RPOS_ECOLI
ID RPOS_ECOLI Reviewed; 330 AA.
AC P13445; Q2MA88; Q79EB7;
DT 01-JAN-1990, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1996, sequence version 3.
DT 03-AUG-2022, entry version 192.
DE RecName: Full=RNA polymerase sigma factor RpoS {ECO:0000255|HAMAP-Rule:MF_00959};
DE AltName: Full=Sigma S {ECO:0000255|HAMAP-Rule:MF_00959};
DE AltName: Full=Sigma-38 {ECO:0000255|HAMAP-Rule:MF_00959};
GN Name=rpoS {ECO:0000255|HAMAP-Rule:MF_00959};
GN Synonyms=appR, katF, nur, otsX, sigS; OrderedLocusNames=b2741, JW5437;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=2690013; DOI=10.1093/nar/17.23.9979;
RA Mulvey M.R., Loewen P.C.;
RT "Nucleotide sequence of katF of Escherichia coli suggests KatF protein is a
RT novel sigma transcription factor.";
RL Nucleic Acids Res. 17:9979-9991(1989).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, AND INDUCTION.
RX PubMed=8475100; DOI=10.1073/pnas.90.8.3511;
RA Tanaka K., Takayanagi Y., Fujita N., Ishihama A., Takahashi H.;
RT "Heterogeneity of the principal sigma factor in Escherichia coli: the rpoS
RT gene product, sigma 38, is a second principal sigma factor of RNA
RT polymerase in stationary-phase Escherichia coli.";
RL Proc. Natl. Acad. Sci. U.S.A. 90:3511-3515(1993).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=1437569; DOI=10.1093/nar/20.20.5479;
RA Ivanova A., Renshaw M., Guntaka R.V., Eisenstark A.;
RT "DNA base sequence variability in katF (putative sigma factor) gene of
RT Escherichia coli.";
RL Nucleic Acids Res. 20:5479-5480(1992).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [6]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-72.
RC STRAIN=K12 / DH1 / ATCC 33849 / DSM 4235 / NCIB 12045;
RX PubMed=8208244; DOI=10.1007/bf00284200;
RA Takayanagi Y., Tanaka K., Takahashi H.;
RT "Structure of the 5' upstream region and the regulation of the rpoS gene of
RT Escherichia coli.";
RL Mol. Gen. Genet. 243:525-531(1994).
RN [7]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-11.
RC STRAIN=MP180;
RX PubMed=8132457; DOI=10.1128/jb.176.6.1630-1638.1994;
RA Ichikawa J.K., Li C., Fu J.C., Clarke S.;
RT "A gene at 59 minutes on the Escherichia coli chromosome encodes a
RT lipoprotein with unusual amino acid repeat sequences.";
RL J. Bacteriol. 176:1630-1638(1994).
RN [8]
RP INDUCTION.
RC STRAIN=K12 / MC4100 / ATCC 35695 / DSM 6574;
RX PubMed=8637901; DOI=10.1073/pnas.93.6.2488;
RA Pratt L.A., Silhavy T.J.;
RT "The response regulator SprE controls the stability of RpoS.";
RL Proc. Natl. Acad. Sci. U.S.A. 93:2488-2492(1996).
RN [9]
RP INDUCTION, INTERACTION WITH RSSB, AND MUTAGENESIS OF LYS-173; GLU-174;
RP VAL-177 AND TYR-178.
RC STRAIN=K12 / MC4100 / ATCC 35695 / DSM 6574;
RX PubMed=10339606; DOI=10.1073/pnas.96.11.6439;
RA Becker G., Klauck E., Hengge-Aronis R.;
RT "Regulation of RpoS proteolysis in Escherichia coli: the response regulator
RT RssB is a recognition factor that interacts with the turnover element in
RT RpoS.";
RL Proc. Natl. Acad. Sci. U.S.A. 96:6439-6444(1999).
RN [10]
RP INDUCTION, AND INTERACTION WITH RSSB.
RC STRAIN=K12 / MC4100 / ATCC 35695 / DSM 6574;
RX PubMed=10672187; DOI=10.1046/j.1365-2958.2000.01736.x;
RA Becker G., Klauck E., Hengge-Aronis R.;
RT "The response regulator RssB, a recognition factor for sigmaS proteolysis
RT in Escherichia coli, can act like an anti-sigmaS factor.";
RL Mol. Microbiol. 35:657-666(2000).
RN [11]
RP FUNCTION.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=15558318; DOI=10.1007/s00438-004-1089-2;
RA Patten C.L., Kirchhof M.G., Schertzberg M.R., Morton R.A., Schellhorn H.E.;
RT "Microarray analysis of RpoS-mediated gene expression in Escherichia coli
RT K-12.";
RL Mol. Genet. Genomics 272:580-591(2004).
RN [12]
RP FUNCTION.
RC STRAIN=K12 / MC4100 / ATCC 35695 / DSM 6574;
RX PubMed=15716429; DOI=10.1128/jb.187.5.1591-1603.2005;
RA Weber H., Polen T., Heuveling J., Wendisch V.F., Hengge R.;
RT "Genome-wide analysis of the general stress response network in Escherichia
RT coli: sigmaS-dependent genes, promoters, and sigma factor selectivity.";
RL J. Bacteriol. 187:1591-1603(2005).
RN [13]
RP FUNCTION.
RC STRAIN=K12 / BW25113;
RX PubMed=16511888; DOI=10.1002/bit.20858;
RA Rahman M., Hasan M.R., Oba T., Shimizu K.;
RT "Effect of rpoS gene knockout on the metabolism of Escherichia coli during
RT exponential growth phase and early stationary phase based on gene
RT expressions, enzyme activities and intracellular metabolite
RT concentrations.";
RL Biotechnol. Bioeng. 94:585-595(2006).
RN [14]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=K12 / MC4100 / ATCC 35695 / DSM 6574;
RX PubMed=19251848; DOI=10.1128/jb.00011-09;
RA Kolodkin-Gal I., Engelberg-Kulka H.;
RT "The stationary-phase sigma factor sigma(S) is responsible for the
RT resistance of Escherichia coli stationary-phase cells to mazEF-mediated
RT cell death.";
RL J. Bacteriol. 191:3177-3182(2009).
RN [15]
RP INDUCTION, AND REVIEW.
RX PubMed=21639793; DOI=10.1146/annurev-micro-090110-102946;
RA Battesti A., Majdalani N., Gottesman S.;
RT "The RpoS-mediated general stress response in Escherichia coli.";
RL Annu. Rev. Microbiol. 65:189-213(2011).
RN [16]
RP INDUCTION.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=21516113; DOI=10.1038/nchembio.560;
RA Wang X., Kim Y., Hong S.H., Ma Q., Brown B.L., Pu M., Tarone A.M.,
RA Benedik M.J., Peti W., Page R., Wood T.K.;
RT "Antitoxin MqsA helps mediate the bacterial general stress response.";
RL Nat. Chem. Biol. 7:359-366(2011).
RN [17]
RP FUNCTION.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=21398637; DOI=10.1093/nar/gkr129;
RA Maciag A., Peano C., Pietrelli A., Egli T., De Bellis G., Landini P.;
RT "In vitro transcription profiling of the sigmaS subunit of bacterial RNA
RT polymerase: re-definition of the sigmaS regulon and identification of
RT sigmaS-specific promoter sequence elements.";
RL Nucleic Acids Res. 39:5338-5355(2011).
CC -!- FUNCTION: Sigma factors are initiation factors that promote the
CC attachment of RNA polymerase to specific initiation sites and are then
CC released. This sigma factor is the master transcriptional regulator of
CC the stationary phase and the general stress response. Controls,
CC positively or negatively, the expression of several hundred genes,
CC which are mainly involved in metabolism, transport, regulation and
CC stress management. {ECO:0000255|HAMAP-Rule:MF_00959,
CC ECO:0000269|PubMed:15558318, ECO:0000269|PubMed:15716429,
CC ECO:0000269|PubMed:16511888, ECO:0000269|PubMed:21398637,
CC ECO:0000269|PubMed:8475100}.
CC -!- FUNCTION: Protects stationary phase cells from killing induced by
CC endoribonuclease MazF. {ECO:0000269|PubMed:19251848}.
CC -!- SUBUNIT: Interacts with the RNA polymerase core enzyme and RssB.
CC {ECO:0000255|HAMAP-Rule:MF_00959, ECO:0000269|PubMed:10339606,
CC ECO:0000269|PubMed:10672187}.
CC -!- INTERACTION:
CC P13445; P0A8V2: rpoB; NbExp=5; IntAct=EBI-557581, EBI-544996;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00959}.
CC -!- INDUCTION: Subject to complex regulation at multiple levels
CC (transcription, translation, regulation of activity and degradation).
CC Transcription is induced during entry into stationary phase and in
CC response to different stresses. Transcription is repressed by antitoxin
CC MqsA (PubMed:21516113). mRNA stability is regulated by small RNA
CC regulators and various proteins such as Hfq, CsdA, CspC and CspE.
CC Finally, the cellular level of RpoS is regulated by proteolysis via
CC RssB and the ClpXP protease. {ECO:0000269|PubMed:10339606,
CC ECO:0000269|PubMed:10672187, ECO:0000269|PubMed:21516113,
CC ECO:0000269|PubMed:21639793, ECO:0000269|PubMed:8475100,
CC ECO:0000269|PubMed:8637901}.
CC -!- DOMAIN: The sigma-70 factor domain-2 mediates sequence-specific
CC interaction with the -10 element in promoter DNA, and plays an
CC important role in melting the double-stranded DNA and the formation of
CC the transcription bubble. The sigma-70 factor domain-2 mediates
CC interaction with the RNA polymerase subunits RpoB and RpoC (By
CC similarity). {ECO:0000250}.
CC -!- DOMAIN: The sigma-70 factor domain-4 contains a helix-turn-helix (H-T-
CC H) motif that mediates interaction with the -35 element in promoter
CC DNA. The domain also mediates interaction with the RNA polymerase
CC subunit RpoA (By similarity). {ECO:0000250}.
CC -!- DISRUPTION PHENOTYPE: Stationary phase cells lose resistance to killing
CC by endoribonuclease MazF. {ECO:0000269|PubMed:19251848}.
CC -!- SIMILARITY: Belongs to the sigma-70 factor family. RpoS subfamily.
CC {ECO:0000255|HAMAP-Rule:MF_00959}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAE76818.1; Type=Erroneous termination; Note=Truncated C-terminus.; Evidence={ECO:0000305};
CC Sequence=CAA34435.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
CC Sequence=CAA78692.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; X16400; CAA34435.1; ALT_INIT; Genomic_DNA.
DR EMBL; D13548; BAA02747.1; -; Genomic_DNA.
DR EMBL; Z14969; CAA78692.1; ALT_INIT; Genomic_DNA.
DR EMBL; U29579; AAA69251.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75783.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE76818.1; ALT_SEQ; Genomic_DNA.
DR EMBL; D17549; BAA21003.1; -; Genomic_DNA.
DR EMBL; L07869; AAA17876.1; -; Unassigned_DNA.
DR PIR; A65055; RNECKF.
DR RefSeq; NP_417221.1; NC_000913.3.
DR RefSeq; WP_000081586.1; NZ_CP047127.1.
DR RefSeq; WP_000081588.1; NZ_CP014272.1.
DR PDB; 5IPL; X-ray; 3.60 A; F=1-328.
DR PDB; 5IPM; X-ray; 4.20 A; F=1-328.
DR PDB; 5IPN; X-ray; 4.61 A; F=1-328.
DR PDB; 6FI7; NMR; -; A=245-330.
DR PDB; 6IDO; X-ray; 3.75 A; A/B=256-330.
DR PDB; 6KJ6; EM; 3.80 A; F=1-330.
DR PDB; 6UTV; X-ray; 3.45 A; FFF=1-328.
DR PDB; 6UTW; X-ray; 3.85 A; FFF=1-328.
DR PDB; 6UTX; X-ray; 4.05 A; FFF=1-328.
DR PDB; 6UTY; X-ray; 4.15 A; FFF=1-328.
DR PDB; 6UTZ; X-ray; 3.80 A; FFF=1-328.
DR PDB; 6UU0; X-ray; 3.90 A; FFF=1-328.
DR PDB; 6UU1; X-ray; 4.10 A; FFF=1-328.
DR PDB; 6UU2; X-ray; 4.40 A; FFF=1-328.
DR PDB; 6UU3; X-ray; 4.00 A; FFF=1-328.
DR PDB; 6UU4; X-ray; 4.30 A; FFF=1-328.
DR PDB; 6UU5; X-ray; 5.40 A; FFF=1-328.
DR PDB; 6UU6; X-ray; 4.20 A; FFF=1-328.
DR PDB; 6UU7; X-ray; 4.40 A; FFF=1-328.
DR PDB; 6UUA; X-ray; 4.00 A; FFF=1-328.
DR PDB; 6UUB; X-ray; 3.96 A; FFF=1-328.
DR PDB; 6UUC; X-ray; 4.10 A; FFF=1-328.
DR PDBsum; 5IPL; -.
DR PDBsum; 5IPM; -.
DR PDBsum; 5IPN; -.
DR PDBsum; 6FI7; -.
DR PDBsum; 6IDO; -.
DR PDBsum; 6KJ6; -.
DR PDBsum; 6UTV; -.
DR PDBsum; 6UTW; -.
DR PDBsum; 6UTX; -.
DR PDBsum; 6UTY; -.
DR PDBsum; 6UTZ; -.
DR PDBsum; 6UU0; -.
DR PDBsum; 6UU1; -.
DR PDBsum; 6UU2; -.
DR PDBsum; 6UU3; -.
DR PDBsum; 6UU4; -.
DR PDBsum; 6UU5; -.
DR PDBsum; 6UU6; -.
DR PDBsum; 6UU7; -.
DR PDBsum; 6UUA; -.
DR PDBsum; 6UUB; -.
DR PDBsum; 6UUC; -.
DR AlphaFoldDB; P13445; -.
DR SMR; P13445; -.
DR BioGRID; 4262274; 308.
DR BioGRID; 851542; 1.
DR ComplexPortal; CPX-4883; DNA-directed RNA polymerase holoenzyme complex, SigmaS variant.
DR ComplexPortal; CPX-5024; rpoS-rssB sigma-antisigma complex.
DR DIP; DIP-10777N; -.
DR IntAct; P13445; 10.
DR STRING; 511145.b2741; -.
DR jPOST; P13445; -.
DR PaxDb; P13445; -.
DR PRIDE; P13445; -.
DR EnsemblBacteria; AAC75783; AAC75783; b2741.
DR EnsemblBacteria; BAE76818; BAE76818; BAE76818.
DR GeneID; 947210; -.
DR KEGG; ecj:JW5437; -.
DR KEGG; eco:b2741; -.
DR PATRIC; fig|511145.12.peg.2835; -.
DR EchoBASE; EB0505; -.
DR eggNOG; COG0568; Bacteria.
DR HOGENOM; CLU_014793_3_5_6; -.
DR InParanoid; P13445; -.
DR OMA; RRVQREF; -.
DR PhylomeDB; P13445; -.
DR BioCyc; EcoCyc:RPOS-MON; -.
DR BioCyc; MetaCyc:RPOS-MON; -.
DR PHI-base; PHI:7256; -.
DR PRO; PR:P13445; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IDA:EcoCyc.
DR GO; GO:1903865; C:sigma factor antagonist complex; IPI:ComplexPortal.
DR GO; GO:0001000; F:bacterial-type RNA polymerase core enzyme binding; IDA:EcoCyc.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0016987; F:sigma factor activity; IDA:EcoCyc.
DR GO; GO:0006352; P:DNA-templated transcription, initiation; IDA:EcoCyc.
DR GO; GO:0045892; P:negative regulation of transcription, DNA-templated; IC:ComplexPortal.
DR Gene3D; 1.10.10.10; -; 2.
DR HAMAP; MF_00959; Sigma70_RpoS; 1.
DR InterPro; IPR014284; RNA_pol_sigma-70_dom.
DR InterPro; IPR000943; RNA_pol_sigma70.
DR InterPro; IPR009042; RNA_pol_sigma70_r1_2.
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; IPR012761; RNA_pol_sigma_RpoS.
DR InterPro; IPR036388; WH-like_DNA-bd_sf.
DR Pfam; PF00140; Sigma70_r1_2; 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; SSF88659; SSF88659; 2.
DR SUPFAM; SSF88946; SSF88946; 1.
DR TIGRFAMs; TIGR02394; rpoS_proteo; 1.
DR TIGRFAMs; TIGR02937; sigma70-ECF; 1.
DR PROSITE; PS00715; SIGMA70_1; 1.
DR PROSITE; PS00716; SIGMA70_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; DNA-binding; Reference proteome; Sigma factor;
KW Stress response; Transcription; Transcription regulation.
FT CHAIN 1..330
FT /note="RNA polymerase sigma factor RpoS"
FT /id="PRO_0000093970"
FT DNA_BIND 288..307
FT /note="H-T-H motif"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00959"
FT REGION 56..89
FT /note="Sigma-70 factor domain-1"
FT REGION 94..164
FT /note="Sigma-70 factor domain-2"
FT REGION 174..249
FT /note="Sigma-70 factor domain-3"
FT REGION 262..315
FT /note="Sigma-70 factor domain-4"
FT MOTIF 118..121
FT /note="Interaction with polymerase core subunit RpoC"
FT MUTAGEN 173
FT /note="K->E: Eliminates RpoS proteolysis. Lack of
FT interaction with RssB."
FT /evidence="ECO:0000269|PubMed:10339606"
FT MUTAGEN 174
FT /note="E->T: 2-fold increase in RpoS half-life. Does not
FT affect interaction with RssB."
FT /evidence="ECO:0000269|PubMed:10339606"
FT MUTAGEN 177
FT /note="V->K: 3-fold increase in RpoS half-life."
FT /evidence="ECO:0000269|PubMed:10339606"
FT MUTAGEN 178
FT /note="Y->L: Does not affect RpoS half-life."
FT /evidence="ECO:0000269|PubMed:10339606"
FT CONFLICT 25
FT /note="F -> L (in Ref. 3; CAA78692)"
FT /evidence="ECO:0000305"
FT CONFLICT 29
FT /note="A -> P (in Ref. 1; CAA34435)"
FT /evidence="ECO:0000305"
FT CONFLICT 33
FT /note="Q -> L (in Ref. 2; BAA02747 and 6; BAA21003)"
FT /evidence="ECO:0000305"
FT CONFLICT 196
FT /note="E -> V (in Ref. 1; CAA34435)"
FT /evidence="ECO:0000305"
FT CONFLICT 328..330
FT /note="FRE -> LPRVSKHLSERPVSSEAGFFCAQ (in Ref. 1;
FT CAA34435)"
FT /evidence="ECO:0000305"
FT HELIX 253..255
FT /evidence="ECO:0007829|PDB:6FI7"
FT HELIX 256..261
FT /evidence="ECO:0007829|PDB:6FI7"
FT TURN 262..266
FT /evidence="ECO:0007829|PDB:6FI7"
FT HELIX 268..278
FT /evidence="ECO:0007829|PDB:6FI7"
FT HELIX 288..295
FT /evidence="ECO:0007829|PDB:6FI7"
FT HELIX 299..318
FT /evidence="ECO:0007829|PDB:6FI7"
FT TURN 319..321
FT /evidence="ECO:0007829|PDB:6FI7"
FT HELIX 324..326
FT /evidence="ECO:0007829|PDB:6FI7"
SQ SEQUENCE 330 AA; 37972 MW; 4E6E675E4CA6BC6F CRC64;
MSQNTLKVHD LNEDAEFDEN GVEVFDEKAL VEQEPSDNDL AEEELLSQGA TQRVLDATQL
YLGEIGYSPL LTAEEEVYFA RRALRGDVAS RRRMIESNLR LVVKIARRYG NRGLALLDLI
EEGNLGLIRA VEKFDPERGF RFSTYATWWI RQTIERAIMN QTRTIRLPIH IVKELNVYLR
TARELSHKLD HEPSAEEIAE QLDKPVDDVS RMLRLNERIT SVDTPLGGDS EKALLDILAD
EKENGPEDTT QDDDMKQSIV KWLFELNAKQ REVLARRFGL LGYEAATLED VGREIGLTRE
RVRQIQVEGL RRLREILQTQ GLNIEALFRE
