Rv0867c (rpfA)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: resuscitation-promoting factor rpfA
- REFSEQ: resuscitation-promoting factor RpfA
- PATRIC: FIG00820555: hypothetical protein
- TUBERCULIST: Possible resuscitation-promoting factor RpfA
- NCBI: Possible resuscitation-promoting factor RpfA
- updated information (H37Rv4):
  - gene name: rpfA
  - function:
  - reference:
Type: Not Target
Start: 964312
End: 965535
Operon:

Trans-membrane region:
Role: II.C.5 - Other membrane proteins
GO terms:
- GO:0040010 - positive regulation of growth rate (Uniprot)
- GO:0016787 - hydrolase activity (Uniprot)
- GO:0010629 - negative 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
4CGE	67%	MYCOBACTERIUM TUBERCULOSIS	Crystal structure of Mycobacterium tuberculosis Resuscitation promoting factor E
4OW1	65%	Mycobacterium tuberculosis	Crystal Structure of Resuscitation Promoting Factor C
2N5Z	65%	Mycobacterium tuberculosis	Mycobacterium tuberculosis: a dynamic view of the resuscitation promoting factor RpfC catalytic domain
5E27	64%	Mycobacterium tuberculosis	The structure of Resuscitation Promoting Factor B from M. tuberculosis reveals unexpected ubiquitin-like domains
4KPM	64%	Mycobacterium tuberculosis	Crystal structure of the catalytic domain of RpfB from Mycobacterium tuberculosis in complex with triNAG
4KL7	64%	Mycobacterium tuberculosis	Crystal structure of the catalytic domain of RpfB from Mycobacterium tuberculosis
4EMN	64%	Mycobacterium tuberculosis	Crystal structure of RpfB catalytic domain in complex with benzamidine
3EO5	64%	Mycobacterium tuberculosis	Crystal structure of the resuscitation promoting factor RpfB
1XSF	64%	Mycobacterium tuberculosis	Solution structure of a resuscitation promoting factor domain from Mycobacterium tuberculosis

Links to additional information on rpfA:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = -0.782 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

MSGRHRKPTTSNVSVAKIAFTGAVLGGGGIAMAAQATAATDGEWDQVARCESGGNWSINTGNGYLGGLQFTQSTWAAHGGGEFAPSAQLASREQQIAVGE
RVLATQGRGAWPVCGRGLSNATPREVLPASAAMDAPLDAAAVNGEPAPLAPPPADPAPPVELAANDLPAPLGEPLPAAPADPAPPADLAPPAPADVAPPV
ELAVNDLPAPLGEPLPAAPADPAPPADLAPPAPADLAPPAPADLAPPAPADLAPPVELAVNDLPAPLGEPLPAAPAELAPPADLAPASADLAPPAPADLA
PPAPAELAPPAPADLAPPAAVNEQTAPGDQPATAPGGPVGLATDLELPEPDPQPADAPPPGDVTEAPAETPQVSNIAYTKKLWQAIRAQDVCGNDALDSL
AQPYVIG

(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
Uncertain	Sodium Oleate	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.160300; 4 non-insertions in a row out of 11 sites
Uncertain	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.259350; 4 non-insertions in a row out of 11 sites
Uncertain	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.287150; 4 non-insertions in a row out of 11 sites
Non-Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 11 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 11 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: 0.31
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:
- Rv0967 (csoR) (Direct binding)
- Rv1353c (-) (Direct binding)
- Rv2034 (-) (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:

Property	Value	Creator	Evidence	PMID	Comment
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
Citation	The resuscitation-promoting factors of Mycobacterium tuberculosis are required for virulence and resuscitation from dormancy but are collectively dispensable for growth in vitro. BD. Kana, BG. Gordhan et al. Mol. Microbiol. 2008	girishgene07	IPI	18186793	Affinity purification (Physical interaction)
Interaction	PhysicalInteraction Rv1477	girishgene07	IPI		Affinity purification (Physical interaction) BD. Kana, BG. Gordhan et al. The resuscitation-promoting factors of Mycobacterium tuberculosis are required for virulence and resuscitation from dormancy but are collectively dispensable for growth in vitro. Mol. Microbiol. 2008
Citation	A mycobacterial enzyme essential for cell division synergizes with resuscitation-promoting factor. EC. Hett, MC. Chao et al. PLoS Pathog. 2008	girishgene07	IPI	18463693	Affinity purification (Physical interaction)
Interaction	PhysicalInteraction Rv1477	girishgene07	IPI		Affinity purification (Physical interaction) EC. Hett, MC. Chao et al. A mycobacterial enzyme essential for cell division synergizes with resuscitation-promoting factor. PLoS Pathog. 2008
Citation	Specialized transduction: an efficient method for generating marked and unmarked targeted gene disruptions in Mycobacterium tuberculosis, M. bovis BCG and M. smegmatis. S. Bardarov, S. Bardarov Jr et al. Microbiology (Reading, Engl.) 2002	girishgene07	IPI	12368434	Affinity purification (Physical interaction)
Interaction	PhysicalInteraction Rv1477	girishgene07	IPI		Affinity purification (Physical interaction) S. Bardarov, S. Bardarov Jr et al. Specialized transduction: an efficient method for generating marked and unmarked targeted gene disruptions in Mycobacterium tuberculosis, M. bovis BCG and M. smegmatis. Microbiology (Reading, Engl.) 2002
Interaction	Regulatory Rv0616c	akankshajain.21	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	RegulatedBy Rv3676	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 Rv0491	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.. T. Parish, DA. Smith et al. The senX3-regX3 two-component regulatory system of Mycobacterium tuberculosis is required for virulence. Microbiology (Reading, Engl.) 2003
Name	Resuscitation-promoting factor	mjackson	IMP		Peptidoglycan turnover

TB Genome Annotation Portal