Menu
▾
▴
#10773 flocculation and adhesion
open
5
2014-09-25
2014-04-14
No
I know there is some history here, but I cannot remember why flocculation cannot be a child of cell-cell adhesion (and I can't locate the old tickets due to the SF search issues).
But based on current defs, it really seems as though it could/should be?
Assuming the lack of relationship is deliberate, this may be because cell-cell adhesion is a binary interaction and flocculation involves the formation of aggregates consisting of large numbers of cells. In this is the case, we could make a new term: cell-cell adhesion involved in agglomeration. This would be a subclass of cell-cell adhesion and a part_of flocculation. Would this work for you?
BTW - I'm wondering whether the def of flocculation might be too specific.
The current def is: "The reversible, calcium-dependent non-sexual aggregation of single-celled organisms."
I assume the calcium-dependency clause is there to fit with flocculation in yeast, but do (can?!) we know whether this is dependency is true for other flocculating microbes?
'cell-cell adhesion involved in flocculation' has been there for quite a while - GO:0043689
Diff:
GO:0000128 flocculation is a multi-organism cellular process. GO:0016337 cell-cell adhesion is a single-organism cellular process. Is it even appropriate to make an MOCP a child of a SOCP?
Regarding the calcium dependency, flocculation in Candida famata seems to not depend on calcium but on peptone. PMID:8740415. There may be others but I'd have to spend time looking.
Diane
Hi Diane,
Nope. Just checked. This would cause a disjointness violation. But, as Midori just pointed out, we do have a term for 'cell-cell adhesion involved in flocculation' (I really should have checked...). This is clearly a multi-organismal process. It's just not asserted to be so. I think we should either broaden cell-cell adhesion to make it neutral as to whether it is single or multi-organismal or make a new broader term.
Thanks for this. I'll remove the Ca2+ dependency clause.
The reason I asked is because yesterday I requested a FYPO phenotype term
"abnormal galactose-specific cell adhesion". In the experiment I was curating, this is not shown to be "flocculation specific" (although it probably is)
There are GO terms for "galactose-specific flocculation" and "mannose specific flocculation". I wanted to ensure that if phenotype terms for
"abnormal galactose-specific flocculation" were requested,
they would be somehow be children " of abnormal galactose-specific cell adhesion" which seems to need to happen at the level of GO.
I remember now that I always struggled with this branch. I don't really understand what flocculation is, apart from being a type os "cell-cell adhesion". Does it have any other 'parts'? If so what are they? all of the children seem to describe types of adhesion.
I guess the question is, where does flocculation start and end?
All of the definitions I can find for yeast flocculation define it as:
the "reversible, asexual and calcium dependent process by which cells adhere to form flocs", or similar.
which as far as I can figure, is describing a specific type of adhesion + its regulation.
From PMID: 18708514
"Flocculation in S. cerevisiae is mediated by specific cell surface lectins (or flocculins) that are capable of binding directly to mannose residues of mannan molecules on adjacent cells. This interaction leads to cellular aggregation and finally settling.
So it seems that lectins binding sugars on adjacent cells is the first step, cell aggregation is the second step and settling is the end result.
That's just my interpretation from what I know and can find online.
Diane
cell-cell adhesion is the mechanism of flocculation, but if cell-cell adhesion happened at a sufficiently low level (perhaps in a very dilute culture, resulting mostly in pairs or very small clusters of bound cells?), then presumably the result would not count as flocculation. So, I think it is correct that these be kept as separate terms. I can make the related cell-cell adhesion terms for the various subclasses of flocculation. These could be used to formally define the flocculation classes.
I think it makes sense for most annotations to be to the cell-cell adhesion terms. I can add comments to the flocculation terms to recommend this to annotators.
I still don't understand :(
Everything I read describes flocculation as a type of calcium dependent cell-cell adhesion. These are the defining features of flocculation.
This makes it seem as though this parent- child relation to cell-cell adhesion would be OK the single organsism restriction was removed from cell-cell adhesion (maybe then a child term would be needed to group all of the developmental cell-cell adhesion which could have this single organism parentage?).
GO:0000771 agglutination involved in conjugation
could also have the exact synonym
"sexual flocculation"
and has
has a cell adhesion parentage
see for example PMID:23311928
"Yeast flocculation is the process, by which cells aggregate, mediated by cell wall-associated adhesive proteins. Two types of flocculations are recognized in yeast, namely sexual and nonsexual flocculation. Flocculation is best characterized
in budding yeast Saccharomyces cerevisiae, in which cell wall proteins (Aga1 and Sag1) bound to glycosylphosphatidylinositol (GPI) are required for mating,
and the Flo1, Flo5, Flo9 and Flo11 flocculins play roles in nonsexual flocculation, invasive growth, and filamentous growth (Soares, 2011). While sexual flocculation in fission yeast Schizosaccharomyces pombe is mediated by an adhesin (Map4; Sharifmoghadam & Valdivieso, 2008), nonsexual flocculation is mediated by the recently identified
flocculin Gsf2."
but also lots of other pubs
http://ec.asm.org/content/12/3/450.full
http://link.springer.com/article/10.1023/A%3A1000166426509#page-1
http://www.ncbi.nlm.nih.gov/pubmed/23284084
I don't think we can treat sexual and no sexual flooculation differently
Diff: