NTR: chitin-based cuticle etc

[gocentral]

Sorry - this is a multi-issue request relating to cuticles that stems from the fact I would like a new cellular component term for insect cuticle.

1. We have terms for both ‘cuticle development’ and ‘protein-based cuticle development’, given that the ‘insect’ chitin-based cuticles also contains many proteins I think that it should be a child of ‘protein-based cuticle development’ rather than directly under ‘cuticle development’. This would be consistent with the fact that ‘cuticle development involved in chitin-based cuticle molting cycle’ is already a grandchild of ‘protein-based cuticle development’. I did wonder ‘protein-based cuticle development’ had been made to distinguish chitin-based cuticles from collagen and cuticulin-based cuticles, in which case I was going to suggest merging it with ‘cuticle development’ but I guess maybe plant cuticles have no protein at all so it is still a useful distinction?

2. New term request for chitin-based cuticle

I would like a new cellular component term to annotate proteins in fly cuticles. We already have the term collagen and cuticulin-based cuticle extracellular matrix ; GO:0060102 for worm so can we have a corresponding chitin-based cuticle extracellular matrix term?

My only problem with the term names are they sound like an extracellular matrix of a cuticle whereas the cuticle itself is an extracellular matrix. So the words ‘extracellular matrix’ in the term name are redundant and potentially confusing. Assuming I have understood correctly! Any chance of changing these to simply ‘collagen and cuticulin-based cuticle’ and ‘chitin-based cuticle’?

Given point 1 above, I thought that it would be ok to have ‘chitin-based cuticle’ as a sib of ‘collagen and cuticulin-based cuticle’ under its current parent ‘proteinaceous extracellular matrix’ but looking at the def I don’t think it works for fly. ‘Proteinaceous extracellular matrix’ is a example of a term name that sounds very general but turns out to have a unexpectedly specific def: “A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.” It sounds like this term was originally for mammalian usage. ‘Especially collagen’ is ok for worm but not for insects. Also chitin is a aminoglycan but I’m not sure it is necessarily a glycosaminoglycan. I’m not sure I’d describe the fly cuticle as a ‘sheet’ and given that the collagen and cuticulin-based cuticle extracellular matrix consists of several layers (see child terms) it jars slightly to define is ‘a layer’ or ‘sheet’.

Can we tweak the def of ‘proteinaceous extracellular matrix’ to make it a bit more general? Maybe there is a more appropriate term that would gather a subset of the more mammalian type children if necc.

3. NTR for cuticle (extracellular matrix)? Is it also worth grouping ‘collagen and cuticulin-based cuticle’ and chitin-based cuticle’ under a new grouping term ‘cuticle’ is_a extracellular matrix - this is consistent with other parts of GO (assuming every cuticle is an extracellular matrix).

4. If every cuticle is an extracellular matrix, should ‘structural constituent of cuticle’ be a child of ‘extracellular matrix structural constituent’ rather than a sib?

5. Minor request... there are three children of structural constituent of chitin-based cuticle:

structural constituent of adult chitin-based cuticle structural constituent of chitin-based larval cuticle structural constituent of pupal chitin-based cuticle

Could they be standardized so that the stage is in the same place in each term name?

6. Sclerotization is defined in Hendersons biological dictionary ISBN:0582227089 as the process of hardening and darkening the new exoskeleton which occurs in insects after moulting. Could sclerotization be added as a synonym to chitin-based cuticle tanning ; GO:0007593?

Thanks, Susan

Reported by: stweedie

Original Ticket: geneontology/ontology-requests/8590

[gocentral]

Regarding adding cuticle to GO: Where is the dividing line between GO CC and gross anatomy?

should terms like "glomerular basement membrane" (FMA:74274, ZFA:0005285, MA:0001659) be added to GO, if they are subtypes of basal lamina?

One way to cut it is that GO has terms representing portions of cuticles, basal laminae, etc, and the AOs have terms representing the entire structure. Thus GO CC is still "at the level of" one cell or a small number of cells.

I don't have strong opinions one way or another, but it would be good to establish some clear principles.

Original comment by: cmungall

[gocentral]

• assigned_to: nobody --> paolaroncaglia

Original comment by: paolaroncaglia

[gocentral]

The cuticle is both an anatomical structure and an extracellular matrix and I hadn't considered the overlap with anatomy in this case. I was influenced by the existing cuticle terms (and my somewhat GO-centric view of the world!) On reflection I think most people would primarily think that cuticle sits more naturally in an anatomy ontology than in GO and I think Chris's suggested rule for where to draw the line sounds pretty good. As no particular part of the cuticle is identified in the paper that I am currently annotating, I would be happy to stick with annotations to 'extracellular matrix' in this case. I've emailed David Osumi-Sutherland for his anatomy-based opinion.

Original comment by: stweedie

[gocentral]

Hi all,

Good timing. I'm in the process of adding terms for cuticle to draft arthropod and insect ontologies. These can be found here:

"http://code.google.com/p/arthropod-anatomy-ontology/"

The draft definition of "arthropod cuticle" is: "The outer, acellular, chitinous layer of the arthropod integument."

The Drosophila anatomy ontology also contains terms for cuticle and its various layers.

I hadn't thought before that cuticle could be in GO. While Chris's suggestion is not unreasonable:

"One way to cut it is that GO has terms representing portions of cuticles, basal laminae, etc, and the AOs have terms representing the entire structure. Thus GO CC is still "at the level of" one cell or a small number of cells."

... I worry that this distinction is going to be too subtle for biologists. So - perhaps best to keep this stuff in anatomy ontologies after all?

Note - a related case is chorion.

One of the most important distinctions we need to make between regions of arthropod integument is between regions of high and low sclerotization. The relatively more hardened regions are called sclerites. Broadly, sclerotized simply means hardened (cf sclerosis). Various methods are used to harden arthropod cuticle. Crustaceans mineralise their their sclerites with calcium carbonate (+ protein cross-linking). Insect sclerotization involves protein cross-linking and dehydration. This appears to be tightly coupled to tanning. Having a good term for sclerotization of cuticle would be very useful in formalising the definition of sclerites.

GO has:

id: GO:0007593 name: chitin-based cuticle tanning def: "The cross-linking of chitin and other cuticle proteins, rendering them insoluble and hardening the cuticle. This process generally darkens the color of the cuticle."

This is a good start, but there are various things wrong.

1. Chitin is not a protein (http://en.wikipedia.org/wiki/Chitin) - so 'other' is not correct here.
2. Given that this term is defined primarily in terms of hardening, perhaps it should be re-named chitin-based cuticle sclerotization with tanning as a synonym?
3. The def looks like it's written for insects. It won't work for sclerotization of crustacean cuticle, which is also chitinous.

The challenge, as ever with GO, is to come up with a way to make relevant classes without mentioning taxonomy. Here's one suggestion based on some brief reading round:

[Term] name: chitin-based cuticle sclerotization def: "The process of hardening of a chitin-based cuticle." synonym: "chitin-based cuticle hardening"

[Term] name: chitin-based cuticle sclerotization by biomineralisation def: "The process of hardening a chitin-based cuticle by mineral incorporation. For example, the cuticle of crustaceans is hardened by the incorporation of calcium carbonate." synonym: "chitin-based cuticle hardening by biomineralisation"

[Note - I don't thing this should be a child of biomineral tissue development as I think cuticle is not a tissue (no cells). But this probably also means that enamel mineralisation (GO:0071529) is not biomineral tissue development either].

[Term] name: chitin-based cuticle sclerotization by protein cross-linking and tanning. def: "The process of hardening of a chitin-based cuticle by protein cross-linking, dehydration and the incorporation of phenolic precursors. This mechanism of cuticle hardening occurs in insects and is usually accompanied by darkening of the cuticle."

[It may be worth separating this last one into two separate classes - one for tanning and one for cross-linking, not least because my suggested name is so ugly and long! Note - sclerotisation of crustacean cuticle also involves protein cross-linking.]

Finally, wondering whether GO terms should be for cuticle secretion and assembly rather than development. For the anatomical relationship develops_from, we've been considering restricting A develops_from B to cases where at least some cells in A are from B or from the lineage of cells in B. I notice that 'assembles' is used for.

How to proceed?

I suggest:

1. "chitinous cuticle" stays in anatomy
2. GO works with my suggestions to improve existing terms.
3. We ask the arthropod anatomy list folks to review the suggestion and suggest good references.

- David

Original comment by: dosumis

[gocentral]

Note for self: see also https://sourceforge.net/tracker/?func=detail&aid=2990107&group\_id=36855&atid=440764

Original comment by: paolaroncaglia

[gocentral]

• assigned_to: paolaroncaglia --> rfoulger

Original comment by: paolaroncaglia

[gocentral]

Getting back to cuticles: thanks for your comments, and here's a proposal based on your suggestions for the process terms:

1. I'm not convinced that the protein-based cuticle terms are useful. Some (but not all) of the chitin-based cuticle terms are under them (odd since chitin is a polysaccharide- presumably because the chitin-based cuticles also contain protein). Seems like an unnecessary grouping term.

Propose to obsolete: protein-based cuticle attachment to epithelium ; GO:0040006 0 direct annotations cuticle development involved in protein-based cuticle molting cycle ; GO:0042336 0 direct annotations ecdysis, protein-based cuticle ; GO:0042394 0 direct annotations molting cycle, protein-based cuticle ; GO:0018988 0 direct annotations protein-based cuticle development ; GO:0007592 2 worm annotations

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2. Keep 'cuticle' as an anatomy not a GO CC term.

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3. [Term] id: GO:0007593 name: chitin-based cuticle tanning namespace: biological_process alt_id: GO:0045452 def: "The cross-linking of chitin and other cuticle proteins, rendering them insoluble and hardening the cuticle. This process generally darkens the color of the cuticle." [GOC:bf, GOC:jid, GOC:mtg_sensu] synonym: "cuticle hardening" NARROW [] is_a: GO:0021700 ! developmental maturation is_a: GO:0040006 ! protein-based cuticle attachment to epithelium relationship: part_of GO:0008365 ! adult chitin-based cuticle development > [Term] id: GO:0007593 name: chitin-based cuticle sclerotization namespace: biological_process alt_id: GO:0045452 def: "The process of hardening of a chitin-based cuticle." [GOC:mtg_sensu, GOC:dos] synonym: "cuticle hardening" EXACT [] synonym: "chitin-based cuticle tanning" RELATED [GOC:dos] is_a: GO:0021700 ! developmental maturation is_a: GO:0040006 ! protein-based cuticle attachment to epithelium

Q: Removed the relationship 'part_of GO:0008365' (PMID: 19932179: in some Diterans, sclerotization occurs during puparium formation).

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4. New terms:

name: chitin-based cuticle sclerotization by biomineralization ; GO:NEW def: The process of hardening a chitin-based cuticle by mineral incorporation. For example, the cuticle of crustaceans is hardened by the incorporation of calcium carbonate." synonym: "chitin-based cuticle hardening by biomineralisation" EXACT is_a: chitin-based cuticle sclerotization ; GO:0007593 maybe is_a: biomineral tissue development ; GO:0031214 (would need to move GO:0031214 from under 'tissue development'… will cover this separately. There is a biomineralization SF item already open).

[Term] name: chitin-based cuticle sclerotization by protein cross-linking ; GO:NEW synonym: chitin-based cuticle sclerotization by protein cross-linking and cuticle tanning NARROW def: "The process of hardening of a chitin-based cuticle by protein cross-linking, and the incorporation of phenolic precursors. This mechanism of cuticle hardening occurs in insects and is usually accompanied by darkening of the cuticle."

Q: Does tanning occur w/o protein cross-linking?

(I am working from the basis that the term "tanning" is often used synonymously with sclerotization, but sometimes it is specifically used for the processes whereby brownish (tan) cuticles are formed, and we are referring to the latter here).

I'm inclined not to make two terms as I think it would be difficult to separate them at the annotation stage since they're often coupled.

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5. Tidy up the terms:

structural constituent of adult chitin-based cuticle structural constituent of chitin-based larval cuticle structural constituent of pupal chitin-based cuticle

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Let me know if you've any edits. thanks Becky

Original comment by: rebeccafoulger

[gocentral]

The PO has terms for plant cuticle, plant cuticle proper, cuticular wax, and cutin, all as children of portion of plant substance. We thought the PO was the appropriate place for these terms, as they are extracellular.

Original comment by: rlwalls2008

[gocentral]

Have updated definition, name and parentage of GO:0007593, as described below.

New terms: chitin-based cuticle sclerotization by biomineralization ; GO:0036340 chitin-based cuticle sclerotization by protein cross-linking ; GO:0036341

Have sent obsoletion notice for the five protein-based cuticle process terms. OBSOLETION DUE DATE: 21ST SEPTEMBER 2012.

Just the obsoletion to do for this SF item.

Original comment by: rebeccafoulger

[gocentral]

• status: open --> pending

Original comment by: rebeccafoulger

[gocentral]

Obsoleted: protein-based cuticle attachment to epithelium ; GO:0040006 cuticle development involved in protein-based cuticle molting cycle ; GO:0042336 ecdysis, protein-based cuticle ; GO:0042394 molting cycle, protein-based cuticle ; GO:0018988 protein-based cuticle development ; GO:0007592

Original comment by: rebeccafoulger

[gocentral]

• status: pending --> closed-fixed

Original comment by: rebeccafoulger