Spore terms

[gocentral]

Several terms have been created by Swiss-Prot for subcellular locations that I would like to map to GO.

The terms are perispore, spore cortex, spore outer (or cortex) membrane, spore coat, spore core, spore core membrane. Definitions as created by SP curators are pasted at the end.

The terms perispore, spore coat, spore core and spore core membrane were created as non-species specific and as such they cover spores in bacteria, yeast, algae and non-flowering plants. The terms spore cortex and spore outer (or cortex) membrane appear to be specific for bacteria.

GO has a species non-specific term for spore wall (GO:0031160) so would the following be appropriate?;

GO:0031160 spore wall -part_of GO:new perispore -part_of GO:new spore coat

However, I notice that GO:0031160 spore wall has a synonym 'spore coat', would this need to be removed?

For the bacterial-specific terms, they could be children of GO:0055030 peptidoglycan-based spore wall;

GO:0055030 peptidoglycan-based spore wall -part_of GO:new spore cortex --part_of GO:new spore cortex membrane (syn: spore outer membrane)

As for the spore core terms, I'm not sure what GO term spore core would be a child of, maybe just 'intracellular part'? then you would have;

GO:0044424intracellular part -part_of GO:new spore core --part_of GO:new spore core membrane

GO:0016020 membrane -is_a GO:new spore core membrane

Perispore. The perispore corresponds to the outer surface layer of mature bacterial spores and eukaryotic spores. The perispore, also called perine or exosporium, represents the primary contact surface between the spore and environment/host and is a site of spore antigens. Synonyms: Perine; Exosporium.

Spore coat. The spore coat is the thick layer found beneath the perispore of some eukaryotic spores and bacterial mature spores. It is made up of highly cross-linked keratin and layers of specific proteins. The coat is composed of several electron-dense and lamella-like layers, differing between species.

Spore cortex. The spore cortex is a loosely cross-linked peptidoglycan layer localized between the spore core and the outer membrane or cortex membrane of bacterial mature spores. The cortex maintains heat resistance and dormancy.

Spore outer membrane. The outer membrane, also called the cortex membrane, is a membrane localized between the cortex and the inner layer of the coat of bacterial mature spores. Synonym: Spore cortex membrane.

Spore core. The core also called spore matrix is the central part of the spore and contains normal cell structures, such as DNA, proteins and ribosomes, but is metabolically inactive.

Spore core membrane. The spore core membrane is the membrane surrounding the innermost spore cell or spore core.

Thanks, Rachael.

Reported by: rachhuntley

Original Ticket: "geneontology/ontology-requests/5843":https://sourceforge.net/p/geneontology/ontology-requests/5843

[gocentral]

Hi,

Do you know (or can you find out) which references the proposed definitions come from?

I don't think I understand the difference between 'spore coat' and the existing 'spore wall' term, especially since the def of 'peptidoglycan-based spore wall' includes 'An exosporium may be present as an extreme outer layer.' Can you or the S-P curators clarify?

There are some other definition wordings that I'd be inclined to tweak to ensure that they don't give the impression that certain features are always present. For example, not all spores have a perispore; not all spore walls/coats are known to contain keratin (or a "keratin-like" protein, as in Bacillus).

I've also asked Chris to comment.

m

Original comment by: mah11

[gocentral]

The PAMGO group and I spent quite a lot of time working on the structure of the 'sporulation' terms - might be useful to look at those. Also, should probably look at the children of 'endospore external encapsulating structure ; GO:0043591' which describe the outer layers of a bacterial spore.

Original comment by: jl242

[gocentral]

Midori,

My (limited)understanding is that a spore coat is just one of the layers of the spore wall, the others being exosporium, perispore and cortex. Inside the spore wall is the spore core. PMID:4551752 shows the ultrastructure of a bacterial spore (Fig. 2) showing the spore coat within several other layers including the exosporium. I can only find use of the term 'exosporium' for bacterial and pollen spores.

I have also sent your comments to the Swiss-Prot curators involved and will post any replies I get.

Rachael.

Original comment by: rachhuntley

[gocentral]

Hi Rachael,

Thanks; since posting that comment I've done a little bit of searching myself, and reached a similar conclusion regarding bacterial spores. It's not quite that simple, however, because it appears that for Dictystelium 'spore wall' and 'spore coat' are used interchangeably; in budding yeast, and I think also fission yeast, 'spore coat' is simply hardly ever used. The budding yeast spore wall layers are not referred to by the same names as those of bacterial spores, and the fission yeast spore wall structure isn't well characterized.

That said, we can add spore parts to the ontology, and they can be used or not depending on which structures exist in the species of interest. The main worry is

Among the terms Jane referred to is 'exosporium' GO:0043592; the others explicitly refer to endospores, so I'm not sure how applicable they are to eukaryotic spores, but they'll certainly do for bacterial spores.

I'm also going to wait for Debby to have a chance to comment here or on the email thread before I do anything. Maybe we should try to collar another plant person as well?

m

Original comment by: mah11

[gocentral]

Hi Midori,

It looks like your second paragraph got truncated. Looking at the definition of exosporium, this is also very bacteria-specific - "The outer-most layer of a bacterial endospore, which is loosely attached and located outside of the endospore coat. It is generally composed of protein, carbohydrate, and perhaps lipid." Would you be able to alter this to encompass plant spores? If they have the same composition?...a plant person (who knows about spores, unlike me!) would be good. There doesn't seem to be any annotation to this term yet. (Although this isn't one of the subcell terms Swiss-Prot has created)

Rachael.

Original comment by: rachhuntley

[gocentral]

Ah, yes, oops. That paragraph should've said "the main worry is avoiding confusion between different spore wall/spore coat usages, given the Dicty situation".

I think we need a spore-knowledgeable plant person to comment on whether the same terms should be used for plant and bacterial spore parts. (I can say that yeast spores have different parts, but with different names so no risk of a clash.) I'll ask Tanya, Donghui, and Jen if they know of anyone.

m

Original comment by: mah11

[gocentral]

Reply from Marc, the Swiss-Prot curator involved with making the spore terms, regarding definitions of the terms; "Thanks for the "report". To be honest, it is not so easy to give a clear answer. Our definitions are not coming from specific papers, but are the result of many discussions and reading of many papers. Every paper has its own definitions so it was not possible to choose just one. Especially the spore wall composition differs so much between species. This is why we tried to avoid details. The aim was to get a clear, simple global view, and not a list of all the possible existing terms concerning spores. As an example spore wall = spore coat + other layers + perispore (so everything exterior to the spore core membrane). Sometimes there is just a spore coat, sometimes you can find additional layers. Spore wall is a general term that's why it can co-exist with the term spore coat, even of the wall just consists of the coat. All the spores have a wall, but you can find hundreds of kind of walls around spores. At the beginning of this work, we did not take into account all the already existing GO terms, and especially those like "chitosan layer of spore wall", "dityrosine layer of spore wall", .... Just getting a look a look at the literature, you may find hundreds of terms like that, specific for each species. At the final you may have as many terms as there are proteins. I just realize that if we mix our general definitions with the already existing detailed definitions in GO (like the example of "peptidoglycan-based spore wall") we will clearly find conflicts. I think that if we want to do this properly, we will have to check all the terms (including the existing GO terms) to avoid overlaps or conflicts."

He is prepared to discuss this further, so I will ask him to monitor this SF request. Rachael.

Original comment by: rachhuntley

[gocentral]

Reply from Marc, the Swiss-Prot curator involved with making the spore terms, regarding definitions of the terms; "Thanks for the "report". To be honest, it is not so easy to give a clear answer. Our definitions are not coming from specific papers, but are the result of many discussions and reading of many papers. Every paper has its own definitions so it was not possible to choose just one. Especially the spore wall composition differs so much between species. This is why we tried to avoid details. The aim was to get a clear, simple global view, and not a list of all the possible existing terms concerning spores. As an example spore wall = spore coat + other layers + perispore (so everything exterior to the spore core membrane). Sometimes there is just a spore coat, sometimes you can find additional layers. Spore wall is a general term that's why it can co-exist with the term spore coat, even of the wall just consists of the coat. All the spores have a wall, but you can find hundreds of kind of walls around spores. At the beginning of this work, we did not take into account all the already existing GO terms, and especially those like "chitosan layer of spore wall", "dityrosine layer of spore wall", .... Just getting a look a look at the literature, you may find hundreds of terms like that, specific for each species. At the final you may have as many terms as there are proteins. I just realize that if we mix our general definitions with the already existing detailed definitions in GO (like the example of "peptidoglycan-based spore wall") we will clearly find conflicts. I think that if we want to do this properly, we will have to check all the terms (including the existing GO terms) to avoid overlaps or conflicts."

He is prepared to discuss this further, so I will ask him to monitor this SF request. Rachael.

Original comment by: rachhuntley

[gocentral]

Hi,

These terms that you are mapping are not ones that I would use for plant spores and even where there are parts that might be shared with plant spores, like 'spore wall', the types of spores are so incredibly different that I don't really feel that is makes sense to group them in any way. If you are making new terms it would probably be best to be quite explicit and just say fungal spore wall or bacterial spore wall and that way it will be clear that these terms are not meant to refer to plants.

Jen

Original comment by: jenclark

[gocentral]

We've discussed this item on the ontology developers' mailing list; thread starts here:

http://fafner.stanford.edu/pipermail/ontology-editors/2009-February/000356.html

I'm still hoping Debby can contribute for bacterial spore parts, but if she doesn't have time we should be able to find enough information in literature.

Rachael - can you check with the SP curators whether they would be able to cope if GO decides not to group spore part terms representing different species/taxa? In the email thread Alex suggested adding terms like "bacterial spore cortex" and "bacterial spore outer membrane" rather than trying to shoehorn all spore cortexes into a single term and definition. Chris hasn't commented on that, but we do have precedents in GO. In light of comments from Alex, Jim, and Jen, it does seem more GO's style not to lump these components artificially.

thanks, m

Original comment by: mah11

[gocentral]

Hi Marc,

Thanks for your comments. The SP-SL terms you've settled on make sense given the way SP uses keywords, so I don't think I can ask you to change them -- you have a system that works for you.

But I also don't think we can do exactly the same thing in GO, because of the criteria that GO terms and relationships have to meet -- for example, we don't have any taxonomy built into the ontology (although for some we do note which taxa a component or process has been observed in). We also have to ensure that every term, and all paths to the root, avoid inferring "path violations", i.e. leading from one term that is applicable to a given taxon to a parent that isn't applicable. We also have to group specific terms under parents based on explicitly described shared features. Given all this, it's both less useful and more risky for us to convert specific terms to more general terms in cases where

The one possible problem, or at least inconvenience, is that some of the spore-related SP-SL terms won't map exactly onto a single GO term. For a general term like "spore cortex" might correspond to "endospore cortex" for bacteria, but to a different term (yet to be added to GO) for fungi or plants. It's not ideal, but not too horrible to contemplate either.

midori

Original comment by: mah11

[gocentral]

Hi Midori,

Thanks for your understanding. Of course we understand the criteria that GO terms and relationships have to meet, and we are aware about the problem that some of the spore-related SP-SL terms won't map exactly onto a single GO term, but we also think that this won't be really a big problem.

Marc.

Original comment by: marcfeuermann

[gocentral]

one option is to extend the syntax of the mapping files

keyword + taxon --> GO term

Original comment by: cmungall

[gocentral]

From GO's point of view, we're in pretty good shape already -- I think we have reasonably good coverage for our purposes of parts of bacterial and budding yeast spores. I've added a new term, GO:0070477, for the (bacterial) endospore core.

Jen, should we add terms for plant spore parts?

A brief summary of what we have:

• bacterial spores - use GO:0043591 and children, and GO:0070477 (for bacterial spores, the spore core membrane is the same as the "inner endospore membrane", which is a narrow synonym for plasma membrane in GO, and I've now added another synonym)

* budding yeast spores - use GO:0005619 and children; "spore coat", "spore cortex", "spore core" not used by community

* fission yeast spores - use GO:0005619; structure not known in enough detail to support using existing or adding new child terms

* other fungi - will add specific terms upon request (none requested so far; I don't know how well studied most are with respect to subcellular structure)

* plants - will add specific terms upon guidance from Jen, or upon request from annotators

midori

Original comment by: mah11

[gocentral]

closing, since there were some additions, and no more comments have come in; can reopen or start a new item for any further modifications needed.

Original comment by: mah11

[gocentral]

• assigned_to: nobody --> gomidori
• status: open --> closed-accepted

Original comment by: mah11