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Search term: Rv3223c

General annotation | Coordinates | Sequence | Structural information | Orthologs/Cross-references | Interacting Drugs/Compounds | Bibliography
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General annotation
Gene namesigH
Rv numberRv3223c
Synonym(s)rpoE
TypeCDS
FunctionAlternative sigma factor that plays a role in the oxidative-stress response (regulation of thioredoxin recycling). The sigma factor is an initiation factor that promotes attachment of the RNA polymerase to specific initiation sites and then is released. This sigma factor is involved in heat shock and oxidative stress response; it is believed to control protein processing in the extracytoplasmic compartment. Regulates positively DNAK and CLPB genes. Regulates TRXB2, TRXC, Rv2466c and SIGB genes, and probably SIGB gene. SigH may mediate the transcription of at least 31 genes directly and modulates the expression of about 150 others.
ProductAlternative RNA polymerase sigma-E factor (sigma-24) SigH (RPOE)
CommentsRv3223c, (MTCY07D11.03), len: 216 aa. SigH (alternate gene name: rpoE), alternative RNA polymerase sigma factor (see citations below), similar to many e.g. Q9XCD8|sigh from Mycobacterium smegmatis (215 aa), FASTA scores: opt: 1187, E(): 8.1e-69, (87.75% identity in 212 aa overlap); O87834|SIGR from Streptomyces coelicolor (227 aa), FASTA scores: opt: 913, E(): 2.6e-51, (68.8% identity in 202 aa overlap); O68520|RPOE1 from Myxococcus xanthus (213 aa), FASTA scores: opt: 452, E(): 6.7e-22, (42.8% identity in 187 aa overlap); Q06198|RPSH_PSEAE|ALGU|ALGT|PA0762 from Pseudomonas aeruginosa (193 aa), FASTA scores: opt: 301, E(): 2.7e-12, (29.9% identity in 194 aa overlap); etc. Equivalent to AAK47662 RNA polymerase sigma-70 factor from Mycobacterium tuberculosis strain CDC1551 (284 aa), but shorter 68 aa. Has sigma-70 factors ECF subfamily signature (PS01063). So belongs to the sigma-70 factor family, ECF subfamily. Start chosen on basis of similarity, other potential starts upstream.
Molecular mass (Da)24225.1
Isoelectric point4.7174
Gene length (bp)651
Protein length216
Location (kb)3598.9


Functional categoryinformation pathways


ProteomicsThe product of this CDS corresponds to a spot identified in cytosol by proteomics at the Statens Serum Institute (Denmark) (see proteomics citations). Identified by mass spectrometry in Triton X-114 extracts of M. tuberculosis H37Rv (See Malen et al., 2010). Identified by mass spectrometry in the membrane protein fraction and whole cell lysates of M. tuberculosis H37Rv but not the culture filtrate (See de Souza et al., 2011). Translational start site supported by proteomics data (See Kelkar et al., 2011).
TranscriptomemRNA identified by SCOTS method, during infection of cultured human primary macrophages (see Graham & Clark-Curtiss 1999). mRNA also identified by real-time quantitative RT-PCR during exponential growing cultures. mRNA level increases after heat shock (see Manganelli et al., 1999; Stewart et al., 2002).
Mutationnon essential gene by Himar1-based transposon mutagenesis in H37Rv strain (see Sassetti et al., 2003). Required for survival in primary murine macrophages, by transposon site hybridization (TraSH) in H37Rv (See Rengarajan et al., 2005). Non-essential gene for in vitro growth of H37Rv, by sequencing of Himar1-based transposon mutagenesis (See Griffin et al., 2011). Transposon mutant is hypersensitive to acidified nitrite (See Darwin et al., 2003). Check for mutants available at TARGET website


Coordinates
TypeStartEndOrientation
CDS35989013599551-
RBS35995683599571-


Protein sequence in FASTA format
>M. tuberculosis H37Rv|Rv3223c|sigH
MADIDGVTGSAGLQPGPSEETDEELTARFERDAIPLLDQLYGGALRMTRNPADAEDLLQE
TMVKAYAGFRSFRHGTNLKAWLYRILTNTYINSYRKKQRQPAEYPTEQITDWQLASNAEH
SSTGLRSAEVEALEALPDTEIKEALQALPEEFRMAVYYADVEGFPYKEIAEIMDTPIGTV
MSRLHRGRRQLRGLLADVARDRGFARGEQAHEGVSS
Blastp: Pre-computed results
TransMembrane prediction using Hidden Markov Models: TMHMM
Genomic sequence

Add extra bases upstream (5') and downstream (3')



Structural information
Protein Data BankNo structure available
PFAMP66807


Orthologs/Cross-references
CDC1551MT3320
Gene Ontologytranscription factor activity
transcription initiation
regulation of transcription, DNA-dependent
response to stress
sigma factor activity
M. bovisMb3250c
M. lepraeML0801
M. marinumMMAR_1334
M. smegmatisMSMEG_1914
UniProtP66807
Multiple Sequences Alignment: between orthologs


Interacting Drugs/Compounds
TDR TargetsRv3223c


Expression Data
TBDBRv3223c


Bibliography
Manganelli R, Dubnau E, Tyagi S, Kramer FR, Smith I,
Differential expression of 10 sigma factor genes in Mycobacterium tuberculosis
Mol Microbiol (1999) 31(2):715-24
Cited for: Transcriptome
Fernandes ND, Wu QL, Kong D, Puyang X, Garg S, Husson RN,
A mycobacterial extracytoplasmic sigma factor involved in survival following heat shock and oxidative stress
J Bacteriol (1999) 181(14):4266-74
Cited for: Homolog/Mutant
Graham JE, Clark-Curtiss JE,
Identification of Mycobacterium tuberculosis RNAs synthesized in response to phagocytosis by human macrophages by selective capture of transcribed sequences (SCOTS)
Proc Natl Acad Sci U S A (1999) 96(20):11554-9
Cited for: Transcriptome
Rosenkrands I, Weldingh K, Jacobsen S, Hansen CV, Florio W, Gianetri I, Andersen P,
Mapping and identification of Mycobacterium tuberculosis proteins by two-dimensional gel electrophoresis, microsequencing and immunodetection
Electrophoresis (2000) 21(5):935-48
Cited for: Proteomics
Rosenkrands I, King A, Weldingh K, Moniatte M, Moertz E, Andersen P,
Towards the proteome of Mycobacterium tuberculosis
Electrophoresis (2000) 21(17):3740-56
Cited for: Proteomics
Raman S, Song T, Puyang X, Bardarov S, Jacobs Jr WR, Husson RN,
The alternative sigma factor SigH regulates major components of oxidative and heat stress responses in Mycobacterium tuberculosis
J Bacteriol (2001) 183(20):6119-25
Cited for: Mutant/Regulation
Paget MS, Molle V, Cohen G, Aharonowitz Y, Buttner MJ,
Defining the disulphide stress response in Streptomyces coelicolor A3(2): identification of the sigmaR regulon
Mol Microbiol (2001) 42(4):1007-20
Cited for: Homolog/Sequence
Kaushal D, Schroeder BG, Tyagi S, Yoshimatsu T, Scott C, Ko C, Carpenter L, Mehrotra J, Manabe YC, Fleischmann RD, Bishai WR,
Reduced immunopathology and mortality despite tissue persistence in a Mycobacterium tuberculosis mutant lacking alternative sigma factor, SigH
Proc Natl Acad Sci U S A (2002) 99(12):8330-5
Cited for: Mutant/Regulation
Manganelli R, Voskuil MI, Schoolnik GK, Dubnau E, Gomez M, Smith I,
Role of the extracytoplasmic-function sigma factor sigma(H) in Mycobacterium tuberculosis global gene expression
Mol Microbiol (2002) 45(2):365-74
Cited for: Mutant/Regulation/Transcriptome
Stewart GR, Wernisch L, Stabler R, Mangan JA, Hinds J, Laing KG, Young DB, Butcher PD,
Dissection of the heat-shock response in Mycobacterium tuberculosis using mutants and microarrays
Microbiology (2002) 148(Pt 10):3129-3138
Cited for: Transcriptome/Mutant/Regulation
Sassetti CM, Boyd DH, Rubin EJ,
Genes required for mycobacterial growth defined by high density mutagenesis.
Mol Microbiol (2003) 48(1):77-84
Cited for: Mutant
Song T, Dove SL, Lee KH, Husson RN,
RshA, an anti-sigma factor that regulates the activity of the mycobacterial stress response sigma factor SigH.
Mol Microbiol (2003) 50(3):949-59
Cited for: Biochemistry
Darwin KH, Ehrt S, Gutierrez-Ramos JC, Weich N, Nathan CF,
The proteasome of Mycobacterium tuberculosis is required for resistance to nitric oxide.
Science (2003) 302(5652):1963-6
Cited for: Mutant
Rengarajan J, Bloom BR, Rubin EJ,
Genome-wide requirements for Mycobacterium tuberculosis adaptation and survival in macrophages.
Proc Natl Acad Sci U S A (2005) 102(23):8327-32
Cited for: Mutant
Jeong EH, Son YM, Hah YS, Choi YJ, Lee KH, Song T, Kim DR,
RshA mimetic peptides inhibiting the transcription driven by a Mycobacterium tuberculosis sigma factor SigH.
Biochem Biophys Res Commun (2006) 339(1):392-8
Cited for: Biochemistry
Park ST, Kang CM, Husson RN,
Regulation of the SigH stress response regulon by an essential protein kinase in Mycobacterium tuberculosis.
Proc Natl Acad Sci U S A (2008) 105(35):13105-10
Cited for: Biochemistry
Mehra S, Kaushal D,
Functional genomics reveals extended roles of the Mycobacterium tuberculosis stress response factor sigmaH.
J Bacteriol (2009) 191(12):3965-80
Cited for: Transcriptome
Malen H, Pathak S, Softeland T, de Souza GA, Wiker HG,
Definition of novel cell envelope associated proteins in Triton X-114 extracts of Mycobacterium tuberculosis H37Rv.
BMC Microbiol (2010) 10:132
Cited for: Proteomics
de Souza GA, Leversen NA, Malen H, Wiker HG,
Bacterial proteins with cleaved or uncleaved signal peptides of the general secretory pathway.
J Proteomics (2011) 75(2):502-10
Cited for: Proteomics
Kelkar DS, Kumar D, Kumar P, Balakrishnan L, Muthusamy B, Yadav AK, Shrivastava P, Marimuthu A, Anand S, Sundaram H, Kingsbury R, Harsha HC, Nair B, Prasad TS, Chauhan DS, Katoch K, Katoch VM, Kumar P, Chaerkady R, Ramachandran S, Dash D, Pandey A,
Proteogenomic analysis of Mycobacterium tuberculosis by high resolution mass spectrometry.
Mol Cell Proteomics (2011) 10(12):M111.011627
Cited for: Proteomics/Sequence
Griffin JE, Gawronski JD, Dejesus MA, Ioerger TR, Akerley BJ, Sassetti CM,
High-resolution phenotypic profiling defines genes essential for mycobacterial growth and cholesterol catabolism.
PLoS Pathog (2011) 7(9):e1002251
Cited for: Mutant
Gomez JE, Chen JM, Bishai WR,
Sigma factors of Mycobacterium tuberculosis
Tuber Lung Dis (1997) 78(3-4):175-83
Cited for: Review
Chen P, Gomez J, Bishai WR,
Molecular Genetics of Mycobacteria; Ninth chapter: Mycobacterial Transcription Regulation in Stationary Phase
ASM Press (2000) 1-55581-191-4:149-156
Cited for: Review