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A manual collection of Syt, Esyt, Rph3a, Rph3al, Doc2, and Dblc2 genes from 46 metazoan genomes--an open access resource for neuroscience and evolutionary biology.

Craxton M - BMC Genomics (2010)

Bottom Line: Synaptotagmins were subsequently found to form a large family, some members of which play important roles in calcium triggered exocytic events.One definition does not necessarily imply the other.Current understanding does not explain why this is so.

View Article: PubMed Central - HTML - PubMed

Affiliation: Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB20QH, UK. mollycraxton@btinternet.com

ABSTRACT

Background: Synaptotagmin proteins were first identified in nervous tissue, residing in synaptic vesicles. Synaptotagmins were subsequently found to form a large family, some members of which play important roles in calcium triggered exocytic events. These members have been investigated intensively, but other family members are not well understood, making it difficult to grasp the meaning of family membership in functional terms. Further difficulty arises as families are defined quite legitimately in different ways: by common descent or by common possession of distinguishing features. One definition does not necessarily imply the other. The evolutionary range of genome sequences now available, can shed more light on synaptotagmin gene phylogeny and clarify family relationships. The aim of compiling this open access collection of synaptotagmin and synaptotagmin-like sequences, is that its use may lead to greater understanding of the biological function of these proteins in an evolutionary context.

Results: 46 metazoan genomes were examined and their complement of Syt, Esyt, Rph3a, Rph3al, Doc2 and Dblc2 genes identified. All of the sequences were compared, named, then examined in detail. Esyt genes were formerly named Fam62. The species in this collection are Trichoplax, Nematostella, Capitella, Helobdella, Lottia, Ciona, Strongylocentrotus, Branchiostoma, Ixodes, Daphnia, Acyrthosiphon, Tribolium, Nasonia, Apis, Anopheles, Drosophila, Caenorhabditis, Takifugu, Tetraodon, Gasterosteus, Oryzias, Danio, Xenopus, Anolis, Gallus, Taeniopygia,Ornithorhynchus, Monodelphis, Mus and Homo. All of the data described in this paper is available as additional files.

Conclusions: Only a subset of synaptotagmin proteins appear able to function as calcium triggers. Syt1, Syt7 and Syt9 are ancient conserved synaptotagmins of this type. Some animals carry extensive repertoires of synaptotagmin genes. Other animals of no less complexity, carry only a small repertoire. Current understanding does not explain why this is so. The biological roles of many synaptotagmins remain to be understood. This collection of genes offers prospects for fruitful speculation about the functional roles of the synaptotagmin repertoires of different animals and includes a great range of biological complexity. With reference to this gene collection, functional relationships among Syt, Esyt, Rph3a, Rph3al, Doc2 and Dblc2 genes, which encode similar proteins, can better be assessed in future.

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Summary of the genes collected from marine invertebrate genomes. The website of the organisation which sequenced the genome is listed below the organism name. Underneath the Gene Name heading, gene symbols are listed. Red symbols indicate sequences containing all ten acidic amino acid positions required for function as a calcium trigger for exocytosis.
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Figure 1: Summary of the genes collected from marine invertebrate genomes. The website of the organisation which sequenced the genome is listed below the organism name. Underneath the Gene Name heading, gene symbols are listed. Red symbols indicate sequences containing all ten acidic amino acid positions required for function as a calcium trigger for exocytosis.

Mentions: On finding uniquely metazoan Syt homologues, with their characteristic gene structures, in the genomes of T. adhaerens and N. vectensis [50,51] I decided to compile afresh, the Syt repertoire of the currently available genomes of evolutionary significance. In addition to Syt genes, I set out to gather Esyt, Rph3a, Rph3al and Doc2 homologues. These gene families, while clearly distinct from the Syt family at the gene structure level, encode proteins with high level sequence similarity to the tandem C2 domain region of Syt (Rph3a and Doc2) or with similarity, in common with NTMC2 proteins, at a more crude domain architecture level (Esyt). Because of these similarities in form, there will be common functions. A collection like this can be used to further define these functions, by revealing the patterns of sequence conservation (indicating selection and functional importance) and sequence divergence, apparent in: 1. the individual domains of an orthologous group of proteins, 2. the equivalent domain in different groups, not necessarily homologous. Such knowledge can provide clues about how these proteins function as molecular machines in cells and about how these functions have developed over evolutionary time. I used the annotation facilities at DOE-JGI to create and annotate gene models where possible. Full details of all genes are listed in additional files 1, 2, 3 and 4. Figures 1, 2 and 3 summarise the genes in additional files 1, 2 and 3 respectively.


A manual collection of Syt, Esyt, Rph3a, Rph3al, Doc2, and Dblc2 genes from 46 metazoan genomes--an open access resource for neuroscience and evolutionary biology.

Craxton M - BMC Genomics (2010)

Summary of the genes collected from marine invertebrate genomes. The website of the organisation which sequenced the genome is listed below the organism name. Underneath the Gene Name heading, gene symbols are listed. Red symbols indicate sequences containing all ten acidic amino acid positions required for function as a calcium trigger for exocytosis.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2823689&req=5

Figure 1: Summary of the genes collected from marine invertebrate genomes. The website of the organisation which sequenced the genome is listed below the organism name. Underneath the Gene Name heading, gene symbols are listed. Red symbols indicate sequences containing all ten acidic amino acid positions required for function as a calcium trigger for exocytosis.
Mentions: On finding uniquely metazoan Syt homologues, with their characteristic gene structures, in the genomes of T. adhaerens and N. vectensis [50,51] I decided to compile afresh, the Syt repertoire of the currently available genomes of evolutionary significance. In addition to Syt genes, I set out to gather Esyt, Rph3a, Rph3al and Doc2 homologues. These gene families, while clearly distinct from the Syt family at the gene structure level, encode proteins with high level sequence similarity to the tandem C2 domain region of Syt (Rph3a and Doc2) or with similarity, in common with NTMC2 proteins, at a more crude domain architecture level (Esyt). Because of these similarities in form, there will be common functions. A collection like this can be used to further define these functions, by revealing the patterns of sequence conservation (indicating selection and functional importance) and sequence divergence, apparent in: 1. the individual domains of an orthologous group of proteins, 2. the equivalent domain in different groups, not necessarily homologous. Such knowledge can provide clues about how these proteins function as molecular machines in cells and about how these functions have developed over evolutionary time. I used the annotation facilities at DOE-JGI to create and annotate gene models where possible. Full details of all genes are listed in additional files 1, 2, 3 and 4. Figures 1, 2 and 3 summarise the genes in additional files 1, 2 and 3 respectively.

Bottom Line: Synaptotagmins were subsequently found to form a large family, some members of which play important roles in calcium triggered exocytic events.One definition does not necessarily imply the other.Current understanding does not explain why this is so.

View Article: PubMed Central - HTML - PubMed

Affiliation: Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB20QH, UK. mollycraxton@btinternet.com

ABSTRACT

Background: Synaptotagmin proteins were first identified in nervous tissue, residing in synaptic vesicles. Synaptotagmins were subsequently found to form a large family, some members of which play important roles in calcium triggered exocytic events. These members have been investigated intensively, but other family members are not well understood, making it difficult to grasp the meaning of family membership in functional terms. Further difficulty arises as families are defined quite legitimately in different ways: by common descent or by common possession of distinguishing features. One definition does not necessarily imply the other. The evolutionary range of genome sequences now available, can shed more light on synaptotagmin gene phylogeny and clarify family relationships. The aim of compiling this open access collection of synaptotagmin and synaptotagmin-like sequences, is that its use may lead to greater understanding of the biological function of these proteins in an evolutionary context.

Results: 46 metazoan genomes were examined and their complement of Syt, Esyt, Rph3a, Rph3al, Doc2 and Dblc2 genes identified. All of the sequences were compared, named, then examined in detail. Esyt genes were formerly named Fam62. The species in this collection are Trichoplax, Nematostella, Capitella, Helobdella, Lottia, Ciona, Strongylocentrotus, Branchiostoma, Ixodes, Daphnia, Acyrthosiphon, Tribolium, Nasonia, Apis, Anopheles, Drosophila, Caenorhabditis, Takifugu, Tetraodon, Gasterosteus, Oryzias, Danio, Xenopus, Anolis, Gallus, Taeniopygia,Ornithorhynchus, Monodelphis, Mus and Homo. All of the data described in this paper is available as additional files.

Conclusions: Only a subset of synaptotagmin proteins appear able to function as calcium triggers. Syt1, Syt7 and Syt9 are ancient conserved synaptotagmins of this type. Some animals carry extensive repertoires of synaptotagmin genes. Other animals of no less complexity, carry only a small repertoire. Current understanding does not explain why this is so. The biological roles of many synaptotagmins remain to be understood. This collection of genes offers prospects for fruitful speculation about the functional roles of the synaptotagmin repertoires of different animals and includes a great range of biological complexity. With reference to this gene collection, functional relationships among Syt, Esyt, Rph3a, Rph3al, Doc2 and Dblc2 genes, which encode similar proteins, can better be assessed in future.

Show MeSH
Related in: MedlinePlus