MP: membrane terms

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See http://wiki.geneontology.org/index.php/XP:cellular\_component\_xp\_self\#X\_membrane

Here are some potential MPs in CC for X-membrane terms. Many of these are false positives but I bring them up to highlight areas of the text definitions requiring clarification.

? "acrosomal membrane" [GO:0002080] is_a "lysosomal membrane" [GO:0005765] This is probably wrong, but I'd like to know exactly why to get the xp def correct. The def of acrosome says it is derived_from the lysosome. So presumably the relation between the membranes is also one of derivation? Also the def of AM is: "The membrane that surrounds the acrosomal lumen". So perhaps this is just the inner membrane....?

? "plasma membrane-derived thylakoid membrane" [GO:0031676] is_a "cytoplasmic vesicle membrane" [GO:0030659] This inference would be true if the def of PMDTM was "a M that sourrounds a PMDT". This would seem to be suggested by the text def: The pigmented membrane of a plasma membrane-derived thylakoid." However, the DAG structure suggests that the genus of the definition should be a portion of the plasma membrane that.... The use of derivation is confusing. Do we just need to use derives_from in GO?

"COPI coated vesicle membrane" [GO:0030663] is_a "Golgi-associated vesicle membrane" [GO:0030660] "synaptic vesicle membrane" [GO:0030672] is_a "clathrin coated vesicle membrane" [GO:0030665] "cyanelle thylakoid membrane" [GO:0033115] part_of "cyanelle thylakoid" [GO:0009843] "prothylakoid membrane" [GO:0042650] is_a "plastid thylakoid membrane" [GO:0055035] "presynaptic active zone membrane" [GO:0048787] is_a "organelle membrane" [GO:0031090]

? "cortical microtubule cytoskeleton" [GO:0030981] part_of "microtubule cytoskeleton" [GO:0015630]

? "flagellin-based flagellum basal body" [GO:0009425] is_a "basal body" [GO:0005932]

? "virion membrane" [GO:0055036] is_a "membrane" [GO:0016020] This one is presumably excluded since the definition of membrane does not mention virions:

"Double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles"

However, it does not exclude virus particles either. It would be nice if we could keep "membrane" univocal

? "cell soma membrane" [GO:0032809] is_a "membrane" [GO:0016020] This inference is definitely based on a wrong xp def; it would be good if the text definition were changed from:

"The plasma membrane of a cell that bears surface projections such as..." to "The portion of the plasma membrane of a cell..."

Switching between count nouns and mass nouns will cause confusion

? "chlorosome envelope" [GO:0033105] is_a "envelope" [GO:0031975]

I think this one is wrong, but it would be good to have univocal use of envelope, and one informative non-part is_a parent. Why not "membrane"? The def is:

"The membrane-like structure, composed of glycolipids and proteins, that encloses the pigments and other contents of the chlorosome." Not membrane-like enough to be a membrane?

? "axolemma" [GO:0030673] is_a "plasma membrane" [GO:0005886] This would seem to be correct from the text def: "The plasma membrane of an axon; it is a specialized trilaminar random mosaic of protein molecules floating within a fluid matrix of highly mobile phospholipid molecules, 7-8 nm in thickness."

However, from the DAG it would seem that the def should be "The portion of plasma membrane covering an axon"

? "flagellar membrane" [GO:0020017] is_a "cell projection membrane" [GO:0031253]

This inference is wrong. I bring it up as the xp def was based on the text def: "The lipid bilayer surrounding the flagellum; continuous with the plasma membrane."

This makes it sound like a separate lipid bilayer, numerically distinct from, but continuous with the PM. In fact this term seems analagous to all the other PM portion terms - so why the difference in wording of the def?

Reported by: cmungall

Original Ticket: "geneontology/ontology-requests/5187":https://sourceforge.net/p/geneontology/ontology-requests/5187

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Original comment by: mah11

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> "acrosomal membrane" [GO:0002080] is_a "lysosomal membrane" [GO:0005765]

It would be perfectly consistent with acrosome is_a lysosome, and the acrosomal membrane def says "The acrosome is a special type of lysosome ...". Obviously I agree they should be consistent, but I don't know which -- is_a or derived_from -- is better.

The acrosomal membrane is a single lipid bilayer, so I don't see any reason why it couldn't have the standard organelle lumen def wording (e.g. see http://worms.zoology.wisc.edu/urchins/SUfert\_acrosome.html). The inner and outer acrosomal membranes aren't separate bilayers, but the portions of the membrane distal and proximal, respectively, to the plasma membrane. This isn't univocal with our use of inner and outer membrane for the parts of a double-membrane organelle envelope, but it is apparently the acrosome-reaction community usage.

I'll ask David to look at all of this, since he did the terms and defs.

> plasma membrane-derived thylakoid membrane" [GO:0031676] is_a "cytoplasmic vesicle membrane" [GO:0030659]

Oh ugh, there are some other problems here too. The DAG structure and text definition for chromatophore (GO:0042716, parent of GO:0031676) don't quite agree -- the text says some, but NOT all, chromatophores are complete vesicles. I'll ask our plant and bacteria people for advice.

> "COPI coated vesicle membrane" [GO:0030663] is_a "Golgi-associated > vesicle membrane" [GO:0030660] > "synaptic vesicle membrane" [GO:0030672] is_a "clathrin coated vesicle > membrane" [GO:0030665] > "cyanelle thylakoid membrane" [GO:0033115] part_of "cyanelle > thylakoid" [GO:0009843] > "prothylakoid membrane" [GO:0042650] is_a "plastid thylakoid membrane" > [GO:0055035]

added

> "presynaptic active zone membrane" [GO:0048787] is_a "organelle > membrane" [GO:0031090]

instead, removed presynaptic active zone GO:0048786 is_a intracellular non-membrane-bounded organelle GO:0043232

> "cortical microtubule cytoskeleton" [GO:0030981] part_of "microtubule cytoskeleton" [GO:0015630]

added

> "flagellin-based flagellum basal body" [GO:0009425] is_a "basal body" [GO:0005932]

two quite different "basal bodies", so I renamed GO:0005932 and two other terms to make the distinction

> "virion membrane" [GO:0055036] is_a "membrane" [GO:0016020] > This one is presumably excluded since the definition of membrane does > not mention virions

The other thing is that membrane is_a cell part, but virion isn't a cell or cell part. Although I agree that univocality would be good, and I'm not opposed to broadening the text or DAG definition of membrane, maybe this should happen in conjunction with a more extensive revamp of the virus-related terms (because I don't know whether the position of virion would change).

> cell soma membrane" [GO:0032809]

def reworded

> "chlorosome envelope" [GO:0033105] is_a "envelope" [GO:0031975] > Not membrane-like enough to be a membrane?

That is actually the case -- it's got lots of lipids, like a membrane, but isn't a lipid bilayer and therefore doesn't fit GO's definition of membrane. It also doesn't quite fit the definition of 'envelope', so I'm willing to consider renaming it if we can come up with something sensible.

Apparently the chlorosome is surrounded by a lipid monolayer with embedded proteins (see PMID: 17303128; that makes the most similar CC term GO:0034430, which has the unwieldy name 'monolayer-surrounded lipid storage body outer lipid monolayer'. We can alter the GO:0033105 definition accordingly, and add a term that can be an is_a parent of GO:0033105 and GO:0034430, but I'm struggling to come up with a decent name. We may have to settle for 'organelle-enclosing lipid monolayer' or something equally clunky.

> "axolemma" [GO:0030673]

def reworded

> "flagellar membrane" [GO:0020017]

def reworded (original wording dates back to about 2002 ...) also added relationship GO:0020017 is_a cell projection membrane GO:0031253

m

Original comment by: mah11

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Original comment by: mah11

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further correspondence on thylakoids, etc

from Debby Siegele, July31:

Hi Midori,

>From scanning the literature and talking with colleagues who work on photosynthesis, I think that the term thylakoid is used almost exclusively for the photosynthetic membranes found in chloroplasts and in cyanobacteria. Personally, I find it confusing that the word "thylakoid" is being used for all photosynthetic organisms. I think of a thylakoid as the stacked photosynthetic membranes that are characteristic of chloroplasts and cyanobacteria.

I think I would modify the first sentence of the definition of GO:0009579 thylakoid to read: " A membraneous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria." Another reason for grouping these together is that chloroplasts are generally accepted to have evolved from an ancestral cyanobacterial endosymbiont.

Could GO:0030075 plasma membrane-derived thylakoid be renamed? Plasma membrane-derived photosynthetic membrane is redundant, but that is all I can think of right now. What sorts of structures are supposed to be annotated to this term? that might help in naming it.

I think the definition and synonyms for GO:0030075 also need to be modified. The current definition is: "A membraneous cellular structure derived from, but not necessarily continuous with, the plasma membrane. It bears the photosynthetic pigments in photosynthetic bacteria." I would change it to "A membraneous cellular structure bearing the photosynthetic apparatus that is derived from, but not necessarily continuous with, the plasma membrane of prokaryotic cells."

> [Should we add this relationship?] > ? "plasma membrane-derived thylakoid membrane" [GO:0031676] is_a > "cytoplasmic vesicle membrane" [GO:0030659]

I'm not sure that this relationship should be added,because I'm not sure that the word vesicle would be used to describe all the membraneous cellular structures bearing the photosynthetic apparatus that are found in photosynthetic prokaryotes. For example, I've attached a jpg file of a diagram of a Chlorobium tepidum cell. The picture was taken from <http://kchf-45.karlov.mff.cuni.cz/~jakub/chlorosome.htm&gt;. I wouldn't call this structure a vesicle, but maybe my mental image of a vesicle is too restricted.

Regards,

Debby

Original comment by: mah11

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more correspondence - my response to previous, Aug. 4:

Hi Debby,

Thanks for your very informative reply, and sorry I haven't got back to it until now. From your mail, the GO structure, and some things I've found online, I think we should have three terms for photosynthetic membrane structures:

- one for thylakoids in plants; 'plastid thylakoid' covers this

• one for thylakoids in cyanobacteria
• one for the photosynthetic membranes in other photosynthetic bacteria

The first two would be grouped under thylakoid (GO:0009579; I've edited the def as you recommended). The second two can be grouped under a term for plasma membrane-derived photosynthetic membrane -- assuming that's biologically accurate. If not, they don't need to be grouped, and the cyanobacterial thylakoid term can have just one parent.

In any case, all three would be descendants of the most general term, 'photosynthetic membrane' (GO:0034357).

Despite the definition wording, I think -- based on the term name and parents -- that GO:0030075 may have been originally intended to represent cyanobacterial thylakoids. But I also suspect that we didn't fully appreciate that the other photosynthetic bacteria have such different photosynthetic membrane structures, whence the muddied specificity of the definition and parents (it was done by me and a former TAIR curator -- neither of us experts on bacteria!).

It might be safest to use GO:0030075 as the broader 'plasma membrane-derived photosynthetic membrane' because of the def/name inconsistency. But if we do that, would there be any difference between GO:0030075 and 'chromatophore' (GO:0042716, defined as "A pigment bearing structure found in certain photosynthetic bacteria and cyanobacteria which is derived from the cytoplasmic membrane, sometimes consisting of simple invaginations and sometimes a complete vesicle.")? If not, they can be merged. The other option is to dclare it to be the term for cyanobacterial thylakoids, and rephrase the definition accordingly. Any preference?

No matter what we do with this term, we can remove the broad synonym 'thylakoid (sensu Bacteria)' because it's a bit misleading; I'll also edit the comment on the obsolete term 'thylakoid (sensu Bacteria)'. We can also move 'chromatophore' from under 'vesicle', since that would fit with both the existing definition and your comments. Can it go under 'plasma membrane-derived photosynthetic membrane'?

Thanks again, Midori

Original comment by: mah11

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Aug. 4th:

Hi Midori,

I haven't finished digesting everything you wrote, but I do have one immediate suggestion. I think that 'plasma-membrane derived photosynthetic membrane structure' might be a better name than 'plasma-membrane derived photosynthetic membrane', which is what I first suggested.

I'll contact a colleague who works on cyanobacteria and ask whether it is accurate to give thylakoids in cyanobacteria the parent of plasma-membrane derived photosynthetic membrane.

>From what I've read, I don't think there is a difference in prokaryotes between chromatophore and photosynthetic membrane. I think the distinction comes from plants, which have plastids that synthesize and store pigments but aren't photosynthetic. In the recent literature, these plastids seems to be more commonly called chromoplasts rather than chromatophores, probably to avoid confusion with "chromatophore" used to refer to pigmented cells in animals.

Regards,

Debby

Original comment by: mah11

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Aug. 5th:

Hi Debby,

> I haven't finished digesting everything you wrote, but I do have one > immediate suggestion. I think that 'plasma-membrane derived > photosynthetic membrane structure' might be a better name than > 'plasma-membrane derived photosynthetic membrane', which is what I first > suggested.

Fine on both counts; I don't mind a bit of time to digest all this myself.

> I'll contact a colleague who works on cyanobacteria and ask whether it > is accurate to give thylakoids in cyanobacteria the parent of > plasma-membrane derived photosynthetic membrane.

Thanks! I'll wait for the expert reply.

Midori

Original comment by: mah11

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Aug 11th:

Hi,

I spoke with Susan Golden in my department who works on photosynthesis in cyanobacteria. She says that oxygenic vs anoxygenic is the key distinction between the photosynthetic membranes of cyanobacteria/chloroplasts and other organisms and suggested that the photosynthetic membrane in prokaryotes other than cyanobacteria be called 'anoxygenic photosynthetic membrane.' Because of the evolutionary relationship and similarities between chloroplasts and cyanobacteria, she didn't like having two separate thylakoid terms for plants and cyanobacteria. She was dubious about connecting the chloroplast photosynthetic membrane to 'plasma-membrane derived photosynthetic membrane' because even though it is likely that it originates from the plasma membrane she doesn't know of any experimental evidence one way or the other.

Susan suggested some names of experts who might be interested in providing input on these GO terms: Robert Blankenship (blankenship@WUSTL.EDU), Don Bryant (dab14@psu.edu), or Carl Bauer (bauer@indiana.edu).

By the way, I was wrong in thinking that chlorosomes were an example of photosynthetic membranes. They're light-harvesting complexes (antennas), but don't have any photosynthetic reaction centers.

Regards,

Debby

Original comment by: mah11

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Aug 13th:

Hi Debby,

On Mon, 11 Aug 2008, Deborah Siegele wrote:

> Hi, > > I spoke with Susan Golden in my department who works on photosynthesis > in cyanobacteria. She says that oxygenic vs anoxygenic is the key > distinction between the photosynthetic membranes of > cyanobacteria/chloroplasts and other organisms and suggested that the > photosynthetic membrane in prokaryotes other than cyanobacteria be > called 'anoxygenic photosynthetic membrane.' Because of the evolutionary > relationship and similarities between chloroplasts and cyanobacteria, > she didn't like having two separate thylakoid terms for plants and > cyanobacteria.

I understand, but I think for GO purposes we can't really avoid having two terms, because of the differences in location: plant thylakoids are located in plastids, whereas cyanobacteria have no plastids. So we have two separate terms, both of which are subtypes of the general 'thylakoid' term, one for thylakoids in plastids and one for thylakoids not found as parts of plastids.

> She was dubious about connecting the chloroplast > photosynthetic membrane to 'plasma-membrane derived photosynthetic > membrane' because even though it is likely that it originates from the > plasma membrane she doesn't know of any experimental evidence one way or > the other.

OK; in that case it would be safer for GO not to make any connection between 'plastid thylakoid' and 'plasma-membrane derived photosynthetic membrane'. That's no problem.

> Susan suggested some names of experts who might be interested in
> providing input on these GO terms: Robert Blankenship > (blankenship@WUSTL.EDU), Don Bryant (dab14@psu.edu), or Carl Bauer
> (bauer@indiana.edu).

Excellent! I'll get in touch if any further questions come up. I think my initial questions are more or less in hand now.

> By the way, I was wrong in thinking that chlorosomes were an example of > photosynthetic membranes. They're light-harvesting complexes > (antennas), but don't have any photosynthetic reaction centers.

OK, I'll make sure that is reflected in the ontology (all I'll have to "do" is leave it as is).

Thanks again for all your help, Midori

Original comment by: mah11

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work done Aug 13th:

moved chromatophore GO:0042716 from is_a cytoplasmic membrane-bounded vesicle GO:0016023 to (direct) is_a cytoplasmic part GO:0044444

removed relationship is_a cytoplasmic vesicle part GO:0044433 from plasma membrane-derived photosystem I GO:0030094 plasma membrane-derived thylakoid membrane GO:0031676 plasma membrane-derived thylakoid photosystem II GO:0030096 plasma membrane-derived thylakoid ribulose bisphosphate carboxylase complex GO:0048493 removed relationships GO:0030094 is_a plastid part GO:0044435 GO:0030096 is_a plastid part GO:0044435

GO:0030075 - removed broad synonym, reworded def to g+d

added organelle-enclosing lipid monolayer GO:0034646 ; made it is_a parent of GO:0033105 and GO:0034430

reworded def GO:0033105

---

I think that fixes everything except the virion membrane item, and I still think that one's going to need at least a bit of the viral-term overhaul, so for now I'll close this.

m

Original comment by: mah11

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Original comment by: mah11

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Hi Midori,

The issue with the acrosomal membrane is just as you say. The community calls the area of the membrane that will contact the egg, the outer membrane and the area away from the egg the inner membrane. They specify this because of the mechanics of the way the acrosomal reaction occurs during fertilization. So these spatial descriptions don't really reflect on the topology of the membrane around the vesicle.

David

Original comment by: ukemi

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Hi David,

Chris and I just had a quick chat about the acrosomal membrane. He says it's OK to keep the acrosome term names as they are, since the 'acrosomal' qualifier provides some distiguishing text, and the definitions are clear. I'll add comments as well.

The original question was about this suggested addition:

> "acrosomal membrane" [GO:0002080] is_a "lysosomal membrane" [GO:0005765]

Is it OK to add this relationship? If so, I will.

m

Original comment by: mah11

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Hi Midori,

According to Gilbert (ISBN:0-87893-243-7)and Alberts (ISBN:0-8240-7282-0) the acrosomal vesicle is actually a modified secretory vesicle. I think it would make more sense to move it to be a child of GO:0030141. Then make the membrane a child of GO:0030667.According to Gilbert, it is derived from the golgi, like all other secretory vesicles.

David

Original comment by: ukemi

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OK, done. Thanks!

Original comment by: mah11

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I think there is still a problem with GO:0009843 ! cyanelle thylakoid

......is_a GO:0031976 ! plastid thylakoid [DEF: "Any thylakoid within a plastid."] .......is_a GO:0009843 ! cyanelle thylakoid [DEF: "Photosynthetic membrane resembling that of cyanobacteria found in the cyanelles of certain algae."] ........is_a GO:0033115 ! cyanelle thylakoid membrane [DEF: "The lipid bilayer membrane of any thylakoid within a cyanelle."] c

The def looks odd in the context of it's is_a parents. Should it not mirror the def of it's parent? Also, should the membrane not be part of rather than is_a the thing it is a membrane of?

Another one: "plasma membrane-derived thylakoid membrane" [GO:0031676] is_a "chromatophore membrane" [GO:0042717]

Original comment by: cmungall

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Original comment by: cmungall

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> GO:0009843 ! cyanelle thylakoid

ouch, it looks like I got the relationship types backwards when I added the term. now fixed; also improved the def.

> "plasma membrane-derived thylakoid membrane" [GO:0031676] is_a > "chromatophore membrane" [GO:0042717]

added.

did a few other fixes in this area as well; details in CVS log and go-diff

Original comment by: mah11

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• status: open-fixed --> closed-fixed

Original comment by: mah11