ID SIGE_ARATH Reviewed; 517 AA.
AC Q9ZNX9; Q56Y78; Q94AW4;
DT 11-JUL-2012, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-1999, sequence version 1.
DT 27-MAR-2024, entry version 160.
DE RecName: Full=RNA polymerase sigma factor sigE, chloroplastic/mitochondrial;
DE Short=Sigma factor E;
DE Short=Sigma-E;
DE AltName: Full=RNA polymerase sigma factor sig5;
DE Short=Atsig5;
DE Short=Sigma factor 5;
DE Flags: Precursor;
GN Name=SIGE; Synonyms=SIG5; OrderedLocusNames=At5g24120; ORFNames=MLE8.4;
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 [GENOMIC DNA].
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 [2]
RP NUCLEOTIDE SEQUENCE [MRNA].
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 [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=9679202; DOI=10.1093/dnares/5.2.131;
RA Kaneko T., Kotani H., Nakamura Y., Sato S., Asamizu E., Miyajima N.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. V. Sequence
RT features of the regions of 1,381,565 bp covered by twenty one physically
RT assigned P1 and TAC clones.";
RL DNA Res. 5:131-145(1998).
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=19423640; DOI=10.1093/dnares/dsp009;
RA Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M.,
RA Shinozaki K.;
RT "Analysis of multiple occurrences of alternative splicing events in
RT Arabidopsis thaliana using novel sequenced full-length cDNAs.";
RL DNA Res. 16:155-164(2009).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-281.
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 [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-269.
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases.
RN [8]
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 [9]
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 [10]
RP FUNCTION, DISRUPTION PHENOTYPE, TISSUE SPECIFICITY, SUBCELLULAR LOCATION,
RP AND ISOFORMS 1 AND 2.
RC STRAIN=cv. Columbia, and cv. Wassilewskija;
RX PubMed=12805603; DOI=10.1104/pp.102.017913;
RA Yao J., Roy-Chowdhury S., Allison L.A.;
RT "AtSig5 is an essential nucleus-encoded Arabidopsis sigma-like factor.";
RL Plant Physiol. 132:739-747(2003).
RN [11]
RP FUNCTION, DISRUPTION PHENOTYPE, TISSUE SPECIFICITY, AND INDUCTION BY BLUE
RP LIGHT.
RC STRAIN=cv. Columbia;
RX PubMed=14976253; DOI=10.1073/pnas.0308362101;
RA Tsunoyama Y., Ishizaki Y., Morikawa K., Kobori M., Nakahira Y., Takeba G.,
RA Toyoshima Y., Shiina T.;
RT "Blue light-induced transcription of plastid-encoded psbD gene is mediated
RT by a nuclear-encoded transcription initiation factor, AtSig5.";
RL Proc. Natl. Acad. Sci. U.S.A. 101:3304-3309(2004).
RN [12]
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 [13]
RP FUNCTION, INDUCTION BY LIGHT, AND MUTAGENESIS OF ASN-484 AND ARG-493.
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 [14]
RP DISRUPTION PHENOTYPE, INTERACTION WITH PIA2/ANK6, SUBCELLULAR LOCATION, AND
RP DEVELOPMENTAL STAGE.
RC STRAIN=cv. Columbia;
RX PubMed=21123745; DOI=10.1073/pnas.1015911107;
RA Yu F., Shi J., Zhou J., Gu J., Chen Q., Li J., Cheng W., Mao D., Tian L.,
RA Buchanan B.B., Li L., Chen L., Li D., Luan S.;
RT "ANK6, a mitochondrial ankyrin repeat protein, is required for male-female
RT gamete recognition in Arabidopsis thaliana.";
RL Proc. Natl. Acad. Sci. U.S.A. 107:22332-22337(2010).
CC -!- FUNCTION: Essential protein. Sigma factors are initiation factors that
CC promote the attachment of plastid-encoded RNA polymerase (PEP) to
CC specific initiation sites (e.g. psbA and psbD) and are then released.
CC Essential for blue light-mediated transcription of psbD, which encodes
CC the photosystem II reaction center protein D2. Plays a role in
CC reproduction. Required during female gametophyte development
CC (PubMed:21123745). {ECO:0000269|PubMed:12805603,
CC ECO:0000269|PubMed:14976253, ECO:0000269|PubMed:18532976,
CC ECO:0000269|PubMed:21123745}.
CC -!- SUBUNIT: Interacts with PIA2/ANK6 in mitochondrion.
CC {ECO:0000269|PubMed:21123745}.
CC -!- INTERACTION:
CC Q9ZNX9; Q9FNP4: PIA2; NbExp=4; IntAct=EBI-15343551, EBI-4435148;
CC -!- SUBCELLULAR LOCATION: [Isoform 1]: Plastid, chloroplast.
CC -!- SUBCELLULAR LOCATION: [Isoform 2]: Mitochondrion
CC {ECO:0000269|PubMed:21123745}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q9ZNX9-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9ZNX9-2; Sequence=VSP_043972;
CC -!- TISSUE SPECIFICITY: Mostly expressed in siliques and flowers, to a
CC lesser extent in leaves and stems, and barely expressed in roots (at
CC protein level). Isoform 2 accumulates specifically in flowers, whereas
CC isoform 1 is expressed in both leaves and flowers. Present in old
CC seedlings (8 days). {ECO:0000269|PubMed:10946105,
CC ECO:0000269|PubMed:12805603, ECO:0000269|PubMed:14976253,
CC ECO:0000269|PubMed:15807777}.
CC -!- DEVELOPMENTAL STAGE: Highly expressed in the male and female
CC gametophytes and in seedlings. {ECO:0000269|PubMed:21123745}.
CC -!- INDUCTION: Induced by blue light illumination (470 nm), especially
CC after dark adaptation. Induction is mediated through both cryptochrome
CC 1 and cryptochrome 2 at lower light intensities and mainly through
CC cryptochrome 1 at higher light intensities.
CC {ECO:0000269|PubMed:10946105, ECO:0000269|PubMed:11959137,
CC ECO:0000269|PubMed:14976253, ECO:0000269|PubMed:18532976}.
CC -!- DISRUPTION PHENOTYPE: Lethal. In heterozygous plants, aborted embryos
CC and unfertilized ovules. Defects in female gametophyte development at
CC the one-nucleate stage and white shriveled ovule (PubMed:12805603,
CC PubMed:14976253, PubMed:21123745). Loss of transcription activation of
CC psbD in chloroplasts in response to light (PubMed:12805603,
CC PubMed:14976253). {ECO:0000269|PubMed:12805603,
CC ECO:0000269|PubMed:14976253, ECO:0000269|PubMed:21123745}.
CC -!- SIMILARITY: Belongs to the sigma-70 factor family. {ECO:0000305}.
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DR EMBL; AB021120; BAA78109.1; -; Genomic_DNA.
DR EMBL; Y18550; CAA77213.1; -; mRNA.
DR EMBL; AB010696; BAB11572.1; -; Genomic_DNA.
DR EMBL; CP002688; AED93259.1; -; Genomic_DNA.
DR EMBL; CP002688; ANM68680.1; -; Genomic_DNA.
DR EMBL; CP002688; ANM68681.1; -; Genomic_DNA.
DR EMBL; AK316888; BAH19595.1; -; mRNA.
DR EMBL; AY045660; AAK74018.1; -; mRNA.
DR EMBL; AK221445; BAD94495.1; -; mRNA.
DR PIR; T51328; T51328.
DR RefSeq; NP_001330408.1; NM_001343842.1. [Q9ZNX9-1]
DR RefSeq; NP_001330409.1; NM_001343841.1. [Q9ZNX9-1]
DR RefSeq; NP_197800.1; NM_122317.4. [Q9ZNX9-1]
DR AlphaFoldDB; Q9ZNX9; -.
DR SMR; Q9ZNX9; -.
DR BioGRID; 17752; 3.
DR DIP; DIP-60440N; -.
DR IntAct; Q9ZNX9; 3.
DR STRING; 3702.Q9ZNX9; -.
DR PaxDb; 3702-AT5G24120-1; -.
DR ProteomicsDB; 234546; -. [Q9ZNX9-1]
DR EnsemblPlants; AT5G24120.1; AT5G24120.1; AT5G24120. [Q9ZNX9-1]
DR EnsemblPlants; AT5G24120.2; AT5G24120.2; AT5G24120. [Q9ZNX9-1]
DR EnsemblPlants; AT5G24120.3; AT5G24120.3; AT5G24120. [Q9ZNX9-1]
DR GeneID; 832477; -.
DR Gramene; AT5G24120.1; AT5G24120.1; AT5G24120. [Q9ZNX9-1]
DR Gramene; AT5G24120.2; AT5G24120.2; AT5G24120. [Q9ZNX9-1]
DR Gramene; AT5G24120.3; AT5G24120.3; AT5G24120. [Q9ZNX9-1]
DR KEGG; ath:AT5G24120; -.
DR Araport; AT5G24120; -.
DR TAIR; AT5G24120; SIGE.
DR eggNOG; ENOG502QRMD; Eukaryota.
DR HOGENOM; CLU_014793_3_4_1; -.
DR InParanoid; Q9ZNX9; -.
DR OMA; KITPERY; -.
DR OrthoDB; 33789at2759; -.
DR PhylomeDB; Q9ZNX9; -.
DR PRO; PR:Q9ZNX9; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9ZNX9; baseline and differential.
DR Genevisible; Q9ZNX9; AT.
DR GO; GO:0009507; C:chloroplast; IDA:UniProtKB.
DR GO; GO:0005739; C:mitochondrion; IDA:UniProtKB.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0016987; F:sigma factor activity; IMP:UniProtKB.
DR GO; GO:0071483; P:cellular response to blue light; IEP:UniProtKB.
DR GO; GO:0071472; P:cellular response to salt stress; IMP:TAIR.
DR GO; GO:0009658; P:chloroplast organization; IMP:TAIR.
DR GO; GO:0006352; P:DNA-templated transcription initiation; ISS:UniProtKB.
DR GO; GO:0009553; P:embryo sac development; IMP:UniProtKB.
DR GO; GO:0010207; P:photosystem II assembly; IMP:UniProtKB.
DR GO; GO:0045893; P:positive regulation of DNA-templated transcription; IMP:TAIR.
DR GO; GO:2001141; P:regulation of RNA biosynthetic process; IMP:UniProtKB.
DR GO; GO:0010218; P:response to far red light; IEP:TAIR.
DR GO; GO:0010114; P:response to red light; IEP:TAIR.
DR Gene3D; 1.10.601.10; RNA Polymerase Primary Sigma Factor; 1.
DR Gene3D; 1.10.10.10; Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain; 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; IPR036388; WH-like_DNA-bd_sf.
DR NCBIfam; TIGR02937; sigma70-ECF; 1.
DR PANTHER; PTHR30603; RNA POLYMERASE SIGMA FACTOR RPO; 1.
DR PANTHER; PTHR30603:SF4; RNA POLYMERASE SIGMA FACTOR SIGE, CHLOROPLASTIC_MITOCHONDRIAL; 1.
DR Pfam; PF04542; Sigma70_r2; 1.
DR Pfam; PF04539; Sigma70_r3; 1.
DR Pfam; PF04545; Sigma70_r4; 1.
DR PRINTS; PR00046; SIGMA70FCT.
DR SUPFAM; SSF88946; Sigma2 domain of RNA polymerase sigma factors; 1.
DR SUPFAM; SSF88659; Sigma3 and sigma4 domains of RNA polymerase sigma factors; 2.
PE 1: Evidence at protein level;
KW Alternative splicing; Chloroplast; DNA-binding; Mitochondrion; Plastid;
KW Reference proteome; Sigma factor; Transcription; Transcription regulation;
KW Transit peptide.
FT TRANSIT 1..34
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 35..517
FT /note="RNA polymerase sigma factor sigE,
FT chloroplastic/mitochondrial"
FT /id="PRO_5000147343"
FT DNA_BIND 478..497
FT /note="H-T-H motif"
FT /evidence="ECO:0000250"
FT REGION 62..85
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 119..144
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 310..323
FT /note="Polymerase core binding"
FT COMPBIAS 121..144
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT VAR_SEQ 1
FT /note="M -> MRYVSACSTSELALRKIQFLSLKIVM (in isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_043972"
FT MUTAGEN 484
FT /note="N->R: Attenuation of psbD promoter recognition."
FT /evidence="ECO:0000269|PubMed:18532976"
FT MUTAGEN 493
FT /note="R->H: No effect on psbD promoter recognition."
FT /evidence="ECO:0000269|PubMed:18532976"
SQ SEQUENCE 517 AA; 58813 MW; 09FD115934E4FBDD CRC64;
MGVVSISSSA ARSPLGLGND LLTHRSSLKK PSIVAFKADD SSNSALIIPP REQVLIPAEK
HNEKKREVTR RKPCKTPKKP LSLEHNSAPS CSLGVDYNEA AARLESIYKL SPATTTLVED
DVEDGGSKAK VSRRRKRKES GEEKKVVVRN NVKKEKRMSL DKRIALKRNV QEKPVVASVD
KKVTKRQQEE EKIERLVRDY SASNDIVSLD WKKMKIPPVL SSTEHAWLFK LMQPMKALLE
VKDVLQKSLG REPREAEIAG EINMTAGEVK KKIEIGRAAR NKLIKHNLRL VLFVMNKYFH
EFTNGPKFQD LCQAGMRGLI TAIDRFEPKR KFRLSTYGLF WIRHAIIRSM TTSNFTRVPF
GLESVRVEIY KAKTELWFEM GRPPTEDEVV ERLKITPERY REVLRAAKPV LSLNSKHSVT
QEEFINGITD VDGVGANNSR QPALLRLALD DVLDSLKPKE SLVIRQRYGL DGKGDRTLGE
IAGNLNISRE MVRKHEVKAL MKLKHQARVD YLRQYIV
//
