chitin-based cuticle extracellular matrix

[gocentral]

Hi, I'd like to request a new term to annotate gene products to the C. elegans pharnygeal cuticle, a chitin-based extracellular matrix.

GO:0005578 proteinaceous extracellular matrix

GO:new chitin-based cuticle extracellular matrix

Definition: A chitin-based, noncellular structure that is synthesized by an underlying cell layer. An example of this type of cuticle is found in the pharynx of the nematode Caenorhabditis elegans. The C. elegans pharyngeal cuticle lines the pharyngeal lumen and contains specialized structures that function as sieves and grinders to transport and break down food, respectively. PMID:25361578 PMID:25262818 PMID:16098962

It might also be good to broaden the definition of the parent term to be more inclusive:

An extracellular layer consisting of proteins (such as collagens) and carbohydrate-containing molecules (such as proteoglycans or chitin) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity.

Thanks, --Kimberly

Reported by: vanaukenk

Original Ticket: geneontology/ontology-requests/11791

[gocentral]

This is at the interface of anatomy and GO CC. Uberon and FBbt have cuticle terms. Wondering if WBbt should. How is chitin-based cuticle extracellular matrix different from plain chitin-based cuticle?

Original comment by: dosumis

[gocentral]

• assigned_to: David Osumi-Sutherland

Original comment by: dosumis

[gocentral]

Hi David,

Yes, I can see where these terms are at the interface of anatomy and GO CC.

We had originally defined the body (collagen- and cuticulin-based) cuticle as an extracellular matrix, which I think is correct, so that is why I gave the new term the suggested name of 'chitin-based cuticle extracellular matrix'.

Would you prefer term names like 'chitin-based cuticle' and 'collagen- and cuticulin-based cuticle'? Or do you not think these terms should be in GO CC at all?

We do have a number of gene products that localize to the C. elegans body cuticle, and now there are gene products that have been shown to localize to the pharyngeal, chitin-based cuticle, so these terms are helpful for annotating CC.

There is a cuticle term in the WBbt, WBbt:0005755, that seems to refer solely to the body cuticle.

Thanks, --Kimberly

Original comment by: vanaukenk

[gocentral]

It would be good to co-ordinate a solution with FlyBase, who I think mostly treat this as anatomy - whether internal (e.g. pharyngeal sclerite or chitinous intima) or external. Presumably some chance of conserved mechanisms here. I'm worried that if I add the terms, then FlyBase will have a bunch more cases that are duplicate with anatomy - they also presumably have a large number of annotations the could add to this new term.

Original comment by: dosumis

[gocentral]

Co-ordinated solution sounds good. How would you like to proceed?

Original comment by: vanaukenk

[pgaudet]

@ukemi was this addressed in the work you did on the ECM ?

[ukemi]

Not specifically, but would this term work?

collagen and cuticulin-based cuticle extracellular matrix GO:0060102?

[ukemi]

Actually, it looks like the pharyngeal cuticle is different. It has chitin in it, but do we want to distinguish that or would it be done at the level of the anatomical structure as indicated above? Chitin is not a gene product. @vanaukenk

[hattrill]

Very timely :) It would be good to distinguish 'cuticle' as a cellular component.

'collagen and cuticulin-based cuticle extracellular matrix' not good for arthopods where collagens are basement membrane components (whereas in C.elegans there are collagens that make up a substantial component of the cuticle). Cuticulin is more of a concept than a thing, I think - tends to belong to the waxy covering of the chitineous cuticle and is prob some lipidy mix.

I think either we would want a simple: cuticle, that would have the basic definition: cuticle: The cuticle is an apical extracellular matrix. It provides protective, skeletal and structural functions, forming part of the exoskeleton and barrier between tissues and the environment.

Or a separate arthopod/chitin-based cuticle (if composition matters): chitin-based cuticle: an apical extracellular matrix principally composed of chitin and cuticular proteins. It provides protective, skeletal and structural functions, forming part of the exoskeleton and barrier between tissues and the environment. Ref:PMID:17628275 PMID:15453918 PMID:20347980

Note that we have collagen and cuticulin-based cuticle and chitin-based cuticle distinctions in process ontology already: e.g. GO:0018996 molting cycle, collagen and cuticulin-based cuticle
GO:0007591 molting cycle, chitin-based cuticle ditto for cuticle development, &etc

[cmungall]

Seems fine but either the AOs would need to cede the label 'cuticle' (renaming to something like 'cuticular covering'...?) or GO should keep the more awkward 'cuticle ECM'

[ukemi]

I think cuticle fits better as an anatomical structure.

[hattrill]

As a structural component? how about a combination of EC location, and composition:

-apical ECM --chitin-based cuticle (which is actually a part of the cuticle not the whole structure - procuticle, but in practice, little emphiasis given to distinguishing) --collagen and cuticulin-based cuticle

[ukemi]

It would make sense to me to have an ECM as a cellular component that is part of an anatomical structures that is a cuticle. The question is whether we want to go to the level of chitin-based ECM and how it would differ or group with the existing terms. Do they still all contain collagen?

[hattrill]

The arthropod cuticle is devoid of collagens, the nematode cuticle is packed full of collagens - they've got tonnes of cuticle-specific collagens. (WormBook says: "It is a highly structured extra-cellular matrix (ECM), composed predominantly of cross-linked collagens, additional insoluble proteins termed cuticlins, associated glycoproteins and lipids.").
I think I'd have to go through this with Kimberly to get to the bottom of the difference and whether it is worth making the distinction.

[ukemi]

OK. I'm happy to add the new ECM types if you let me know what to add and where to add them. I still think it would be best to have the terms represent an ECM at the cellular level rather than a cuticle, which seems like the gross anatomical level.

[hattrill]

@vanaukenk do you want to have a chat about this?

[hattrill]

Hi @ukemi, having mulled this over an done some curation, would like to request this term:

chitin-based cuticle extracellular matrix is_a extracellular matrix GO:0031012 def: Any constituent part of a chitin-based noncellular, hardened, or membranous extracellular matrix secreted from the apical surface of an epithelial sheet. Ref: PMID:23955854

Thanks

[ukemi]

HI @hattrill,

Would there ever be a need for a chitin based ECM that is not in the cuticle? That is, would it be better to just make the chitin-based extracellular matrix?

[ukemi]

I think your def would fit that.

[ukemi]

Looking back at my old Invertebrate Zoology book (brings back fond memories), I can confirm that the teeth on the radula of a mollusc are made of chitin. Is it composed of an an ECM? I'm not sure about that but it wouldn't hurt to broaden the term. If you concur I will make it so.

[hattrill]

There is also the peritrophic matrix or membrane which lines the midgut of most insects (PMID: 30902530). So I am fine with making it "chitin-based extracellular matrix" as it can cover a multitude of things.

[hattrill]

Thanks!