Rv2450c (rpfE)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: hypothetical protein
- REFSEQ: resuscitation-promoting factor RpfE
- PATRIC: Putative saccharopine dehydrogenase
- TUBERCULIST: Probable resuscitation-promoting factor RpfE
- NCBI: Probable resuscitation-promoting factor RpfE
- updated information (H37Rv4):
  - gene name: rpfE
  - function:
  - reference:
Type: Not Target
Start: 2751662
End: 2752180
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
4CGE	100%	MYCOBACTERIUM TUBERCULOSIS	Crystal structure of Mycobacterium tuberculosis Resuscitation promoting factor E
4OW1	66%	Mycobacterium tuberculosis	Crystal Structure of Resuscitation Promoting Factor C
2N5Z	66%	Mycobacterium tuberculosis	Mycobacterium tuberculosis: a dynamic view of the resuscitation promoting factor RpfC catalytic domain
4KPM	63%	Mycobacterium tuberculosis	Crystal structure of the catalytic domain of RpfB from Mycobacterium tuberculosis in complex with triNAG
4KL7	63%	Mycobacterium tuberculosis	Crystal structure of the catalytic domain of RpfB from Mycobacterium tuberculosis
4EMN	63%	Mycobacterium tuberculosis	Crystal structure of RpfB catalytic domain in complex with benzamidine
5E27	59%	Mycobacterium tuberculosis	The structure of Resuscitation Promoting Factor B from M. tuberculosis reveals unexpected ubiquitin-like domains
3EO5	59%	Mycobacterium tuberculosis	Crystal structure of the resuscitation promoting factor RpfB
1XSF	59%	Mycobacterium tuberculosis	Solution structure of a resuscitation promoting factor domain from Mycobacterium tuberculosis

Links to additional information on rpfE:
- TBDB (updated)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

LKNARTTLIAAAIAGTLVTTSPAGIANADDAGLDPNAAAGPDAVGFDPNLPPAPDAAPVDTPPAPEDAGFDPNLPPPLAPDFLSPPAEEAPPVPVAYSVN
WDAIAQCESGGNWSINTGNGYYGGLRFTAGTWRANGGSGSAANASREEQIRVAENVLRSQGIRAWPVCGRRG

(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 8 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 8 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 8 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 8 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 8 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: 0.55
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:
- Rv2021c (-) (Direct binding)

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

Upregulates:
- Does not upregulate other genes.
Upregulated by:
- Rv0081 (-)
Downregulates:
- Does not downregulate other genes.
Downregulated by:
- Not downregulated by other genes.

Property	Value	Creator	Evidence	PMID	Comment
Interaction	Operon Rv2948c	ashwinigbhat	NAS		Co-expression (Functional linkage) B. Abomoelak, EA. Hoye et al. mosR, a novel transcriptional regulator of hypoxia and virulence in Mycobacterium tuberculosis. J. Bacteriol. 2009
Interaction	PhysicalInteraction Rv1477	singhpankaj2116	IMP		Co-expression (Functional linkage) 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 partner for the resuscitation-promoting factors of Mycobacterium tuberculosis. EC. Hett, MC. Chao et al. Mol. Microbiol. 2007	singhpankaj2116	IMP	17919286	Co-expression (Functional linkage)
Interaction	PhysicalInteraction Rv1477	singhpankaj2116	IMP		Co-expression (Functional linkage) EC. Hett, MC. Chao et al. A partner for the resuscitation-promoting factors of Mycobacterium tuberculosis. Mol. Microbiol. 2007
Citation	A bacterial cytokine. authors,GV. Mukamolova,AS. Kaprelyants,DI. Young,M. Young,DB. Kell Proc. Natl. Acad. Sci. U.S.A. 1998	singhpankaj2116	IMP	9671779	Co-expression (Functional linkage)
Interaction	PhysicalInteraction Rv1477	singhpankaj2116	IMP		Co-expression (Functional linkage) authors,GV. Mukamolova,AS. Kaprelyants,DI. Young,M. Young,DB. Kell A bacterial cytokine. Proc. Natl. Acad. Sci. U.S.A. 1998
Citation	Global expression profiling of strains harbouring null mutations reveals that the five rpf-like genes of Mycobacterium tuberculosis show functional redundancy. KJ. Downing, JC. Betts et al. Tuberculosis (Edinburgh, Scotland) 2004	richasinha4u	IDA	15207486	Yeast two-hybrid (Physical interaction)
Interaction	PhysicalInteraction Rv1477	richasinha4u	IDA		Yeast two-hybrid (Physical interaction) 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	richasinha4u	IDA	18186793	Yeast two-hybrid (Physical interaction)
Interaction	PhysicalInteraction Rv1477	richasinha4u	IDA		Yeast two-hybrid (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	Individual Mycobacterium tuberculosis resuscitation-promoting factor homologues are dispensable for growth in vitro and in vivo. authors,JM. Tufariello,WR. Jacobs,J. Chan Infect. Immun. 2004	richasinha4u	IDA	14688133	Yeast two-hybrid (Physical interaction)
Interaction	PhysicalInteraction Rv1477	richasinha4u	IDA		Yeast two-hybrid (Physical interaction) authors,JM. Tufariello,WR. Jacobs,J. Chan Individual Mycobacterium tuberculosis resuscitation-promoting factor homologues are dispensable for growth in vitro and in vivo. Infect. Immun. 2004
Citation	A partner for the resuscitation-promoting factors of Mycobacterium tuberculosis. EC. Hett, MC. Chao et al. Mol. Microbiol. 2007	richasinha4u	IDA	17919286	Yeast two-hybrid (Physical interaction)
Interaction	PhysicalInteraction Rv1477	richasinha4u	IDA		Yeast two-hybrid (Physical interaction) EC. Hett, MC. Chao et al. A partner for the resuscitation-promoting factors of Mycobacterium tuberculosis. Mol. Microbiol. 2007
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	singhpankaj2116	IMP	18186793	Co-expression (Functional linkage)
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	ActivatedBy Rv1477	vijayachitra	IPI		Yeast two-hybrid (Physical interaction) EC. Hett, MC. Chao et al. A partner for the resuscitation-promoting factors of Mycobacterium tuberculosis. Mol. Microbiol. 2007
Name	Resuscitation-promoting factor	mjackson	IMP		Peptidoglycan turnover

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