Instituto Nacional de Medicina Genómica (INMEGEN), México City, México.
PLoS One. 2013 Aug 12;8(8):e70582. doi: 10.1371/journal.pone.0070582. eCollection 2013.
After the surprisingly low number of genes identified in the human genome, alternative splicing emerged as a major mechanism to generate protein diversity in higher eukaryotes. However, it is still not known if its prevalence along the genome evolution has contributed to the overall functional protein diversity or if it simply reflects splicing noise. The (βα)8 barrel or TIM barrel is one of the most frequent, versatile, and ancient fold encountered among enzymes. Here, we analyze the structural modifications present in TIM barrel proteins from the human genome product of alternative splicing events. We found that 87% of all splicing events involved deletions; most of these events resulted in protein fragments that corresponded to the (βα)2, (βα)4, (βα)5, (βα)6, and (βα)7 subdomains of TIM barrels. Because approximately 7% of all the splicing events involved internal β-strand substitutions, we decided, based on the genomic data, to design β-strand and α-helix substitutions in a well-studied TIM barrel enzyme. The biochemical characterization of one of the chimeric variants suggests that some of the splice variants in the human genome with β-strand substitutions may be evolving novel functions via either the oligomeric state or substrate specificity. We provide results of how the splice variants represent subdomains that correlate with the independently folding and evolving structural units previously reported. This work is the first to observe a link between the structural features of the barrel and a recurrent genetic mechanism. Our results suggest that it is reasonable to expect that a sizeable fraction of splice variants found in the human genome represent structurally viable functional proteins. Our data provide additional support for the hypothesis of the origin of the TIM barrel fold through the assembly of smaller subdomains. We suggest a model of how nature explores new proteins through alternative splicing as a mechanism to diversify the proteins encoded in the human genome.
在人类基因组中鉴定出的基因数量之少令人惊讶之后，选择性剪接成为高等真核生物产生蛋白质多样性的主要机制。然而，目前尚不清楚其在基因组进化过程中的普遍存在是否有助于整体功能蛋白质多样性，或者它是否仅仅反映了剪接噪音。（βα）8 桶或 TIM 桶是酶中最常见、最多样化和最古老的折叠之一。在这里，我们分析了来自人类基因组选择性剪接事件的产物中 TIM 桶蛋白的结构修饰。我们发现，所有剪接事件中有 87%涉及缺失；这些事件中的大多数导致相应的（βα）2、（βα）4、（βα）5、（βα）6 和（βα）7 TIM 桶亚结构域的蛋白片段。因为大约 7%的剪接事件涉及内部β-链取代，所以我们根据基因组数据决定设计在一个研究良好的 TIM 桶酶中进行β-链和α-螺旋取代。对一个嵌合变体的生化特征分析表明，人类基因组中具有β-链取代的一些剪接变体可能通过寡聚状态或底物特异性来进化新的功能。我们提供了有关剪接变体如何代表与以前报道的独立折叠和进化结构单元相关的亚结构域的结果。这项工作首次观察到桶的结构特征与反复出现的遗传机制之间的联系。我们的结果表明，有理由期望在人类基因组中发现的相当一部分剪接变体代表具有结构可行性的功能蛋白。我们的数据为通过组装较小的亚结构域来解释 TIM 桶折叠起源的假设提供了额外的支持。我们提出了一种模型，即自然界如何通过选择性剪接作为一种多样化人类基因组编码蛋白的机制来探索新的蛋白。
