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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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Syt orthologues and paralogues in M. musculus. Percent identity scores produced by the align facility at EBI, of pairwise comparisons of full length protein sequences, are listed. Top scores from mouse versus lizard comparisons are highlighted in blue, indicating an orthologous relationship between the mouse gene and the evolutionarily more ancient lizard gene. Top scores from comparisons between mouse and the much more evolutionarily ancient polychaete worm, Capitella, are highlighted in green, indicating that of these mouse genes, Syt1, Syt4, Syt9 and Syt16 are orthologous to genes in Capitella.
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Figure 4: Syt orthologues and paralogues in M. musculus. Percent identity scores produced by the align facility at EBI, of pairwise comparisons of full length protein sequences, are listed. Top scores from mouse versus lizard comparisons are highlighted in blue, indicating an orthologous relationship between the mouse gene and the evolutionarily more ancient lizard gene. Top scores from comparisons between mouse and the much more evolutionarily ancient polychaete worm, Capitella, are highlighted in green, indicating that of these mouse genes, Syt1, Syt4, Syt9 and Syt16 are orthologous to genes in Capitella.

Mentions: Deciding whether relationships of orthology or some other kind exist among a group of similar genes, can be complicated. The processes of duplication, deletion, and rearrangement of genes, plus the action of selection or absence of selection on gene sequences, can obscure relationships. Whether absence from a genome assembly reflects true absence, or incompleteness of the assembly, presents a further problem of some seriousness [68]. In M. musculus and H. sapiens there are several groups of duplicated Syt genes: group 1 [Syt1, Syt2, Syt5, Syt8] group 2 [Syt4, Syt11] group 3 [Syt3, Syt6, Syt9, Syt10] and group 4 [Syt14, Syt16]. Each group contains genes which share a distinct gene structure. Additional files 5, 6, 7, 8 and figure 4, indicate that the parental gene of group 1 is Syt1. The parental gene of group 2 is Syt4, that of group 3 is Syt9 and that of group 4 is Syt16. In each of these cases, the parental gene is more similar to a gene present in an evolutionarily more ancient genome than it is to another member of the mammalian group, which is to say, orthologous [39]. Orthologous genes in different organisms, are related by vertical descent from a common ancestor. Relevant pairwise comparison scores are listed in figure 4. It is worthwhile trying to determine the phylogenetic relationships between the Syt genes of mammals and those of other animals because it is the rodent Syt proteins which are best characterised functionally. However, because mammalian organisms and their brains in particular, represent biological systems of such complexity, modelling these systems by using simpler systems is essential. The relationships and nomenclature proposed here, are in good general agreement with the Syt data at Treefam [69,70] which does not include many of the invertebrate Syt genes in this collection.


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)

Syt orthologues and paralogues in M. musculus. Percent identity scores produced by the align facility at EBI, of pairwise comparisons of full length protein sequences, are listed. Top scores from mouse versus lizard comparisons are highlighted in blue, indicating an orthologous relationship between the mouse gene and the evolutionarily more ancient lizard gene. Top scores from comparisons between mouse and the much more evolutionarily ancient polychaete worm, Capitella, are highlighted in green, indicating that of these mouse genes, Syt1, Syt4, Syt9 and Syt16 are orthologous to genes in Capitella.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Syt orthologues and paralogues in M. musculus. Percent identity scores produced by the align facility at EBI, of pairwise comparisons of full length protein sequences, are listed. Top scores from mouse versus lizard comparisons are highlighted in blue, indicating an orthologous relationship between the mouse gene and the evolutionarily more ancient lizard gene. Top scores from comparisons between mouse and the much more evolutionarily ancient polychaete worm, Capitella, are highlighted in green, indicating that of these mouse genes, Syt1, Syt4, Syt9 and Syt16 are orthologous to genes in Capitella.
Mentions: Deciding whether relationships of orthology or some other kind exist among a group of similar genes, can be complicated. The processes of duplication, deletion, and rearrangement of genes, plus the action of selection or absence of selection on gene sequences, can obscure relationships. Whether absence from a genome assembly reflects true absence, or incompleteness of the assembly, presents a further problem of some seriousness [68]. In M. musculus and H. sapiens there are several groups of duplicated Syt genes: group 1 [Syt1, Syt2, Syt5, Syt8] group 2 [Syt4, Syt11] group 3 [Syt3, Syt6, Syt9, Syt10] and group 4 [Syt14, Syt16]. Each group contains genes which share a distinct gene structure. Additional files 5, 6, 7, 8 and figure 4, indicate that the parental gene of group 1 is Syt1. The parental gene of group 2 is Syt4, that of group 3 is Syt9 and that of group 4 is Syt16. In each of these cases, the parental gene is more similar to a gene present in an evolutionarily more ancient genome than it is to another member of the mammalian group, which is to say, orthologous [39]. Orthologous genes in different organisms, are related by vertical descent from a common ancestor. Relevant pairwise comparison scores are listed in figure 4. It is worthwhile trying to determine the phylogenetic relationships between the Syt genes of mammals and those of other animals because it is the rodent Syt proteins which are best characterised functionally. However, because mammalian organisms and their brains in particular, represent biological systems of such complexity, modelling these systems by using simpler systems is essential. The relationships and nomenclature proposed here, are in good general agreement with the Syt data at Treefam [69,70] which does not include many of the invertebrate Syt genes in this collection.

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