TB Genome Annotation Portal

Rv1033c (trcR)

Amino Acid Sequence

MTTMSGYTRSQRPRQAILGQLPRIHRADGSPIRVLLVDDEPALTNLVKMALHYEGWDVEVAHDGQEAIAKFDKVGPDVLVLDIMLPDVDGLEILRRVRES
DVYTPTLFLTARDSVMDRVTGLTSGADDYMTKPFSLEELVARLRGLLRRSSHLERPADEALRVGDLTLDGASREVTRDGTPISLSSTEFELLRFLMRNPR
RALSRTEILDRVWNYDFAGRTSIVDLYISYLRKKIDSDREPMIHTVRGIGYMLRPPE
(Nucleotide sequence available on KEGG)

Additional Information
















Analysis of Positive Selection in Clinical Isolates
*new*






Moldova (2,057)global set (5,195)

under significant positive selection?NONO

omega peak height (95%CI lower bound)0.64 (0.01)1.02 (0.4)

codons under selection

omega plots

genetic variants*linklink

statistics at each codonlinklink



* 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

Rv1033c/trcR,
gene len: 773 bp, num TA sites: 15



conditiondatasetcallmediummethodnotes

in-vitroDeJesus 2017 mBiogrowth advantage7H9HMMfully saturated, 14 TnSeq libraries combined

in-vitroSassetti 2003 Mol Micronon-essential 7H9TRASHessential if hybridization ratio<0.2

in-vivo (mice)Sassetti 2003 PNASnon-essential BL6 miceTRASHessential if hybridization ratio<0.4, min over 4 timepoints (1-8 weeks)

in-vitro (glycerol)Griffin 2011 PPathnon-essentialM9 minimal+glycerolGumbel2 replicates; Padj<0.05

in-vitro (cholesterol)Griffin 2011 PPathnon-essentialM9 minimal+cholesterolGumbel3 replicates; Padj<0.05

differentially essential in cholesterol Griffin 2011 PPathNO (LFC=0.71)cholesterol vs glycerolresampling-SRYES if Padj<0.05, else not significant; LFC<0 means less insertions/more essential in cholesterol

in-vitroSmith 2022 eLifenon-essential7H9HMM6 replicates (raw data in Subramaniam 2017, PMID 31752678)

in-vivo (mice)Smith 2022 eLifenon-essentialBL6 miceHMM6 replicates (raw data in Subramaniam 2017, PMID 31752678)

differentially essential in miceSmith 2022 eLifeNO (LFC=-0.018)in-vivo vs in-vitroZINBYES if Padj<0.05, else not significant; LFC<0 means less insertions/more essential in mice

in-vitro (minimal)Minato 2019 mSysnon-essentialminimal mediumHMM

in-vitro (YM rich medium)Minato 2019 mSysnon-essentialYM rich mediumHMM7H9 supplemented with ~20 metabolites (amino acids, cofactors)

differentially essential in YM rich mediumMinato 2019 mSysNO (LFC=-0.3)YM rich vs minimal mediumresampling







    












 





    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
    

    
    

    
    
    

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




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














    

    






    


    


    


    TBCAP
    
Tubculosis Community Annotation Project (    Slayden et al., 2013)
    
Rv1033c (trcR)

    

    PropertyValueCreatorEvidencePMIDComment
    
InteractionInhibits Rv1057ashwinigbhatIDADNase I and hydroxyl radical footprinting analyses
    SE. Haydel & JE. Clark-Curtiss The Mycobacterium tuberculosis TrcR response regulator represses transcription of the intracellularly expressed Rv1057 gene, encoding a seven-bladed beta-propeller. J. Bacteriol. 2006
    
InteractionRegulatory Rv1032cdarhnguIEPCo-expression (Functional linkage)
    SE. Haydel, NE. Dunlap et al. In vitro evidence of two-component system phosphorylation between the Mycobacterium tuberculosis TrcR/TrcS proteins. Microb. Pathog. 1999
    
InteractionRegulatory Rv1032cdarhnguIEPCo-expression (Functional linkage)
    L. Wernisch, SL. Kendall et al. Analysis of whole-genome microarray replicates using mixed models. Bioinformatics 2003
    
CitationThe Mycobacterium tuberculosis TrcR response regulator represses transcription of the intracellularly expressed Rv1057 gene, encoding a seven-bladed beta-propeller. SE. Haydel & JE. Clark-Curtiss J. Bacteriol. 2006ahal4789IEP16352831Co-expression (Functional linkage)
    
InteractionRegulatory Rv1057ahal4789IEPCo-expression (Functional linkage)
    SE. Haydel & JE. Clark-Curtiss The Mycobacterium tuberculosis TrcR response regulator represses transcription of the intracellularly expressed Rv1057 gene, encoding a seven-bladed beta-propeller. J. Bacteriol. 2006
    
CitationThe Mycobacterium tuberculosis TrcR response regulator represses transcription of the intracellularly expressed Rv1057 gene, encoding a seven-bladed beta-propeller. SE. Haydel & JE. Clark-Curtiss J. Bacteriol. 2006sourish10IEP16352831Co-expression (Functional linkage)
    
InteractionRegulatory Rv1057sourish10IEPCo-expression (Functional linkage)
    SE. Haydel & JE. Clark-Curtiss The Mycobacterium tuberculosis TrcR response regulator represses transcription of the intracellularly expressed Rv1057 gene, encoding a seven-bladed beta-propeller. J. Bacteriol. 2006
    
CitationIn vitro evidence of two-component system phosphorylation between the Mycobacterium tuberculosis TrcR/TrcS proteins. SE. Haydel, NE. Dunlap et al. Microb. Pathog. 1999akankshajain.21IEP10089160Co-expression (Functional linkage)
    
InteractionRegulatory Rv1032cakankshajain.21IEPCo-expression (Functional linkage)
    SE. Haydel, NE. Dunlap et al. In vitro evidence of two-component system phosphorylation between the Mycobacterium tuberculosis TrcR/TrcS proteins. Microb. Pathog. 1999
    
CitationAnalysis of whole-genome microarray replicates using mixed models. L. Wernisch, SL. Kendall et al. Bioinformatics 2003akankshajain.21IEP12499293Co-expression (Functional linkage)
    
InteractionRegulatory Rv1032cakankshajain.21IEPCo-expression (Functional linkage)
    L. Wernisch, SL. Kendall et al. Analysis of whole-genome microarray replicates using mixed models. Bioinformatics 2003
    
CitationThe temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. G. Balzsi, AP. Heath et al. Mol. Syst. Biol. 2008yamir.morenoTAS18985025Literature previously reported link (from Balazsi et al. 2008). Traceable author statement to experimental support.
    
InteractionRegulates Rv1033cyamir.morenoTASLiterature 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
    
InteractionRegulatedBy Rv1033cyamir.morenoTASLiterature 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
    
CitationThe temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. G. Balzsi, AP. Heath et al. Mol. Syst. Biol. 2008yamir.morenoTAS18985025Literature previously reported link (from Balazsi et al. 2008). Traceable author statement to experimental support.
    
InteractionRegulates Rv1057yamir.morenoTASLiterature 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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