Evolutionary genomics of plant genes encoding N-terminal-TM-C2 domain proteins and the similar FAM62 genes and synaptotagmin genes of metazoans.
Evolutionary genomics of plant genes encoding N-terminal-TM-C2 domain proteins and the similar FAM62 genes and synaptotagmin genes of metazoans.
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DOI：
10.1186/1471-2164-8-259
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发表时间：
2007-07-31
期刊：
影响因子：
4.4
通讯作者：
Craxton M
中科院分区：
文献类型：
--
作者：
Craxton M
Synaptotagmin基因存在于动物基因组中，已知在神经系统中起作用。在植物基因组中也发现了与synaptotagmin C2结构域具有相似结构域结构和序列相似性的基因。植物基因与一组名为FAM62的动物基因有一个额外的序列相似性区域。FAM62基因也具有类似的结构域结构。植物和动物FAM62基因的功能尚不清楚。事实上，Syt基因家族的许多成员正在等待功能鉴定。了解这些基因之间的进化关系将有助于实现功能研究的全部含义，并导致改进的基因组注释。我从NCBI的初级核苷酸序列数据库中收集并比较了植物syt样序列。该集合包括六组在胚胎中保守的植物基因：NTMC2Type1至NTMC2Type6。我收集和比较了后生动物的FAM62序列，并从其他真核生物谱系中鉴定了一些类似的序列。我发现了RNA编辑和选择性剪接的证据。我比较了Syt基因的内含子模式。我还比较了Rabphilin和Doc2基因。编码具有类似于synaptotagmins的n端跨膜c2结构域结构的蛋白质的基因在真核生物中广泛存在。这里展示了这些基因的集合。该集合为内含子进化的研究提供了资源。根据不同的序列保守模式和内含子位置，我将收集的基因分类为同源基因家族。这些基因家族的进化史可以通过不同真核谱系中家族成员的出现来追溯。假设一个富含内含子的真核生物祖先，个体基因家族特有的保守内含子模式表明Syt， FAM62和NTMC2基因的独立起源。这些大型多结构域蛋白之间的相似性不仅源于共同的祖先（同源性），而且源于趋同进化（相似性）。在这些基因家族的进化过程中，随着序列分化，重复和其他影响结构域组成的基因重排也随之发生，导致了复杂的家族关系和相应的复杂功能影响。这些基因之间的功能同源性和相似性仍有待于经验证实。
Synaptotagmin genes are found in animal genomes and are known to function in the nervous system. Genes with a similar domain architecture as well as sequence similarity to synaptotagmin C2 domains have also been found in plant genomes. The plant genes share an additional region of sequence similarity with a group of animal genes named FAM62. FAM62 genes also have a similar domain architecture. Little is known about the functions of the plant genes and animal FAM62 genes. Indeed, many members of the large and diverse Syt gene family await functional characterization. Understanding the evolutionary relationships among these genes will help to realize the full implications of functional studies and lead to improved genome annotation. I collected and compared plant Syt-like sequences from the primary nucleotide sequence databases at NCBI. The collection comprises six groups of plant genes conserved in embryophytes: NTMC2Type1 to NTMC2Type6. I collected and compared metazoan FAM62 sequences and identified some similar sequences from other eukaryotic lineages. I found evidence of RNA editing and alternative splicing. I compared the intron patterns of Syt genes. I also compared Rabphilin and Doc2 genes. Genes encoding proteins with N-terminal-transmembrane-C2 domain architectures resembling synaptotagmins, are widespread in eukaryotes. A collection of these genes is presented here. The collection provides a resource for studies of intron evolution. I have classified the collection into homologous gene families according to distinctive patterns of sequence conservation and intron position. The evolutionary histories of these gene families are traceable through the appearance of family members in different eukaryotic lineages. Assuming an intron-rich eukaryotic ancestor, the conserved intron patterns distinctive of individual gene families, indicate independent origins of Syt, FAM62 and NTMC2 genes. Resemblances among these large, multi-domain proteins are due not only to shared ancestry (homology) but also to convergent evolution (analogy). During the evolution of these gene families, duplications and other gene rearrangements affecting domain composition, have occurred along with sequence divergence, leading to complex family relationships with accordingly complex functional implications. The functional homologies and analogies among these genes remain to be established empirically.
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