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ECF RNA polymerase sigma factor SigR (ECF sigma factor SigR) (Alternative RNA polymerase sigma factor SigR) (RNA polymerase sigma-R factor) (Sigma-R factor)

 SIGR_STRCO              Reviewed;         227 AA.
Q7AKG9; O87834;
16-OCT-2013, integrated into UniProtKB/Swiss-Prot.
16-MAY-2012, sequence version 1.
12-SEP-2018, entry version 45.
RecName: Full=ECF RNA polymerase sigma factor SigR;
Short=ECF sigma factor SigR;
AltName: Full=Alternative RNA polymerase sigma factor SigR;
AltName: Full=RNA polymerase sigma-R factor;
Short=Sigma-R factor;
Name=sigR; OrderedLocusNames=SCO5216;
Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145).
Bacteria; Actinobacteria; Streptomycetales; Streptomycetaceae;
Streptomyces; Streptomyces albidoflavus group.
NCBI_TaxID=100226;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 5-24, FUNCTION
AS A SIGMA FACTOR, INDUCTION, AUTOREGULATION, AND DISRUPTION
PHENOTYPE.
STRAIN=ATCC BAA-471 / A3(2) / M145;
PubMed=9755177; DOI=10.1093/emboj/17.19.5776;
Paget M.S., Kang J.G., Roe J.H., Buttner M.J.;
"sigmaR, an RNA polymerase sigma factor that modulates expression of
the thioredoxin system in response to oxidative stress in Streptomyces
coelicolor A3(2).";
EMBO J. 17:5776-5782(1998).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC BAA-471 / A3(2) / M145;
PubMed=12000953; DOI=10.1038/417141a;
Bentley S.D., Chater K.F., Cerdeno-Tarraga A.-M., Challis G.L.,
Thomson N.R., James K.D., Harris D.E., Quail M.A., Kieser H.,
Harper D., Bateman A., Brown S., Chandra G., Chen C.W., Collins M.,
Cronin A., Fraser A., Goble A., Hidalgo J., Hornsby T., Howarth S.,
Huang C.-H., Kieser T., Larke L., Murphy L.D., Oliver K., O'Neil S.,
Rabbinowitsch E., Rajandream M.A., Rutherford K.M., Rutter S.,
Seeger K., Saunders D., Sharp S., Squares R., Squares S., Taylor K.,
Warren T., Wietzorrek A., Woodward J.R., Barrell B.G., Parkhill J.,
Hopwood D.A.;
"Complete genome sequence of the model actinomycete Streptomyces
coelicolor A3(2).";
Nature 417:141-147(2002).
[3]
FUNCTION AS A SIGMA-FACTOR, INTERACTION WITH RSRA, AND SUBUNIT.
STRAIN=ATCC BAA-471 / A3(2) / M145;
PubMed=10428967; DOI=10.1093/emboj/18.15.4292;
Kang J.G., Paget M.S.B., Seok Y.J., Hahn M.Y., Bae J.B., Hahn J.S.;
"RsrA, an anti-sigma factor regulated by redox change.";
EMBO J. 18:4292-4298(1999).
[4]
FUNCTION, SUBUNIT, AND REGULON.
STRAIN=ATCC BAA-471 / A3(2) / M145;
PubMed=11737643; DOI=10.1046/j.1365-2958.2001.02675.x;
Paget M.S.B., Molle V., Cohen G., Aharonowitz Y., Buttner M.J.;
"Defining the disulphide stress response in Streptomyces coelicolor
A3(2): identification of the sigmaR regulon.";
Mol. Microbiol. 42:1007-1020(2001).
[5]
FUNCTION AS A SIGMA FACTOR, AND INTERACTION WITH RSRA.
STRAIN=ATCC BAA-471 / A3(2) / M145;
PubMed=14529630; DOI=10.1016/j.jmb.2003.08.038;
Li W., Bottrill A.R., Bibb M.J., Buttner M.J., Paget M.S.,
Kleanthous C.;
"The role of zinc in the disulphide stress-regulated anti-sigma factor
RsrA from Streptomyces coelicolor.";
J. Mol. Biol. 333:461-472(2003).
[6]
REGULON, INDUCTION, AND DISRUPTION PHENOTYPE.
STRAIN=ATCC BAA-471 / A3(2) / M145;
PubMed=18430082; DOI=10.1111/j.1365-2958.2008.06191.x;
Park J.H., Roe J.H.;
"Mycothiol regulates and is regulated by a thiol-specific antisigma
factor RsrA and sigma(R) in Streptomyces coelicolor.";
Mol. Microbiol. 68:861-870(2008).
[7]
INDUCTION, ALTERNATIVE INITIATION (SIGR PRIME), AND PROBABLE CLEAVAGE.
STRAIN=ATCC BAA-471 / A3(2) / M145;
PubMed=19682253; DOI=10.1111/j.1365-2958.2009.06824.x;
Kim M.S., Hahn M.Y., Cho Y., Cho S.N., Roe J.H.;
"Positive and negative feedback regulatory loops of thiol-oxidative
stress response mediated by an unstable isoform of sigmaR in
actinomycetes.";
Mol. Microbiol. 73:815-825(2009).
[8]
REGULON.
PubMed=22651816; DOI=10.1111/j.1365-2958.2012.08115.x;
Kim M.S., Dufour Y.S., Yoo J.S., Cho Y.B., Park J.H., Nam G.B.,
Kim H.M., Lee K.L., Donohue T.J., Roe J.H.;
"Conservation of thiol-oxidative stress responses regulated by SigR
orthologues in actinomycetes.";
Mol. Microbiol. 85:326-344(2012).
[9]
X-RAY CRYSTALLOGRAPHY (2.38 ANGSTROMS) OF 23-109, AND INTERACTION WITH
RSRA.
STRAIN=ATCC BAA-471 / A3(2) / M145;
PubMed=12381317; DOI=10.1016/S0022-2836(02)00948-8;
Li W., Stevenson C.E., Burton N., Jakimowicz P., Paget M.S.,
Buttner M.J., Lawson D.M., Kleanthous C.;
"Identification and structure of the anti-sigma factor-binding domain
of the disulphide-stress regulated sigma factor sigma(R) from
Streptomyces coelicolor.";
J. Mol. Biol. 323:225-236(2002).
-!- FUNCTION: Sigma factors are initiation factors that promote the
attachment of RNA polymerase to specific initiation sites and are
then released. Extracytoplasmic function (ECF) sigma factors are
held in an inactive form by an anti-sigma factor (RsrA) until
released. Responds to thiol-oxidative stress, involved in
regulation of about 30 genes and operons, including the
thioredoxin system (trxB-trxA, trxC), ribosomal protein L31, RNA
polymerase-binding protein RbpA and mycothiol (MSH) biosynthetic
(mshA) and recycling genes (mca). In conjunction with its cognate
anti-sigma factor RsrA may sense the intracellular level of
reduced MSH. {ECO:0000269|PubMed:10428967,
ECO:0000269|PubMed:11737643, ECO:0000269|PubMed:14529630,
ECO:0000269|PubMed:9755177}.
-!- SUBUNIT: Interacts transiently with the RNA polymerase catalytic
core formed by RpoA, RpoB, RpoC and RpoZ (2 alpha, 1 beta, 1 beta'
and 1 omega subunit) to form the RNA polymerase holoenzyme that
can initiate transcription. Interacts with cognate anti-sigma
factor RsrA under reducing but not oxiding conditions, which
prevents it binding to RNA polymerase. Treatment with the thiol-
oxidzing agent diamide inhibits the interaction.
{ECO:0000269|PubMed:10428967, ECO:0000269|PubMed:11737643,
ECO:0000269|PubMed:12381317, ECO:0000269|PubMed:14529630}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative initiation; Named isoforms=2;
Name=SigR;
IsoId=Q7AKG9-1; Sequence=Displayed;
Note=Constitutively expressed major isoform, not induced by
diamide (at protein level), contributes about half of the
diamide-induced expression of the regulon.;
Name=SigR prime;
IsoId=Q7AKG9-2; Sequence=VSP_053231;
Note=Present in low amounts in unstressed cells, strongly but
transiently produced upon diamide induction. Functions as a
sigma factor, contributes about half of the diamide-induced
expression of the regulon. Unstable, half-life of about 10
minutes.;
-!- INDUCTION: Expressed from 2 promoters, 1 of which (sigRp2)
positively regulates its own expression. The same promoter is
transiently induced (about 70-fold) by the thiol-oxiding agent
diamide. Also induced when mycothiol is oxidized or conjugated.
{ECO:0000269|PubMed:18430082, ECO:0000269|PubMed:19682253,
ECO:0000269|PubMed:9755177}.
-!- DOMAIN: The sigma-70 factor domain-2 mediates sequence-specific
interaction with the -10 element in promoter DNA, and plays an
important role in melting the double-stranded DNA and the
formation of the transcription bubble. The sigma-70 factor domain-
2 mediates interaction with the RNA polymerase subunits RpoB and
RpoC (By similarity). Interactions between sigma-70 factor domain-
2 and anti-sigma factors prevents interaction of sigma factors
with the RNA polymerase catalytic core (Probable). {ECO:0000250,
ECO:0000305}.
-!- DOMAIN: The sigma-70 factor domain-4 contains a helix-turn-helix
(H-T-H) motif that mediates interaction with the -35 element in
promoter DNA. The domain also mediates interaction with the RNA
polymerase subunit RpoA (By similarity). {ECO:0000250}.
-!- PTM: SigR is present in multiple forms of different pI, suggesting
other unknown post-translational modifications.
-!- PTM: SigR prime is probably partially degraded by ClpP1-ClpP2.
-!- DISRUPTION PHENOTYPE: Increased sensitivity to redox-cycling
compounds menadione and plumbagin, and to diamide. Loss of
expression of mycothiol biosynthetic and recycling genes.
{ECO:0000269|PubMed:18430082, ECO:0000269|PubMed:9755177}.
-!- SIMILARITY: Belongs to the sigma-70 factor family. ECF subfamily.
{ECO:0000305}.
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EMBL; AJ010320; CAA09088.1; -; Genomic_DNA.
EMBL; AL939122; CAB94601.1; -; Genomic_DNA.
PIR; T42015; T42015.
RefSeq; NP_629363.1; NC_003888.3. [Q7AKG9-1]
RefSeq; WP_003973756.1; NC_003888.3.
PDB; 1H3L; X-ray; 2.38 A; A/B=23-109.
PDB; 5FGM; X-ray; 2.60 A; A=143-207.
PDBsum; 1H3L; -.
PDBsum; 5FGM; -.
ProteinModelPortal; Q7AKG9; -.
SMR; Q7AKG9; -.
STRING; 100226.SCO5216; -.
PRIDE; Q7AKG9; -.
EnsemblBacteria; CAB94601; CAB94601; CAB94601.
GeneID; 1100657; -.
KEGG; sco:SCO5216; -.
PATRIC; fig|100226.15.peg.5300; -.
eggNOG; ENOG4105EMN; Bacteria.
eggNOG; COG1595; LUCA.
HOGENOM; HOG000094755; -.
InParanoid; Q7AKG9; -.
KO; K03088; -.
OMA; TYINLYR; -.
OrthoDB; POG091H04ZH; -.
PhylomeDB; Q7AKG9; -.
Proteomes; UP000001973; Chromosome.
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; IDA:UniProtKB.
GO; GO:0006352; P:DNA-templated transcription, initiation; IEA:InterPro.
GO; GO:0006979; P:response to oxidative stress; IDA:UniProtKB.
Gene3D; 1.10.10.10; -; 1.
InterPro; IPR014284; RNA_pol_sigma-70_dom.
InterPro; IPR014293; RNA_pol_sigma70_actinobac.
InterPro; IPR000838; RNA_pol_sigma70_ECF_CS.
InterPro; IPR007627; RNA_pol_sigma70_r2.
InterPro; IPR013249; RNA_pol_sigma70_r4_t2.
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; PF08281; Sigma70_r4_2; 1.
SUPFAM; SSF88659; SSF88659; 1.
SUPFAM; SSF88946; SSF88946; 1.
TIGRFAMs; TIGR02947; SigH_actino; 1.
TIGRFAMs; TIGR02937; sigma70-ECF; 1.
PROSITE; PS01063; SIGMA70_ECF; 1.
1: Evidence at protein level;
3D-structure; Alternative initiation; Complete proteome;
Direct protein sequencing; DNA-binding; Reference proteome;
Sigma factor; Transcription; Transcription regulation.
CHAIN 1 227 ECF RNA polymerase sigma factor SigR.
/FTId=PRO_0000423649.
DNA_BIND 173 192 H-T-H motif. {ECO:0000250}.
REGION 43 106 Sigma-70 factor domain-2.
REGION 148 198 Sigma-70 factor domain-4.
MOTIF 63 66 Polymerase core binding. {ECO:0000255}.
VAR_SEQ 1 1 M -> MGSAFCPSRSSRADLDWTVLHAAKTAPIRAAGGPDR
RLSSDSSETGLGFTTTSEEM (in isoform SigR
prime). {ECO:0000305}.
/FTId=VSP_053231.
HELIX 29 42 {ECO:0000244|PDB:1H3L}.
HELIX 44 55 {ECO:0000244|PDB:1H3L}.
HELIX 58 75 {ECO:0000244|PDB:1H3L}.
HELIX 76 78 {ECO:0000244|PDB:1H3L}.
STRAND 81 83 {ECO:0000244|PDB:1H3L}.
HELIX 85 99 {ECO:0000244|PDB:1H3L}.
HELIX 148 153 {ECO:0000244|PDB:5FGM}.
HELIX 157 167 {ECO:0000244|PDB:5FGM}.
HELIX 173 180 {ECO:0000244|PDB:5FGM}.
HELIX 184 204 {ECO:0000244|PDB:5FGM}.
SEQUENCE 227 AA; 25218 MW; AE89C2EF0ED4F366 CRC64;
MGPVTGTDAG TEHGQAEQPE GRGTGAESTA ERSARFERDA LEFLDQMYSA ALRMTRNPAD
AEDLVQETYA KAYASFHQFR EGTNLKAWLY RILTNTFINS YRKKQREPQR SAAEEIEDWQ
LARAESHMST GLRSAESQAL DHLPDSDVKQ ALQAIPEEFR IAVYLADVEG FAYKEIADIM
GTPIGTVMSR LHRGRRQLRG MLEDYARDRG LVPAGAGESN EAKGSGS


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