New term 'organelle' for component ontology

[gocentral]

Add a new term 'organelle' to the component ontology. Should be useful for filling in missing is-a links and for searching. This arose from August content meeting.

Reported by: jl242

Original Ticket: "geneontology/ontology-requests/1980":https://sourceforge.net/p/geneontology/ontology-requests/1980

[gocentral]

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We had a think about this and came up with the following:

organelle def: Organized cytoplasmic structures of distinctive morphology and function. Including the nucleus, mitochondria, plastids, vacuoles, vesicles and ribosomes. Excluding the plasma membrane and cytoskeleton.

dag as follows:

%cellular_component -%organelle --%intracellular organelle --%extracellular organelle

The extracellular organelle that we thought of is "extracellular membrane vesicles (EMVs)" explained at http://www.postech.ac.kr/bk21/mls/en\_dmls/ e_faculty/e_facu_gys.html.

Original comment by: jenclark

[gocentral]

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picky language bit: should say 'includes|excludes' rather than 'including|excluding', and both can be put in one sentence instead of two fragments

biological content bit: the process ontology has this:

%cell organization and biogenesis ; GO:0016043 -%cytoplasm organization and biogenesis ; GO:0007028 --%organelle organization and biogenesis ; GO:0006996 ---%cytoskeleton organization and biogenesis ; GO:0007010 ---%plasma membrane organization and biogenesis ; GO:0007009

... the ontologies should be consistent with each other (I don't have strong feelings about which gets changed, tho I'd never heard of those extracellular vesicles before)

Original comment by: mah11

[gocentral]

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I think we should change the process ontology - most biologists wouldn't think of the cytoskeleton as an organelle I don't think.

I'd never heard of that extracellular vesicle thing either, but there's bound to be some weird organism that has one sooner or later! There are also other references in the literature to other extracellular organelles, so think we do need the child terms.

Original comment by: jl242

[gocentral]

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I think we should define organelles as

A membrane-bound structure within the cytoplasm of a cell that is organised to perform a specific cellular function. These are separated from each other and the cytoplasm of the cell by their own membranes. In other words, organelles partition the cell into regions which carry out different cellular functions.

Thus excluding plasma membrane, cytoskeleton and ribosomes.

for extra cellular vesicles see refs http://jcs.biologists.org/cgi/reprint/106/2/657.pdf http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=216700

Original comment by: jaiswalp

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Pankaj - we'd like to include ribosomes though really - they're often referred to as organelles in the literature e.g. PMID: 15112238, http://en.wikipedia.org/wiki/Ribosome, http://cancerweb.ncl.ac.uk/cgi-bin/omd?ribosome

Original comment by: jl242

[gocentral]

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Ribosomes are definitely thought of as organelles. Interestingly, I had a student ask me about what exactly is an organelle a couple of weeks ago. Certainly the membrane-bound stuff; but, ribosomes are listed as organelles. Some dictionaries merely say that an organelle is a discrete structure within a cell, or any complex structure that froms in the cell. and ribosomes are listed, as well as spindles and centrioles (defined as a elf- reproducing cellular organelle composed of peripher microtubles..), which are formed by components of the microtubule cytoskeleton. Thus, we have to be careful about excluding the cytoskeleton. Actually, a chromsome should be counted as an organelle also. Although a usual distinction between prokaryotes and eukaryotes is the presence or absence of membrane-bound organelles, they aren't the only organelles.

Original comment by: hdrabkin

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I don't really have any feelings as to whether or not we should include the cytoskeleton - do you think we should Harold?

Original comment by: jl242

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Hi Jane I just got off the phone with Paul Matsudaira, co-author of the Lodish, et al. Moelcular Cell Biology texts. He is also an expert in the cytoskeleton field. Although the ribosomes, spindles, asters, etc. have been thought by some to be considered organelles. he currently things of these as "machines" that carry out complex functions; organelles, on the other hand, have an aspect of compartmentalizating a subset of processes and functions; hence, he would think of them as "membrane bound" (although, he thought having organelle, with non-membrane enclosed and membrane-enclosed might work; but then, the mitochondrial ribosomes would be organelles within an organelle.

He also suggested looking at the Nature encyclopedia of life science. Nancy J. Lane wrote:

"Cells are living entities made up of a central nuclear region which contains the hereditary material, surrounded on all sides by cytoplasm,
which, encompassed by a delimiting membrane, contains all the structures
required for biological processes, such as making protein and extracting
utilizable energy from food. These events may occur in separate compartments, the organelles, which include the endoplasmic reticulum, the Golgi apparatus, the mitochondria, the chloroplasts and the lysosomes; there is also an internal cytoskeleton."

Note that the cytoskeleton is considered separately. I can't read more of the article without paying; we don't have an access subscription; perhaps you guys do?

Original comment by: hdrabkin

[gocentral]

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I am afraid by including ribosomes and cytoskeleton we are getting into a situation where organelles are part of organelles, which should avoid.

-both ribosomes and cytoskeletons are for example found in plastid and mitochondria. -ribosomes are found bound to the ER (rough ER) and nuleolemma and may be to the plasma membrane in some organisms.

Though some authors have used "organell" terms to classify their cell part, I think in GO the "organelle" should be limited to the components, which have their own envelope (membrane) and self replicative.

Original comment by: jaiswalp

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I don't really have any particular opinion about which way we define organelle as long as we can reach a consensus,

but

I don't see the problem with having an organelle within an organelle, we can handle it fine within our structure:

organelle ---[i] ribosome ------[i] mitochondrial ribosome ---[i] mitochondrion ------[p] mitochondrial ribosome

Original comment by: jl242

[gocentral]

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Thinking about it over the weekend, I think it might be safe to go orgnaelle ...membrane-bound organelle ...non-membrane-bound organelle

simply because even after talking with Paul, and reading that article he suggesed, I know that there are biologists that will be expecting a search on organelle to include ribosomes, centrioles, asters, etc. (I could not convince serveral people here that they were not organelles).

Original comment by: hdrabkin

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May be we should seek the opinion from other experts on ribosomes. As I said, based on the membrane bound ("bound" probably means enveloped by a membrane and NOT stuck to a membrane), definition, ribosomes are not suggested to be organelles. They are nucleoprotein complexes just like any other protein complex.

I a sure plant people will never search for ribosomes under Organelles as instances (is_a). As part_of is fine.

-Pankaj

Original comment by: jaiswalp

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Pankaj: unfortunately, if you look in "Plant Biology", by Rost, et al, a fairly new textbook, they refer to ribosomes as organelles of protein synthesis.
I think wemay have to accomodate some history. -hjd

Original comment by: hdrabkin

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I think having membrane bound and non-membrane bound organelle would be fine.

Pankaj - ribosome will still have its current parents - organelle will just be additional. So I can't see a problem with people not finding the correct terms. And if some biologists think of ribosomes as organelles, it seems sensible to have them listed under organelle.

Original comment by: jl242

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Fine with me. -Pankaj

Original comment by: jaiswalp

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Added the following new terms:

organelle ; GO:0043226 ---[i] extracellular organelle ; GO:0043230 ---[i] intracellular organelle ; GO:0043229 ------[i] intracellular membrane-bound organelle ; GO:0043231 ------[i] intracellular non-membrane-bound organelle ; GO:0043232 ---[i] membrane-bound organelle ; GO:0043227 ------[i] intracellular membrane-bound organelle ; GO:0043231 ---[i] non-membrane-bound organelle ; GO:0043228 ------[i] intracellular non-membrane-bound organelle ; GO:0043232

And made the appropriate parenatge. Please let me know if I've missed anything...

Original comment by: jl242

[gocentral]

• status: open --> closed-accepted

Original comment by: jl242