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 .
Status of the Claims
Claims 1, 3-10 and 12-19 are pending (claim set filed 05/05/2025). Claims 9, 10, 12 and 14-19 are withdrawn. Claims 2 and 11 are cancelled. Claims 1, 3-8 and 13 are amended.
Claims 1, 3-8 and 13 are examined on the merits herein.
Priority
This application is a CON of PCT/JP2020/035137 filed 09/16/2020.
Acknowledgment is made of applicant’s claim for foreign priority under 35 U.S.C. 119 (a)-(d) based on JAPAN 2019-168805 filed 09/17/2019. Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 02/11/2025 complies with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Withdrawal of Rejections
The response and amendment filed on 05/05/2025 are acknowledged. The Declaration under 37 C.F.R. 1.132 of Yosuke Masakari supporting amendment of claim 1 is acknowledged. All of the amendment and arguments have been thoroughly reviewed and considered.
For the purposes of clarity of the record, the reasons for the Examiner's withdrawal and/or maintaining if applicable, of the substantive or essential claim rejections are detailed directly below and/or in the Examiner's response to arguments section.
The previous claims 2-8, 11 and 13 objections have been withdrawn necessitated by amendment of claims 3-8 and 13 and cancellation of claims 2 and 11.
The previous claims 1-8, 11 and 13 rejections under 35 U.S.C. 112(b) have been withdrawn necessitated by amendment of claim 1 and cancellation of claims 2 and 11.
The previous claim 11 rejection under 35 U.S.C. 112(a) has been withdrawn necessitated by cancellation of claim 11.
The previous claims 1, 4 and 13 rejections under 35 U.S.C. 102 (a)(1), claims 1-4, 6, 8 and 11 rejections under 35 U.S.C. 102 (a)(1) and (a)(2) and claim 7 rejection under 35 U.S.C. 102 (a)(1) and (a) (2)/103 have been withdrawn necessitated by amendment of claim 1 and cancellation of claims 2 and 11.
New Rejections
Claim Rejections - 35 USC § 112
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 1, 3-8 and 13 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 applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
First Rejection
Claim 1 recites the limitation for the purified citrulline oxidoreductase to have at least 90% sequence identity with SEQ ID NO: 60. Claim 1 is interpreted as the method for quantifying citrulline in a sample comprising the citrulline oxidoreductase with the sequence 10% or less of which vary from SEQ ID NO: 60.
Thus, claim 1 broadly encompasses a genus of citrulline oxidoreductase, retaining functional activity and having 90% or more sequence identity to SEQ ID NO:60. This would represent a large pool of variant protein sequences for citrulline oxidoreductase that are functional. At the same time citrulline oxidoreductase can have 10% or less of sequences that can differ from SEQ ID NO:60 that represents 59 amino acid residues (from complete sequence of 590 amino acid residues). The Specification does not provide structure function correlation for citrulline oxidoreductase and does not describe domains and/or amino acid residues essential for citrulline oxidoreductase function and domain and/or amino acid residues which can be modified without loss of citrulline oxidoreductase function. The Specification provides examples of four citrulline oxidoreductases including citrulline oxidoreductase with SEQ ID NO: 60 with 67% or more sequence identity and several functionally active mutants for each citrulline oxidoreductase. However, examples of the domains or amino acid residues modification of which results in the loss of citrulline oxidoreductase function are not described.
Thus, one of ordinary skill in the art would not be able to identify without further testing which amino acid sequences that have at least 90% identity to SEQ ID NO:60 encode for functional citrulline oxidoreductase. One of ordinary skill in the art would conclude based on the lack of representative number of species and the lack of describing the domains or amino acid residues of SEQ ID NO: 60 critical for the function of citrulline oxidoreductase that the Applicant was not in possession of the claimed genus and the specification fails to satisfy the requirements of written description under 35 U.S.C. 112 (a).
Claims 3-8 and 13, dependent on claim 1, do not resolve the issue mentioned above and are rejected.
Second Rejection
Claim 7 is directed to citrulline oxidoreductase derived from Pseudomonas japonica, Pseudomonas putida or Pseudomonas mosselii. Claim 7 is dependent on claim1, which recites citrulline oxidoreductase with at least 90% sequence identity to SEQ ID NO: 60 and either having sequence of SEQ ID NO: 60 or recited mutations.
The specification describes the citrulline oxidoreductase with SEQ ID NO: 60 to derive from Pseudomonas sp. WCHPs060044 strain (paragraph 0038), however, does not provide information of Pseudomonas species. The specification describes three other citrulline oxidoreductases. The citrulline oxidoreductases with SEQ ID NO:1 and SEQ ID NO:81 are derived from Pseudomonas genus, however, species are not identified (paragraphs 0030 and 0041). The citrulline oxidoreductase with SEQ ID NO: 31 is derived from P. japonica (paragraph 0035). However, the sequence identity between SEQ ID NO:60 and SEQ ID NO: 31 is 86% which is lower than 90%. Therefore, the specification does not provide description for citrulline oxidoreductase derived from P. putida or P. mosselii and provides example of citrulline oxidoreductase derived P. japonica with less than 90% sequence identity to SEQ ID NO:60 that does not correspond to claim 7 limitation.
The prior art of Geueke (Geueke and Hummel, Enzyme and Microbial Technology, 2002, 31, 77-87) teaches L-amino acid oxidase from Rhodococcus opacus DSM 43250 with a very broad substrate specificity, that can oxidize citrulline (Abstract). However, no citrulline-specific amino acid oxidase was reported as evidenced by Yamamoto (Yamamoto et al. AMB Express, 2023, 13, 137, 1-9; p. 3, left column, 1st paragraph). Thus the prior art does not describe citrulline oxidoreductase from P. japonica, P. putida or P. mosselii.
Therefore, the citrulline oxidoreductase derived from P. japonica, P. putida or P. mosselii and having at least 90% sequence identity to SEQ ID NO: 60 is not described in the specification in such a way as to confirm to one skilled in the relevant art that the inventors, at the time the application was filed, had possession of the claimed invention.
Maintained/Modified/New Rejections
The following rejections are maintained and/or modified or newly added taking into consideration amendment to claim 1 filed on 05/05/2025.
Claim Rejections - 35 USC § 103
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claims 1, 3, 4, 6-8 and 13 are rejected under 35 U.S.C. 103 as being unpatentable over Asano (WO 2014129529 A1 on record in IDS) in view of NCBI WP_110972968.1 (NCBI, WP_110972968.1, 19-Jun-2018 [retrieved on 07/29/2025]. Retrieved from the Internet: <amine oxidoreductase [Pseudomonas sp. WCHPs060044] - Protein - NCBI>).
Regarding claim 1, Asano teaches L-arginine oxidase that can be used to measure L-arginine, a microorganism producing L-arginine oxidase and an enzyme sensor (Abstract). Asano provides example of measurement of arginine in plasma samples with purified L-arginine oxidase (lines 722-729). Asano discloses that L-arginine oxidase is produced by novel Pseudomonas sp. strain BYC41-1 and has sequence of SEQ ID NO: 2 (lines 364-366). Amino acid sequence of SEQ ID NO: 2 in Asano teaching is 100% identical to instant SEQ ID NO:1 for citrulline oxidoreductase derived from Pseudomonas sp. BYC41-1 strain as described in the specification (paragraph 0030).
MPEP 2112.01 states: “Products of identical chemical composition cannot have mutually exclusive properties." In re Spada, 911 F.2d 705, 709, 15 USPQ2d 1655, 1658 (Fed. Cir. 1990). A chemical composition and its properties are inseparable. Therefore, if the prior art teaches the identical chemical structure, the properties applicant discloses and/or claims are necessarily present.” Therefore, since L-arginine oxidase of Asano teaching has the same structure as disclosed citrulline oxidoreductase, it can be used for instant method for quantifying citrulline.
The SEQ ID NO:2 (line 170) of Asano teaching has 85.6% identity to instant SEQ ID NO: 60. However, Asano does not teach citrulline oxidoreductase with at least 90% sequence identity to SEQ ID NO:60 and either having SEQ ID NO:60 or recited mutations.
NCBI WP_110972968.1 teaches the sequence for amine oxidoreductase derived from Pseudomonas sp. WCHPs060044 which is 100% identical to SEQ ID NO:60. Besides the citrulline oxidoreductase with SEQ ID NO:60 is described in the specification as derived from the same strain, i.e. Pseudomonas sp. WCHPs060044 (paragraph 0038) as taught in NCBI WP_110972968.1. Therefore, the NCBI WP_110972968.1 teaches the citrulline oxidoreductase of claim 1.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine teachings of Asano and NCBI WP_110972968.1 and use citrulline oxidoreductase of NCBI WP_110972968.1 to quantify citrulline in a sample as described by Asano for quantification of L-arginine. One would have been motivated to do so since NCBI WP_110972968.1 provides sequence for citrulline oxidoreductase that inherently can oxidize citrulline and can be used for quantification of citrulline in the sample and Asano provides method of L-arginine quantification with the enzyme which can be applied for citrulline detection. A skilled artisan would have reasonably expected success in this combination because Asano and GenBank and NCBI WP_110972968.1 teach citrulline oxidoreductases with 85.6% identity derived from Pseudomonas.
Regarding claim 3, Asano teaches that the product of reaction, hydrogen peroxide can be measured with hydrogen peroxide detection electrode. Asano further describes electrode to have immobilized on glutaraldehyde peroxidase that reacts with hydrogen peroxide (lines 432-436). Asano mentions that L-arginine oxidase corresponding to citrulline oxidoreductase as described above can be immobilized on the surface of detection electrode to be used repeatedly (lines 484-486). Thus, Asano and NCBI WP_110972968.1 teachings render claim 3 obvious.
Regarding claim 4, Asano teaches that the product of the reaction is hydrogen peroxide that can be measured with peroxidase reaction comprising color-developing agent used as a peroxidase substrate (lines 420-428). Thus, Asano and NCBI WP_110972968.1 teachings render claim 4 obvious.
Regarding claim 6, Asano teaches L-arginine oxidase corresponding to citrulline oxidoreductase as described above to be derived from Pseudomonas sp. (lines 179-181) and WP_110972968.1 teaches sequence derived from Pseudomonas sp. Thus, Asano and NCBI WP_110972968.1 teachings render claim 6 obvious.
Regarding claim 7, Asano teaches that Pseudomonas sp. strain BYC41-1 from which L-arginine oxidase gene corresponding to citrulline oxidoreductase as described above was derived has the highest homology of 99.6% to Pseudomonas japonica. It clustered with Pseudomonas japonica based on 16S rDNA sequence and appeared to be closely related (lines 531-540). It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention that citrulline oxidoreductase taught by NCBI WP_110972968.1 may be derived from P. japonica. One would have been motivated to assume that with reasonably expected success since Pseudomonas strain in Asano teaching has the highest homology to P. japonica and Pseudomonas strains in Asano and NCBI WP_110972968.1 teachings have 85.6% identity and can catalyze the same reaction as described above. Thus, Asano and NCBI WP_110972968.1 teachings render claim 7 obvious.
Regarding claim 8, Asano teaches the preparation of transformed microorganism by introduction a recombinant vector containing gene of L-arginine oxidase corresponding to citrulline oxidoreductase as described above into a suitable host (lines 310-311) and describes purification method for expressed L-arginine oxidase (lines 346-363) that can be applied to citrulline oxidoreductase of NCBI WP_110972968.1 teaching. Thus, Asano and NCBI WP_110972968.1 teachings render claim 8 obvious.
Regarding claim 13, since the NCBI WP_110972968.1 teaches the same sequence as claimed SEQ ID NO:60, the citrulline oxidoreductase of NCBI WP_110972968.1 will inherently possess the property of having higher substrate specificity for citrulline than for arginine. Thus, Asano and NCBI WP_110972968.1 teachings render claim 13 obvious.
Claims 5 is rejected under 35 U.S.C. 103 as being unpatentable over Asano (WO 2014129529 A1 on record in IDS) in view of NCBI WP_110972968.1 (NCBI, WP_110972968.1, 19-Jun-2018 [retrieved on 07/29/2025]. Retrieved from the Internet: <amine oxidoreductase [Pseudomonas sp. WCHPs060044] - Protein - NCBI>) as applied to claim 1 above, and further in view of Frew (Frew and Hill Eur. J. Biochem., 1988, 172, 261-269).
The teachings of Asano and NCBI WP_110972968.1 have been set forth above.
Asano and NCBI WP_110972968.1 do not teach measurement of activity of citrulline oxidoreductase by reduction of a mediator further reacting with a reagent.
Frew teaches direct and indirect electron transfer between redox proteins and electrodes (Title). Frew describes the role of mediators in electron transfer: “In systems where direct electron transfer is very slow, small electron carriers, or mediators, may be employed to enhance the rate of electron exchange with the electrode.” (Abstract). Few mentions ferrocene as a mediator: “The organometallic compound ferrocene and its derivatives have proved particularly effective in this role.” (Abstract). Frew discloses that ferrocene compounds have been shown to be effective mediators to a variety of oxidoreductase enzymes (p. 267, left column, last paragraph). Frew describes that ferrocene can be either present in a solution or can be immobilized to the electrode in the presence of oxidoreductase and provides example of glucose oxidase (p. 267, right column, 1st paragraph). Thus, Frew describes mediator which is reduced during oxidoreductase reaction and react with electrode as a reagent.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to add mediator to measure oxidoreductase reaction as described by Frew to method of detection of citrulline based on combination of Asano and NCBI WP_110972968.1 teachings by measurement of the product of reaction, hydrogen peroxide with hydrogen peroxide detection electrode. One would have been motivated to do so since Frew teaches that mediator can enhance the rate of electron exchange with the electrode and provides example of ferrocene as effective mediator for oxidoreductase enzymes. A skilled artisan would have reasonably expected success in the combination because Asano and Frew describe measurement of the activity of oxidase/oxidoreductase enzymes involving electrodes. Thus, Asano, NCBI WP_110972968.1 and Frew teachings render claim 5 obvious.
Response to Arguments
Applicant's arguments filed 05/05/2025 have been fully considered but they are not persuasive.
The Declaration under 37 C.F.R. 1.132 of Yosuke Masakari is acknowledged. The Declaration supports amendment to claim 1 in particular E62Q mutation of citrulline oxidoreductase with SEQ ID NO:60.
Applicant’s arguments with respect to amended claims have been considered but are moot because the new ground of rejection does not rely only on Asano reference applied in the prior rejection of record for any teaching or matter specifically challenged in the argument. The current rejection is based on combination of prior art of Asano and NCBI WP_110972968.1 as described above.
Conclusion
No claims are allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to LIOUBOV G KOROTCHKINA whose telephone number is (571)270-0911. The examiner can normally be reached Monday-Friday: 8:00-5:30.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Sharmila G Landau can be reached at (571)272-0614. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/L.G.K./ Examiner, Art Unit 1653
/SHARMILA G LANDAU/ Supervisory Patent Examiner, Art Unit 1653