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#10987 negative regulation of protein localization to cell tip involved in positive regulation of establishment of cell polarity regulating cell shape

None
open
David Osumi-Sutherland
None
8
2014-10-10
2014-07-08
David Osumi-Sutherland
No

This ticket is for discussion and resolution of a TermGenie request for a pair of compound terms with very long names with multiple clauses. The term genie requests have been rejected (=> obsoletion of the terms).

"protein localization to cell tip involved in positive regulation of establishment of cell polarity regulating cell shape"
intersection_of: GO:1990151 ! protein localization to cell tip
intersection_of: part_of GO:2000784 ! positive regulation of establishment of cell polarity regulating cell shape

"negative regulation of protein localization to cell tip involved in positive regulation of establishment of cell polarity regulating cell shape"
intersection_of: GO:1903067 ! negative regulation of protein localization to cell tip
intersection_of: par\t_of GO:2000784 ! positive regulation of establishment of cell polarity regulating cell shape

These terms were requested for curation of Kokkoris et al., 2014. PMID:24554432

Critique of term names:

These terms are hard for most people to read and understand. The main problem is not their length (although that doesn't help), it is the multiple occurences of 'regulates' (positive, negative and neutral) combined with involved in.

Brief summary of the biology:

The big picture:

"microtubule organization and cell shape form a self-reinforcing system, in which the cell shape provides physical constraints that align microtubules along the length of the cell to deliver landmarks to cell extremities, which in turn reinforce the rod shape by marking the cell ends for growth"

Can we simplify/clarify the terms by changing the way we capture this context?

  • Doesn't all establishment/maintenance of cell polarity have some effect on cell shape? If so, do we need to mention most in the term?

  • Given that we're talking about a self-reinforcing system rather than de novo establishment of a state, wouldn't it be clearer to use 'maintenance' to describe this, rather than regulation?

  • What about the relationship to polarised growth? We have a variety of terms for this (e.g. bipolar cell growth; cell tip growth), but the requested terms lack this context. Presumably polarised cell growth is always dependent on a prior establishment of cell polarity followed by ongoing maintenance of cell polarity. It should be possible to reflect this in the ontology.

  • Would be enough to capture a smaller slice of this big picture? Rather than establishement of cell polarity regualting cell shape, perhaps: 'maintenance of cell polarity' OR 'maintenance of polarised cell growth'

The molecular details:

Microtubules deliver Tea1-Tea4 to the poles where it activates Cdc42. This activation drives localised growth. e.g. via promoting polarised exocytosis of cell wall remodelling enzymes.

The paper focuses on how Tea4 activates Cdc42. It does this by binding and recruiting an activator of Cdc42 (the GEF, gef1), while locally excluding a inhibitor of Cdc42 (the GAP, Rga4)

Some suggestions

Tea4 capable_of protein localisation to cell tip involved in maintenance of polarised cell growth (localizes Gef1)
Tea4 capable_of negative regulation of protein localisation to cell tip involved in maintenance of polarised cell growth (some relationship to Rga4 ?)

Discussion

  • David Osumi-Sutherland

    David Osumi-Sutherland - 2014-07-08
    • Description has changed:

    Diff:

    --- old
+++ new
@@ -12,7 +12,7 @@

 ## Critique of term names:

-These terms are hard for most people to read and understand.  The main problem is not their lenght (although that doesn't help), it is the multiple occurences of 'regulates'  (positive, negative and neutral) combined with involved in.
+These terms are hard for most people to read and understand.  The main problem is not their length (although that doesn't help), it is the multiple occurences of 'regulates'  (positive, negative and neutral) combined with involved in.

 ## Brief summary of the biology:
     

  • Valerie Wood

    Valerie Wood - 2014-09-03
    • Doesn't all establishment/maintenance of cell polarity have some effect on cell shape? If so, do we need to mention most in the term?

    not necessarily, you can polarize actin cytoskeleton elements or other aspects of the cell withough affecting cell shape...apparently...there is an old ticket about this where David H introduced the 'regulating cell shape' string to the terms where shape was affected.

    • Given that we're talking about a self-reinforcing system rather than de novo establishment of a state, wouldn't it be clearer to use 'maintenance' to describe this, rather than regulation?

    Yes I think you are right. I got hooked on establishment because the experiment was setting up a new growth zone at an ectopic location, but in the WT cell it could be 'maintenance'

    • What about the relationship to polarised growth? We have a variety of terms for this (e.g. bipolar cell growth; cell tip growth), but the requested terms lack this context. Presumably polarised cell growth is always dependent on a prior establishment of cell polarity followed by ongoing maintenance of cell polarity. It should be possible to reflect this in the ontology.

    • Would be enough to capture a smaller slice of this big picture? Rather than establishement of cell polarity regulting cell shape, perhaps: 'maintenance of cell polarity' OR 'maintenance of polarised cell growth'

    I'm not sure. Although I get confused by this. I avoided the 'growth terms" is because they are defined as the increase in cell size. The "cell polarity" terms are about shape.
    This process isn't abut the size increase (although obviously the size increase happens concurrently). If this pathway wasn't working the cell size would still increase, only the shape would be different, it would be round instead of cylindrical.
    I need this term to have parentage up the cell shape branch but not the cell growth branch. Does that make sense?

    Actually the term
    unidimensional cell growth
    has this comment
    Unidimensional cell growth refers to a change in both cell size and cell shape. For cell shape changes where cell size is not affected, consider instead the term 'regulation of cell shape ; GO:0008360' and its children.

    Now I think it is wrong to have a term which represents cell size and cell shape increase simultaneously. These are totally separate processes, they just occur simultaneously.

    hmmm....can of worms...

     

  • Diane Inglis

    Diane Inglis - 2014-09-05

    The new suggested terms are good for the annotation being made but i have to question the placement of the term "unidirectional cell growth" under "cell morphogenesis" though. All the other child terms under "cell morphogenesis" have something to do with a "change" in the way cells are growing or the generation of a new state. "Unidirectional cell growth" seems out of place here because no actual change, transition or morphogenesis is required for this process to occur (at least in fungi) and only one of its child terms have anything to do with a process that involves change.

    Unidirectional cell growth is the standard growth mode for filamentous fungi which do not have any other mode to change to or from. This mode causes short cylindrical hyphal cells to elongate and become long cylindrical hyphal cells. A short cylinder that grows to be a long cylinder is not truly undergoing morphogenesis (or changing cell shape) so I think that last part of the definition will not always true. The unidirectional cell growth term could be reasonably placed as a child of GO:0051211 anisotropic cell growth

    There's also the synonym "cell morphogenesis by unidimensional growth" which is a change in cell shape term and not a great synonym for unidimentional cell growth. It could be considered for it's own separate term as a child of "cell morphogenesis."

    What is the evidence that "unidimensional cell growth" actually requires a change in "both cell size and cell shape?" Is it from nonfungal species where that occurs?

    GO:0007163 establishment or maintenance of cell polarity definition: "Any cellular process that results in the specification, formation or maintenance of anisotropic intracellular organization or cell growth patterns."

    Another source of confusion is the similar combinations of the words used for "cell polarity," "cell polarization" or "polarized cell growth."

    The definition for "establishment and maintenance of cell polarity" terms specifically broadens the usage of the term "cell polarity" to include the establishment or maintenance of anisotropic cell growth patterns in addition to the polarity of cell growth. Since the cell growth pattern can refer to the location where new daughter cells emerge from the mother cell and thus the process of determining a pattern of cell emergence is now also described with similar terms as the process of polarized cell growth.

     

  • David Osumi-Sutherland

    David Osumi-Sutherland - 2014-09-08

    Still thinking this all through, but one thing strikes me from Diane's comments:

    "Unidirectional cell growth is the standard growth mode for filamentous fungi which do not have any other mode to change to or from. This mode causes short cylindrical hyphal cells to elongate and become long cylindrical hyphal cells."

    Arguably, a long thing cylinder is a different shape from a short dumpy one. I can see that it might be a little odd for fungi as this makes all hyphal growth a type of morphogenesis (not currently reflected in the structure of GO). But we'd treat this as morphogenesis in other metazoan contexts (e.g. apico-basal elongation of columnar epithelial cells).

     

  • Valerie Wood

    Valerie Wood - 2014-09-08

    I've been continuing to think about this too. When David H and I talked about this in the past, I think the conclusion was that morphogenesis can be maintenance of a shape in addition to change of a shape. Diane, presumably there are mutants in the filamentous fungi which result in shape changes, and indicate a programe for maintaining the hyphal morphology?

     

  • Diane Inglis

    Diane Inglis - 2014-09-08

    In filamentous fungi some mutations cause hyphae to meander which results in squiggly hyphae instead of straight (unidirectional) hyphae. I'd call that a change in hyphal morphology

     

  • Valerie Wood

    Valerie Wood - 2014-10-10

    I think these terms would work:

    "protein localization to cell tip involved in establishment of
    cell shape and polarity"

    "negative regulation of protein localization to cell tip involved establishment of cell shape and polarity"

    where "cell shape and polarity" is basically any polarity process affecting cell shape to distinguish it from things which affect the internal poliarity of the cell but do not affect cell shape.

    However, I think that there is still some confusion in the ontology with the current parantage,
    because of the different usage of the term "growth" (i.e polarized growth, seems to be coupling 2 processes which occur simultaneously, determination of polarity, and cell size increase). The terms that I need should have no relationship to cell size. The cell will grow independently of growth site selection. The volume will be the same. Only the shape will be different.

    I think we need to have a look at this portion of the graph, maybe in Barcelona if time, or on an editorial call.

     

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