Golgi membrane budding, please!

gocentral commented 21 years ago

Hi,

GO has 'Golgi membrane viral budding' and many other viral budding terms - but how about 'Golgi membrane budding', normal budding that is nothing to do with viruses??

thanks Nellie

Reported by: eleanor

Original Ticket: "geneontology/ontology-requests/679":https://sourceforge.net/p/geneontology/ontology-requests/679

gocentral commented 21 years ago

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Hi Eleanor - just to let you know, we're not ignoring this request (honest!) but it's going to mean adding quite a few new terms because, as you pointed out, we have good viral terms here but nothing else! Will get to this soon though - promise!

Original comment by: jl242

gocentral commented 21 years ago

assigned_to: nobody --> jenclark

Original comment by: jenclark

gocentral commented 21 years ago

Logged In: YES user_id=735846

Is there one specific term that you need urgently, because I could do that first? In the meantime I am working on a whole set as you suggest.

Thanks, Jen

Original comment by: jenclark

gocentral commented 21 years ago

Logged In: YES user_id=735846

Hiya,

Here the changes I have planned for Golgi budding. The DAG shown includes many terms that are already there as context for the ones I am adding. Down below I have included the definition for the new terms and some synonyms for old terms. Ths synonyms are mostly just the dictyosome version of the term's name. 'Dictyosome' is the plant name for the Golgi apparatus.

If everbody's happy with what I've done then I'll add the terms on Monday 11th August.

Thanks,

Jen

Golgi budding

All definitions have reference: ISBN 0-7167-3136-3 1 PMID: 10219233

$intracellular transport ; GO:0046907
--%vacuolar transport ; GO:0007034 ----<endocytosed protein transport to the vacuole ; GO:0007038 ; synonym:delivery of endocytosed proteins to the vacuole-% intracellular protein transport ; GO:0006886 ----%Golgi to vacuole transport ; GO:0006896 ----%retrograde transport from the vacuole ; GO:0045018 --%Golgi vesicle transport ----%intra-Golgi transport ; GO:0006891 ------%cisternal progression ; GO:0045057 ; synonym:cisternal maturation ------%retrograde (vesicle recycling within Golgi) transport ; GO:0000301 -------%protein-Golgi targeting ; GO:0000042 --------%protein-Golgi retention ; GO:0045053 ----%post-Golgi transport ; GO:0006892 -----%Golgi to endosome transport ; GO:0006895 ; synonym:TGN to endosome transport -----%Golgi to plasma membrane transport ; GO:0006893 -----%Golgi to secretory vesicle transport ; GO:0006894 -----%Golgi to vacuole transport ; GO:0006896 ----%retrograde (Golgi to ER) transport ; GO:0006890 ----%ER to Golgi transport ; GO:0006888 ----<Golgi vesicle budding ; GO:newx ------<GTPase activation and membrane binding prior to vesicle budding ; GO:new ------<formation of Golgi membrane priming complex ; GO:newx PMID: 10219233 ------<Golgi membrane bud coat oligomerisation ; GO:newx PMID: 10219233 ------<Golgi membrane binding by cytosolic coat proteins ; GO:newx PMID: 10219233 ------<Golgi vesicle bud deformation and release ; GO:newx PMID: 10219233 ------<Golgi vesicle targeting --------<Golgi transport vesicle coating ; GO:newx--PMID: 10219233 (also child of trans-Golgi network vesicle formation) --------%plasma membrane to endosomes targeting ----------<clathrin vesicle coating --------%trans-Golgi to endosomes targeting ----------<clathrin vesicle coating --------%inter-Golgi cisterna targeting ----------<COPI vesicle coating --------%cis-Golgi to rough ER targeting ---------<COPI vesicle coating --------%rough ER to the cis-Golgi targeting ---------<COPII vesicle coating --------<Regulation of vesicle targeting ----------<positive regulation of vesicle targeting ----------<negative regulation of vesicle targeting ----<Golgi vesicle docking and fusion to target membrane ------<Golgi vesicle coat depolymerization
------<Golgi vesicle coat release and V-SNARE protein exposure ------<Golgi vesicle V-SNARE to T-SNARE protein binding ------<Golgi vesicle prefusion complex stabilisation ------<Golgi vesicle fusion to target membrane --------<regulation of vesicle fusion ----------<positive regulation of vesicle fusion ----------<negative regulation of vesicle fusion ------<dissociation of the Golgi T-SNARE/V-SNARE/SNAP25 complex

Additional parents:

%Golgi transport vesicle coating --%clathrin vesicle coating --%clathrin vesicle coating --%COP I vesicle coating --%COP I vesicle coating --%COP II vesicle coating

%plasma membrane to endosomes transport --<clathrin vesicle coating %trans-Golgi to endosomes transport --<clathrin vesicle coating %inter-Golgi cisterna transport --<COP I vesicle coating %cis-Golgi to rough ER transport -<COP I vesicle coating %rough ER to the cis-Golgi -<COP II vesicle coating

Definitions:

Golgi to vacuole transport ; GO:0006896 new synonym: dictyosome to vacuole transport

Golgi vesicle transport def:The directed movement of substances to, from or within the Golgi, mediated by small transport vesicles. new synonym: dictyosome vesicle transport

intra-Golgi transport ; GO:0006891 new synonym: dictyosome vesicle transport

retrograde (vesicle recycling within Golgi) transport ; GO:0000301 new synonym: retrograde (vesicle recycling within dictyosome) transport

protein-Golgi targeting ; GO:0000042 new synonym: protein-dictyosome targeting

protein-Golgi retention ; GO:0045053 new synonym: protein-dictyosome retention

post-Golgi transport ; GO:0006892 new synonym: post-dictyosome transport

Golgi to endosome transport ; GO:0006895 ; new synonym: dictyosome to endosome transport

Golgi to secretory vesicle transport ; GO:0006894 new synonym: dictyosome to secretory vesicle transport

Golgi to vacuole transport ; GO:0006896 new synonym: dictyosome to vacuole transport

retrograde (Golgi to ER) transport ; GO:0006890 new synonym: retrograde (dictyosome to ER) transport

ER to Golgi transport ; GO:0006888 new synonym: ER to dictyosome transport

Golgi vesicle budding ; GO:new def:The evagination of the Golgi membrane, resulting in formation of a vesicle. new synonym: dictyosome vesicle budding

GTPase activation prior to vesicle budding ; GO:new def: The first stage of membrane budding is GTPase activation; the recruitment of a small GTPase to the donor membrane by it's cognate guanine nucleotide exchange factor (GEF). PMID: 10219233

formation of Golgi membrane priming complex ; GO:new PMID: 10219233 def: Formation of Golgi membrane priming complex: an incoming coat component containing a GTPase activating protein recognises both the GTPase and a membrane protein (e.g. a v-SNARE). The membrane protein acts as a primer to form this priming complex. new synonym:formation of dictyosome membrane priming complex PMID: 7969419

Golgi membrane binding by cytosolic coat proteins ; GO:new PMID: 10219233 def:Following membrane priming, the priming complexes associate laterally and further coat proteins are bound. Cargo proteins diffuse into the budding site and become trapped by their interactions with the coat. ISBN0815316194 new synonym:dictyosome membrane binding by cytosolic coat proteins, dictyosome membrane bud coat oligomerisation, Golgi membrane bud coat oligomerisation

Golgi vesicle bud deformation and release; GO:new PMID: 10219233 def:Cytosolic coat proteins fit together in a basketlike convex framework of hexagons and pentagons to form a coated deformed region on the cytoplasmic surface of the membrane. Finally the deformed region forms into a complete vesicle and is released. new synonym:dictyosome vesicle bud deformation

Golgi vesicle targeting def:Vesicles are targeted to or from the Golgi by the addition of specific coat proteins. Some examples of types of coat proteins include COPI and COPII protein. new synonym:dictyosome vesicle targeting

Golgi transport vesicle coating ; GO:new PMID:10219233 (also child of trans-Golgi network vesicle formation) def:The addition of specific coat proteins to transport vesicles. new synonym:dictyosome transport vesicle coating

plasma membrane to endosomes targeting def:The trageting of vesicles from the plasma membrane to the endosome.

clathrin vesicle coating def:The coating of a vesicle with clathrin.

trans-Golgi to endosomes targeting def:The targeting of a transport vesicle from the trans-Golgi to the endosome. new synonym:trans-dictyosome to endosomes targeting

inter-Golgi cisterna targeting def:The targeting of a transport vesicle from one cisterna of the Golgi apparatus to another. new synonym:inter-dictyosome cisterna targeting

COP I vesicle coating def:The coating of a transport vesicle with COPI protein.

cis-Golgi to rough ER targeting def:The targeting of a transport vesicle from the cis-Golgi to the rough-ER. new synonym:cis-dictyosome to rough ER targeting

rough ER to the cis-Golgi targeting def:The targeting of a transport vesicle from the rough-ER to the cis-Golgi. new synonym:rough ER to the cis-dictyosome targeting

COPII vesicle coating def:The coating of a transport vesicle with COPII protein.

Regulation of vesicle targeting def:Any process that modulates the frequency, rate or extent of vesicle targeting.

positive regulation of vesicle targeting def:Any process that activates or increases the rate of vesicle targeting.

negative regulation of vesicle targeting def:Any process that stops, prevents or reduces the rate of vesicle targeting.

Golgi vesicle coat depolymerization def:Once transport vesicles have budded off, the coat is depolymerized, releasing the coat proteins for reuse. new synonym:dictyosome vesicle coat depolymerization

Golgi vesicle coat release and VSNARE protein exposure def:Uncoating of transport vesicles exposes specific V-SNARE proteins on the surface of each type of vesicle. new synonym:dictyosome vesicle coat release and VSNARE protein exposure

Golgi vesicle V-SNARE to T-SNARE protein binding def:Each V-SNARE on a transport vesicle specifically binds to cognate T-SNARE proteins complexed with SNAP25 on the target membrane. new synonym:dictyosome vesicle VSNARE to TSNARE protein binding

Golgi vesicle prefusion complex stabilisation def:Specific proteins bind to the T-SNARE/V-SNARE/SNAP25 complex, stabilizing the prefusion complex and/or catalyzing dissociation of the T-SNARE/V-SNARE/SNAP25 complex after vesicle fusion. new synonym:dictyosome vesicle prefusion complex stabilisation

Golgi vesicle fusion to target membrane def: When the transport vesicle has docked with it's target membrane, the two membranes fuse. new synonym:dictyosome vesicle fusion to target membrane

Golgi vesicle docking and fusion to target membrane def: When the transport vesicle has moved to it's target location, it docks with the target membrane and then the two membrane's fuse. new synonym:dictyosome vesicle docking and fusion to target membrane

regulation of vesicle fusion def: Any process that modulates the frequency, rate or extent of vesicle fusion. GTP-binding Rab proteins serve as regulators of vesicle targeting and fusion.

positive regulation of vesicle fusion def: Any process that activates or increases the rate of vesicle fusion.

negative regulation of vesicle fusion def: Any process that stops, prevents or reduces the rate of vesicle fusion.

dissociation of the Golgi TSNARE/VSNARE/SNAP25 complex def: Following fusion of the transport vesicle to the target membrane the TSNARE/VSNARE/SNAP25 complex dissociates. new synonym:dissociation of the dictyosome TSNARE/VSNARE/SNAP25 complex

Original comment by: jenclark

gocentral commented 21 years ago

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Hi,

Lots of nice work; thanks! But as usual I have a batch of mostly small comments, this time marked with **.

Golgi budding

All definitions have reference: ISBN 0-7167-3136-3 1

** don't forget to delete the hyphens :)

PMID: 10219233

$intracellular transport ; GO:0046907
--%vacuolar transport ; GO:0007034 ----<endocytosed protein transport to the vacuole ; GO:0007038 ; synonym:delivery of endocytosed proteins to the vacuole-% intracellular protein transport ; GO:0006886 ----%Golgi to vacuole transport ; GO:0006896 ----%retrograde transport from the vacuole ; GO:0045018

** remove 'the'

--%Golgi vesicle transport ----%intra-Golgi transport ; GO:0006891 ------%cisternal progression ; GO:0045057 ; synonym:cisternal maturation ------%retrograde (vesicle recycling within Golgi) transport ; GO:0000301 -------%protein-Golgi targeting ; GO:0000042 --------%protein-Golgi retention ; GO:0045053 ----%post-Golgi transport ; GO:0006892 -----%Golgi to endosome transport ; GO:0006895 ; synonym:TGN to endosome transport -----%Golgi to plasma membrane transport ; GO:0006893 -----%Golgi to secretory vesicle transport ; GO:0006894 -----%Golgi to vacuole transport ; GO:0006896 ----%retrograde (Golgi to ER) transport ; GO:0006890 ----%ER to Golgi transport ; GO:0006888

----<Golgi vesicle budding ; GO:newx ------<GTPase activation and membrane binding prior to vesicle budding ; GO:new

** really a process? sounds like two functions just listed together

------<formation of Golgi membrane priming complex ; GO:newx PMID: 10219233 ------<Golgi membrane bud coat oligomerisation ; GO:newx PMID: 10219233 ------<Golgi membrane binding by cytosolic coat proteins ; GO:newx PMID: 10219233

** really a process? sounds like an interaction

------<Golgi vesicle bud deformation and release ; GO:newx PMID: 10219233 ------<Golgi vesicle targeting

** looks misplaced - is targeting really part of budding? I'd have thought not....

--------<Golgi transport vesicle coating ; GO:newx--PMID: 10219233 (also child of trans-Golgi network vesicle formation) --------%plasma membrane to endosomes targeting

** use 'endosome' (i.e. singular) for this and all similar terms

----------<clathrin vesicle coating --------%trans-Golgi to endosomes targeting ----------<clathrin vesicle coating --------%inter-Golgi cisterna targeting ----------<COPI vesicle coating --------%cis-Golgi to rough ER targeting ---------<COPI vesicle coating --------%rough ER to the cis-Golgi targeting

** remove 'the'

---------<COPII vesicle coating --------<Regulation of vesicle targeting ----------<positive regulation of vesicle targeting ----------<negative regulation of vesicle targeting

** not sure positive and negative really make sense here (also see comments on defs)

----<Golgi vesicle docking and fusion to target membrane

** should this be split into two terms?

------<Golgi vesicle coat depolymerization
------<Golgi vesicle coat release and V-SNARE protein exposure ------<Golgi vesicle V-SNARE to T-SNARE protein binding

is this a bona fide process? wording sounds like just an interaction t-SNARE and v-SNARE use lower-case 't' and 'v'

------<Golgi vesicle prefusion complex stabilisation

** use american spelling of 'stabilization'

------<Golgi vesicle fusion to target membrane --------<regulation of vesicle fusion

** term sounds more generic than parent (cos other vesicles fuse to target membranes); could either move up or change wording to 'regulation of Golgi vesicle fusion'

----------<positive regulation of vesicle fusion ----------<negative regulation of vesicle fusion ------<dissociation of the Golgi T-SNARE/V-SNARE/SNAP25 complex

** really a process?

Additional parents:

%Golgi transport vesicle coating --%clathrin vesicle coating --%clathrin vesicle coating --%COP I vesicle coating --%COP I vesicle coating --%COP II vesicle coating

** some of these will lead to true path violations - e.g. endocytic vesicles have clathrin coats

%plasma membrane to endosomes transport --<clathrin vesicle coating %trans-Golgi to endosomes transport --<clathrin vesicle coating %inter-Golgi cisterna transport --<COP I vesicle coating %cis-Golgi to rough ER transport -<COP I vesicle coating %rough ER to the cis-Golgi -<COP II vesicle coating

Definitions: (** I deleted ones that are already OK.)

Golgi vesicle budding ; GO:new def:The evagination of the Golgi membrane, resulting in formation of a vesicle. new synonym: dictyosome vesicle budding

GTPase activation prior to vesicle budding ; GO:new def: The first stage of membrane budding is GTPase activation; the recruitment of a small GTPase to the donor membrane by it's cognate guanine nucleotide exchange factor (GEF). PMID: 10219233

change it's --> its wording isn't quite what we usually use for definitions - it should state what the process is, e.g. with a 'process by which x happens' style wording (not that it's bad to mention that it's the first stage of parent process x or essential for process y, but the primary purpose of a GO def is to answer the question 'what the $$#@* do you mean by that bunch of words?' ;) )

formation of Golgi membrane priming complex ; GO:new PMID: 10219233 def: Formation of Golgi membrane priming complex: an incoming coat component containing a GTPase activating protein recognises both the GTPase and a membrane protein (e.g. a v-SNARE). The membrane protein acts as a primer to form this priming complex. new synonym:formation of dictyosome membrane priming complex PMID: 7969419

** don't repeat the term in its own def! this one also needs a more process-y wording

Golgi membrane binding by cytosolic coat proteins ; GO:new PMID: 10219233 def:Following membrane priming, the priming complexes associate laterally and further coat proteins are bound. Cargo proteins diffuse into the budding site and become trapped by their interactions with the coat. ISBN0^8153^1619^4 new synonym:dictyosome membrane binding by cytosolic coat proteins, dictyosome membrane bud coat oligomerisation, Golgi membrane bud coat oligomerisation

** same again; this series of defs reads like a narrative describing the successive steps - very informative but doesn't quite do the exact thing that defs should

Golgi vesicle bud deformation and release; GO:new PMID: 10219233 def:Cytosolic coat proteins fit together in a basketlike convex framework of hexagons and pentagons to form a coated deformed region on the cytoplasmic surface of the membrane. Finally the deformed region forms into a complete vesicle and is released. new synonym:dictyosome vesicle bud deformation

** yep, another one for same comments

Golgi vesicle targeting def:Vesicles are targeted to or from the Golgi by the addition of specific coat proteins. Some examples of types of coat proteins include COPI and COPII protein. new synonym:dictyosome vesicle targeting

** and again

Golgi transport vesicle coating ; GO:new PMID:10219233 (also child of trans-Golgi network vesicle formation) def:The addition of specific coat proteins to transport vesicles. new synonym:dictyosome transport vesicle coating

** def sounds more generic than term (def isn't Golgi-specific)

plasma membrane to endosomes targeting def:The trageting of vesicles from the plasma membrane to the endosome.

** typo 'trageting' --> targeting

clathrin vesicle coating def:The coating of a vesicle with clathrin.

COP I vesicle coating def:The coating of a transport vesicle with COPI protein.

** the wording implies that COP I is a single protein, when in fact it's a complex; also, might want to mention that the coat contains adapter proteins as well

COPII vesicle coating def:The coating of a transport vesicle with COPII protein.

** same sort of thing as for COP I - COP II is a complex

Regulation of vesicle targeting def:Any process that modulates the frequency, rate or extent of vesicle targeting.

** not sure the Standard Definition Wording really works for this - vesicle targeting is regulated as to when and especially where, not how much. For the same reason positive & negative regulation don't seem to fit the process either

positive regulation of vesicle targeting def:Any process that activates or increases the rate of vesicle targeting.

negative regulation of vesicle targeting def:Any process that stops, prevents or reduces the rate of vesicle targeting.

Golgi vesicle coat depolymerization def:Once transport vesicles have budded off, the coat is depolymerized, releasing the coat proteins for reuse. new synonym:dictyosome vesicle coat depolymerization

** another one that sounds narrative rather than explanatory

Golgi vesicle coat release and VSNARE protein exposure def:Uncoating of transport vesicles exposes specific V-SNARE proteins on the surface of each type of vesicle. new synonym:dictyosome vesicle coat release and VSNARE protein exposure

** and another

Golgi vesicle V-SNARE to T-SNARE protein binding def:Each V-SNARE on a transport vesicle specifically binds to cognate T-SNARE proteins complexed with SNAP25 on the target membrane. new synonym:dictyosome vesicle VSNARE to TSNARE protein binding

** narrative

Golgi vesicle prefusion complex stabilisation def:Specific proteins bind to the T-SNARE/V-SNARE/SNAP25 complex, stabilizing the prefusion complex and/or catalyzing dissociation of the T-SNARE/V-SNARE/SNAP25 complex after vesicle fusion. new synonym:dictyosome vesicle prefusion complex stabilisation

** narrative

Golgi vesicle fusion to target membrane def: When the transport vesicle has docked with it's target membrane, the two membranes fuse. new synonym:dictyosome vesicle fusion to target membrane

Golgi vesicle docking and fusion to target membrane def: When the transport vesicle has moved to it's target location, it docks with the target membrane and then the two membrane's fuse. new synonym:dictyosome vesicle docking and fusion to target membrane

narrative also it's --> its

regulation of vesicle fusion def: Any process that modulates the frequency, rate or extent of vesicle fusion. GTP-binding Rab proteins serve as regulators of vesicle targeting and fusion.

** move the bit about Rab proteins to a comment

positive regulation of vesicle fusion def: Any process that activates or increases the rate of vesicle fusion.

negative regulation of vesicle fusion def: Any process that stops, prevents or reduces the rate of vesicle fusion.

dissociation of the Golgi TSNARE/VSNARE/SNAP25 complex def: Following fusion of the transport vesicle to the target membrane the TSNARE/VSNARE/SNAP25 complex dissociates. new synonym:dissociation of the dictyosome TSNARE/VSNARE/SNAP25 complex

** narrative

cheers, m (hope this lot isn't overwhelming!)

Original comment by: mah11

gocentral commented 21 years ago

Logged In: YES user_id=735846

New improved version:

Golgi budding

All definitions have reference: ISBN 0-7167-3136-3 1

PMID: 10219233

$intracellular transport ; GO:0046907
--%vacuolar transport ; GO:0007034 ----<endocytosed protein transport to the vacuole ; GO:0007038 synonym:delivery of endocytosed proteins to the vacuole --%intracellular protein transport ; GO:0006886 ----%Golgi to vacuole transport ; GO:0006896 ----%retrograde transport from vacuole ; GO:0045018 --%Golgi vesicle transport ; GO:new ----%intra-Golgi transport ; GO:0006891 ------%cisternal progression ; GO:0045057 ; synonym:cisternal maturation ------%retrograde (vesicle recycling within Golgi) transport ; GO:0000301 -------%protein-Golgi targeting ; GO:0000042 --------%protein-Golgi retention ; GO:0045053 ----%post-Golgi transport ; GO:0006892 -----%Golgi to endosome transport ; GO:0006895 ; synonym:TGN to endosome transport -----%Golgi to plasma membrane transport ; GO:0006893 -----%Golgi to secretory vesicle transport ; GO:0006894 -----%Golgi to vacuole transport ; GO:0006896 ----%retrograde (Golgi to ER) transport ; GO:0006890 ----%ER to Golgi transport ; GO:0006888 ----<Golgi vesicle budding ; GO:new ------<formation of Golgi membrane priming complex ; GO:new PMID: 10219233 ------<Golgi membrane bud coat oligomerisation ; GO:new PMID:10219233 ------<Golgi membrane coating with cytosolic coat proteins ; GO:newx PMID: 10219233 ------<Golgi vesicle bud deformation and release ; GO:new PMID:10219233 ------<Golgi vesicle targeting --------<Golgi transport vesicle coating ; GO:new PMID:10219233 (also child of trans-Golgi network vesicle formation) --------%plasma membrane to endosome targeting ----------<clathrin coating of Golgi vesicle --------%trans-Golgi to endosomes targeting ----------<clathrin coating of Golgi vesicle --------%inter-Golgi cisterna targeting ----------<COPI coating of Golgi vesicle --------%cis-Golgi to rough ER targeting ---------<COPI coating of Golgi vesicle --------%rough ER to cis-Golgi targeting ---------<COPII coating of Golgi vesicle --------<Regulation of Golgi vesicle targeting ----<Golgi vesicle fusion to target membrane ------<Golgi vesicle docking with target membrane ------<Golgi vesicle coat depolymerization
------<Golgi vesicle prefusion complex stabilization ------<regulation of Golgi vesicle fusion to target membrane ----------<positive regulation of vesicle fusion ----------<negative regulation of vesicle fusion

Additional parents:

%Golgi transport vesicle coating --%clathrin coating of Golgi vesicle --%clathrin coating of Golgi vesicle --%COPI coating of Golgi vesicle --%COPI coating of Golgi vesicle --%COPII coating of Golgi vesicle

%plasma membrane to endosomes transport --<clathrin coating of Golgi vesicle %trans-Golgi to endosomes transport --<clathrin coating of Golgi vesicle %inter-Golgi cisterna transport --<COPI coating of Golgi vesicle %cis-Golgi to rough ER transport -<COPI coating of Golgi vesicle %rough ER to the cis-Golgi -<COPII coating of Golgi vesicle

Definitions:

Golgi vesicle budding ; GO:new def:The evagination of the Golgi membrane, resulting in formation of a vesicle. new synonym: dictyosome vesicle budding

formation of Golgi membrane priming complex ; GO:new PMID: 10219233 def: A process by which an incoming coat component recognises both GTPase and a membrane protein to form the membrane priming complex. new synonym:formation of dictyosome membrane priming complex PMID: 7969419

Golgi membrane coating with cytosolic coat proteins ; GO:new PMID: 10219233 def:The process by which the priming complexes associate laterally and further coat proteins are bound. Cargo proteins diffuse into the budding site and become trapped by their interactions with the coat.
new synonym:dictyosome membrane binding by cytosolic coat proteins, dictyosome membrane bud coat oligomerisation, Golgi membrane bud coat oligomerisation

Golgi vesicle bud deformation and release; GO:new PMID: 10219233 def:The process by which cytosolic coat proteins fit together in a basketlike convex framework to form a coated deformed region on the cytoplasmic surface of the membrane. The deformed region forms into a complete vesicle and is released. new synonym:dictyosome vesicle bud deformation

Golgi vesicle targeting def:The process by which the addition of specific coat proteins to vesicles causes the vesicles to be targeted to or from the Golgi. Types of coat proteins include COPI and COPII protein and clathrin. new synonym:dictyosome vesicle targeting

Golgi transport vesicle coating ; GO:new PMID:10219233 (also child of trans-Golgi network vesicle formation) def:The addition of specific coat proteins to Golgi transport vesicles. new synonym:dictyosome transport vesicle coating

plasma membrane to endosomes targeting def:The targeting of vesicles from the plasma membrane to the endosome.

clathrin coating of Golgi vesicle def:The coating of a Golgi transport vesicle with clathrin.

COPI coating of Golgi vesicle def:The coating of a Golgi transport vesicle with COPI protein complexes. The coat also contains adapter proteins.

COPII coating of Golgi vesicle def:The coating of a Golgi transport vesicle with COPII protein complexes. The coat also contains adapter proteins.

Regulation of Golgi vesicle targeting def:Any process that modulates the timing and destination of Golgi transport vesicles.

Golgi vesicle coat depolymerization def:The process by which Golgi vesicle coat proteins are depolymerized, and released for reuse. new synonym:dictyosome vesicle coat depolymerization

Golgi vesicle prefusion complex stabilisation def:The binding of specific proteins to the t-SNARE/v-SNARE/SNAP25 complex, by which the Golgi vesicle prefusion complex is stabilised. new synonym:dictyosome vesicle prefusion complex stabilisation

Golgi vesicle fusion to target membrane def: Fusion of the membrane of a Golgi transport vesicle with it's target membrane. new synonym:dictyosome vesicle fusion to target membrane

Golgi vesicle docking with target membrane def: Linking of a Golgi transport vesicle membrane with its target membrane. new synonym:dictyosome vesicle docking and fusion to target membrane

regulation of vesicle fusion def: Any process that modulates the frequency, rate or extent of vesicle fusion. Comment: GTP-binding Rab proteins serve as regulators of vesicle targeting and fusion.

positive regulation of vesicle fusion def: Any process that activates or increases the rate of vesicle fusion.

negative regulation of vesicle fusion def: Any process that stops, prevents or reduces the rate of vesicle fusion.

dissociation of the Golgi t-SNARE/v-SNARE/SNAP25 complex def: Dissociation of the t-SNARE/v-SNARE/SNAP25 complex, following fusion of the transport vesicle to its target membrane. new synonym:dissociation of the dictyosome t-SNARE/v-SNARE/SNAP25 complex

Original comment by: jenclark

gocentral commented 21 years ago

Logged In: YES user_id=735846

This is what was finally done:

Golgi budding

All definitions have reference: ISBN 07167313631

PMID: 10219233

$intracellular transport ; GO:0046907
--%vacuolar transport ; GO:0007034 ----<endocytosed protein transport to the vacuole ; GO:0007038 synonym:delivery of endocytosed proteins to the vacuole --%intracellular protein transport ; GO:0006886 ----%retrograde transport from vacuole ; GO:0045018 ----%plasma membrane to endosome transport GO:new GO:0048217 --%Golgi vesicle transport ; GO:new GO:0048193 x added as new ----%Golgi to vacuole transport ; GO:0006896 x added as child ----%intra-Golgi transport ; GO:0006891 x added as child ------%cisternal progression ; GO:0045057 ; synonym:cisternal maturation ------%retrograde (vesicle recycling within Golgi) transport ; GO:0000301 -------%protein-Golgi targeting ; GO:0000042 x added as child --------%protein-Golgi retention ; GO:0045053 x added as child ----%post-Golgi transport ; GO:0006892 added as child -----%Golgi to endosome transport ; GO:0006895 ; synonym:TGN to endosome transport -----%Golgi to plasma membrane transport ; GO:0006893 -----%Golgi to secretory vesicle transport ; GO:0006894 -----%Golgi to vacuole transport ; GO:0006896 ----%retrograde (Golgi to ER) transport ; GO:0006890 added as child ----%ER to Golgi transport ; GO:0006888 added as child ----<Golgi vesicle budding ; GO:new GO:0048194 ------<formation of Golgi membrane priming complex ; GO:new GO:0048195 PMID: 10219233 ------<Golgi membrane coating with cytosolic coat proteins ; GO:newx
GO:0048197 PMID: 10219233 ------<Golgi vesicle bud deformation and release ; GO:new GO:0048198 PMID:10219233 ------<Golgi vesicle targeting GO:new GO:0048199 --------<Golgi transport vesicle coating ; GO:new GO:0048200 PMID:10219233 (not done: also child of trans-Golgi network vesicle formation) --------%plasma membrane to endosome targeting GO:new GO:0048201 ----------<clathrin coating of Golgi vesicle GO:new GO:0048202 --------%trans-Golgi to endosome targeting GO:new GO:0048203 ----------<clathrin coating of Golgi vesicle
--------%inter-Golgi cisterna targeting GO:new GO:0048204 ----------<COPI coating of Golgi vesicle GO:new GO:0048205 --------%cis-Golgi to rough ER targeting GO:new GO:0048206 ---------<COPI coating of Golgi vesicle GO:new --------%rough ER to cis-Golgi targeting GO:new GO:0048207 ---------<COPII coating of Golgi vesicle GO:new GO:0048208 --------<Regulation of Golgi vesicle targeting GO:new GO:0048209 ----<Golgi vesicle fusion to target membrane GO:new GO:0048210 ------<Golgi vesicle docking with target membrane GO:new GO:0048211 ------<Golgi vesicle coat depolymerization GO:new GO:0048212 ------<Golgi vesicle prefusion complex stabilization GO:new GO:0048213 ------<regulation of Golgi vesicle fusion to target membrane GO:new GO:0048214 ----------<positive regulation of Golgi vesicle fusion to target membrane GO:new GO:0048215 ----------<negative regulation of Golgi vesicle fusion to target membrane GO:new GO:0048216 ----%trans-Golgi to endosome transport GO:new GO:0048218 -----<clathrin coating of Golgi vesicle GO:new ----%inter-Golgi cisterna transport GO:new GO:0048219 -----<COPI coating of Golgi vesicle GO:new ----%cis-Golgi to rough ER transport GO:new GO:0048220 -----<COPI coating of Golgi vesicle GO:new ----%rough ER to cis-Golgi transport GO:new GO:0048221 -----<COPII coating of Golgi vesicle GO:new

Additional parents:

%Golgi transport vesicle coating GO:new --%clathrin coating of Golgi vesicle GO:new --%COPI coating of Golgi vesicle GO:new --%COPII coating of Golgi vesicle GO:new

Definitions:

Golgi vesicle budding ; GO:new def:The evagination of the Golgi membrane, resulting in formation of a vesicle. new synonym: dictyosome vesicle budding

formation of Golgi membrane priming complex ; GO: new PMID: 10219233 def: A process by which an incoming coat component recognises both GTPase and a membrane protein to form the membrane priming complex. new synonym:formation of dictyosome membrane priming complex PMID: 7969419

Golgi membrane coating with cytosolic coat proteins ; GO: new PMID: 10219233 def:The process by which the priming complexes associate laterally and further coat proteins are bound. Cargo proteins diffuse into the budding site and become trapped by their interactions with the coat. new synonym:dictyosome membrane binding by cytosolic coat proteins , dictyosome membrane bud coat oligomerisation, Golgi membrane bud coat oligomerisation

Golgi vesicle bud deformation and release; GO: new PMID: 10219233 def:The process by which cytosolic coat proteins fit together in a basketlike convex framework to form a coated deformed region on the cytoplasmic surface of the membrane. The deformed region forms into a complete vesicle and is released. new synonym:dictyosome vesicle bud deformation

Golgi vesicle targeting def:The process by which the addition of specific coat proteins to vesicles causes the vesicles to be targeted to or from the Golgi. Types of coat proteins include COPI and COPII protein and clathrin. new synonym:dictyosome vesicle targeting

Golgi transport vesicle coating ; GO: new PMID:10219233 (also child of trans-Golgi network vesicle formation) def:The addition of specific coat proteins to Golgi transport vesicles. new synonym:dictyosome transport vesicle coating