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 .
DETAILED ACTION
Claims 1-15 are cancelled. Claims 16-25 are pending and under examination.
Claim Objections
Claims 16-25 are objected to because of the following informalities: the claims contain extraneous and convoluted language.
Claim 16 recites protein name acronyms and should recite the full names of each protein.
All preambles of claims 17-25 should be amended to recite: the method of claim 16… instead of: he method for fermentative production of recombinant proteins as claimed in claim 16, or: the method as claimed in claim 16.
Appropriate correction is required.
Claim Rejections – 35 USC § 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 16-25 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 16 recites the limitation “the cells” in line 7. Claim 16 recites the limitation “the culture medium” in line . There is insufficient antecedent basis for these limitations in the claim.
Claim 16 further recites an indefinite claim limitation in lines 2-5: a bacterial strain containing an open reading frame encoding a signal peptide and a recombinant protein under the control of a functional promoter, contains an additional open reading frame encoding a signal peptide and a peptidoglycan peptidase under the control of a functional promoter, wherein the peptidoglycan peptidase is (i) Spr, (ii) YdhO or (iii) Spr and YdhO. It is uncertain whether the cultured bacterial strain, an alternative bacterial strain, or more than one bacterial strain, is required to contain two open reading frames (OPRs): OPR1 encoding a signal peptide and a recombinant protein under the control of a functional promoter; and OPR2 encoding a signal peptide, and Spr and/or YdhO, under the control of a functional promoter.
Claim 16 also recites: wherein…the yield of the recombinant protein which is released into the culture medium is at least 1.1 times as high as the yield which can be achieved with corresponding bacteria strains without overproduction of the peptidoglycan peptidase. However, the claim only requires that Spr and YdhO are under the control of a functional promoter, but does not recite any structural feature, any method condition, or any active method step that results in overexpression or the yield of recombinant protein which is released into the culture medium is at least 1.1 times as high as the yield which can be achieved with corresponding bacterial strains without overproduction of the peptidoglycan peptidase.
Claims 17-25 are also rejected as they depend from claim 16.
Claim 19 recites: wherein Spr is the sequence specified by amino acids of 27-188 in SEQ ID NO:5. It is unclear if the claim means that the bacterial strain comprises a Spr protein that contains only the amino acids of 27-188 of SEQ ID NO:5, or if the claim means that amino acids 27-188 of SEQ ID NO:5 are the amino acids that make up the catalytic portion of the protein.
Claim 20 recites: wherein YdhO is the sequence specified by the amino acids of 28-271 in SEQ ID NO:7. It is unclear if the claim means that the bacterial strain comprises a YdhO protein that contains only the amino acids of 28-271 of SEQ ID NO:7, or if the claim means that amino acids 28-271 of SEQ ID NO:7 are the amino acids that make up the catalytic portion of the protein.
Claim 25 recites the limitation “the additional peptidoglycan peptidase” in line 2. There is insufficient antecedent basis for this limitation in the claim. It is unclear if the claim requires the expression of more than one peptidoglycan peptidase.
Claim Rejections - 35 USC § 112(d)
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 25 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 25 recites results that occur because of the method of claim 16, but does not recite any additional method steps or further limit any of the steps in claim 16. Therefore, the claim fails to further limit the method of claim 16. Applicant may cancel the claim, amend the claim to place the claim in proper dependent form, rewrite the claim in independent form, or present a sufficient showing that the dependent claim complies with the statutory requirements.
Claim Rejections – 35 USC § 112(a)
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 16-25 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claims contain subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventors, at the time the application was filed, had possession of the claimed invention.
Claims 16 and 23-25 are drawn to method for fermentative production of recombinant proteins comprising culturing a bacterial strain containing an open reading frames encoding signal peptides and a recombinant protein under the control of a functional promoter, and an additional open reading frame encoding a signal peptide and a peptidoglycan peptidase under control of a functional promoter, wherein the peptidoglycan peptidase is Spr, YdhO, or Spr and YdhO. The claims are not specific to a particular bacterial strain, particular signal peptides, particular recombinant proteins, particular promoters, or particular Spr and YdhO variants. Claim 17 limits the bacterial strain to Gram-negative bacteria. Claim 18 limits the bacterial strain to an Escherichia coli strain. Claims 19 and 20 limit the amino acid sequences of the Spr and YdhO proteins, respectively. Claim 21 limits the promoter controlling peptidoglycan peptidase expression to an inducible promoter. Claim 22 limits the recombinant protein to a heterologous protein.
MPEP 2163.05 II states “the written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species. A ‘representative number of species’ means that the species which are adequately described are representative of the entire genus. Thus, when there is substantial variation within the genus, one must describe a sufficient variety of species to reflect the variation within the genus. See AbbVie Deutschland GmbH & Co., KG v. Janssen Biotech, Inc., 759 F.3d 1285, 1300, 111 USPQ2d 1780, 1790 (Fed. Cir. 2014) (Claims directed to a functionally defined genus of antibodies were not supported by a disclosure that ‘only describe[d] one type of structurally similar antibodies’ that ‘are not representative of the full variety or scope of the genus.’). The disclosure of only one species encompassed within a genus adequately describes a claim directed to that genus only if the disclosure “indicates that the patentee has invented species sufficient to constitute the gen[us].’”
The instant specification reduces to practice the production of recombinant proteins using E. coli cells transformed with plasmids containing the gene for CGTase and its native signal sequence under control of the tac promoter, an arabinose promoter (pBAD) controlling expression of a nucleotide fragment encoding a fusion of either E. coli Spr or YdhO and the terminator of the E. coli trpA gene (pages 22 and 23); or, with the pJF118ut-CD154 plasmid containing a fusion consisting of the signal sequence of SEQ ID NO:2, the reading frame for the heavy chain of the Fab fragment of the humanized monoclonal anti-CD154 antibody, the phoA signal sequence of SEQ ID NO:3, the reading frame for the light chain of the Fab fragment of the humanized monoclonal anti-CD154 antibody, and a DNA fragment encoding E. coli Spr under control of the arabinose promoter and flanked by the E. coli trpA terminator. The specification discloses that inducible expression of E. coli Spr and/or YdhO allows for release of the recombinant protein at higher yields without causing host cell lysis (p. 3, lines 20-23). The specification does not disclose the entire genus of bacterial strains, signal peptides, promoters, or Spr/YdhO variants as claimed. Therefore, the disclosed species are not representative of the entire claimed genus of bacterial strains, signal peptides, promoters, and Spr/YdhO variants that may be combined to successfully produce recombinant proteins at an increased yield compared to those without overproduction of the peptidoglycan peptidase.
Dasler et al., (EP2204441A1) teaches a process for the fermentative production of heterologous proteins by E. coli expressing (p)ppGpp synthetase II (para. [0001]) and a heterologous protein linked to a signal sequence, wherein the E. coli strain secretes the heterologous protein into the fermentation medium (para. [0011]). Dasler also teaches the use of E. coli strains with mutations in the gene for Braun lipoprotein that expel overproduced heterologous proteins into the medium (para. [0004]). Dasler and no other prior art reference teach a bacterial strain encoding Spr and/or YdhO for the production of recombinant proteins at higher yields compared to those without overproduction of the peptidoglycan peptidase.
In summary, neither the instant specification, nor the prior art, discloses all bacterial strains, promoters, or Spr/YdhO variants that may be combined to successfully produce recombinant proteins at an increased yield without overproduction of the peptidoglycan peptidase. One of ordinary skill in the art cannot reasonably predict what specific bacterial strains, promoters, and Spr/YdhO variants may be used to perform the method as claimed. Based on the instant disclosure, those skilled in the art would not conclude that the applicant was in possession of all claimed variants.
Pertinent Prior Art
The closest prior art references are: Dasler et al., (EP2204441A1; cited in the IDS filed 04/19/2022), Singh et al., 2012 (cited in the IDS filed 04/19/2022), and Vollmer et al (Bacterial growth does require peptidoglycan hydrolases. Dec. 2012. Molecular Microbiology Vol. 86, Issue 5, p. 1031-1035.).
Dasler teaches a process for the fermentative production of heterologous proteins by E. coli expressing (p)ppGpp synthetase II (para. [0001]) and a heterologous protein linked to a signal sequence, wherein the E. coli strain secretes the heterologous protein into the fermentation medium (para. [0011]). Dasler also teaches the use of E. coli strains with mutations in the gene for Braun lipoprotein that expel overproduced heterologous proteins into the medium (para. [0004]). Dasler does not teach that the E. coli strain encodes E. coli Spr and/or YdhO.
Singh teaches that Spr and YdhO belong to a peptidase superfamily (Abstract). Singh teaches that Spr is a murein endopeptidase that cleaves D-ala-mDAP cross-links (Figure 2), and that YdhO is a DD-endopeptidase (Fig. 4). Singh does not teach a method of using Spr and/or YdhO for the fermentative production of recombinant proteins.
Vollmer (Bacterial growth does require peptidoglycan hydrolases. Dec. 2012. Molecular Microbiology Vol. 86, Issue 5, p. 1031-1035.) teaches the identification in Escherichia coli of three new DD-endopeptidases, Spr, YdhO and YebA, which are collectively required for peptidoglycan growth (Abstract).
The inventors have demonstrated a novel method of producing proteins at increased yield in E. coli. Said method relies on the expression of peptidoglycan peptidases Spr and/or YdhO, which cleave and weaken the peptidoglycan layer, subsequently resulting in the release of the recombinant proteins from the E. coli cells without causing E. coli i.e., host cell, lysis (p. 1, last paragraph; p. 3, lines 20-23; Table 1). The Examiner is unaware of any prior art references that teach a plasmid encoding a recombinant protein combined with Spr and/or YdhO.
Allowable Subject Matter
Based on the instant specification (p. 22, lines 15-34; p. 23, lines 5-24; Examples 1 and 2), the following claim amendment is suggested to place this application in condition for allowance:
16. A method for comprising:
a) fermenting an Escherichia coli strain transformed with a plasmid encoding:
1) a first fusion protein comprising a recombinant protein and a cyclodextrin glycosyltransferase (CGTase) signal sequence from Klebsiella pneumoniae, wherein the first fusion protein is under control of a tac promoter; and
2) a second fusion protein comprising an E. coli peptidoglycan peptidase selected from Spr, YdhO, or Spr and YdhO, flanked by the E. coli trpA terminator, wherein the second fusion protein is under control of an arabinose promoter;
b) removing the fermentation medium E. coli cells after ; and,
c) isolating the recombinant proteinE. coli cell and the yield of recombinant protein which is released into the culture medium is at least 1.1 times as high as the yield which can be achieved with corresponding bacterial strains that do not express the plasmid.
17. Cancelled.
18. Cancelled.
19. The method of the amino acid sequence of Spr consists of amino acids 27-188 of
20. The method ofthe amino acid sequence of YdhO consists of amino acids 28-271 of
21. Cancelled.
22. The method of
23. Cancelled.
24. The method of
25. Cancelled.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to RACHEL EMILY MARTIN whose telephone number is (703)756-1416. The examiner can normally be reached M-Th 8:30-16:00, F 8:30-10:00 EST.
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, Louise Humphrey can be reached at (571) 272-5543. 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.
/LOUISE W HUMPHREY/Supervisory Patent Examiner, Art Unit 1657
/RACHEL EMILY MARTIN/Examiner, Art Unit 1657
Prosecution Insights