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 .
Election/Restrictions
Applicant’s election without traverse of Group I and withdrawal of claims 14-17 and 24-27 in the reply filed on May 29. 2026 is acknowledged.
Claims 1-7, 14-17, and 24-27 are currently pending. Claims 1-7 are herein examined on their merits.
Priority
It is acknowledged that the instant application is a 371 of international PCT Application No. PCT/KR2022/007860, filed June 2, 2022, and that it claims benefit of foreign applications KR10-2021-0070803 (filed June 1, 2021), KR10-2021-0076938 (filed June 14, 2021), KR10-2021-0076939 (filed Jun3 14, 2021), KR10-2022-0067642 (filed June 2, 2022), and KR10-2022-0067643 (filed June 2, 2022). It is noted, however, that the foreign priority date is the effective filing date of the claimed invention if:
the foreign application supports the claimed invention under 112(a), and
the applicant has perfected the right of priority by providing
a certified copy of the priority application, and
a translation of the priority application (if not in English)
In the instant case, the applicant has submitted a certified copy of each of the priority applications but they are not in English and the examiner cannot determine if they fully support the claimed invention.
The effective filing date of the claims under examination is considered to be June 2, 2022, which is the filing date of PCT/KR2022/007860.
Claim Objections
Claims 3 and 4 objected to because of the following informalities: improper tense. Claim 3 should read “…in which a Cra-binding site has been deleted.” Appropriate correction is required.
Drawings
The drawings are objected to because text (labels, legend, etc.) in several of the figures are illegible (see especially Fig. 1ab, Fig. 4, and Fig. 5). Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
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.
Claims 3-7 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 3 and 4 are rejected for the recitation of “deletion”/”deleted” as indefinite. It is unclear whether the claims requires the inclusion in the expression vector of sequences from which Cra-binding site(s) have been removed, or if the claim is merely requiring that the Cra-binding site sequence(s) simply not be present in the expression vector. If the claim is requiring that the site(s) have been present and subsequently removed, it is not clear how one would assess that limitation. For example, there is no obvious or disclosed list of sequences containing Cra-binding sites, or of sequences which have had the Cra-binding site removed, and there is no discussion in the instant specification of how one might assess this property of an expression vector. As a result, one of skill in the art would not be able to determine the metes and bounds of the claimed subject matter so as to avoid infringement.
Claims 5-7 are rejected for the recitation of “a mutation sequence” as indefinite. It is unclear what is meant be ‘a mutation sequence’ in this context. For example, is the claim intended to require that a sequence is mutated relative to some wildtype or reference sequence? If so, it is not clear what the wildtype or reference sequence would be and how one would determine that a sequence was ‘a mutation sequence.’ It is also unclear whether the claims are requiring the mutation sequence only, or the mutation sequence as well as sequences encoding lacI and T7 RNAP. As written, the claim is ambiguous and may require either of the following:
An expression cassette comprising the required mutation sequence has merely been derived from a sequence containing lacI, the mutation sequence, and T7 RNAP, OR
An expression cassette comprising lacI, a mutation sequence, and T7 RNAP, wherein the mutation sequence lies between lacI and T7 RNAP in the claimed expression cassette
As a result, one of skill in the art would not be able to determine the metes and bounds of the claimed subject matter so as to avoid infringement.
Claim 6 is rejected for the recitation of “wherein the mutation sequence between the sequence encoding LacI and the sequence encoding T7 RNAP is mutation in a T7 RNAP core promoter region,” as indefinite. It is unclear whether “T7 RNAP core promoter region” is meant to indicate a sequence which is bound by T7 RNAP or if it is meant to indicate a sequence which controls the expression of T7 RNAP itself. If it is meant to be s sequence which is bound by T7 RNAP, is the limitation meant to indicate a specific, critical sequence to which T7 RNAP binds for polymerization or can the limitation be met by any sequence of residues which can be bound by or provide specificity for the T7 RNAP? It is not apparent what the specific, critical sequence (the ‘core’) would be in either interpretation. As a result, one of skill in the art would not be able to determine the metes and bounds of the claimed subject matter so as to avoid infringement.
Claim 7 is rejected because it is unclear what is intended by the claim. SEQ ID NO: 4 corresponds with a sequence between 749,737-750,053bp in the genome of C41(DE3) strain of Escherichia coli (GenBank: CP010585.1). Said sequence is annotated as including: 1) a portion of lacI, 2) an intervening sequence, and 3) a portion of lacZ (beta-galactosidase). Given that the composition of SEQ ID NO: 4 apparently already includes a portion of lacI, is lacI meant to be partially duplicated in the claimed expression cassette (i.e. the expression cassette contains a full lacI sequence + SEQ ID NO: 4 + T7 RNAP), or is claim 7 meant to require only that the intervening sequence of SEQ ID NO: 4 (and not the elements encoding parts of lacI/lacZ) be comprised in the expression cassette, or is there some other meaning intended by the claim? As a result, one of skill in the art would not be able to determine the metes and bounds of the claimed subject matter so as to avoid infringement. Clarification is requested.
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 pre-AIA 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter pertains. Patentability shall not be negated by the manner in which the invention was made.
This application currently names joint inventors. In considering patentability of the claims under pre-AIA 35 U.S.C. 103(a), the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the examiner to consider the applicability of pre-AIA 35 U.S.C. 103(c) and potential pre-AIA 35 U.S.C. 102(e), (f) or (g) prior art under pre-AIA 35 U.S.C. 103(a).
Claims 1-4 are rejected under 35 U.S.C. 103 as unpatentable over Klaenhammer et al. (published Jan 4, 2007; Klaenhammer et al. US Publication No. 2007/0003668) in view of Bork et al. (published Jan 1993; Bork P et al. Protein Sci. 1993 Jan;2(1):31-40) and Ahler et al (published April 18, 2020; Ahler et al. Mol Cell. 2019 Apr 18;74(2):393-408.e20).
Regarding claim 1, Klaenhammer teaches an expression cassette comprising a gene (par. 117) encoding a fructose-1-kinase (par. 30; Table 1: pg. 26, col. 1 – ‘FruK’).
Regarding claim 1, Klaenhammer does not teach a novel fructose-1- phosphate kinase in which alanine (A) at position 39 in the amino acid sequence of SEQ ID NO: 1 is substituted with serine (S). Klaenhammer instead teaches fructose-1-phosphate kinases from Lactobacillus acidophilus (‘fruK’ – reference’s SEQ ID NO: 185/186 in Table 1, pg. 26, col. 1).
Regarding claim 2, Klaenhammer does not teach that the gene encoding the novel fructose-1-phosphate kinase is SEQ ID NO: 2.
Bork teaches fructose-1-phosphate kinase (also known as 1-phosphofructokinase) from Escherichia coli (pg. 32, Table 1: K1PF_ECOLI). Bork teaches that the sequence came from SWISSPROT, which is now part of UniProt. The corresponding sequence K1PF_ECOLI was aligned to SEQ ID NO: 1 (shown below), and has 100% identity to the claimed sequence.
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It would have been obvious to a person with ordinary skill in the art before the effective filing date of the instant invention to replace the fructose-1-phosphate kinase from Lactobacillus with the fructose-1-phosphate kinase from Escherichia coli because the kinases are used for the same purpose (i.e. they are both fructose-1-phosphate kinases having the same carbohydrate utilization-related enzymatic activity), and therefore the kinases are considered functional equivalents. One would have had reasonable expectation of success because Klaenhammer demonstrates expression constructs using the Lactobacillus fructose-1-kinase (par. 265), and because Klaenhammer teaches the generation of expression constructs using generic and conventional methods (par. 61, 115, 158).
Regarding claim 2, Bork does not explicitly teach that the gene encoding the novel fructose-1-phosphate kinase is SEQ ID NO: 2. However, when the nucleotide sequence of SEQ ID NO: 2 is translated to its corresponding amino acid sequence (using Expasy or other accessible translation tools), it is clear that Bork teaches a single nucleotide variant of the sequences required by claim 1 (i.e. SEQ ID NO: 1 without the A39S mutation). The alignment of SEQ ID NO: 1 (“Sbjct”) to the translated SEQ ID NO: 2 (“Query”) is shown below:
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Since Bork teaches the sequence corresponding to SEQ ID NO: 1 (an amino acid sequence), it would be obvious to use the corresponding nucleotide sequence to encode the fructose-1-phosphate kinase.
Regarding claims 1 and 2, neither Klaenhammer nor Bork teaches a sequence wherein alanine (A) at position 39 in the amino acid sequence of SEQ ID NO: 1 is substituted with serine (S), nor the mutation in the corresponding nucleotide sequence. However, Klaenhammer does teach mutating the sequence of specific carbohydrate-utilizing coding sequences along the entire length of the sequence, using techniques like saturation mutagenesis (par. 57) to generate combinatorial libraries of mutants (par. 61).
Furthermore, Ahler teaches the use of ‘deep mutational scanning’ to probe the phenotypic effects of all possible variants at all single-amino-acid positions in the kinase Src (pg. 3, last par.). This method requires the generation of library constructs transformed into yeast for expression and phenotype analysis. However, a person with ordinary skill in the art would understand that the general strategy of deep mutational scanning may be applied in other systems, such as bacterial expression systems, as discussed in Klaenhammer (see par. 115 and 118, for example).
It would have been obvious to a person with ordinary skill in the art before the effective filing date of the instant invention to try mutating any position of fructose-1-phosphate kinase to any amino acid, including the claimed A39S mutation. One would have been motivated to do so in order to investigate intramolecular kinase regulation or phosphotransferase-independent function (Ahler: pg. 12, last par.). One would have had reasonable expectation of success because Klaenhammer states that methods of making and testing variants of carbohydrate utilization-related proteins are well known in the art (Klaenhammer: par. 168) and Ahler demonstrates deep mutational scanning in another kinase (Ahler: Figure 2).
Regarding claims 3 and 4, Klaenhammer, Bork, and Ahler do not explicitly teach that the expression cassette is one in which a Cra-binding site has been deleted. Klaenhammer and Bork are silent regarding Cra-binding sites. Although they discuss Cra itself (which is also known as FruR), they do not discuss binding sites for Cra/FruR. Furthermore, none of the sequences from Klaenhammer or Bork relied upon in these rejections contain the sequence of SEQ ID NO: 3, which is a Cra-binding site. Therefore, barring evidence to the contrary, the limitations of claims 3 and 4 are considered to have been met.
Claims 5 and 7 are rejected under 35 U.S.C. 103 as unpatentable over Klaenhammer et al. (published Jan 4, 2007; Klaenhammer et al. US Publication No. 2007/0003668) in view of Bork et al. (published Jan 1993; Bork P et al. Protein Sci. 1993 Jan;2(1):31-40) and Ahler et al (published April 18, 2020; Ahler et al. Mol Cell. 2019 Apr 18;74(2):393-408.e20), as applied to claim 1 above, and further in view of Miroux et al. (published July 19, 1996; Miroux et al. J Mol Biol. 1996 Jul 19;260(3):289-98).
Klaenhammer, Bork, and Ahler teach the limitations of claim 1, as discussed in the rejection of claims 1-4 above.
Regarding claim 5, Klaenhammer teaches expression cassettes further comprising sequences encoding LacI (par. 122) and T7 RNAP (par. 119, 121). Klaenhammer teaches expression cassettes further comprising sequences encoding LacI (par. 122) and T7 RNAP (par. 119, 121). Klaenhammer teaches that the sequence elements in an expression cassette are subject to manipulation so as to provide the sequences in the proper orientation (par. 129).
Regarding claims 5 and 7, Klaenhammer, Bork, and Ahler do not explicitly teach expression cassettes comprising mutation sequences between sequences encoding LacI and T7 RNAP, nor that the mutation sequence is SEQ ID NO: 4.
Regarding claims 5 and 7, Miroux teaches a mutated derivative of the wild-type Escherichia coli lac operon promoter which controls expression of T7 RNAP (pg. 290, col. 1) as part of an expression system for Escherichia coli strain C41(DE3). NCBI’s complete genome of E. coli strain C41(DE3) (GenBank CP010585.1) contains a sequence encoding portions of LacI, an intervening sequence, and a portion of LacZ (CP010585.1: 749737-750053). This sequence aligns to SEQ ID NO: 4 with 100% identity, as shown below (the query is the claimed sequence):
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This sequence (SEQ ID NO: 4 corresponding to CP010585.1: 749737-750053) represents a single nucleotide variant sequence which differs between strain C41(DE3) and the originating strain (BL21(DE3); Abstract). The originating strain’s corresponding sequence is represented by GenBank’s NC_012971.2:335766-336044). The alignment of these sequences is shown below (the query is the claimed sequence):
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Therefore, Miroux is considered to have met the limitation of comprising a mutation sequence corresponding to SEQ ID NO: 4.
A view of the genome of CD41(DE3) from a larger range shows that the order of elements is: lacI – the rest of SEQ ID NO: 4 – T7 RNAP. This is shown below
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Here, the coding sequence element AJF76079.1 represents a sequence with 100% identity to NCBI’s NC_001604.1: 3139-5887, which is the sequence for T7 RNAP. Thus, Miroux is considered to have met the limitation that the mutation sequence represented by SEQ ID NO: 4 (corresponding to CP010585.1: 749737-750053) lies between a sequence encoding LacI and a sequence encoding T7 RNAP.
It would have been obvious to a person with ordinary skill in the art before the effective filing date of the instant invention to combine the teachings of Klaenhammer, Bork, and Ahler with the teachings of Miroux. One would have been motivated to do so in order to overcome potential toxic effects observed in the production of some proteins using E. coli-T7 RNAP expression systems (Miroux: Abstract). One would have had reasonable expectation of success because Miroux demonstrates the successful use of C41(DE3) in producing otherwise toxic proteins, including several globular proteins (Miroux: Abstract).
Claim 6 is rejected under 35 U.S.C. 103 as unpatentable over Klaenhammer et al. (published Jan 4, 2007; Klaenhammer et al. US Publication No. 2007/0003668) in view of Bork et al. (published Jan 1993; Bork P et al. Protein Sci. 1993 Jan;2(1):31-40) and Ahler et al (published April 18, 2020; Ahler et al. Mol Cell. 2019 Apr 18;74(2):393-408.e20), as applied to claim 1 above, further in view of Miroux et al. (published July 19, 1996; Miroux et al. J Mol Biol. 1996 Jul 19;260(3):289-98), as applied to claim 5 above, and further in view of Raskin et al. (published Apr 15 1993; Raskin et al. Proc Natl Acad Sci U S A. 1993 Apr 15;90(8):3147-51).
Klaenhammer, Bork, and Ahler teach the limitations of claim 1, as discussed in the rejection of claims 1-4 above. Klaenhammer, Bork, Ahler, and Miroux teach the limitations of claim 5, as discussed in the rejection of claims 5 and 7 above.
Regarding claim 6, Klaenhammer, Bork, Ahler, and Miroux do not explicitly teach expression cassettes comprising mutation sequences between sequences encoding LacI and T7 RNAP, wherein the mutation sequence is a mutation in a T7 RNAP core promoter region.
Raskin teaches mutation sequences of the T7 promoter which are in a critical region for specific binding of T7 RNAPs (pg. 3147, col. 1, par. 3-4).
It would have been obvious to a person with ordinary skill in the art before the effective filing date of the instant invention to combine the teachings of Klaenhammer, Bork, Ahler, and Miroux with the teachings of Raskin, in order to expand the usable repertoire of specific RNAPs that are available for use in phage RNAP-based expression systems (pg. 3149, col. 1 – col. 2, 1st par.). One would have had reasonable expectation of success because Raskin shows that mutation of the promoter at critical positions is functional in many difference combinations of altered promoters with RNAP variants (pg. 3147, col. 1, last par. – col. 2, 1st par.; Fig. 3).
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Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Christine M Jones whose telephone number is (571)272-2585. The examiner can normally be reached Monday - Friday, 8AM - 4PM.
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/C.M.J./Examiner, Art Unit 1682
/WU CHENG W SHEN/Supervisory Patent Examiner, Art Unit 1682
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