Gene Rv3414c
in Mycobacterium tuberculosis H37Rv
General annotation
| Type | CDS |
| Function | The sigma factor is an initiation factor that promotes attachment of the RNA polymerase to specific initiation sites and then is released. |
| Product | Probable alternative RNA polymerase sigma-D factor SigD |
| Comments | Rv3414c, (MTCY78.15), len: 212 aa. Probable sigD, alternative RNA polymerase sigma-D factor (see citations below), similar to others (notably from Streptomyces coelicolor) e.g. Q9L0I8|SCD63.01 from Streptomyces coelicolor (195 aa), FASTA scores: opt: 533, E(): 9.6e-28, (47.25% identity in 182 aa overlap); Q9FDS3|ADSA from Streptomyces griseus (258 aa), FASTA scores: opt: 223, E(): 1.8e-07, (28.95% identity in 183 aa overlap); BAB48649|MLL1224 from Rhizobium loti (Mesorhizobium loti) (187 aa), FASTA scores: opt: 202, E(): 3.2e-06, (30.4% identity in 194 aa overlap); P38133|RPOE_STRCO|SIGE|SCE94.07 from Streptomyces coelicolor (176 aa), FASTA scores: opt: 200, E(): 4.1e-06, (35.25% identity in 156 aa overlap); P37978|CNRH_ALCEU from Alcaligenes eutrophus (Ralstonia eutropha), FASTA scores: opt: 197, E(): 6.9e-06, (30.35% identity in 191 aa overlap); etc. C-terminus strongly similar to N-terminal part of Q49727|S1620B|B1620_C3_233 hypothetical 6.2 KDA protein from Mycobacterium leprae (59 aa), FASTA scores: opt: 217, E(): 1.3e-07, (90.25% identity in 41 aa overlap). Belongs to the sigma-70 factor family. |
| Functional category | Information pathways |
| 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 decreased after heat shock (see Manganelli et al., 1999). |
| 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 and CDC1551 strains (see Sassetti et al., 2003 and Lamichhane et al., 2003). Non-essential gene for in vitro growth of H37Rv, by Himar1 transposon mutagenesis (See Griffin et al., 2011). M. tuberculosis H37Rv sigD|Rv3414c mutant is attenuated in BALB/c mice; growth in vitro, in hypoxic conditions, under oxidative stress (plumbagin, cumene hydroperoxide, diamide) is comparable to wild-type; slightly more susceptible to INH (See Raman et al., 2004). Check for mutants available at TARGET website |
Coordinates
| Type | Start | End | Orientation |
|---|---|---|---|
| CDS | 3833038 | 3833676 | - |
Genomic sequence
Feature type
Upstream flanking region (bp)
Downstream flanking region (bp)
Update
Protein sequence
>Mycobacterium tuberculosis H37Rv|Rv3414c|sigD
MVDPGVSPGCVRFVTLEISPSMTMQGERLDAVVAEAVAGDRNALREVLETIRPIVVRYCRARVGTVERSGLSADDVAQEVCLATITALPRYRDRGRPFLAFLYGIAAHKVADAHRAAGRDRAYPAETLPERWSADAGPEQMAIEADSVTRMNELLEILPAKQREILILRVVVGLSAEETAAAVGSTTGAVRVAQHRALQRLKDEIVAAGDYA
Bibliography
- Gomez JE et al. [1997]. Sigma factors of Mycobacterium tuberculosis. Review
- 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
- Manganelli R et al. [1999]. Differential expression of 10 sigma factor genes in Mycobacterium tuberculosis. Transcriptome
- Chen P, Gomez J and Bishai WR [2000]. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids=&dopt=Abstract Review
- Sassetti CM et al. [2003]. Genes required for mycobacterial growth defined by high density mutagenesis. Mutant
- Lamichhane G et al. [2003]. A postgenomic method for predicting essential genes at subsaturation levels of mutagenesis: application to Mycobacterium tuberculosis. Mutant
- Raman S, Hazra R, Dascher CC and Husson RN [2004]. Transcription regulation by the Mycobacterium tuberculosis alternative sigma factor SigD and its role in virulence. Mutant Regulon
- 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
