a deleted alanine racemase dal gene and comprising a plasmid comprising a mutated dal gene to express the dal gene and a plasmid comprising nucleic acid molecules encoding a target enzyme (at least examples 1-4).
Therefore, while Rij et al. do not explicitly teach that the Bacillus host cell in the working examples is Bacillus licheniformis, the teachings of Rij et al. still fairly disclose a Bacillus host cell belonging to the species Bacillus licheniformis or a Bacillus pumilus, in which the alr gene has been inactivated and which comprises a plasmid comprising at least one autonomous replication sequence, a first polynucleotide encoding at least one polypeptide of interest, wherein the first polynucleotide is operably linked to a promoter, and a second polynucleotide encoding an alanine racemase which is not native to the host cell, where the second polynucleotide is operably linked to a promoter.
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to arrive at the claimed Bacillus host belonging to the species Bacillus licheniformis or a Bacillus pumilus, in which the alr gene has been inactivated and which comprises a plasmid comprising at least one autonomous replication sequence, a first polynucleotide encoding at least one polypeptide of interest, wherein the first polynucleotide is operably linked to a promoter, and a second polynucleotide encoding an alanine racemase which is not native to the host cell, where the second polynucleotide is operably linked to a promoter, wherein the alanine racemase not native to the host cell has at least 99% sequence identity to the sequence identity of the essential polypeptide (alr) having the amino acid sequence of SEQ ID NO: 45 (or instant SEQ ID NO: 4) (instant claim 16). The motivation to do so is given by the prior art, which disclose it has been surprisingly found that a host cell deficient in an essential gene coding for an essential polypeptide comprising a vector (or plasmid) carrying a mutated essential gene complementing at least in part said deficiency can be used for the production of a compound of interest with high yield (Rij et al. at least p. 4 lines 10-13, p. 11). One of ordinary skill would have a reasonable expectation of success because the prior art discloses a Bacillus host cell having a deleted alanine racemase dal gene and comprising a non-native alanine racemase results in increased target enzyme production.
Regarding instant claim 17, Rij et al. disclose a nutrient medium comprising the Bacillus host cell noted above, where suitable nutrient mediums comprise carbon and nitrogen sources, and inorganic salts, known in the art, where it would be obvious that known nutrient mediums contain glucose as a carbon source (at least p. 56-59).
Regarding instant claims 1, 5, Rij et al. disclose a method for producing the polypeptide of interest, comprising providing a Bacillus host cell belonging to the species Bacillus licheniformis or a Bacillus pumilus, in which the alr gene has been inactivated and which comprises a plasmid comprising at least one autonomous replication sequence, a first polynucleotide encoding at least one polypeptide of interest, wherein the first polynucleotide is operably linked to a promoter, and a second polynucleotide encoding an alanine racemase which is not native to the host cell, where the second polynucleotide is operably linked to a promoter, wherein the alanine racemase not native to the host cell has at least 99% sequence identity to the sequence identity of the essential polypeptide (alr) having the amino acid sequence of SEQ ID NO: 45 (or instant SEQ ID NO: 4); and culturing the host cell under conditions conducive for expressing the polypeptide of interest (at least p. 56-59).
Regarding instant claim 2, Rij et al. disclose that prior to culturing the host cell deficient in the essential gene (alr) coding for the essential gene (alr), methods for providing and providing the host cell deficient in the essential gene (alr) coding for the essential gene (alr) (p. 57 lines 22-27), comprising inactivating the essential gene (alr) of the host cell and introducing into the host cell deficient in the essential gene (alr) a plasmid comprising at least one autonomous replication sequence, a first polynucleotide encoding at least one polypeptide of interest, wherein the first polynucleotide is operably linked to a promoter, and a second polynucleotide encoding an alanine racemase which is not native to the host cell, where the second polynucleotide is operably linked to a promoter (at least p. 53-55).
Regarding instant claim 4, Rij et al. disclose deletion of the alr gene (at least p. 54, 63, 70).
Regarding instant claim 6, Rij et al. disclose a host cell of Bacillus licheniformis; therefore, Rij et al. can be deemed to disclose a system having a recognition sequence GCNGC.
Regarding instant claim 8, Rij et al. disclose that the alanine racemase not native to the host cell has at least 99% sequence identity to the sequence identity of the essential polypeptide (alr) having the amino acid sequence of SEQ ID NO: 45 (at least p. 12-13, 16-17), where SEQ ID NO: 45 has 100% sequence identity to instant SEQ ID NO: 4.
Regarding instant claim 9, Rij et al. disclose that the promoter is a constitutive promoter (at least p. 31 lines 30-31, p. 33-35, p. 42).
Regarding instant claim 10, Rij et al. disclose the promoter is from a bacterial source, including Bacillus subtilis (at least p. 33-34), where the promoter of the non-native essential gene is not mutated (at least p. 4-6, 11-12), where Rij et al. disclose SEQ ID NO: 44 is the sequence of the Bacillus subtilis alr gene (p. 10, p. 45-47) and comprises a sequence having 100% sequence identity to instant SEQ ID NO: 46.
Regarding instant claim 12, Rij et al. disclose the polypeptide of interest is an enzyme (at least p. 26-28).
Regarding instant claim 13, Rij et al. disclose the polypeptide of interest is a protease, including an aminopeptidase (at least p. 27-28).
Regarding instant claims 14-15, Rij et al. disclose the polypeptide of interest is secreted into the nutrient medium and isolated from the medium (at least p. 57 lines 19-20).
Reply: In view of Applicants’ amendments/remarks, the previous 35 U.S.C. 102(a)(1) rejection as being anticipated by Rij et al. has been withdrawn. However, Rij et al. is relevant as a 103 reference for the reasons noted above.
Applicants assert that Rij et al. do not render obvious any of the claims. Applicants assert that for example, the application discloses unexpected results. Applicants assert that specifically, the B. subtilis alr gene was introduced into a host cell belonging to the species B. licheniformis in which the endogenous alr gene has been inactivated; as B. pumilus, B. licheniformis comprises two endogenous genes encoding for an alanine racemase: alr and yncD; interestingly, the expression enhancing effect was more pronounced when the alr gene was inactivated, as compared to when the yncD gene was inactivated (instant specification p. 4, example 2).
Applicants’ remarks are not persuasive. In this instance, Rij et al. already disclose that it has been surprisingly found that a host cell deficient in an essential gene coding for an essential polypeptide comprising a vector (or plasmid) carrying a mutated essential gene complementing at least in part said deficiency can be used for the production of a compound of interest with high yield (Rij et al. at least p. 4 lines 10-13, p. 11). It is further expressly disclosed in Rij et al. that the deficient essential gene in the host cell is an alanine racemase, specifically dal or alr (abstract, p. 2, p. 7) and that the deficient essential gene is D-alanine racemase in B. licheniformis (at least p. 16 lines 7-8) and that the essential gene in the introduced plasmid is a B. subtilis alr gene (p. 16-17).
The instant specification discloses that it is known that the D-alanine racemase gene dal is also referred to as alr (application publication paragraph 0013).
Therefore, Rij et al. disclose the same inventive features of introducing a B. subtilis alr gene into a host cell belonging to the species B. licheniformis in which the endogenous alr gene has been inactivated and further disclose that such a feature surprisingly results in the production of a compound of interest with high yield.
Regarding Applicants’ remarks that interestingly, the expression enhancing effect was more pronounced when the alr gene was inactivated, as compared to when the yncD gene was inactivated, the remarks are not persuasive. In this instance, the prior art Rij et al. has already specifically disclosed the alr gene for inactivation in a Bacillus host cell for high yield and production of a compound of interest.
Further, it is known that B. licheniformis has two alanine racemase genes and that dal is the main alanine racemase in B. licheniformis (He et al. p. 1390-1391; IDS 06.07.23).
Therefore, it would not be surprising or unexpected that deletion of the endogenous dal or alr in B. licheniformis has a more pronounced effect since it is the main alanine racemase.
Further, as already noted, Rij et al. also disclose that it has been surprisingly found that a Bacillus host cell deficient in the essential gene dal (alr) and comprising a plasmid encoding a B. subtilis dal (alr) gene can be used for the production of a compound of interest with high yield (see the teachings of Rij et al. noted above).
For at least these reasons, the claims are unpatentable under 103 over Rij et al.
Claims 1-2, 4-6, 8-10, 12-17 are rejected under 35 U.S.C. 103 as being unpatentable over Jorgensen et al. (WO 0200907; IDS 06.07.23, previously cited) in view of Rij et al. (WO 2015055558; IDS 06.07.23, previously cited). Jorgensen et al. disclose providing a Bacillus licheniformis host cell, in which the alanine racemase (dal) gene has been deleted (example 3), and which comprises an integration plasmid comprising an autonomous replication sequence (p. 18 lines 1-5), a first polynucleotide encoding a polypeptide of interest (amylase), where the first polypeptide is operably linked to a promoter, and a second polynucleotide comprising a truncated dal gene which is not native to the host cell, where the second polynucleotide is operably linked to a promoter (example 3, p. 59-68, also Fig. 3, see also pages 10-16). It is disclosed in the instant specification that the alanine racemase gene dal (is also referred to as alr gene) (application publication paragraph 0013). Jorgensen et al. do not teach that the second polynucleotide comprises a non-native dal gene.
The teachings of Rij et al. are noted above. Rij et al. disclose it has been surprisingly found that a host cell deficient in an essential gene coding for an essential polypeptide comprising a vector (or plasmid) carrying a mutated essential gene complementing at least in part said deficiency can be used for the production of a compound of interest with high yield (Rij et al. at least p. 4 lines 10-13, p. 11). Rij et al. disclose a Bacillus host cell, where the essential gene codes for an alanine racemase not native to the host cell has at least 99% sequence identity to the sequence identity of the essential polypeptide (alr) having the amino acid sequence of SEQ ID NO: 45 (at least p. 12-13, 16-17), where SEQ ID NO: 45 has 100% sequence identity to instant SEQ ID NO: 4.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine references and arrive at the claimed Bacillus host belonging to the species Bacillus licheniformis, in which the alr gene has been inactivated and which comprises a plasmid comprising at least one autonomous replication sequence, a first polynucleotide encoding at least one polypeptide of interest, wherein the first polynucleotide is operably linked to a promoter, and a second polynucleotide encoding an alanine racemase which is not native to the host cell, where the second polynucleotide is operably linked to a promoter, wherein the alanine racemase not native to the host cell has at least 99% sequence identity to the sequence identity of the essential polypeptide (alr) having the amino acid sequence of SEQ ID NO: 45 (or instant SEQ ID NO: 4) (instant claim 16). The motivation to do so is given by the prior art, which disclose it has been surprisingly found that a host cell deficient in an essential gene coding for an essential polypeptide comprising a vector (or plasmid) carrying a mutated essential gene complementing at least in part said deficiency can be used for the production of a compound of interest with high yield (Rij et al. at least p. 4 lines 10-13, p. 11). Therefore, one of ordinary skill would have reasonable motivation to incorporate the non-native dal gene encoding the polypeptide comprising the amino acid sequence of SEQ ID NO: 45 of Rij et al. for the truncated dal gene in the Bacillus licheniformis host cell in which the alanine racemase (dal) gene has been deleted and encoding an amylase of Jorgensen et al. noted above. One of ordinary skill would have a reasonable expectation of success because the prior art discloses a Bacillus host cell having a deleted alanine racemase dal gene and comprising a non-native alanine racemase results in increased target enzyme production.
Regarding instant claim 17, Jorgensen et al. disclose a culture medium comprising the Bacillus licheniformis host cell noted above and in glucose (example 3, also p. 65).
Regarding instant claims 1, 5, 15, Jorgensen et al. disclose a process for producing an enzyme or polypeptide of interest, comprising providing the Bacillus licheniformis host cell above and cultivating the Bacillus licheniformis host above and purifying the enzyme (at least p. 39 lines 15-18, p. 102 lines 30-33). Therefore, it would have been obvious to produce an enzyme or polypeptide of interest comprising providing the Bacillus licheniformis host cell in which the alanine racemase (dal) gene has been deleted and comprising the non-native dal gene encoding the polypeptide comprising the amino acid sequence of SEQ ID NO: 45 of Jorgensen et al. in view of Rij et al. noted above and cultivating the Bacillus licheniformis host above and purifying the enzyme.
Regarding instant claim 2, Jorgensen et al. disclose providing the Bacillus licheniformis host cell comprising inactivating the dal gene in the host cell (example 3) and introducing into the host cell an integration plasmid comprising an autonomous replication sequence (p. 18 lines 1-5), a first polynucleotide encoding a polypeptide of interest (amylase), where the first polypeptide is operably linked to a promoter, and a second polynucleotide encoding a alanine racemase which is not native to the host cell, where the second polynucleotide is operably linked to a promoter (example 3, p. 59-68, also Fig. 3, see also pages 10-16).
Regarding instant claim 4, Jorgensen et al. disclose deletion of the dal gene (at least example 3).
Regarding instant claim 6, Jorgensen et al. disclose a host cell of Bacillus licheniformis; therefore, Jorgensen et al. can be deemed to disclose a system having a recognition sequence GCNGC.
Regarding instant claim 8, Rij et al. disclose that the alanine racemase not native to the host cell has at least 99% sequence identity to the sequence identity of the essential polypeptide (alr) having the amino acid sequence of SEQ ID NO: 45 (at least p. 12-13, 16-17), where SEQ ID NO: 45 has 100% sequence identity to instant SEQ ID NO: 4.
Regarding instant claim 9, Jorgensen et al. disclose suitable known promoters, which include constitutive promoters (at least p. 15).
Regarding instant claim 10, Jorgensen et al. disclose the promoter is from a bacterial source, including Bacillus subtilis (at least p. 15), where Jorgensen et al. disclose the Bacillus subtilis dal gene, which would therefore, comprise a promoter sequence having a sequence as shown in the recited sequence(s).
Regarding instant claim 12, Jorgensen et al. disclose the polypeptide of interest is an enzyme (at least p. 38).
Regarding instant claim 13, Jorgensen et al. disclose the polypeptide of interest is a protease, including an aminopeptidase (at least p. 38).
Regarding instant claims 14-15, Jorgensen et al. disclose the polypeptide of interest is secreted into the culture medium and purified from the medium (at least p. 21).
Reply: In view of Applicants’ amendments/remarks, the previous 35 U.S.C. 102(a)(1) rejection as being anticipated by Jorgensen et al. has been withdrawn. However, Jorgensen et al. is relevant as a 103 reference in view of Rij et al. for the reasons noted above.
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
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Claims 1-2, 4-6, 8-10, 12-17 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-3, 6-11 of copending Application No. 18017430 (’430) (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because both the instant claims and the ‘430 application claims are drawn to a method of producing a polypeptide of interest comprising providing a Bacillus host cell, in which the alr gene has been inactivated and which comprises a plasmid comprising at least one autonomous replication sequence, a first polynucleotide encoding at least one polypeptide of interest, wherein the first polynucleotide is operably linked to a promoter, and a second polynucleotide encoding an alanine racemase which is not native to the host cell, where the second polynucleotide is operably linked to a promoter; and culturing the host cell under conditions conducive for expressing the polypeptide of interest; and a Bacillus host cell comprising the features noted above. The features recited in the instant dependent claims are also reasonably recited or obvious in the ‘430 application claims.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Reply: Applicants’ remarks regarding the provisional nonstatutory double patenting rejection have been considered; however, the provisional nonstatutory double patenting rejection is maintained for the reasons noted above.
No claim is allowed.
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.
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/Marsha Tsay/Primary Examiner, Art Unit 1656
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