Severing Edouard I, van Dijk Aalt D J, Stiekema Willem J, van Ham Roeland C H J
Applied Bioinformatics, Plant Research International, PO Box 16, 6700 AA Wageningen, The Netherlands.
BMC Genomics. 2009 Apr 9;10:154. doi: 10.1186/1471-2164-10-154.
Alternative splicing (AS) is a widespread phenomenon in higher eukaryotes but the extent to which it leads to functional protein isoforms and to proteome expansion at large is still a matter of debate. In contrast to animal species, for which AS has been studied extensively at the protein and functional level, protein-centered studies of AS in plant species are scarce. Here we investigate the functional impact of AS in dicot and monocot plant species using a comparative approach.
Detailed comparison of AS events in alternative spliced orthologs from the dicot Arabidopsis thaliana and the monocot Oryza sativa (rice) revealed that the vast majority of AS events in both species do not result from functional conservation. Transcript isoforms that are putative targets for the nonsense-mediated decay (NMD) pathway are as likely to contain conserved AS events as isoforms that are translated into proteins. Similar results were obtained when the same comparison was performed between the two more closely related monocot species rice and Zea mays (maize).Genome-wide computational analysis of functional protein domains encoded in alternatively and constitutively spliced genes revealed that only the RNA recognition motif (RRM) is overrepresented in alternatively spliced genes in all species analyzed. In contrast, three domain types were overrepresented in constitutively spliced genes. AS events were found to be less frequent within than outside predicted protein domains and no domain type was found to be enriched with AS introns. Analysis of AS events that result in the removal of complete protein domains revealed that only a small number of domain types is spliced-out in all species analyzed. Finally, in a substantial fraction of cases where a domain is completely removed, this domain appeared to be a unit of a tandem repeat.
The results from the ortholog comparisons suggest that the ability of a gene to produce more than one functional protein through AS does not persist during evolution. Cross-species comparison of the results of the protein-domain oriented analyses indicates little correspondence between the analyzed species. Based on the premise that functional genetic features are most likely to be conserved during evolution, we conclude that AS has only a limited role in functional expansion of the proteome in plants.
可变剪接（AS）在高等真核生物中普遍存在，但它在多大程度上导致功能性蛋白质异构体以及整体蛋白质组扩张仍是一个有争议的问题。与在蛋白质和功能水平上对可变剪接进行广泛研究的动物物种不同，以蛋白质为中心对植物物种可变剪接的研究很少。在这里，我们使用比较方法研究可变剪接在双子叶和单子叶植物物种中的功能影响。
对双子叶植物拟南芥和单子叶植物水稻（Oryza sativa）中可变剪接直系同源物的可变剪接事件进行详细比较发现，两个物种中的绝大多数可变剪接事件并非源于功能保守。作为无义介导的衰变（NMD）途径假定靶点的转录异构体与被翻译成蛋白质的异构体一样，都可能包含保守的可变剪接事件。当在两个亲缘关系更近的单子叶植物物种水稻和玉米（Zea mays）之间进行相同比较时，也得到了类似的结果。对可变剪接和组成型剪接基因中编码的功能蛋白质结构域进行全基因组计算分析表明，在所分析的所有物种中，只有RNA识别基序（RRM）在可变剪接基因中过度富集。相比之下，三种结构域类型在组成型剪接基因中过度富集。发现可变剪接事件在预测的蛋白质结构域内比在其外更不频繁，并且没有发现哪种结构域类型富含可变剪接内含子。对导致完整蛋白质结构域被去除的可变剪接事件进行分析发现，在所分析的所有物种中，只有少数几种结构域类型会被剪接掉。最后，在相当一部分结构域被完全去除的情况下，该结构域似乎是串联重复的一个单元。
直系同源物比较的结果表明，基因通过可变剪接产生多种功能蛋白质的能力在进化过程中并不持续存在。对面向蛋白质结构域分析结果的跨物种比较表明，所分析的物种之间几乎没有对应关系。基于功能遗传特征在进化过程中最有可能保守这一前提，我们得出结论，可变剪接在植物蛋白质组功能扩展中仅起有限作用。
