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RNA polymerase sigma factor SigF (Sigma factor SigF) (Alternative RNA polymerase sigma factor SigF) (RNA polymerase sigma-F factor) (Sigma-F factor) (Stress response/stationary phase sigma factor SigF)

 SIGF_MYCTU              Reviewed;         261 AA.
P9WGI3; F2GKV9; Q50547; Q798K1; Q7D5S2;
16-APR-2014, integrated into UniProtKB/Swiss-Prot.
16-APR-2014, sequence version 1.
28-MAR-2018, entry version 25.
RecName: Full=RNA polymerase sigma factor SigF;
Short=Sigma factor SigF;
AltName: Full=Alternative RNA polymerase sigma factor SigF;
AltName: Full=RNA polymerase sigma-F factor;
Short=Sigma-F factor;
AltName: Full=Stress response/stationary phase sigma factor SigF;
Name=sigF; OrderedLocusNames=Rv3286c;
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
Mycobacterium; Mycobacterium tuberculosis complex.
NCBI_TaxID=83332;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=ATCC 25618 / H37Rv;
PubMed=8610119; DOI=10.1073/pnas.93.7.2790;
DeMaio J., Zhang Y., Ko C., Young D.B., Bishai W.R.;
"A stationary-phase stress-response sigma factor from Mycobacterium
tuberculosis.";
Proc. Natl. Acad. Sci. U.S.A. 93:2790-2794(1996).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 25618 / H37Rv;
PubMed=9634230; DOI=10.1038/31159;
Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M.,
Harris D.E., Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III,
Tekaia F., Badcock K., Basham D., Brown D., Chillingworth T.,
Connor R., Davies R.M., Devlin K., Feltwell T., Gentles S., Hamlin N.,
Holroyd S., Hornsby T., Jagels K., Krogh A., McLean J., Moule S.,
Murphy L.D., Oliver S., Osborne J., Quail M.A., Rajandream M.A.,
Rogers J., Rutter S., Seeger K., Skelton S., Squares S., Squares R.,
Sulston J.E., Taylor K., Whitehead S., Barrell B.G.;
"Deciphering the biology of Mycobacterium tuberculosis from the
complete genome sequence.";
Nature 393:537-544(1998).
[3]
INDUCTION.
STRAIN=ATCC 25618 / H37Rv;
PubMed=10027986; DOI=10.1046/j.1365-2958.1999.01212.x;
Manganelli R., Dubnau E., Tyagi S., Kramer F.R., Smith I.;
"Differential expression of 10 sigma factor genes in Mycobacterium
tuberculosis.";
Mol. Microbiol. 31:715-724(1999).
[4]
INDUCTION FOLLOWING STARVATION.
STRAIN=ATCC 25618 / H37Rv / NCTC 7416;
PubMed=11929527; DOI=10.1046/j.1365-2958.2002.02779.x;
Betts J.C., Lukey P.T., Robb L.C., McAdam R.A., Duncan K.;
"Evaluation of a nutrient starvation model of Mycobacterium
tuberculosis persistence by gene and protein expression profiling.";
Mol. Microbiol. 43:717-731(2002).
[5]
FUNCTION AS A SIGMA FACTOR, REGULATION, AND INTERACTION WITH RSBW.
PubMed=12354223; DOI=10.1046/j.1365-2958.2002.03135.x;
Beaucher J., Rodrigue S., Jacques P.E., Smith I., Brzezinski R.,
Gaudreau L.;
"Novel Mycobacterium tuberculosis anti-sigma factor antagonists
control sigmaF activity by distinct mechanisms.";
Mol. Microbiol. 45:1527-1540(2002).
[6]
DISRUPTION PHENOTYPE IN GUINEA PIGS.
STRAIN=ATCC 25618 / H37Rv;
PubMed=16735723; DOI=10.1099/mic.0.28591-0;
Karls R.K., Guarner J., McMurray D.N., Birkness K.A., Quinn F.D.;
"Examination of Mycobacterium tuberculosis sigma factor mutants using
low-dose aerosol infection of guinea pigs suggests a role for SigC in
pathogenesis.";
Microbiology 152:1591-1600(2006).
[7]
SUBUNIT, AND INTERACTION WITH RSBW.
PubMed=19130906; DOI=10.1016/j.bbapap.2008.11.007;
Malik S.S., Luthra A., Ramachandran R.;
"Interactions of the M. tuberculosis UsfX with the cognate sigma
factor SigF and the anti-anti sigma factor RsfA.";
Biochim. Biophys. Acta 1794:541-553(2009).
[8]
FUNCTION AS A SIGMA FACTOR, AND DISRUPTION PHENOTYPE.
STRAIN=ATCC 25618 / H37Rv;
PubMed=20729364; DOI=10.1128/JB.00687-10;
Hartkoorn R.C., Sala C., Magnet S.J., Chen J.M., Pojer F., Cole S.T.;
"Sigma factor F does not prevent rifampin inhibition of RNA polymerase
or cause rifampin tolerance in Mycobacterium tuberculosis.";
J. Bacteriol. 192:5472-5479(2010).
[9]
INTERACTION WITH RSBW.
PubMed=20600947; DOI=10.1016/j.pep.2010.06.018;
Thakur K.G., Jaiswal R.K., Shukla J.K., Praveena T., Gopal B.;
"Over-expression and purification strategies for recombinant multi-
protein oligomers: a case study of Mycobacterium tuberculosis
sigma/anti-sigma factor protein complexes.";
Protein Expr. Purif. 74:223-230(2010).
[10]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
STRAIN=ATCC 25618 / H37Rv;
PubMed=21969609; DOI=10.1074/mcp.M111.011627;
Kelkar D.S., Kumar D., Kumar P., Balakrishnan L., Muthusamy B.,
Yadav A.K., Shrivastava P., Marimuthu A., Anand S., Sundaram H.,
Kingsbury R., Harsha H.C., Nair B., Prasad T.S., Chauhan D.S.,
Katoch K., Katoch V.M., Kumar P., Chaerkady R., Ramachandran S.,
Dash D., Pandey A.;
"Proteogenomic analysis of Mycobacterium tuberculosis by high
resolution mass spectrometry.";
Mol. Cell. Proteomics 10:M111.011627-M111.011627(2011).
[11]
FUNCTION, AND REGULON.
STRAIN=ATCC 25618 / H37Rv;
PubMed=22307756; DOI=10.1128/JB.06692-11;
Hartkoorn R.C., Sala C., Uplekar S., Busso P., Rougemont J.,
Cole S.T.;
"Genome-wide definition of the SigF regulon in Mycobacterium
tuberculosis.";
J. Bacteriol. 194:2001-2009(2012).
[12]
FUNCTION AS A SIGMA FACTOR.
STRAIN=ATCC 25618 / H37Rv;
PubMed=22570422; DOI=10.1093/nar/gks346;
Hu Y., Morichaud Z., Chen S., Leonetti J.P., Brodolin K.;
"Mycobacterium tuberculosis RbpA protein is a new type of
transcriptional activator that stabilizes the sigma A-containing RNA
polymerase holoenzyme.";
Nucleic Acids Res. 40:6547-6557(2012).
-!- FUNCTION: Sigma factors are initiation factors that promote the
attachment of RNA polymerase to specific initiation sites and are
then released. Held in an inactive form by a cognate anti-sigma
factor RsbW (UsfX) until released. Increased expression decreases
growth rate, and after 3 days increases the expression of 51 loci
encoding 33 protein-coding genes as well as some non-coding RNA
(PubMed:22307756). {ECO:0000269|PubMed:12354223,
ECO:0000269|PubMed:20729364, ECO:0000269|PubMed:22307756,
ECO:0000269|PubMed:22570422}.
-!- SUBUNIT: Monomer. 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 (via sigma-
70 factor domain 4) with anti-sigma-F factor RsbW (UsfX) with a
possible 2:1 RbsW:SigF stoichiometry, which inhibits SigF
activity. {ECO:0000269|PubMed:12354223,
ECO:0000269|PubMed:19130906, ECO:0000269|PubMed:20600947}.
-!- INDUCTION: Constitutively expressed at a low level under all
conditions tested, including stationary phase and several
stresses. 3-fold induced during starvation (PubMed:11929527).
Positively controls expression of its own operon (rsbW-sigF).
{ECO:0000269|PubMed:10027986, ECO:0000269|PubMed:11929527}.
-!- 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). {ECO:0000250}.
-!- 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. Interactions between sigma-70 factor
domain-4 and anti-sigma factors prevents interaction of sigma
factors with the RNA polymerase catalytic core (By similarity).
{ECO:0000250}.
-!- DISRUPTION PHENOTYPE: Infected guinea pigs mutant and wild-type
bacteria grow comparably (PubMed:16735723). A double rsbW-sigF
disruption shows no effect in the presence or absence of
rifampicin (PubMed:20729364). {ECO:0000269|PubMed:16735723,
ECO:0000269|PubMed:20729364}.
-!- SIMILARITY: Belongs to the sigma-70 factor family. {ECO:0000305}.
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EMBL; U41061; AAC44103.1; -; Genomic_DNA.
EMBL; AL123456; CCP46105.1; -; Genomic_DNA.
RefSeq; NP_217803.1; NC_000962.3.
RefSeq; WP_003417158.1; NZ_KK339370.1.
ProteinModelPortal; P9WGI3; -.
SMR; P9WGI3; -.
IntAct; P9WGI3; 5.
STRING; 83332.Rv3286c; -.
PaxDb; P9WGI3; -.
EnsemblBacteria; CCP46105; CCP46105; Rv3286c.
GeneID; 888727; -.
KEGG; mtu:Rv3286c; -.
TubercuList; Rv3286c; -.
eggNOG; ENOG4105E65; Bacteria.
eggNOG; COG1191; LUCA.
KO; K03090; -.
OMA; RGEIQHY; -.
PhylomeDB; P9WGI3; -.
Proteomes; UP000001584; Chromosome.
GO; GO:0016987; F:bacterial sigma factor activity; IGI:MTBBASE.
GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
GO; GO:0003700; F:DNA binding transcription factor activity; IEA:InterPro.
GO; GO:0043175; F:RNA polymerase core enzyme binding; IDA:MTBBASE.
GO; GO:0070417; P:cellular response to cold; IEP:MTBBASE.
GO; GO:0006995; P:cellular response to nitrogen starvation; IEP:MTBBASE.
GO; GO:0006352; P:DNA-templated transcription, initiation; IEA:InterPro.
GO; GO:0006629; P:lipid metabolic process; IMP:MTBBASE.
GO; GO:0045893; P:positive regulation of transcription, DNA-templated; IDA:MTBBASE.
GO; GO:0034059; P:response to anoxia; IMP:MTBBASE.
GO; GO:0046677; P:response to antibiotic; IMP:MTBBASE.
GO; GO:0009409; P:response to cold; IMP:MTBBASE.
GO; GO:0006979; P:response to oxidative stress; IMP:MTBBASE.
Gene3D; 1.10.10.10; -; 2.
InterPro; IPR014284; RNA_pol_sigma-70_dom.
InterPro; IPR014322; RNA_pol_sigma-B/F/G.
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.
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; TIGR02980; SigBFG; 1.
TIGRFAMs; TIGR02937; sigma70-ECF; 1.
1: Evidence at protein level;
Complete proteome; DNA-binding; Reference proteome; Sigma factor;
Transcription; Transcription regulation.
CHAIN 1 261 RNA polymerase sigma factor SigF.
/FTId=PRO_0000422954.
DNA_BIND 231 250 H-T-H motif. {ECO:0000255}.
REGION 43 112 Sigma-70 factor domain-2.
REGION 123 189 Sigma-70 factor domain-3.
REGION 209 258 Sigma-70 factor domain-4.
MOTIF 67 70 Interaction with polymerase core subunit
RpoC. {ECO:0000250}.
CONFLICT 248 248 L -> V (in Ref. 1; AAC44103).
{ECO:0000305}.
SEQUENCE 261 AA; 28794 MW; 7FD4AA6AB64061AB CRC64;
MTARAAGGSA SRANEYADVP EMFRELVGLP AGSPEFQRHR DKIVQRCLPL ADHIARRFEG
RGEPRDDLIQ VARVGLVNAA VRFDVKTGSD FVSFAVPTIM GEVRRHFRDN SWSVKVPRRL
KELHLRLGTA TADLSQRLGR APSASELAAE LGMDRAEVIE GLLAGSSYHT LSIDSGGGSD
DDARAITDTL GDVDAGLDQI ENREVLRPLL EALPERERTV LVLRFFDSMT QTQIAERVGI
SQMHVSRLLA KSLARLRDQL E


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