Rv2763c (dfrA)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: dihydrofolate reductase
- REFSEQ: dihydrofolate reductase DFRA (DHFR) (tetrahydrofolate dehydrogenase)
- PATRIC: Dihydrofolate reductase (EC 1.5.1.3)
- TUBERCULIST: Dihydrofolate reductase DfrA (DHFR) (tetrahydrofolate dehydrogenase)
- NCBI: Dihydrofolate reductase DfrA (DHFR) (tetrahydrofolate dehydrogenase)
- updated information (H37Rv4):
  - gene name: dfrA
  - function:
  - reference:
Type: Not Target
Start: 3073130
End: 3073609
Operon:

Trans-membrane region:
Role: I.G.2 - Folic acid
GO terms:
- GO:0070401 - NADP+ binding (Uniprot)
- GO:0055114 - oxidation-reduction process (Uniprot)
- GO:0050661 - NADP binding (Uniprot)
- GO:0046654 - tetrahydrofolate biosynthetic process (Uniprot)
- GO:0016491 - oxidoreductase activity (Uniprot)
- GO:0006730 - one-carbon metabolic process (Uniprot)
- GO:0006545 - glycine biosynthetic process (Uniprot)
- GO:0004146 - dihydrofolate reductase activity (Uniprot)
Reaction(s) (based on iSM810 metabolic model):
- NADPH[c] + DHF[c] -> NADP[c] + THF[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: 1dg5, 1dg7, 1dg8, 1df7, 2cig
Search for Homologs in PDB

Top 10 Homologs in PDB (as of Nov 2020):

PDB	aa ident	species	PDB title
6VVB	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Mycobacterium tuberculosis dihydrofolate reductase in complex with 6-methyl-5-(4-phenylthiazol-2-yl)-2- (trifluoromethyl)nicotinic acid (fragment 10)
6VV9	100%	Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra)	Mycobacterium tuberculosis dihydrofolate reductase in complex with JEB300
6VV8	100%	Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra)	Mycobacterium tuberculosis dihydrofolate reductase in complex with JEB285
6VV7	100%	Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra)	Mycobacterium tuberculosis dihydrofolate reductase in complex with JEB136
6VV6	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Mycobacterium tuberculosis dihydrofolate reductase in complex with JEB113
6VSG	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Mycobacterium tuberculosis dihydrofolate reductase in complex with 4-(trifluoromethyl)benzene-1,2-diamine(fragment 17)
6VSF	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Mycobacterium tuberculosis dihydrofolate reductase in complex with 4-(3,4-dihydro-2H-benzo[b][1,4]dioxepin-7-yl)-4-oxobutanoic acid(fragment 16)
6VSE	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Mycobacterium tuberculosis dihydrofolate reductase in complex with 3-(phenoxymethyl)benzoic acid(fragment 14)
6VSD	100%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Mycobacterium tuberculosis dihydrofolate reductase in complex with 3-((thiophen-2-ylthio)methyl)benzoic acid (fragment 13)
6VS9	100%	Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra)	Mycobacterium tuberculosis dihydrofolate reductase in complex with 3-(piperidin-1-ylmethyl)benzoic acid(fragment 11)

Links to additional information on dfrA:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = -7.65 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

MVGLIWAQATSGVIGRGGDIPWRLPEDQAHFREITMGHTIVMGRRTWDSLPAKVRPLPGRRNVVLSRQADFMASGAEVVGSLEEALTSPETWVIGGGQVY
ALALPYATRCEVTEVDIGLPREAGDALAPVLDETWRGETGEWRFSRSGLRYRLYSYHRS

(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)	1.87 (0.3)	0.88 (0.28)
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

Rv2763c/dfrA, gene len: 479 bp, num TA sites: 9

condition	dataset	call	medium	method	notes
in-vitro	DeJesus 2017 mBio	growth defect	7H9	HMM	fully saturated, 14 TnSeq libraries combined
in-vitro	Sassetti 2003 Mol Micro	no data	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

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv3417c (groEL1)

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:
- Rv3417c (groEL1)

Property	Value	Creator	Evidence	PMID	Comment
Symbol	DHFR	jlew			interacts with Rv3097c. Using an in vivo pull-down assay, for the first time we have confirmed the presence of three pairs of PE/PPE-related novel protein interactions in this pathogen. J. Zeng, L. Zhang et al. Over-producing soluble protein complex and validating protein-protein interaction through a new bacterial co-expression system. Protein Expr. Purif. 2010
Citation	Over-producing soluble protein complex and validating protein-protein interaction through a new bacterial co-expression system. J. Zeng, L. Zhang et al. Protein Expr. Purif. 2010	jlew		19747546	interacts with Rv3097c. Using an in vivo pull-down assay, for the first time we have confirmed the presence of three pairs of PE/PPE-related novel protein interactions in this pathogen.
Citation	The folate pathway is a target for resistance to the drug para-aminosalicylic acid (PAS) in mycobacteria. J. Rengarajan, CM. Sassetti et al. Mol. Microbiol. 2004	jjmcfadden		15225321	Inferred from direct assay
Term	EC:1.5.1.3 Dihydrofolate reductase. - NR	jjmcfadden	NR		Inferred from direct assay J. Rengarajan, CM. Sassetti et al. The folate pathway is a target for resistance to the drug para-aminosalicylic acid (PAS) in mycobacteria. Mol. Microbiol. 2004

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