Rv1884c (rpfC)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: hypothetical protein
- REFSEQ: resuscitation-promoting factor RpfC
- PATRIC: Resuscitation-promoting factor RpfC
- TUBERCULIST: Probable resuscitation-promoting factor RpfC
- NCBI: Probable resuscitation-promoting factor RpfC
- updated information (H37Rv4):
  - gene name: rpfC
  - function:
  - reference:
Type: Not Target
Start: 2133731
End: 2134261
Operon:

Trans-membrane region:
Role: V - Conserved hypotheticals
GO terms:
- GO:0040010 - positive regulation of growth rate (Uniprot)
- GO:0016787 - hydrolase activity (Uniprot)
- GO:0010629 - negative regulation of gene expression (Uniprot)
- GO:0010628 - positive regulation of gene expression (Uniprot)
- GO:0009405 - pathogenesis (Uniprot)
- GO:0005576 - extracellular region (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
4OW1	100%	Mycobacterium tuberculosis	Crystal Structure of Resuscitation Promoting Factor C
2N5Z	100%	Mycobacterium tuberculosis	Mycobacterium tuberculosis: a dynamic view of the resuscitation promoting factor RpfC catalytic domain
4CGE	66%	MYCOBACTERIUM TUBERCULOSIS	Crystal structure of Mycobacterium tuberculosis Resuscitation promoting factor E
5E27	57%	Mycobacterium tuberculosis	The structure of Resuscitation Promoting Factor B from M. tuberculosis reveals unexpected ubiquitin-like domains
4KPM	57%	Mycobacterium tuberculosis	Crystal structure of the catalytic domain of RpfB from Mycobacterium tuberculosis in complex with triNAG
4KL7	57%	Mycobacterium tuberculosis	Crystal structure of the catalytic domain of RpfB from Mycobacterium tuberculosis
4EMN	57%	Mycobacterium tuberculosis	Crystal structure of RpfB catalytic domain in complex with benzamidine
3EO5	57%	Mycobacterium tuberculosis	Crystal structure of the resuscitation promoting factor RpfB
1XSF	57%	Mycobacterium tuberculosis	Solution structure of a resuscitation promoting factor domain from Mycobacterium tuberculosis

Links to additional information on rpfC:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 1.322 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

VHPLPADHGRSRCNRHPISPLSLIGNASATSGDMSSMTRIAKPLIKSAMAAGLVTASMSLSTAVAHAGPSPNWDAVAQCESGGNWAANTGNGKYGGLQFK
PATWAAFGGVGNPAAASREQQIAVANRVLAEQGLDAWPTCGAASGLPIALWSKPAQGIKQIINEIIWAGIQASIPR

(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 6 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 6 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 6 sites
Non-Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 6 sites
Non-Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 6 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: 1.04
Growth-Advantage	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:
- Rv2011c (-)
- Rv3849 (espR)

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

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv0047c (-) (Direct binding)
- Rv0678 (-) (Direct binding)
- Rv1816 (-) (Direct binding)
- Rv2011c (-) (Direct binding)
- Rv2324 (-) (Direct binding)
- Rv3246c (mtrA) (Direct binding)
- Rv3736 (-) (Direct binding)
- Rv3830c (-) (Direct binding)
- Rv0023 (-) (Upstream of operon)
- Rv0967 (csoR) (Upstream of operon)
- Rv1990c (-) (Upstream of operon)
- Rv3133c (devR) (Upstream of operon)
- Rv3597c (lsr2) (Upstream of operon)

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:
- Rv2011c (-)
- Rv3849 (espR)

Property	Value	Creator	Evidence	Comment
Interaction	Regulatory Rv3414c	swatigandhi19	IMP	Co-expression(Functional Linkage) H. Calamita, C. Ko et al. The Mycobacterium tuberculosis SigD sigma factor controls the expression of ribosome-associated gene products in stationary phase and is required for full virulence. Cell. Microbiol. 2005
Interaction	Regulatory Rv3414c	swatigandhi19	IMP	Co-expression(Functional Linkage) S. Raman, R. Hazra et al. Transcription regulation by the Mycobacterium tuberculosis alternative sigma factor SigD and its role in virulence. J. Bacteriol. 2004
Interaction	Regulatory Rv2389c	sourish10	IMP	Co-expression (Functional linkage) KJ. Downing, JC. Betts et al. Global expression profiling of strains harbouring null mutations reveals that the five rpf-like genes of Mycobacterium tuberculosis show functional redundancy. Tuberculosis (Edinburgh, Scotland) 2004
Interaction	RegulatedBy Rv0182c	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.. JH. Lee, DE. Geiman et al. Role of stress response sigma factor SigG in Mycobacterium tuberculosis. J. Bacteriol. 2008
Interaction	RegulatedBy Rv0981	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.. H. He, R. Hovey et al. MprAB is a stress-responsive two-component system that directly regulates expression of sigma factors SigB and SigE in Mycobacterium tuberculosis. J. Bacteriol. 2006
Interaction	RegulatedBy Rv1221	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.. 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
Interaction	RegulatedBy Rv3414c	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
Name	Resuscitation-promoting factor	mjackson	IMP	Peptidoglycan turnover

TB Genome Annotation Portal