polarized growth related comments and synonyms

[gocentral]

GO:0042815 : bipolar cell growth GO:0009826 unidimensional cell growth

note I originally requested the term "bipolar cell growth" to curate fission yeast genes involved in "bipolar growth" but this term is used by the fission yeast community to refer to the "direction" of growth (i.e. shape change) rather than increase in cell size. When genes involved in "bipolar growth are knocked out, the cells still grow but there is a loss of shape.

perhaps it would be useful to add a comment to these 2 terms "bipolar cell growth refers to the change in size, not a change in shape, for shape changes resulting from changes in bipolar growth patterns, please use GO:2000100

...and similal for unidimensional cell growth

also the def of "bipolar cell growth" should be standardized to reflect the "increase in size"

GO:0061246 establishment or maintenance of bipolar cell polarity resulting in cell shape add exact: polarized cell growth exact: polarized growth

establishment or maintenance of monopolar cell polarity resulting in cell shape related: monopolar cell growth related: unidimensional cell growth

Reported by: ValWood

Original Ticket: geneontology/ontology-requests/7809

[gocentral]

Hi Val,

The change in size is linked to a change in shape though: it can't grow in one-direction without changing shape (hence the morphogenesis parent for GO:0009826):

GO:0009826 unidimensional cell growth The process by which a cell irreversibly increases in size in one [spatial] dimension or along one axis, resulting in the morphogenesis of the cell.

To make the definition of GO:0042815 more similar to its parent and get the size info in, we could: GO:0042815 : bipolar cell growth Simultaneous polarized growth from opposite ends of a cell > The process by which a cell irreversibly increases in size along one axis through simultaneous polarized growth from opposite ends of a cell, resulting in morphogenesis of the cell.

I don't completely understand GO:0061246: you can't result in cell shape. You can regulate cell shape.

thanks, Becky

Original comment by: rebeccafoulger

[gocentral]

• assigned_to: nobody --> rfoulger

Original comment by: rebeccafoulger

[gocentral]

Hi Becky,

This is another head hurt. I might have made a mess here but I hope not. I was meant to assign to David as he knows the history, but it would be good to have someone else look.

Here is the "back story" in more detail:

There is a lot of work i the area of " cell polarity" in fission yeast. This is often referred to as "polarized growth (growth in a specific direction). I created the term bipolar growth as a child of unidemensional cell growth as I thought I was annotating in the correct part of the graph.

Over the next couple of years it became apparent to me that there were 2 problems causing TPVs for yeast for these annotations.

Firstly, most genes known to be involed in these "polarlized growth" terms I was using do not affect growth. The genes I am annotating appear to grow at the normal rate, they just loose their shape. I therefore needed a term which was not under growth (the use of the phrase "polarized growth" led me to think it was a cell size increase, but it wasn't)

The second issue was that in yeast, vegetative growth is not referred to as development, but is referred to as "cell morphogenesis" so we have 2 different uses of "morphogenesis", the common use, where it is part of developemnt and the way the yeast community use it which is not. David believes strongly that morphogenesis has to be part of development which I think is correct.

We therefore created the new terms which I could use to describe these processes, which had neither violating parent,

I think the existing terms for "unidimensional cell growth" and bipolar cell growth are fine to use for annotating genes which are really involved in "growth in a single direction". gene which regulate size and shape simultaneously but I have moved all of my annotations from this term to the newer terms:

GO:0061246 establishment or maintenance of bipolar cell polarity resulting in cell shape (you are right here, I think regulation fo cell shape would be more appropriate term name).

I agree that : The change in size is linked to a change in shape though: it can't grow in one-direction without changing shape (hence the morphogenesis parent for GO:0009826):

ah, my comment should say

"bipolar cell growth refers to the change in size AND shape. To annotate shape changes resulting from changes in bipolar growth patterns, where cell size is NOT affected use GO:2000100

Does that make sense?

Original comment by: ValWood

[gocentral]

I've updated the definition of bipolar cell growth ; GO:0042815 to make it clear that cell size is altered.

And I've added comments to both GO:0042815 bipolar cell growth and GO:0009826 unidimensional cell growth to make it clear that the terms refer to a change in both cell size and cell growth, pointing also to the cell shape change terms for cases where cell size is not affected.

NB: The 'resulting in' terms haven't been looked at by David and Tanya yet (they've done 'by', 'via' and 'during')... so any further rearrangement to should be covered when they go through those.

cheers, Becky

Original comment by: rebeccafoulger

[gocentral]

• status: open --> closed-fixed

Original comment by: rebeccafoulger

[gocentral]

• milestone: --> PomBase

Original comment by: mah11