gas vasicle terms

[gocentral]

Hello,

TIGR annotator MJ Rosovitz alerted me to the need for terms concerning gas vesicles in prokaryotes.

new term 1: "gas vesicle" type: component def: "The gas vesicle is a hollow structure made of protein. It usually has the form of a cylindrical tube closed by conical end caps. Gas vesicles occur in five phyla of the Bacteria and two groups of the Archaea, but they are mostly restricted to planktonic microorganisms, in which they provide buoyancy. By regulating their relative gas vesicle content aquatic microbes are able to perform vertical migrations." (This definition is a direct quote from the abstract of PMID:8177173.) parent: cytoplasmic vesicle (GO:0016023)

NOTE on suggested parent term: "cytoplasmic vesicle" (GO:0016023) currently has the parent "intracellular membrane-bound organelle" (GO:0043231) which seems wrong to me and if that is actually the correct parent then I wil need to request a different parent for the gas vesicle. I think the parent of "cytoplasmic vesicle" should be "intracellular non-membrane-bound organelle" (GO:0043232).

new term 2: "gas vesicle organization and biogenesis" OR "gas vesicle formation" (I'm not sure which name would be best.) type: process def: The process of forming a gas vesicle. parent: cytoplasm organization and biogenesis (GO:0007028)

new term 3: "stuctural constituent of gas vesicle" type: function def: Provides the physical framework for a gas vesicle, a structure containing gases for the purpose of regulating buoyancy in some prokaryotes. parent: structural molecule activity (GO:0005198)

new term 4: "buoyancy regulation" type: process def: The process of regulating an organism's position in a fluid medium by changing the organism's buoyancy, often through the use of stored gases. parent: physiological process (GO:0007582)

Thanks, Michelle

Reported by: mlgwinn

Original Ticket: "geneontology/ontology-requests/2430":https://sourceforge.net/p/geneontology/ontology-requests/2430

[gocentral]

Logged In: YES user_id=436423

Parentage: As far as I know, all eukaryotic vesicles are small membrane-bounded compartments, so the current parentage is correct for eukaryotes. I do not want to lose the information captured in that relationship, so we have two options: we can either have 'sensu' terms for prokaryotic and eukaryotic vesicles, or just put the gas vesicle under 'cytoplasm' or 'intracellular non-membrane- bound organelle', and include a comment explaining why it is not a child of cytoplasmic vesicle.

Which option is better depends in part on what the community would expect. Biologists who work on eukaryotes tend to automatically think of vesicles as membrane-bounded, so will expect the existing arrangement. Do prokaryote biologists have a general concept of 'vesicle' as something not membrane-bounded?

Term #3: We really do not want to add any more 'structural constituent of ...' terms, and we'd like best to obsolete most of the existing ones, because they really represent cellular component or anatomical information (with the possible exception of the parent 'structural molecule activity').

Terms 1, 2, and 4 should be OK once we decide what to do about the varying uses and meanings of 'vesicle'.

midori

Original comment by: mah11

[gocentral]

Logged In: YES user_id=482944

Hi Midori,

How about we change the name of "cytoplasmic vesicle" (GO:0016023) to "cytoplasmic membrane-bound vesicle", since this was the understood nature of this term to begin with, it would not require a change in annotations . Then we can add a new term called "cytoplasmic vesicle" as a child of "intracellular organelle" (GO:0043229). Then my new term "gas vesicle" can be a child of that new cyoplasmic vesicle term and also the old cytoplasmic vesicle term, now named "cytoplasmic membrane-bound vesicle" (GO:0016023) would be a child of the new "cytoplasmic vesicle" term.

I think this would solve it without the creation of any sensu terms and also allowing for the occurance of other non-membrane bound organelles, which are likely to occur in proks.

How does this sound?

Michelle

Original comment by: mlgwinn

[gocentral]

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Hi Michelle,

Thanks for getting back to this. Your idea sounds reasonable. I'd like to run it by the mailing list just because it affects a much-used term, but I'll phrase it as I'll-do-this-next-week- unless-anyone-hollers.

m

Original comment by: mah11

[gocentral]

• assigned_to: nobody --> gomidori

Original comment by: mah11

[gocentral]

Logged In: YES user_id=436423

OK, I've done the changes to 'cytoplasmic vesicle':

• GO:0016023 is now 'cytoplasmic membrane-bound vesicle'
• new term GO:0031410 is 'cytoplasmic vesicle'

also added gas vesicle GO:0031411 gas vesicle organization and biogenesis GO:0031412 buoyancy regulation GO:0031413

G:0031412 has exact synonym 'gas vesicle formation' and is_a 'vesicle organization and biogenesis' (GO:0016050), and therefore indirectly under GO:0007582.

Original comment by: mah11

[gocentral]

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

Original comment by: mah11

[gocentral]

Logged In: YES user_id=482944

This is great - Thanks Midori.

Michelle

Original comment by: mlgwinn

[gocentral]

Logged In: YES user_id=436423 Originator: NO

Note: in the is_a-complete biological process, there will be some changes to GO:0031413 for consistency with other regulation terms and improved parentage.

- renamed to 'regulation of buoyancy' (old wording, 'buoyancy regulation', kept as exact synonym

• reworded definition so it's not mistaken for locomotion
• made is_a regulation of biological quality (GO:0065008)

These changes aren't in the live GO yet, but will be when the is_a-complete work is merged in.

m

Original comment by: mah11