WHIB3_MYCTU
ID WHIB3_MYCTU Reviewed; 102 AA.
AC P9WF41; F2GEG1; L0TCG8; Q50710; Q7D5K3;
DT 16-APR-2014, integrated into UniProtKB/Swiss-Prot.
DT 16-APR-2014, sequence version 1.
DT 03-AUG-2022, entry version 41.
DE RecName: Full=Redox- and pH-responsive transcriptional regulator WhiB3;
GN Name=whiB3; OrderedLocusNames=Rv3416;
OS Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
OC Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC Mycobacterium; Mycobacterium tuberculosis complex.
OX NCBI_TaxID=83332;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=9634230; DOI=10.1038/31159;
RA Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M., Harris D.E.,
RA Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III, Tekaia F., Badcock K.,
RA Basham D., Brown D., Chillingworth T., Connor R., Davies R.M., Devlin K.,
RA Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K.,
RA Krogh A., McLean J., Moule S., Murphy L.D., Oliver S., Osborne J.,
RA Quail M.A., Rajandream M.A., Rogers J., Rutter S., Seeger K., Skelton S.,
RA Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S.,
RA Barrell B.G.;
RT "Deciphering the biology of Mycobacterium tuberculosis from the complete
RT genome sequence.";
RL Nature 393:537-544(1998).
RN [2]
RP FUNCTION, INTERACTION WITH SIGA, AND DISRUPTION PHENOTYPE.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=11880648; DOI=10.1073/pnas.052705399;
RA Steyn A.J., Collins D.M., Hondalus M.K., Jacobs W.R. Jr., Kawakami R.P.,
RA Bloom B.R.;
RT "Mycobacterium tuberculosis WhiB3 interacts with RpoV to affect host
RT survival but is dispensable for in vivo growth.";
RL Proc. Natl. Acad. Sci. U.S.A. 99:3147-3152(2002).
RN [3]
RP INDUCTION IN MOUSE INFECTION.
RX PubMed=16923787; DOI=10.1128/iai.00190-06;
RA Banaiee N., Jacobs W.R. Jr., Ernst J.D.;
RT "Regulation of Mycobacterium tuberculosis whiB3 in the mouse lung and
RT macrophages.";
RL Infect. Immun. 74:6449-6457(2006).
RN [4]
RP FUNCTION AS A REDOX SENSOR, COFACTOR, DINITROSYLATION, DISRUPTION
RP PHENOTYPE, AND MUTAGENESIS OF CYS-23; CYS-53; CYS-56 AND CYS-62.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=17609386; DOI=10.1073/pnas.0700490104;
RA Singh A., Guidry L., Narasimhulu K.V., Mai D., Trombley J., Redding K.E.,
RA Giles G.I., Lancaster J.R. Jr., Steyn A.J.;
RT "Mycobacterium tuberculosis WhiB3 responds to O2 and nitric oxide via its
RT [4Fe-4S] cluster and is essential for nutrient starvation survival.";
RL Proc. Natl. Acad. Sci. U.S.A. 104:11562-11567(2007).
RN [5]
RP FUNCTION AS A DISULFIDE ISOMERASE, COFACTOR, SUBUNIT, AND DISULFIDE BOND.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=18550384; DOI=10.1016/j.pep.2008.04.010;
RA Suhail Alam M., Agrawal P.;
RT "Matrix-assisted refolding and redox properties of WhiB3/Rv3416 of
RT Mycobacterium tuberculosis H37Rv.";
RL Protein Expr. Purif. 61:83-91(2008).
RN [6]
RP FUNCTION, DNA-BINDING, DISULFIDE BONDS, MASS SPECTROMETRY, AND DISRUPTION
RP PHENOTYPE.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=19680450; DOI=10.1371/journal.ppat.1000545;
RA Singh A., Crossman D.K., Mai D., Guidry L., Voskuil M.I., Renfrow M.B.,
RA Steyn A.J.;
RT "Mycobacterium tuberculosis WhiB3 maintains redox homeostasis by regulating
RT virulence lipid anabolism to modulate macrophage response.";
RL PLoS Pathog. 5:E1000545-E1000545(2009).
RN [7]
RP FUNCTION, COFACTOR, AND DISULFIDE BOND.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=19016840; DOI=10.1111/j.1742-4658.2008.06755.x;
RA Alam M.S., Garg S.K., Agrawal P.;
RT "Studies on structural and functional divergence among seven WhiB proteins
RT of Mycobacterium tuberculosis H37Rv.";
RL FEBS J. 276:76-93(2009).
RN [8]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=H37Rv;
RX PubMed=26774486; DOI=10.1016/j.celrep.2015.12.056;
RA Saini V., Cumming B.M., Guidry L., Lamprecht D.A., Adamson J.H.,
RA Reddy V.P., Chinta K.C., Mazorodze J.H., Glasgow J.N.,
RA Richard-Greenblatt M., Gomez-Velasco A., Bach H., Av-Gay Y., Eoh H.,
RA Rhee K., Steyn A.J.;
RT "Ergothioneine maintains redox and bioenergetic homeostasis essential for
RT drug susceptibility and virulence of Mycobacterium tuberculosis.";
RL Cell Rep. 14:572-585(2016).
RN [9]
RP FUNCTION, REGULON, INDUCTION BY ACID STRESS, AND DISRUPTION PHENOTYPE.
RC STRAIN=H37Rv;
RX PubMed=26637353; DOI=10.1074/jbc.m115.684597;
RA Mehta M., Rajmani R.S., Singh A.;
RT "Mycobacterium tuberculosis WhiB3 responds to vacuolar pH-induced changes
RT in mycothiol redox potential to modulate phagosomal maturation and
RT virulence.";
RL J. Biol. Chem. 291:2888-2903(2016).
RN [10]
RP REVIEW.
RX PubMed=22010944; DOI=10.1089/ars.2011.4341;
RA Saini V., Farhana A., Steyn A.J.;
RT "Mycobacterium tuberculosis WhiB3: a novel iron-sulfur cluster protein that
RT regulates redox homeostasis and virulence.";
RL Antioxid. Redox Signal. 16:687-697(2012).
CC -!- FUNCTION: A redox-sensitive transcriptional regulator. Maintains
CC intracellular redox homeostasis by regulating catabolic metabolism and
CC polyketide biosynthesis (PubMed:17609386, PubMed:19680450). Regulates
CC expression of the redox buffer ergothioneine (ERG) in a carbon-source-
CC dependent manner; loss of ERG or mycothiol (MSH, the other major redox
CC buffer in this bacteria) leads to respiratory alterations and
CC bioenergetic deficiencies that negatively impact virulence
CC (PubMed:26774486). In response to low external pH (like that found in
CC host macrophage phagosomes) alters endogenous gene expression leading
CC to acid resistance; MSH and WhiB3 are probably part of a regulatory
CC circuit that mediates gene expression upon acid stress
CC (PubMed:26637353). Regulates pathogenic lipid synthesis, coordinating
CC proprionate flux (and other host-derived fatty acid oxidation
CC intermediates) into methyl-branched fatty acids (polyacyltrehalose,
CC phthiocerol dimycocerosates, sulfolipids) and the storage lipid
CC triacylglycerol, functioning as reductive sink (PubMed:19680450).
CC During intracellular growth M.tuberculosis uses host fatty acids as an
CC energy source, generating large quantities of proprionate and
CC NADH/NADPH, which are toxic and highly reducing respectively. WhiB3 is
CC thought to help dissipate proprionate and NADH/NADPH by switching to
CC the in vivo carbon source and via lipid anabolism (PubMed:19680450).
CC Responds to NO and O(2) (PubMed:17609386). Regulates expression of
CC genes encoding modular polyketide synthases such as pks2, pks3 and fbpA
CC (PubMed:19680450). The oxidized apo-form of WhiB3 binds DNA (with 2
CC intramolecular disulfide bonds); holo-WhiB3 (with the 4Fe-4S cluster)
CC binds DNA considerably less well (PubMed:19680450). Discriminates
CC poorly between specific and non-specific DNA-binding. Plays a role in
CC virulence and nutritional stress (PubMed:11880648, PubMed:17609386,
CC PubMed:26637353). In its apo-form can act as a protein disulfide
CC reductase (PubMed:18550384). {ECO:0000269|PubMed:11880648,
CC ECO:0000269|PubMed:17609386, ECO:0000269|PubMed:18550384,
CC ECO:0000269|PubMed:19016840, ECO:0000269|PubMed:19680450,
CC ECO:0000269|PubMed:26637353, ECO:0000269|PubMed:26774486}.
CC -!- FUNCTION: May respond to mycothiol (MSH) redox potential (E-MSH) which
CC decreases at pH 4.5 for up to 72 hours, indicative of cellular
CC reductive stress; deletion of whiB3 leads to a lesser E-MSH at 72
CC hours, indicative of cellular oxidative stress (PubMed:26637353).
CC Probably via its effects on production of polyketide lipids, regulates
CC host gene expression, leading to blockage of phagosome maturation
CC (PubMed:26637353). Equilibration of extra- and intracytoplasmic pH
CC kills bacteria (PubMed:26637353). {ECO:0000269|PubMed:26637353}.
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000269|PubMed:17609386, ECO:0000269|PubMed:18550384,
CC ECO:0000269|PubMed:19016840};
CC Note=Binds 1 [4Fe-4S] cluster per subunit (PubMed:17609386). Following
CC nitrosylation of the [4Fe-4S] cluster binds 1 [4Fe-8(NO)] cluster per
CC subunit (PubMed:17609386). {ECO:0000269|PubMed:17609386,
CC ECO:0000269|PubMed:18550384, ECO:0000269|PubMed:19016840};
CC -!- SUBUNIT: Homodimer (Probable) (PubMed:18550384). Interacts with the C-
CC terminal 54 residues of sigma factor SigA (RpoV) (PubMed:11880648).
CC {ECO:0000269|PubMed:11880648, ECO:0000305|PubMed:18550384}.
CC -!- INTERACTION:
CC P9WF41; P9WGI1: sigA; NbExp=3; IntAct=EBI-11859434, EBI-11859464;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|UniProtKB:Q9S426}.
CC -!- INDUCTION: 100-fold induced in wild-type C57BL/6 mice 2 weeks after
CC lung infection, RNA levels drop to 30X induced 8 weeks post-infection
CC (PubMed:16923787). Similar but less dramatic induction is seen in
CC immunocompromised mice (PubMed:16923787). Rapidly induced in resting
CC mouse macrophages, remains up-regulated for at least 60 hours,
CC continuing induction is repressed by interferon gamma
CC (PubMed:16923787). Induced by growth at acidic pH (PubMed:26637353).
CC {ECO:0000269|PubMed:16923787, ECO:0000269|PubMed:26637353}.
CC -!- PTM: The 4Fe-4S cluster interacts with NO, forming a protein-bound
CC dinitrosyliron dithiol complex (PubMed:17609386).
CC {ECO:0000269|PubMed:17609386}.
CC -!- PTM: The 4Fe-4S cluster interacts with O(2), leading to its
CC degradation. Cluster loss takes about 2 hours (PubMed:17609386). Once
CC in the apo-form the cysteines oxidize to form 2 intramolecular
CC disulfide bonds (PubMed:18550384). {ECO:0000269|PubMed:17609386,
CC ECO:0000269|PubMed:18550384}.
CC -!- MASS SPECTROMETRY: Mass=14636.76; Method=MALDI; Note=Fully reduced
CC protein.; Evidence={ECO:0000269|PubMed:19680450};
CC -!- MASS SPECTROMETRY: Mass=14407.22; Method=MALDI; Note=Fully oxidized
CC protein.; Evidence={ECO:0000269|PubMed:19680450};
CC -!- DISRUPTION PHENOTYPE: Not essential for growth in culture, or growth in
CC vivo in mouse and guinea pig infections (PubMed:11880648). Disruption
CC significantly enhances survival of immunocompetent mice
CC (PubMed:11880648). Decreased bacterial growth in guinea pig lungs, but
CC not spleen (PubMed:26637353). Growth on minimal media, glucose or
CC succinate is poor, suggesting WhiB3 is involved in starvation response
CC (PubMed:17609386). Growth on acetate is better than wild-type
CC (PubMed:17609386). 55-fold decreased survival at pH 4.5, no difference
CC at pH 5.5 or 6.6 (PubMed:26637353). Altered expression of genes
CC involved in cell wall lipid composition, the ESX-1 secretion system and
CC redox balance, impairs the mycothiol-specific reductive response to
CC acid stress (PubMed:26637353). Dysfunctional respiration when grown in
CC pyruvate, increased intracellular ergothioneine (ERG) production when
CC grown in a number of carbon sources (PubMed:26774486). Upon infection
CC of human THP-1 macrophage-like cells bacteria are localized to
CC acidified lysosomes (M.tuberculosis usually blocks lysosome
CC acidification), do not reduce mycothiol (MSH) and have significantly
CC decreased survival (PubMed:26637353). Leads to up-regulation of host
CC innate immunity genes usually repressed by M.tuberculosis (such as
CC phagosome maturation and TLR signaling) and down-regulation of genes
CC that inhibit autophagy (such as mTOR) (PubMed:26637353). Cell size,
CC shape and surface architecture are perturbed, as is synthesis of cell
CC surface associated virulence lipids both in culture and in cultured
CC macrophages, or in response to oxidizing or reducing agents
CC (PubMed:19680450). Disrupted strains are more resistant to toxic levels
CC of propionate (PubMed:19680450). {ECO:0000269|PubMed:11880648,
CC ECO:0000269|PubMed:17609386, ECO:0000269|PubMed:19680450,
CC ECO:0000269|PubMed:26637353, ECO:0000269|PubMed:26774486}.
CC -!- SIMILARITY: Belongs to the WhiB family. {ECO:0000305}.
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DR EMBL; AL123456; CCP46238.1; -; Genomic_DNA.
DR PIR; E70737; E70737.
DR RefSeq; NP_217933.1; NC_000962.3.
DR RefSeq; WP_003418017.1; NZ_NVQJ01000027.1.
DR AlphaFoldDB; P9WF41; -.
DR SMR; P9WF41; -.
DR IntAct; P9WF41; 1.
DR STRING; 83332.Rv3416; -.
DR PaxDb; P9WF41; -.
DR GeneID; 45427412; -.
DR GeneID; 887598; -.
DR KEGG; mtu:Rv3416; -.
DR TubercuList; Rv3416; -.
DR eggNOG; ENOG5032S23; Bacteria.
DR OMA; WQLHGAC; -.
DR PhylomeDB; P9WF41; -.
DR PHI-base; PHI:5575; -.
DR PHI-base; PHI:7218; -.
DR Proteomes; UP000001584; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0009274; C:peptidoglycan-based cell wall; HDA:MTBBASE.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IDA:MTBBASE.
DR GO; GO:0035731; F:dinitrosyl-iron complex binding; IEA:UniProtKB-UniRule.
DR GO; GO:0003677; F:DNA binding; IDA:UniProtKB.
DR GO; GO:0051536; F:iron-sulfur cluster binding; IDA:MTBBASE.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0047134; F:protein-disulfide reductase (NAD(P)) activity; IBA:GO_Central.
DR GO; GO:0015035; F:protein-disulfide reductase activity; IDA:MTBBASE.
DR GO; GO:0071766; P:Actinobacterium-type cell wall biogenesis; IDA:MTBBASE.
DR GO; GO:0045454; P:cell redox homeostasis; IDA:MTBBASE.
DR GO; GO:0045892; P:negative regulation of transcription, DNA-templated; IBA:GO_Central.
DR GO; GO:0019216; P:regulation of lipid metabolic process; IDA:MTBBASE.
DR HAMAP; MF_01479; WhiB; 1.
DR InterPro; IPR034768; 4FE4S_WBL.
DR InterPro; IPR003482; Whib.
DR PANTHER; PTHR38839; PTHR38839; 1.
DR Pfam; PF02467; Whib; 1.
DR PROSITE; PS51674; 4FE4S_WBL; 1.
PE 1: Evidence at protein level;
KW 4Fe-4S; Cytoplasm; Disulfide bond; DNA-binding; Iron; Iron-sulfur;
KW Metal-binding; Reference proteome; Stress response; Transcription;
KW Transcription regulation; Virulence.
FT CHAIN 1..102
FT /note="Redox- and pH-responsive transcriptional regulator
FT WhiB3"
FT /id="PRO_0000420382"
FT DOMAIN 22..86
FT /note="4Fe-4S Wbl-type"
FT BINDING 23
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000305|PubMed:17609386"
FT BINDING 53
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000305|PubMed:17609386"
FT BINDING 56
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000305|PubMed:17609386"
FT BINDING 62
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000305|PubMed:17609386"
FT MUTAGEN 23
FT /note="C->A: No 4Fe-4S cluster assembly, does not
FT complement growth defects; when associated with A-53; A-56
FT and A-62."
FT /evidence="ECO:0000269|PubMed:17609386"
FT MUTAGEN 53
FT /note="C->A: No 4Fe-4S cluster assembly, does not
FT complement growth defects; when associated with A-23; A-56
FT and A-62."
FT /evidence="ECO:0000269|PubMed:17609386"
FT MUTAGEN 56
FT /note="C->A: No 4Fe-4S cluster assembly, does not
FT complement growth defects; when associated with A-33; A-53
FT and A-62."
FT /evidence="ECO:0000269|PubMed:17609386"
FT MUTAGEN 62
FT /note="C->A: No 4Fe-4S cluster assembly, does not
FT complement growth defects; when associated with A-33; A-53
FT and A-56."
FT /evidence="ECO:0000269|PubMed:17609386"
SQ SEQUENCE 102 AA; 11612 MW; C38A6774457F71BA CRC64;
MPQPEQLPGP NADIWNWQLQ GLCRGMDSSM FFHPDGERGR ARTQREQRAK EMCRRCPVIE
ACRSHALEVG EPYGVWGGLS ESERDLLLKG TMGRTRGIRR TA
