DETAILED ACTION
Application status
Claims 1-9 are pending in this application.
Election/Restrictions
Restriction is required under 35 U.S.C. 121 and 372.
This application contains the following inventions or groups of inventions which
are not so linked as to form a single general inventive concept under PCT Rule 13.1.
In accordance with 37 CFR 1.499, applicant is required, in reply to this action, to elect a single invention to which the claims must be restricted.
Group I, claims 1 and 6-7, drawn to a protein-glutaminase comprising a polypeptide shown in any one of the following (1) to (3): (1) a polypeptide having an amino acid sequence shown in SEQ ID NO: 1 or 2; (2) a polypeptide having an amino acid sequence obtained by substituting, adding, inserting, or deleting one or more amino acid residues in an amino acid sequence shown in SEQ ID NO: 1 or 2, the polypeptide having thermostability equivalent to thermostability of a polypeptide having an amino acid sequence shown in SEQ ID NO: 1 or 2; and (3) a polypeptide having an amino acid sequence having a sequence identity to an amino acid sequence shown in SEQ ID NO: 1 or 2 of 76% or more, the polypeptide having thermostability equivalent to thermostability of a polypeptide having an amino acid sequence shown in SEQ ID NO: 1 or 2.
Group II, claims 2-5, drawn to a DNA encoding the protein-glutaminase according to claim 1.
Group III, claims 8-9, drawn to a method for producing a modified protein material, the method comprising a step of making the protein-glutaminase according to claim 1 act on a protein material.
The groups of inventions listed above do not relate to a single general inventive concept under PCT Rule 13.1 because, under PCT Rule 13.2, they lack the same or corresponding special technical features for the following reasons: The Groups I-III lack unity of invention because even though the inventions of these groups require the technical feature of a protein-glutaminase comprising a polypeptide shown in any one of the following (1) to (3): (1) a polypeptide having an amino acid sequence shown in SEQ ID NO: 1 or 2; (2) a polypeptide having an amino acid sequence obtained by substituting, adding, inserting, or deleting one or more amino acid residues in an amino acid sequence shown in SEQ ID NO: 1 or 2, the polypeptide having thermostability equivalent to thermostability of a polypeptide having an amino acid sequence shown in SEQ ID NO: 1 or 2; and (3) a polypeptide having an amino acid sequence having a sequence identity to an amino acid sequence shown in SEQ ID NO: 1 or 2 of 76% or more, the polypeptide having thermostability equivalent to thermostability of a polypeptide having an amino acid sequence shown in SEQ ID NO: 1 or 2, this technical feature is not a special technical feature as it does not make a contribution over the prior art in view of Zimmermann et al. (UniProt accession no. A0A2S9CPY3, see sequence search result 1 from 20251201_132705_us-18-037-934-1.rup, available in SCV, which has been copied/pasted below for Applicants’ convenience).
Zimmermann et al. teach a polypeptide having 99.2% sequence identity to Applicants’ SEQ ID NO: 1, which meets the limitation of claim 1 (2) and (3), and thus, the shared technical feature of the groups is not a “special technical feature”, unity of invention between the groups does not exist.
RESULT 1
A0A2S9CPY3_CHRCI
ID A0A2S9CPY3_CHRCI Unreviewed; 319 AA.
AC A0A2S9CPY3;
DT 18-JUL-2018, integrated into UniProtKB/TrEMBL.
DT 18-JUL-2018, sequence version 1.
DT 08-OCT-2025, entry version 14.
DE RecName: Full=Protein glutaminase domain-containing protein {ECO:0000259|Pfam:PF18626};
GN ORFNames=CQ022_17855 {ECO:0000313|EMBL:PRB82551.1}, CQ033_16750
GN {ECO:0000313|EMBL:PRB88926.1};
OS Chryseobacterium culicis.
OC Bacteria; Pseudomonadati; Bacteroidota; Flavobacteriia; Flavobacteriales;
OC Weeksellaceae; Chryseobacterium group; Chryseobacterium.
OX NCBI_TaxID=680127 {ECO:0000313|EMBL:PRB82551.1, ECO:0000313|Proteomes:UP000238534};
RN [1] {ECO:0000313|Proteomes:UP000238325, ECO:0000313|Proteomes:UP000238534}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=MYb25 {ECO:0000313|EMBL:PRB82551.1,
RC ECO:0000313|Proteomes:UP000238534}, and MYb44
RC {ECO:0000313|EMBL:PRB88926.1, ECO:0000313|Proteomes:UP000238325};
RA Zimmermann J., Obeng N., Yang W., Obeng O., Kissoyan K., Pees B.,
RA Dirksen P., Hoppner M., Franke A., Rosenstiel P., Leippe M., Dierking K.,
RA Kaleta C., Schulenburg H.;
RT "Genomic, metabolic, and phenotypic characteristics of bacterial isolates
RT from the natural microbiome of the model nematode Caenorhabditis elegans.";
RL Submitted (SEP-2017) to the EMBL/GenBank/DDBJ databases.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:PRB82551.1}.
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DR EMBL; PCPP01000003; PRB82551.1; -; Genomic_DNA.
DR EMBL; PCPH01000004; PRB88926.1; -; Genomic_DNA.
DR RefSeq; WP_105683660.1; NZ_JBBGZD010000003.1.
DR AlphaFoldDB; A0A2S9CPY3; -.
DR OrthoDB; 8417456at2; -.
DR Proteomes; UP000238325; Unassembled WGS sequence.
DR Proteomes; UP000238534; Unassembled WGS sequence.
DR Gene3D; 2.40.50.340; -; 1.
DR Gene3D; 3.10.620.30; -; 1.
DR InterPro; IPR041325; Gln_deamidase_2.
DR NCBIfam; NF040782; PG_glutam_Chrys; 1.
DR Pfam; PF18626; Gln_deamidase_2; 1.
PE 4: Predicted;
KW Reference proteome {ECO:0000313|Proteomes:UP000238325};
KW Signal {ECO:0000256|SAM:SignalP}.
FT SIGNAL 1..21
FT /evidence="ECO:0000256|SAM:SignalP"
FT CHAIN 22..319
FT /note="Protein glutaminase domain-containing protein"
FT /evidence="ECO:0000256|SAM:SignalP"
FT /id="PRO_5015407182"
FT DOMAIN 146..254
FT /note="Protein glutaminase"
FT /evidence="ECO:0000259|Pfam:PF18626"
SQ SEQUENCE 319 AA; 34739 MW; 939C596E4AFEE2CD CRC64;
Query Match 99.2%; Score 1651; Length 319;
Best Local Similarity 99.1%;
Matches 316; Conservative 1; Mismatches 2; Indels 0; Gaps 0;
Qy 1 MKKFLLSMMVFVTMLSFNACSDSAANQDPNLVAKESNEIAMKDFGKTVPVGIEKEEGKFK 60
||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||
Db 1 MKKFLLSMMVFVTMLSFNACSDSGANQDPNLVAKESNEIAMKDFGKTVPVGIEKEEGKFK 60
Qy 61 VSFMVSAQPYHIKDSKENAGYISMIRQAVENETPVHIFLKTNTTEIAKVDKPTDDDIRYF 120
||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||
Db 61 VSFMVSAQPYHIKDSKENAGYISMIRQAVENETPVHIFLKTNTNEIAKVDKPTDDDIRYF 120
Qy 121 KSVFNKEERGDSKKAVSVIPNLATLNSLFTQIKNQACGTSTASSPCITFRYPVDGCYARA 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 KSVFNKEERGDSKKAVSVIPNLATLNSLFTQIKNQACGTSTASSPCITFRYPVDGCYARA 180
Qy 181 HKMRQILLNAGYDCEKQFVYGNLRASTGTCCVSWVYHVAILVSFKNASGIVEKRIIDPSL 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 HKMRQILLNAGYDCEKQFVYGNLRASTGTCCVSWVYHVAILVSFKNASGIVEKRIIDPSL 240
Qy 241 FSSGPVTDAAWRAACTNTSCGSASVSSYANTAGNVYYRSPSGSLLYDNNYVNTNCVLNIF 300
|||||||||||||||||||||||||||:||||||||||||||||||||||||||||||||
Db 241 FSSGPVTDAAWRAACTNTSCGSASVSSFANTAGNVYYRSPSGSLLYDNNYVNTNCVLNIF 300
Qy 301 SSLSGCSPSPAPSVASCGF 319
|||||||||||||||||||
Db 301 SSLSGCSPSPAPSVASCGF 319
The examiner has required restriction between product and process claims. Where applicant elects claims directed to the product, and the product claims are subsequently found allowable, withdrawn process claims that depend from or otherwise require all the limitations of the allowable product claim will be considered for rejoinder. All claims directed to a nonelected process invention must require all the limitations of an allowable product claim for that process invention to be rejoined.
In the event of rejoinder, the requirement for restriction between the product claims and the rejoined process claims will be withdrawn, and the rejoined process claims will be fully examined for patentability in accordance with 37 CFR 1.104. Thus, to be allowable, the rejoined claims must meet all criteria for patentability including the requirements of 35 U.S.C. 101, 102, 103 and 112. Until all claims to the elected product are found allowable, an otherwise proper restriction requirement between product claims and process claims may be maintained. Withdrawn process claims that are not commensurate in scope with an allowable product claim will not be rejoined. See MPEP § 821.04(b). Additionally, in order to retain the right to rejoinder in accordance with the above policy, applicant is advised that the process claims should be amended during prosecution to require the limitations of the product claims. Failure to do so may result in a loss of the right to rejoinder. Further, note that the prohibition against double patenting rejections of 35 U.S.C. 121 does not apply where the restriction requirement is withdrawn by the examiner before the patent issues. See MPEP § 804.01.
Applicant is advised that the reply to this requirement to be complete must include (i) an election of a invention to be examined even though the requirement may be traversed (37 CFR 1.143) and (ii) identification of the claims encompassing the elected invention.
The election of an invention may be made with or without traverse. To reserve a right to petition, the election must be made with traverse. If the reply does not distinctly and specifically point out supposed errors in the restriction requirement, the election shall be treated as an election without traverse. Traversal must be presented at the time of election in order to be considered timely. Failure to timely traverse the requirement will result in the loss of right to petition under 37 CFR 1.144. If claims are added after the election, applicant must indicate which of these claims are readable upon the elected invention.
Should applicant traverse on the ground that the inventions are not patentably distinct, applicant should submit evidence or identify such evidence now of record showing the inventions to be obvious variants or clearly admit on the record that this is the case. In either instance, if the examiner finds one of the inventions unpatentable over the prior art, the evidence or admission may be used in a rejection under 35 U.S.C. 103(a) of the other invention.
Telephonic Election
The attorney of record, Raymond Smith, telephonically elected on 12/05/2025 without traverse of Group I, claims 1 and 6-7.
Claims 2-5 and 8-9 are withdrawn from further consideration by the Examiner, 37 CFR 1.142(b) as being drawn to a non-elected invention.
For the reasons provided above, this restriction requirement is deemed proper, and therefore, it is made final.
Priority
The instant application is the 371 national stage entry of PCT/JP2021/042625, filed on 11/19/2021.
Acknowledgment is made of applicant's claim for foreign priority under 35 U.S.C. 119(a)-(d) to a foreign patent application JAPAN JP2020-193671 filed without English translation on 11/20/2020.
Information Disclosure Statement
The information disclosure statements (IDS) submitted on 05/19/2023, 12/31/2024, 07/15/2025 and 09/15/2025. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statements are being considered by the examiner.
Claim Objections
Claim 1 is objected to because of the following informalities:
Claim 1 is objected to because the recitation of “shown in” can be substantially improved grammar. The Examiner suggests replacing the noted phrase with “of”.
Appropriate correction is required.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1 and 6-7 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (i.e., a natural phenomenon) without significantly more.
Analysis of subject-matter eligibility under 35 U.S.C. § 101 requires consideration of the following steps:
(1) whether the claim is directed to one of the four categories recited in §101 (process, machine, manufacture or composition of matter);
(Revised 2A - Prong 1) do the claims recite an abstract idea (mathematical concepts, mental processes or method of organizing human activity), law of nature or natural phenomenon;
(Revised 2A - Prong 2) do the claims recite additional elements that integrate the judicial exception into a practical application; and
(2B) whether the claim as a whole recites something that amounts to significantly more than the judicial exception. (See 2019 Revised Patent Subject Matter Eligibility Guidance (2019 PEG))
Question 1: Yes; the claims are directed to a composition of matter.
Question 2A – Prong 1: Yes, the claims recite a natural phenomenon, namely, a naturally occurring polypeptide.
Question 2A – Prong 2: No, the claims do not recite anything additional which integrate the naturally occurring polypeptide into a practical application. It is noted, SEQ ID NOs: 1 and 2 are naturally glutaminases derived from Chryseobacterium sp. strain 57594 and strain 61798. There is nothing in the claims and specification which differentiates these naturally occurring enzymes in terms of structure and/or function from the naturally occurring protein-glutaminases found in Chryseobacterium sp. strain 57594 and strain 61798. Thus, there is ultimately nothing in the claims which amounts to significantly more or significantly different from those protein-gIlutaminases found in nature. It is noted by the Examiner that even when there are some insertions, deletions and substitutions, especially with respect to parts (b) and (c) of claim 1, the end result is naturally occurring enzymes. For instance, the sequence search results of SEQ ID NOs: 1 and 2 disclose that a naturally occurring protein-glutaminase having 99.2% or 97.9% sequence identity to SEQ ID NO: 1 or SEQ ID NO: 2, respectively as shown below.
(copied/pasted from Sequence Search Result 20251201_132705_us-18-037-934-1.rup, available in SCV)
RESULT 1
A0A2S9CPY3_CHRCI
ID A0A2S9CPY3_CHRCI Unreviewed; 319 AA.
AC A0A2S9CPY3;
DT 18-JUL-2018, integrated into UniProtKB/TrEMBL.
DT 18-JUL-2018, sequence version 1.
DT 08-OCT-2025, entry version 14.
DE RecName: Full=Protein glutaminase domain-containing protein {ECO:0000259|Pfam:PF18626};
GN ORFNames=CQ022_17855 {ECO:0000313|EMBL:PRB82551.1}, CQ033_16750
GN {ECO:0000313|EMBL:PRB88926.1};
OS Chryseobacterium culicis.
OC Bacteria; Pseudomonadati; Bacteroidota; Flavobacteriia; Flavobacteriales;
OC Weeksellaceae; Chryseobacterium group; Chryseobacterium.
OX NCBI_TaxID=680127 {ECO:0000313|EMBL:PRB82551.1, ECO:0000313|Proteomes:UP000238534};
RN [1] {ECO:0000313|Proteomes:UP000238325, ECO:0000313|Proteomes:UP000238534}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=MYb25 {ECO:0000313|EMBL:PRB82551.1,
RC ECO:0000313|Proteomes:UP000238534}, and MYb44
RC {ECO:0000313|EMBL:PRB88926.1, ECO:0000313|Proteomes:UP000238325};
RA Zimmermann J., Obeng N., Yang W., Obeng O., Kissoyan K., Pees B.,
RA Dirksen P., Hoppner M., Franke A., Rosenstiel P., Leippe M., Dierking K.,
RA Kaleta C., Schulenburg H.;
RT "Genomic, metabolic, and phenotypic characteristics of bacterial isolates
RT from the natural microbiome of the model nematode Caenorhabditis elegans.";
RL Submitted (SEP-2017) to the EMBL/GenBank/DDBJ databases.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:PRB82551.1}.
CC ---------------------------------------------------------------------------
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DR EMBL; PCPP01000003; PRB82551.1; -; Genomic_DNA.
DR EMBL; PCPH01000004; PRB88926.1; -; Genomic_DNA.
DR RefSeq; WP_105683660.1; NZ_JBBGZD010000003.1.
DR AlphaFoldDB; A0A2S9CPY3; -.
DR OrthoDB; 8417456at2; -.
DR Proteomes; UP000238325; Unassembled WGS sequence.
DR Proteomes; UP000238534; Unassembled WGS sequence.
DR Gene3D; 2.40.50.340; -; 1.
DR Gene3D; 3.10.620.30; -; 1.
DR InterPro; IPR041325; Gln_deamidase_2.
DR NCBIfam; NF040782; PG_glutam_Chrys; 1.
DR Pfam; PF18626; Gln_deamidase_2; 1.
PE 4: Predicted;
KW Reference proteome {ECO:0000313|Proteomes:UP000238325};
KW Signal {ECO:0000256|SAM:SignalP}.
FT SIGNAL 1..21
FT /evidence="ECO:0000256|SAM:SignalP"
FT CHAIN 22..319
FT /note="Protein glutaminase domain-containing protein"
FT /evidence="ECO:0000256|SAM:SignalP"
FT /id="PRO_5015407182"
FT DOMAIN 146..254
FT /note="Protein glutaminase"
FT /evidence="ECO:0000259|Pfam:PF18626"
SQ SEQUENCE 319 AA; 34739 MW; 939C596E4AFEE2CD CRC64;
Query Match 99.2%; Score 1651; Length 319;
Best Local Similarity 99.1%;
Matches 316; Conservative 1; Mismatches 2; Indels 0; Gaps 0;
Qy 1 MKKFLLSMMVFVTMLSFNACSDSAANQDPNLVAKESNEIAMKDFGKTVPVGIEKEEGKFK 60
||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||
Db 1 MKKFLLSMMVFVTMLSFNACSDSGANQDPNLVAKESNEIAMKDFGKTVPVGIEKEEGKFK 60
Qy 61 VSFMVSAQPYHIKDSKENAGYISMIRQAVENETPVHIFLKTNTTEIAKVDKPTDDDIRYF 120
||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||
Db 61 VSFMVSAQPYHIKDSKENAGYISMIRQAVENETPVHIFLKTNTNEIAKVDKPTDDDIRYF 120
Qy 121 KSVFNKEERGDSKKAVSVIPNLATLNSLFTQIKNQACGTSTASSPCITFRYPVDGCYARA 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 KSVFNKEERGDSKKAVSVIPNLATLNSLFTQIKNQACGTSTASSPCITFRYPVDGCYARA 180
Qy 181 HKMRQILLNAGYDCEKQFVYGNLRASTGTCCVSWVYHVAILVSFKNASGIVEKRIIDPSL 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 HKMRQILLNAGYDCEKQFVYGNLRASTGTCCVSWVYHVAILVSFKNASGIVEKRIIDPSL 240
Qy 241 FSSGPVTDAAWRAACTNTSCGSASVSSYANTAGNVYYRSPSGSLLYDNNYVNTNCVLNIF 300
|||||||||||||||||||||||||||:||||||||||||||||||||||||||||||||
Db 241 FSSGPVTDAAWRAACTNTSCGSASVSSFANTAGNVYYRSPSGSLLYDNNYVNTNCVLNIF 300
Qy 301 SSLSGCSPSPAPSVASCGF 319
|||||||||||||||||||
Db 301 SSLSGCSPSPAPSVASCGF 319
(copied/pasted from Sequence Search Result 20251201_132705_us-18-037-934-2.rup, available in SCV)
RESULT 1
A0ABX9X9X8_9FLAO
ID A0ABX9X9X8_9FLAO Unreviewed; 319 AA.
AC A0ABX9X9X8;
DT 08-OCT-2025, integrated into UniProtKB/TrEMBL.
DT 08-OCT-2025, sequence version 1.
DT 08-OCT-2025, entry version 1.
DE SubName: Full=Uncharacterized protein {ECO:0000313|EMBL:ROH95086.1};
GN ORFNames=EGI15_04285 {ECO:0000313|EMBL:ROH95086.1};
OS Chryseobacterium cucumeris.
OC Bacteria; Pseudomonadati; Bacteroidota; Flavobacteriia; Flavobacteriales;
OC Weeksellaceae; Chryseobacterium group; Chryseobacterium.
OX NCBI_TaxID=1813611 {ECO:0000313|EMBL:ROH95086.1, ECO:0000313|Proteomes:UP000281899};
RN [1] {ECO:0000313|EMBL:ROH95086.1, ECO:0000313|Proteomes:UP000281899}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=G0235 {ECO:0000313|EMBL:ROH95086.1,
RC ECO:0000313|Proteomes:UP000281899};
RA Nicholson A.C., Gulvik C.A., Whitney A.M., Humrighouse B.W., Bell M.,
RA Holmes B., Steigerwalt A., Villarma A., Sheth M., Batra D., Pryor J.,
RA Bernardet J.-F., Hugo C., Kampfer P., Newman J., Mcquiston J.R.;
RT "Proposal to divide the Flavobacteriaceae and reorganize its genera based
RT on Amino Acid Identity values calculated from whole genome sequences.";
RL Submitted (NOV-2018) to the EMBL/GenBank/DDBJ databases.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:ROH95086.1}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; RJTW01000003; ROH95086.1; -; Genomic_DNA.
DR Proteomes; UP000281899; Unassembled WGS sequence.
PE 4: Predicted;
KW Reference proteome {ECO:0000313|Proteomes:UP000281899}.
SQ SEQUENCE 319 AA; 34587 MW; A4D2CB204924F21F CRC64;
Query Match 97.9%; Score 1618; Length 319;
Best Local Similarity 97.2%;
Matches 310; Conservative 7; Mismatches 2; Indels 0; Gaps 0;
Qy 1 MKKFLLSMMVFVTVLSFNSCSDSSANQDPNLVAKESNEIAMKDFGKTVPVGIEKEDGKFK 60
|||||||||||||||| ||||||:||||||||||||||||||||||||||||||||||||
Db 1 MKKFLLSMMVFVTVLSVNSCSDSAANQDPNLVAKESNEIAMKDFGKTVPVGIEKEDGKFK 60
Qy 61 VSFIVSAQPYQIKDTKENAGYISMIKEAVENETPVQVFLKANSNEIAKVDKATADDIRYF 120
|||:||||||||||||||||:||||||||||||||||||| ||||||||:||||||||||
Db 61 VSFMVSAQPYQIKDTKENAGFISMIKEAVENETPVQVFLKVNSNEIAKVEKATADDIRYF 120
Qy 121 KSVFNKEERGDSRKAVSVIPNLATLNSLFTQIKNQACGTSTASSPCITFRYPVDGCYARA 180
|:||||||||||:|||||||||||||||||||||||||||||||||||||||||||||||
Db 121 KTVFNKEERGDSKKAVSVIPNLATLNSLFTQIKNQACGTSTASSPCITFRYPVDGCYARA 180
Qy 181 HKMRQILLNAGYDCEKQFVYGNLRASTGTCCVSWVYHVAILVSFKNASGIVEKRIIDPSL 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 HKMRQILLNAGYDCEKQFVYGNLRASTGTCCVSWVYHVAILVSFKNASGIVEKRIIDPSL 240
Qy 241 FSSGPVTDTAWRAACTNTSCGSASVSSYANTAGNVYYRSPSGSLLYDNNYVNTNCVLNIF 300
||||||||:|||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 FSSGPVTDSAWRAACTNTSCGSASVSSYANTAGNVYYRSPSGSLLYDNNYVNTNCVLNIF 300
Qy 301 SSLSGCSPSPAPSVASCGF 319
|||||||||||||||||||
Db 301 SSLSGCSPSPAPSVASCGF 319
Question 2B: As noted in answering that of 2A – Prong 2 above, there is nothing in the claims which amounts to significantly more in terms of structure and/or function and the claims read on naturally occurring protein-glutaminases. Thus, the claims are drawn to a judicial exception, namely, a naturally occurring product.
Claim Rejections - 35 U.S.C. § 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.
Claim 1 is rejected under 35 U.S.C. § 112, second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which applicant regards as the invention.
Claim 1 recites the phrase “an amino acid sequence” which is unclear. The reason is that the noted phrase can mean the full-length or any fragment or sequence found within SEQ ID NO: 1 and 2. The Examiner suggests replacing the noted phrase with ---the amino acid sequence---.
The following is a quotation 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.
Claims 1 and 6-7 are rejected under 35 U.S.C. § 112(a), written description, 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(s), at the time the application was filed, had possession of the claimed invention.
The instant claims are directed to a protein-glutaminase comprising a polypeptide shown in any one of the following (1) to (3): (1) a polypeptide having an amino acid sequence shown in SEQ ID NO: 1 or 2; (2) a polypeptide having an amino acid sequence obtained by substituting, adding, inserting, or deleting one or more amino acid residues in an amino acid sequence shown in SEQ ID NO: 1 or 2, the polypeptide having thermostability equivalent to thermostability of a polypeptide having an amino acid sequence shown in SEQ ID NO: 1 or 2; and (3) a polypeptide having an amino acid sequence having a sequence identity to an amino acid sequence shown in SEQ ID NO: 1 or 2 of 76% or more, the polypeptide having thermostability equivalent to thermostability of a polypeptide having an amino acid sequence shown in SEQ ID NO: 1 or 2.
To satisfy the written description aspect of 35 U.S.C. § 112(a) for a claimed genus of [compositions or methods], it must be clear that: (1) the identifying characteristics of the claimed [compositions or methods] have been disclosed, e.g., structure, physical and/or chemical characteristics, functional characteristics when coupled with a known or disclosed correlation between function and structure, or a combination of these; and (2) a representative number of species within the genus must be disclosed.
The Court of Appeals for the Federal Circuit has recently 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 be structure, formula [or] chemical name,’ of the claimed subject matter sufficient to distinguish it from other materials.” University of California v. Eli Lilly and Co., 1997 U.S. App. LEXIS 18221, at *23, quoting Fiers v. Revel, 25 USPQ2d 1601, 1606 (Fed. Cir. 1993) (bracketed material in original). To fully describe a genus of genetic material, which is a chemical compound, applicants must (1) fully describe at least one species of the claimed genus sufficient to represent said genus whereby a skilled artisan, in view of the prior art, could predict the structure of other species encompassed by the claimed genus and (2) identify the common characteristics of the claimed molecules, e.g., structure, physical and/or chemical characteristics, functional characteristics when coupled with a known or disclosed correlation between function and structure, or a combination of these (paraphrased from Enzo Biochemical Inc. v. Gen-Probe Inc. (CAFC (2002) 63 USPQ2d 1609).
The specification discloses two representative species of a protein-glutaminase, SEQ ID NOs: 1 and 2. However, these two disclosed species fail to provide adequate written description for a genus of (2) polypeptides having any amino acid sequence obtained by substituting, adding, inserting, or deleting one or more amino acid residues in an amino acid sequence shown in SEQ ID NO: 1 or 2, the polypeptide having thermostability equivalent to thermostability of a polypeptide having an amino acid sequence shown in SEQ ID NO: 1 or 2; and (3) polypeptides having an amino acid sequence having a sequence identity to an amino acid sequence shown in SEQ ID NO: 1 or 2 of 76% or more, the polypeptides having thermostability equivalent to thermostability of a polypeptide having an amino acid sequence shown in SEQ ID NO: 1 or 2 (italicized for added emphasis), which encompasses any polypeptide obtained by substituting, adding, inserting, or deleting any number of amino acid residues in an amino acid sequence shown in SEQ ID NO: 1 or 2, or any polypeptide sequence having at least 76% sequence identity to SEQ ID NO: 1 or 2, while maintaining the thermostability of SEQ ID NO: 1 or 2. However, the instant specification fails to describe any identification of structural characteristics or properties of [1] any polypeptides that can be obtained by substituting, adding, inserting, or deleting any number of amino acid residues in an amino acid sequence shown in SEQ ID NO: 1 or 2, or [2] amino acids which can be modified in any polypeptides having at least 76% sequence identity to SEQ ID NO: 1 or 2, such that the thermostability of SEQ ID NO: 1 or 2 is maintained. Therefore, the claimed genus of polypeptides encompasses widely variant species, having essentially any structure. While M.P.E.P. section 2163 acknowledges that a single species can describe a genus, it also acknowledges that for a genus that encompasses widely variant species, disclosure of a single species within the genus fails to adequately describe all members of the genus. Please refer to the M.P.E.P. section 2163.05 [R-7.2022] under I, B for more details with respect to sufficient number of representative species that should be disclosed to describe a widely variant genus.
Given the lack of additional representative species of a claimed genus of polypeptides as encompassed by the claims, Applicants have failed to sufficiently describe the claimed invention, in such full, clear, concise, and exact terms that a skilled artisan would recognize Applicants were in possession of the claimed invention.
Applicant is referred to the revised guidelines concerning compliance with the written description requirement of U.S.C. 112(a) published in the Official Gazette and also available at www.uspto.gov.
Claim Rejections - 35 U.S.C. § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale or otherwise available to the public before the effective filing date of the claimed invention.
Claims 1 and 6-7 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Zimmermann et al. (UniProt accession no. A0A2S9CPY3, see sequence search result 1 from 20251201_132705_us-18-037-934-1.rup, available in SCV, which has been copied/pasted below for Applicants’ convenience).
The instant claims are drawn to a protein-glutaminase comprising a polypeptide shown in any one of the following (1) to (3): (1) a polypeptide having an amino acid sequence shown in SEQ ID NO: 1 or 2; (2) a polypeptide having an amino acid sequence obtained by substituting, adding, inserting, or deleting one or more amino acid residues in an amino acid sequence shown in SEQ ID NO: 1 or 2, the polypeptide having thermostability equivalent to thermostability of a polypeptide having an amino acid sequence shown in SEQ ID NO: 1 or 2; and (3) a polypeptide having an amino acid sequence having a sequence identity to an amino acid sequence shown in SEQ ID NO: 1 or 2 of 76% or more, the polypeptide having thermostability equivalent to thermostability of a polypeptide having an amino acid sequence shown in SEQ ID NO: 1 or 2.
Zimmermann et al. teach a polypeptide having 99.2% sequence identity to Applicants’ SEQ ID NO: 1 (see below sequence search result), which meets the limitation of claims 1, 6 and 7. Therefore, the claimed invention is anticipated by teachings of Zimmermann et al.
RESULT 1
A0A2S9CPY3_CHRCI
ID A0A2S9CPY3_CHRCI Unreviewed; 319 AA.
AC A0A2S9CPY3;
DT 18-JUL-2018, integrated into UniProtKB/TrEMBL.
DT 18-JUL-2018, sequence version 1.
DT 08-OCT-2025, entry version 14.
DE RecName: Full=Protein glutaminase domain-containing protein {ECO:0000259|Pfam:PF18626};
GN ORFNames=CQ022_17855 {ECO:0000313|EMBL:PRB82551.1}, CQ033_16750
GN {ECO:0000313|EMBL:PRB88926.1};
OS Chryseobacterium culicis.
OC Bacteria; Pseudomonadati; Bacteroidota; Flavobacteriia; Flavobacteriales;
OC Weeksellaceae; Chryseobacterium group; Chryseobacterium.
OX NCBI_TaxID=680127 {ECO:0000313|EMBL:PRB82551.1, ECO:0000313|Proteomes:UP000238534};
RN [1] {ECO:0000313|Proteomes:UP000238325, ECO:0000313|Proteomes:UP000238534}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=MYb25 {ECO:0000313|EMBL:PRB82551.1,
RC ECO:0000313|Proteomes:UP000238534}, and MYb44
RC {ECO:0000313|EMBL:PRB88926.1, ECO:0000313|Proteomes:UP000238325};
RA Zimmermann J., Obeng N., Yang W., Obeng O., Kissoyan K., Pees B.,
RA Dirksen P., Hoppner M., Franke A., Rosenstiel P., Leippe M., Dierking K.,
RA Kaleta C., Schulenburg H.;
RT "Genomic, metabolic, and phenotypic characteristics of bacterial isolates
RT from the natural microbiome of the model nematode Caenorhabditis elegans.";
RL Submitted (SEP-2017) to the EMBL/GenBank/DDBJ databases.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:PRB82551.1}.
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DR EMBL; PCPP01000003; PRB82551.1; -; Genomic_DNA.
DR EMBL; PCPH01000004; PRB88926.1; -; Genomic_DNA.
DR RefSeq; WP_105683660.1; NZ_JBBGZD010000003.1.
DR AlphaFoldDB; A0A2S9CPY3; -.
DR OrthoDB; 8417456at2; -.
DR Proteomes; UP000238325; Unassembled WGS sequence.
DR Proteomes; UP000238534; Unassembled WGS sequence.
DR Gene3D; 2.40.50.340; -; 1.
DR Gene3D; 3.10.620.30; -; 1.
DR InterPro; IPR041325; Gln_deamidase_2.
DR NCBIfam; NF040782; PG_glutam_Chrys; 1.
DR Pfam; PF18626; Gln_deamidase_2; 1.
PE 4: Predicted;
KW Reference proteome {ECO:0000313|Proteomes:UP000238325};
KW Signal {ECO:0000256|SAM:SignalP}.
FT SIGNAL 1..21
FT /evidence="ECO:0000256|SAM:SignalP"
FT CHAIN 22..319
FT /note="Protein glutaminase domain-containing protein"
FT /evidence="ECO:0000256|SAM:SignalP"
FT /id="PRO_5015407182"
FT DOMAIN 146..254
FT /note="Protein glutaminase"
FT /evidence="ECO:0000259|Pfam:PF18626"
SQ SEQUENCE 319 AA; 34739 MW; 939C596E4AFEE2CD CRC64;
Query Match 99.2%; Score 1651; Length 319;
Best Local Similarity 99.1%;
Matches 316; Conservative 1; Mismatches 2; Indels 0; Gaps 0;
Qy 1 MKKFLLSMMVFVTMLSFNACSDSAANQDPNLVAKESNEIAMKDFGKTVPVGIEKEEGKFK 60
||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||
Db 1 MKKFLLSMMVFVTMLSFNACSDSGANQDPNLVAKESNEIAMKDFGKTVPVGIEKEEGKFK 60
Qy 61 VSFMVSAQPYHIKDSKENAGYISMIRQAVENETPVHIFLKTNTTEIAKVDKPTDDDIRYF 120
||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||
Db 61 VSFMVSAQPYHIKDSKENAGYISMIRQAVENETPVHIFLKTNTNEIAKVDKPTDDDIRYF 120
Qy 121 KSVFNKEERGDSKKAVSVIPNLATLNSLFTQIKNQACGTSTASSPCITFRYPVDGCYARA 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 KSVFNKEERGDSKKAVSVIPNLATLNSLFTQIKNQACGTSTASSPCITFRYPVDGCYARA 180
Qy 181 HKMRQILLNAGYDCEKQFVYGNLRASTGTCCVSWVYHVAILVSFKNASGIVEKRIIDPSL 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 HKMRQILLNAGYDCEKQFVYGNLRASTGTCCVSWVYHVAILVSFKNASGIVEKRIIDPSL 240
Qy 241 FSSGPVTDAAWRAACTNTSCGSASVSSYANTAGNVYYRSPSGSLLYDNNYVNTNCVLNIF 300
|||||||||||||||||||||||||||:||||||||||||||||||||||||||||||||
Db 241 FSSGPVTDAAWRAACTNTSCGSASVSSFANTAGNVYYRSPSGSLLYDNNYVNTNCVLNIF 300
Qy 301 SSLSGCSPSPAPSVASCGF 319
|||||||||||||||||||
Db 301 SSLSGCSPSPAPSVASCGF 319
Claims 1 and 6-7 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by de Groot (UniProt accession no. A0A1H6I911, see sequence search result 3 copied/pasted from Sequence Search Result 20251201_132705_us-18-037-934-2.rup, available in SCV).
The instant claims are drawn to a protein-glutaminase comprising a polypeptide shown in any one of the following (1) to (3): (1) a polypeptide having an amino acid sequence shown in SEQ ID NO: 1 or 2; (2) a polypeptide having an amino acid sequence obtained by substituting, adding, inserting, or deleting one or more amino acid residues in an amino acid sequence shown in SEQ ID NO: 1 or 2, the polypeptide having thermostability equivalent to thermostability of a polypeptide having an amino acid sequence shown in SEQ ID NO: 1 or 2; and (3) a polypeptide having an amino acid sequence having a sequence identity to an amino acid sequence shown in SEQ ID NO: 1 or 2 of 76% or more, the polypeptide having thermostability equivalent to thermostability of a polypeptide having an amino acid sequence shown in SEQ ID NO: 1 or 2.
de Groot teaches a polypeptide having 96.3% sequence identity to Applicants’ SEQ ID NO: 2 (see below sequence search result), which meets the limitation of claims 1, 6 and 7. Therefore, the claimed invention is anticipated by teachings of de Groot.
RESULT 3
A0A1H6I911_CHRCI
ID A0A1H6I911_CHRCI Unreviewed; 312 AA.
AC A0A1H6I911;
DT 22-NOV-2017, integrated into UniProtKB/TrEMBL.
DT 22-NOV-2017, sequence version 1.
DT 02-APR-2025, entry version 20.
DE RecName: Full=Protein glutaminase domain-containing protein {ECO:0000259|Pfam:PF18626};
GN ORFNames=SAMN05421593_4276 {ECO:0000313|EMBL:SEH45085.1};
OS Chryseobacterium culicis.
OC Bacteria; Pseudomonadati; Bacteroidota; Flavobacteriia; Flavobacteriales;
OC Weeksellaceae; Chryseobacterium group; Chryseobacterium.
OX NCBI_TaxID=680127 {ECO:0000313|EMBL:SEH45085.1, ECO:0000313|Proteomes:UP000198561};
RN [1] {ECO:0000313|EMBL:SEH45085.1, ECO:0000313|Proteomes:UP000198561}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 23031 {ECO:0000313|EMBL:SEH45085.1,
RC ECO:0000313|Proteomes:UP000198561};
RA de Groot N.N.;
RL Submitted (OCT-2016) to the EMBL/GenBank/DDBJ databases.
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CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
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DR EMBL; FNWQ01000007; SEH45085.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A1H6I911; -.
DR Proteomes; UP000198561; Unassembled WGS sequence.
DR Gene3D; 2.40.50.340; -; 1.
DR Gene3D; 3.10.620.30; -; 1.
DR InterPro; IPR041325; Gln_deamidase_2.
DR NCBIfam; NF040782; PG_glutam_Chrys; 1.
DR Pfam; PF18626; Gln_deamidase_2; 1.
PE 4: Predicted;
FT DOMAIN 139..247
FT /note="Protein glutaminase"
FT /evidence="ECO:0000259|Pfam:PF18626"
SQ SEQUENCE 312 AA; 33816 MW; 8F837575DC5F7DE4 CRC64;
Query Match 96.3%; Score 1592; Length 312;
Best Local Similarity 96.8%;
Matches 302; Conservative 8; Mismatches 2; Indels 0; Gaps 0;
Qy 8 MMVFVTVLSFNSCSDSSANQDPNLVAKESNEIAMKDFGKTVPVGIEKEDGKFKVSFIVSA 67
||||||:||||:|||||||||||||||||||:||||||||||||||||||||:|||:|||
Db 1 MMVFVTMLSFNACSDSSANQDPNLVAKESNEVAMKDFGKTVPVGIEKEDGKFRVSFMVSA 60
Qy 68 QPYQIKDTKENAGYISMIKEAVENETPVQVFLKANSNEIAKVDKATADDIRYFKSVFNKE 127
||| :||||||||||||||||||||||||:||||||||||||||||||||||||||||||
Db 61 QPYHLKDTKENAGYISMIKEAVENETPVQIFLKANSNEIAKVDKATADDIRYFKSVFNKE 120
Qy 128 ERGDSRKAVSVIPNLATLNSLFTQIKNQACGTSTASSPCITFRYPVDGCYARAHKMRQIL 187
|||||:||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 ERGDSKKAVSVIPNLATLNSLFTQIKNQACGTSTASSPCITFRYPVDGCYARAHKMRQIL 180
Qy 188 LNAGYDCEKQFVYGNLRASTGTCCVSWVYHVAILVSFKNASGIVEKRIIDPSLFSSGPVT 247
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 LNAGYDCEKQFVYGNLRASTGTCCVSWVYHVAILVSFKNASGIVEKRIIDPSLFSSGPVT 240
Qy 248 DTAWRAACTNTSCGSASVSSYANTAGNVYYRSPSGSLLYDNNYVNTNCVLNIFSSLSGCS 307
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 DTAWRAACTNTSCGSASVSSYANTAGNVYYRSPSGSLLYDNNYVNTNCVLNIFSSLSGCS 300
Qy 308 PSPAPSVASCGF 319
||||||| ||||
Db 301 PSPAPSVGSCGF 312
Conclusion
Claims 1 and 6-7 are rejected for the reasons as stated above. Applicants must respond to the objections/rejections in this Office action to be fully responsive in prosecution.
The instant Office action is non-final.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JAE W LEE whose telephone number is (571)272-9949. The examiner can normally be reached on M-F between 9:00-6:00.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Manjunath 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.
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/JAE W LEE/
Examiner, Art Unit 1656
/SUZANNE M NOAKES/Primary Examiner, Art Unit 1656