Applied Bioinformatics, Plant Research International, Wageningen, The Netherlands.
PLoS One. 2012;7(1):e30524. doi: 10.1371/journal.pone.0030524. Epub 2012 Jan 25.
Several genome-wide studies demonstrated that alternative splicing (AS) significantly increases the transcriptome complexity in plants. However, the impact of AS on the functional diversity of proteins is difficult to assess using genome-wide approaches. The availability of detailed sequence annotations for specific genes and gene families allows for a more detailed assessment of the potential effect of AS on their function. One example is the plant MADS-domain transcription factor family, members of which interact to form protein complexes that function in transcription regulation. Here, we perform an in silico analysis of the potential impact of AS on the protein-protein interaction capabilities of MIKC-type MADS-domain proteins. We first confirmed the expression of transcript isoforms resulting from predicted AS events. Expressed transcript isoforms were considered functional if they were likely to be translated and if their corresponding AS events either had an effect on predicted dimerisation motifs or occurred in regions known to be involved in multimeric complex formation, or otherwise, if their effect was conserved in different species. Nine out of twelve MIKC MADS-box genes predicted to produce multiple protein isoforms harbored putative functional AS events according to those criteria. AS events with conserved effects were only found at the borders of or within the K-box domain. We illustrate how AS can contribute to the evolution of interaction networks through an example of selective inclusion of a recently evolved interaction motif in the MADS AFFECTING FLOWERING1-3 (MAF1-3) subclade. Furthermore, we demonstrate the potential effect of an AS event in SHORT VEGETATIVE PHASE (SVP), resulting in the deletion of a short sequence stretch including a predicted interaction motif, by overexpression of the fully spliced and the alternatively spliced SVP transcripts. For most of the AS events we were able to formulate hypotheses about the potential impact on the interaction capabilities of the encoded MIKC proteins.
几项全基因组研究表明，可变剪接（AS）显著增加了植物转录组的复杂性。然而，使用全基因组方法评估 AS 对蛋白质功能多样性的影响是困难的。特定基因和基因家族详细序列注释的可用性允许更详细地评估 AS 对其功能的潜在影响。一个例子是植物 MADS 结构域转录因子家族，其成员相互作用形成蛋白质复合物，在转录调控中发挥作用。在这里，我们对 AS 对 MIKC 型 MADS 结构域蛋白的蛋白质-蛋白质相互作用能力的潜在影响进行了计算机分析。我们首先证实了预测 AS 事件产生的转录本异构体的表达。如果预测的剪接事件可能导致翻译产生表达的转录本异构体，并且其相应的剪接事件要么对预测的二聚化基序有影响，要么发生在已知参与多聚体复合物形成的区域，或者其影响在不同物种中保守，则认为它们是有功能的。根据这些标准，预测产生多个蛋白质异构体的 12 个 MIKC MADS 盒基因中有 9 个具有潜在的功能 AS 事件。具有保守效应的 AS 事件仅在 K 盒结构域的边界或内部发现。我们通过一个最近进化的相互作用模体在 MADS AFFECTING FLOWERING1-3 (MAF1-3) 亚群中选择性包含的例子来说明 AS 如何有助于相互作用网络的进化。此外，我们通过过量表达完全拼接和选择性拼接的 SVP 转录本，证明了 SHORT VEGETATIVE PHASE (SVP) 中的一个 AS 事件的潜在影响，该事件导致包括预测的相互作用模体在内的短序列片段缺失。对于大多数 AS 事件，我们能够对其对编码 MIKC 蛋白的相互作用能力的潜在影响提出假设。
