high-density lipoprotein assembly/disassembly

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Hi

please could the following term be created

Parent: GO:0042159 lipoprotein catabolic process >NTR:high-density lipoprotein catabolic process

definition: The chemical reactions and pathways resulting in the breakdown of high-density lipoproteins, one of the classes of lipoproteins found in the bloodstream of animals, acting as a carrier for cholesterol and fats.

synonyms: HDL catabolic process HDL catabolism high-density lipoprotein breakdown high-density lipoprotein catabolism high-density lipoprotein degradation

Note the term low-density lipoprotein catabolic process already exists.

I would like to add this term to CETP P11597 using IMP PMID: 2586614

Thanks and have a great festive season

Ruth

Reported by: RLovering

Original Ticket: "geneontology/ontology-requests/4672":https://sourceforge.net/p/geneontology/ontology-requests/4672

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Hi Sorry

should have also requested

Parent: GO:0042157 lipoprotein metabolic process > NTR:high-density lipoprotein metabolic process >>NTR:high-density lipoprotein catabolic process > NTR:low-density lipoprotein metabolic process >>GO:0045192: low-density lipoprotein catabolic process

definitions/synonyms: > NTR:high-density lipoprotein metabolic process The chemical reactions and pathways involving high-density lipoproteins. synonym: HDL metabolism, high-density lipoprotein metabolism
> NTR:low-density lipoprotein metabolic process The chemical reactions and pathways involving low-density lipoproteins. synonym: LDL metabolism, low-density lipoprotein metabolism

Original comment by: RLovering

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This sounds wrong (and by implication, so does GO:0045192 low-density lipoprotein catabolic process. Following on from the discussion of CETP function (SourceForge 1852651 2007-12-17 12:18 lipid transfer) most of the actual molecular events to be covered here involve the transfer of an intact lipid or protein molecule from one extracellular lipoprotein complex to another, or between an extracellular lipoprotein complex and a cell. No covalent bonds are made or broken.

There are also lipases that can catalyze the hydrolysis of lipids (mostly, triacylglycerol) associated with an extracellular lipoprotein. Most of these are associated with cells or extracellular matrix and are thought to facilitate the transfer of lipid from the lipoprotein into cells.

A lipoprotein is a dynamic structure. It forms as a nucleation event involving a particular apolipoprotein produced in a particular cell type (the exact type of cell and protein varies according to the kind of lipoprotein) and a number of lipid molecules (again varying in type according to the type of particle being formed) and is released into the blood or lymph where it exchanges proteins and lipids with other particles and cells, and ultimately is endocytosed, mostly by liver cells in humans, and degraded. Thus, the constant, defining feature of a lipoprotein is its original apolipoprotein, and its biological function requires it to change many other features of its composition in the course of its life cycle.

This story is good for humans and, mostly, for rodents. I'm not aware that it's been studied in detail in many other organisms, but there's no reason to expect lipid trafficking to be particularly well conserved evolutionarily among multicellular organisms.

This is also relevant to the new term request for high density lipoprotein (1852674 2007-12-17 13:20 high density lipoprotein).

Peter D'E Reactome

Original comment by: deustp01

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• assigned_to: nobody --> gomidori

Original comment by: mah11

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We've decided on "complex disassembly" terms instead, and will add "complex assembly" terms as well. I'll add details here once Ruth has put the lipoprotein complex terms and definitions (new draft) into SF 1852674.

I think we would also want to make GO:Q0045192 obsolete, to be superseded by "low-density lipoprotein complex disassembly".

m

Original comment by: mah11

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You may not need all of these terms, but take a look and let me know what you think ... m

[Term] id: newGO:0100012 name: plasma lipoprotein particle assembly namespace: cellular_component def: "The aggregation, arrangement and bonding together of proteins and lipids to form a plasma lipoprotein particle." [GOC:mah] is_a: GO:0065005 ! protein-lipid complex assembly

[Term] id: newGO:0100013 name: mature chylomicron assembly namespace: cellular_component def: "The aggregation, arrangement and bonding together of proteins and lipids to form a mature chylomicron." [GOC:mah] is_a: newGO:0100034 ! chylomicron assembly

[Term] id: newGO:0100014 name: nascent chylomicron assembly namespace: cellular_component def: "The aggregation, arrangement and bonding together of proteins and lipids to form a nascent chylomicron." [GOC:mah] is_a: newGO:0100034 ! chylomicron assembly

[Term] id: newGO:0100015 name: chylomicron remnant assembly namespace: cellular_component def: "The aggregation, arrangement and bonding together of proteins and lipids to form a chylomicron remnant." [GOC:mah] is_a: newGO:0100034 ! chylomicron assembly

[Term] id: newGO:0100016 name: low-density lipoprotein class particle assembly namespace: cellular_component def: "The aggregation, arrangement and bonding together of proteins and lipids to form a low-density lipoprotein class particle." [GOC:mah] is_a: newGO:0100012 ! plasma lipoprotein particle assembly

[Term] id: newGO:0100017 name: very-low-density lipoprotein particle assembly namespace: cellular_component def: "The aggregation, arrangement and bonding together of proteins and lipids to form a very-low-density lipoprotein particle." [GOC:mah] is_a: newGO:0100016 ! low-density lipoprotein class particle assembly

[Term] id: newGO:0100018 name: low-density lipoprotein particle assembly namespace: cellular_component def: "The aggregation, arrangement and bonding together of proteins and lipids to form a low-density lipoprotein particle." [GOC:mah] is_a: newGO:0100016 ! low-density lipoprotein class particle assembly

[Term] id: newGO:0100019 name: intermediate-density lipoprotein particle assembly namespace: cellular_component def: "The aggregation, arrangement and bonding together of proteins and lipids to form an intermediate-density lipoprotein particle." [GOC:mah] is_a: newGO:0100016 ! low-density lipoprotein class particle assembly

[Term] id: newGO:0100020 name: high-density lipoprotein class particle assembly namespace: cellular_component def: "The aggregation, arrangement and bonding together of proteins and lipids to form a high-density lipoprotein particle." [GOC:mah] is_a: newGO:0100012 ! plasma lipoprotein particle assembly

[Term] id: newGO:0100021 name: high-density lipoprotein particle, subclass 2 assembly namespace: cellular_component def: "The aggregation, arrangement and bonding together of proteins and lipids to form a high-density lipoprotein particle of subclass 2." [GOC:mah] is_a: newGO:0100020 ! high-density lipoprotein class particle assembly

[Term] id: newGO:0100022 name: high-density lipoprotein particle, subclass 3 assembly namespace: cellular_component def: "The aggregation, arrangement and bonding together of proteins and lipids to form a high-density lipoprotein particle of subclass 3." [GOC:mah] is_a: newGO:0100020 ! high-density lipoprotein class particle assembly

[Term] id: newGO:0100023 name: plasma lipoprotein particle disassembly namespace: cellular_component def: "The disaggregation of a plasma lipoprotein particle into its constituent components." [GOC:mah] is_a: GO:0032987 ! protein-lipid complex disassembly

[Term] id: newGO:0100024 name: mature chylomicron disassembly namespace: cellular_component def: "The disaggregation of a mature chylomicron into its constituent components." [GOC:mah] is_a: newGO:0100035 ! chylomicron disassembly

[Term] id: newGO:0100025 name: nascent chylomicron disassembly namespace: cellular_component def: "The disaggregation of a nascent chylomicron into its constituent components." [GOC:mah] is_a: newGO:0100035 ! chylomicron disassembly

[Term] id: newGO:0100026 name: chylomicron remnant disassembly namespace: cellular_component def: "The disaggregation of a chylomicron remnant into its constituent components." [GOC:mah] is_a: newGO:0100035 ! chylomicron disassembly

[Term] id: newGO:0100027 name: low-density lipoprotein class particle disassembly namespace: cellular_component def: "The disaggregation of a low-density lipoprotein class particle into its constituent components." [GOC:mah] is_a: newGO:0100023 ! plasma lipoprotein particle disassembly

[Term] id: newGO:0100028 name: very-low-density lipoprotein particle disassembly namespace: cellular_component def: "The disaggregation of a very-low-density lipoprotein particle into its constituent components." [GOC:mah] is_a: newGO:0100027 ! low-density lipoprotein class particle disassembly

[Term] id: newGO:0100029 name: low-density lipoprotein particle disassembly namespace: cellular_component def: "The disaggregation of a low-density lipoprotein particle into its constituent components." [GOC:mah] is_a: newGO:0100027 ! low-density lipoprotein class particle disassembly

[Term] id: newGO:0100030 name: intermediate-density lipoprotein particle disassembly namespace: cellular_component def: "The disaggregation of an intermediate-density lipoprotein particle into its constituent components." [GOC:mah] is_a: newGO:0100027 ! low-density lipoprotein class particle disassembly

[Term] id: newGO:0100031 name: high-density lipoprotein class particle disassembly namespace: cellular_component def: "The disaggregation of a high-density lipoprotein particle into its constituent components." [GOC:mah] is_a: newGO:0100023 ! plasma lipoprotein particle disassembly

[Term] id: newGO:0100032 name: high-density lipoprotein particle, subclass 2 disassembly namespace: cellular_component def: "The disaggregation of a high-density lipoprotein particle of subclass 2 into its constituent components." [GOC:mah] is_a: newGO:0100031 ! high-density lipoprotein class particle disassembly

[Term] id: newGO:0100033 name: high-density lipoprotein particle, subclass 3 disassembly namespace: cellular_component def: "The disaggregation of a high-density lipoprotein particle of subclass 3 into its constituent components." [GOC:mah] is_a: newGO:0100031 ! high-density lipoprotein class particle disassembly

[Term] id: newGO:0100034 name: chylomicron assembly namespace: cellular_component def: "The aggregation, arrangement and bonding together of proteins and lipids to form a chylomicron." [GOC:mah] is_a: newGO:0100012 ! plasma lipoprotein particle assembly

[Term] id: newGO:0100035 name: chylomicron disassembly namespace: cellular_component def: "The disaggregation of a chylomicron into its constituent components." [GOC:mah] is_a: newGO:0100023 ! plasma lipoprotein particle disassembly

Original comment by: mah11

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• summary: high-density lipoprotein catabolic process --> high-density lipoprotein assembly/disassembly

Original comment by: mah11

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Hi Midori

I think you may have covered this point by email, but I just thought I would add it here to make sure it doesn't get forgotten.

I like these assembly and disassembly terms, but they are listed as cellular_component and I think should be molecular_process.

Regards

Ruth

Original comment by: RLovering

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Well spotted! That will indeed be corrected when the terms go in.

midori

Original comment by: mah11

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Hi Midori

I had word with Philippa about plasma lipoprotein assembly and disassembly. Although lipoproteins are assembled, the disassembly aspect is more complex, it involves the metabolism of cholesterol and triglycerides and the formation of remnant particles. She does not think that disassembly really describes this process, and certainly I can't find any use of this phrase in the literature. The 'disassembly' of these plasma lipoproteins is probably better covered by the terms relating to cholesterol and triglyceride etc metabolism. Although people do discuss HDL metabolism and catabolism. For example in a book Philippa lent me (a pocket picture book!) it states that CETP catalyses the transfer of Cholesterol esters from mature HDL and LDL particles to triglyceride rich lipoproteins. Triglyceride is simultaneously transferred in the reverse direction to the HDL and LDL particles. So the plasma lipoproteins are not disassembled it is more like they are being constantly rearranged! I think we should try to avoid suggesting GO terms using phrases which aren't used in the literature.

Original comment by: RLovering

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Hi Ruth,

I think the earlier arguments against terms like "HDL catabolism" stand, but if "HDL disassembly" would not be useful, we don't have to add them.

One thing we could do is add 'related' synonyms to the relevant cholesterol, triglyceride, etc. terms. If that would help, I'll be back to ask for specifics of which terms get which synonyms.

midori

Original comment by: mah11

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GO:0045192 and its children, GO:0045193 and GO:0045194 made obsolete.

Original comment by: mah11

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Hi Midori

lipoprotein clearance is a phrase used with these lipoprotein particles (see PMID: 9649566), so perhaps we could have assembly and clearance?

Ruth

Original comment by: RLovering

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"Assembly" is good for the process by which a lipoprotein particle is created, and "clearance" is good for the process by which it's destroyed (after "clearance" via receptor binding into a coated vesicle and then into an endosome, it's just another batch of lipids and proteins to be catabolized, I think).

Is there a term needed for the process(es) by which a circulating lipoprotein particle swaps lipids and proteins with other particles and with cell surfaces? It's certainly a distinct phase of the lipoprotein life cycle; I can't think of a neat term to summarize it.

Peter D'E

Original comment by: deustp01

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I'm happy to use 'clearance' instead of 'disassembly'; for definitions, could they be based on this?

- The process by which a lipoprotein particle is removed from the blood via receptor-mediated and its constituent parts degraded.

Please correct any errors in the above; I just made it up using my own interpretation of comments here!

At some point, GO may add a "has_part" relationship, which we could use to link lipoprotein clearance to the various relevant catabolic processes (using part_of would create true path violations).

I'm intrigued by the suggestion to include terms for the exchange of lipids and proteins during the lipoprotein life cycle, although so far I've also failed to come up with good term names. I'll keep thinking!

m

Original comment by: mah11

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Add a word to your definition?

The process by which a lipoprotein particle is removed from the blood via receptor-mediated endocytosis and its constituent parts degraded.

Peter

Original comment by: deustp01

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Thanks for the additional word -- I'm sure I was thinking it, but apparently I didn't type it. Glad the definition passes muster otherwise.

m

Original comment by: mah11

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As noted in earlier comments, we've decided on 'clearance' terms rather than 'disassembly'.

In a more recent email exchange, we've chosen to add fewer 'assembly' terms, and to include a set of 'remodeling' terms.

Assembly terms included: newGO:0100012 plasma lipoprotein particle assembly newGO:0100013 chylomicron assembly newGO:0100017 very-low-density lipoprotein particle assembly newGO:0100020 high-density lipoprotein class particle assembly

Remodeling terms: [Term] id: newGO:0100030 name: macromolecular complex remodeling namespace: biological_process def: "The acquisition, loss, or modification of molecules within a complex. The remodeling process begins with an existing complex, and ends with an altered complex." [GOC:mah, GOC:rl] is_a: GO:0043170: macromolecule metabolic process

[Term] id: newGO:0100031 name: protein-lipid complex remodeling namespace: biological_process def: "The acquisition, loss or modification of a protein or lipid within a protein-lipid complex." [GOC:mah, GOC:rl] is_a: newGO:0100030 ! macromolecular complex remodeling

[Term] id: newGO:0100032 name: plasma lipoprotein particle remodeling namespace: biological_process def: "The acquisition, loss or modification of a protein or lipid within a plasma lipoprotein particle, including the hydrolysis of triglyceride by hepatic lipase, with the subsequent loss of free fatty acid, and the esterification of cholesterol by phosphatidylcholine-sterol O-acyltransferase (lecithin cholesterol acyltransferase; LCAT)." [GOC:mah, GOC:rl, GOC:expert_pt] is_a: newGO:0100031 ! protein-lipid complex remodeling

[Term] id: newGO:0100033 name: triglyceride-rich lipoprotein particle remodeling namespace: biological_process def: "The acquisition, loss or modification of a protein or lipid within a triglyceride-rich lipoprotein particle, including the hydrolysis of triglyceride by lipoprotein lipase, with the subsequent loss of free fatty acid, and the transfer of cholesterol esters to a triglyceride-rich lipoprotein particle by cholesteryl ester transfer protein (CETP), with the simultaneous transfer of triglyceride from a triglyceride-rich lipoprotein particle." [GOC:mah, GOC:rl, GOC:expert_pt] is_a: newGO:0100032 ! plasma lipoprotein particle remodeling

[Term] id: newGO:0100034 name: chylomicron remodeling namespace: biological_process def: "The acquisition, loss or modification of a protein or lipid within a chylomicron, including the hydrolysis of triglyceride by lipoprotein lipase and the subsequent loss of free fatty acid." [GOC:mah, GOC:rl, GOC:expert_pt] synonym: "chylomicron remnant formation" RELATED [] is_a: newGO:0100033 ! triglyceride-rich lipoprotein particle remodeling

[Term] id: newGO:0100035 name: very-low-density lipoprotein particle remodeling namespace: biological_process def: "The acquisition, loss or modification of a protein or lipid within a very-low-density lipoprotein particle, including the hydrolysis of triglyceride by hepatic lipase or lipoprotein lipase and the subsequent loss of free fatty acid." [GOC:mah, GOC:rl, GOC:expert_pt] synonym: "VLDL remodeling" EXACT [] synonym: "intermediate-density lipoprotein particle formation" RELATED [] synonym: "IDL formation" RELATED [] is_a: newGO:0100033 ! triglyceride-rich lipoprotein particle remodeling

[Term] id: newGO:0100036 name: intermediate-density lipoprotein particle remodeling namespace: biological_process def: "The acquisition, loss or modification of a protein or lipid within an intermediate-density lipoprotein particle." [GOC:mah, GOC:rl, GOC:expert_pt] synonym: "IDL remodeling" EXACT [] synonym: "low-density lipoprotein particle formation" RELATED [] synonym: "LDL formation" RELATED [] is_a: newGO:0100033 ! triglyceride-rich lipoprotein particle remodeling

[Term] id: newGO:0100037 name: low-density lipoprotein particle remodeling namespace: biological_process def: "The acquisition, loss or modification of a protein or lipid within a low-density lipoprotein particle, including the hydrolysis of triglyceride by hepatic lipase, with the subsequent loss of free fatty acid, and the transfer of cholesterol esters from LDL to a triglyceride-rich lipoprotein particle by cholesteryl ester transfer protein (CETP), with the simultaneous transfer of triglyceride to LDL." [GOC:mah, GOC:rl, GOC:expert_pt] synonym: "LDL remodeling" EXACT [] is_a: newGO:0100012 ! plasma lipoprotein particle remodeling

[Term] id: newGO:0100038 name: high-density lipoprotein particle remodeling namespace: biological_process def: "The acquisition, loss or modification of a protein or lipid within a high-density lipoprotein particle, including the hydrolysis of triglyceride by hepatic lipase, with the subsequent loss of free fatty acid, and the transfer of cholesterol esters from LDL to a triglyceride-rich lipoprotein particle by cholesteryl ester transfer protein (CETP), with the simultaneous transfer of triglyceride to LDL." [GOC:mah, GOC:rl, GOC:expert_pt] synonym: "HDL remodeling" EXACT [] is_a: newGO:0100012 ! plasma lipoprotein particle remodeling

[Term] id: newGO:0100039 name: conversion of discoidal high-density lipoprotein to spherical high-density lipoprotein namespace: biological_process def: "The process by which a discoidal high-density lipoprotein (HDL) particle acquires additional lipid or protein molecules, and cholesterol in the particle is converted to tightly bound cholesterol esters by the action of phosphatidylcholine-sterol O-acyltransferase (lecithin cholesterol acyltransferase; LCAT), resulting in the formation of a spherical HDL particle." [GOC:pd; GOC:mah] synonym: "conversion of discoidal HDL to spherical HDL" EXACT [] synonym: "discoidal high-density lipoprotein remodeling" RELATED [] synonym: "discoidal HDL remodeling" RELATED [] is_a: newGO:0100012 ! plasma lipoprotein particle remodeling

Original comment by: mah11

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clearance terms included so far, based on Peter's summary document:

[Term] id: newGO:0100041 name: chylomicron remnant clearance namespace: biological_process def: "The process by which a chylomicron remnant is removed from the blood via receptor-mediated endocytosis into liver cells and its constituent parts degraded." [GOC:mah, GOC:pd] is_a: newGO:0100040

[Term] id: newGO:0100042 name: low-density lipoprotein particle clearance namespace: biological_process def: "The process by which a low-density lipoprotein particle is removed from the blood via receptor-mediated endocytosis and its constituent parts degraded." [GOC:mah] synonym: "LDL clearance" EXACT [] is_a: newGO:0100040

[Term] id: newGO:0100043 name: high-density lipoprotein particle clearance namespace: biological_process def: "The process by which a high-density lipoprotein particle is removed from the blood via receptor-mediated endocytosis and its constituent parts degraded." [GOC:mah] synonym: "HDL clearance" EXACT [] is_a: newGO:0100040

Original comment by: mah11

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added GO:0034367 macromolecular complex remodeling GO:0034368 protein-lipid complex remodeling GO:0034369 plasma lipoprotein particle remodeling GO:0034370 triglyceride-rich lipoprotein particle remodeling GO:0034371 chylomicron remodeling GO:0034372 very-low-density lipoprotein particle remodeling GO:0034373 intermediate-density lipoprotein particle remodeling GO:0034374 low-density lipoprotein particle remodeling GO:0034375 high-density lipoprotein particle remodeling GO:0034376 conversion of discoidal high-density lipoprotein to spherical high-density lipoprotein GO:0034377 plasma lipoprotein particle assembly GO:0034378 chylomicron assembly GO:0034379 very-low-density lipoprotein particle assembly GO:0034380 high-density lipoprotein particle assembly GO:0034381 lipoprotein particle clearance GO:0034382 chylomicron remnant clearance GO:0034383 low-density lipoprotein particle clearance GO:0034384 high-density lipoprotein particle clearance

Original comment by: mah11

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• status: open --> open-accepted

Original comment by: mah11

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Hi Midori have been going back through proteins trying to get these new terms in use. And realised that I could do with the term to cover clearance of VLDL particles. Eg APOE P02649 IMP PMID: 9649566 replacement of mouse Apoe with mutant human APOE leads to defective VLDL clearance.

GO:0034381:lipoprotein particle clearance >is_a NTR:very low-density lipoprotein particle clearance

definition: The process by which a very-low-density lipoprotein particle is removed from the blood via receptor-mediated endocytosis and its constituent parts degraded.

synonym exact: VLDL clearance

Thanks

Ruth

Original comment by: RLovering

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no problem - added very-low-density lipoprotein particle clearance GO:0034447

Original comment by: mah11

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• status: open-accepted --> closed-accepted

Original comment by: mah11