Missing Parent: cell wall catabolic process

[gocentral]

add cell wall organization and biogenesis

Reported by: ValWood

Original Ticket: "geneontology/ontology-requests/4412":https://sourceforge.net/p/geneontology/ontology-requests/4412

[gocentral]

Logged In: YES user_id=516865 Originator: YES

I see this can't have this parent because of the other organims terms....

I need a term under here that I can annotate to (I still have the outstanding problems with the chitin terms from the sensu overhaul (used to be sensu fungi, but now is chitin, pombe doesn't have chitin) is anybody looking into this?

Original comment by: ValWood

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I see this can't have this parent because of the other organims terms....

I need a term under here that I can annotate to (I still have the outstanding problems with the chitin terms from the sensu overhaul (used to be sensu fungi, but now is chitin, pombe doesn't have chitin) is anybody looking into this?

Original comment by: ValWood

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I don't know whose can of worms this is :). an you do 'cellular polysaccharide catabolic process'? Kind of unsatisfying because it doesn't have the cell wall bit in it. If I understand you correctly, you need a term that's more specific than 'cell wall catabolic process' but that's not any of the existing terms, right?

Found a paper that talks about beta-glucan and alpha-galactomannan in the S. pombe cell wall.

http://www.springerlink.com/content/w3481014987354w2/

Maybe it's time for

'beta-glucan containing cell wall biogenesis/catabolism/metabolic process'

?

Original comment by: tberardini

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I can do but I still need a cell wall organization ....term,

What happen was that previusly this was cell wall sensu fungi, which was fine. This was cahnged to the chitin containing cell wall terms but pombe cell walls are not thought to contain chitin (only spores).

We could have beta-glucan containing cell wall (which would also apply to plants right?)....the composition of pombe cell walls in't known in detail, which is part of the problem.

I'd like to use terms which put these cell wall catabolic processes under cell wall org and bio, because we have a big cell wall community (despite not knowing what it is!), and I'd like to ensure cell wall organization capture everything it should ......

Original comment by: ValWood

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Putting the composition-specific child terms aside for a moment ...

The offending term, 'cell wall peptidoglycan catabolic process in another organism', is already a problem because it has parents that violate the disjoint thing anyway, so we'll have to fix it somehow. Adding 'cell wall catabolic process' is_a 'cell wall metabolic process' isn't going to make the disjoint violation any worse, or any harder to fix.

So I've added the relationship cell wall catabolic process GO:0016998 is_a cell wall metabolic process GO:0010382.

m

Original comment by: mah11

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Could it be time to pull in someone from the pombe cell wall community to help us sort this out?

Original comment by: tberardini

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I don't know if this will help, because the is no more information about the conposition at present and I need a term which all my existing annotations can be transferred to (i.e with the same meaning as cell wall sensu fungi) but that doesn't contain the word chitin.

The problem is that in the sensu overhaul the definition of this term was changed to include the word chitin (is this allowed?), and now my annotations are incorrect. They were fine before.....

I can go with the beta glucan term, but I'd need to reannotate everything.

(PS sorry about my appallin typing in this thread, I can barly work out what I mean re-reading)

Original comment by: ValWood

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Arg. I think when the sensu group renamed that term we didn't know that pombe walls don't have chitin (tho you may have told us ... oops). So we will have to rename that term again, and remove the reference to chitin; the current name and def would work for a new term ...

I've emailed David and Jen to look at this and the formerly-sensu-fungi terms.

m

p.s. if you can get someone from the community to help, that would be great!

Original comment by: mah11

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Actually, we had this discussion when we renamed the term and we went round and round about it. I thought it was still controversial whether or not pombe had chitin in its cell wall and Val was going to check with experts. I remember reading a paper where a someone dried down the pombe cell wall and detected chitin, but then other folks said they didn't detect chitin. If the community thinks they do not have chitin, we can remove chitin from the name only if the other types of cell walls in the ontology don't contain beta-glucan. I'm not sure this is true. Otherwise, maybe we need to make a separate type of cell wall for pombe. The issue here would be that we would need to find the distinguishing feature of the pombe cell wall. Questions for the cell wall folks to ask themselves: 1) Do we want to group the fungal cell walls even if if it appears that their structure is not the same? 2) If we do want to group them, what is the distinguishing feature of a shared by all fungal cell walls that separates them from other types of cell walls. For the types in GO right now, it seems like this is bacterial cell walls and plant cell walls. 3) If we don't want to group them, what is the distinguishing feature of a pombe cell wall that separates it from all other fungi other than that its found in pombe?

David

Original comment by: ukemi

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my previous comments were in 1690789 ] cell wall metabolic process overhaul I didn't propose a solution, but pointed out that pombe cell walls don't contain chitin (as far as I'm aware) only the spores do. From the checking I have done so far, I think not, but I have just sent out another e-mail. Will (hopefully) post reply here shortly...

Val

Original comment by: ValWood

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pombe cell wall composition PMID: 12582133 The /Schizosaccharomyces pombe/ cell wall is an extracellular matrix with a layered organization consisting of an outer layer of glycoproteins (9 to 14% -galactomannan) and an inner layer of carbohydrate polymers. This carbohydrate layer is mainly composed of 1,3--glucan (48%) interwoven into a fibrillar network with 1,3--glucan (18 to 28%), although it also contains some 1,6--glucan (2%) (27 <http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12582133\#r27&gt;). Among the polysaccharides, 1,3--glucans are the most prevalent, and it is generally accepted that they are the main structural components responsible for cell wall rigidity (27 <http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12582133\#r27&gt;). In situ localization of three different types of -glucan has indicated that 1,6--branched 1,3--glucan and 1,6--glucan are located throughout the glucan layer (less-dense layer), whereas the linear 1,3--glucan is located exclusively in the primary septum of dividing cells (16 <http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12582133\#r16&gt;).

Original comment by: ValWood

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1. chitin and beta glucan contining cell wall We needed to get rid of chitin and beta-glucan contining cell wall as that does not work for pombe. (pombe cell walls don't have chitin , although spores do).

Propose solution, Change term name to "fungal cell wall". This needs to be defined based on features which distinguish the fungal cell wall, but the def can be refined/clarified to include remarks on features that this type of cell wall does not have (cellulose/pectin) to distinguish from non-fungal cell walls. Maria, were you going to do this?

2. Spore wall Similarly change term spore wall (sensu fungi) to fungal cell wall Val to write new def which distinguished fungal spores from bacterial spores (i.e. include something about being a product of meiosis)

(N.B. There currently is not a term for plant spores. if it turns out that this term is not appropriate for plant spores they can raise a new term later, if required)

3. invasive growth (sensu fungi) change to fungal invasive growth

4. yeast-form cell wall Maria to refine def to include 'budding'

Original comment by: ValWood

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for

spore wall (sensu fungi) how about rename term: fungal spore wall Def: A meiotically produced spore wall formed within an ascus

(I think it may have to be fungal spore wall because:

i) I can't think of a term name to include plant and fungi which excludes bacteria, unless it was called 'meitocally produced spore wall'

BUT also

the current def refers to 'ascospore' which is specific to ascomycetes.

The specialized cell wall of the ascospore (spore). As in, but not restricted to, the fungi (Fungi, ncbi_taxonomy_id:4751).

(Is this a problem as it would not apply to non-ascomycete fungi.???)

Also spotted the term spore wall assembly (sensu fungi) that we need to deal with.

Original comment by: ValWood

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I think this is pretty much fixed now (except for the disjoint violation, which isn't directly related to the yeasty terms and will be sorted out in its own right fairly soon).

whew! m

Original comment by: mah11

[gocentral]

• labels: --> Other term-related request
• milestone: --> 224410
• assigned_to: nobody --> gomidori
• status: open --> closed-fixed

Original comment by: mah11

[gocentral]

• milestone: 224410 --> PomBase

Original comment by: mah11