SIGF_ARATH
ID SIGF_ARATH Reviewed; 547 AA.
AC Q9LD95; Q9SJK8; Q9SMV8;
DT 11-JUL-2012, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 146.
DE RecName: Full=RNA polymerase sigma factor sigF, chloroplastic;
DE Short=Sigma factor F;
DE Short=Sigma-F;
DE AltName: Full=Protein SINGLET OXYGEN-LINKED DEATH ACTIVATOR 8;
DE AltName: Full=RNA polymerase sigma factor sig6;
DE Short=Atsig6;
DE Short=Sigma factor 6;
DE Flags: Precursor;
GN Name=SIGF; Synonyms=SIG6, SOLDAT8; OrderedLocusNames=At2g36990;
GN ORFNames=T1J8;
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], AND SUBCELLULAR LOCATION.
RX PubMed=10984613; DOI=10.1016/s0014-5793(00)01965-7;
RA Fujiwara M., Nagashima A., Kanamaru K., Tanaka K., Takahashi H.;
RT "Three new nuclear genes, sigD, sigE and sigF, encoding putative plastid
RT RNA polymerase sigma factors in Aarabidopsis thaliana.";
RL FEBS Lett. 481:47-52(2000).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC STRAIN=cv. Columbia;
RA Hoffmann M., Binder S.;
RT "Arabidopsis thaliana gene for sigma factor-like protein.";
RL Submitted (APR-2000) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10617197; DOI=10.1038/45471;
RA Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL Nature 402:761-768(1999).
RN [4]
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 [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [6]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 61-547.
RC STRAIN=cv. C24;
RX PubMed=10734058; DOI=10.1074/jbc.275.13.9215;
RA Hakimi M.-A., Privat I., Valay J.-G., Lerbs-Mache S.;
RT "Evolutionary conservation of C-terminal domains of primary sigma(70)-type
RT transcription factors between plants and bacteria.";
RL J. Biol. Chem. 275:9215-9221(2000).
RN [7]
RP GENE FAMILY, AND NOMENCLATURE.
RC STRAIN=cv. Columbia; TISSUE=Seedling hypocotyl;
RX PubMed=10946105; DOI=10.1016/s0300-9084(00)00611-8;
RA Allison L.A.;
RT "The role of sigma factors in plastid transcription.";
RL Biochimie 82:537-548(2000).
RN [8]
RP INDUCTION BY BLUE LIGHT.
RC STRAIN=cv. Columbia;
RX PubMed=11959137; DOI=10.1016/s0014-5793(02)02538-3;
RA Tsunoyama Y., Morikawa K., Shiina T., Toyoshima Y.;
RT "Blue light specific and differential expression of a plastid sigma factor,
RT Sig5 in Arabidopsis thaliana.";
RL FEBS Lett. 516:225-228(2002).
RN [9]
RP FUNCTION, DISRUPTION PHENOTYPE, TISSUE SPECIFICITY, AND INDUCTION BY LIGHT.
RC STRAIN=cv. Columbia;
RX PubMed=15807777; DOI=10.1111/j.1365-313x.2005.02362.x;
RA Ishizaki Y., Tsunoyama Y., Hatano K., Ando K., Kato K., Shinmyo A.,
RA Kobori M., Takeba G., Nakahira Y., Shiina T.;
RT "A nuclear-encoded sigma factor, Arabidopsis SIG6, recognizes sigma-70 type
RT chloroplast promoters and regulates early chloroplast development in
RT cotyledons.";
RL Plant J. 42:133-144(2005).
RN [10]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=17118361; DOI=10.1016/j.febslet.2006.11.010;
RA Schweer J., Loschelder H., Link G.;
RT "A promoter switch that can rescue a plant sigma factor mutant.";
RL FEBS Lett. 580:6617-6622(2006).
RN [11]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=16905663; DOI=10.1104/pp.106.085878;
RA Loschelder H., Schweer J., Link B., Link G.;
RT "Dual temporal role of plastid sigma factor 6 in Arabidopsis development.";
RL Plant Physiol. 142:642-650(2006).
RN [12]
RP INDUCTION BY LIGHT.
RX PubMed=18532976; DOI=10.1111/j.1365-313x.2008.03567.x;
RA Onda Y., Yagi Y., Saito Y., Takenaka N., Toyoshima Y.;
RT "Light induction of Arabidopsis SIG1 and SIG5 transcripts in mature leaves:
RT differential roles of cryptochrome 1 and cryptochrome 2 and dual function
RT of SIG5 in the recognition of plastid promoters.";
RL Plant J. 55:968-978(2008).
RN [13]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=19273469; DOI=10.1093/pcp/pcp036;
RA Coll N.S., Danon A., Meurer J., Cho W.K., Apel K.;
RT "Characterization of soldat8, a suppressor of singlet oxygen-induced cell
RT death in Arabidopsis seedlings.";
RL Plant Cell Physiol. 50:707-718(2009).
RN [14]
RP PHOSPHORYLATION AT SER-94; SER-95; SER-174; SER-176; SER-177; SER-180 AND
RP THR-249 BY CK2, AND MUTAGENESIS OF SER-94; SER-95; 94-SER-SER-95; SER-174;
RP SER-176; SER-177; SER-180 AND THR-249.
RX PubMed=20088902; DOI=10.1111/j.1365-313x.2010.04138.x;
RA Schweer J., Tuerkeri H., Link B., Link G.;
RT "AtSIG6, a plastid sigma factor from Arabidopsis, reveals functional impact
RT of cpCK2 phosphorylation.";
RL Plant J. 62:192-202(2010).
RN [15]
RP FUNCTION, AND INTERACTION WITH DG1.
RX PubMed=20626654; DOI=10.1111/j.1365-313x.2010.04304.x;
RA Chi W., Mao J., Li Q., Ji D., Zou M., Lu C., Zhang L.;
RT "Interaction of the pentatricopeptide-repeat protein DELAYED GREENING 1
RT with sigma factor SIG6 in the regulation of chloroplast gene expression in
RT Arabidopsis cotyledons.";
RL Plant J. 64:14-25(2010).
CC -!- FUNCTION: Sigma factors are initiation factors that promote the
CC attachment of plastid-encoded RNA polymerase (PEP) to specific
CC initiation sites and are then released. Regulates transcription in
CC chloroplast in a DG1-dependent manner. Involved in light-dependent
CC chloroplast development. Required during early plant development and
CC primary leaf formation. {ECO:0000269|PubMed:15807777,
CC ECO:0000269|PubMed:16905663, ECO:0000269|PubMed:17118361,
CC ECO:0000269|PubMed:19273469, ECO:0000269|PubMed:20626654}.
CC -!- SUBUNIT: Interacts (via N-terminus) with DG1 (via C-terminus).
CC {ECO:0000269|PubMed:20626654}.
CC -!- INTERACTION:
CC Q9LD95; Q9LQT8: GAI; NbExp=4; IntAct=EBI-4455937, EBI-963606;
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000269|PubMed:10984613}.
CC -!- TISSUE SPECIFICITY: Expressed in seedling, accumulating progressively.
CC Present in leaves but not in roots. {ECO:0000269|PubMed:15807777}.
CC -!- INDUCTION: Induced by red light. Slightly induced by blue light.
CC {ECO:0000269|PubMed:11959137, ECO:0000269|PubMed:15807777,
CC ECO:0000269|PubMed:18532976}.
CC -!- PTM: Phosphorylated to acquire sigma activity; site-specific
CC phosphorylation regulates promoter affinity. Phosphorylation at Ser-174
CC by chloroplastic CK2 requires prior phosphorylation at Ser-177.
CC Phosphorylation at either Ser-94, Ser-95 or Ser-174 is required for
CC sigma activation. {ECO:0000269|PubMed:20088902}.
CC -!- DISRUPTION PHENOTYPE: Chlorophyll-defective seedlings with reduced
CC levels of chloroplast-encoded transcripts (e.g. atpB, atpE and rbcL).
CC Delayed light-dependent chloroplast development. Constitutive
CC acclimation to light stress. Suppressor of FLU disruption phenotype;
CC seedlings missing both FLU and SIGF do not bleach when grown under non-
CC permissive dark/light conditions. {ECO:0000269|PubMed:15807777,
CC ECO:0000269|PubMed:16905663, ECO:0000269|PubMed:17118361,
CC ECO:0000269|PubMed:19273469}.
CC -!- SIMILARITY: Belongs to the sigma-70 factor family. {ECO:0000305}.
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DR EMBL; AB029916; BAA92288.1; -; mRNA.
DR EMBL; AJ277389; CAB89775.1; -; mRNA.
DR EMBL; AC006922; AAD31584.2; -; Genomic_DNA.
DR EMBL; CP002685; AEC09332.1; -; Genomic_DNA.
DR EMBL; AY059768; AAL24116.1; -; mRNA.
DR EMBL; AY091182; AAM14121.1; -; mRNA.
DR EMBL; AJ250812; CAB60192.1; -; mRNA.
DR PIR; B84787; B84787.
DR PIR; T52653; T52653.
DR RefSeq; NP_565856.1; NM_129255.3.
DR AlphaFoldDB; Q9LD95; -.
DR SMR; Q9LD95; -.
DR BioGRID; 3617; 7.
DR IntAct; Q9LD95; 7.
DR MINT; Q9LD95; -.
DR STRING; 3702.AT2G36990.1; -.
DR iPTMnet; Q9LD95; -.
DR PaxDb; Q9LD95; -.
DR PRIDE; Q9LD95; -.
DR ProteomicsDB; 234579; -.
DR EnsemblPlants; AT2G36990.1; AT2G36990.1; AT2G36990.
DR GeneID; 818273; -.
DR Gramene; AT2G36990.1; AT2G36990.1; AT2G36990.
DR KEGG; ath:AT2G36990; -.
DR Araport; AT2G36990; -.
DR TAIR; locus:2057996; AT2G36990.
DR eggNOG; ENOG502QVXR; Eukaryota.
DR HOGENOM; CLU_014793_11_1_1; -.
DR InParanoid; Q9LD95; -.
DR OMA; IYANFRL; -.
DR OrthoDB; 1191135at2759; -.
DR PhylomeDB; Q9LD95; -.
DR PRO; PR:Q9LD95; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; Q9LD95; baseline and differential.
DR Genevisible; Q9LD95; AT.
DR GO; GO:0009507; C:chloroplast; IDA:TAIR.
DR GO; GO:0009536; C:plastid; IDA:TAIR.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0016987; F:sigma factor activity; IDA:TAIR.
DR GO; GO:0071483; P:cellular response to blue light; IEP:UniProtKB.
DR GO; GO:0071482; P:cellular response to light stimulus; IMP:UniProtKB.
DR GO; GO:0006352; P:DNA-templated transcription, initiation; ISS:UniProtKB.
DR GO; GO:0045893; P:positive regulation of transcription, DNA-templated; IMP:TAIR.
DR GO; GO:0090351; P:seedling development; IMP:TAIR.
DR Gene3D; 1.10.10.10; -; 2.
DR InterPro; IPR014284; RNA_pol_sigma-70_dom.
DR InterPro; IPR000943; RNA_pol_sigma70.
DR InterPro; IPR007627; RNA_pol_sigma70_r2.
DR InterPro; IPR007624; RNA_pol_sigma70_r3.
DR InterPro; IPR007630; RNA_pol_sigma70_r4.
DR InterPro; IPR013325; RNA_pol_sigma_r2.
DR InterPro; IPR013324; RNA_pol_sigma_r3/r4-like.
DR InterPro; IPR016262; RNA_pol_sigma_SigB/C/D/F.
DR InterPro; IPR036388; WH-like_DNA-bd_sf.
DR Pfam; PF04542; Sigma70_r2; 1.
DR Pfam; PF04539; Sigma70_r3; 1.
DR Pfam; PF04545; Sigma70_r4; 1.
DR PIRSF; PIRSF000767; RNA_pol_sigma_SigB/C/D; 1.
DR PRINTS; PR00046; SIGMA70FCT.
DR SUPFAM; SSF88659; SSF88659; 2.
DR SUPFAM; SSF88946; SSF88946; 1.
DR TIGRFAMs; TIGR02937; sigma70-ECF; 1.
DR PROSITE; PS00715; SIGMA70_1; 1.
DR PROSITE; PS00716; SIGMA70_2; 1.
PE 1: Evidence at protein level;
KW Chloroplast; DNA-binding; Phosphoprotein; Plastid; Reference proteome;
KW Sigma factor; Transcription; Transcription regulation; Transit peptide.
FT TRANSIT 1..55
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 56..547
FT /note="RNA polymerase sigma factor sigF, chloroplastic"
FT /id="PRO_0000418097"
FT DNA_BIND 505..524
FT /note="H-T-H motif"
FT /evidence="ECO:0000250"
FT REGION 1..28
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 54..79
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 163..226
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 335..348
FT /note="Polymerase core binding"
FT COMPBIAS 65..79
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 167..184
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 200..226
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 94
FT /note="Phosphoserine; by CK2"
FT /evidence="ECO:0000269|PubMed:20088902"
FT MOD_RES 95
FT /note="Phosphoserine; by CK2"
FT /evidence="ECO:0000269|PubMed:20088902"
FT MOD_RES 174
FT /note="Phosphoserine; by CK2"
FT /evidence="ECO:0000269|PubMed:20088902"
FT MOD_RES 176
FT /note="Phosphoserine; by CK2"
FT /evidence="ECO:0000269|PubMed:20088902"
FT MOD_RES 177
FT /note="Phosphoserine; by CK2"
FT /evidence="ECO:0000269|PubMed:20088902"
FT MOD_RES 180
FT /note="Phosphoserine; by CK2"
FT /evidence="ECO:0000269|PubMed:20088902"
FT MOD_RES 249
FT /note="Phosphothreonine; by CK2"
FT /evidence="ECO:0000269|PubMed:20088902"
FT MUTAGEN 94..95
FT /note="SS->AA: Chlorophyll-defective seedlings."
FT /evidence="ECO:0000269|PubMed:20088902"
FT MUTAGEN 94
FT /note="S->A: Loss of sigma factor activity but green
FT seedlings."
FT /evidence="ECO:0000269|PubMed:20088902"
FT MUTAGEN 95
FT /note="S->A: Loss of sigma factor activity but green
FT seedlings."
FT /evidence="ECO:0000269|PubMed:20088902"
FT MUTAGEN 174
FT /note="S->A: Loss of sigma factor activity and chlorophyll-
FT defective seedlings."
FT /evidence="ECO:0000269|PubMed:20088902"
FT MUTAGEN 174
FT /note="S->Q: Chlorophyll-defective seedlings."
FT /evidence="ECO:0000269|PubMed:20088902"
FT MUTAGEN 176
FT /note="S->A: Normal sigma factor activity upon
FT phosphorylation but green seedlings."
FT /evidence="ECO:0000269|PubMed:20088902"
FT MUTAGEN 177
FT /note="S->A,D: Chlorophyll-defective seedlings."
FT /evidence="ECO:0000269|PubMed:20088902"
FT MUTAGEN 180
FT /note="S->A: Loss of sigma factor activity but green
FT seedlings."
FT /evidence="ECO:0000269|PubMed:20088902"
FT MUTAGEN 249
FT /note="T->A: Reduced sigma factor activity upon
FT phosphorylation but green seedlings."
FT /evidence="ECO:0000269|PubMed:20088902"
SQ SEQUENCE 547 AA; 61797 MW; DA75EC67B4542CB6 CRC64;
MEATRNLVSS SPSFQTKTHL KSSYSSPSSV VMLHDQTTTP VVNSRHLNSL SRHFPASVLS
QEPREESRPL SHALRDDRTS QLTLERRQFD ELVSSREDEK FEQQLLHSTG LWNLLISPLT
SETKLPAVVS PLADAELCDV VALAQKALSA SKQAALLVDD TEANPSDNIK DSLSTSSSMS
LPEKGNIVRS KRQLERRAKN RRAPKSNDVD DEGYVPQKTS AKKKYKQGAD NDDALQLFLW
GPETKQLLTA KEEAELISHI QHLLKLEKVK TKLESQNGCE PTIGEWAEAM GISSPVLKSD
IHRGRSSREK LITANLRLVV HIAKQYQNRG LNFQDLLQEG SMGLMKSVEK FKPQSGCRFA
TYAYWWIRQS IRKSIFQNSR TIRLPENVYM LLGKVSEARK TCVQEGNYRP SKEELAGHVG
VSTEKLDKLL YNTRTPLSMQ QPIWSDQDTT FQEITPDSGI ETPTMSVGKQ LMRNHVRNLL
NVLSPKERRI IKLRFGIDGG KQRSLSEIGE IYGLSKERVR QLESRALYRL KQNMNSHGLH
AYADLLV
