Rv1955 (higB)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: toxin
- REFSEQ: hypothetical protein
- PATRIC: FIG00822499: hypothetical protein
- TUBERCULIST: Possible toxin HigB
- NCBI: Possible toxin HigB
- updated information (H37Rv4):
  - gene name: higB
  - function:
  - reference:
Type: Not Target
Start: 2201719
End: 2202096
Operon:

Trans-membrane region:
Role: VI - Unknowns
GO terms:
- GO:0090502 - RNA phosphodiester bond hydrolysis, endonucleolytic (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:0005515 - protein binding (Uniprot)
- GO:0004521 - endoribonuclease activity (Uniprot)
- GO:0004519 - endonuclease activity (Uniprot)
- GO:0004518 - nuclease activity (Uniprot)
- GO:0001666 - response to hypoxia (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): (none with >35% aa id)
Links to additional information on higB:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 1.691 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

VPPPDPAAMGTWKFFRASVDGRPVFKKEFDKLPDQARAALIVLMQRYLVGDLAAGSIKPIRGDILELRWHEANNHFRVLFFRWGQHPVALTAFYKNQQKT
PKTKIETALDRQKIWKRAFGDTPPI

(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 9 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 9 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 9 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 7 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 7 sites
No-Data	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Too-Short	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: -1
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:
- Rv1423 (whiA) (Direct binding)

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

Upregulates:
- Does not upregulate other genes.
Upregulated by:
Downregulates:
- Does not downregulate other genes.
Downregulated by:

Property	Value	Creator	Evidence	PMID	Comment
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
Interaction	InhibitedBy Rv1956	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 Rv1956	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 Rv1956	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 Rv1956	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	RegulatedBy Rv0348	yamir.moreno	IEP		Microarrays. mRNA levels of regulated element measured and compared between wild-type and trans-element mutation (knockout, over expression etc.) performed by using microarray (or macroarray) experiments.. B. Abomoelak, EA. Hoye et al. mosR, a novel transcriptional regulator of hypoxia and virulence in Mycobacterium tuberculosis. J. Bacteriol. 2009
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	HigA homolog, Toxic when expressed in Msmeg, rescued by antitoxin (Rv1956)
Symbol	higB	jlew			In Ecoli, HigB expression blocks growth but not if HigA and Rv1957 are also present; HigA or Rv1957 alone does not rescue. authors,P. Bordes,AM. Cirinesi,R. Ummels,A. Sala,S. Sakr,W. Bitter,P. Genevaux SecB-like chaperone controls a toxin-antitoxin stress-responsive system in Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. U.S.A. 2011
Citation	SecB-like chaperone controls a toxin-antitoxin stress-responsive system in Mycobacterium tuberculosis. authors,P. Bordes,AM. Cirinesi,R. Ummels,A. Sala,S. Sakr,W. Bitter,P. Genevaux Proc. Natl. Acad. Sci. U.S.A. 2011	jlew		21536872	In Ecoli, HigB expression blocks growth but not if HigA and Rv1957 are also present; HigA or Rv1957 alone does not rescue.
Symbol	higB	jlew			higB-higA-Rv1957 could be deleted, but not higA alone authors,AS. Fivian-Hughes,EO. Davis Analyzing the regulatory role of the HigA antitoxin within Mycobacterium tuberculosis. J. Bacteriol. 2010
Citation	Analyzing the regulatory role of the HigA antitoxin within Mycobacterium tuberculosis. authors,AS. Fivian-Hughes,EO. Davis J. Bacteriol. 2010	jlew		20585061	higB-higA-Rv1957 could be deleted, but not higA alone
Other	start:2201741	rslayden			Hypothetical unknown protein, start overlaps another ORF, Rv1954c (MTCY09F9.10).
Other	stop:2202091	rslayden			Hypothetical unknown protein, start overlaps another ORF, Rv1954c (MTCY09F9.10).
Other	strand:+	rslayden			Hypothetical unknown protein, start overlaps another ORF, Rv1954c (MTCY09F9.10).

TB Genome Annotation Portal