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RNA polymerase sigma factor sigE, chloroplastic/mitochondrial (Sigma factor E) (Sigma-E) (RNA polymerase sigma factor sig5) (Atsig5) (Sigma factor 5)

 SIGE_ARATH              Reviewed;         517 AA.
Q9ZNX9; Q56Y78; Q94AW4;
11-JUL-2012, integrated into UniProtKB/Swiss-Prot.
01-MAY-1999, sequence version 1.
12-SEP-2018, entry version 138.
RecName: Full=RNA polymerase sigma factor sigE, chloroplastic/mitochondrial;
Short=Sigma factor E;
Short=Sigma-E;
AltName: Full=RNA polymerase sigma factor sig5;
Short=Atsig5;
Short=Sigma factor 5;
Flags: Precursor;
Name=SIGE; Synonyms=SIG5; OrderedLocusNames=At5g24120;
ORFNames=MLE8.4;
Arabidopsis thaliana (Mouse-ear cress).
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
Arabidopsis.
NCBI_TaxID=3702;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=10984613; DOI=10.1016/S0014-5793(00)01965-7;
Fujiwara M., Nagashima A., Kanamaru K., Tanaka K., Takahashi H.;
"Three new nuclear genes, sigD, sigE and sigF, encoding putative
plastid RNA polymerase sigma factors in Aarabidopsis thaliana.";
FEBS Lett. 481:47-52(2000).
[2]
NUCLEOTIDE SEQUENCE [MRNA].
PubMed=10734058; DOI=10.1074/jbc.275.13.9215;
Hakimi M.-A., Privat I., Valay J.-G., Lerbs-Mache S.;
"Evolutionary conservation of C-terminal domains of primary sigma(70)-
type transcription factors between plants and bacteria.";
J. Biol. Chem. 275:9215-9221(2000).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=9679202; DOI=10.1093/dnares/5.2.131;
Kaneko T., Kotani H., Nakamura Y., Sato S., Asamizu E., Miyajima N.,
Tabata S.;
"Structural analysis of Arabidopsis thaliana chromosome 5. V. Sequence
features of the regions of 1,381,565 bp covered by twenty one
physically assigned P1 and TAC clones.";
DNA Res. 5:131-145(1998).
[4]
GENOME REANNOTATION.
STRAIN=cv. Columbia;
PubMed=27862469; DOI=10.1111/tpj.13415;
Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
Town C.D.;
"Araport11: a complete reannotation of the Arabidopsis thaliana
reference genome.";
Plant J. 89:789-804(2017).
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=cv. Columbia;
PubMed=19423640; DOI=10.1093/dnares/dsp009;
Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M.,
Seki M., Shinozaki K.;
"Analysis of multiple occurrences of alternative splicing events in
Arabidopsis thaliana using novel sequenced full-length cDNAs.";
DNA Res. 16:155-164(2009).
[6]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-281.
STRAIN=cv. Columbia;
PubMed=14593172; DOI=10.1126/science.1088305;
Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J.,
Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F.,
Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.,
Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J.,
Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y.,
Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P.,
Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F.,
Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M.,
Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J.,
Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T.,
Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y.,
Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.;
"Empirical analysis of transcriptional activity in the Arabidopsis
genome.";
Science 302:842-846(2003).
[7]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-269.
STRAIN=cv. Columbia;
Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J.,
Hayashizaki Y., Shinozaki K.;
"Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases.
[8]
TISSUE SPECIFICITY, INDUCTION BY LIGHT, GENE FAMILY, AND NOMENCLATURE.
STRAIN=cv. Columbia; TISSUE=Seedling hypocotyl;
PubMed=10946105; DOI=10.1016/S0300-9084(00)00611-8;
Allison L.A.;
"The role of sigma factors in plastid transcription.";
Biochimie 82:537-548(2000).
[9]
INDUCTION BY BLUE LIGHT.
STRAIN=cv. Columbia;
PubMed=11959137; DOI=10.1016/S0014-5793(02)02538-3;
Tsunoyama Y., Morikawa K., Shiina T., Toyoshima Y.;
"Blue light specific and differential expression of a plastid sigma
factor, Sig5 in Arabidopsis thaliana.";
FEBS Lett. 516:225-228(2002).
[10]
FUNCTION, DISRUPTION PHENOTYPE, TISSUE SPECIFICITY, SUBCELLULAR
LOCATION, AND ISOFORMS 1 AND 2.
STRAIN=cv. Columbia, and cv. Wassilewskija;
PubMed=12805603; DOI=10.1104/pp.102.017913;
Yao J., Roy-Chowdhury S., Allison L.A.;
"AtSig5 is an essential nucleus-encoded Arabidopsis sigma-like
factor.";
Plant Physiol. 132:739-747(2003).
[11]
FUNCTION, DISRUPTION PHENOTYPE, TISSUE SPECIFICITY, AND INDUCTION BY
BLUE LIGHT.
STRAIN=cv. Columbia;
PubMed=14976253; DOI=10.1073/pnas.0308362101;
Tsunoyama Y., Ishizaki Y., Morikawa K., Kobori M., Nakahira Y.,
Takeba G., Toyoshima Y., Shiina T.;
"Blue light-induced transcription of plastid-encoded psbD gene is
mediated by a nuclear-encoded transcription initiation factor,
AtSig5.";
Proc. Natl. Acad. Sci. U.S.A. 101:3304-3309(2004).
[12]
TISSUE SPECIFICITY.
STRAIN=cv. Columbia;
PubMed=15807777; DOI=10.1111/j.1365-313X.2005.02362.x;
Ishizaki Y., Tsunoyama Y., Hatano K., Ando K., Kato K., Shinmyo A.,
Kobori M., Takeba G., Nakahira Y., Shiina T.;
"A nuclear-encoded sigma factor, Arabidopsis SIG6, recognizes sigma-70
type chloroplast promoters and regulates early chloroplast development
in cotyledons.";
Plant J. 42:133-144(2005).
[13]
FUNCTION, INDUCTION BY LIGHT, AND MUTAGENESIS OF ASN-484 AND ARG-493.
PubMed=18532976; DOI=10.1111/j.1365-313X.2008.03567.x;
Onda Y., Yagi Y., Saito Y., Takenaka N., Toyoshima Y.;
"Light induction of Arabidopsis SIG1 and SIG5 transcripts in mature
leaves: differential roles of cryptochrome 1 and cryptochrome 2 and
dual function of SIG5 in the recognition of plastid promoters.";
Plant J. 55:968-978(2008).
[14]
DISRUPTION PHENOTYPE, INTERACTION WITH PIA2/ANK6, SUBCELLULAR
LOCATION, AND DEVELOPMENTAL STAGE.
STRAIN=cv. Columbia;
PubMed=21123745; DOI=10.1073/pnas.1015911107;
Yu F., Shi J., Zhou J., Gu J., Chen Q., Li J., Cheng W., Mao D.,
Tian L., Buchanan B.B., Li L., Chen L., Li D., Luan S.;
"ANK6, a mitochondrial ankyrin repeat protein, is required for male-
female gamete recognition in Arabidopsis thaliana.";
Proc. Natl. Acad. Sci. U.S.A. 107:22332-22337(2010).
-!- FUNCTION: Essential protein. Sigma factors are initiation factors
that promote the attachment of plastid-encoded RNA polymerase
(PEP) to specific initiation sites (e.g. psbA and psbD) and are
then released. Essential for blue light-mediated transcription of
psbD, which encodes the photosystem II reaction center protein D2.
Plays a role in reproduction. Required during female gametophyte
development (PubMed:21123745). {ECO:0000269|PubMed:12805603,
ECO:0000269|PubMed:14976253, ECO:0000269|PubMed:18532976,
ECO:0000269|PubMed:21123745}.
-!- SUBUNIT: Interacts with PIA2/ANK6 in mitochondrion.
{ECO:0000269|PubMed:21123745}.
-!- INTERACTION:
Q9FNP4:PIA2; NbExp=4; IntAct=EBI-15343551, EBI-4435148;
-!- SUBCELLULAR LOCATION: Isoform 1: Plastid, chloroplast.
-!- SUBCELLULAR LOCATION: Isoform 2: Mitochondrion
{ECO:0000269|PubMed:21123745}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=2;
Name=1;
IsoId=Q9ZNX9-1; Sequence=Displayed;
Name=2;
IsoId=Q9ZNX9-2; Sequence=VSP_043972;
-!- TISSUE SPECIFICITY: Mostly expressed in siliques and flowers, to a
lesser extent in leaves and stems, and barely expressed in roots
(at protein level). Isoform 2 accumulates specifically in flowers,
whereas isoform 1 is expressed in both leaves and flowers. Present
in old seedlings (8 days). {ECO:0000269|PubMed:10946105,
ECO:0000269|PubMed:12805603, ECO:0000269|PubMed:14976253,
ECO:0000269|PubMed:15807777}.
-!- DEVELOPMENTAL STAGE: Highly expressed in the male and female
gametophytes and in seedlings. {ECO:0000269|PubMed:21123745}.
-!- INDUCTION: Induced by blue light illumination (470 nm), especially
after dark adaptation. Induction is mediated through both
cryptochrome 1 and cryptochrome 2 at lower light intensities and
mainly through cryptochrome 1 at higher light intensities.
{ECO:0000269|PubMed:10946105, ECO:0000269|PubMed:11959137,
ECO:0000269|PubMed:14976253, ECO:0000269|PubMed:18532976}.
-!- DISRUPTION PHENOTYPE: Lethal. In heterozygous plants, aborted
embryos and unfertilized ovules. Defects in female gametophyte
development at the one-nucleate stage and white shriveled ovule
(PubMed:12805603, PubMed:14976253, PubMed:21123745). Loss of
transcription activation of psbD in chloroplasts in response to
light (PubMed:12805603, PubMed:14976253).
{ECO:0000269|PubMed:12805603, ECO:0000269|PubMed:14976253,
ECO:0000269|PubMed:21123745}.
-!- SIMILARITY: Belongs to the sigma-70 factor family. {ECO:0000305}.
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EMBL; AB021120; BAA78109.1; -; Genomic_DNA.
EMBL; Y18550; CAA77213.1; -; mRNA.
EMBL; AB010696; BAB11572.1; -; Genomic_DNA.
EMBL; CP002688; AED93259.1; -; Genomic_DNA.
EMBL; CP002688; ANM68680.1; -; Genomic_DNA.
EMBL; CP002688; ANM68681.1; -; Genomic_DNA.
EMBL; AK316888; BAH19595.1; -; mRNA.
EMBL; AY045660; AAK74018.1; -; mRNA.
EMBL; AK221445; BAD94495.1; -; mRNA.
PIR; T51328; T51328.
RefSeq; NP_001330408.1; NM_001343842.1. [Q9ZNX9-1]
RefSeq; NP_001330409.1; NM_001343841.1. [Q9ZNX9-1]
RefSeq; NP_197800.1; NM_122317.4. [Q9ZNX9-1]
UniGene; At.5425; -.
ProteinModelPortal; Q9ZNX9; -.
SMR; Q9ZNX9; -.
BioGrid; 17752; 1.
DIP; DIP-60440N; -.
IntAct; Q9ZNX9; 3.
STRING; 3702.AT5G24120.1; -.
PaxDb; Q9ZNX9; -.
EnsemblPlants; AT5G24120.1; AT5G24120.1; AT5G24120. [Q9ZNX9-1]
EnsemblPlants; AT5G24120.2; AT5G24120.2; AT5G24120. [Q9ZNX9-1]
EnsemblPlants; AT5G24120.3; AT5G24120.3; AT5G24120. [Q9ZNX9-1]
GeneID; 832477; -.
Gramene; AT5G24120.1; AT5G24120.1; AT5G24120. [Q9ZNX9-1]
Gramene; AT5G24120.2; AT5G24120.2; AT5G24120. [Q9ZNX9-1]
Gramene; AT5G24120.3; AT5G24120.3; AT5G24120. [Q9ZNX9-1]
KEGG; ath:AT5G24120; -.
Araport; AT5G24120; -.
TAIR; locus:2167413; AT5G24120.
eggNOG; ENOG410IIZS; Eukaryota.
eggNOG; COG0568; LUCA.
HOGENOM; HOG000241625; -.
InParanoid; Q9ZNX9; -.
KO; K03093; -.
OMA; CSLGVDY; -.
OrthoDB; EOG09360EWV; -.
PhylomeDB; Q9ZNX9; -.
PRO; PR:Q9ZNX9; -.
Proteomes; UP000006548; Chromosome 5.
ExpressionAtlas; Q9ZNX9; baseline and differential.
Genevisible; Q9ZNX9; AT.
GO; GO:0009507; C:chloroplast; IDA:UniProtKB.
GO; GO:0005739; C:mitochondrion; IDA:UniProtKB.
GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
GO; GO:0003700; F:DNA-binding transcription factor activity; IEA:InterPro.
GO; GO:0016987; F:sigma factor activity; IMP:UniProtKB.
GO; GO:0071483; P:cellular response to blue light; IEP:UniProtKB.
GO; GO:0071472; P:cellular response to salt stress; IMP:TAIR.
GO; GO:0009658; P:chloroplast organization; IMP:TAIR.
GO; GO:0006352; P:DNA-templated transcription, initiation; ISS:UniProtKB.
GO; GO:0009553; P:embryo sac development; IMP:UniProtKB.
GO; GO:0010207; P:photosystem II assembly; IMP:UniProtKB.
GO; GO:0045893; P:positive regulation of transcription, DNA-templated; IMP:TAIR.
GO; GO:2001141; P:regulation of RNA biosynthetic process; IMP:UniProtKB.
GO; GO:0010218; P:response to far red light; IEP:TAIR.
GO; GO:0010114; P:response to red light; IEP:TAIR.
Gene3D; 1.10.10.10; -; 2.
InterPro; IPR014284; RNA_pol_sigma-70_dom.
InterPro; IPR000943; RNA_pol_sigma70.
InterPro; IPR007627; RNA_pol_sigma70_r2.
InterPro; IPR007624; RNA_pol_sigma70_r3.
InterPro; IPR007630; RNA_pol_sigma70_r4.
InterPro; IPR013325; RNA_pol_sigma_r2.
InterPro; IPR013324; RNA_pol_sigma_r3/r4-like.
InterPro; IPR036388; WH-like_DNA-bd_sf.
Pfam; PF04542; Sigma70_r2; 1.
Pfam; PF04539; Sigma70_r3; 1.
Pfam; PF04545; Sigma70_r4; 1.
PRINTS; PR00046; SIGMA70FCT.
SUPFAM; SSF88659; SSF88659; 2.
SUPFAM; SSF88946; SSF88946; 1.
TIGRFAMs; TIGR02937; sigma70-ECF; 1.
1: Evidence at protein level;
Alternative splicing; Chloroplast; Complete proteome; DNA-binding;
Mitochondrion; Plastid; Reference proteome; Sigma factor;
Transcription; Transcription regulation; Transit peptide.
TRANSIT 1 34 Chloroplast. {ECO:0000255}.
CHAIN 35 517 RNA polymerase sigma factor sigE,
chloroplastic/mitochondrial.
/FTId=PRO_5000147343.
DNA_BIND 478 497 H-T-H motif. {ECO:0000250}.
MOTIF 310 323 Polymerase core binding.
VAR_SEQ 1 1 M -> MRYVSACSTSELALRKIQFLSLKIVM (in
isoform 2). {ECO:0000305}.
/FTId=VSP_043972.
MUTAGEN 484 484 N->R: Attenuation of psbD promoter
recognition.
{ECO:0000269|PubMed:18532976}.
MUTAGEN 493 493 R->H: No effect on psbD promoter
recognition.
{ECO:0000269|PubMed:18532976}.
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


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