Obsoletion: GO:0051278 fungal-type cell wall polysaccharide biosynthetic process & related children

[rozaru]

Please provide as much information as you can:

• Suggested term label: peritrophic membrane chitin biosynthetic process

• Definition (free text) The chemical reactions and pathways resulting in the formation of peritrophic membrane chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues, found in peritrophic membrane, a tubular sheath of cuticle that shields the epithelial cells of the midgut from the gut contents. An example of this is found in Drosophila melanogaster.

• Reference, in format PMID:####### PMID: 11376452

• Gene product name and ID to be annotated to this term Chs2 FBgn0029091 (Q9VNW7) CHS2 Q530Z6 CHS2 Q6WD24

• Parent term(s) GO:0006031 chitin biosynthetic process

• Children terms (if applicable) Should any existing terms that should be moved underneath this new proposed term?

• Synonyms (please specify, EXACT, BROAD, NARROW or RELATED) peritrophic matrix chitin biosynthesis EXACT peritrophic matrix synthesis BROAD

• Cross-references

• For enzymes, please provide RHEA and/or EC numbers.

• Can also provide MetaCyc, KEGG, Wikipedia, and other links.

• Any other information There is a related MF term - GO:0016490 structural constituent of peritrophic membrane -

[pgaudet]

Hi @rozaru

I suppose you're asking this because other children of chitin biosynthetic process describe where the chitin is located? ie:

• 'cuticle chitin biosynthetic process'
• 'fungal-type cell wall chitin biosynthetic process'
• 'cell wall chitin biosynthetic process'

Or are these different pathways? It seem like these terms are mixing BP and CC, and should be obsoleted and replaced by their parent. What do you think ?

Thanks, Pascale

[rozaru]

@pgaudet The composition of these chitin-containing structures is different. However, the chitin biosynthesis pathway itself is the same. Chitin synthase in all the species that can make chitin uses UDP-GlcNAc as precursor. In fly, there are 2 genes for chitin synthase, one responsible for chitin synthesis in the epidermis, trachea and joints (cuticle) and one for chitin synthesis in the midgut (peritrophic matrix). C.elegans has also 2 genes that differ in where they make chitin.

For the moment, I used an extension to convey the information: FB Q9VNW7 Chs2 involved_in GO:0006031 chitin biosynthetic process ECO:0000250 (ISS) GO_REF:0000024 UniProtKB:Q6WD24 occurs_in(FBbt:00005383)

FBbt:00005383 = midgut

I agree with you that the terms appear to be mixing a biosynthetic process and a CC term and maybe a general GO term combined with an extension to CC term would be better. I don't know of WormBase, SDG and PomBase would feel about simplifying the annotation, though....

[ValWood]

yes from me, cel wall is a mess, lots of extra terms

[pgaudet]

Hi @rozaru

Thanks for the quick reply. From what I can see, the appropriate terms would be:

• 'GO:0040003 chitin-based cuticle development' rather than 'cuticle chitin biosynthetic process'
• GO:0009272 fungal-type cell wall biogenesis or GO:0031505 fungal-type cell wall organization (I am not clear what the difference is between these 2 terms, in practice) rather than 'fungal-type cell wall chitin biosynthetic process'
• GO:0042546 cell wall biogenesis or GO:0071555 cell wall organization rather than 'cell wall chitin biosynthetic process'

This way we keep synthesis of the indivial component molecules separate from the organization of the structure itself. What do you think?

If we decide to do that, the same should apply to GO:0071966 fungal-type cell wall polysaccharide metabolic process GO:0034218 ascospore wall chitin metabolic process GO:0070599 fungal-type cell wall (1->3)-alpha-glucan metabolic process GO:0070879 fungal-type cell wall beta-glucan metabolic process GO:0051278 fungal-type cell wall polysaccharide biosynthetic process

Thanks, Pascale

[rozaru]

@pgaudet

This way we keep synthesis of the indivial component molecules separate from the organization of the structure itself. What do you think?

I agree with you, it would make more sense.

Just to be sure that I understood correctly. For example, in the chitin synthesis case:

The idea would be to obsolete the following terms: GO:0006037 cell wall chitin metabolic process and its children GO:0006034 cuticle chitin metabolic process and its children

This would leave the following terms:

chitin metabolic process
|chitin biosynthetic process | |regulation of chitin biosynthetic process |chitin catabolic process |regulation of chitin metabolic process |__regulation of chitin biosynthetic process

This would cover the metabolism of chitin independently of which structure it is incorporated in and it would cover crustacean, insect, nematodes, fungi etc..

Separately (or in an extension) I could add a term that describes the development or organisation of the structure that contains chitin: GO:0040003 chitin-based cuticle development and children (which would be appropriate for insects and nematodes) GO:0007591 molting cycle, chitin-based cuticle and children

Does it make sense?

Thanks

[raymond91125]

PMID:31102247 shows lists of steps in metabolic process.

[raymond91125]

I think these terms are not all simply superfluous. @ValWood What do you think?

If we decide to do that, the same should apply to GO:0071966 fungal-type cell wall polysaccharide metabolic process GO:0070599 fungal-type cell wall (1->3)-alpha-glucan metabolic process GO:0070879 fungal-type cell wall beta-glucan metabolic process GO:0051278 fungal-type cell wall polysaccharide biosynthetic process

[ValWood]

I have often wondered if we need the individual terms and we could just have

"cell wall polysaccharide biosynthetic process"

i.e.
beta 1-3 glucan synthase part_of cell wall polysaccharide biosynthetic process alpha-1,3-glucan synthase activity part_of cell wall polysaccharide biosynthetic process

since these are all single steps part of the broader process of cell wall polysaccharide biosynthetic process

Do we need the individual types of glucan represented as separate processes at all?

The issue might be that they could have separate regulatory pathways IIRC, we would need to look at that...

[pgaudet]

I also wonder if we need "cell wall polysaccharide biosynthetic process" can the same polysaccharide end up in the cell wall or in another place? Or is this a real class of polysaccharides?

[ValWood]

these cases are specifically making polysaccharides for cell wall. They are positioned to make polysaccharides only as part of cell wall biosynthesis. i.e. https://www.researchgate.net/publication/328338096_Fission_Yeast_Cell_Wall_Biosynthesis_and_Cell_Integrity_Signalling/figures?lo=1

https://www.sciencedirect.com/science/article/pii/S1087184515300529 https://ars.els-cdn.com/content/image/1-s2.0-S1087184515300529-gr1.jpg

.....there are other types of polysaccharide that are not cell wall (i.e starch, glycogen)

so I think cell wall polysaccharide biosynthesis should be a class..... so that it can be part_of cell wall biosynthesis.

Otherwise, we need to make lots of unnecessary concurrent annotations and BP part of BP annotations

[ValWood]

but I'm not fussed about the individual component metabolism terms if they can be captured as MF terms.... I haven't looked if this will work across the entire process (clearly not for chitin because it is used for other cell structures in addition to cell walls)

[ValWood]

There is also other grouping terms to consider https://github.com/geneontology/go-ontology/issues/22008

[raymond91125]

I think this ticket may be closed as obsoletion has been done. If needed, please start new tickets. Thanks.

[pgaudet]

@raymond91125 I dont see that GO:0051278 fungal-type cell wall polysaccharide biosynthetic process has been obsoleted ; should it be?

[raymond91125]

It wasn't clear to me that decision has been made. The original focus on chitin was done.

[ValWood]

A thought: I often wonder why the fungal-type and plant-type cell wall terms are necessary? Why not just cell wall? The composition of the cell wall may be different but any differences can be determined by specific terms. For example, we don't have bacterial-cell wall type terms. A lot of the inconsistencies I have in PomBase annotation are because of terms not being available in the fungal branch or vice versa, so I end up with annotations in 2 branches (although this is likely to improve a lot once these polysaccharide terms go).

[raymond91125]

@ValWood Are we good to obsolete the following terms? GO:0071966 fungal-type cell wall polysaccharide metabolic process GO:0070599 fungal-type cell wall (1->3)-alpha-glucan metabolic process GO:0070879 fungal-type cell wall beta-glucan metabolic process GO:0051278 fungal-type cell wall polysaccharide biosynthetic process

[ValWood]

good for me...

[pgaudet]

My question was a bit different: why have 'organelle' + 'compound' + metabolic process? For example I see

• plant-type cell wall cellulose biosynthetic process : this is certainly the same biosynthetic process as its parent 'GO:0030244 cellulose biosynthetic process' ? The synthesis of these compounds is unrelated to where they end up in the cell, isn't it?

[ValWood]

I have been thinking about this and there are some other considerations.

When these compounds are synthesised in fungi they are always cell wall compounds, and are synthesised in pathways that operate at the cell wall and extrude the growing molecules.

If they are not placed under "cell wall biosynthetic process" we need to make 2 annotations (i.e. the specific polysaccharide, and to cell wall biosynthesis) to say one thing (and this will generate a lot of annotation inconsistency across the fungi).

We could place the beta glucan biosynthetic process under cell wall biosynthesis (I think?) because it is only found in cell walls.

However, alpha glucans are different, they include a variety of compounds (cell wall alpha glycan, starch, glycogen), for this reason I preferred the old specificity.

Ideally, we would still be able to have the fungal pathways directly under cell wall biosynthesis. The structures are slightly different anyway, fungal cell wall alpha glucans are α-1,3-glycosidic bonds with less branching than glycogen branching points can involve α-1,3 or sometimes α-1,6-glycosidic bonds. Glycogen is α-1,4-glycosidic bonds with branching points created by α-1,6-glycosidic bonds.

So sometimes, it might be useful to keep the physiological context (i.e. cell wall). i don't consider this as a label to define where it ends up, rather to define the entire pathway, the catalytic enzymes and any accessory proteins and the signalling (which will probably be different in different physiological contexts).

[ValWood]

I would remove the genus groupings if possible and remove the 'physiological context' groupings only if they do not distinguish between different contexts.

[pgaudet]

Two questions:

1. Is this valid for all organisms? ie are these compounds only present in fungus?
2. Are there other compounds that are not only present in the cell wall and that need co-annotation? It seems this could lead to inconsistent annotations.

[ValWood]

Is this valid for all organisms? ie are these compounds only present in fungus?

I don't know (see above). I think beta glugans may only be in cell walls but alpha glucans comprse alpha glucans, glycogen and startch). Now we will lump them all together?

Are there other compounds that are not only present in the cell wall and that need co-annotation? It seems this could lead to inconsistent annotations.

I don't understand. At the moment, all of the polysaccharides that we need to annotate for yeast ARE already positioned under cell wall biosynthesis. I would like to keep it like that if possible, not just for fission yeast; otherwise, many fungi will lose their cell wall biosynthesis annotations. Cell wall biosynthesis is important for antifungal drug targets, and so it wouldn't be good to lose large numbers of annotations. This might mean keeping some of the cell wall grouping terms.

This would probably mean not losing the distinction alpha-glucan, glycogen and starch are different compounds.

I'm more bothered about the connection to cell wall biosynthesis (the process they are involved in) than I am about the connections to the specific polysaccharide biosynthesis.

I still think the larger problem with the cell wall process was the plant/fungi/bacterial specific groupings. These groupings would only be required IF a polysaccharide is used in different contexts (i.e. chitin which is used in a non-cell wall context).

I am struggling to see what would be under cell wall biosynthesis if we remove the cell wall polysaccharide biosynthesis terms, because that's what cell wall biosynthesis is?