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 .
Claim status
Claims 1, 8-11, 13-14 and 17-20 are pending.
Claims 14 and 17-20 are withdrawn.
Claims 1, 8-11 and 13 are examined.
Withdrawn rejections
The rejection of claims 1-3, 7-11 and 13 under 35 USC 112(a) for failing to comply with the written description requirement is withdrawn in light of amendments made by Applicant.
The rejection of claims 1-3, 7-11 and 13 under 35 USC 112(a) for failing to comply with the enablement requirement is withdrawn in light of amendments made by Applicant.
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 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.
Claims 1, 8-11 and 13 remain rejected under 35 U.S.C. 103 as being unpatentable over Wang (Wang et al. Applied Environmental Microbiology. 2010. 76(8):2524-2530) in view of Chauhan (Chauhan D., Yennamalli R.M., Priyadarshini R. Accession A0A246BJ83_9DEIO. Submitted (MAY-2017) to the EMBL/GenBank/DDBJ databases), Wang 2012 (Wang et al. Applied Environmental Microbiology. 2012 Nov. 78(22):7985-7992) and Meng (Meng et al. Plant Disease. 2017. 101:279-287).
Due to Applicant's amendment of the claims, the rejection is modified from the rejection set forth in the Office action mailed 3/18/2026, as applied to claims 1-3, 7-11 and 13.
An embodiment of claim 1 requires a method of contacting a potato with a composition including a quorum quenching lactonase comprising at least 95% identity with SEQ ID NO: 1 by degrading acyl-homoserine lactone (AHL) wherein the AHL is a C6-homoserine lactone or a C8-homoserine lactone.
Claim 8 specifies that the potato of claim 1 is suspected of being infected with a pathogen.
Claim 9 is drawn to the pathogen of claim 8 comprising Pectobacterium.
Claim 10 is drawn to the pathogen of claim 8 comprising Erwinia.
Claim 11 specifies that the lactonase of claim 1 is from Deinococcus.
An embodiment of claim 13 specifies that the contacting of claim 1 includes immersing.
Regarding claim 1, Wang teaches contacting a potato with the N-Acylhomoserine lactone (AHL)-degrading lactonase, AiiM, on the surfaces of potato slices (Abstract). Wang teaches the AHLs used include a C6-homoserine lactone and a C8-homoserine lactone (paragraph bridging pages 2524-2525). Wang teaches that AiiM quenched the virulence in Pectobacterium carotovorum (page 2529, left column, paragraph 2). N-Acylhomoserine lactones (AHLs) are used by many bacteria for cell-cell communication referred to as quorum sensing (Wang, page 2524, left column, paragraph 1). Therefore, the method of Wang is interpreted as encompassing contacting with an isolated quorum quenching lactonase.
Regarding claims 8-9, Wang teaches the potato sample comprised both the lactonase AiiM and Pectobacterium carotovorum (page 2529, paragraph bridging left and right columns).
Regarding claim 10, Wang teaches that Pectobacterium carotovorum was formerly referred to as Erwinia carotovora (page 2524, left column, paragraph 1). Because the instant disclosure is also drawn to Pectobacterium, this limitation is interpreted as being met by Pectobacterium carotovorum.
Regarding claim 13, the method of Wang teaches inoculation of a potato slice (page 2526, left column, paragraph 4; page 2529, paragraph bridging left and right columns). This is interpreted as reading on “immersing”.
Wang 2012 teaches that AHL lactonases comprise metallo-β-lactamases and α/β-hydrolase-folds (page 7988, right column, paragraph 2). Wang 2012 teaches that AiiA is an AHL-degrading lactonase that has been shown to attenuate pathogenicity of P. carotovorum in crops. Wang 2012 teaches that AiiA is a metallo-β-lactamase (page 7985, left column, paragraph 2). Wang 2012 teaches that zinc (Zn2+) is essential for the AHL-degrading activity AiiA (page 7990, right column, paragraph 2).
Regarding claim 1, Wang does not teach that the lactonase shares at least 95% identity with SEQ ID NO: 1.
Regarding claim 11, Wang does not teach that the lactonase is from Deinococcus.
Regarding claims 1 and 11, Chauhan teaches A0A246BJ83_9DEIO, a MBL fold metallo-hydrolase sequence from Deinococcus sharing 97.6% identity with instant SEQ ID NO: 1. See alignment below.
At time of filing, it would have been prima facie obvious to one of ordinary skill in the art to modify the method of contacting a plant with a quorum quenching lactonase such as AiiM taught by Wang by contacting a plant with the enzyme of Chauhan because the enzyme was known to comprise a MBL metallo-hydrolase fold. The enzyme of Chauhan would be expected to have AHL lactonase activity given the teaching of Wang 2012. One would have expected that contacting a plant with this enzyme would result in less damage caused by P. carotovorum due to the quorum sensing of P. carotovorum being quenched by the degradation of AHL. One would have been motivated to degrade AHLs of P. carotovorum to reduce its virulence.
Therefore, the claims are made obvious in view of the teachings and suggestions of the prior art.
Alignment of A0A246BJ83_9DEIO taught by Chauhan with instant SEQ ID NO: 1:
RESULT 1
A0A246BJ83_9DEIO
ID A0A246BJ83_9DEIO Unreviewed; 213 AA.
AC A0A246BJ83;
DT 25-OCT-2017, integrated into UniProtKB/TrEMBL.
DT 25-OCT-2017, sequence version 1.
DT 08-OCT-2025, entry version 17.
DE SubName: Full=Hydrolase {ECO:0000313|EMBL:OWL95384.1};
GN ORFNames=CBQ26_12365 {ECO:0000313|EMBL:OWL95384.1};
OS Deinococcus indicus.
OC Bacteria; Thermotogati; Deinococcota; Deinococci; Deinococcales;
OC Deinococcaceae; Deinococcus.
OX NCBI_TaxID=223556 {ECO:0000313|EMBL:OWL95384.1, ECO:0000313|Proteomes:UP000197208};
RN [1] {ECO:0000313|EMBL:OWL95384.1, ECO:0000313|Proteomes:UP000197208}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DR1 {ECO:0000313|EMBL:OWL95384.1,
RC ECO:0000313|Proteomes:UP000197208};
RA Chauhan D., Yennamalli R.M., Priyadarshini R.;
RT "De novo genome assembly of Deniococcus indicus strain DR1.";
RL Submitted (MAY-2017) to the EMBL/GenBank/DDBJ databases.
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000256|ARBA:ARBA00001947};
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:OWL95384.1}.
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DR EMBL; NHMK01000017; OWL95384.1; -; Genomic_DNA.
DR RefSeq; WP_088248942.1; NZ_BNAM01000012.1.
DR AlphaFoldDB; A0A246BJ83; -.
DR OrthoDB; 9802248at2; -.
DR Proteomes; UP000197208; Unassembled WGS sequence.
DR GO; GO:0016787; F:hydrolase activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR Gene3D; 3.60.15.10; Ribonuclease Z/Hydroxyacylglutathione hydrolase-like; 1.
DR InterPro; IPR051453; MBL_Glyoxalase_II.
DR InterPro; IPR001279; Metallo-B-lactamas.
DR InterPro; IPR036866; RibonucZ/Hydroxyglut_hydro.
DR PANTHER; PTHR46233; HYDROXYACYLGLUTATHIONE HYDROLASE GLOC; 1.
DR PANTHER; PTHR46233:SF3; HYDROXYACYLGLUTATHIONE HYDROLASE GLOC; 1.
DR Pfam; PF00753; Lactamase_B; 1.
DR SMART; SM00849; Lactamase_B; 1.
DR SUPFAM; SSF56281; Metallo-hydrolase/oxidoreductase; 1.
PE 4: Predicted;
KW Hydrolase {ECO:0000256|ARBA:ARBA00022801, ECO:0000313|EMBL:OWL95384.1};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723};
KW Reference proteome {ECO:0000313|Proteomes:UP000197208};
KW Zinc {ECO:0000256|ARBA:ARBA00022833}.
FT DOMAIN 21..197
FT /note="Metallo-beta-lactamase"
FT /evidence="ECO:0000259|SMART:SM00849"
FT REGION 192..213
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 203..213
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 213 AA; 22329 MW; EA6C5465FEADBAAA CRC64;
Query Match 97.6%; Score 1115; Length 213;
Best Local Similarity 97.7%;
Matches 208; Conservative 1; Mismatches 4; Indels 0; Gaps 0;
Qy 1 MTAPFTHGPLRVWSLPTGPIQENAVLIAGEQGQGFLIDPGDDAGRIAALVAASGVTVTGI 60
||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||
Db 1 MTAPFTHGPLRVWSLPTGPIQENAVLIAGEQGQGFLIDPGDDAGRIAALVAGSGVTVTGI 60
Qy 61 LLTHAHFDHIGAVQPLREQLGVPVWLHPDDRELYALGAQSAARWNLPFTQPAPPDHDITG 120
|||||||||||||||||||||||||||| ||:|||||||||||||||||||||||||||
Db 61 LLTHAHFDHIGAVQPLREQLGVPVWLHPADRDLYALGAQSAARWNLPFTQPAPPDHDITD 120
Qy 121 GQTFTAGDLTLTARHLPGHAPGHVVFVAPGVVIAGDTLFQGGIGRTDLPGGNHPQLLAGI 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 GQTFTAGDLTLTARHLPGHAPGHVVFVAPGVVIAGDTLFQGGIGRTDLPGGNHPQLLAGI 180
Qy 181 RTQLLTLPDDTAVYPGHGPRTSVGHERRSNPFL 213
| |||||||||||||||||||||||||||||||
Db 181 RAQLLTLPDDTAVYPGHGPRTSVGHERRSNPFL 213
Applicant’s arguments regarding rejection under 35 USC 103
Applicant argues on pages 6-7 of the Remarks filed 6/18/2026 that none of the references teach the same limitation as instantly claimed, an isolated quorum quenching lactonase having at least 95% identity to the protein SEQ ID NO: 12. Applicant notes that the Specification provides, “[a]s disclosed herein, putative QQ enzymes from seven bacterial genomes where characterized for their ability to degrade acyl-homoserine lactones (AHLs, a QS chemical signal).” Applicant also notes that the Specification discloses that an enzyme with SEQ ID NO: 12 is useful in the compositions and methods to cause loss of one or more AHLs. Therefore, Applicant argues, the instantly claimed invention was not obvious over the references cited by Examiner.
This argument has been fully considered but it is not persuasive. In response to applicant's arguments against the references individually, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986). It would have been obvious to modify the teaching of Wang to use the lactonase taught by Chauhan, which shares over 97% identity with SEQ ID NO: 2, because the enzyme of Chauhan would be expected to have AHL lactonase activity given the teaching of Wang 2012. One would have expected that contacting a plant with the enzyme of Chauhan would result in less damage caused by P. carotovorum due to the quorum sensing of P. carotovorum being quenched by the degradation of AHL. One would have been motivated to degrade AHLs of P. carotovorum to reduce its virulence.
Conclusion
Claims 1, 8-11 and 13 remain rejected.
THIS ACTION IS MADE FINAL. 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 DAVID R BYRNES whose telephone number is (571)270-3935. The examiner can normally be reached 9:00 - 5:00 M-F.
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/DAVID R BYRNES/Examiner, Art Unit 1662
/MYKOLA V. KOVALENKO/Primary Examiner, Art Unit 1662
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