DETAILED CORRESPONDENCE
Status of the Application
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claims 1-11 are pending in the application.
Applicant’s amendment to the claims, filed November 19, 2025, is acknowledged. This listing of the claims replaces all prior versions and listings of the claims.
Applicant’s amendments to the specification, filed November 19, 2025, November 20, 2025, and November 24, 2025, are acknowledged.
Applicant’s submissions of substitute sequence listings, filed November 19, 2025, November 20, 2025, and November 24, 2025, are acknowledged.
Applicant’s remarks filed November 19, 2025, November 20, 2025, and November 24, 2025 in response to the non-final rejection mailed August 21, 2025 are acknowledged and have been fully considered.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Restriction/Election
In response to a requirement for restriction/election mailed May 28, 2025, applicant elected with traverse the invention of Group I, claims 1-8, and species (A), the Gram-positive bacterium is a Streptococcus thermophilus, in the reply filed July 28, 2025.
Claims 9-11 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention, there being no allowable generic or linking claim.
Claims 5-7 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected species, there being no allowable generic or linking claim.
Claims 1-4 and 8 are being examined on the merits with claim 1 being examined only to the extent the claim reads on the elected subject matter.
Specification/Informalities
The amendment to the specification filed November 19, 2025 is objected to because it contains an embedded hyperlink and/or other form of browser-executable code (see line 3 of the amended paragraph beginning with “Of these, 11 are predicted…). Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
RESPONSE TO REMARKS: Applicant argues the specification has been amended to delete the embedded hyperlink. However, as stated above, an embedded hyperlink remains in line 3 of the amended paragraph beginning with “Of these, 11 are predicted…”
Drawings
The objection to Figures 2 and 5 is withdrawn in view of applicant’s amendments to insert sequence identifiers in the descriptions of Figures 2 and 5.
Claim Objections
The objection to claims 1-4 is withdrawn in view of applicant’s amendments to recite “80% sequence identity” and “70% sequence identity.”
Claims 1, 3, and 4 are objected to in the recitation of “as compared to a non-modified strain” and in the interest of improving claim form, it is suggested that the noted phrase be amended to recite “as compared to a Streptococcus thermophilus or Lactococcus lactis bacterium that has not been modified to decrease or abolish expression and/or activity of the endogenous surface protease by mutagenesis.”
Claim 4 is objected to in the recitation of “protease” in line 3 and in the interest of improving claim form and grammar, it is suggested that “protease” be amended to the plural “proteases.”
Claim Rejections - 35 USC § 112(b)
The rejection of claims 1-3 and 8 under 35 U.S.C. 112(b) for reciting “decreased…expression and/or activity” is withdrawn in view of applicant’s amendments to recite “as compared to a non-modified strain” in claim 1.
The rejection of claims 1-4 and 8 under 35 U.S.C. 112(b) for reciting “by the use of specific inhibitors of serine proteases or by the use of a strain such that the gene encoding said protease is absent or is present in a truncated form” is withdrawn in view of applicant’s amendment to claims 1, 3, and 4 to delete the phrase at issue.
The rejection of claims 3 and 4 under 35 U.S.C. 112(b) for being confusing because sequences with at least 70% identity to SEQ ID NO: 8 and/or SEQ ID NO: 9 do not share at least 70% sequence identity to SEQ ID NO: 2 is withdrawn in view of applicant’s amendment to claims 3 and 4 to recite “at least one other endogenous surface protease…”
The rejection of claim 4 under 35 U.S.C. 112(b) as being indefinite in the recitation of “decreased…expression and/or activity” is maintained for the reasons of record (see p. 7 of the Office action mailed August 21, 2025). Applicant’s amendment to claim 4 to recite “as compared to a non-modified strain” is acknowledged. However, as written, this phrase appears to be directed only to “the second other endogenous surface protease” of part (ii) and not to apply to “the first other endogenous surface protease” of part (i). As such, there is no reference for comparison of “decreased…expression and/or activity” of the first other endogenous surface protease in part (i) and the recitation of “decreased…expression and/or activity” in line 2 of claim 4 renders the claim indefinite.
Claims 2-4 are newly rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention. This rejection is necessitated by amendment.
Claim 2 (claims 3 and 4 dependent therefrom) recites the limitation “wherein the at least one endogenous surface protease…” in lines 3-4. There is insufficient antecedent basis for this limitation in the claim. Applicant may consider amending claim 2 to recite “The bacterium according to claim 1, wherein the gram-positive bacterium is a Streptococcus thermophilus, and wherein the endogenous surface protease has at least 70% sequence identity with the sequence of SEQ ID NO: 2 of Ster_1612 when the sequences are aligned along their entire length.”
Claim 3 is indefinite in the recitation of “wherein the bacterium has a decreased or abolished expression and/or activity by mutagenesis as compared to a non-modified strain” in lines 7-8 because it is unclear as to whether this phrase is in reference to the endogenous surface protease recited in claim 1 or is in reference to the at least one other endogenous surface protease recited in claim 3.
Claim Rejections - 35 USC § 102/103
The rejection of claims 1-4 and 8 under 35 U.S.C. 102(a)(1) as anticipated by or, in the alternative, under 35 U.S.C. 103 as obvious over Hafeez et al. (Appl. Microbiol. Biotechnol. 97:9787-9799, 2013; cited on the IDS filed on August 31, 2022; hereafter “Hafeez”) is withdrawn in view of applicant’s amendments to recite “as compared to a non-modified strain” in claims 1, 3, and 4.
Claim Rejections - 35 USC § 103
Claims 1-3 and 8 are rejected under 35 U.S.C. 103 as being unpatentable over Lecomte et al. (Food Microbiology 53:2-9, 2016; cited on Form PTO-892 mailed August 21, 2025; hereafter “Lecomte”) in view of Maehara et al. (Extremophiles 12:285-296, 2008; cited on Form PTO-892 mailed August 21, 2025; hereafter “Maehara”) and UniProt Database Accession Number Q5M2Z4 (February 2020, 2 pages; cited on Form PTO-892 mailed August 21, 2025; hereafter “UniProt Q5M2Z4”), and as evidenced by UniProt Database Accession Number Q5M228 (February 2020, 2 pages; cited on Form PTO-892 mailed August 21, 2025; hereafter “UniProt Q5M228”).
As amended, the claims are drawn to (in relevant part) a gram-positive bacterium of the species Streptococcus thermophilus such that the endogenous surface protease comprising an amino acid motif and having at least 80% sequence identity with the sequence SEQ ID NO: 1, has a decreased or abolished expression and/or activity by mutagenesis as compared to a non-modified strain,
wherein SEQ ID NO: 1 is defined as follows:
I-A-G-T-G-T-I-E-X1-D-G-X2-X3-G-X4-I-G-G-X5-X6-X7-K
with
X1 is histidine (H) or lysine (K);
X2 is serine (S), alanine (A) or threonine (T);
X3 is isoleucine (I), leucine (L) or valine (V);
X4 is aspartic acid (D) or glutamine (Q);
X5 is alanine (A) or valine (V);
X6 is aspartic acid (D) or tyrosine (Y);
and X7 is lysine (K) or leucine (L).
Regarding claims 1-3 and 8, Lecomte teaches Streptococcus thermophilus presents many features that make it a good candidate for the production of heterologous proteins (p. 2, Abstract). Lecomte teaches deleting the gene encoding the cell surface protease HtrA to avoid protein degradation (p. 5, column 2, bottom). Lecomte does not teach or suggest the amino acid sequence of HtrA, however, evidentiary reference UniProt Q5M228 is cited to show that the sequence of S. thermophilus HtrA has at least 70% sequence identity to instant SEQ ID NO: 8 (see Appendix A at pp. 17-18 of the Office action mailed August 21, 2025).
The difference between Lecomte and claims 1-3 and 8 is that Lecomte does not teach or suggest deleting a gene encoding a protease comprising an amino acid motif having at least 80% identity with the sequence of SEQ ID NO: 1.
Maehara teaches Lon protease was reported to degrade heterologous gene products in E. coli (p. 286, column 1, middle) and E. coli strains deficient in Lon protease were used to direct expression of heterologous gene products, which improved production of some heterologous proteins (p. 294, paragraph bridging columns 1-2). Maehara teaches development of a strain of Thermus thermophilus for expression of heterologous genes (p. 286, column 1, bottom) and teaches improving production of heterologous gene products using T. thermophilus by deleting genes annotated as Lon protease (p. 286, column 2, middle; p. 294, column 2, middle; p. 293, Table 3).
UniProt Q5M2Z4 teaches a S. thermophilus polypeptide annotated as a Lon protease (see entire document). The sequence of UniProt Q5M2Z4 has 99% sequence identity to instant SEQ ID NO: 2 and the sequence of amino acids 270 to 290 of UniProt Q5M2Z4 is encompassed by instant SEQ ID NO: 1 (see Appendix B at pp. 19-20 of the Office action mailed August 21, 2025).
In view of Lecomte, Maehara, and UniProt Q5M2Z4, it would have been obvious to one of ordinary skill in the art before the effective filing date for a S. thermophilus with a deletion of a gene encoding an annotated Lon protease, e.g., the annotated Lon protease of UniProt Q5M2Z4. One would have been motivated and would have expected success because Lecomte teaches S. thermophilus as a host for the production of heterologous proteins, Maehara teaches the concept of deleting a gene encoding an annotated Lon protease to improve heterologous protein production, and, as exemplified by UniProt Q5M2Z4, the prior art taught a S. thermophilus polypeptide annotated as a Lon protease. Therefore, the invention of claims 1-3 and 8 would have been obvious to one of ordinary skill in the art before the effective filing date.
Claim 4 is rejected under 35 U.S.C. 103 as being unpatentable over Lecomte in view of Maehara and UniProt Q5M2Z4 and evidentiary reference UniProt Q5M228 as applied to claims 1-3 and 8 above, and further in view of Lecomte et al. (Microbial Cell Factories 13:82, 2014, 14 pages; cited on Form PTO-892 mailed August 21, 2025; hereafter “Lecomte-2”) and UniProt Database Accession Number B9UZ65 (December 2019, 3 pages; cited on Form PTO-892 mailed August 21, 2025; hereafter “UniProt B9UZ65”).
The relevant teachings of the combination of Lecomte, UniProt Q5M2Z4, and Maehara and evidentiary reference UniProt Q5M228 as applied to claims 1-3 and 8 are set forth above.
The difference between the combination of cited prior art and claim 4 is that the combination does not teach or suggest deleting a gene encoding a protease comprising an amino acid sequence having at least 70% identity with the sequence of SEQ ID NO: 9 of PrtS.
Similar to Lecomte, Lecomte-2 teaches S. thermophilus as a host for expression of heterologous proteins (p. 1, Abstract). Lecomte-2 teaches heterologous expression of a prtH gene by replacing the prtS gene encoding the pro-protein sequence of PrtS of S. thermophilus with a prtH gene encoding the pro-protein sequence of PrtH (p. 3, columns 1 and 2). According to Lecomte-2, the study demonstrated that S. thermophilus is able to secrete and probably anchor heterologous proteins on its cell wall (p. 9, column 2, bottom).
UniProt B9UZ65 teaches a S. thermophilus PrtS polypeptide (see entire document). The sequence of UniProt B9UZ65 has 99% sequence identity to instant SEQ ID NO: 9 (see Appendix C at pp. 21-24 of the Office action mailed August 21, 2025).
In view of Lecomte-2 and UniProt B9UZ65, it would have been obvious to one of ordinary skill in the art before the effective filing date to replace the prtS gene encoding the pro-protein sequence of PrtS of the S. thermophilus of the combination of Lecomte, Maehara, and UniProt Q5M2Z4 with a desired heterologous gene. One would have been motivated and would have expected success because Lecomte-2 teaches expressing a recombinant protein using S. thermophilus as an expression host by replacing the prtS gene encoding the pro-protein sequence of PrtS of S. thermophilus with a desired heterologous gene. Therefore, the invention of claim 4 would have been obvious to one of ordinary skill in the art before the effective filing date.
RESPONSE TO REMARKS: Applicant argues that because Lecomte’s teachings are directed to S. thermophilus while Maehara’s teachings are directed to a T. thermophilus, there would have been no motivation to combine Lecomte with Maehara.
Applicant’s argument is not found persuasive. As stated above, Lecomte teaches S. thermophilus as a host for heterologous protein production and teaches deleting the gene encoding the protease HtrA to avoid protein degradation. Similar to Lecomte, Maehara acknowledges E. coli and T. thermophilus as hosts for heterologous protein production, and teaches E. coli strains deficient in Lon protease and T. thermophilus with deletion of genes annotated as Lon protease, which reduced heterologous protein degradation, thus improving the production of the heterologous protein. Given the benefit of deleting genes annotated as Lon protease for heterologous protein production and that UniProt Q5M2Z4 is annotated as a Lon protease, one would have been motivated to delete the gene encoding UniProt Q5M2Z4 in a S. thermophilus intended for heterologous protein production.
Applicant argues Lecomte’s teachings are directed to deletion of a cell surface protease while Maehara’s teachings are directed to deletion of a protein annotated as a Lon protease, and Lon protease is an intracellular protease, there would have been no motivation to combine Lecomte with Maehara.
Applicant’s argument is not found persuasive. First, there is no teaching that UniProt Q5M2Z4 is an intracellular protease. Rather, UniProt Q5M2Z4 teaches the protease has a transmembrane domain (p. 3, top) and one of ordinary skill would have recognized that it is just as likely than not that the protease of UniProt Q5M2Z4 is a surface protease.
Second, even if one would have assumed that the protease of UniProt Q5M2Z4 is an intracellular protease, based on the teachings of Lecomte and Maehara, one of ordinary skill in the art would have recognized that heterologous proteins produced by a bacterial host cell can be maintained in the cytoplasm or secreted from the cell. As such, one would have recognized that a bacterial host cell for production of heterologous proteins would benefit from removing intracellular proteases (such as Lon) and proteases that are present on the cell surface (such as HtrA) for improved versatility as an expression host. Moreover, even if a bacterial host cell is used strictly for production of heterologous proteins intended for secretion, such heterologous proteins are expressed in the cytoplasm and one of ordinary skill in the art would recognize that even a bacterial host cell for production of only secreted heterologous proteins would benefit from removing intracellular proteases (such as Lon).
Applicant argues that because of differences in length and sequence identity between the proteases of T. thermophilus and UniProt Q5M2Z4, the teachings of Maehara would not have led one of ordinary skill in the art to predict that the protease of UniProt Q5M2Z4 is a surface protease and there would have been no motivation to delete the gene encoding UniProt Q5M2Z4 to abolish surface proteolysis in S. thermophilus.
Applicant’s argument is not found persuasive. Motivation to make a S. thermophilus polypeptide modified by deleting the gene encoding the protease of UniProt Q5M2Z4 is not based on prediction or empirical knowledge of the protease of UniProt Q5M2Z4 being a surface protease. Rather, as stated above, one would have been motivated for a S. thermophilus with a deletion of a gene encoding an annotated Lon protease, e.g., the annotated Lon protease of UniProt Q5M2Z4, because Lecomte teaches S. thermophilus as a host for the production of heterologous proteins, Maehara teaches the concept of deleting a gene encoding an annotated Lon protease in a bacterial expression host to improve heterologous protein production, and UniProt Q5M2Z4 taught a S. thermophilus polypeptide annotated as a Lon protease.
Applicant argues combining the ΔSter_1612 mutation with ΔhtrA and/or ΔprtS mutation(s) resulted in a surprising and unexpected reduction in proteolytic activity as shown in the experimental data of example 4 and figure 4 of the application.
Applicant’s argument and allegation of unexpected results are not found persuasive. First, applicant’s results are not unexpected as required by MPEP 716.02. Given that UniProt Q5M2Z4 teaches the protease has a transmembrane domain (p. 3, top), it would not have been unexpected that the protease of UniProt Q5M2Z4 is a surface protease. Also, as stated above, Maehara taught deleting genes annotated as Lon protease in a bacterial expression host had the effect of reducing proteolytic degradation of a heterologous protein, thus improving production of the heterologous protein. Given Maehara’s noted teaching and because UniProt Q5M2Z4 is annotated as a Lon protease in S. thermophilus, it would not have been unexpected that a S. thermophilus with a deletion of a gene encoding UniProt Q5M2Z4 would also have the effect of reducing proteolytic degradation of a heterologous protein in a S. thermophilus expression host, thus improving production of the heterologous protein.
Second, even assuming applicant’s results were unexpected, the applicant’s results are not commensurate in scope with the claimed invention as required by MPEP 716.02(d). “Commensurate in scope” means that the evidence provides a reasonable basis for concluding that the untested embodiments encompassed by the claims would behave in the same manner as the tested embodiments. See In re Lindner, 457 F.2d 506, 508 (CCPA 1972). The results of example 4 and figure 4 are based on a S. thermophilus with a deletion of Ster_1612 gene alone and in combination with deletion(s) of htrA and/or prtS gene(s). These results are not commensurate in scope with the claims, which encompass any level or amount – even the slightest, most miniscule level or amount – of decreased or abolished expression and/or activity of any endogenous surface protease comprising an amino acid motif and having at least 80% sequence identity with the sequence SEQ ID NO: 1. While nonobviousness of a broader claimed range can be supported by evidence based on unexpected results from testing a narrower range (MPEP 716.02(d).I), there is no evidence of record that the untested embodiments encompassed by the claims would behave in the same manner as the tested embodiments. As such, applicant’s results fail to rebut a prima facie case of obviousness.
Applicant argues Lecomte-2 and UniProt B9UZ65 fail to cure the alleged deficiencies of the combination of Lecomte, Maehara, and UniProt Q5M2Z4 and the combination of Lecomte, Maehara, UniProt Q5M2Z4, Lecomte-2, and UniProt B9UZ65 fails to render obvious the invention of claim 4.
Applicant’s argument is not found persuasive because the combination of Lecomte, Maehara, and UniProt Q5M2Z4 is not deficient and for the reasons set forth above, the gram-positive bacterium of claim 4 would have been obvious in view of the combined teachings of Lecomte, Maehara, UniProt Q5M2Z4, Lecomte-2, and UniProt B9UZ65.
For these reasons, it is the examiner’s position that the claimed invention would have been obvious to one of ordinary skill in the art before the effective filing date.
Claim Rejections - 35 USC § 101
The rejection of claims 1-4 under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception is withdrawn in view of applicant’s amendment to recite “as compared to a non-modified strain” in claim 1.
Conclusion
Status of the claims:
Claims 1-11 are pending.
Claims 5-7 and 9-11 are withdrawn from consideration.
Claims 1-4 and 8 are rejected.
No claim is in condition for allowance.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). 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 DAVID J STEADMAN whose telephone number is (571)272-0942. The examiner can normally be reached Monday to Friday, 7:30 AM to 4:00 PM.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, MANJUNATH N RAO can be reached on 571-272-0939. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/David Steadman/Primary Examiner, Art Unit 1656