Limits...
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.

Show MeSH

Related in: MedlinePlus

Pairwise comparisons of Syt1 paralogues in vertebrates. Percent identity scores produced by the align facility at EBI, of pairwise comparisons of full length protein sequences, are listed. Top scores are highlighted in blue, indicating an orthologous relationship between the compared genes.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2823689&req=5

Figure 5: Pairwise comparisons of Syt1 paralogues in vertebrates. Percent identity scores produced by the align facility at EBI, of pairwise comparisons of full length protein sequences, are listed. Top scores are highlighted in blue, indicating an orthologous relationship between the compared genes.

Mentions: Additional files 11, 12 and 13 show multiple alignments of the vertebrate Syt2, Syt5 and Syt8 protein sequences, respectively. For Syt2, Syt5 and Syt8 genes, there is transcript evidence of alternatively expressed forms which lack the TM domain. Syt1, Syt2, Syt5 and Syt8 are all related by duplication, with Syt1 being the parental gene (figure 4). In the fish genomes, there are yet more duplicates. In order to distinguish the relationships among these duplicates, pairwise comparison scores (figure 5) and syntenic relationships (figure 6) were examined. The top scores highlighted in blue in figure 5, indicate that D. rerio syt1a is orthologous to the Syt1 gene of other vertebrates and that D. rerio syt8 is orthologous to the Syt8 gene of other vertebrates. The pairwise comparison scores do not however, indicate orthology for the other duplicates. Figure 6 shows that relationships of orthology, are indeed present. The neighbouring genes of Syt1, Syt2, Syt5 and Syt8, in the genomes of H. sapiens, X. tropicalis and D. rerio, reveal conserved syntenic blocks in each genome. This synteny indicates that the four genomic segments share ancestry. Orthologous relationships exist between: H. sapiens SYT1 and the duplicated syt1a/syt1b in D. rerio, between SYT2 and syt2/syt2b and between SYT5 and syt5a/syt5b, respectively. Since there is so much interest in the mechanism of Syt1 function, close examination of the Syt1 orthologues and paralogues in this collection, to see how they have been shaped by evolution, may prove productive.


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)

Pairwise comparisons of Syt1 paralogues in vertebrates. Percent identity scores produced by the align facility at EBI, of pairwise comparisons of full length protein sequences, are listed. Top scores are highlighted in blue, indicating an orthologous relationship between the compared genes.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 5: Pairwise comparisons of Syt1 paralogues in vertebrates. Percent identity scores produced by the align facility at EBI, of pairwise comparisons of full length protein sequences, are listed. Top scores are highlighted in blue, indicating an orthologous relationship between the compared genes.
Mentions: Additional files 11, 12 and 13 show multiple alignments of the vertebrate Syt2, Syt5 and Syt8 protein sequences, respectively. For Syt2, Syt5 and Syt8 genes, there is transcript evidence of alternatively expressed forms which lack the TM domain. Syt1, Syt2, Syt5 and Syt8 are all related by duplication, with Syt1 being the parental gene (figure 4). In the fish genomes, there are yet more duplicates. In order to distinguish the relationships among these duplicates, pairwise comparison scores (figure 5) and syntenic relationships (figure 6) were examined. The top scores highlighted in blue in figure 5, indicate that D. rerio syt1a is orthologous to the Syt1 gene of other vertebrates and that D. rerio syt8 is orthologous to the Syt8 gene of other vertebrates. The pairwise comparison scores do not however, indicate orthology for the other duplicates. Figure 6 shows that relationships of orthology, are indeed present. The neighbouring genes of Syt1, Syt2, Syt5 and Syt8, in the genomes of H. sapiens, X. tropicalis and D. rerio, reveal conserved syntenic blocks in each genome. This synteny indicates that the four genomic segments share ancestry. Orthologous relationships exist between: H. sapiens SYT1 and the duplicated syt1a/syt1b in D. rerio, between SYT2 and syt2/syt2b and between SYT5 and syt5a/syt5b, respectively. Since there is so much interest in the mechanism of Syt1 function, close examination of the Syt1 orthologues and paralogues in this collection, to see how they have been shaped by evolution, may prove productive.

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