Rv0490 (senX3)
Current annotations:
TBCAP: (community-based annotations - see table at bottom of page )
TBDB: sensor-like histidine kinase senX3
REFSEQ: putative two component sensor histidine kinase SENX3
PATRIC: Phosphate regulon sensor protein PhoR (SphS) (EC 2.7.13.3); Sensor-like histidine kinase senX3 (EC 2.7.13.3)
TUBERCULIST: Putative two component sensor histidine kinase SenX3
NCBI: Putative two component sensor histidine kinase SenX3
updated information (H37Rv4):
gene name: senX3
function:
reference:
Type: Not Target
Start: 579349
End: 580581
Operon:
Trans-membrane region:
Role: I.J.2 - Two component systems
GO terms:
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 3SL2 44% Bacillus subtilis ATP Forms a Stable Complex with the Essential Histidine Kinase WalK (YycG) Domain 6BLK 36% Mycobacterium hassiacum (strain DSM 44199 / CIP 105218 / JCM 12690 / 3849) Mycobacterial sensor histidine kinase MprB 5C93 35% Lactobacillus plantarum 16 Histidine kinase with ATP 4ZKI 35% Lactobacillus plantarum JDM1 The crystal structure of Histidine Kinase YycG with ADP 4U7O 35% Lactobacillus plantarum Active histidine kinase bound with ATP 4U7N 35% Lactobacillus plantarum Inactive structure of histidine kinase
Links to additional information on senX3:
Amino Acid Sequence
VTVFSALLLAGVLSALALAVGGAVGMRLTSRVVEQRQRVATEWSGITVSQMLQCIVTLMPLGAAVVDTHRDVVYLNERAKELGLVRDRQLDDQAWRAARQ
ALGGEDVEFDLSPRKRSATGRSGLSVHGHARLLSEEDRRFAVVFVHDQSDYARMEAARRDFVANVSHELKTPVGAMALLAEALLASADDSETVRRFAEKV
LIEANRLGDMVAELIELSRLQGAERLPNMTDVDVDTIVSEAISRHKVAADNADIEVRTDAPSNLRVLGDQTLLVTALANLVSNAIAYSPRGSLVSISRRR
RGANIEIAVTDRGIGIAPEDQERVFERFFRGDKARSRATGGSGLGLAIVKHVAANHDGTIRVWSKPGTGSTFTLALPALIEAYHDDERPEQAREPELRSN
RSQREEELSR
(
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) 1.71 (0.33) 1.07 (0.39)
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"
MtbTnDB - interactive tool for exploring a database of published TnSeq datasets for Mtb
TnSeqCorr - genes with correlated TnSeq profiles across ~100 conditions
Rv0490/senX3,
gene len: 1232 bp, num TA sites: 16
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 non-essential 7H9 TRASH essential if hybridization ratio<0.2
in-vivo (mice) Sassetti 2003 PNAS essential BL6 mice TRASH essential if hybridization ratio<0.4, min over 4 timepoints (1-8 weeks)
in-vitro (glycerol) Griffin 2011 PPath non-essential M9 minimal+glycerol Gumbel 2 replicates; Padj<0.05
in-vitro (cholesterol) Griffin 2011 PPath non-essential M9 minimal+cholesterol Gumbel 3 replicates; Padj<0.05
differentially essential in cholesterol Griffin 2011 PPath NO (LFC=0.28) 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=-0.86) 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=0.83) 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
RNA processing and modification
Energy production and conversion
Chromatin structure and dynamics
Amino acid transport and metabolism
Cell cycle control, cell division, chromosome partitioning
Carbohydrate transport and metabolism
Nucleotide transport and metabolism
Lipid transport and metabolism
Coenzyme transport and metabolism
Translation, ribosomal structure and biogenesis
Cell wall/membrane/envelope biogenesis
Replication, recombination and repair
Posttranslational modification, protein turnover, chaperones
Secondary metabolites biosynthesis, transport and catabolism
Inorganic ion transport and metabolism
General function prediction only
Intracellular trafficking, secretion, and vesicular transport
Signal transduction mechanisms
Differentially expressed as result of RNASeq in glycerol environment (Only top 20 genes shown sorted by log fold change with p_adj 0.05).
Conditionally essential as result of TNSeq (Only top 20 genes shown sorted by log fold change with p_adj 0.05).
Binds To:
No bindings to other targets were found.
Bound By:
No bindings from other targets were found.
Binds To:
No bindings to other targets were found.
Bound By:
Upregulates:
Does not upregulate other genes.
Upregulated by:
Not upregulated by other genes.
Downregulates:
Does not downregulate other genes.
Downregulated by:
Not downregulated by other genes.
Property Value Creator Evidence PMID Comment
Interaction Transcription Rv3750c sourish10 IMP Co-expression (Functional linkage)T. Parish, DA. Smith et al. The senX3-regX3 two-component regulatory system of Mycobacterium tuberculosis is required for virulence. Microbiology (Reading, Engl.) 2003
Interaction Transcription Rv3749c sourish10 IMP Co-expression (Functional linkage)T. Parish, DA. Smith et al. The senX3-regX3 two-component regulatory system of Mycobacterium tuberculosis is required for virulence. Microbiology (Reading, Engl.) 2003
Interaction Transcription Rv2337c girishgene07 IEP Co-expression (Functional linkage)T. Parish, DA. Smith et al. The senX3-regX3 two-component regulatory system of Mycobacterium tuberculosis is required for virulence. Microbiology (Reading, Engl.) 2003
Interaction Transcription Rv2337c girishgene07 IEP Co-expression (Functional linkage)authors,KG. Mawuenyega,CV. Forst,KM. Dobos,JT. Belisle,J. Chen,EM. Bradbury,AR. Bradbury,X. Chen Mycobacterium tuberculosis functional network analysis by global subcellular protein profiling. Mol. Biol. Cell 2005
Interaction Transcription Rv2337c girishgene07 IEP Co-expression (Functional linkage)authors,CM. Sassetti,DH. Boyd,EJ. Rubin Genes required for mycobacterial growth defined by high density mutagenesis. Mol. Microbiol. 2003
Interaction Regulatory Rv2069 ashwinigbhat IEP Co-expression (Functional linkage)R. Sun, PJ. Converse et al. Mycobacterium tuberculosis ECF sigma factor sigC is required for lethality in mice and for the conditional expression of a defined gene set. Mol. Microbiol. 2004
Interaction Regulatory Rv2069 priti.priety IEP Co-expression (Functional linkage)R. Sun, PJ. Converse et al. Mycobacterium tuberculosis ECF sigma factor sigC is required for lethality in mice and for the conditional expression of a defined gene set. Mol. Microbiol. 2004
Interaction Transcription Rv1433 sourish10 IEP Co-expression (Functional linkage)T. Parish, DA. Smith et al. The senX3-regX3 two-component regulatory system of Mycobacterium tuberculosis is required for virulence. Microbiology (Reading, Engl.) 2003
Interaction Regulatory Rv1355c swetha.r IEP Co-expression (Functional linkage)T. Parish, DA. Smith et al. The senX3-regX3 two-component regulatory system of Mycobacterium tuberculosis is required for virulence. Microbiology (Reading, Engl.) 2003
Interaction Regulatory Rv1355c swetha.r IEP Co-expression (Functional linkage)L. Vera-Cabrera, CA. Molina-Torres et al. Genetic characterization of Mycobacterium tuberculosis clinical isolates with deletions in the plcA-plcB-plcC locus. Tuberculosis (Edinburgh, Scotland) 2007
Citation Molecular characterization of the mycobacterial SenX3-RegX3 two-component system: evidence for autoregulation. authors,S. Himpens,C. Locht,P. Supply Microbiology (Reading, Engl.) 2000 akankshajain.21 IEP 11101667 Affinity purification (Physical interaction)
Interaction Regulatory Rv0491 akankshajain.21 IEP Affinity purification (Physical interaction)authors,S. Himpens,C. Locht,P. Supply Molecular characterization of the mycobacterial SenX3-RegX3 two-component system: evidence for autoregulation. Microbiology (Reading, Engl.) 2000
Citation The senX3-regX3 two-component regulatory system of Mycobacterium tuberculosis is required for virulence. T. Parish, DA. Smith et al. Microbiology (Reading, Engl.) 2003 prabhakarsmail IEP 12777483 Affinity purification (Physical interaction)
Interaction Regulatory Rv0491 prabhakarsmail IEP Affinity purification (Physical interaction)T. Parish, DA. Smith et al. The senX3-regX3 two-component regulatory system of Mycobacterium tuberculosis is required for virulence. Microbiology (Reading, Engl.) 2003
Citation Molecular characterization of the mycobacterial SenX3-RegX3 two-component system: evidence for autoregulation. authors,S. Himpens,C. Locht,P. Supply Microbiology (Reading, Engl.) 2000 prabhakarsmail IEP 11101667 Affinity purification (Physical interaction)
Interaction Regulatory Rv0491 prabhakarsmail IEP Affinity purification (Physical interaction)authors,S. Himpens,C. Locht,P. Supply Molecular characterization of the mycobacterial SenX3-RegX3 two-component system: evidence for autoregulation. Microbiology (Reading, Engl.) 2000
Citation The senX3-regX3 two-component regulatory system of Mycobacterium tuberculosis is required for virulence. T. Parish, DA. Smith et al. Microbiology (Reading, Engl.) 2003 akankshajain.21 IEP 12777483 Affinity purification (Physical interaction)
Interaction Regulatory Rv0491 akankshajain.21 IEP Affinity purification (Physical interaction)T. Parish, DA. Smith et al. The senX3-regX3 two-component regulatory system of Mycobacterium tuberculosis is required for virulence. Microbiology (Reading, Engl.) 2003
Interaction RegulatedBy Rv0491 yamir.moreno TAS Literature previously reported link (from Balazsi et al. 2008). Traceable author statement to experimental support. E.coli orthology based inference. Orthologous pair regulator-target found in E.coli.G. Balzsi, AP. Heath et al. The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. Mol. Syst. Biol. 2008
Interaction RegulatedBy Rv0491 yamir.moreno ISO Literature previously reported link (from Balazsi et al. 2008). Traceable author statement to experimental support. E.coli orthology based inference. Orthologous pair regulator-target found in E.coli.G. Balzsi, AP. Heath et al. The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. Mol. Syst. Biol. 2008
Interaction RegulatedBy Rv0491 yamir.moreno ISO E.coli orthology based inference. Orthologous pair regulator-target found in E.coli.authors,M. Madan Babu,SA. Teichmann,L. Aravind Evolutionary dynamics of prokaryotic transcriptional regulatory networks. J. Mol. Biol. 2006