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Auxin response factor 2A (SlARF2A)

 ARF2A_SOLLC             Reviewed;         846 AA.
Q2LAJ3;
05-JUL-2017, integrated into UniProtKB/Swiss-Prot.
21-FEB-2006, sequence version 1.
31-JAN-2018, entry version 85.
RecName: Full=Auxin response factor 2A {ECO:0000303|PubMed:26716451, ECO:0000303|PubMed:26959229};
Short=SlARF2A {ECO:0000303|PubMed:26716451};
Name=ARF2A {ECO:0000303|PubMed:26716451, ECO:0000303|PubMed:26959229};
Synonyms=ARF2 {ECO:0000303|PubMed:21735233,
ECO:0000312|EMBL:ABC69711.1};
OrderedLocusNames=Solyc03g118290 {ECO:0000305|PubMed:26716451};
Solanum lycopersicum (Tomato) (Lycopersicon esculentum).
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae;
Solaneae; Solanum; Lycopersicon.
NCBI_TaxID=4081 {ECO:0000312|EMBL:ABC69711.1};
[1] {ECO:0000312|EMBL:ABC69711.1}
NUCLEOTIDE SEQUENCE [MRNA].
STRAIN=cv. M82 {ECO:0000312|EMBL:ABC69711.1};
Mah S.A., Swanson W.J., Moy G.W., Vacquier V.D.;
Submitted (JAN-2017) to the EMBL/GenBank/DDBJ databases.
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Heinz 1706;
PubMed=22660326; DOI=10.1038/nature11119;
Tomato Genome Consortium;
"The tomato genome sequence provides insights into fleshy fruit
evolution.";
Nature 485:635-641(2012).
[3]
TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, AND PHYLOGENETIC ANALYSIS.
PubMed=21735233; DOI=10.1007/s00299-011-1113-z;
Wu J., Wang F., Cheng L., Kong F., Peng Z., Liu S., Yu X., Lu G.;
"Identification, isolation and expression analysis of auxin response
factor (ARF) genes in Solanum lycopersicum.";
Plant Cell Rep. 30:2059-2073(2011).
[4]
FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, INDUCTION, AND
DISRUPTION PHENOTYPE.
PubMed=26716451; DOI=10.1371/journal.pgen.1005649;
Hao Y., Hu G., Breitel D., Liu M., Mila I., Frasse P., Fu Y.,
Aharoni A., Bouzayen M., Zouine M.;
"Auxin response factor SlARF2 is an essential component of the
regulatory mechanism controlling fruit ripening in tomato.";
PLoS Genet. 11:E1005649-E1005649(2015).
[5]
FUNCTION, SUBUNIT, INTERACTION WITH ASR1, SUBCELLULAR LOCATION,
DEVELOPMENTAL STAGE, INDUCTION, AND DISRUPTION PHENOTYPE.
PubMed=26959229; DOI=10.1371/journal.pgen.1005903;
Breitel D.A., Chappell-Maor L., Meir S., Panizel I., Puig C.P.,
Hao Y., Yifhar T., Yasuor H., Zouine M., Bouzayen M.,
Granell Richart A., Rogachev I., Aharoni A.;
"AUXIN RESPONSE FACTOR 2 intersects hormonal signals in the regulation
of tomato fruit ripening.";
PLoS Genet. 12:E1005903-E1005903(2016).
[6]
FUNCTION, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, INDUCTION, AND
DISRUPTION PHENOTYPE.
PubMed=27645097; DOI=10.1038/srep33728;
Xu T., Liu X., Wang R., Dong X., Guan X., Wang Y., Jiang Y., Shi Z.,
Qi M., Li T.;
"SlARF2a plays a negative role in mediating axillary shoot
formation.";
Sci. Rep. 6:33728-33728(2016).
[7]
FUNCTION, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, INDUCTION, AND
PHYLOGENETIC ANALYSIS.
PubMed=28167023; DOI=10.1016/j.plantsci.2016.12.008;
Ren Z., Liu R., Gu W., Dong X.;
"The Solanum lycopersicum auxin response factor SlARF2 participates in
regulating lateral root formation and flower organ senescence.";
Plant Sci. 256:103-111(2017).
-!- FUNCTION: Auxin response factors (ARFs) are transcriptional
factors that bind specifically to the DNA sequence 5'-TGTCTC-3'
found in the auxin-responsive promoter elements (AuxREs) (By
similarity). Could act as transcriptional activator or repressor
(PubMed:26959229, PubMed:26716451, PubMed:27645097,
PubMed:28167023). Involved in the control of fruit ripening
process (PubMed:26959229, PubMed:26716451, PubMed:28167023).
Regulates expression of a number of ripening regulators,
transcription factors, and ethylene biosynthesis and signaling
components (PubMed:26959229, PubMed:26716451). May act as a
transcriptional repressor of auxin-responsive genes
(PubMed:26716451). Regulates vegetative growth, lateral root
formation and flower organ senescence, possibly partially by
regulating gene expression of auxin and ethylene response factor
(ERF) genes (PubMed:28167023). Plays a negative role in axillary
shoot meristem formation (PubMed:27645097).
{ECO:0000255|RuleBase:RU004561, ECO:0000269|PubMed:26716451,
ECO:0000269|PubMed:26959229, ECO:0000269|PubMed:27645097,
ECO:0000269|PubMed:28167023}.
-!- SUBUNIT: Homodimers and heterodimers. Interacts with ASR1.
{ECO:0000269|PubMed:26959229}.
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-
ProRule:PRU00326, ECO:0000255|RuleBase:RU004561,
ECO:0000255|SAAS:SAAS00552270, ECO:0000269|PubMed:26716451,
ECO:0000269|PubMed:26959229}.
-!- TISSUE SPECIFICITY: Expressed in root, leaf and flower
(PubMed:26716451, PubMed:27645097, PubMed:28167023,
PubMed:21735233). Expressed in flower buds about three days before
opening including ovary, petal and sepal with the highest in
stamen (PubMed:21735233). Expressed in stem (PubMed:26716451,
PubMed:28167023, PubMed:21735233). Expressed in fruit
(PubMed:26716451, PubMed:27645097, PubMed:28167023). Expressed in
seeds (PubMed:27645097). {ECO:0000269|PubMed:21735233,
ECO:0000269|PubMed:26716451, ECO:0000269|PubMed:27645097,
ECO:0000269|PubMed:28167023}.
-!- DEVELOPMENTAL STAGE: Expression increases at the orange (Or) and
red (R) fruit stages. Expression is increased with ethylene at
mature green (MG) stage, but only after six days post-treatment.
Expression is increased three days post-treatment with plant
hormone abscisic acid (ABA) at the Or stage, but not at the MG or
breaker (Br) stages. No change in expression level up to six days
post-treatment with ABA at the MG fruit stage (PubMed:26959229).
Expressed during floral development (PubMed:21735233,
PubMed:28167023, PubMed:27645097). During bud-anthesis stages
flowers exhibit dynamic expression pattern in sepal, stamen, ovary
and petal (PubMed:28167023). Expressed during ovary development
with the highest expression on the third day after the flower
fully opened (PubMed:21735233). During seed germination, expressed
in the cotyledon. Expressed strongly in the pollen grain.
Expressed in the developing fruits, in which mainly expressed in
the vascular tissues and seeds. During growth, strongly expressed
in leaf, where mainly expressed in the trichome and in the root
tip and lateral root formation sites. Expressed in the vascular
tissue and the epicycle of the root. Also expressed in branch
(PubMed:27645097). {ECO:0000269|PubMed:21735233,
ECO:0000269|PubMed:26959229, ECO:0000269|PubMed:27645097,
ECO:0000269|PubMed:28167023}.
-!- INDUCTION: By tomato fruit ripening. Expression in tomato fruits
is up-regulated by exogenous application of ethylene and down-
regulated by inhibition of ethylene receptors with 1-
methylcyclopropene (1-MCP) (PubMed:26959229, PubMed:26716451). Up-
regulated by plant hormone abscisic acid (ABA) in tomato fruits
(PubMed:26959229). Expression is not up-regulated by plant hormone
auxin in tomato fruits (PubMed:26716451). Up-regulated by auxin
and gibberellic acid (GA), and down-regulated by ethylene in
seedlings (PubMed:28167023). Down-regulated during decapitation-
induced axillary shoot development and by excision of immature
leaves. Down-regulation is inhibited by the application of auxin
on the cut surface (PubMed:27645097).
{ECO:0000269|PubMed:26716451, ECO:0000269|PubMed:26959229,
ECO:0000269|PubMed:27645097, ECO:0000269|PubMed:28167023}.
-!- DISRUPTION PHENOTYPE: Simultaneous RNAi-mediated silencing of both
ARF2A and ARF2B results in severe defects in tomato fruit ripening
process (PubMed:26959229, PubMed:26716451). Plants form triple
cotyledons and have enhanced root branching. Tomatoes have reduced
pigment accumulation, enhanced fruit firmness, low climacteric
ethylene production and inability to ripen upon exogenous
application of ethylene (PubMed:26716451). The fruits are either
parthenocarpic or contain only a few seeds, and the time from
anthesis to breaker (Br) developmental stage is significantly
extended compared to wild type fruit (PubMed:26959229). Altered
expression of ethylene biosynthesis, signaling and ethylene
response factor (ERF) genes and genes involved in the carotenoid
pathway and ripening-related cell wall metabolism. Up-regulates
auxin-responsive genes (PubMed:26716451). Down-regulated
expression levels of ripening regulators, including RIN, AP2a,
NOR, TAGL1, ETR3, ERF1 and CNR at the red (R) fruit stage.
Expression levels of hormones such as abscisates, cytokinins and
salicyclic acid are altered, and levels of carotenoids phytoene,
phytofluene and lycopene are reduced in red fruits. Gibberellic
acid (GA) and auxin expression levels are unchanged. Compounds
normally reduced upon ripening show higher levels than wild type
fruit as a result of simultaneous silencing of ARF2A and ARF2B
(PubMed:26959229). RNAi-mediated silencing of ARF2A results in
increased frequency of polycotyledons and significantly increased
lateral organ development. Lateral shoot emergence occurs at the
first leaf node compared to eighth leaf node in wild type. An
unusual meristem appears in the mature leaf and lateral shoot
development appears below the position of the cotyledon nodes.
Unusual lateral branches also appear in the stem, which is located
far from the leaf node. Epiderm is split along the axis at the
site of the unusual meristem. Abnormally enlarged interfascicular
cambia and phloem. Altered auxin distribution, and expression of
auxin transporter PIN genes and ectopic axillary shoot-related
transcriptional factors (PubMed:27645097).
{ECO:0000269|PubMed:26716451, ECO:0000269|PubMed:26959229,
ECO:0000269|PubMed:27645097}.
-!- SIMILARITY: Belongs to the ARF family.
{ECO:0000255|RuleBase:RU004561, ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; DQ340255; ABC69711.1; -; mRNA.
EMBL; CM001066; -; NOT_ANNOTATED_CDS; Genomic_DNA.
RefSeq; NP_001233765.1; NM_001246836.2.
UniGene; Les.20300; -.
SMR; Q2LAJ3; -.
STRING; 4081.Solyc03g118290.2.1; -.
PaxDb; Q2LAJ3; -.
EnsemblPlants; Solyc03g118290.2.1; Solyc03g118290.2.1; Solyc03g118290.2.
GeneID; 778240; -.
Gramene; Solyc03g118290.2.1; Solyc03g118290.2.1; Solyc03g118290.2.
KEGG; sly:778240; -.
eggNOG; ENOG410IE1Z; Eukaryota.
eggNOG; ENOG4110RNJ; LUCA.
OMA; HESAYTD; -.
OrthoDB; EOG09360207; -.
Proteomes; UP000004994; Chromosome 3.
GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
GO; GO:0046982; F:protein heterodimerization activity; IPI:UniProtKB.
GO; GO:0042803; F:protein homodimerization activity; IPI:UniProtKB.
GO; GO:0009734; P:auxin-activated signaling pathway; IEA:UniProtKB-KW.
GO; GO:0009835; P:fruit ripening; IEP:UniProtKB.
GO; GO:0009836; P:fruit ripening, climacteric; IMP:UniProtKB.
GO; GO:0009911; P:positive regulation of flower development; IEP:UniProtKB.
GO; GO:0006355; P:regulation of transcription, DNA-templated; IEA:UniProtKB-KW.
GO; GO:0006351; P:transcription, DNA-templated; IEA:UniProtKB-KW.
CDD; cd10017; B3_DNA; 1.
Gene3D; 2.40.330.10; -; 1.
InterPro; IPR033389; AUX/IAA_dom.
InterPro; IPR010525; Auxin_resp.
InterPro; IPR003340; B3_DNA-bd.
InterPro; IPR015300; DNA-bd_pseudobarrel_sf.
InterPro; IPR000270; PB1_dom.
Pfam; PF02309; AUX_IAA; 1.
Pfam; PF06507; Auxin_resp; 1.
Pfam; PF02362; B3; 1.
SMART; SM01019; B3; 1.
SUPFAM; SSF101936; SSF101936; 1.
PROSITE; PS50863; B3; 1.
PROSITE; PS51745; PB1; 1.
1: Evidence at protein level;
Auxin signaling pathway; Complete proteome; Developmental protein;
DNA-binding; Fruit ripening; Nucleus; Reference proteome;
Transcription; Transcription regulation.
CHAIN 1 846 Auxin response factor 2A.
/FTId=PRO_0000441018.
DOMAIN 720 804 PB1. {ECO:0000255|PROSITE-
ProRule:PRU01081}.
DNA_BIND 146 248 TF-B3. {ECO:0000255|PROSITE-
ProRule:PRU00326}.
SEQUENCE 846 AA; 94014 MW; D432F0CC4D7B5793 CRC64;
MAASEVSIQG YSEPSDGSRP VSETGRSSSG VGIVDADTAL YTELWRSCAG PLVTVPREGE
LVYYFPQGHI EQVEASTNQV ADQQMPLYNL PSKILCRVVN VLLKAEPDTD EVYAQVTLMP
EPNQDENAVK KEPMRPPPPR FHVHSFCKTL TASDTSTHGG FSVLRRHADE CLPQLDMSRQ
PPTQELVAKD LHGNEWRFRH IFRGQPRRHL LQSGWSVFVS SKRLVAGDAF IFLRGENGEL
RVGVRRAMRQ QGNAPSSVIS SHSMHLGVLA TAWHAIQTKT MFTVYYKPRT SPAEFIVPYD
HYMESVKNNY SIGMRFKMRF EGEEAPEQRF TGTIVGIEDA DPQRWLESKW RCLKVRWDEN
SSIPRPDRVS PWKIEPALSP PALNVPPVAR PKRPRSSILP TSPDSSVLTR EGSSRATADH
SQASGFPRVL QGQELSTFRG GFAEINETDL SEKPMIWQTS VNDEKNDIHS ASKRYLPDKW
LPLGRPESSL TDLLSGFGSS HGFCLPSADQ AAFGARLVKQ QTQDQEKDFS LLGKPWSLLS
SGLSLNLMDS GSKAPGIGGD TPYQMRGDAR YSGYGEFSVL PGHRVANQQG SWIMPQPVSP
YMQLSSHSRE MMHKPSVVKQ PEAVKPKEGN YKLFGIPLTS NVCTDAVMMR KSSLIDPASD
MNIGIHPHQS LATDSDQRSE QSKGSKVDDG VAANDHDKQF HTFHLAARDK DGKGHSSSTR
SCTKVHKQGT ALGRSVDLAK FNNYDELIAE LDQLFDFNGE LKARSKSWLV VYTDDEGDMM
LVGDDPWQEF CGMVRKIFIY TKEEVQRMNP GTLNSKGEDT SSVAEGSDAK EVKNLQLPSE
SGQAES


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