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ECF RNA polymerase sigma factor SigE (ECF sigma factor SigE) (Alternative RNA polymerase sigma factor SigE) (RNA polymerase sigma-E factor) (Sigma-E factor)

 SIGE_MYCTU              Reviewed;         257 AA.
P9WGG7; F2GFW7; O06289; Q79FQ9; Q7D8K8;
16-APR-2014, integrated into UniProtKB/Swiss-Prot.
16-APR-2014, sequence version 1.
25-APR-2018, entry version 25.
RecName: Full=ECF RNA polymerase sigma factor SigE;
Short=ECF sigma factor SigE;
AltName: Full=Alternative RNA polymerase sigma factor SigE;
AltName: Full=RNA polymerase sigma-E factor;
Short=Sigma-E factor;
Name=sigE; OrderedLocusNames=Rv1221;
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
Mycobacterium; Mycobacterium tuberculosis complex.
NCBI_TaxID=83332;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND FUNCTION AS A SIGMA FACTOR.
STRAIN=ATCC 25618 / H37Rv;
PubMed=9139909; DOI=10.1128/jb.179.9.2922-2929.1997;
Wu Q.L., Kong D., Lam K., Husson R.N.;
"A mycobacterial extracytoplasmic function sigma factor involved in
survival following stress.";
J. Bacteriol. 179:2922-2929(1997).
[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 BY SIGH.
STRAIN=ATCC 25618 / H37Rv;
PubMed=11567012; DOI=10.1128/JB.183.20.6119-6125.2001;
Raman S., Song T., Puyang X., Bardarov S., Jacobs W.R. Jr.,
Husson R.N.;
"The alternative sigma factor SigH regulates major components of
oxidative and heat stress responses in Mycobacterium tuberculosis.";
J. Bacteriol. 183:6119-6125(2001).
[5]
FUNCTION, INDUCTION, AND DISRUPTION PHENOTYPE IN MACROPHAGES.
STRAIN=ATCC 25618 / H37Rv;
PubMed=11489128; DOI=10.1046/j.1365-2958.2001.02525.x;
Manganelli R., Voskuil M.I., Schoolnik G.K., Smith I.;
"The Mycobacterium tuberculosis ECF sigma factor sigmaE: role in
global gene expression and survival in macrophages.";
Mol. Microbiol. 41:423-437(2001).
[6]
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).
[7]
DISRUPTION PHENOTYPE IN MICE.
STRAIN=ATCC 25618 / H37Rv;
PubMed=15102817; DOI=10.1128/IAI.72.5.3038-3041.2004;
Manganelli R., Fattorini L., Tan D., Iona E., Orefici G.,
Altavilla G., Cusatelli P., Smith I.;
"The extra cytoplasmic function sigma factor sigma(E) is essential for
Mycobacterium tuberculosis virulence in mice.";
Infect. Immun. 72:3038-3041(2004).
[8]
REGULATION BY MPRAB.
STRAIN=ATCC 25618 / H37Rv;
PubMed=16513743; DOI=10.1128/JB.188.6.2134-2143.2006;
He H., Hovey R., Kane J., Singh V., Zahrt T.C.;
"MprAB is a stress-responsive two-component system that directly
regulates expression of sigma factors SigB and SigE in Mycobacterium
tuberculosis.";
J. Bacteriol. 188:2134-2143(2006).
[9]
REGULATION BY MPRAB.
STRAIN=ATCC 25618 / H37Rv;
PubMed=17379732; DOI=10.1099/mic.0.29281-0;
Pang X., Vu P., Byrd T.F., Ghanny S., Soteropoulos P.,
Mukamolova G.V., Wu S., Samten B., Howard S.T.;
"Evidence for complex interactions of stress-associated regulons in an
mprAB deletion mutant of Mycobacterium tuberculosis.";
Microbiology 153:1229-1242(2007).
[10]
FUNCTION, AND DISRUPTION PHENOTYPE IN MACROPHAGES.
STRAIN=ATCC 25618 / H37Rv;
PubMed=18657035; DOI=10.1086/591098;
Fontan P.A., Aris V., Alvarez M.E., Ghanny S., Cheng J.,
Soteropoulos P., Trevani A., Pine R., Smith I.;
"Mycobacterium tuberculosis sigma factor E regulon modulates the host
inflammatory response.";
J. Infect. Dis. 198:877-885(2008).
[11]
REGULATION, INTERACTION WITH RSEA, AND ALTERNATIVE PROMOTER USAGE
(ISOFORMS 2 AND 3).
STRAIN=ATCC 25618 / H37Rv;
PubMed=18606740; DOI=10.1128/JB.00622-08;
Dona V., Rodrigue S., Dainese E., Palu G., Gaudreau L., Manganelli R.,
Provvedi R.;
"Evidence of complex transcriptional, translational, and
posttranslational regulation of the extracytoplasmic function sigma
factor sigmaE in Mycobacterium tuberculosis.";
J. Bacteriol. 190:5963-5971(2008).
[12]
FUNCTION AS A SIGMA FACTOR, REGULATION, AND INTERACTION WITH RSEA.
STRAIN=ATCC 25618 / H37Rv;
PubMed=20025669; DOI=10.1111/j.1365-2958.2009.07008.x;
Barik S., Sureka K., Mukherjee P., Basu J., Kundu M.;
"RseA, the SigE specific anti-sigma factor of Mycobacterium
tuberculosis, is inactivated by phosphorylation-dependent ClpC1P2
proteolysis.";
Mol. Microbiol. 75:592-606(2010).
[13]
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).
-!- 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 until released.
Responds to heat shock and surface stress (detergent exposure).
When combined with isolated core RNA polymerase from M.smegmatis
is able to guide initiation from the sigB promoter. Required for
full expression of sigB, and for sigB induction after detergent
exposure but not after heat shock. Controls a regulon of about 38
genes in culture (PubMed:11489128) and about 16 genes during
macrophage infection (PubMed:18657035), most of which have
decreased expression in a disruption mutant. Probably down
regulates the host immune response to mycobacterial infection.
{ECO:0000269|PubMed:11489128, ECO:0000269|PubMed:18657035,
ECO:0000269|PubMed:20025669, ECO:0000269|PubMed:9139909}.
-!- 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 (via sigma-70 factor domain
4) with cognate anti-sigma-E factor RseA under reducing
conditions, which stops the sigma factor from functioning.
Inhibition is specific; RsaH and RsaL (anti-sigma-H and -L
factors) do not inhibit SigE. {ECO:0000269|PubMed:18606740,
ECO:0000269|PubMed:20025669}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative promoter usage; Named isoforms=3;
Name=1; Synonyms=Sigma-E 257;
IsoId=P9WGG7-1; Sequence=Displayed;
Note=Produced following surface stress.;
Name=2; Synonyms=Sigma-E 218;
IsoId=P9WGG7-2; Sequence=VSP_047441, VSP_047443;
Note=Produced following oxidative stress and heat shock. Shown
by mutagenesis of the start codon and subsequent loss of
translationally fused LacZ.;
Name=3; Synonyms=Sigma-E 215;
IsoId=P9WGG7-3; Sequence=VSP_047440, VSP_047442;
Note=Produced following oxidative stress and heat shock. Able to
interact with RseA. Shown by mutagenesis of the start codon and
subsequent loss of translationally fused LacZ.;
-!- INDUCTION: Unlike many sigma factors not directly autoregulated.
Expressed from 3 promoters. P1 is 55 nucleotides upstream of the
major start codon, used during normal growth, repressed by surface
stress, P2 is at the start codon, under control of MprAB and is
induced following surface stress and alkaline pH leading to a
leader-less RNA, while P3 is 63 nucleotides downstream of the
major start codon, transcribed from a SigH-responsive promoter
under conditions of oxidative stress and heat shock. Expressed in
exponential phase; further induced by detergent (6-fold) and heat
shock (3-fold, 45 degrees Celsius) under control of SigH.
Positively regulated by MprAB, as is induction by detergent. 6-
fold induced by starvation, not known by which promoter.
{ECO:0000269|PubMed:10027986, ECO:0000269|PubMed:11489128,
ECO:0000269|PubMed:11567012, 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 (Probable).
{ECO:0000305}.
-!- DISRUPTION PHENOTYPE: Increased susceptibility to detergent and
heat shock, slighty decreased resistance to oxidative stress. Poor
growth in both human and mouse macrophage-derived cell lines.
Attenuated infection in both SCID and BALB/c mice. 13-fold
decreased transcription of sigB, no change in its own transcript
in culture. The sigE mutant induced the up-regulation of human and
mouse macrophage gene expression, which correlated with an
increased innate immune response. {ECO:0000269|PubMed:11489128,
ECO:0000269|PubMed:15102817, ECO:0000269|PubMed:18657035}.
-!- SIMILARITY: Belongs to the sigma-70 factor family. ECF subfamily.
{ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; U87242; AAC45268.1; -; Genomic_DNA.
EMBL; AL123456; CCP43977.1; -; Genomic_DNA.
PIR; H70507; H70507.
RefSeq; NP_215737.1; NC_000962.3. [P9WGG7-1]
RefSeq; WP_003406257.1; NZ_KK339370.1.
ProteinModelPortal; P9WGG7; -.
SMR; P9WGG7; -.
STRING; 83332.Rv1221; -.
PaxDb; P9WGG7; -.
EnsemblBacteria; CCP43977; CCP43977; Rv1221.
GeneID; 888751; -.
KEGG; mtu:Rv1221; -.
TubercuList; Rv1221; -.
eggNOG; ENOG4105DU6; Bacteria.
eggNOG; COG1595; LUCA.
KO; K03088; -.
OMA; EHADRVY; -.
PhylomeDB; P9WGG7; -.
Proteomes; UP000001584; Chromosome.
GO; GO:0016987; F:bacterial sigma factor activity; IDA:MTBBASE.
GO; GO:0003677; F:DNA binding; IDA:MTBBASE.
GO; GO:0003700; F:DNA binding transcription factor activity; IEA:InterPro.
GO; GO:0006352; P:DNA-templated transcription, initiation; IEA:InterPro.
GO; GO:0044119; P:growth of symbiont in host cell; IMP:MTBBASE.
GO; GO:0009405; P:pathogenesis; IMP:MTBBASE.
GO; GO:0090034; P:regulation of chaperone-mediated protein complex assembly; IDA:MTBBASE.
GO; GO:0009408; P:response to heat; IEP:MTBBASE.
GO; GO:0052572; P:response to host immune response; IEP:MTBBASE.
GO; GO:0042542; P:response to hydrogen peroxide; IEP:MTBBASE.
GO; GO:0009410; P:response to xenobiotic stimulus; IEP:MTBBASE.
Gene3D; 1.10.10.10; -; 1.
InterPro; IPR014284; RNA_pol_sigma-70_dom.
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; TIGR02937; sigma70-ECF; 1.
1: Evidence at protein level;
Alternative promoter usage; Complete proteome; DNA-binding;
Reference proteome; Sigma factor; Transcription;
Transcription regulation.
CHAIN 1 257 ECF RNA polymerase sigma factor SigE.
/FTId=PRO_0000422945.
DNA_BIND 211 230 H-T-H motif. {ECO:0000250}.
REGION 87 153 Sigma-70 factor domain-2.
REGION 186 236 Sigma-70 factor domain-4.
MOTIF 111 114 Polymerase core binding. {ECO:0000255}.
VAR_SEQ 1 42 Missing (in isoform 2). {ECO:0000305}.
/FTId=VSP_047441.
VAR_SEQ 1 39 Missing (in isoform 3). {ECO:0000305}.
/FTId=VSP_047440.
VAR_SEQ 40 40 I -> M (in isoform 3). {ECO:0000305}.
/FTId=VSP_047442.
VAR_SEQ 43 43 L -> M (in isoform 2). {ECO:0000305}.
/FTId=VSP_047443.
SEQUENCE 257 AA; 28877 MW; E7AB77CAECBF6CE7 CRC64;
MELLGGPRVG NTESQLCVAD GDDLPTYCSA NSEDLNITTI TTLSPTSMSH PQQVRDDQWV
EPSDQLQGTA VFDATGDKAT MPSWDELVRQ HADRVYRLAY RLSGNQHDAE DLTQETFIRV
FRSVQNYQPG TFEGWLHRIT TNLFLDMVRR RARIRMEALP EDYDRVPADE PNPEQIYHDA
RLGPDLQAAL ASLPPEFRAA VVLCDIEGLS YEEIGATLGV KLGTVRSRIH RGRQALRDYL
AAHPEHGECA VHVNPVR


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