fungal differentiation/ for pending/consideration

[gocentral]

I think that the fungal switches from proliferative growth to different 'cell types' should have terms under 'cell differentiation' (this will help to make links between gene products involved in conserved eukaryotic pathways (like TOR and PKA etc) and processes involved in these differentiation switches between fungi and higher eukaryotes.

I'm thinking of

i) cellular morphogenesis during conjugation with cellular fusion ii) the switch to filamentous growth iii) G1 to G0 transition (there is not a term for this, although there is a term for G0-G1) perhaps cellular morphogenesis during vegetative growth ?

This is non urgent, so I'll think about it so more (also it seems a bit of a mish mash where the terms are positioned (development/morphogenesis etc) depending on the way the terms are defined for the different types of growth. I just wanted to flag this in case anyone is working on (or thinking of working on) these areas.

Reported by: ValWood

Original Ticket: "geneontology/ontology-requests/4484":https://sourceforge.net/p/geneontology/ontology-requests/4484

[gocentral]

Logged In: YES user_id=436423 Originator: NO

Another thing to take into account is whether the def of 'cell differentiation' really works for fungi ... it's written from a bigger-eukaryote point of view, and makes plenty of sense for multicellular organisms. I'm not sure it works as well for yeasts ... might be better to put the yeasty/fungal terms under 'cell morphogenesis' instead (some already have this parentage).

cell differentiation def: The process whereby relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate.

m

Original comment by: mah11

[gocentral]

Logged In: YES user_id=516865 Originator: YES

that would work, but as fungal researchers use the study of the transition from vegetative to resting state to draw paralleles broader eukaryotic differention it seems a shame not to capture this in some way (particularly the signalling aspects) in GO

Original comment by: ValWood

[gocentral]

Logged In: YES user_id=436423 Originator: NO

Hmmm, I wonder if the differentiation def could be broadened while still maintaining a distinction from the other terms? One for the dev biol crowd ... I don't think I'd be much help ...

Original comment by: mah11

[gocentral]

Logged In: YES user_id=616548 Originator: NO

I don't think 'differentiation' applies to these processes; I'd call them 'morphogenesis'. To me, differentiation implies an irreversible change from one stable state to another stable state, and the definition of the GO term implies this too. The fungal processes (and there are additional ones, such as the white-opaque switch in Candida which involves a drastic change in cell morphology) are reversible, and the states are not maintained for the rest of the organism's life.

Original comment by: mariacostanzo

[gocentral]

Logged In: YES user_id=631592 Originator: NO

I'm not working on them, but I very much agree that these types of terms should be added to the development portion of GO. The matA matalpha switch is another classic model for cell differentiation and development.

David

Original comment by: ukemi

[gocentral]

• assigned_to: nobody --> ukemi

Original comment by: mah11

[gocentral]

Now that we have a cell morphogenesis term outside of development, I think it covers much of what is being discussed in this item. However, I still wonder if it wouldn't be worthwhile to have a 'fungal mating type cell differentiation' term or maybe the terms for the differentiation of 'a' and alpha cells. What do you guys think?

As an aside, we also heard a really interesting talk at the ASCB meeting by someone who described budding yeast as differentiating. Apparently the daughter cell of a budding division inherits cytoplasmic components (I can't remember what they are at the moment, we should ask Tanya) making the daughter cells different from the mother cell. It was pretty cool.

D

Original comment by: ukemi

[gocentral]

• status: open --> closed-works-for-me

Original comment by: ukemi

[gocentral]

> Now that we have a cell morphogenesis term outside of development

sorry, could you remind me which term you mean here?

> [is it] worthwhile to have a 'fungal mating type cell differentiation' term ...?

Might be useful ... what would the term encompass? Seems we'd probably want some kind of connection to 'mating type switching' (GO:0007533).

Oh, and I'd find it clearer to use 'fungal mating type-specific cell differentiation' because nobody refers to a 'mating type cell'.

> daughter cell of a budding division inherits cytoplasmic components (I > can't remember what they are at the moment

Ash1 mRNA is one, iirc

m

Original comment by: mah11

[gocentral]

there is quite a lot of stuff on cellular asymmetry in yeasts coming out at the moment PMID: 20066112

There is also some exciting stuff in pombe, conserved spindle pole components which affect left right symmetry developmentally in Metazoa... watch this space....

Original comment by: ValWood

[gocentral]

• milestone: --> PomBase

Original comment by: mah11