Rv3019c (esxR)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: ESAT-6-like protein esxR
- REFSEQ: secreted ESAT-6 like protein ESXR (TB10.3) (ESAT-6 like protein 9)
- PATRIC: 10 kDa antigen CFP7
- TUBERCULIST: Secreted ESAT-6 like protein EsxR (TB10.3) (ESAT-6 like protein 9)
- NCBI: Secreted ESAT-6 like protein EsxR (TB10.3) (ESAT-6 like protein 9)
- updated information (H37Rv4):
  - gene name: esxR
  - function:
  - reference:
Type: Not Target
Start: 3378711
End: 3379001
Operon:

Trans-membrane region:
Role: II.C.2 - Surface polysaccharides, lipopolysaccharides, proteins and antigens
GO terms:
- GO:0032991 - protein-containing complex (Uniprot)
- GO:0005576 - extracellular region (Uniprot)
- GO:0005515 - protein 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: 3h6p
Search for Homologs in PDB

Top 10 Homologs in PDB (as of Nov 2020):

PDB	aa ident	species	PDB title
3H6P	100%	Mycobacterium tuberculosis	Crystal structure of Rv3019c-Rv3020c from Mycobacterium tuberculosis
2KG7	84%	Mycobacterium tuberculosis	Structure and features of the complex formed by the tuberculosis virulence factors Rv0287 and Rv0288
3Q4H	71%	Mycobacterium smegmatis	Crystal structure of the Mycobacterium smegmatis EsxGH complex (MSMEG_0620-MSMEG_0621)

Links to additional information on esxR:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = -0.011 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

MSQIMYNYPAMMAHAGDMAGYAGTLQSLGADIASEQAVLSSAWQGDTGITYQGWQTQWNQALEDLVRAYQSMSGTHESNTMAMLARDGAEAAKWGG

(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
Non-Essential	Sodium Oleate	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 9 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000100; 3 non-insertions in a row out of 9 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000100; 3 non-insertions in a row out of 9 sites
Non-Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 3 non-insertions in a row out of 10 sites
Non-Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 10 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: 1.46
Non-Essential	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:
- No bindings to other targets were found.
Bound By:

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

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv0081 (-) (Direct binding)
- Rv0678 (-) (Direct binding)
- Rv1033c (trcR) (Direct binding)
- Rv1985c (-) (Direct binding)
- Rv3488 (-) (Direct binding)
- Rv3765c (tcrX) (Direct binding)
- Rv3597c (lsr2) (Upstream of operon)
- Rv3849 (espR) (Upstream of operon)

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

Upregulates:
- Does not upregulate other genes.
Upregulated by:
- Rv2595 (vapB40)
Downregulates:
- Does not downregulate other genes.
Downregulated by:

Property	Value	Creator	Evidence	PMID	Comment
Citation	Epitope mapping of the immunodominant antigen TB10.4 and the two homologous proteins TB10.3 and TB12.9, which constitute a subfamily of the esat-6 gene family. RL. Skjt, I. Brock et al. Infect. Immun. 2002	ilamathi.raja	IEP	12228269	Co-expression (Functional linkage)
Interaction	Regulatory Rv2359	ilamathi.raja	IEP		Co-expression (Functional linkage) RL. Skjt, I. Brock et al. Epitope mapping of the immunodominant antigen TB10.4 and the two homologous proteins TB10.3 and TB12.9, which constitute a subfamily of the esat-6 gene family. Infect. Immun. 2002
Citation	Transcriptional analysis of ESAT-6 cluster 3 in Mycobacterium smegmatis. A. Maciag, A. Piazza et al. BMC Microbiol. 2009	ilamathi.raja	IEP	19257911	Co-expression (Functional linkage)
Interaction	Regulatory Rv2359	ilamathi.raja	IEP		Co-expression (Functional linkage) A. Maciag, A. Piazza et al. Transcriptional analysis of ESAT-6 cluster 3 in Mycobacterium smegmatis. BMC Microbiol. 2009
Interaction	RegulatedBy Rv2359	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
Interaction	RegulatedBy Rv2711	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.. GM. Rodriguez, MI. Voskuil et al. ideR, An essential gene in mycobacterium tuberculosis: role of IdeR in iron-dependent gene expression, iron metabolism, and oxidative stress response. Infect. Immun. 2002

TB Genome Annotation Portal