Cryptococcus NTR: protein secretion phenotype

[Achchuthan]

1) NTR

Arrested protein secretion (is_a: OMP:0007346! protein secretion phenotype)

2) Xref

protein secretion phenotype xref: GO:0009306 " protein secretion" APO cross-refs: id: APO:0000078 name: protein secretion namespace: observable alt_id: YPO:0000078 def: "Transport of proteins out of the cell by fusion of a membrane-bounded vesicle containing the proteins by fusion of the vesicle with the plasma membrane." [SGD:mcc] subset: AspGD subset: CGD subset: CryptoGD subset: SGD synonym: "exocytosis" RELATED [] is_a: APO:0000129 ! protein transport

[dsiegele]

APO:0000078 def: "Transport of proteins out of the cell by fusion of a membrane-bounded vesicle containing the proteins by fusion of the vesicle with the plasma membrane." [SGD:mcc]

I added APO:0000078 as a narrow synonym of OMP:0007346 protein secretion phenotype. I did this because in bacteria protein secretion usually doesn't involve fusion of vesicles with the plasma membrane.

[Achchuthan]

Thanks a lot Debby for adding as synonym. This makes sense!

[dsiegele]

I added exocytosis as a narrow synonym of protein secretion phenotype.

[dsiegele]

What would the definition of 'arrested protein secretion' be?

[Achchuthan]

Hi Debby,

This is my envisaged definition for the arrested phenotype:

Arrested protein secretion phenotype is an altered protein secretion phenotype where protein secretion was not observed in a given time period relative to a designated control.

[dsiegele]

In other OMP terms, we have called phenotypes like this decreased protein secretion and abolished protein secretion. Would that be OK?

[Achchuthan]

You're right Debby. As I read the decreased protein secretion definition, it describes the timing as well! So, this sounds good!

[dianeoinglis]

When SGD (Saccharomyces Genome Database) uses the APO term "protein secretion", a "Reporter" field is ALWAYS used to name the specific protein or fusion protein is the readout such as "heterologous B. licheniformis alpha-amylase," "precursor carboxypeptidase Y," "alpha-factor," etc.

CGD (Candida Genome Database) is less consistent at indicating a reporter. But Candida species have families of secreted proteins such as secreted aspartyl protease (SAP genes or SAPs) and lipases, some of which are important for virulence. Sometimes "secreted aspartyl protease" will be recorded as the Reporter and other times "secreted aspartyl protease" or "secreted aspartyl protease activity" will be in the "Details" field where curators can add free text, depending whether the assay measured protein or protein activity.. http://www.candidagenome.org/cgi-bin/phenotype/phenotype.pl?observable=protein%20secretion

AspGD (Aspergillus Genome Database) also uses the Reporter field or the Details field. http://www.aspergillusgenome.org/cgi-bin/phenotype/phenotype.pl?observable=protein%20secretion

This term is a child of APO "protein transport" which is somewhat restrictive and most often the specific protein recorded as the reporter, is actually a readout for the process of "exocytosis." Exocytosis is referenced as "synonym: "exocytosis" RELATED []"but, in my opinion, "exocytosis" is preferable as the "term name" and should be a parent of terms for siblings "protein secretion" and "non-protein secretion." Cryptococcus synthesizes "glucuronoxylomannan" which is the major sugar component of the capsule. Glucuronoxylomannan is secreted by exocytosis but the structure of the APO precludes a term for non-protein exocytosis by its placement under "protein transport."

I think the actual term request should be "exocytosis phenotype" with "protein secretion phenotype" and either "glucuronoxylomannan secretion phenotype" or just "carbohydrate secretion phenotype" as child terms of "exocytosis phenotype." As I commented previously, some proteins are so important to the biology of the organism they deserve a specific term such as "secreted phospholipase B secretion phenotype."

Thoughts or comments? Diane