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
A restriction requirement was posted on 24 February 2023. Applicant elected without traverse SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:28, SEQ ID NO:1, SEQ ID NO:2 and SEQ ID NO:17 along with Group I in the reply filed on 18 April 2023. Claims 1-3 and 9-20 were examined in an Office action posted on 19 July 2023 with 4-8 withdrawn as being drawn to a non-elected invention. Claim 9 was also examined.
Applicant responded on 19 October 2023 adding 4 claims. Claims 22-24 depended from withdrawn claims and thus were also withdrawn. Claims 1-3 and 9-21 as of 19 October 2023 were examined and rejected in an Office action posted on 7 February 2024.
Applicant responded after final and an advisory action was posted.
Applicant filed an RCE as above adding a new claim. Claims 1-3, 9-21 and 25 were examined and rejected in an Office action posted 26 September 2024. Claims 4-8 and 22-24 remained withdrawn. Applicant responded on 17 December 2024.
A new non-final rejection was posted on 9 April 2025 examining claims 1-6, 9-19 and 21-25. The Office action allowed claims 1-6,9-13, 18 and 21-25 but rejected claims 14-17 and 19. No claims were withdrawn.
Applicant responded on 7 July 2025. In a Final Rejection posted on 7 October 2025. Claims 1-6, 9-19 and 21-25 were pending. Claims 1-6, 9-13, 16-18 and 21-25 were allowed. (Claim 19 was marked as “allowed” in the Office Action Summary but was rejected in the body of the Office action.)
Claims 14, 15 and 19 were rejected in the Office action posted on 7 October 2025. Applicant responded with an RCE and claim amendments plus new claim 26 on 6 January 2026.
Claims 1-6, 9-13, 14, 15, 16-18, 19 and 21-25 are pending. Claims 1-6, 9-13, 16-18 and 21-26 are allowed.
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action was withdrawn pursuant to 37 CFR 1.114. The Office enters Applicant's submission filed on 6 January 2026.
Withdrawal of Objections and Rejections
The rejection of claim 19 under 35 USC U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph is withdrawn in view of Applicant’s amendments to the claims.
Examiner’s Notes
Citations to Applicant’s specification are abbreviated herein “Spec.”
Occasionally, “SIN:” is used as an abbreviation “SEQ ID NO:” herein.
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 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:
§ 103. Conditions for patentability; non-obvious subject matter
A patent for a claimed invention may not be obtained, . . . . 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 14,15 and 19 are rejected under 35 U.S.C. 103 as being obvious over
Alexandrov et al.’s. US Patent Pub. No. 20170037426 A1.
in view of Papdi et al. (2008) Plant Physiol. 147(2):528-42.
The factual inquiries set forth in Graham v. John Deere Co., 383 U.S. 1, 18, 148 USPQ 459, 467 (1966), that are applied for establishing a background for determining obviousness under 35 U.S.C. 103(a) are summarized as follows:
a. Determining the scope and contents of the prior art.
b. Ascertaining the differences between the prior art and the claims at issue.
c. Resolving the level of ordinary skill in the pertinent art.
d. Considering objective evidence present in the application indicating obviousness or nonobviousness.
As seen in the first alignment below, instant SEQ ID NO:3 was known in the prior art as SEQ ID NO:3523837 in Alexandrov et al.’s SEQ ID NO:3523837. US Patent Pub. No. 2017/0037426 A1.
As seen in the second alignment below, a sequence falling within the scope of the claimed variants of instant SEQ ID NO:4 was known in the prior art as SEQ ID NO 1392711. The same patent publication as the alignment of SEQ ID NO:3 above.
Alexandrov et al. teaches that both proteins are from Arabidopsis (para. 0131)
Papdi et al. teaches creating Arabidopsis cDNA libraries under the control of a heterologous inducible promoter. Page 529, lower right corner. The authors also cite to the previously cited LeClere & Bartel (2001) (misspelled as “LeClerc in prior Office action).
Creating a cDNA library in the experimental plant Arabidopsis is obvious.
Thus it would have been prima facie obvious to one of ordinary skill in the art as of the effective filing date of the claimed invention create a composition with the Arabidopsis genes encoding those two proteins controlled by a heterologous inducible promoter.
Given the level of skill in the art as of the effective filing date of the claimed invention one of ordinary skill in the art would have had a reasonable expectation of success.
Claim 14 uses the open transitional phrase “comprising.” Reciting two signposts within the library is not patentable over the prior art.
Therefore claim 14 is obvious. Claim 15 is also obvious because it only requires a higher degree of sequence identity to SEQ ID NO:4.
In contrast, claim 16 requires both genes on the same construct molecule / backbone.
Given the above, placing the two genes as independent DNA molecules in a plant cell given the subject matter is also obvious and therefore claim 19 is obvious.
Applicant’s Argument
Applicant traverses the rejection under 35 USC 103 on pages 6-7.
Applicant cites to a Federal Circuit decision – a footnote on page 1346. The footnote is an argument between the author’s opinion and the dissent. (Response, p, 7 (citing to In re Stepan Co., 868 F.3d 1342, 1346 n. 1.).
Response to Applicant’s Argument
In further support of this rejection is the following analysis of Arabidopsis genetics.
A search of SEQ ID NO:3 reveals it is the At3g11260 gene. (the third alignment below) It was also identified as “WUSCHEL-RELATED HOMEOBOX 5” protein. A BLAST® search reveals GenBank (2000) NP_187735.
Additionally, a search of SEQ ID NO:4 reveals it is the At3g20840 gene. (fourth alignment immediately below).
Again claim 14 uses open language. Thus Applicant’s claim 14 reads on a library of Arabidopsis genes. Arabidopsis is a renowned experimental plant.
Merely articulating two members does not provide a patentable distinction over an obvious-to-create library. Further, one of the genes IS taught by Santuari et al. (2016) under the control of inducible promoter.
Santuari et al. teaches expression Arabidopsis PLETHORA genes under the control of an inducible promoter. Santuari et al. (2016) Plant Cell, 28:2937–51 (2nd para. of “Results” section on page 2938). At3g20840 is taught as a PLETHORA gene under “Accession Numbers” on page 2949.
Rashid et al. teaches expressing another Arabidopsis WUS gene under the control of an inducible promoter. (1st paragraph). (Rashid et al. (2007) Plant Cell Rep 26:1449-55, 1st paragraph. Even though Rashid et al. does not teach SEQ ID NO:3, it suggests placing it, as another WUS gene, under the control of a inducible promoter.
Finally, if allowed, creating a new Arabidopsis cDNA library using an inducible promoter would infringe at least claim 14.
Therefore Applicant’s argument was fully considered but is not persuasive.
Alexandrov et al.’s SEQ ID NO:3523837
Listed by serail no., U.S. Patent Publication No. is 20170/037426 A1
US-11-006-231-3523837
Filing date in PALM: 2004-12-06
Sequence 3523837, US/11006231
GENERAL INFORMATION
APPLICANT: ALEXANDROV, Nickolai
APPLICANT: APUYA, Nestor
APPLICANT: BROVER, Vyacheslav
APPLICANT: CHEN, Xianfeng
APPLICANT: DUMAS, Jean-Baptiste
APPLICANT: FANG, Yiwen
APPLICANT: FELDMANN, Kenneth
APPLICANT: MASCIA, Peter
APPLICANT: OKAMURO, Jack
APPLICANT: PENNELL, Roger
APPLICANT: SCHNEEBERGER, Richard
APPLICANT: SUBRAMANIAN,Gopalakrishnan
APPLICANT: TROUKHAN, Maxim
APPLICANT: ZHANG, Liansheng
TITLE OF INVENTION: SEQUENCE DETERMINED DNA FRAGMENTS AND CORRESPONDING POLYPEPTIDES
TITLE OF INVENTION: ENCODED THEREBY
FILE REFERENCE: 2750-1571PUS2
CURRENT APPLICATION NUMBER: US/11/006,231
CURRENT FILING DATE: 2004-12-06
PRIOR APPLICATION NUMBER: US 60/099,671
PRIOR FILING DATE: 1998-09-04
PRIOR APPLICATION NUMBER: US 60/099,672
PRIOR FILING DATE: 1998-09-04
PRIOR APPLICATION NUMBER: US 60/099,933
PRIOR FILING DATE: 1998-09-11
PRIOR APPLICATION NUMBER: US 60/100,864
PRIOR FILING DATE: 1998-09-17
PRIOR APPLICATION NUMBER: US 60/101,042
PRIOR FILING DATE: 1998-09-18
PRIOR APPLICATION NUMBER: US 60/101,682
PRIOR FILING DATE: 1998-09-24
PRIOR APPLICATION NUMBER: US 60/102,460
PRIOR FILING DATE: 1998-09-30
PRIOR APPLICATION NUMBER: US 60/102,533
PRIOR FILING DATE: 1998-09-30
PRIOR APPLICATION NUMBER: US 60/103,116
PRIOR FILING DATE: 1998-10-05
PRIOR APPLICATION NUMBER: US 60/103,141
PRIOR FILING DATE: 1998-10-05
Remaining Prior Application data removed - See File Wrapper or PALM.
NUMBER OF SEQ ID NOS: 4140943
SEQ ID NO 3523837
LENGTH: 182
TYPE: PRT
ORGANISM: Arabidopsis thaliana
FEATURE:
NAME/KEY: misc_feature
LOCATION: (1)..(182)
OTHER INFORMATION: Ceres Seq. ID no. 4812818
Query Match 100.0%; Score 969; Length 182;
Best Local Similarity 100.0%;
Matches 182; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MSFSVKGRSLRGNNNGGTGTKCGRWNPTVEQLKILTDLFRAGLRTPTTDQIQKISTELSF 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MSFSVKGRSLRGNNNGGTGTKCGRWNPTVEQLKILTDLFRAGLRTPTTDQIQKISTELSF 60
Qy 61 YGKIESKNVFYWFQNHKARERQKRRKISIDFDHHHHQPSTRDVFEISEEDCQEEEKVIET 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 YGKIESKNVFYWFQNHKARERQKRRKISIDFDHHHHQPSTRDVFEISEEDCQEEEKVIET 120
Qy 121 LQLFPVNSFEDSNSKVDKMRARGNNQYREYIRETTTTSFSPYSSCGAEMEHPPPLDLRLS 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 LQLFPVNSFEDSNSKVDKMRARGNNQYREYIRETTTTSFSPYSSCGAEMEHPPPLDLRLS 180
Qy 181 FL 182
||
Db 181 FL 182
Alexandrov et al.’s SEQ ID NO: 1392711
Listed by serail no., U.S. Patent Publication No. is 20170/037426 A1
US-11-006-231-1392711
Filing date in PALM: 2004-12-06
Sequence 1392711, US/11006231
GENERAL INFORMATION
APPLICANT: ALEXANDROV, Nickolai
APPLICANT: APUYA, Nestor
APPLICANT: BROVER, Vyacheslav
APPLICANT: CHEN, Xianfeng
APPLICANT: DUMAS, Jean-Baptiste
APPLICANT: FANG, Yiwen
APPLICANT: FELDMANN, Kenneth
APPLICANT: MASCIA, Peter
APPLICANT: OKAMURO, Jack
APPLICANT: PENNELL, Roger
APPLICANT: SCHNEEBERGER, Richard
APPLICANT: SUBRAMANIAN,Gopalakrishnan
APPLICANT: TROUKHAN, Maxim
APPLICANT: ZHANG, Liansheng
TITLE OF INVENTION: SEQUENCE DETERMINED DNA FRAGMENTS AND CORRESPONDING POLYPEPTIDES
TITLE OF INVENTION: ENCODED THEREBY
FILE REFERENCE: 2750-1571PUS2
CURRENT APPLICATION NUMBER: US/11/006,231
CURRENT FILING DATE: 2004-12-06
PRIOR APPLICATION NUMBER: US 60/099,671
PRIOR FILING DATE: 1998-09-04
PRIOR APPLICATION NUMBER: US 60/099,672
PRIOR FILING DATE: 1998-09-04
PRIOR APPLICATION NUMBER: US 60/099,933
PRIOR FILING DATE: 1998-09-11
PRIOR APPLICATION NUMBER: US 60/100,864
PRIOR FILING DATE: 1998-09-17
PRIOR APPLICATION NUMBER: US 60/101,042
PRIOR FILING DATE: 1998-09-18
PRIOR APPLICATION NUMBER: US 60/101,682
PRIOR FILING DATE: 1998-09-24
PRIOR APPLICATION NUMBER: US 60/102,460
PRIOR FILING DATE: 1998-09-30
PRIOR APPLICATION NUMBER: US 60/102,533
PRIOR FILING DATE: 1998-09-30
PRIOR APPLICATION NUMBER: US 60/103,116
PRIOR FILING DATE: 1998-10-05
PRIOR APPLICATION NUMBER: US 60/103,141
PRIOR FILING DATE: 1998-10-05
Remaining Prior Application data removed - See File Wrapper or PALM.
NUMBER OF SEQ ID NOS: 4140943
SEQ ID NO 1392711
LENGTH: 571
TYPE: PRT
ORGANISM: Arabidopsis thaliana
FEATURE:
NAME/KEY: misc_feature
LOCATION: (1)..(571)
OTHER INFORMATION: Ceres Seq. ID no. 2163113
Query Match 99.1%; Score 3016.5; Length 571;
Best Local Similarity 99.5%;
Matches 571; Conservative 0; Mismatches 0; Indels 3; Gaps 1;
Qy 1 MNSNNWLGFPLSPNNSSLPPHEYNLGLVSDHMDNPFQTQEWNMINPHGGGGDEGGEVPKV 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MNSNNWLGFPLSPNNSSLPPHEYNLGLVSDHMDNPFQTQEWNMINPHGGGGDEGGEVPKV 60
Qy 61 ADFLGVSKPDENQSNHLVAYNDSDYYFHTNSLMPSVQSNDVVVAACDSNTPNNSSYHELQ 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 ADFLGVSKPDENQSNHLVAYNDSDYYFHTNSLMPSVQSNDVVVAACDSNTPNNSSYHELQ 120
Qy 121 ESAHNLQSLTLSMGTTAGNNVVDKASPSETTGDNASGGALAVVETATPRRALDTFGQRTS 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 ESAHNLQSLTLSMGTTAGNNVVDKASPSETTGDNASGGALAVVETATPRRALDTFGQRTS 180
Qy 181 IYRGVTRHRWTGRYEAHLWDNSCRREGQSRKGRQVYLGGYDKEDKAARSYDLAALKYWGP 240
|||||||||||||||||||||||||||||||||| |||||||||||||||||||||||
Db 181 IYRGVTRHRWTGRYEAHLWDNSCRREGQSRKGRQ---GGYDKEDKAARSYDLAALKYWGP 237
Qy 241 STTTNFPITNYEKEVEEMKHMTRQEFVAAIRRKSSGFSRGASMYRGVTRHHQHGRWQARI 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 238 STTTNFPITNYEKEVEEMKHMTRQEFVAAIRRKSSGFSRGASMYRGVTRHHQHGRWQARI 297
Qy 301 GRVAGNKDLYLGTFSTEEEAAEAYDIAAIKFRGLNAVTNFEINRYDVKAILESSTLPIGG 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 298 GRVAGNKDLYLGTFSTEEEAAEAYDIAAIKFRGLNAVTNFEINRYDVKAILESSTLPIGG 357
Qy 361 GAAKRLKEAQALESSRKREAEMIALGSSFQYGGGSSTGSGSTSSRLQLQPYPLSIQQPLE 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 358 GAAKRLKEAQALESSRKREAEMIALGSSFQYGGGSSTGSGSTSSRLQLQPYPLSIQQPLE 417
Qy 421 PFLSLQNNDISHYNNNNAHDSSSFNHHSYIQTQLHLHQQTNNYLQQQSSQNSQQLYNAYL 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 418 PFLSLQNNDISHYNNNNAHDSSSFNHHSYIQTQLHLHQQTNNYLQQQSSQNSQQLYNAYL 477
Qy 481 HSNPALLHGLVSTSIVDNNNNNGGSSGSYNTAAFLGNHGIGIGSSSTVGSTEEFPTVKTD 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 478 HSNPALLHGLVSTSIVDNNNNNGGSSGSYNTAAFLGNHGIGIGSSSTVGSTEEFPTVKTD 537
Qy 541 YDMPSSDGTGGYSGWTSESVQGSNPGGVFTMWNE 574
||||||||||||||||||||||||||||||||||
Db 538 YDMPSSDGTGGYSGWTSESVQGSNPGGVFTMWNE 571
At3g11260 / NP_187735
A0A384KT15_ARATH
ID A0A384KT15_ARATH Unreviewed; 182 AA.
AC A0A384KT15; A0A5S9XB94;
DT 07-NOV-2018, integrated into UniProtKB/TrEMBL.
DT 07-NOV-2018, sequence version 1.
DT 22-FEB-2023, entry version 23.
DE SubName: Full=(thale cress) hypothetical protein {ECO:0000313|EMBL:CAD5322709.1};
DE SubName: Full=WOX5B {ECO:0000313|EMBL:OAP04775.1};
GN OrderedLocusNames=AXX17_At3g11140 {ECO:0000313|EMBL:OAP04775.1};
GN ORFNames=AN1_LOCUS12445 {ECO:0000313|EMBL:VYS56994.1},
GN AT9943_LOCUS10702 {ECO:0000313|EMBL:CAD5322709.1}, C24_LOCUS12274
GN {ECO:0000313|EMBL:CAA0382040.1};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702 {ECO:0000313|EMBL:OAP04775.1, ECO:0000313|Proteomes:UP000078284};
RN [1] {ECO:0000313|Proteomes:UP000078284}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Landsberg erecta {ECO:0000313|Proteomes:UP000078284};
RX PubMed=27354520; DOI=10.1073/pnas.1607532113;
RA Zapata L., Ding J., Willing E.M., Hartwig B., Bezdan D., Jiao W.B.,
RA Patel V., Velikkakam James G., Koornneef M., Ossowski S., Schneeberger K.;
RT "Chromosome-level assembly of Arabidopsis thaliana Ler reveals the extent
RT of translocation and inversion polymorphisms.";
RL Proc. Natl. Acad. Sci. U.S.A. 113:E4052-E4060(2016).
RN [2] {ECO:0000313|EMBL:OAP04775.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC TISSUE=Leaf {ECO:0000313|EMBL:OAP04775.1};
RA Zapata L., Schneeberger K., Ossowski S.;
RT "Full-length assembly of Arabidopsis thaliana Ler reveals the complement of
RT translocations and inversions.";
RL Submitted (MAR-2016) to the EMBL/GenBank/DDBJ databases.
RN [3] {ECO:0000313|EMBL:CAA0382040.1, ECO:0000313|Proteomes:UP000434276}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. An-1 {ECO:0000313|Proteomes:UP000426265}, and cv. C24
RC {ECO:0000313|Proteomes:UP000434276};
RA Jiao W.-B., Schneeberger K.;
RL Submitted (DEC-2019) to the EMBL/GenBank/DDBJ databases.
RN [4] {ECO:0000313|EMBL:CAD5322709.1, ECO:0000313|Proteomes:UP000516314}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Cdm-0 {ECO:0000313|Proteomes:UP000516314};
RA Ashkenazy H.;
RL Submitted (SEP-2020) to the EMBL/GenBank/DDBJ databases.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000256|ARBA:ARBA00004123,
CC ECO:0000256|PROSITE-ProRule:PRU00108, ECO:0000256|RuleBase:RU000682}.
CC -!- SIMILARITY: Belongs to the WUS homeobox family.
CC {ECO:0000256|ARBA:ARBA00024040}.
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DR EMBL; CACSHJ010000089; CAA0382040.1; -; Genomic_DNA.
DR EMBL; LR881468; CAD5322709.1; -; Genomic_DNA.
DR EMBL; LUHQ01000003; OAP04775.1; -; Genomic_DNA.
DR EMBL; CACRSJ010000106; VYS56994.1; -; Genomic_DNA.
DR RefSeq; NP_187735.2; NM_111961.4.
DR AlphaFoldDB; A0A384KT15; -.
DR SMR; A0A384KT15; -.
DR EnsemblPlants; AT3G11260.1; AT3G11260.1; AT3G11260.
DR GeneID; 820297; -.
DR Gramene; AT3G11260.1; AT3G11260.1; AT3G11260.
DR KEGG; ath:AT3G11260; -.
DR OMA; FSPYSSC; -.
DR OrthoDB; 411854at2759; -.
DR Proteomes; UP000078284; Chromosome 3.
DR Proteomes; UP000426265; Unassembled WGS sequence.
DR Proteomes; UP000434276; Unassembled WGS sequence.
DR Proteomes; UP000516314; Chromosome 3.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0003700; F:DNA-binding transcription factor activity; IEA:InterPro.
DR GO; GO:0099402; P:plant organ development; IEA:InterPro.
DR CDD; cd00086; homeodomain; 1.
DR Gene3D; 1.10.10.60; Homeodomain-like; 1.
DR InterPro; IPR009057; Homeobox-like_sf.
DR InterPro; IPR001356; Homeobox_dom.
DR InterPro; IPR044555; WUSCHEL-like.
DR PANTHER; PTHR45940; WUSCHEL-RELATED HOMEOBOX 1-RELATED; 1.
DR PANTHER; PTHR45940:SF41; WUSCHEL-RELATED HOMEOBOX 5; 1.
DR Pfam; PF00046; Homeodomain; 1.
DR SMART; SM00389; HOX; 1.
DR SUPFAM; SSF46689; Homeodomain-like; 1.
DR PROSITE; PS50071; HOMEOBOX_2; 1.
PE 3: Inferred from homology;
KW DNA-binding {ECO:0000256|PROSITE-ProRule:PRU00108,
KW ECO:0000256|RuleBase:RU000682};
KW Homeobox {ECO:0000256|ARBA:ARBA00023155, ECO:0000256|PROSITE-
KW ProRule:PRU00108};
KW Nucleus {ECO:0000256|PROSITE-ProRule:PRU00108,
KW ECO:0000256|RuleBase:RU000682}.
FT DOMAIN 18..83
FT /note="Homeobox"
FT /evidence="ECO:0000259|PROSITE:PS50071"
FT DNA_BIND 20..84
FT /note="Homeobox"
FT /evidence="ECO:0000256|PROSITE-ProRule:PRU00108"
FT REGION 1..24
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 182 AA; 21226 MW; 70502169709BB91D CRC64;
Query Match 100.0%; Score 969; Length 182;
Best Local Similarity 100.0%;
Matches 182; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MSFSVKGRSLRGNNNGGTGTKCGRWNPTVEQLKILTDLFRAGLRTPTTDQIQKISTELSF 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MSFSVKGRSLRGNNNGGTGTKCGRWNPTVEQLKILTDLFRAGLRTPTTDQIQKISTELSF 60
Qy 61 YGKIESKNVFYWFQNHKARERQKRRKISIDFDHHHHQPSTRDVFEISEEDCQEEEKVIET 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 YGKIESKNVFYWFQNHKARERQKRRKISIDFDHHHHQPSTRDVFEISEEDCQEEEKVIET 120
Qy 121 LQLFPVNSFEDSNSKVDKMRARGNNQYREYIRETTTTSFSPYSSCGAEMEHPPPLDLRLS 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 LQLFPVNSFEDSNSKVDKMRARGNNQYREYIRETTTTSFSPYSSCGAEMEHPPPLDLRLS 180
Qy 181 FL 182
||
Db 181 FL 182
At3g20840 / NP_187735
PLET1_ARATH
ID PLET1_ARATH Reviewed; 574 AA.
AC Q5YGP8; Q6PQQ6; Q9LT37;
DT 21-AUG-2007, integrated into UniProtKB/Swiss-Prot.
DT 23-NOV-2004, sequence version 1.
DT 22-FEB-2023, entry version 116.
DE RecName: Full=AP2-like ethylene-responsive transcription factor PLT1 {ECO:0000303|PubMed:15454085};
DE AltName: Full=Protein AINTEGUMENTA-LIKE 3 {ECO:0000303|PubMed:15988559};
DE AltName: Full=Protein PLETHORA 1 {ECO:0000303|PubMed:15454085};
GN Name=PLT1 {ECO:0000303|PubMed:15454085};
GN Synonyms=AIL3 {ECO:0000303|PubMed:15988559};
GN OrderedLocusNames=At3g20840 {ECO:0000312|Araport:AT3G20840};
GN ORFNames=MOE17.15 {ECO:0000312|EMBL:BAB02492.1};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, TISSUE SPECIFICITY, DEVELOPMENTAL
RP STAGE, AND INDUCTION.
RC STRAIN=cv. Columbia;
RX PubMed=15454085; DOI=10.1016/j.cell.2004.09.018;
RA Aida M., Beis D., Heidstra R., Willemsen V., Blilou I., Galinha C.,
RA Nussaume L., Noh Y.-S., Amasino R., Scheres B.;
RT "The PLETHORA genes mediate patterning of the Arabidopsis root stem cell
RT niche.";
RL Cell 119:109-120(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10819329; DOI=10.1093/dnares/7.2.131;
RA Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 3. I. Sequence
RT features of the regions of 4,504,864 bp covered by sixty P1 and TAC
RT clones.";
RL DNA Res. 7:131-135(2000).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [4]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 43-574.
RA Pan Y., Gong W., Liu D., Fu Q., Mei W.-Q., Song W.-Q., Ma L.-G., Luo J.-C.,
RA Deng X.-W., Zhu Y.-X.;
RT "Molecular cloning, expression, phylogenetic and functional
RT characterization of the Arabidopsis AP2/EREBP transcription factor
RT family.";
RL Submitted (MAR-2004) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP FUNCTION, AND TISSUE SPECIFICITY.
RX PubMed=15635403; DOI=10.1038/nature03184;
RA Blilou I., Xu J., Wildwater M., Willemsen V., Paponov I., Friml J.,
RA Heidstra R., Aida M., Palme K., Scheres B.;
RT "The PIN auxin efflux facilitator network controls growth and patterning in
RT Arabidopsis roots.";
RL Nature 433:39-44(2005).
RN [6]
RP TISSUE SPECIFICITY.
RX PubMed=15988559; DOI=10.1007/s11103-005-0955-6;
RA Nole-Wilson S., Tranby T.L., Krizek B.A.;
RT "AINTEGUMENTA-like (AIL) genes are expressed in young tissues and may
RT specify meristematic or division-competent states.";
RL Plant Mol. Biol. 57:613-628(2005).
RN [7]
RP GENE FAMILY, AND NOMENCLATURE.
RX PubMed=16407444; DOI=10.1104/pp.105.073783;
RA Nakano T., Suzuki K., Fujimura T., Shinshi H.;
RT "Genome-wide analysis of the ERF gene family in Arabidopsis and rice.";
RL Plant Physiol. 140:411-432(2006).
RN [8]
RP FUNCTION, AND TISSUE SPECIFICITY.
RX PubMed=16424342; DOI=10.1126/science.1121790;
RA Xu J., Hofhuis H., Heidstra R., Sauer M., Friml J., Scheres B.;
RT "A molecular framework for plant regeneration.";
RL Science 311:385-388(2006).
RN [9]
RP FUNCTION, TISSUE SPECIFICITY, AND DEVELOPMENTAL STAGE.
RX PubMed=20190735; DOI=10.1038/nature08843;
RA Smith Z.R., Long J.A.;
RT "Control of Arabidopsis apical-basal embryo polarity by antagonistic
RT transcription factors.";
RL Nature 464:423-426(2010).
RN [10]
RP REGULATION BY RGF.
RX PubMed=20798316; DOI=10.1126/science.1191132;
RA Matsuzaki Y., Ogawa-Ohnishi M., Mori A., Matsubayashi Y.;
RT "Secreted peptide signals required for maintenance of root stem cell niche
RT in Arabidopsis.";
RL Science 329:1065-1067(2010).
CC -!- FUNCTION: Probably acts as a transcriptional activator. Binds to the
CC GCC-box pathogenesis-related promoter element. May be involved in the
CC regulation of gene expression by stress factors and by components of
CC stress signal transduction pathways (By similarity). Master regulator
CC of basal/root fate. Essential for root quiescent center (QC) and
CC columella specification, stem cell activity, as well as for
CC establishment of the stem cell niche during embryogenesis. Modulates
CC the root polar auxin transport by regulating the distribution of PIN
CC genes. Essential role in respecifying pattern and polarity in damaged
CC roots. Direct target of the transcriptional corepressor TPL. Expression
CC levels and patterns regulated post-transcriptionally by root meristem
CC growth factors (RGFs). {ECO:0000250|UniProtKB:Q9LND1,
CC ECO:0000269|PubMed:15454085, ECO:0000269|PubMed:15635403,
CC ECO:0000269|PubMed:16424342, ECO:0000269|PubMed:20190735}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}.
CC -!- TISSUE SPECIFICITY: Expressed in roots, seedlings, flowers, and
CC siliques. Also detected at low levels in leaves. In roots, specifically
CC detected in the distal root meristem, including the QC. This tissue
CC specificity is regulated by auxin gradient and depends on PIN proteins.
CC {ECO:0000269|PubMed:15454085, ECO:0000269|PubMed:15635403,
CC ECO:0000269|PubMed:15988559, ECO:0000269|PubMed:16424342,
CC ECO:0000269|PubMed:20190735}.
CC -!- DEVELOPMENTAL STAGE: Accumulates in the basal embryo region that gives
CC rise to hypocotyl, root, and root stem cells. Expressed in the root
CC meristem throughout embryo development. {ECO:0000269|PubMed:15454085,
CC ECO:0000269|PubMed:20190735}.
CC -!- INDUCTION: By auxin accumulation. {ECO:0000269|PubMed:15454085}.
CC -!- PTM: Stabilized in root meristems by reactive oxygen species (ROS)
CC mediated oxidative post-translational modification triggered by RGF1
CC hormone peptide in a RITF1-dependent manner.
CC {ECO:0000250|UniProtKB:Q5YGP7}.
CC -!- SIMILARITY: Belongs to the AP2/ERF transcription factor family. AP2
CC subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAB02492.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AY506549; AAS86335.1; -; mRNA.
DR EMBL; AB025629; BAB02492.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002686; AEE76430.1; -; Genomic_DNA.
DR EMBL; AY585682; AAS97939.1; -; mRNA.
DR RefSeq; NP_188720.2; NM_112975.3.
DR AlphaFoldDB; Q5YGP8; -.
DR SMR; Q5YGP8; -.
DR STRING; 3702.AT3G20840.1; -.
DR PaxDb; Q5YGP8; -.
DR ProteomicsDB; 234769; -.
DR EnsemblPlants; AT3G20840.1; AT3G20840.1; AT3G20840.
DR GeneID; 821632; -.
DR Gramene; AT3G20840.1; AT3G20840.1; AT3G20840.
DR KEGG; ath:AT3G20840; -.
DR Araport; AT3G20840; -.
DR TAIR; locus:2091891; AT3G20840.
DR eggNOG; ENOG502QSTN; Eukaryota.
DR HOGENOM; CLU_013549_5_0_1; -.
DR InParanoid; Q5YGP8; -.
DR OMA; KTDYDMP; -.
DR OrthoDB; 397053at2759; -.
DR PhylomeDB; Q5YGP8; -.
DR PRO; PR:Q5YGP8; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q5YGP8; baseline and differential.
DR Genevisible; Q5YGP8; AT.
DR GO; GO:0005634; C:nucleus; IDA:TAIR.
DR GO; GO:0003700; F:DNA-binding transcription factor activity; ISS:TAIR.
DR GO; GO:0000976; F:transcription cis-regulatory region binding; IPI:TAIR.
DR GO; GO:0009734; P:auxin-activated signaling pathway; IEA:UniProtKB-KW.
DR GO; GO:0009873; P:ethylene-activated signaling pathway; IEA:UniProtKB-KW.
DR GO; GO:0007389; P:pattern specification process; IMP:TAIR.
DR GO; GO:0048364; P:root development; IMP:TAIR.
DR GO; GO:0010449; P:root meristem growth; IGI:TAIR.
DR GO; GO:0019827; P:stem cell population maintenance; IMP:TAIR.
DR GO; GO:0000723; P:telomere maintenance; IDA:TAIR.
DR CDD; cd00018; AP2; 2.
DR Gene3D; 3.30.730.10; AP2/ERF domain; 2.
DR InterPro; IPR001471; AP2/ERF_dom.
DR InterPro; IPR036955; AP2/ERF_dom_sf.
DR InterPro; IPR016177; DNA-bd_dom_sf.
DR PANTHER; PTHR32467; AP2-LIKE ETHYLENE-RESPONSIVE TRANSCRIPTION FACTOR; 1.
DR PANTHER; PTHR32467:SF102; AP2-LIKE ETHYLENE-RESPONSIVE TRANSCRIPTION FACTOR PLT1; 1.
DR Pfam; PF00847; AP2; 2.
DR PRINTS; PR00367; ETHRSPELEMNT.
DR SMART; SM00380; AP2; 2.
DR SUPFAM; SSF54171; DNA-binding domain; 2.
DR PROSITE; PS51032; AP2_ERF; 2.
PE 2: Evidence at transcript level;
KW Activator; Auxin signaling pathway; Developmental protein; DNA-binding;
KW Ethylene signaling pathway; Nucleus; Reference proteome; Repeat;
KW Stress response; Transcription; Transcription regulation.
FT CHAIN 1..574
FT /note="AP2-like ethylene-responsive transcription factor
FT PLT1"
FT /id="PRO_0000297930"
FT DNA_BIND 181..247
FT /note="AP2/ERF 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00366"
FT DNA_BIND 283..341
FT /note="AP2/ERF 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00366"
FT REGION 536..566
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 549..566
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CONFLICT 347
FT /note="V -> L (in Ref. 4; AAS97939)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 574 AA; 62875 MW; 3904AF3BD26B7E1C CRC64;
Conclusion
Claims 14, 15 and 19 are rejected. All other pending claims are allowed.
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/RUSSELL T BOGGS/
Examiner, Art Unit 1663
Prosecution Insights