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#10588 NTRs: Piccolo-Bassoon transport vesicle and Synaptic vesicle protein transport vesicle

None
closed-accepted
Paola Roncaglia
New term request (5530)
5
2013-12-20
2013-12-17
Paola Roncaglia
No

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)

Related

Ontology requests: #10588

Discussion

  • Paola Roncaglia

    Paola Roncaglia - 2013-12-17
    • 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
     

  • Daniela Raciti

    Daniela Raciti - 2013-12-18

    Thanks Paola

     

  • Paola Roncaglia

    Paola Roncaglia - 2013-12-18

    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

     

    • Daniela Raciti

      Daniela Raciti - 2013-12-18

      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)

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

      To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/

       

      Related

      Ontology requests: #10588

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  • Paola Roncaglia

    Paola Roncaglia - 2013-12-19

    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

     

    • Daniela Raciti

      Daniela Raciti - 2013-12-19

      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/

      To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/

       
      alternate

  • Daniela Raciti

    Daniela Raciti - 2013-12-20

    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

     

  • Paola Roncaglia

    Paola Roncaglia - 2013-12-20

    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

     

  • Paola Roncaglia

    Paola Roncaglia - 2013-12-20
    • status: open --> closed-accepted
     

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