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

Analysis of Positive Selection in Clinical Isolates new

Analysis of dN/dS (omega) in two collections of Mtb clinical isolates using GenomegaMap (Window model) (see description of methods)
- Moldova: 2,057 clinical isolates
- global set: 5,195 clinical isolates from 15 other countries
In the omega plots, the black line shows the mean estimate of omega (dN/dS) at each codon, and the blue lines are the bounds for the 95% credible interval (95%CI, from MCMC sampling).
A gene is under significant positive selection if the lower-bound of the 95%CI of omega (lower blue line) exceeds 1.0 at any codon.

	Moldova (2,057)	global set (5,195)
under significant positive selection?	NO	NO
omega peak height (95%CI lower bound)	1.54 (0.28)	2.19 (0.9)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link

* example format for variants: "D27 (GAC): D27H (CAC,11)" means "Asp27 (native codon GAC) mutated to His (codon CAC) in 11 isolates"

ESSENTIALITY

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

TnSeqCorr - genes with correlated TnSeq profiles across ~100 conditions

Rv1189/sigI, gene len: 872 bp, num TA sites: 9

condition	dataset	call	medium	method	notes
in-vitro	DeJesus 2017 mBio	non-essential	7H9	HMM	fully saturated, 14 TnSeq libraries combined
in-vitro	Sassetti 2003 Mol Micro	no data	7H9	TRASH	essential if hybridization ratio<0.2
in-vivo (mice)	Sassetti 2003 PNAS	non-essential	BL6 mice	TRASH	essential if hybridization ratio<0.4, min over 4 timepoints (1-8 weeks)
in-vitro (glycerol)	Griffin 2011 PPath	uncertain	M9 minimal+glycerol	Gumbel	2 replicates; Padj<0.05
in-vitro (cholesterol)	Griffin 2011 PPath	uncertain	M9 minimal+cholesterol	Gumbel	3 replicates; Padj<0.05
differentially essential in cholesterol	Griffin 2011 PPath	NO (LFC=-0.59)	cholesterol vs glycerol	resampling-SR	YES if Padj<0.05, else not significant; LFC<0 means less insertions/more essential in cholesterol
in-vitro	Smith 2022 eLife	non-essential	7H9	HMM	6 replicates (raw data in Subramaniam 2017, PMID 31752678)
in-vivo (mice)	Smith 2022 eLife	non-essential	BL6 mice	HMM	6 replicates (raw data in Subramaniam 2017, PMID 31752678)
differentially essential in mice	Smith 2022 eLife	NO (LFC=0.441)	in-vivo vs in-vitro	ZINB	YES if Padj<0.05, else not significant; LFC<0 means less insertions/more essential in mice
in-vitro (minimal)	Minato 2019 mSys	non-essential	minimal medium	HMM
in-vitro (YM rich medium)	Minato 2019 mSys	non-essential	YM rich medium	HMM	7H9 supplemented with ~20 metabolites (amino acids, vitamins)
differentially essential in YM rich medium	Minato 2019 mSys	NO (LFC=1.21)	YM rich vs minimal medium	resampling

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