NTRs: Piccolo-Bassoon transport vesicle and Synaptic vesicle protein transport vesicle

[gocentral]

From an email from Daniela Raciti (WormBase):

Piccolo-Bassoon transport vesicle (synonym:PVT). Dense-core vesicle or aggregates of vesicles and proteins that range in size from approximately 80 nm in diameter for dense core vesicles to 130 nm by 220 nm in area for aggregates. Proteins transported by PTVs include piccolo, bassoon, N-cadherin and syntaxin. PVT are packaged via the trans-Golgi network before being transported through the axon.

Synaptic vesicle protein transport vesicle (Synonym:STV). Vesicle heterogeneous in size and shape composed of both tubulovesicular and clear core vesicles that transport synaptic vesicle-associated proteins. Proteins carried by STVs include synaptophysin, synapsin Ia, synaptotagmin and synaptobrevin/vesicle-associated membrane protein 2 (VAMP2). STVs are packaged via the trans-Golgi network before being transported through the axon.

Both terms should be children of "cytoplasmic vesicle".

reference: Bury LA, Sabo SL. Coordinated trafficking of synaptic vesicle and active zone proteins prior to synapse formation. Neural Dev. 2011 May 10;6:24. doi: 10.1186/1749-8104-6-24. PubMed PMID: 21569270; PubMed Central PMCID: PMC3103415.

Additional references:

Ahmari SE, Buchanan J, Smith SJ: Assembly of presynaptic active zones from cytoplasmic transport packets. Nat Neurosci 2000, 3:445-451

Dresbach T, Torres V, Wittenmayer N, Altrock WD, Zamorano P, Zuschratter W, Nawrotzki R, Ziv NE, Garner CC, Gundelfinger ED: Assembly of active zone precursor vesicles: obligatory trafficking of presynaptic cytomatrix proteins Bassoon and Piccolo via a trans-Golgi compartment. J Biol Chem 2006, 281:6038-6047.

Kraszewski K, Mundigl O, Daniell L, Verderio C, Matteoli M, De Camilli P: Synaptic vesicle dynamics in living cultured hippocampal neurons visualized with CY3-conjugated antibodies directed against the lumenal domain of synaptotagmin. J Neurosci 1995, 15:4328-4342

Nakata T, Terada S, Hirokawa N: Visualization of the dynamics of synaptic vesicle and plasma membrane proteins in living axons. J Cell Biol 1998, 140:659-674.

Sabo SL, Gomes RA, McAllister AK: Formation of presynaptic terminals at predefined sites along axons.J Neurosci 2006, 26:10813-10825.

Tao-Cheng JH: Ultrastructural localization of active zone and synaptic vesicle proteins in a preassembled multi-vesicle transport aggregate. Neuroscience 2007, 150:575-584.

Zhai et al, 2001 neuron (http://www.sciencedirect.com/science/article/pii/S0896627301001854)

Reported by: paolaroncaglia

Original Ticket: geneontology/ontology-requests/10588

[gocentral]

• Description has changed:

Diff:

--- old
+++ new
@@ -4,6 +4,7 @@

 Synaptic vesicle protein transport vesicle (Synonym:STV). Vesicle heterogeneous in size and shape composed of both tubulovesicular and clear core vesicles that transport synaptic vesicle-associated proteins. Proteins carried by STVs include synaptophysin, synapsin Ia, synaptotagmin and synaptobrevin/vesicle-associated membrane protein 2 (VAMP2). STVs are packaged via the trans-Golgi network before being transported through the axon. 

+Both terms should be children of "cytoplasmic vesicle".

 reference:
 Bury LA, Sabo SL. Coordinated trafficking of synaptic vesicle and active zone 

Original comment by: paolaroncaglia

[gocentral]

Thanks Paola

Original comment by: draciti

[gocentral]

Hi Daniela,

I have a question on your second request:

"Synaptic vesicle protein transport vesicle (Synonym:STV). Vesicle heterogeneous in size and shape composed of both tubulovesicular and clear core vesicles that transport synaptic vesicle-associated proteins. Proteins carried by STVs include synaptophysin, synapsin Ia, synaptotagmin and synaptobrevin/vesicle-associated membrane protein 2 (VAMP2). STVs are packaged via the trans-Golgi network before being transported through the axon."

I'd like to make sure that this is not, in fact, the same as GO:0008021 synaptic vesicle. I see that your term would refer to aggregates of smaller vesicles rather than just one vesicle, but I'm not sure how well resolution techniques can distinguish between the two... current annotations to GO:0008021 synaptic vesicle include e.g. VAMP2. Is GO:0008021 synaptic vesicle the only term we need? If not, how should we differentiate between the two.

Thanks, Paola

Original comment by: paolaroncaglia

[gocentral]

Ok Paola, I will take a closer look and get back to you Thanks Daniela

On Dec 18, 2013, at 6:05 AM, Paola Roncaglia wrote:

Hi Daniela,

I have a question on your second request:

"Synaptic vesicle protein transport vesicle (Synonym:STV). Vesicle heterogeneous in size and shape composed of both tubulovesicular and clear core vesicles that transport synaptic vesicle-associated proteins. Proteins carried by STVs include synaptophysin, synapsin Ia, synaptotagmin and synaptobrevin/vesicle-associated membrane protein 2 (VAMP2). STVs are packaged via the trans-Golgi network before being transported through the axon."

I'd like to make sure that this is not, in fact, the same as GO:0008021 synaptic vesicle. I see that your term would refer to aggregates of smaller vesicles rather than just one vesicle, but I'm not sure how well resolution techniques can distinguish between the two... current annotations to GO:0008021 synaptic vesicle include e.g. VAMP2. Is GO:0008021 synaptic vesicle the only term we need? If not, how should we differentiate between the two.

Thanks, Paola

[ontology-requests:#10588] NTRs: Piccolo-Bassoon transport vesicle and Synaptic vesicle protein transport vesicle

Status: open Labels: New term request Created: Tue Dec 17, 2013 03:18 PM UTC by Paola Roncaglia Last Updated: Wed Dec 18, 2013 09:33 AM UTC Owner: Paola Roncaglia

From an email from Daniela Raciti (WormBase):

Piccolo-Bassoon transport vesicle (synonym:PVT). Dense-core vesicle or aggregates of vesicles and proteins that range in size from approximately 80 nm in diameter for dense core vesicles to 130 nm by 220 nm in area for aggregates. Proteins transported by PTVs include piccolo, bassoon, N-cadherin and syntaxin. PVT are packaged via the trans-Golgi network before being transported through the axon.

Synaptic vesicle protein transport vesicle (Synonym:STV). Vesicle heterogeneous in size and shape composed of both tubulovesicular and clear core vesicles that transport synaptic vesicle-associated proteins. Proteins carried by STVs include synaptophysin, synapsin Ia, synaptotagmin and synaptobrevin/vesicle-associated membrane protein 2 (VAMP2). STVs are packaged via the trans-Golgi network before being transported through the axon.

Both terms should be children of "cytoplasmic vesicle".

reference: Bury LA, Sabo SL. Coordinated trafficking of synaptic vesicle and active zone proteins prior to synapse formation. Neural Dev. 2011 May 10;6:24. doi: 10.1186/1749-8104-6-24. PubMed PMID: 21569270; PubMed Central PMCID: PMC3103415.

Additional references:

Ahmari SE, Buchanan J, Smith SJ: Assembly of presynaptic active zones from cytoplasmic transport packets. Nat Neurosci 2000, 3:445-451

Dresbach T, Torres V, Wittenmayer N, Altrock WD, Zamorano P, Zuschratter W, Nawrotzki R, Ziv NE, Garner CC, Gundelfinger ED: Assembly of active zone precursor vesicles: obligatory trafficking of presynaptic cytomatrix proteins Bassoon and Piccolo via a trans-Golgi compartment. J Biol Chem 2006, 281:6038-6047.

Kraszewski K, Mundigl O, Daniell L, Verderio C, Matteoli M, De Camilli P: Synaptic vesicle dynamics in living cultured hippocampal neurons visualized with CY3-conjugated antibodies directed against the lumenal domain of synaptotagmin. J Neurosci 1995, 15:4328-4342

Nakata T, Terada S, Hirokawa N: Visualization of the dynamics of synaptic vesicle and plasma membrane proteins in living axons. J Cell Biol 1998, 140:659-674.

Sabo SL, Gomes RA, McAllister AK: Formation of presynaptic terminals at predefined sites along axons.J Neurosci 2006, 26:10813-10825.

Tao-Cheng JH: Ultrastructural localization of active zone and synaptic vesicle proteins in a preassembled multi-vesicle transport aggregate. Neuroscience 2007, 150:575-584.

Zhai et al, 2001 neuron (http://www.sciencedirect.com/science/article/pii/S0896627301001854)

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Original comment by: draciti

[gocentral]

In the meantime, here's the other term:

[Term] id: GO:1990257 name: piccolo-bassoon transport vesicle namespace: cellular_component def: "A cytoplasmic dense-core vesicle, or aggregate of vesicles and proteins, that range in size from approximately 80 nm in diameter for dense core vesicles to 130 nm by 220 nm in area for aggregates. Proteins transported by piccolo-bassoon transport vesicle (PTVs) include piccolo, bassoon, N-cadherin and syntaxin. PTVs are packaged via the trans-Golgi network before being transported through the axon." [GOC:dr, PMID:21569270] synonym: "PTV" EXACT [] is_a: GO:0031410 ! cytoplasmic vesicle

Thanks, Paola

Original comment by: paolaroncaglia

[gocentral]

thanks! d

On Dec 19, 2013, at 6:16 AM, Paola Roncaglia wrote:

In the meantime, here's the other term:

[Term] id: GO:1990257 name: piccolo-bassoon transport vesicle namespace: cellular_component def: "A cytoplasmic dense-core vesicle, or aggregate of vesicles and proteins, that range in size from approximately 80 nm in diameter for dense core vesicles to 130 nm by 220 nm in area for aggregates. Proteins transported by piccolo-bassoon transport vesicle (PTVs) include piccolo, bassoon, N-cadherin and syntaxin. PTVs are packaged via the trans-Golgi network before being transported through the axon." [GOC:dr, PMID:21569270] synonym: "PTV" EXACT [] is_a: GO:0031410 ! cytoplasmic vesicle

Thanks, Paola

[ontology-requests:#10588] NTRs: Piccolo-Bassoon transport vesicle and Synaptic vesicle protein transport vesicle

Status: open Labels: New term request Created: Tue Dec 17, 2013 03:18 PM UTC by Paola Roncaglia Last Updated: Wed Dec 18, 2013 02:04 PM UTC Owner: Paola Roncaglia

From an email from Daniela Raciti (WormBase):

Piccolo-Bassoon transport vesicle (synonym:PVT). Dense-core vesicle or aggregates of vesicles and proteins that range in size from approximately 80 nm in diameter for dense core vesicles to 130 nm by 220 nm in area for aggregates. Proteins transported by PTVs include piccolo, bassoon, N-cadherin and syntaxin. PVT are packaged via the trans-Golgi network before being transported through the axon.

Synaptic vesicle protein transport vesicle (Synonym:STV). Vesicle heterogeneous in size and shape composed of both tubulovesicular and clear core vesicles that transport synaptic vesicle-associated proteins. Proteins carried by STVs include synaptophysin, synapsin Ia, synaptotagmin and synaptobrevin/vesicle-associated membrane protein 2 (VAMP2). STVs are packaged via the trans-Golgi network before being transported through the axon.

Both terms should be children of "cytoplasmic vesicle".

reference: Bury LA, Sabo SL. Coordinated trafficking of synaptic vesicle and active zone proteins prior to synapse formation. Neural Dev. 2011 May 10;6:24. doi: 10.1186/1749-8104-6-24. PubMed PMID: 21569270; PubMed Central PMCID: PMC3103415.

Additional references:

Ahmari SE, Buchanan J, Smith SJ: Assembly of presynaptic active zones from cytoplasmic transport packets. Nat Neurosci 2000, 3:445-451

Dresbach T, Torres V, Wittenmayer N, Altrock WD, Zamorano P, Zuschratter W, Nawrotzki R, Ziv NE, Garner CC, Gundelfinger ED: Assembly of active zone precursor vesicles: obligatory trafficking of presynaptic cytomatrix proteins Bassoon and Piccolo via a trans-Golgi compartment. J Biol Chem 2006, 281:6038-6047.

Kraszewski K, Mundigl O, Daniell L, Verderio C, Matteoli M, De Camilli P: Synaptic vesicle dynamics in living cultured hippocampal neurons visualized with CY3-conjugated antibodies directed against the lumenal domain of synaptotagmin. J Neurosci 1995, 15:4328-4342

Nakata T, Terada S, Hirokawa N: Visualization of the dynamics of synaptic vesicle and plasma membrane proteins in living axons. J Cell Biol 1998, 140:659-674.

Sabo SL, Gomes RA, McAllister AK: Formation of presynaptic terminals at predefined sites along axons.J Neurosci 2006, 26:10813-10825.

Tao-Cheng JH: Ultrastructural localization of active zone and synaptic vesicle proteins in a preassembled multi-vesicle transport aggregate. Neuroscience 2007, 150:575-584.

Zhai et al, 2001 neuron (http://www.sciencedirect.com/science/article/pii/S0896627301001854)

Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/geneontology/ontology-requests/10588/

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Original comment by: draciti

[gocentral]

Paola STVs indeed differ from Synaptic vesicles. Whenever you can you can generate the term. From the authors

Dear Daniela, You are correct that STVs differ from synaptic vesicles, and the definition of STVs below is accurate. There is both a morphological and functional distinction between STVs and synaptic vesicles. Functionally, STVs are transport vesicles that deliver synaptic vesicle proteins to synapses, while synaptic vesicles are responsible for transmitter release at synapses. Morphologically, synaptic vesicles are very homogeneous, while STVs are very heterogeneous. STVs might be a precursor for synaptic vesicles.

thanks Daniela

Original comment by: draciti

[gocentral]

Thanks Daniela, that's very helpful. I've added the new term:

GO:0097547 synaptic vesicle protein transport vesicle

And I've added definition comments to both the new term and the existing 'synaptic vesicle' to underline the differences between the two.

Happy holidays! Paola

Original comment by: paolaroncaglia

[gocentral]

• status: open --> closed-accepted

Original comment by: paolaroncaglia