Rv3219 (whiB1)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: transcriptional regulator whib-like whiB1
- REFSEQ: transcriptional regulatory protein WHIB-like WHIB1
- PATRIC: WhiB-like transcription regulator
- TUBERCULIST: Transcriptional regulatory protein WhiB-like WhiB1. Contains [4FE-4S]2+ cluster.
- NCBI: Transcriptional regulatory protein WhiB-like WhiB1 Contains [4FE-4S]2+ cluster
- updated information (H37Rv4):
  - gene name: whiB1
  - function:
  - reference:
Type: Not Target
Start: 3595713
End: 3595967
Operon:

Trans-membrane region:
Role: I.J.1 - Repressors/activators
GO terms:
- GO:0071731 - response to nitric oxide (Uniprot)
- GO:0055114 - oxidation-reduction process (Uniprot)
- GO:0051539 - 4 iron, 4 sulfur cluster binding (Uniprot)
- GO:0051536 - iron-sulfur cluster binding (Uniprot)
- GO:0047134 - protein-disulfide reductase activity (Uniprot)
- GO:0046872 - metal ion binding (Uniprot)
- GO:0045892 - negative regulation of transcription, DNA-templated (Uniprot)
- GO:0015035 - protein disulfide oxidoreductase activity (Uniprot)
- GO:0006355 - regulation of transcription, DNA-templated (Uniprot)
- GO:0006351 - transcription, DNA-templated (Uniprot)
- GO:0005737 - cytoplasm (Uniprot)
- GO:0005515 - protein binding (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
6ONU	100%	Mycobacterium tuberculosis H37Rv	Complex structure of WhiB1 and region 4 of SigA in P21 space group.
6ONO	100%	Mycobacterium tuberculosis H37Rv	Complex structure of WhiB1 and region 4 of SigA in C2221 space group
5OAY	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	M. tuberculosis [4Fe-4S] protein WhiB1 is a four-helix bundle that forms a NO-sensitive complex with sigmaA and regulates the major virulence factor ESX-1

Links to additional information on whiB1:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = -10.916 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

MDWRHKAVCRDEDPELFFPVGNSGPALAQIADAKLVCNRCPVTTECLSWALNTGQDSGVWGGMSEDERRALKRRNARTKARTGV

(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: 0.965050; 4 non-insertions in a row out of 4 sites
Uncertain	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.981800; 4 non-insertions in a row out of 4 sites
Uncertain	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.985200; 4 non-insertions in a row out of 4 sites
Uncertain	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.982450; 4 non-insertions in a row out of 4 sites
Uncertain	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.981350; 4 non-insertions in a row out of 4 sites
Non-Essential	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Non-Essential	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: 1.44
Growth-Defect	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

Binds To:
Bound By:
- Rv0818 (-)

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

Binds To:
- Rv0510 (hemC) (Direct binding)
- Rv0511 (hemD) (Direct binding)
- Rv0578c (PE_PGRS7) (Direct binding)
- Rv0579 (-) (Direct binding)
- Rv0667 (rpoB) (Direct binding)
- Rv0682 (rpsL) (Direct binding)
- Rv0700 (rpsJ) (Direct binding)
- Rv0714 (rplN) (Direct binding)
- Rv0756c (-) (Direct binding)
- Rv0842 (-) (Direct binding)
- Rv1074c (fadA3) (Direct binding)
- Rv1173 (fbiC) (Direct binding)
- Rv1374c (-) (Direct binding)
- Rv1397c (vapC10) (Direct binding)
- Rv1398c (vapB10) (Direct binding)
- Rv2274c (mazF8) (Direct binding)
- Rv2275 (-) (Direct binding)
- Rv2783c (gpsI) (Direct binding)
- Rv2785c (rpsO) (Direct binding)
- Rv3462c (infA) (Direct binding)
- Rv3463 (-) (Direct binding)
- Rv3908 (mutT4) (Direct binding)
- Rv0683 (rpsG) (Upstream of operon)
- Rv0701 (rplC) (Upstream of operon)
- Rv0702 (rplD) (Upstream of operon)
- Rv0703 (rplW) (Upstream of operon)
- Rv0715 (rplX) (Upstream of operon)
- Rv0716 (rplE) (Upstream of operon)
- Rv0717 (rpsN1) (Upstream of operon)
- Rv0843 (-) (Upstream of operon)
- Rv2276 (cyp121) (Upstream of operon)
- Rv2782c (pepR) (Upstream of operon)
- Rv2784c (lppU) (Upstream of operon)
- Rv3461c (rpmJ) (Upstream of operon)
- Rv3909 (-) (Upstream of operon)
- Rv3910 (MviN) (Upstream of operon)
- Rv3911 (sigM) (Upstream of operon)
- Rv3912 (-) (Upstream of operon)
Bound By:
- Rv0023 (-) (Direct binding)
- Rv0081 (-) (Direct binding)
- Rv0135c (-) (Direct binding)
- Rv0324 (-) (Direct binding)
- Rv0576 (-) (Direct binding)
- Rv0678 (-) (Direct binding)
- Rv0757 (phoP) (Direct binding)
- Rv1033c (trcR) (Direct binding)
- Rv1219c (-) (Direct binding)
- Rv1985c (-) (Direct binding)
- Rv2034 (-) (Direct binding)
- Rv2069 (sigC) (Direct binding)
- Rv2250c (-) (Direct binding)
- Rv2324 (-) (Direct binding)
- Rv2989 (-) (Direct binding)
- Rv3597c (lsr2) (Direct binding)
- Rv3681c (whiB4) (Direct binding)
- Rv3765c (tcrX) (Direct binding)

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

Upregulates:
- Does not upregulate other genes.
Upregulated by:
- Not upregulated by other genes.
Downregulates:
- Rv1258c (-)
- Rv1473A (-)
Downregulated by:
- Rv0818 (-)

Property	Value	Creator	Evidence	Comment
Interaction	PhysicalInteraction Rv1326c	ahal4789	IPI	Yeast two-hybrid (Physical interaction) SK. Garg, MS. Alam et al. Redox Biology of Mycobacterium tuberculosis H37Rv: protein-protein interaction between GlgB and WhiB1 involves exchange of thiol-disulfide. BMC Biochem. 2009
Interaction	PhysicalInteraction Rv1326c	sourish10	IPI	Yeast two-hybrid (Physical interaction) SK. Garg, MS. Alam et al. Redox Biology of Mycobacterium tuberculosis H37Rv: protein-protein interaction between GlgB and WhiB1 involves exchange of thiol-disulfide. BMC Biochem. 2009
Interaction	RegulatedBy Rv0757	yamir.moreno	IEP	Microarrays. mRNA levels of regulated element measured and compared between wild-type and trans-element mutation (knockout, over expression etc.) performed by using microarray (or macroarray) experiments.. SB. Walters, E. Dubnau et al. The Mycobacterium tuberculosis PhoPR two-component system regulates genes essential for virulence and complex lipid biosynthesis. Mol. Microbiol. 2006
Interaction	RegulatedBy Rv1221	yamir.moreno	IEP	Microarrays. mRNA levels of regulated element measured and compared between wild-type and trans-element mutation (knockout, over expression etc.) performed by using microarray (or macroarray) experiments.. R. Manganelli, MI. Voskuil et al. The Mycobacterium tuberculosis ECF sigma factor sigmaE: role in global gene expression and survival in macrophages. Mol. Microbiol. 2001
Interaction	RegulatedBy Rv3676	yamir.moreno	TAS	Literature previously reported link (from Balazsi et al. 2008). Traceable author statement to experimental support. G. Balzsi, AP. Heath et al. The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. Mol. Syst. Biol. 2008

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