SIGD_ARATH
ID SIGD_ARATH Reviewed; 419 AA.
AC Q9ZSL6; Q9SXP8;
DT 11-JUL-2012, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-1999, sequence version 1.
DT 03-AUG-2022, entry version 147.
DE RecName: Full=RNA polymerase sigma factor sigD, chloroplastic;
DE Short=Sigma factor D;
DE Short=Sigma-D;
DE AltName: Full=RNA polymerase sigma factor sig4;
DE Short=Atsig4;
DE Short=Sigma factor 4;
DE Flags: Precursor;
GN Name=SIGD; Synonyms=SIG4; OrderedLocusNames=At5g13730; ORFNames=MSH12.20;
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] (ISOFORM 1), TISSUE SPECIFICITY, AND INDUCTION
RP BY LIGHT.
RA Yao J., Allison L.A.;
RT "The cDNA sequence of AtSIG4, a new member of the nuclear-encoded sigma-
RT like factor gene family in Arabidopsis thaliana.";
RL (er) Plant Gene Register PGR98-212(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORMS 1 AND 2).
RC STRAIN=cv. Columbia;
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 [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=9405937; DOI=10.1093/dnares/4.4.291;
RA Kotani H., Nakamura Y., Sato S., Kaneko T., Asamizu E., Miyajima N.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. II. Sequence
RT features of the regions of 1,044,062 bp covered by thirteen physically
RT assigned P1 clones.";
RL DNA Res. 4:291-300(1997).
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] (ISOFORM 2).
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 TISSUE SPECIFICITY, INDUCTION BY LIGHT, 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 [7]
RP INDUCTION BY 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 [8]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia, and cv. Wassilewskija;
RX PubMed=16243785; DOI=10.1093/nar/gki908;
RA Favory J.-J., Kobayshi M., Tanaka K., Peltier G., Kreis M., Valay J.-G.,
RA Lerbs-Mache S.;
RT "Specific function of a plastid sigma factor for ndhF gene transcription.";
RL Nucleic Acids Res. 33:5991-5999(2005).
RN [9]
RP TISSUE SPECIFICITY.
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 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).
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 of the
CC ndhF gene which codes for a subunit of the plastid NDH [NAD(P)H
CC dehydrogenase] complex. {ECO:0000269|PubMed:16243785}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast {ECO:0000250}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q9ZSL6-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9ZSL6-2; Sequence=VSP_043970, VSP_043971;
CC -!- TISSUE SPECIFICITY: Mostly expressed in leaves, and to a lesser extent
CC in roots. Present in seedlings. {ECO:0000269|PubMed:10946105,
CC ECO:0000269|PubMed:15807777, ECO:0000269|Ref.1}.
CC -!- INDUCTION: Slightly induced by blue light, especially after dark
CC adaptation. {ECO:0000269|PubMed:10946105, ECO:0000269|PubMed:11959137,
CC ECO:0000269|PubMed:18532976, ECO:0000269|Ref.1}.
CC -!- DISRUPTION PHENOTYPE: Reduced transcription of the plastid ndhF gene.
CC {ECO:0000269|PubMed:16243785}.
CC -!- SIMILARITY: Belongs to the sigma-70 factor family. {ECO:0000305}.
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DR EMBL; AF101075; AAC97954.1; -; mRNA.
DR EMBL; AB021119; BAA78110.1; -; Genomic_DNA.
DR EMBL; AB021119; BAA78111.1; -; Genomic_DNA.
DR EMBL; AB006704; BAB08700.1; -; Genomic_DNA.
DR EMBL; CP002688; AED91933.1; -; Genomic_DNA.
DR EMBL; AY059907; AAL24389.1; -; mRNA.
DR EMBL; AY114689; AAM48008.1; -; mRNA.
DR PIR; T51715; T51715.
DR RefSeq; NP_196877.1; NM_121376.4. [Q9ZSL6-1]
DR AlphaFoldDB; Q9ZSL6; -.
DR SMR; Q9ZSL6; -.
DR BioGRID; 16496; 1.
DR IntAct; Q9ZSL6; 1.
DR STRING; 3702.AT5G13730.1; -.
DR PaxDb; Q9ZSL6; -.
DR PRIDE; Q9ZSL6; -.
DR EnsemblPlants; AT5G13730.1; AT5G13730.1; AT5G13730. [Q9ZSL6-1]
DR GeneID; 831218; -.
DR Gramene; AT5G13730.1; AT5G13730.1; AT5G13730. [Q9ZSL6-1]
DR KEGG; ath:AT5G13730; -.
DR Araport; AT5G13730; -.
DR TAIR; locus:2173249; AT5G13730.
DR eggNOG; ENOG502QPRS; Eukaryota.
DR HOGENOM; CLU_014793_3_4_1; -.
DR InParanoid; Q9ZSL6; -.
DR OMA; AFFKEMA; -.
DR OrthoDB; 1191135at2759; -.
DR PhylomeDB; Q9ZSL6; -.
DR PRO; PR:Q9ZSL6; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9ZSL6; baseline and differential.
DR Genevisible; Q9ZSL6; AT.
DR GO; GO:0009507; C:chloroplast; ISS:UniProtKB.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0016987; F:sigma factor activity; IMP:UniProtKB.
DR GO; GO:0071482; P:cellular response to light stimulus; IEP:UniProtKB.
DR GO; GO:0006352; P:DNA-templated transcription, initiation; ISS:UniProtKB.
DR GO; GO:2001141; P:regulation of RNA biosynthetic process; IMP:UniProtKB.
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.
PE 2: Evidence at transcript level;
KW Alternative splicing; Chloroplast; DNA-binding; Plastid;
KW Reference proteome; Sigma factor; Transcription; Transcription regulation;
KW Transit peptide.
FT TRANSIT 1..52
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 53..419
FT /note="RNA polymerase sigma factor sigD, chloroplastic"
FT /id="PRO_0000418096"
FT DNA_BIND 377..396
FT /note="H-T-H motif"
FT /evidence="ECO:0000250"
FT MOTIF 207..220
FT /note="Polymerase core binding"
FT VAR_SEQ 258..267
FT /note="GSMWELTAKV -> LVVCREACGS (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14593172"
FT /id="VSP_043970"
FT VAR_SEQ 268..419
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14593172"
FT /id="VSP_043971"
SQ SEQUENCE 419 AA; 47165 MW; A64364EA914CE895 CRC64;
MATTIPTTAT ATMCPSPPVP TISPLLRTTH QCQPSPSLSS PFSIKLSTAL VCGDTTVDRV
VDSSVMIKPE KWGIQSEKRR KRRRRRRVGY ERLEPEEEEN AGVEAEAETI SVPVVGASRS
GFLSRLEEVQ LCLYLKEGAK LENLGTSVEE NEMVSVLLAS GRGKKKRSAN EILCRRKEAR
EKITRCYRRL VVSIATGYQG KGLNLQDLIQ EGSIGLLRGA ERFDPDRGYK LSTYVYWWIK
QAILRAIAHK SRLVKLPGSM WELTAKVAEA SNVLTRKLRR QPSCEEIAEH LNLNVSAVRL
AVERSRSPVS LDRVASQNGR MTLQEIVRGP DETRPEEMVK REHMKHEIEQ LLGSLTARES
RVLGLYFGLN GETPMSFEEI GKSLKLSRER VRQINGIALK KLRNVHNVND LKIYYSSSE
