Gene Rv3223c (rpoE)
in Mycobacterium tuberculosis H37Rv
General annotation
| Type | CDS |
| Function | Alternative 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. |
| Product | Alternative RNA polymerase sigma-E factor (sigma-24) SigH (RPOE) |
| Comments | Rv3223c, (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. |
| Functional category | Information pathways |
| Proteomics | The 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). |
| Transcriptomics | mRNA 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). |
| Mutant | Non-essential gene for in vitro growth of H37Rv in a MtbYM rich medium, by Himar1 transposon mutagenesis (see Minato et al. 2019). Non-essential gene for in vitro growth of H37Rv, by analysis of saturated Himar1 transposon libraries (see DeJesus et al. 2017). Non essential gene by Himar1 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 Himar1 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
| Type | Start | End | Orientation |
|---|---|---|---|
| CDS | 3598901 | 3599551 | - |
Genomic sequence
Feature type
Upstream flanking region (bp)
Downstream flanking region (bp)
Update
Protein sequence
>Mycobacterium tuberculosis H37Rv|Rv3223c|sigH
MADIDGVTGSAGLQPGPSEETDEELTARFERDAIPLLDQLYGGALRMTRNPADAEDLLQETMVKAYAGFRSFRHGTNLKAWLYRILTNTYINSYRKKQRQPAEYPTEQITDWQLASNAEHSSTGLRSAEVEALEALPDTEIKEALQALPEEFRMAVYYADVEGFPYKEIAEIMDTPIGTVMSRLHRGRRQLRGLLADVARDRGFARGEQAHEGVSS
Bibliography
- Gomez JE et al. [1997]. Sigma factors of Mycobacterium tuberculosis. Review
- Manganelli R et al. [1999]. Differential expression of 10 sigma factor genes in Mycobacterium tuberculosis. Transcriptome
- Fernandes ND et al. [1999]. A mycobacterial extracytoplasmic sigma factor involved in survival following heat shock and oxidative stress. Homolog Mutant
- Graham JE and Clark-Curtiss JE [1999]. Identification of Mycobacterium tuberculosis RNAs synthesized in response to phagocytosis by human macrophages by selective capture of transcribed sequences (SCOTS). Transcriptome
- Rosenkrands I et al. [2000]. Towards the proteome of Mycobacterium tuberculosis. Proteomics
- Chen P, Gomez J and Bishai WR [2000]. Review
- Rosenkrands I, Weldingh K, Jacobsen S, Hansen CV, Florio W, Gianetri I and Andersen P [2000]. Mapping and identification of Mycobacterium tuberculosis proteins by two-dimensional gel electrophoresis, microsequencing and immunodetection. Proteomics
- Raman S, Song T, Puyang X, Bardarov S, Jacobs Jr WR and Husson RN [2001]. The alternative sigma factor SigH regulates major components of oxidative and heat stress responses in Mycobacterium tuberculosis. Mutant Regulation
- Paget MS et al. [2001]. Defining the disulphide stress response in Streptomyces coelicolor A3(2): identification of the sigmaR regulon. Homolog Sequence
- Stewart GR et al. [2002]. Dissection of the heat-shock response in Mycobacterium tuberculosis using mutants and microarrays. Transcriptome Mutant Regulation
- Kaushal D et al. [2002]. Reduced immunopathology and mortality despite tissue persistence in a Mycobacterium tuberculosis mutant lacking alternative sigma factor, SigH. Mutant Regulation
- Manganelli R et al. [2002]. Role of the extracytoplasmic-function sigma factor sigma(H) in Mycobacterium tuberculosis global gene expression. Mutant Regulation Transcriptome
- Song T et al. [2003]. RshA, an anti-sigma factor that regulates the activity of the mycobacterial stress response sigma factor SigH. Biochemistry
- Sassetti CM et al. [2003]. Genes required for mycobacterial growth defined by high density mutagenesis. Mutant
- Darwin KH et al. [2003]. The proteasome of Mycobacterium tuberculosis is required for resistance to nitric oxide. Mutant
- Rengarajan J et al. [2005]. Genome-wide requirements for Mycobacterium tuberculosis adaptation and survival in macrophages. Mutant
- Jeong EH et al. [2006]. RshA mimetic peptides inhibiting the transcription driven by a Mycobacterium tuberculosis sigma factor SigH. Biochemistry
- Park ST et al. [2008]. Regulation of the SigH stress response regulon by an essential protein kinase in Mycobacterium tuberculosis. Biochemistry
- Mehra S et al. [2009]. Functional genomics reveals extended roles of the Mycobacterium tuberculosis stress response factor sigmaH. Transcriptome
- Målen H et al. [2010]. Definition of novel cell envelope associated proteins in Triton X-114 extracts of Mycobacterium tuberculosis H37Rv. Proteomics
- Kelkar DS et al. [2011]. Proteogenomic analysis of Mycobacterium tuberculosis by high resolution mass spectrometry. Proteomics Sequence
- de Souza GA et al. [2011]. Bacterial proteins with cleaved or uncleaved signal peptides of the general secretory pathway. Proteomics
- Griffin JE et al. [2011]. High-resolution phenotypic profiling defines genes essential for mycobacterial growth and cholesterol catabolism. Mutant
- DeJesus MA et al. [2017]. Comprehensive Essentiality Analysis of the Mycobacterium tuberculosis Genome via Saturating Transposon Mutagenesis. Mutant
- Minato Y et al. [2019]. Genomewide Assessment of Mycobacterium tuberculosis Conditionally Essential Metabolic Pathways. Mutant
