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 .
Claim Status Summary
Claims 1- 10, and 12- 15 are pending.
Claims 1- 10, and 12- 15 are considered on the merits.
Claims 4 and 5 are objected.
Claims 1- 10, and 12- 15 are rejected.
No Claims are allowed.
Claim Objections
Claim 4 is objected to because of the following informalities: Claim 4 recites “wherein the genetic construct further comprises a nucleic sequence encoding the Rgg protein.” The phrase “nucleic sequence” is grammatically incorrect. This examiner interprets this to read “wherein the genetic construct further comprises a nucleic acid sequence encoding the Rgg protein.”
Claim 5 is objected to because of the following informalities: Claim 5 recites “wherein the genetic construct further comprises a nucleic sequence encoding the SHP peptide.” The phrase “nucleic sequence” is grammatically incorrect. This examiner interprets this to read “wherein the genetic construct further comprises a nucleic acid sequence encoding the SHP peptide.”
Appropriate correction is required.
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.
Claim 8 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.
The limitation “no or low surface proteolytic activity” is indefinite and the specification fails to provide clear scope of the claim; in particular what proteolysis activity occurs and what is the rate and/or extent of proteolysis from a given reference point. The specification provides some guidance toward “no or low surface proteolytic activity” stating “a bacterium having no or low surface proteolytic activity is a bacterium of the species Streptococcus thermophilus, wherein an endogenous surface protease homologous to the protein designated STR_RS07745 [SepM] in Streptococcus thermophilus CNRZ1066 has a reduced or abolished expression and/or activity” (page 12, 6th paragraph) as well as Example II (page 26, line 20) and Figure 3. Further reference is directed toward “PCT/EP2021/055561” [WO2021176039]. However, the terms “low” and “reduced” found in these citations from the specification are absent quantitative values and are merely relative terminology that provide no meaningful manner to determine the extent of proteolysis so as to make the claim limitation definite. Furthermore, the reference to PCT/EP2021/055561 similarly does not clarify the extent of proteolysis nor does it reference STR_RS07745.
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 1- 5, 7- 10, and 12- 15 are rejected under 35 U.S.C. 103 as being unpatentable over Fleuchot (Fleuchot et al. Mol Microbiol. 2011 May;80(4):1102-19.), and further in view of WP_100262537.1 (NCBI reference sequence Rgg/GadR/MutR family transcriptional regulator [Streptococcus thermophilus]; priority to April 17, 2018).
Regarding claims 1, Fleuchot teaches TIL 773, the Δeep genetically modified bacteria (GMB) strain of S. thermophilus LMD-9 (Table 3, and page 1114, 1st column, bottom). They teach further that their GMB comprises a genetic construct, comprising nucleic acid, operably linked and regulated as claimed, “binding of the SHP1358(15–23)/Rgg1358 complex to the promoter region of the … target genes, shp1358 …, leads to the activation of their transcription”(Fig. 7 legend). This quote also highlights the limitation “the GMB expresses the Rgg protein.” Fleuchot further teaches “The putative binding site for the Rgg1358 protein is boxed”(Fig. 5 legend, see figure below).
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The boxed region of the promoter shown in the figure matches a variant of instant claim’s SEQ ID NO 1 with 100% identity.
Fleuchot does not teach “the Rgg protein has at least 80% sequence identity with an amino acid sequence selected from the group consisting of: SEQ ID NO: 4- 13.”
However Fleuchot does teach the Rgg1358 protein.
WP_100262537.1 is the NCBI reference sequence Rgg/GadR/MutR family transcriptional regulator of the bacteria Streptococcus thermophilus. WP_100262537.1 Is a 287 AA protein that shares 96.86% identity with instant 287 AA SEQ ID NO 7 and shares 81.27% identity with the instant 286 AA SEQ ID NO 6.
It would have been obvious for a person having ordinary skill in the art (PHOSITA) at the time of filing to have taken the engineered S. thermophilus bacteria of Fleuchot and used Rgg protein WP_100262537.1 because it is a simple substitution of one known element for another to obtain predictable results. The Rgg protein and its sequence WP_100262537.1, were known and available within the NCBI database at the time of filing the instant invention. A PHOSITA would have recognized the Rgg of Fleuchot and the Rgg WP_100262537.1 share similar structure and function. Therefore, a PHOSITA would have predicted the substituted Rgg would function (express and regulate) satisfactorily within the engineered bacteria.
Regarding claims 2, 4, 5, SHP1358(15–23)/Rgg1358 is a naturally (native) occurring/expressed peptide/protein complex, therefore “the SHP1358(15–23)/Rgg1358 complex” described in claim 1 above is evidence “the bacterium expresses a native form of the SHP peptide” (claim 2) and is evidence “the genetic construct further comprises a nucleic sequence encoding the Rgg protein” (claim 4) and is evidence “wherein the genetic construct further comprises a nucleic sequence encoding the SHP peptide” (claim 5).
Regarding claim 3, Fleuchot teaches “At low cell density, we hypothesize that the SHP1358(15–23) is present in a negligible amount and the Rgg1358 protein is bound alone to the promoter region of shp1358 … in an inactivated state that does not allow their [shp1358] transcription” (page 1111, Fig. 7 legend).
Regarding claim 7, Fleuchot teaches “Strain TIL 773 (Δeep) was constructed by deleting an internal fragment of the gene”(page 1114, 1st column, bottom).
Regarding claim 8, the claim is rejected for being indefinite as described above. However, for the purpose of prior art comparison, this examiner currently interprets the claim language “no or low surface proteolytic activity” to include membrane protease gene knockdowns. Fleuchot teaches “[lipoproteins] may be matured by the Eep [surface membrane] protease and therefore tested their functionality in a Δeep mutant. (page 1107, 2nd column, bottom).”
Regarding claim 9, all of the limitations of claim 9 are taught by Fleuchot- WP_100262537.1 as described in claim 1.
The additional limitation of claim 9 recites, “at least one genetic element selected from the group consisting of a nucleic acid sequence encoding the SHP peptide, said SHP peptide being selected from the group consisting of: SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31 and SEQ ID NO: 32.”
Fleuchot teaches this limitation, “…a highly hydrophobic nonapeptide [a fragment of SHP1358] with the amino acid sequence EGIIVIVVG.”(page 1105, 2nd column, middle). Fleuchot’s nonapeptide SHP1358 shares 100% identity with the instant 9 AA SEQ ID NO 24.
Regarding claim 10, the bacterial cell as described above in claim 9 (and claim 1) is the genetic vector.
Regarding claim 12, Fleuchot teaches a method for producing a protein of interest, culturing a GMB sufficient for expressing protein of interest in detail in their “Experimental procedures” section, specifically the sections “Bacterial strains and growth conditions,” and “Plasmid and strain constructions” (pages 1113, 1114).
Regarding claim 13, Fleuchot teaches supplementing culture media with SHP peptide by introducing a plasmid into the bacteria that self-supplements the culture media “A replicative plasmid containing the shp1358 gene under the control of a constitutive promoter was introduced into the Δeep …, leading to strains TIL 1206 ... The effects of culture supernatants from both these strains were then tested on reporter strain” (page 1108, 1st column, middle).
Regarding claim 14, the instant claimed invention is similar to the inventions of claims 1 and 9. All of the limitations of claims 1 and 9 are taught by Fleuchot- WP_100262537.1 as described in claims 1 and 9 with the following variation, “A genetic vector for inducibly expressing a nucleic acid sequence of interest comprising:” and
Fleuchot teaches a genetic vector in the form of the genetically modified bacteria (GMB) strain of S. thermophilus LMD-9, TIL 773, the Δeep (Table 3, and page 1114, 1st column, bottom). Fleuchot further teaches that their GMB vector comprises a nucleic acid, operably linked and regulated as described above in claims 1 and 9.
Fleuchot does not teach “a promoter… being located in 5' of a cloning site allowing the insertion of the nucleic acid sequence of interest.”
However Fleuchot teaches their familiarity with cloning in their Experimental procedures section DNA manipulation and sequencing and the section Plasmid and strain constructions, “Standard methods were used for DNA purification, restriction digestion, PCR, ligation and sequencing. E. coli TG1 or TG1 repA+ strains were used as hosts for cloning experiments.” They further exemplify this in Table 1 by listing more than a dozen different bacteria clones where they inserted a nucleic acid sequence of interest, for example the reporter gene LuxAB.
It would have been obvious for a person having ordinary skill in the art (PHOSITA) at the time of filing to have taken the genetic vector comprising S. thermophilus bacteria of Fleuchot- WP_100262537.1 comprising the SHP/Rgg system and designed the vector such that a promoter is located in 5' of a cloning site allowing the insertion of the nucleic acid sequence of interest because it is simply combining prior art elements according to known methods to yield predictable result. Cloning strategies were known as described above by Fleuchot. Fleuchot further showed success cloning in their different genes of interest into their vectors. Therefore, a person having ordinary skill in the art would have predicted the placement of a promoter in 5’ of a nucleic acid of interest would result in a functional vector.
Regarding claim 15, Fleuchot- WP_100262537.1 teaches all of the elements of claim 14 (and claims 1 and 9) as described above.
The additional limitation “A kit” is given no patentable weight. As claimed, “A kit” provides no additional structural limitations. Furthermore, the instant specification does not provide any additional guidance toward the meaning or structure of “A kit.” The specification merely recites “A kit” in the same usage as the instant claim [page 16, line 13).
Furthermore, Fleuchot- WP_100262537.1 teaches “a SHP peptide,” and “a bacterium, optionally a Streptococcus bacterium” as described in claim 14 above.
Claim 6 is rejected under 35 U.S.C. 103 as being unpatentable over Fleuchot and WP_100262537.1 as applied to claims 1 above, and further in view of Chang (Chang et al. PLoS One. 2016 Dec 19;11(12):e0168461.).
Fleuchot and WP_100262537.1 teach all of the elements of claim 1.
Fleuchot and WP_100262537.1 do not teach the limitation “wherein an ABC-type transporter called "PptAB", which enables export of the SHP peptide to the extracellular medium, is not functional or is inactivated.”
However, Fleuchot teaches “an oligopeptide permease transport system called … Ami, member of the ubiquitous ATP-binding cassette superfamily (ABC transporters) (page 1102, 2nd column, bottom).” Furthermore, Fleuchot teaches transporter inactivation via gene deletion, “we introduced the Pshp1358-luxAB transcriptional fusion into various Δami mutants, (page 1107, 1st column, middle). Additionally, Fleuchot’s investigative curiosity and lack of understanding provides motivation for inactivating this and potentially other transporters in their discussion, “Further study of two steps of this mechanism would be particularly interesting. First, the secretion mechanism responsible for the export of SHP pheromones is unknown (page 1109, 2nd column, bottom).”
Chang teaches “A transposon mutagenesis screen designed to identify mutants that were defective in peptide-pheromone signaling of the Rgg2/Rgg3 pathway in Streptococcus pyogenes … the pheromones known as SHPs (short hydrophobic peptides) were no longer detected in cell-free culture supernatants in a generated deletion mutant of pptAB (Abstract).”
It would have been obvious for a person having ordinary skill in the art (PHOSITA) at the time of filing to have taken the engineered S. thermophilus bacteria of Fleuchot- WP_100262537.1 and inactivated the PptaB transporter as taught by Chang because there was some teaching, suggestion, or motivation in the prior art that would have led one of ordinary skill to modify the prior art reference or to combine prior art reference teachings to arrive at the claimed invention (“TSM”). Both Fleuchot and Chang are in the same field of endeavor, molecular biology research of the SHP/Rgg pathway of Streptococcus bacteria. As stated above, researcher Fleuchot provides explicit motivation for inactivating the SHP export pathway of their bacteria. The researcher Chang was successful in their research experiments inactivating the PptaB exporter of Streptococcus bacteria. Therefore, a PHOSITA would similarly have a reasonable expectation of success inactivating the PptaB exporter of Fleuchot-WP_100262537.1’s Streptococcus bacteria to arrive at the instant claim limitation.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to AARON DUREL WARD whose telephone number is (571)272-8495. The examiner can normally be reached Monday to Thursday 8:00AM 6:00PM.
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/AARON DUREL WARD/ Examiner, Art Unit 1636
/NEIL P HAMMELL/Supervisory Patent Examiner, Art Unit 1636
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