Rv1959c (parE1)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: toxin
- REFSEQ: hypothetical protein
- PATRIC: plasmid stabilization protein ParE
- TUBERCULIST: Possible toxin ParE1
- NCBI: Possible toxin ParE1
- updated information (H37Rv4):
  - gene name: parE1
  - function:
  - reference:
Type: Not Target
Start: 2203681
End: 2203977
Operon:

Trans-membrane region:
Role: V - Conserved hypotheticals
GO terms:
- GO:0045926 - negative regulation of growth (Uniprot)
- GO:0005515 - protein 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

3KXE 43% Caulobacter crescentus NA1000 A conserved mode of protein recognition and binding in a ParD-ParE toxin-antitoxin complex
Links to additional information on parE1:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 0.579 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

PDB	aa ident	species	PDB title
3KXE	43%	Caulobacter crescentus NA1000	A conserved mode of protein recognition and binding in a ParD-ParE toxin-antitoxin complex

Amino Acid Sequence

VSSRYLLSPAAQAHLEEIWDCTYDRWGVDQAEQYLRELQHAIDRAAANPRIGRACDEIRPGYRKLSAGSHTLFYRVTGEGTIDVVRVLHQRMDVDRNL

(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; 0 non-insertions in a row out of 7 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 7 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 7 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 7 sites
Non-Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000050; 3 non-insertions in a row out of 7 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: 1.98
Growth-Advantage	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:
- Rv2034 (-) (Upstream of operon)
- Rv3574 (kstR) (Upstream of operon)

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

Upregulates:
- Does not upregulate other genes.
Upregulated by:
- Rv0023 (-)
- Rv1960c (parD1)
Downregulates:
- Does not downregulate other genes.
Downregulated by:

Property	Value	Creator	Evidence	PMID	Comment
Interaction	InhibitedBy Rv1960c	akankshajain.21	IDA		Spectrophotometric analysis 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	prabhakarsmail	IDA	19016878	Spectrophotometric analysis
Interaction	InhibitedBy Rv1960c	prabhakarsmail	IDA		Spectrophotometric analysis authors,A. Gupta Killing activity and rescue function of genome-wide toxin-antitoxin loci of Mycobacterium tuberculosis. FEMS Microbiol. Lett. 2009
Interaction	InhibitedBy Rv1960c	akankshajain.21	IDA		Spectrophotometric analysis authors,A. Gupta Killing activity and rescue function of genome-wide toxin-antitoxin loci of Mycobacterium tuberculosis. FEMS Microbiol. Lett. 2009
Interaction	InhibitedBy Rv1960c	prabhakarsmail	IDA		Spectrophotometric analysis 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	akankshajain.21	IDA	19016878	Spectrophotometric analysis
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	ParE homolog, Not toxic when expressed in Msmeg
Symbol	ParE1	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.
Other	start:2203681	rslayden			Plasmid stabilization system protein. Conserved hypothetical protein, similar to other hypothetical plasmid proteins e.g. AL117189
Other	stop:2203977	rslayden			Plasmid stabilization system protein. Conserved hypothetical protein, similar to other hypothetical plasmid proteins e.g. AL117189
Other	strand:+	rslayden			Plasmid stabilization system protein. Conserved hypothetical protein, similar to other hypothetical plasmid proteins e.g. AL117189
Other	start:2203681	rslayden			YPCD1.08 from Yersinia pestis (99 aa), FASTA scores: opt: 162, E(): 7.3e-05, (33.0% identity in 91 aa overlap); also some similarity to E145339 hypothetical protein (103 aa), FASTA scores: opt: 142, E(): 0.0003, (33.0% identity in 91 aa overlap).
Other	stop:2203977	rslayden			YPCD1.08 from Yersinia pestis (99 aa), FASTA scores: opt: 162, E(): 7.3e-05, (33.0% identity in 91 aa overlap); also some similarity to E145339 hypothetical protein (103 aa), FASTA scores: opt: 142, E(): 0.0003, (33.0% identity in 91 aa overlap).
Other	strand:+	rslayden			YPCD1.08 from Yersinia pestis (99 aa), FASTA scores: opt: 162, E(): 7.3e-05, (33.0% identity in 91 aa overlap); also some similarity to E145339 hypothetical protein (103 aa), FASTA scores: opt: 142, E(): 0.0003, (33.0% identity in 91 aa overlap).

TB Genome Annotation Portal