DETAILED ACTION
Status of Application
Claims 2-4 and 9-12 are pending.
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Amendment of claims 2, 9-12, and cancellation of claims 1,5-8, 13-14 as submitted in a communication filed on 03/13/2026 is acknowledged.
Applicant’s election without traverse of Group VI, claims 2-4 and 9-12, drawn
to a method of use of an RNA Binding Protein (RBP) AbrP and a complex that comprises said protein and the translation promoting factor Era, as submitted in communication filed on 03-13-2016 is acknowledged.
Claims 2-4 and 9-12 are at issue and will be examined to the extent they encompass the elected invention.
Priority
Acknowledgment is made of a claim for foreign priority under 35 U.S.C. 119(a)-(d) to 2023112177340 filed on 09/20/2023. Receipt is acknowledged of papers submitted under 35 U.S.C. 119(a)-(d), which papers have been placed of record in the file.
Drawings
The drawings submitted on 12/07/2023 have been reviewed and are accepted by the examiner for examination purposes.
Claim Rejections - 35 USC § 112(b) or Second Paragraph (pre-AIA )
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 2, 3, 4, 9, 10, 11, 12 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.
Claims 2, 9, and 11 (claims 3, 4, 10, and 12 dependent thereon) provide for the use of an RNA binding protein and an AbrP protein translation-promoting complex, but since the claim does not set forth any steps involved in the method/process, it is unclear what method/process applicant is intending to encompass. A claim is indefinite where it merely recites a use without any active, positive steps delimiting how this use is actually practiced. Correction is required.
Claim 3 (claim 4 dependent thereon) is indefinite in the recitation of “recombinant protein translation comprises expression of an exogenous protein in a host cell” for the following reasons: Translation is a process where ribosomes in the cytoplasm decode messenger RNA (mRNA) sequences to synthesize specific polypeptide chains (proteins). Expression is the overall, regulated process by which cells generate functional proteins based on genetic instructions, encompassing transcription and translation. Therefore, it is unclear as to how the process of protein translation can comprise expression of a protein in a cell. Correction is required.
Claim 4 is indefinite in the recitation "wherein the host cell comprises a prokaryotic cell and/or a eukaryotic cell" for the following reason: The host cell can only be a prokaryotic cell or a eukaryotic cell, not both. For examination purposes, the recitation will be interpreted as “wherein the host cell comprises a prokaryotic cell or a eukaryotic cell". Correction is required.
Claims 9 and 11 (claims 10 and 12 dependent thereon) are indefinite due to the terms "prokaryotic chassis cell" and "eukaryotic chassis cell" being unclear as one cannot determine how the term “chassis” further limits the genus of prokaryotic or eukaryotic cells. As written, it is unclear as to what is included or excluded from the genus of prokaryotic or eukaryotic cells. For examination purposes, no patentable weight will be given to the terms “prokaryotic chassis cell” and "eukaryotic chassis cell". Correction is required.
Claims 10 and 12 are indefinite in the recitation of “Era, FusA, LepA”, for the following reasons. The terms as written, appear to be generic and not limited to a specific organism. While the gene nomenclature used may be appropriate for E. coli genes, the use of this nomenclature for (i) genes encoding proteins of identical function in other organisms, or (ii) proteins of identical function from other organisms may not be accurate. As known in the art, genes encoding proteins of identical function in two different organisms may use different designations. For example, the ARO4 gene of Candida albicans encodes a DAHP synthase whereas the E. coli counterpart is the aroF gene. See the abstract of Sousa et al. (Microbiology 148(Pt5):1291-1303, 2002). As such, the use of gene/protein terminology which is applicable to some organisms and not to others as used herein is confusing since one cannot determine if by using this nomenclature, the claims are limiting the organism from which these genes/proteins derive to those that use the same nomenclature. For examination purposes, the terms “Era”, “FusA”, “LepA” will be interpreted as proteins with GTP hydrolase translation-promoting activity. If applicant wishes to use the recited terminology in the claims, it is suggested that the claims be amended to clearly indicate the organism associated with the specific gene/protein designation. Correction is required.
Claim Rejections - 35 USC § 112(a) or First Paragraph (pre-AIA )
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(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 2-4 and 9-12 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 claim(s) contains 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 pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention.
As stated in MPEP 2111.01, during examination, the claims must be interpreted as broadly as their terms reasonably allow.
Claims 2-4 and 9-12 are directed in part to a method of use of an RNA-binding protein that comprises SEQ ID NO: 1 for promoting translation of any protein by any means, and a method of use of an AbrP protein translation system wherein the AbrP protein translation-promoting system comprises an mRNA translation-promoting complex comprising an RBP AbrP having the amino acid sequence of SEQ ID NO: 1 combined with a genus of translation-promoting factors having any structure. See claim rejections under 35 USC § 112(b) for claim interpretation.
In University of California v. Eli Lilly & Co., 43 USPQ2d 1938, the Court of Appeals for the Federal Circuit has held that “A written description of an invention involving a chemical genus, like a description of a chemical species, ‘requires a precise definition, such as by structure, formula, [or] chemical name,’ of the claimed subject matter sufficient to distinguish it from other materials”. As indicated in MPEP § 2163, the written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice, reduction to drawings, or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show that Applicant was in possession of the claimed genus. In addition, MPEP § 2163 states that 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.
According to the specification, the RBP AbrP having the amino acid sequence of SEQ ID NO: 1 requires a translation promoting factor and a sRNA/gRNA to obtain enhancement of protein translation. The specification fails to indicate (i) the structural element of any translation-promoting factor and any sRNA/gRNA that binds to the protein of SEQ ID: 1 that can be used in the recited methods, and (ii) how to obtain enhancement of protein translation solely by using the protein of SEQ ID NO: 1 as required by claims 2-4. There is no structural limitation with regard to the genus of translation-promoting factors required by the claims and the sRNA/gRNA required for the RBP to be used in the method. While the specification in the instant application discloses that the protein of SEQ ID NO: 1 binds to a sRNA/gRNA at the protein’s binding part encoded by SEQ ID NO: 4, the specification is silent with regard to the structure of a sRNA/gRNA that can bind to the protein of SEQ ID NO: 1 at the binding part encoded by SEQ ID NO: 4, it provides no clue as to the structural elements required in any translation-promoting factors to activate translation, including any Era protein, and any sRNA/gRNA that is able to bind to the binding part of the polypeptide of SEQ ID NO: 1 encoded by SEQ ID NO: 4. No disclosure of a structure/function correlation has been provided which would allow one of skill in the art to recognize which translation-promotion factors will work by any means as recited in the specification and which sRNA/gRNA will to bind the RBP AbrP with SEQ ID NO: 1 at the binding part of SEQ ID NO:4 while binding to any mRNA.
The claims encompass a large genus of translation-promoting factors and sRNA/gRNAs that can bind to the protein of SEQ ID NO: 1 that are structurally unrelated. A sufficient written description of a genus of translation-promoting factors and sRNA/gRNAs may be achieved by a recitation of a representative number of translation-promoting factors and sRNA/gRNAs defined by the recitation of structural elements common to members of the genus, which features constitute a substantial portion of the genus. However, in the instant case, there is no recited structural element which is representative of all the members of the genus of translation-promoting factors and sRNA/gRNAs required by the claimed method and there is no information as to which are the structural elements required in any translation-promoting factor that is essential for translation-promoting activity by any means with the recited protein complex. Furthermore, while one could argue that the species disclosed is representative of the structure of all the members of the genus of translation-promoting factors and sRNA/gRNAs required to promote translation by any means, it is noted that the art teaches several examples of how different translation-promoting factors carry out different translation-promoting activities and functions, and how different sRNA/gRNAs have different affinities and targets. For example, Sonenberg et al. (Cell 136(4):731–745, 2009) teach that eIF2a promotes translation by initiating translation (Page 732, left column, full paragraph 1). Xu et al. (Front. Mol. Biosci 8:816398, 1-20, 2013) teach that EF-Ts/eEF1B promotes translation by affecting the overall rate of elongation (Abstract; page 1). Veluchamy et al. (Scientific reports, 13:19717, page 1-12, 2023) disclose that gRNAs are designed for unique loci (Page 1, Abstract). Mekler et al. (Journal of Biological Chemistry, Vol 295, (Issue 19, 6059-6517, 2020) teach that gRNA variants have different binding affinities (Page 6513, right column, line 10-18).
Therefore, since structural differences in translational-promoting factors and sRNA/gRNA may result in changes affecting function and the means by which the RBP AbrP protein promote translation, and no additional information correlating structure with the desired functional characteristics has been provided, one cannot reasonably conclude that the species disclosed is representative of the structure of all the translation-promoting factors and sRNA/gRNAs required by the claimed method.
Due to the fact that the specification only discloses a limited species of the genus of translation-promoting factors and sRNA/gRNA required by the claimed process, the lack of description of any additional species by any relevant structural features, lack of description of additional ways the recited system promotes translation with the protein encoded by SEQ ID: 1, lack of description of the structural features required in any sRNA/gRNA so that it can bind to the protein of SEQ ID NO: 1 and translation-promoting factors that are required for this method to work as described, one of skill in the art would not recognize from the disclosure that applicant was in possession of the claimed invention.
Claims 2-4 and 9-12 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for the method of improving protein translation in (a) E. coli expressing the protein of SEQ ID NO: 1, wherein said E. coli expresses a sRNA/gRNA that comprises SEQ ID NO: 6 or 7, (b) B. subtilis expressing the protein of SEQ ID NO: 1, wherein said B. subtilis expresses a sRNA/gRNA that comprises SEQ ID NO: 8, 9, or 10, or (c) C. glutamicum expressing the protein of SEQ ID NO: 1, wherein said C. glutamicum expresses a sRNA/gRNA that comprises SEQ ID NO: 11, does not reasonably provide enablement for (a) a method for promoting protein translation by solely providing the protein of SEQ ID NO: 1 in any host cell, (b) a method for promoting translation of any recombinant protein in any host cell, wherein said method requires any translation promoting factor and does not require a sRNA/gRNA that binds to the protein of SEQ ID NO: 1. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention commensurate in scope with these claims.
Factors to be considered in determining whether undue experimentation is required are summarized in In re Wands (858 F.2d 731, 737, 8 USPQ2nd 1400 (Fed. Cir. 1988)) as follows: 1) quantity of experimentation necessary, 2) the amount of direction or guidance presented, 3) the presence and absence of working examples, 4) the nature of the invention, 5) the state of prior art, 6) the relative skill of those in the art, 7) the predictability or unpredictability of the art, and 8) the breadth of the claims. The factors which have led the Examiner to conclude that the specification fails to teach how to make and/or use the claimed invention without undue experimentation, are addressed in detail below.
The breadth of the claims. Claims 2-4 and 9-12 broadly encompass a method of use of an RNA-binding protein that comprises SEQ ID NO: 1 for promoting translation of any protein by any means, and a method of use of an AbrP protein translation system wherein the AbrP protein translation-promoting system comprises an mRNA translation-promoting complex comprising an RBP AbrP having the amino acid sequence of SEQ ID NO: 1 combined with a genus of translation-promoting factors and sRNA/gRNA having any structure. See Claim Rejections - 35 USC § 112(b) or Second Paragraph (pre-AIA ) for claim interpretation. The enablement provided is not commensurate in scope with the claims due to the lack of information as to the structural features required in any translation-promotion factor to promote translation with the protein of SEQ ID NO: 1. In the instant case, the specification enables for the method of use of an RNA-binding protein and a method of use of an AbrP protein translation system wherein the AbrP protein translation-promoting system comprises an mRNA translation-promoting complex comprising an RBP AbrP having the amino acid sequence of SEQ ID NO: 1 combined with translation-promoting factor, Era, using sRNA/gRNA selected from SEQ ID NO: 5-11.
The amount of direction or guidance presented and the existence of working examples. The specification discloses a method of use of an RNA-binding protein and a method of use of an AbrP protein translation system wherein the AbrP protein translation-promoting system comprises an mRNA translation-promoting complex comprising an RBP AbrP having the amino acid sequence of SEQ ID NO: 1 with the sRNA/gRNA binding part of SEQ ID NO:4, combined with translation-promoting factor, Era, using sRNA/gRNA selected from SEQ ID NO: 5-11. However, the specification fails to provide any clue as to the structural elements required in any translation-promoting factor or any sRNA/gRNA to bind to the protein of SEQ ID NO: 1 that can be used in the recited method, along with the means by which the AbrP protein translation promoting system is promoting translation. No correlation between structure and function has been presented.
The state of prior art, the relative skill of those in the art, and the predictability or unpredictability of the art. The amino acid sequence of a polypeptide determines its structural and functional properties, and the nucleic acid sequence of sRNA/gRNA determines its affinity to proteins and its overall target. While the art discloses a limited number of translation-promoting factors and sRNA/gRNA, neither the specification nor the art provides a correlation between structure and function such that one of skill in the art can envision the structure of any translation-promoting factors and sRNA/gRNAs that can be used in the claimed method. In addition, the art does not provide any teaching or guidance as to which changes can be made to the translation-promoting factors or sRNA/gRNA such that the resulting translation-promoting factors and sRNA/gRNA would work in the recited methods, or the general tolerance of translation-promoting factors and sRNA/gRNA to structural modifications and the extent of such tolerance. The art clearly teaches that (a) modifications of a gRNA sequence to obtain the desired activity without any guidance/knowledge as to which nucleic acids in a gRNA are tolerant of modification and which will bind to the target are highly unpredictable, (b) modifications of a protein’s amino acid sequence to obtain the desired activity without any guidance/knowledge as to which amino acids in a protein are tolerant of modification and which ones are conserved are highly unpredictable, and (c) the modifications of a gRNA sequence to obtain the desired affinity and target without any guidance/knowledge as to which nucleic acids in a gRNA are tolerant of modification and which ones are conserved are highly unpredictable. For example, Sonenberg et al. (Cell 136(4):731–745, 2009) teach that eIF2a promotes translation by initiating translation (Page 732, left column, full paragraph 1). Xu et al. (Front. Mol. Biosci 8:816398, 1-20, 2013) teach that EF-Ts/eEF1B promotes translation by affecting the overall rate of elongation (Abstract; page 1). Veluchamy et al. (Scientific reports, 13:19717, page 1-12, 2023) disclose that gRNA are designed for unique loci (Page 1, Abstract). Mekler et al. (Journal of Biological Chemistry, Vol 295, (Issue 19, 6059-6517, 2020) teach that gRNA variants have different binding affinities (Page 6513, right column, line 10-18).
The quantity of experimentation required to practice the claimed invention based on the teachings of the specification. While methods of generating or isolating variants of polypeptides and nucleotides, assays to assess translation promoting activity, and assays to select specific sRNA/gRNAs were known in the art at the time of the invention, it was not routine in the art to screen by a trial-and-error process for an essentially infinite number of translation promoting factors and sRNA/gRNA to find a translation-promoting system that can be used as claimed. In the absence of (i) a rational and predictable scheme for selecting those translation-promotion factors and sRNA/gRNA most likely to have the desired functional features, and/or (ii) a correlation between structure and translation-promoting activity, one of skill in the art would have to test an essentially infinite number of translational-promoting factors and sRNA/gRNA to determine which ones have the desired functional characteristics to be used in the recited method.
Therefore, taking into consideration the extremely broad scope of the claims, the lack of guidance, the amount of information provided, the lack of knowledge about a correlation between structure and the desired function, the lack of knowledge of the specific means of how the recited method promotes translation, and the high degree of unpredictability of the prior art in regard to structural changes and their effect on function, one of ordinary skill in the art would have to go through the burden of undue experimentation in order to practice the claimed invention. Thus, applicant has not provided sufficient guidance to enable one of ordinary skill in the art to make and use the invention in a manner reasonably correlated with the scope of the claims.
Claim Rejections - 35 USC § 103 (AIA )
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.
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.
Claims 2, 3, and 4 are rejected under 35 U.S.C. 103 as being unpatentable over He et al. (Microbial pathogenesis 41.6 (2006): 199-206), in view of De Gregorio et al. (The EMBO journal 18.17 (1999): 4865-4874)
He teaches that Tex proteins are transcriptional accessory proteins, wherein said proteins can bind DNA directly, or work in concert with other proteins to regulate gene expression. (Page 203, right column, first full paragraph). He teaches that Tex proteins are RNA-Binding proteins (Page 203, right column, first full paragraph). He teaches that Tex proteins are involved in protein translation initiation (Page 203, left column, second full paragraph). He teaches the ability of Tex to bind to RNA in prokaryotic cells (Page 203, right column, first full paragraph). He does not teach the use of an RNA-binding protein to promote expression of an exogenous protein. De Gregorio teaches the use of RNA binding protein to promote expression (Page 4865, abstract). De Gregorio teaches that the protein expressed was a reporter exogenous protein in a eukaryotic host cell (Page 4873 left column, second paragraph).
Claims 2, 3, and 4 are directed in part to a method of use of an RNA binding protein AbrP having the amino acid sequence of SEQ ID NO: 1 in promoting recombinant protein translation, wherein the recombinant protein translation comprises expression of an exogenous protein in a host cell, wherein the host cell comprises a prokaryotic cell or a eukaryotic cell. Additionally, SEQ ID NO: 1 is a 100% identity match to UniProt ID: K0CBE7_ALCDB, which is identified as a transcriptional accessory factor. Since the transcriptional accessory factor is identical to the amino acid sequence of SEQ ID NO:1, the transcriptional accessory factor of UniProt ID: K0CBE7_ALCDB is inherently an RNA binding AbrP polypeptide.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to use an RNA-binding protein or a transcriptional accessory factor to promote translation of an exogenous protein in a prokaryotic cell or a eukaryotic cell. These teachings would suggest to a person of ordinary skill in the art that an RNA-Binding protein would be useful in promoting the translation of an endogenous or exogenous protein in either a prokaryotic or eukaryotic host cell. One of ordinary skill in the art has a reasonable expectation of success at arriving to using an RNA-binding protein to promote translation because all that is required is introducing the desired target mRNA to a host cell with an RNA-binding protein that has an affinity to the target RNA. Therefore, the invention as a whole would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention.
Claims 9-12 are rejected under 35 U.S.C. 103 as being unpatentable over He (Microbial pathogenesis 41.6 (2006): 199-206) and De Gregorio (The EMBO journal 18.17 (1999): 4865-4874) in further view of Verstraeten (Microbiology and Molecular Biology Reviews 75.3 (2011): 507-542)
Claims 9-12 are directed in part to a method of use of an AbrP protein translation-promoting system in metabolic engineering regulation of a prokaryotic or eukaryotic cell, wherein the AbrP protein translation-promoting system comprises an mRNA translation-promoting complex comprising an RBP AbrP having the amino acid sequence of SEQ ID NO: 1 combined with a translation-promoting factor, wherein the translation-promoting factor comprises Era. Additionally, instant SEQ ID NO: 1 is a 100% identity match to UniProt ID: K0CBE7_ALCDB, which is identified as a transcriptional accessory factor. Since the transcriptional accessory factor is identical to the amino acid sequence of SEQ ID NO:1, the transcriptional accessory factor of UniProt ID: K0CBE7_ALCDB is inherently an RNA binding AbrP polypeptide.
The teachings of He and De Gregorio have been taught above. Neither He or De Gregorio teach of the translation-promoting factor, Era. Verstraeten teaches that Era plays a central role in the initiation of protein synthesis (Page 520, left column, first 3 lines). Verstraeten teaches that many properties of bacterial Era are conserved in eukaryotes (Page 520, 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 use an AbrP protein translation-promoting system that comprises an RNA-binding protein or a transcriptional accessory factor combined with a translation-promoting factor to promote translation of a protein in a prokaryotic cell or a eukaryotic cell. These teachings would motivate a person of ordinary skill in the art to modify the promotion of protein translation taught by He and De Gregorio and add the translation-promoting factor, Era, to further promote protein translation, as suggested by Verstraeten. One of ordinary skill in the art has a reasonable expectation of success at arriving to using an RNA-binding protein combined with translation-promoting factor, Era, to promote translation because all that is required is introducing the desired target mRNA to a host cell with Era and an RNA-binding protein that has an affinity to the target. Therefore, the invention as a whole would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention.
Conclusion
No claim is in condition for allowance
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/SYNPHANE L SHELTON/Examiner, Art Unit 1652
/ROBERT B MONDESI/Supervisory Patent Examiner, Art Unit 1652
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