Rv2006 (otsB1)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: trehalose-phosphatase
- REFSEQ: trehalose-6-phosphate phosphatase OtsB1
- PATRIC: Uncharacterized glycosyl hydrolase Rv2006/MT2062 (EC 3.2.1.-)
- TUBERCULIST: Probable trehalose-6-phosphate phosphatase OtsB1 (trehalose-phosphatase) (TPP)
- NCBI: Probable trehalose-6-phosphate phosphatase OtsB1 (trehalose-phosphatase) (TPP)
- updated information (H37Rv4):
  - gene name: otsB1
  - function:
  - reference:
Type: Not Target
Start: 2252002
End: 2255985
Operon:

Trans-membrane region:
Role: III.E - Adaptations and atypical conditions
GO terms:
- GO:0030246 - carbohydrate binding (Uniprot)
- GO:0016798 - hydrolase activity, acting on glycosyl bonds (Uniprot)
- GO:0016787 - hydrolase activity (Uniprot)
- GO:0008152 - metabolic process (Uniprot)
- GO:0005992 - trehalose biosynthetic process (Uniprot)
- GO:0005975 - carbohydrate metabolic process (Uniprot)
- GO:0005886 - plasma membrane (Uniprot)
- GO:0005618 - cell wall (Uniprot)
- GO:0005576 - extracellular region (Uniprot)
- GO:0003824 - catalytic activity (Uniprot)
Reaction(s) (based on iSM810 metabolic model):
- TREHALOSEMONOMYCOLATE[P][c] -> PI[c] + TREHALOSEMONOMYCOLATE_40_CY_41_[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

5GVX 56% Mycobacterium tuberculosis Structural insight into dephosphorylation by Trehalose 6-phosphate Phosphatase (OtsB2) from Mycobacterium Tuberculosis
Links to additional information on otsB1:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 1.444 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

PDB	aa ident	species	PDB title
5GVX	56%	Mycobacterium tuberculosis	Structural insight into dephosphorylation by Trehalose 6-phosphate Phosphatase (OtsB2) from Mycobacterium Tuberculosis

Amino Acid Sequence

VRCGIVVNVTGPPPTIDRRYHDAVIVGLDNVVDKATRVHAAAWTKFLDDYLTRRPQRTGEDHCPLTHDDYRRFLAGKPDGVADFLAARGIRLPPGSPTDL
TDDTVYGLQNLERQTFLQLLNTGVPEGKSIASFARRLQVAGVRVAAHTSHRNYGHTLDATGLAEVFAVFVDGAVTAELGLPAEPNPAGLIETAKRLGANP
GRCVVIDSCQTGLRAGRNGGFALVIAVDAHGDAENLLSSGADAVVADLAAVTVGSGDAAISTIPDALQVYSQLKRLLTGRRPAVFLDFDGTLSDIVERPE
AATLVDGAAEALRALAAQCPVAVISGRDLADVRNRVKVDGLWLAGSHGFELVAPDGSHHQNAAATAAIDGLAEAAAQLADALREIAGAVVEHKRFAVAVH
YRNVADDSVDNLIAAVRRLGHAAGLRVTTGRKVVELRPDIAWDKGKALDWIGERLGPAEVGPDLRLPIYIGDDLTDEDAFDAVRFTGVGIVVRHNEHGDR
RSAATFRLECPYTVCQFLSQLACDLQEAVQHDDPWTLVFHGYDPGQERLREALCAVGNGYLGSRGCAPESAESEAHYPGTYVAGVYNQLTDHIEGCTVDN
ESLVNLPNWLSLTFRIDGGAWFNVDTVELLSYRQTFDLRRATLTRSLRFRDAGGRVTTMTQERFASMNRPNLVALQTRIESENWSGTVDFRSLVDGGVHN
TLVDRYRQLSSQHLTTAEIEVLADSVLLRTQTSQSGIAIAVAARSTLWRDGQRVDAQYRVARDTNRGGHDIQVTLSAGQSVTLEKVATIFTSRDAATLTA
AISAQRCLGEAGRYAELCQQHVRAWARLWERCAIDLTGNTEELRLVRLHLLHLLQTISPHTAELDAGVPARGLNGEAYRGHVFWDALFVAPVLSLRMPKV
ARSLLDYRYRRLPAARRAAHRAGHLGAMYPWQSGSDGSEVSQQLHLNPRSGRWTPDPSDRAHHVGLAVAYNAWHYYQVTGDRQYLVDCGAELLVEIARFW
VGLAKLDDSRGRYLIRGVIGPDEFHSGYPGNEYDGIDNNAYTNVMAVWVILRAMEALDLLPLTDRRHLIEKLGLTTQERDQWDDVSRRMFVPFHDGVISQ
FEGYSELAELDWDHYRHRYGNIQRLDRILEAEGDSVNNYQASKQADALMLLYLLSSDELIGLLARLGYRFAPTQIPGTVDYYLARTSDGSTLSAVVHAWV
LARANRSNAMEYFRQVLRSDIADVQGGTTQEGIHLAAMAGSIDLLQRCYSGLELRDDRLVLSPQWPEALGPLEFPFVYRRHQLSLRISGRSATLTAESGD
AEPIEVECRGHVQRLRCGHTIEVGCSR

(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)	2.59 (0.65)	1.55 (0.82)
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

Rv2006/otsB1, gene len: 3983 bp, num TA sites: 82

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	essential	M9 minimal+glycerol	Gumbel	2 replicates; Padj<0.05
in-vitro (cholesterol)	Griffin 2011 PPath	uncertain	M9 minimal+cholesterol	Gumbel	3 replicates; Padj<0.05
differentially essential in cholesterol	Griffin 2011 PPath	NO (LFC=0.54)	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=0.037)	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, vitamins)
differentially essential in YM rich medium	Minato 2019 mSys	NO (LFC=-0.12)	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:
- Rv0302 (-) (Direct binding)
- Rv0678 (-) (Direct binding)
- Rv1985c (-) (Direct binding)
- Rv3133c (devR) (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	Three pathways for trehalose biosynthesis in mycobacteria. KA. De Smet, A. Weston et al. Microbiology (Reading, Engl.) 2000	njamshidi	IDA	10658666	PMID: 10658666
Term	EC:3.1.3.12 Trehalose-phosphatase. - IDA	njamshidi	IDA	10658666	PMID: 10658666 KA. De Smet, A. Weston et al. Three pathways for trehalose biosynthesis in mycobacteria. Microbiology (Reading, Engl.) 2000
Term	TBRXN:TRE6PP trehalose-phosphatase - IDA	njamshidi	IDA	10658666	PMID: 10658666 KA. De Smet, A. Weston et al. Three pathways for trehalose biosynthesis in mycobacteria. Microbiology (Reading, Engl.) 2000
Citation	Three pathways for trehalose biosynthesis in mycobacteria. KA. De Smet, A. Weston et al. Microbiology (Reading, Engl.) 2000	njamshidi	ISS	10658666	PMID: 10658666
Term	EC:3.1.3.12 Trehalose-phosphatase. - ISS	njamshidi	ISS	10658666	PMID: 10658666 KA. De Smet, A. Weston et al. Three pathways for trehalose biosynthesis in mycobacteria. Microbiology (Reading, Engl.) 2000
Term	TBRXN:TRE6PP trehalose-phosphatase - ISS	njamshidi	ISS	10658666	PMID: 10658666 KA. De Smet, A. Weston et al. Three pathways for trehalose biosynthesis in mycobacteria. Microbiology (Reading, Engl.) 2000
Interaction	RegulatedBy Rv3133c	yamir.moreno	TAS		Literature previously reported link (from Balazsi et al. 2008). Traceable author statement to experimental support. G. Balzsi, AP. Heath et al. The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. Mol. Syst. Biol. 2008
Interaction	RegulatedBy Rv3133c	yamir.moreno	TAS		Literature previously reported link (from Balazsi et al. 2008). Traceable author statement to experimental support. G. Balzsi, AP. Heath et al. The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. Mol. Syst. Biol. 2008
Name	probable trehalose-6P-phosphatase, apparently inactive in MTB: INVOLVED IN TREHALOSE BIOSYNTHESIS FROM GLUCOSE 6-PHOSPHATE AND UDP-GLUCOSE	mjackson	ISS		Trehalose biosynthesis
Name	probable trehalose-6P-phosphatase, apparently inactive in MTB: INVOLVED IN TREHALOSE BIOSYNTHESIS FROM GLUCOSE 6-PHOSPHATE AND UDP-GLUCOSE	mjackson	IMP		Trehalose biosynthesis
Citation	Pathway to synthesis and processing of mycolic acids in Mycobacterium tuberculosis. K. Takayama, C. Wang et al. Clin. Microbiol. Rev. 2005	extern:JZUCKER		15653820	Inferred by a human based on computational evidence
Term	EC:3.1.3.12 Trehalose-phosphatase. - NR	extern:JZUCKER	NR		Inferred by a human based on computational evidence K. Takayama, C. Wang et al. Pathway to synthesis and processing of mycolic acids in Mycobacterium tuberculosis. Clin. Microbiol. Rev. 2005

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