Rv3791 (dprE2)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: oxidoreductase
- REFSEQ: short chain dehydrogenase
- PATRIC: 3-oxoacyl-[acyl-carrier protein] reductase paralog (EC 1.1.1.100)
- TUBERCULIST: Decaprenylphosphoryl-D-2-keto erythro pentose reductase
- NCBI: Decaprenylphosphoryl-D-2-keto erythro pentose reductase
- updated information (H37Rv4):
  - gene name: dprE2
  - function:
  - reference:
Type: Essential
Start: 4237165
End: 4237929
Operon:

Trans-membrane region:
Role: I.B.7 - Miscellaneous oxidoreductases and oxygenases
GO terms:
- GO:0071555 - cell wall organization (Uniprot)
- GO:0070592 - cell wall polysaccharide biosynthetic process (Uniprot)
- GO:0055114 - oxidation-reduction process (Uniprot)
- GO:0045227 - capsule polysaccharide biosynthetic process (Uniprot)
- GO:0042597 - periplasmic space (Uniprot)
- GO:0040007 - growth (Uniprot)
- GO:0035884 - arabinan biosynthetic process (Uniprot)
- GO:0016491 - oxidoreductase activity (Uniprot)
- GO:0005886 - plasma membrane (Uniprot)
Reaction(s) (based on iSM810 metabolic model):
- DPPR[c] -> ARAFDPP[c]
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

6TQ8 36% Starmerella magnoliae Alcohol dehydrogenase from Candida magnoliae DSMZ 70638 (ADHA): thermostable 10fold mutant
Links to additional information on dprE2:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = -7.197 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

PDB	aa ident	species	PDB title
6TQ8	36%	Starmerella magnoliae	Alcohol dehydrogenase from Candida magnoliae DSMZ 70638 (ADHA): thermostable 10fold mutant

Amino Acid Sequence

MVLDAVGNPQTVLLLGGTSEIGLAICERYLHNSAARIVLACLPDDPRREDAAAAMKQAGARSVELIDFDALDTDSHPKMIEAAFSGGDVDVAIVAFGLLG
DAEELWQNQRKAVQIAEINYTAAVSVGVLLAEKMRAQGFGQIIAMSSAAGERVRRANFVYGSTKAGLDGFYLGLSEALREYGVRVLVIRPGQVRTRMSAH
LKEAPLTVDKEYVANLAVTASAKGKELVWAPAAFRYVMMVLRHIPRSIFRKLPI

(Nucleotide sequence available on KEGG)

Additional Information

Analysis of Positive Selection in Clinical Isolates new

Analysis of dN/dS (omega) in two collections of Mtb clinical isolates using GenomegaMap (Window model) (see description of methods)
- Moldova: 2,057 clinical isolates
- global set: 5,195 clinical isolates from 15 other countries
In the omega plots, the black line shows the mean estimate of omega (dN/dS) at each codon, and the blue lines are the bounds for the 95% credible interval (95%CI, from MCMC sampling).
A gene is under significant positive selection if the lower-bound of the 95%CI of omega (lower blue line) exceeds 1.0 at any codon.

	Moldova (2,057)	global set (5,195)
under significant positive selection?	NO	NO
omega peak height (95%CI lower bound)	1.11 (0.14)	1.23 (0.43)
codons under selection
omega plots
genetic variants*	link	link
statistics at each codon	link	link

* example format for variants: "D27 (GAC): D27H (CAC,11)" means "Asp27 (native codon GAC) mutated to His (codon CAC) in 11 isolates"

ESSENTIALITY

MtbTnDB - interactive tool for exploring a database of published TnSeq datasets for Mtb

TnSeqCorr - genes with correlated TnSeq profiles across ~100 conditions

Rv3791/dprE2, gene len: 764 bp, num TA sites: 12

condition	dataset	call	medium	method	notes
in-vitro	DeJesus 2017 mBio	essential	7H9	HMM	fully saturated, 14 TnSeq libraries combined
in-vitro	Sassetti 2003 Mol Micro	essential	7H9	TRASH	essential if hybridization ratio<0.2
in-vivo (mice)	Sassetti 2003 PNAS	non-essential	BL6 mice	TRASH	essential if hybridization ratio<0.4, min over 4 timepoints (1-8 weeks)
in-vitro (glycerol)	Griffin 2011 PPath	essential	M9 minimal+glycerol	Gumbel	2 replicates; Padj<0.05
in-vitro (cholesterol)	Griffin 2011 PPath	essential	M9 minimal+cholesterol	Gumbel	3 replicates; Padj<0.05
differentially essential in cholesterol	Griffin 2011 PPath	NO (LFC=0.0)	cholesterol vs glycerol	resampling-SR	YES if Padj<0.05, else not significant; LFC<0 means less insertions/more essential in cholesterol
in-vitro	Smith 2022 eLife	essential	7H9	HMM	6 replicates (raw data in Subramaniam 2017, PMID 31752678)
in-vivo (mice)	Smith 2022 eLife	essential	BL6 mice	HMM	6 replicates (raw data in Subramaniam 2017, PMID 31752678)
differentially essential in mice	Smith 2022 eLife	NO (LFC=0.0)	in-vivo vs in-vitro	ZINB	YES if Padj<0.05, else not significant; LFC<0 means less insertions/more essential in mice
in-vitro (minimal)	Minato 2019 mSys	growth defect	minimal medium	HMM
in-vitro (YM rich medium)	Minato 2019 mSys	essential	YM rich medium	HMM	7H9 supplemented with ~20 metabolites (amino acids, cofactors)
differentially essential in YM rich medium	Minato 2019 mSys	NO (LFC=0.0)	YM rich vs minimal medium	resampling

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

RNA processing and modification

Energy production and conversion

Chromatin structure and dynamics

Amino acid transport and metabolism

Cell cycle control, cell division, chromosome partitioning

Carbohydrate transport and metabolism

Nucleotide transport and metabolism

Lipid transport and metabolism

Coenzyme transport and metabolism

Transcription

Translation, ribosomal structure and biogenesis

Cell wall/membrane/envelope biogenesis

Replication, recombination and repair

Posttranslational modification, protein turnover, chaperones

Cell motility

Secondary metabolites biosynthesis, transport and catabolism

Inorganic ion transport and metabolism

Function unknown

General function prediction only

Intracellular trafficking, secretion, and vesicular transport

Signal transduction mechanisms

Extracellular structures

Defense mechanisms

Nuclear structure

Cytoskeleton

BioCyc Co-regulated genes based on gene expression profiling (Systems Biology, Inferelator Network)

Differentially expressed as result of RNASeq in glycerol environment (Only top 20 genes shown sorted by log fold change with p_adj 0.05).

Conditionally essential as result of TNSeq (Only top 20 genes shown sorted by log fold change with p_adj 0.05).

BioCyc Transcription factor binding based on ChIP-Seq (Systems Biology)

Binds To:
- No bindings to other targets were found.
Bound By:
- No bindings from other targets were found.

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

Binds To:
- No bindings to other targets were found.
Bound By:
- No bindings to other targets were found.

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:
- Not downregulated by other genes.

Property	Value	Creator	Evidence	PMID	Comment
Citation	Decaprenylphosphoryl arabinofuranose, the donor of the D-arabinofuranosyl residues of mycobacterial arabinan, is formed via a two-step epimerization of decaprenylphosphoryl ribose. K. Mikusov, H. Huang et al. J. Bacteriol. 2005	njamshidi	IDA	16291675	see PMID: 16291675. lumped reaction, believed to be two step epimerization of ribose to arabinofuranose
Term	TBRXN:DCPE decaprenylphosphoryl ribose, arabinofuranose isomerization - IDA	njamshidi	IDA	16291675	see PMID: 16291675. lumped reaction, believed to be two step epimerization of ribose to arabinofuranose K. Mikusov, H. Huang et al. Decaprenylphosphoryl arabinofuranose, the donor of the D-arabinofuranosyl residues of mycobacterial arabinan, is formed via a two-step epimerization of decaprenylphosphoryl ribose. J. Bacteriol. 2005
Citation	Decaprenylphosphoryl arabinofuranose, the donor of the D-arabinofuranosyl residues of mycobacterial arabinan, is formed via a two-step epimerization of decaprenylphosphoryl ribose. K. Mikusov, H. Huang et al. J. Bacteriol. 2005	njamshidi	IPI	16291675	see PMID: 16291675. lumped reaction, believed to be two step epimerization of ribose to arabinofuranose
Term	TBRXN:DCPE decaprenylphosphoryl ribose, arabinofuranose isomerization - IPI	njamshidi	IPI	16291675	see PMID: 16291675. lumped reaction, believed to be two step epimerization of ribose to arabinofuranose K. Mikusov, H. Huang et al. Decaprenylphosphoryl arabinofuranose, the donor of the D-arabinofuranosyl residues of mycobacterial arabinan, is formed via a two-step epimerization of decaprenylphosphoryl ribose. J. Bacteriol. 2005
Symbol	dprE2	mjackson	IDA		Decaprenyl phosphoarabinose synthesis
Name	decaprenylphosphoryl-D-arabinose synthase (AKA decaprenylphosphoryl-D-2-keto erythro pentuose reductase) forming decaprenyl-P-arabinose	mjackson	IDA		Decaprenyl phosphoarabinose synthesis
Symbol	dprE2	mmcneil			decaprenylphosphoryl-D-arabinose synthase (AKA decaprenylphosphoryl-D-2-keto erythro pentuose reductase) forming decaprenyl-P-arabinose; enzymatic evidence K. Mikusov, H. Huang et al. Decaprenylphosphoryl arabinofuranose, the donor of the D-arabinofuranosyl residues of mycobacterial arabinan, is formed via a two-step epimerization of decaprenylphosphoryl ribose. J. Bacteriol. 2005
Citation	Decaprenylphosphoryl arabinofuranose, the donor of the D-arabinofuranosyl residues of mycobacterial arabinan, is formed via a two-step epimerization of decaprenylphosphoryl ribose. K. Mikusov, H. Huang et al. J. Bacteriol. 2005	mmcneil		16291675	decaprenylphosphoryl-D-arabinose synthase (AKA decaprenylphosphoryl-D-2-keto erythro pentuose reductase) forming decaprenyl-P-arabinose; enzymatic evidence
Term	GO:0009247 glycolipid biosynthetic process - NR	mmcneil	NR		decaprenylphosphoryl-D-arabinose synthase (AKA decaprenylphosphoryl-D-2-keto erythro pentuose reductase) forming decaprenyl-P-arabinose; enzymatic evidence K. Mikusov, H. Huang et al. Decaprenylphosphoryl arabinofuranose, the donor of the D-arabinofuranosyl residues of mycobacterial arabinan, is formed via a two-step epimerization of decaprenylphosphoryl ribose. J. Bacteriol. 2005
Citation	Identification and active expression of the Mycobacterium tuberculosis gene encoding 5-phospho-{alpha}-d-ribose-1-diphosphate: decaprenyl-phosphate 5-phosphoribosyltransferase, the first enzyme committed to decaprenylphosphoryl-d-arabinose synthesis. H. Huang, MS. Scherman et al. J. Biol. Chem. 2005	jjmcfadden		15878857	Inferred from direct assay
Term	EC:1.-.-.- Oxidoreductases. - NR	jjmcfadden	NR		Inferred from direct assay H. Huang, MS. Scherman et al. Identification and active expression of the Mycobacterium tuberculosis gene encoding 5-phospho-{alpha}-d-ribose-1-diphosphate: decaprenyl-phosphate 5-phosphoribosyltransferase, the first enzyme committed to decaprenylphosphoryl-d-arabinose synthesis. J. Biol. Chem. 2005
Citation	Identification and active expression of the Mycobacterium tuberculosis gene encoding 5-phospho-{alpha}-d-ribose-1-diphosphate: decaprenyl-phosphate 5-phosphoribosyltransferase, the first enzyme committed to decaprenylphosphoryl-d-arabinose synthesis. H. Huang, MS. Scherman et al. J. Biol. Chem. 2005	extern:JZUCKER		15878857	Inferred from direct assay
Term	EC:1.-.-.- Oxidoreductases. - NR	extern:JZUCKER	NR		Inferred from direct assay H. Huang, MS. Scherman et al. Identification and active expression of the Mycobacterium tuberculosis gene encoding 5-phospho-{alpha}-d-ribose-1-diphosphate: decaprenyl-phosphate 5-phosphoribosyltransferase, the first enzyme committed to decaprenylphosphoryl-d-arabinose synthesis. J. Biol. Chem. 2005

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