Rv3097c (lipY)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: triacylglycerol lipase
- REFSEQ: triacylglycerol lipase
- PATRIC: (MTCY164.08c) len: 436. Esterase/lipase identical to TR:P77909 (EMBL:U76006) ESTERASE/LIPASE (EC 3.1.1.3) (TRIACYLGLYCEROL LIPASE) (437 aa); N-terminal similar to N-terminal of M. tuberculosis PE family members eg Y03A_MYCTU Q10637 hypothetical glycine-rich 49.6 kd pro (603 aa) fasta scores opt: 334 E(): 4.8e-13 (43.4% identity in 152 aa overlap). Other relatives include MTCY1A11.25c 7.8e-14; MTCY21B4.13c 2.4e-12; MTCY270.06 5.4e-12; MTCY359.33 1.2e-11; MTC1A11.04 1.2ee-11; cY130.seq 1.3e-11
- TUBERCULIST: PE-PGRS family protein triacylglycerol lipase LipY (esterase/lipase) (triglyceride lipase) (tributyrase)
- NCBI: PE-PGRS family protein, triacylglycerol lipase LipY (esterase/lipase) (triglyceride lipase) (tributyrase)
- updated information (H37Rv4):
  - gene name: lipY
  - function: primiary TAG lipase
  - reference: Maurya (2018) PMID: 30687647
Type: Not Target
Start: 3465778
End: 3467091
Operon:

Trans-membrane region:
Role: IV.C.1.a - PE subfamily
GO terms:
- GO:0016787 - hydrolase activity (Uniprot)
- GO:0016042 - lipid catabolic process (Uniprot)
- GO:0008152 - metabolic process (Uniprot)
- GO:0006629 - lipid metabolic process (Uniprot)
- GO:0005576 - extracellular region (Uniprot)
- GO:0004806 - triglyceride lipase activity (Uniprot)
Reaction(s) (based on iSM810 metabolic model):
- TAGcat[c] -> 0.2 HEXADECANOATE[c] + 0.1 OCTADECANOATE[c] + 0.1 9_OCTADECENOATE[c] + 0.1 EICOSANOATE[c] + 0.1 TETRACOSANOATE[c] ... <Preview truncated at 128 characters>
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 lipY:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 0.663 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

VVSYVVALPEVMSAAATDVASIGSVVATASQGVAGATTTVLAAAEDEVSAAIAALFSGHGQDYQALSAQLAVFHERFVQALTGAAKGYAAAELANASLLQ
SEFASGIGNGFATIHQEIQRAPTALAAGFTQVPPFAAAQAGIFTGTPSGAAGFDIASLWPVKPLLSLSALETHFAIPNNPLLALIASDIPPLSWFLGNSP
PPLLNSLLGQTVQYTTYDGMSVVQITPAHPTGEYVVAIHGGAFILPPSIFHWLNYSVTAYQTGATVQVPIYPLVQEGGTAGTVVPAMAGLISTQIAQHGV
SNVSVVGDSAGGNLALAAAQYMVSQGNPVPSSMVLLSPWLDVGTWQISQAWAGNLAVNDPLVSPLYGSLNGLPPTYVYSGSLDPLAQQAVVLEHTAVVQG
APFSFVLAPWQIHDWILLTPWGLLSWPQINQQLGIAA

(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)	2.55 (0.63)	1.53 (0.7)
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

Rv3097c/lipY, gene len: 1313 bp, num TA sites: 28

condition	dataset	call	medium	method	notes
in-vitro	DeJesus 2017 mBio	growth advantage	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=-0.16)	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	growth advantage	7H9	HMM	6 replicates (raw data in Subramaniam 2017, PMID 31752678)
in-vivo (mice)	Smith 2022 eLife	growth advantage	BL6 mice	HMM	6 replicates (raw data in Subramaniam 2017, PMID 31752678)
differentially essential in mice	Smith 2022 eLife	NO (LFC=0.074)	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	growth advantage	YM rich medium	HMM	7H9 supplemented with ~20 metabolites (amino acids, vitamins)
differentially essential in YM rich medium	Minato 2019 mSys	NO (LFC=0.2)	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

RNA processing and modification

Energy production and conversion

Chromatin structure and dynamics

Amino acid transport and metabolism

Cell cycle control, cell division, chromosome partitioning

Carbohydrate transport and metabolism

Nucleotide transport and metabolism

Lipid transport and metabolism

Coenzyme transport and metabolism

Transcription

Translation, ribosomal structure and biogenesis

Cell wall/membrane/envelope biogenesis

Replication, recombination and repair

Posttranslational modification, protein turnover, chaperones

Cell motility

Secondary metabolites biosynthesis, transport and catabolism

Inorganic ion transport and metabolism

Function unknown

General function prediction only

Intracellular trafficking, secretion, and vesicular transport

Signal transduction mechanisms

Extracellular structures

Defense mechanisms

Nuclear structure

Cytoskeleton

BioCyc Co-regulated genes based on gene expression profiling (Systems Biology, Inferelator Network)

Differentially expressed as result of RNASeq in glycerol environment (Only top 20 genes shown sorted by log fold change with p_adj 0.05).

Conditionally essential as result of TNSeq (Only top 20 genes shown sorted by log fold change with p_adj 0.05).

BioCyc Transcription factor binding based on ChIP-Seq (Systems Biology)

Binds To:
- No bindings to other targets were found.
Bound By:
- No bindings from other targets were found.

Interactions based on ChIPSeq data (Minch et al. 2014)

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv0767c (-) (Direct binding)
- Rv2989 (-) (Direct binding)

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:
- Not downregulated by other genes.

Property	Value	Creator	Evidence	PMID	Comment
Citation	Mycobacterium tuberculosis uses host triacylglycerol to accumulate lipid droplets and acquires a dormancy-like phenotype in lipid-loaded macrophages. authors,J. Daniel,H. Maamar,C. Deb,TD. Sirakova,PE. Kolattukudy PLoS Pathog. 2011	jlew		21731490	Among genes upregulated in Mtb in hypoxic lipid loaded macrophages.
Symbol	lipY	jlew			The role of the PE domain in ESX-5 secretion was confirmed in a whole cell lipase assay, in which wild-type bacteria expressing full-length LipYtub, but not LipYtub lacking its PE domain, were shown to hydrolyze extracellular lipids. In conclusion, both PE and PPE domains contain a signal required for secretion of LipY by the ESX-5 system, and these domains are proteolytically removed upon translocation. authors,MH. Daleke,A. Cascioferro,K. de Punder,R. Ummels,AM. Abdallah,N. van der Wel,PJ. Peters,J. Luirink,R. Manganelli,W. Bitter Conserved Pro-Glu (PE) and Pro-Pro-Glu (PPE) protein domains target LipY lipases of pathogenic mycobacteria to the cell surface via the ESX-5 pathway. J. Biol. Chem. 2011
Citation	Conserved Pro-Glu (PE) and Pro-Pro-Glu (PPE) protein domains target LipY lipases of pathogenic mycobacteria to the cell surface via the ESX-5 pathway. authors,MH. Daleke,A. Cascioferro,K. de Punder,R. Ummels,AM. Abdallah,N. van der Wel,PJ. Peters,J. Luirink,R. Manganelli,W. Bitter J. Biol. Chem. 2011	jlew		21471225	The role of the PE domain in ESX-5 secretion was confirmed in a whole cell lipase assay, in which wild-type bacteria expressing full-length LipYtub, but not LipYtub lacking its PE domain, were shown to hydrolyze extracellular lipids. In conclusion, both PE and PPE domains contain a signal required for secretion of LipY by the ESX-5 system, and these domains are proteolytically removed upon translocation.
Symbol	lipY	jlew			Rv3097c of Mycobacterium tuberculosis encoding lipase (LipY) was overexpressed in Mycobacterium bovis BCG. Immunogenicity of BCG vaccine was impaired by LipY-induced hydrolysis of specific lipids leading to suppression of host immune responses. authors,VK. Singh,V. Srivastava,V. Singh,N. Rastogi,R. Roy,AK. Shaw,AK. Dwivedi,R. Srivastava,BS. Srivastava Overexpression of Rv3097c in Mycobacterium bovis BCG abolished the efficacy of BCG vaccine to protect against Mycobacterium tuberculosis infection in mice. Vaccine 2011
Citation	Overexpression of Rv3097c in Mycobacterium bovis BCG abolished the efficacy of BCG vaccine to protect against Mycobacterium tuberculosis infection in mice. authors,VK. Singh,V. Srivastava,V. Singh,N. Rastogi,R. Roy,AK. Shaw,AK. Dwivedi,R. Srivastava,BS. Srivastava Vaccine 2011	jlew		21565242	Rv3097c of Mycobacterium tuberculosis encoding lipase (LipY) was overexpressed in Mycobacterium bovis BCG. Immunogenicity of BCG vaccine was impaired by LipY-induced hydrolysis of specific lipids leading to suppression of host immune responses.
Symbol	lipY	jlew			Among genes upregulated in Mtb in hypoxic lipid loaded macrophages. authors,J. Daniel,H. Maamar,C. Deb,TD. Sirakova,PE. Kolattukudy Mycobacterium tuberculosis uses host triacylglycerol to accumulate lipid droplets and acquires a dormancy-like phenotype in lipid-loaded macrophages. PLoS Pathog. 2011
Symbol	PE_PGRS/LipY	jlew			interacts with Rv2763c and Rv3733c. 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 Rv2763c and Rv3733c. 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.
Symbol	lipY	jlew			We have characterized the triacylglycerol (TAG) hydrolase LipY from Mycobacterium tuberculosis. Results suggest that the PE domain modulates enzyme activity. authors,KC. Mishra,C. de Chastellier,Y. Narayana,P. Bifani,AK. Brown,GS. Besra,VM. Katoch,B. Joshi,KN. Balaji,L. Kremer Functional role of the PE domain and immunogenicity of the Mycobacterium tuberculosis triacylglycerol hydrolase LipY. Infect. Immun. 2008
Citation	Functional role of the PE domain and immunogenicity of the Mycobacterium tuberculosis triacylglycerol hydrolase LipY. authors,KC. Mishra,C. de Chastellier,Y. Narayana,P. Bifani,AK. Brown,GS. Besra,VM. Katoch,B. Joshi,KN. Balaji,L. Kremer Infect. Immun. 2008	jlew		17938218	We have characterized the triacylglycerol (TAG) hydrolase LipY from Mycobacterium tuberculosis. Results suggest that the PE domain modulates enzyme activity.
Citation	PE is a functional domain responsible for protein translocation and localization on mycobacterial cell wall. A. Cascioferro, G. Delogu et al. Mol. Microbiol. 2007	jlew		18028308	Protein is surface exposed and localizes in the cell wall.
Citation	Macrophage-specific Mycobacterium tuberculosis genes: identification by green fluorescent protein and kanamycin resistance selection. V. Srivastava, C. Rouanet et al. Microbiology (Reading, Engl.) 2007	jlew		17322185	Reporter finds TB promoters that are upregulated in macrophages compared to in vitro growth.
Citation	A novel lipase belonging to the hormone-sensitive lipase family induced under starvation to utilize stored triacylglycerol in Mycobacterium tuberculosis. C. Deb, J. Daniel et al. J. Biol. Chem. 2006	jlew		16354661	We show that Rv3097c (LIPY) hydrolyzed long-chain TG with high specific activity. We demonstrate that hypoxic cultures of M. tuberculosis, which had accumulated TG, hydrolyzed the stored TG when subjected to nutrient starvation. Under such conditions, lipY was induced more than all lipases, suggesting a central role for it in the utilization of stored TG. We also show that in the lipY-deficient mutant, TG utilization was drastically decreased under nutrient deprived condition.
Symbol	lipY	jlew			We show that Rv3097c (LIPY) hydrolyzed long-chain TG with high specific activity. We demonstrate that hypoxic cultures of M. tuberculosis, which had accumulated TG, hydrolyzed the stored TG when subjected to nutrient starvation. Under such conditions, lipY was induced more than all lipases, suggesting a central role for it in the utilization of stored TG. We also show that in the lipY-deficient mutant, TG utilization was drastically decreased under nutrient deprived condition. C. Deb, J. Daniel et al. A novel lipase belonging to the hormone-sensitive lipase family induced under starvation to utilize stored triacylglycerol in Mycobacterium tuberculosis. J. Biol. Chem. 2006
Citation	A novel lipase belonging to the hormone-sensitive lipase family induced under starvation to utilize stored triacylglycerol in Mycobacterium tuberculosis. C. Deb, J. Daniel et al. J. Biol. Chem. 2006	extern:JZUCKER		16354661	Assay of protein purified to homogeneity from its native host
Term	EC:3.1.1.3 Triacylglycerol lipase. - NR	extern:JZUCKER	NR		Assay of protein purified to homogeneity from its native host C. Deb, J. Daniel et al. A novel lipase belonging to the hormone-sensitive lipase family induced under starvation to utilize stored triacylglycerol in Mycobacterium tuberculosis. J. Biol. Chem. 2006

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