Rv2050 (-)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: hypothetical protein
- REFSEQ: hypothetical protein
- PATRIC: FIG00820327: hypothetical protein
- TUBERCULIST: Conserved protein
- NCBI: hypothetical protein
- updated information (H37Rv4):
  - gene name: rbpA
  - function: stabilizes RNA polymerase
  - reference: Hu (2012) PMID: 22570422; Bortoluzzi (2013) PMID: 23548911
Type: Not Target
Start: 2307821
End: 2308156
Operon:

Trans-membrane region:
Role: V - Conserved hypotheticals
GO terms:
- GO:0045893 - positive regulation of transcription, DNA-templated (Uniprot)
- GO:0006355 - regulation of transcription, DNA-templated (Uniprot)
- GO:0006351 - transcription, DNA-templated (Uniprot)
- GO:0005515 - protein binding (Uniprot)
- GO:0001108 - bacterial-type RNA polymerase holo enzyme binding (Uniprot)
- GO:0001000 - bacterial-type RNA polymerase core enzyme 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
6VW0	100%	Mycobacterium tuberculosis	Mycobacterium tuberculosis RNAP S456L mutant open promoter complex
6VVZ	100%	Mycobacterium tuberculosis	Mycobacterium tuberculosis RNAP S456L mutant transcription initiation intermediate structure with Sorangicin
6VVY	100%	Mycobacterium tuberculosis	Mycobacterium tuberculosis WT RNAP transcription open promoter complex with Sorangicin
6VVX	100%	Mycobacterium tuberculosis	Mycobacterium tuberculosis WT RNAP transcription initiation intermediate structure with Sorangicin
6M7J	100%	Mycobacterium tuberculosis	Mycobacterium tuberculosis RNAP with RbpA/us fork and Corallopyronin
6EEC	100%	Mycobacterium tuberculosis	Mycobacterium tuberculosis RNAP promoter unwinding intermediate complex with RbpA/CarD and AP3 promoter captured by Corallopyronin
6EE8	100%	Mycobacterium tuberculosis	Mycobacterium tuberculosis RNAP promoter unwinding intermediate complex with RbpA/CarD and AP3 promoter
6EDT	100%	Mycobacterium tuberculosis	Mycobacterium tuberculosis RNAP open promoter complex with RbpA/CarD and AP3 promoter
6C06	100%	Mycobacterium tuberculosis	Mycobacterium tuberculosis RNAP Holo/RbpA/Fidaxomicin
6C05	100%	Mycobacterium tuberculosis	Mycobacterium tuberculosis RNAP Holo/RbpA in relaxed state

Links to additional information on Rv2050:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = -2.007 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

MADRVLRGSRLGAVSYETDRNHDLAPRQIARYRTDNGEEFEVPFADDAEIPGTWLCRNGMEGTLIEGDLPEPKKVKPPRTHWDMLLERRSIEELEELLKE
RLELIRSRRRG

(Nucleotide sequence available on KEGG)

Additional Information

RbpA (binds RNA polymerase, like CarD)
http://www.ncbi.nlm.nih.gov/pubmed/22570422

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: 0.982350; 5 non-insertions in a row out of 5 sites
Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.993700; 5 non-insertions in a row out of 5 sites
Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.994950; 5 non-insertions in a row out of 5 sites
Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.993000; 5 non-insertions in a row out of 5 sites
Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.992350; 5 non-insertions in a row out of 5 sites
Essential	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Essential	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: 0.19
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:
- No bindings to other targets were found.
Bound By:
- Rv0452 (-)

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

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv0767c (-) (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:
- Does not downregulate other genes.
Downregulated by:
- Rv0452 (-)

Property	Value	Creator	Evidence	PMID	Comment
Citation	Global transcriptional response to vancomycin in Mycobacterium tuberculosis. R. Provvedi, F. Boldrin et al. Microbiology (Reading, Engl.) 2009	shahanup86	TAS	19332811	None
Interaction	Regulatory Rv3223c	shahanup86	TAS		R. Provvedi, F. Boldrin et al. Global transcriptional response to vancomycin in Mycobacterium tuberculosis. Microbiology (Reading, Engl.) 2009
Citation	The Mycobacterium tuberculosis ECF sigma factor sigmaE: role in global gene expression and survival in macrophages. R. Manganelli, MI. Voskuil et al. Mol. Microbiol. 2001	shahanup86	TAS	11489128	None
Interaction	Regulatory Rv1221	shahanup86	TAS		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

TB Genome Annotation Portal