Rv1991c (mazF6)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: toxin
- REFSEQ: hypothetical protein
- TUBERCULIST: Toxin MazF6
- NCBI: Toxin MazF6
- updated information (H37Rv4):
  - gene name: mazF6
  - function:
  - reference:
Type: Not Target
Start: 2234305
End: 2234649
Operon:

Trans-membrane region:
Role: V - Conserved hypotheticals
GO terms:
- GO:0090501 - RNA phosphodiester bond hydrolysis (Uniprot)
- GO:0090305 - nucleic acid phosphodiester bond hydrolysis (Uniprot)
- GO:0045927 - positive regulation of growth (Uniprot)
- GO:0045926 - negative regulation of growth (Uniprot)
- GO:0016787 - hydrolase activity (Uniprot)
- GO:0016075 - rRNA catabolic process (Uniprot)
- GO:0006402 - mRNA catabolic process (Uniprot)
- GO:0005576 - extracellular region (Uniprot)
- GO:0005515 - protein binding (Uniprot)
- GO:0004540 - ribonuclease activity (Uniprot)
- GO:0004519 - endonuclease activity (Uniprot)
- GO:0004518 - nuclease activity (Uniprot)
- GO:0003677 - DNA binding (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
5HK0	99%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of M. tuberculosis MazF-mt3 (Rv1991c) in complex with RNA
5HKC	97%	Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)	Crystal structure of M. tuberculosis MazF-mt3 T52D-F62D mutant in complex with 8-mer RNA
5HK3	97%	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Crystal structure of M. tuberculosis MazF-mt3 T52D-F62D mutant in complex with DNA
4HKE	37%	Bacillus anthracis	Crystal Structure of MoxT of Bacillus anthracis
4ME7	36%	Bacillus subtilis subsp. subtilis	Crystal structure of Bacillus subtilis toxin MazF in complex with cognate antitoxin MazE
4MDX	36%	Bacillus subtilis subsp. subtilis	Crystal structure of Bacillus subtilis MazF in complex with RNA
1NE8	36%	Bacillus subtilis	YDCE protein from Bacillus subtilis
5DLO	36%	Staphylococcus aureus	S. aureus MazF in complex with substrate analogue
4MZT	36%	Staphylococcus aureus subsp. aureus	MazF from S. aureus crystal form II, C2221, 2.3 A
4MZP	36%	Staphylococcus aureus subsp. aureus	MazF from S. aureus crystal form III, C2221, 2.7 A

Links to additional information on mazF6:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 0.054 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

VVISRAEIYWADLGPPSGSQPAKRRPVLVIQSDPYNASRLATVIAAVITSNTALAAMPGNVFLPATTTRLPRDSVVNVTAIVTLNKTDLTDRVGEVPASL
MHEVDRGLRRVLDL

(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)	1.4 (0.22)	2.0 (0.5)
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

Rv1991c/mazF6, gene len: 344 bp, num TA sites: 6

condition	dataset	call	medium	method	notes
in-vitro	DeJesus 2017 mBio	non-essential	7H9	HMM	fully saturated, 14 TnSeq libraries combined
in-vitro	Sassetti 2003 Mol Micro	non-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	non-essential	M9 minimal+glycerol	Gumbel	2 replicates; Padj<0.05
in-vitro (cholesterol)	Griffin 2011 PPath	non-essential	M9 minimal+cholesterol	Gumbel	3 replicates; Padj<0.05
differentially essential in cholesterol	Griffin 2011 PPath	NO (LFC=1.14)	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	non-essential	7H9	HMM	6 replicates (raw data in Subramaniam 2017, PMID 31752678)
in-vivo (mice)	Smith 2022 eLife	non-essential	BL6 mice	HMM	6 replicates (raw data in Subramaniam 2017, PMID 31752678)
differentially essential in mice	Smith 2022 eLife	NO (LFC=0.088)	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	non-essential	minimal medium	HMM
in-vitro (YM rich medium)	Minato 2019 mSys	non-essential	YM rich medium	HMM	7H9 supplemented with ~20 metabolites (amino acids, cofactors)
differentially essential in YM rich medium	Minato 2019 mSys	NO (LFC=0.11)	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:

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:
- Rv0023 (-)
- Rv0818 (-)
Downregulates:
- Does not downregulate other genes.
Downregulated by:
- Rv2788 (sirR)
- Rv2887 (-)

Property	Value	Creator	PMID	Comment
Citation	Comprehensive functional analysis of Mycobacterium tuberculosis toxin-antitoxin systems: implications for pathogenesis, stress responses, and evolution. authors,HR. Ramage,LE. Connolly,JS. Cox PLoS Genet. 2009	jlew	20011113	MazF homolog, Toxic when expressed in Msmeg, rescued by antitoxin (Rv1991A)
Symbol	mazF-mt3	jlew		mRNA levels elevated in Mtb in limited O2.. No growth when mazF-mt1 expressed in Ecoli but restored when mazE-mt1 was co-induced. mazF-mt1 could also be partially neutralized by vapB-mt24 or vapB-mt25. Growth inhibition by mazF-mt3; normal growth if mazE-mt1, mazE-mt3, vapB-mt24 or vapB-mt25 were co-expressed. Each pair shows interaction by pull-down. authors,L. Zhu,JD. Sharp,H. Kobayashi,NA. Woychik,M. Inouye Noncognate Mycobacterium tuberculosis toxin-antitoxins can physically and functionally interact. J. Biol. Chem. 2010
Citation	Noncognate Mycobacterium tuberculosis toxin-antitoxins can physically and functionally interact. authors,L. Zhu,JD. Sharp,H. Kobayashi,NA. Woychik,M. Inouye J. Biol. Chem. 2010	jlew	20876537	mRNA levels elevated in Mtb in limited O2.. No growth when mazF-mt1 expressed in Ecoli but restored when mazE-mt1 was co-induced. mazF-mt1 could also be partially neutralized by vapB-mt24 or vapB-mt25. Growth inhibition by mazF-mt3; normal growth if mazE-mt1, mazE-mt3, vapB-mt24 or vapB-mt25 were co-expressed. Each pair shows interaction by pull-down.
Symbol	MazF6	jlew		Toxic to Ecoli growth. We report the heterologous toxicity of these TA loci in Escherichia coli and show that only a few of the M. tuberculosis-encoded toxins can inhibit E. coli growth and have a killing effect. This killing effect can be suppressed by coexpression of the cognate antitoxin. authors,A. Gupta Killing activity and rescue function of genome-wide toxin-antitoxin loci of Mycobacterium tuberculosis. FEMS Microbiol. Lett. 2009
Citation	Killing activity and rescue function of genome-wide toxin-antitoxin loci of Mycobacterium tuberculosis. authors,A. Gupta FEMS Microbiol. Lett. 2009	jlew	19016878	Toxic to Ecoli growth. We report the heterologous toxicity of these TA loci in Escherichia coli and show that only a few of the M. tuberculosis-encoded toxins can inhibit E. coli growth and have a killing effect. This killing effect can be suppressed by coexpression of the cognate antitoxin.
Symbol	mazF-mt3	jlew		Caused cell growth arrest when induced in Ecoli. authors,L. Zhu,Y. Zhang,JS. Teh,J. Zhang,N. Connell,H. Rubin,M. Inouye Characterization of mRNA interferases from Mycobacterium tuberculosis. J. Biol. Chem. 2006
Citation	Characterization of mRNA interferases from Mycobacterium tuberculosis. authors,L. Zhu,Y. Zhang,JS. Teh,J. Zhang,N. Connell,H. Rubin,M. Inouye J. Biol. Chem. 2006	jlew	16611633	Caused cell growth arrest when induced in Ecoli.
Citation	Expression of Mycobacterium tuberculosis Rv1991c using an arabinose-inducible promoter demonstrates its role as a toxin. P. Carroll, AC. Brown et al. FEMS Microbiol. Lett. 2007	jlew	17623030	Expression of Rv1991c inhibits growth of EC but not when expressed with adjacent antitoxin and expression of 1991c in Msmeg resulted in reduction of cell viability.
Citation	Biochemical characterization of a chromosomal toxin-antitoxin system in Mycobacterium tuberculosis. L. Zhao & J. Zhang FEBS Lett. 2008	jlew	18258191	show it's a toxin with ribonuclease activity. Rv1991c and Rv1991A form a complex that can bind its own promoter.
Other	start:2234305	rslayden		Conserved hypothetical protein, showing some similarity to P13976
Other	stop:2234649	rslayden		Conserved hypothetical protein, showing some similarity to P13976
Other	strand:+	rslayden		Conserved hypothetical protein, showing some similarity to P13976
Other	start:2234305	rslayden		PEMK_ECOLI pemk protein (133 aa), FASTA scores: opt: 113, E(): 0.043, (29.2% identity in 113 aa overlap); and P96622
Other	stop:2234649	rslayden		PEMK_ECOLI pemk protein (133 aa), FASTA scores: opt: 113, E(): 0.043, (29.2% identity in 113 aa overlap); and P96622
Other	strand:+	rslayden		PEMK_ECOLI pemk protein (133 aa), FASTA scores: opt: 113, E(): 0.043, (29.2% identity in 113 aa overlap); and P96622
Other	start:2234305	rslayden		YDCE PROTEIN from Bacillus subtilis (116 aa), FASTA scores: opt: 227, E(): 6.9e-09, (37.4% identity in 115 aa overlap). Also similar to Mycobacterium tuberculosis Rv2801c, and Rv0659c.
Other	stop:2234649	rslayden		YDCE PROTEIN from Bacillus subtilis (116 aa), FASTA scores: opt: 227, E(): 6.9e-09, (37.4% identity in 115 aa overlap). Also similar to Mycobacterium tuberculosis Rv2801c, and Rv0659c.
Other	strand:+	rslayden		YDCE PROTEIN from Bacillus subtilis (116 aa), FASTA scores: opt: 227, E(): 6.9e-09, (37.4% identity in 115 aa overlap). Also similar to Mycobacterium tuberculosis Rv2801c, and Rv0659c.

TB Genome Annotation Portal