lipase activity edits - Githubissues

sjm41 commented 1 week ago

Our lipase activity term and immediate child terms look like this:

hydrolase activity, acting on ester bonds
    |__lipase activity
           |__acylglycerol lipase activity
           |__galactolipase activity
           |__phospholipase activity
           |__sterol esterase activity
           |__triglyceride lipase activity
               |__lipoprotein lipase activity

After chatting with Lucila Aimo at RHEA and @pgaudet, there are several corrections to make:

id: GO:0016298 name: lipase activity def: "Catalysis of the hydrolysis of a lipid or phospholipid." [GOC:mah, ISBN:0198506732] is_a: GO:0016788 ! hydrolase activity, acting on ester bonds

[x] All lipases are carboxylic ester hydrolase, so change parent here to 'GO:0052689 ! carboxylic ester hydrolase activity'
[x] No need to specify 'phospholipid' (but not other lipid types) in the definition, so remove that bit.

id: GO:0047372 name: acylglycerol lipase activity def: "Catalysis of the reaction: H2O + acylglycerol = a fatty acid + glycerol." [EC:3.1.1.23, MetaCyc:3.1.1.23-RXN] xref: EC:3.1.1.23 xref: MetaCyc:3.1.1.23-RXN xref: RHEA:34019 is_a: GO:0016298 ! lipase activity is_a: GO:0052689 ! carboxylic ester hydrolase activity

[x] Following point above, remove redundant parent 'GO:0052689 ! carboxylic ester hydrolase activity'
[x] This is specifically for monoacylglycerol lipase (which is the alternative EC name), so change GO name to 'monoacylglycerol lipase activity'
[x] RHEA xref here should be RHEA:15245
[x] Update def to match RHEA:15245 "a monoacylglycerol + H2O = a fatty acid + glycerol + H+"
[x] Change MetaCyc xref to MetaCyc:RXN-19280

id: GO:0004806 name: triglyceride lipase activity def: "Catalysis of the reaction: triacylglycerol + H2O = diacylglycerol + a carboxylate." [EC:3.1.1.3] xref: EC:3.1.1.3 xref: MetaCyc:TRIACYLGLYCEROL-LIPASE-RXN xref: RHEA:12044 is_a: GO:0016298 ! lipase activity is_a: GO:0052689 ! carboxylic ester hydrolase activity

[x] Following point above, remove redundant parent 'GO:0052689 ! carboxylic ester hydrolase activity'
[x] Change GO name to 'triacylglycerol lipase activity'
[x] Update def to match RHEA:12044 "a triacylglycerol + H2O = a diacylglycerol + a fatty acid + H+"
[x] Change MetaCyc xref to MetaCyc:RXN-19278

id: GO:0004465 name: lipoprotein lipase activity def: "Catalysis of the reaction: triacylglycerol + H2O = diacylglycerol + a carboxylate, where the triacylglycerol is part of a lipoprotein." [EC:3.1.1.34, GOC:bf] xref: EC:3.1.1.34 is_a: GO:0004806 ! triglyceride lipase activity

EC:3.1.1.34 says: Hydrolyzes triacylglycerols and diacylglycerol in chylomicrons and low-density lipoprotein particles (VLDL). Human protein purified from post-heparin plasma (LPL) shows no activity against triglyceride in the absence of added lipoprotein. The principal reaction sequence of that enzyme is triglyceride -> 1,2-diglyceride -> 2-monoglyceride. The hepatic enzyme (LIPC) also hydrolyzes triglycerides and phospholipids present in circulating plasma lipoproteins.

[x] Append some text to the def to indicate these additional activities.

[x] Make new term for 'diacylglycerol lipase activity': name: diacylglycerol lipase activity def: "Catalysis of the reaction: a diacylglycerol + H2O = a fatty acid + a monoacylglycerol + H+ [RHEA:32731] xref: RHEA:32731 xref: MetaCyc:RXN-19279 is_a: GO:0016298 ! lipase activity

id: GO:0033878 name: hormone-sensitive lipase activity def: "Catalysis of the reactions: diacylglycerol + H2O = monoacylglycerol + a carboxylate; triacylglycerol + H2O = diacylglycerol + a carboxylate; and monoacylglycerol + H2O = glycerol + a carboxylate." [EC:3.1.1.79] xref: EC:3.1.1.79 xref: MetaCyc:TRIACYLGLYCEROL-LIPASE-RXN is_a: GO:0052689 ! carboxylic ester hydrolase activity

This is really a gene product that can catalyse hydrolysis of monoacylglycerols, diacylglycerols, and triacylglycerol - ie. three of the GO terms listed above.

[ ] obsolete this GO term (5 EXP annotations to human LIPE, rat Lipe, human ABHD2, and Arabidopis AtOBL1)
[x] add EC:3.1.1.79 as a broadMatch xref on the three mono/di/triacylglycerol lipase activity GO terms above

id: GO:0004771 name: sterol esterase activity def: "Catalysis of the reaction: a steryl ester + H2O = a sterol + a fatty acid." [EC:3.1.1.13] xref: EC:3.1.1.13 xref: MetaCyc:STEROL-ESTERASE-RXN xref: RHEA:10100 is_a: GO:0016298 ! lipase activity is_a: GO:0052689 ! carboxylic ester hydrolase activity

[x] change name to 'sterol ester esterase activity'
[x] update def to RHEA:10100 'a sterol ester + H2O = a fatty acid + a sterol + H+'
[x] Following point above, remove redundant parent 'GO:0052689 ! carboxylic ester hydrolase activity'

id: GO:0047714 name: galactolipase activity def: "Catalysis of the reaction: 1,2-diacyl-3-beta-D-galactosyl-sn-glycerol + 2 H2O = 3-beta-D-galactosyl-sn-glycerol + 2 carboxylates." [EC:3.1.1.26, MetaCyc:GALACTOLIPASE-RXN] xref: EC:3.1.1.26 xref: MetaCyc:GALACTOLIPASE-RXN xref: RHEA:13189 is_a: GO:0016298 ! lipase activity is_a: GO:0052689 ! carboxylic ester hydrolase activity

[x] update def to RHEA:13189 'a 1,2-diacyl-3-O-(beta-D-galactosyl)-sn-glycerol + 2 H2O = 3-beta-D-galactosyl-sn-glycerol + 2 a fatty acid + 2 H+'
[x] Following point above, remove redundant parent 'GO:0052689 ! carboxylic ester hydrolase activity'
[ ] Merge GO:0102549 (see below) into GO:0047714 (same EC, specific substrate, no EXP annotations)

id: GO:0102549 name: 1-18:1-2-16:0-monogalactosyldiacylglycerol lipase activity def: "Catalysis of the reaction: 1-18:1-2-16:0-monogalactosyldiacylglycerol + H2O = sn-1-lyso-2-16:0-monogalactosyldiacylglycerol + oleate + H+." [EC:3.1.1.26, GOC:pz] xref: EC:3.1.1.26 xref: MetaCyc:RXN-14912 is_a: GO:0052689 ! carboxylic ester hydrolase activity

sjm41 commented 1 week ago

Also:

[x] remove redundant parent 'GO:0052689 ! carboxylic ester hydrolase activity' on GO:0008970 phospholipase A1 activity and GO:0004623 phospholipase A2 activity and GO:0004622 lysophospholipase activity and GO:0052739 phosphatidylserine 1-acylhydrolase activity and GO:0052740 1-acyl-2-lysophosphatidylserine acylhydrolase activity
[x] change parent of GO:0102545 phosphatidyl phospholipase B activity from carboxylic ester hydrolase activity to phospholipase activity

sjm41 commented 1 week ago

[ ] Merge the two terms below into the new term 'diacylglycerol lipase activity' since they represent specific substrates:

id: GO:0102259 (7 annotations, 1 IDA) name: 1,2-diacylglycerol acylhydrolase activity namespace: molecular_function def: "Catalysis of the reaction: H2O + a 1,2-diacyl-sn-glycerol = a monoglyceride + a fatty acid." [GOC:pz, PMID:1477884] xref: MetaCyc:RXN-12434 is_a: GO:0052689 ! carboxylic ester hydrolase activity

id: GO:0102258 (7 annotations, 1 IDA) name: 1,3-diacylglycerol acylhydrolase activity namespace: molecular_function def: "Catalysis of the reaction: H2O + a 1,3-diglyceride = a monoglyceride + a fatty acid." [GOC:pz, PMID:21477884] xref: MetaCyc:RXN-12433 is_a: GO:0052689 ! carboxylic ester hydrolase activity

sjm41 commented 1 week ago

+[Term] +id: GO:0120516 +name: diacylglycerol lipase activity +namespace: molecular_function +def: "Catalysis of the reaction: a diacylglycerol + H2O = a fatty acid + a monoacylglycerol + H+." [RHEA:32731] +xref: EC:3.1.1.79 {source="skos:broadMatch"} +xref: MetaCyc:RXN-19279 {source="skos:exactMatch"} +xref: RHEA:32731 {source="skos:exactMatch"} +is_a: GO:0016298 ! lipase activity +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28339" xsd:anyURI +created_by: sjm +creation_date: 2024-06-28T12:36:24Z +

pgaudet commented 1 week ago

@sjm41 Can you give the reasons for merge? I assume GO:0102549 1-18:1-2-16:0-monogalactosyldiacylglycerol lipase activity is a specific substrate of GO:0102549?

sjm41 commented 1 week ago

Hi @pgaudet Can I leave the merges and obsoletion mentioned above (ie. the open tasks) to you?

pgaudet commented 5 days ago

yes of course

geneontology / go-ontology

lipase activity edits #28339