gocentral
commented
16 years ago Logged In: YES user_id=1101528 Originator: NO
A piece of biology that I tripped over about a year ago - animal cells can take up stuff from the extracellular space by cell surface receptor-mediated endocytosis, forming a clathrin-coated vesicle, which then underges successive modifications, losing its clathrin coat, and fusing with other vesicles which contribute vesicle membrane-associated proton pumps and inactive forms of digestive enzymes. Then, the proton pumps turn on, the digestive enzymes get activated, and the vesicle contents get degraded. Somewhere along the way, the cell surface receptors (now in the endocytic vesicle membrane) may get moved into a separate vesicle so that they are spared from degradation and can be returned to the cell surface. Something like this is the classic pathway for LDL (low density lipoprotein) uptake by liver cells that Brown and Goldstein worked out, but apparently it works for many other receptors and their ligands as well. Somewhere in the process, the evolving vesicle comes to be called a lysosome. (The vesicle that donated the pumps and digestive enzymes is also a distinct sort of lysosome, I think.)
This class of processes can clearly generate diverse vesicles, each with potential variants, and that's a legitimate biological reason for that "any of a group of ..." construction in the lysosome definition.
What's needed clearly is a well-defined taxonomy, or a kind of menu or decision tree that would show what sort of vesicle arises according to receptor and ligand, and what the intracellular fates of each such vesicle are. The experts I talked to about all of this a year ago were pretty vague on these points - there appears still to be a lot of missing information, so people can describe a major fate of a particular ligand, but would feel unhappy with any description / definition that didn't also allow for the less well-described / minor fates.
The discussion of all of this in the current edition of the Alberts et al. cell biology textbook is said by my expert sources to be up-to-date and authoritative.
Peter
Original comment by: deustp01
The differentium between lytic vacuole, and its subtype, lysosome is not clear:
GO:0000323 ! lytic vacuole [DEF: "A vacuole that is maintained at an acidic pH and which contains degradative enzymes, including a wide variety of acid hydrolases."]
GO:0005764 ! lysosome [DEF: "Any of a group of related cytoplasmic, membrane bound organelles that are found in most animal cells and that contain a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions."]
Can we have a def of lysosome in genus-differentia style? "Any group of..." is confusing. Is this an aggregate in the cell, or is group synonym for "class"?
There is a redundant listing of N+S conditions here, with minor adjectival differences ("wide variety" vs "variery" - is this significant or just down to def source)?
the genus of lytic vacuole is "vacuole", and the genus of lysosome is presumably "cytoplasmic, membrane bound organelles" (not "group of..."). This difference in wording is confusing as they are presumably both (1) vacuoles, (2) membrane-bound organnelles and (3) intracellular.
Also GO names "intracellular membrane-bound organelles" but not "cytoplasmic membrane-bound organelles". Is the cytoplasm vs intracellular distinction relevant here? My guess is not.
This seems a little odd:
--is_a GO:0000326 ! protein storage vacuole ---is_a GO:0000327 ! lytic vacuole within protein storage vacuole
should be part_of?
I find this def a little confusing:
GO:0000326 protein storage vacuole [DEF: "A compound organelle of plants where there is a lytic vacuole within a storage vacuole."]
I read this as "a compound organelle of plants that has_part a lytic vacuole"
or even "a storage vacuole that has_part a lytic vacuole. Found in plants"
(I don't know what a "compound" organelle is, and GO only uses this term once, in this definition)
Reported by: cmungall
Original Ticket: "geneontology/ontology-requests/5184":https://sourceforge.net/p/geneontology/ontology-requests/5184