Rv1189 (sigI)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: sigma-70 family RNA polymerase sigma factor
- REFSEQ: RNA polymerase sigma factor SigI
- PATRIC: putative RNA polymerase sigma factor
- TUBERCULIST: Possible alternative RNA polymerase sigma factor SigI
- NCBI: Possible alternative RNA polymerase sigma factor SigI
- updated information (H37Rv4):
  - gene name: sigI
  - function:
  - reference:
Type: Not Target
Start: 1332092
End: 1332964
Operon:

Trans-membrane region:
Role: II.A.7 - RNA synthesis, RNA modification and DNA transcription
GO terms:
- GO:2000142 - regulation of DNA-templated transcription, initiation (Uniprot)
- GO:0016987 - bacterial sigma factor activity (Uniprot)
- GO:0006355 - regulation of transcription, DNA-templated (Uniprot)
- GO:0006352 - DNA-templated transcription, initiation (Uniprot)
- GO:0006351 - transcription, DNA-templated (Uniprot)
- GO:0003700 - DNA binding transcription factor activity (Uniprot)
- GO:0003677 - DNA binding (Uniprot)
Reaction(s) (based on iSM810 metabolic model):
Gene Expression Profile (Transcriptional Responses to Drugs; Boshoff et al, 2004)
Gene Modules extracted from cluster analysis of 249 transcriptomic datasets using ICA
Orthologs among selected mycobacteria
Protein structure:
Search for Homologs in PDB
Top 10 Homologs in PDB (as of Nov 2020):

PDB aa ident species PDB title

5XE7 35% Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) Crystal structure of Mycobacterium tuberculosis extracytoplasmic function sigma factor SigJ
Links to additional information on sigI:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 1.005 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

PDB	aa ident	species	PDB title
5XE7	35%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of Mycobacterium tuberculosis extracytoplasmic function sigma factor SigJ

Amino Acid Sequence

MSQHDPVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGDIDDERGWLIVVTSRLCLDHIKSASTRRERPQDIAAWHDGDASVSSVDPAD
RVTLDDEVRLALLIMLERLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRARRKINESRIAASVEPAQHRVVTRAFIEACSNGDLDTLLEVLD
PGVAGEIDARKGVVVVGADRVGPTILRHWSHPATVLVAQPVCGQPAVLAFVNRALAGVLALSIEAGKITKIHVLVQPSTLDPLRAELGGG

(Nucleotide sequence available on KEGG)

Additional Information

ESSENTIALITY

MtbTnDB - interactive tool for exploring a database of published TnSeq datasets for Mtb

TnSeqCorr - genes with correlated TnSeq profiles across >100 conditions *new*

Classification	Condition	Strain	Method	Reference	Notes
Uncertain	Sodium Oleate	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.059050; 2 non-insertions in a row out of 8 sites
Uncertain	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.049250; 2 non-insertions in a row out of 8 sites
Uncertain	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.052200; 2 non-insertions in a row out of 8 sites
Uncertain	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.046250; 2 non-insertions in a row out of 9 sites
Uncertain	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.047550; 2 non-insertions in a row out of 9 sites
No-Data	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Too-Short	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: -1
Non-Essential	7H09/7H10 + rich media	H37RvMA	MotifHMM	DeJesus et al. (2017)	Fully saturated (14 reps).

TnSeq Data No data currently available.

No TnSeq data currently available for this Target.

RNASeq Data No data currently available.

No RNA-Seq data currently available for this Target.

Metabolomic Profiles No data currently available.

No Metabolomic data currently available for this Target.

Proteomic Data No data currently available.

No Proteomic data currently available for this Target.

Regulatory Relationships from Systems Biology

BioCyc

Gene interactions based on ChIPSeq and Transcription Factor Over-Expression (TFOE) (Systems Biology)

NOTE: Green edges represent the connected genes being classified as differentially essential as a result of the middle gene being knocked out. These interactions are inferred based on RNASeq.

Interactions based on ChIPSeq data

Interactions based on ChIPSeq data (Minch et al. 2014)

Binds To:
- Rv0070c (glyA2) (Direct binding)
- Rv0167 (yrbE1A) (Direct binding)
- Rv0467 (icl1) (Direct binding)
- Rv0667 (rpoB) (Direct binding)
- Rv1116 (-) (Direct binding)
- Rv1374c (-) (Direct binding)
- Rv1586c (-) (Direct binding)
- Rv1587c (-) (Direct binding)
- Rv1665 (pks11) (Direct binding)
- Rv1963c (mce3R) (Direct binding)
- Rv1964 (yrbE3A) (Direct binding)
- Rv2107 (PE22) (Direct binding)
- Rv2307B (-) (Direct binding)
- Rv2768c (PPE43) (Direct binding)
- Rv3290c (lat) (Direct binding)
- Rv3383c (idsB) (Direct binding)
- Rv3425 (PPE57) (Direct binding)
- Rv3746c (PE34) (Direct binding)
- Rv3747 (-) (Direct binding)
- Rv0069c (sdaA) (Upstream of operon)
- Rv0168 (yrbE1B) (Upstream of operon)
- Rv0169 (mce1A) (Upstream of operon)
- Rv0170 (mce1B) (Upstream of operon)
- Rv0171 (mce1C) (Upstream of operon)
- Rv0172 (mce1D) (Upstream of operon)
- Rv0173 (lprK) (Upstream of operon)
- Rv0174 (mce1F) (Upstream of operon)
- Rv0175 (-) (Upstream of operon)
- Rv0176 (-) (Upstream of operon)
- Rv0177 (-) (Upstream of operon)
- Rv0178 (-) (Upstream of operon)
- Rv1965 (yrbE3B) (Upstream of operon)
- Rv1966 (mce3A) (Upstream of operon)
- Rv1967 (mce3B) (Upstream of operon)
- Rv1968 (mce3C) (Upstream of operon)
- Rv1969 (mce3D) (Upstream of operon)
- Rv1970 (lprM) (Upstream of operon)
- Rv1971 (mce3F) (Upstream of operon)
- Rv1972 (-) (Upstream of operon)
- Rv1973 (-) (Upstream of operon)
- Rv1974 (-) (Upstream of operon)
- Rv1975 (-) (Upstream of operon)
- Rv3288c (usfY) (Upstream of operon)
- Rv3289c (-) (Upstream of operon)
- Rv3382c (lytB1) (Upstream of operon)
Bound By:
- No bindings to other targets were found.

Interactions based on TFOE data (Rustad et al. 2014)

Upregulates:
Upregulated by:
Downregulates:
Downregulated by:
- Not downregulated by other genes.

Property	Value	Creator	Evidence	PMID	Comment
Citation	[Quantitative analysis of sigma genes expression in Mycobacterium tuberculosis cultures exposed to rifampicin and isoniazid] J. Pendzich, W. Maksymowicz-Mazur et al. Wiad. Lek. 2004	dreamsbeyondinfinity	IEP	15518067	Co-expression (Functional linkage)
Interaction	Regulatory Rv3328c	dreamsbeyondinfinity	IEP		Co-expression (Functional linkage) J. Pendzich, W. Maksymowicz-Mazur et al. [Quantitative analysis of sigma genes expression in Mycobacterium tuberculosis cultures exposed to rifampicin and isoniazid] Wiad. Lek. 2004
Citation	Identifying sigma factors in Mycobacterium smegmatis by comparative genomic analysis. A. Waagmeester, J. Thompson et al. Trends Microbiol. 2005	dreamsbeyondinfinity	IEP	16140533	Co-expression (Functional linkage)
Interaction	Regulatory Rv3328c	dreamsbeyondinfinity	IEP		Co-expression (Functional linkage) A. Waagmeester, J. Thompson et al. Identifying sigma factors in Mycobacterium smegmatis by comparative genomic analysis. Trends Microbiol. 2005
Citation	Differential expression of 10 sigma factor genes in Mycobacterium tuberculosis. R. Manganelli,E. Dubnau,S. Tyagi,FR. Kramer,I. Smith Mol. Microbiol. 1999	dreamsbeyondinfinity	IEP	10027986	Co-expression (Functional linkage)
Interaction	Regulatory Rv3328c	dreamsbeyondinfinity	IEP		Co-expression (Functional linkage) R. Manganelli,E. Dubnau,S. Tyagi,FR. Kramer,I. Smith Differential expression of 10 sigma factor genes in Mycobacterium tuberculosis. Mol. Microbiol. 1999
Citation	Cascade of extracytoplasmic function sigma factors in Mycobacterium tuberculosis: identification of a sigmaJ-dependent promoter upstream of sigI. D. Homerova, L. Halgasova et al. FEMS Microbiol. Lett. 2008	dreamsbeyondinfinity	IEP	18248429	Co-expression (Functional linkage)
Interaction	Regulatory Rv3328c	dreamsbeyondinfinity	IEP		Co-expression (Functional linkage) D. Homerova, L. Halgasova et al. Cascade of extracytoplasmic function sigma factors in Mycobacterium tuberculosis: identification of a sigmaJ-dependent promoter upstream of sigI. FEMS Microbiol. Lett. 2008

TB Genome Annotation Portal