#1114 O13703 Kw mapping to lipis transport KW:KW-0445

UniProt
closed-fixed
nobody
None
5
2014-09-24
2013-11-03
Valerie Wood
No

O13703
Vps20 associated protein Vts1
is mapping to KW:KW-0445 "lipid transport" but I can't find any evidence in the major models

val

Discussion

  • rach_huntley
    rach_huntley
    2013-11-20

    Sent to UniProt

     
  • Marc Feuermann
    Marc Feuermann
    2013-12-05

    Hi Val,
    I've checked where the mapping to KW:KW-0445 "lipid transport" comes from. In fact it was mapped to the S.cerevisiae ortholog VTA1 from PMID:12953057.
    In the paper they show that:

    "Vps20p and Vta1p are required for efficient endocytosis of fluid-phase and membrane markers from the cell surface to the vacuole".

    "We next examined whether Vps20p and Vta1p are important for bulk membrane transport from
    the cell surface to the vacuole. The lipid dye FM4-64 is a membrane-soluble dye that binds to the plasma membrane and is internalised by endocytosis and delivered to the vacuole
    membrane... By 30 minutes, FM4-64 could clearly be seen on the vacuole limiting membrane in wild-type cells. In contrast, the bulk of FM4-64 remained in large endosomal structures in both the vps20delta and vta1delta cells, indicating a delay in transport from the class E compartment to the vacuole.

    I hope this helps.
    Regards,
    Marc.

     
  • Valerie Wood
    Valerie Wood
    2013-12-05

    I'm never sure what to do in these cases. This logic sort of implies that all genes involved in vesicle-mediated transport (306 in pombe) should be annotated to "lipid transport" because membrane is being moved, but would people really expect this?

    Membrane is moved but is the lipid being transported incidentally during membrane protein internalization and degradation, i.e the vesicle is the agent doing the transporting?

    I will ask...

     
  • Marc Feuermann
    Marc Feuermann
    2013-12-05

    Yes, I was thinking the same. But as they used a lipid dye that was transported, I understand the annotation of lipid transport. This was the reason why I first wanted to send you the information. However, I think it is not a big concern for us to remove the KW if you think that it's really not appropriate.

     
  • Valerie Wood
    Valerie Wood
    2013-12-05

    I asked SGD to take a look. We should include this info in some annotation guidelines somewhere if this is the case, as it isn't obvious that you wouldn't make the annotation.
    VAl

     
  • Valerie Wood
    Valerie Wood
    2014-09-24

    mapping is removed

     
  • Valerie Wood
    Valerie Wood
    2014-09-24

    • Description has changed:

    Diff:

    --- old
    +++ new
    @@ -1,4 +1,3 @@
    -
     O13703
        Vps20 associated protein Vts1
     is mapping to KW:KW-0445 "lipid transport" but I can't find any evidence in the major models
    
    • status: open --> closed-fixed