Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Storrs, CT 06269-3125, USA.
BMC Evol Biol. 2009 Dec 31;9:303. doi: 10.1186/1471-2148-9-303.
Inteins and introns are genetic elements that are removed from proteins and RNA after translation or transcription, respectively. Previous studies have suggested that these genetic elements are found in conserved parts of the host protein. To our knowledge this type of analysis has not been done for group II introns residing within a gene. Here we provide quantitative statistical support from an analyses of proteins that host inteins, group I introns, group II introns and spliceosomal introns across all three domains of life.
To determine whether or not inteins, group I, group II, and spliceosomal introns are found preferentially in conserved regions of their respective host protein, conservation profiles were generated and intein and intron positions were mapped to the profiles. Fisher's combined probability test was used to determine the significance of the distribution of insertion sites across the conservation profile for each protein. For a subset of studied proteins, the conservation profile and insertion positions were mapped to protein structures to determine if the insertion sites correlate to regions of functional activity. All inteins and most group I introns were found to be preferentially located within conserved regions; in contrast, a bacterial intein-like protein, group II and spliceosomal introns did not show a preference for conserved sites.
These findings demonstrate that inteins and group I introns are found preferentially in conserved regions of their respective host proteins. Homing endonucleases are often located within inteins and group I introns and these may facilitate mobility to conserved regions. Insertion at these conserved positions decreases the chance of elimination, and slows deletion of the elements, since removal of the elements has to be precise as not to disrupt the function of the protein. Furthermore, functional constrains on the targeted site make it more difficult for hosts to evolve immunity to the homing endonuclease. Therefore, these elements will better survive and propagate as molecular parasites in conserved sites. In contrast, spliceosomal introns and group II introns do not show significant preference for conserved sites and appear to have adopted a different strategy to evade loss.
内含子和内含子是分别在翻译或转录后从蛋白质和 RNA 中去除的遗传元件。先前的研究表明，这些遗传元件存在于宿主蛋白的保守部分中。据我们所知，这种类型的分析尚未针对位于基因内的 II 组内含子进行。在这里，我们提供了来自所有三个生命领域的含有内含子、I 组内含子、II 组内含子和剪接体内含子的宿主蛋白的定量统计支持。
为了确定内含子、I 组、II 组和剪接体内含子是否优先存在于其各自宿主蛋白的保守区域，生成了保守谱，并将内含子和内含子位置映射到谱上。Fisher 联合概率检验用于确定每个蛋白质的保守谱内插入位点分布的显著性。对于研究的蛋白质子集，将保守谱和插入位置映射到蛋白质结构上，以确定插入位点是否与功能活性区域相关。所有内含子和大多数 I 组内含子都被发现优先位于保守区域内；相比之下，一种细菌内含子样蛋白、II 组和剪接体内含子则没有表现出对保守位点的偏好。
这些发现表明，内含子和 I 组内含子优先存在于其各自宿主蛋白的保守区域。归巢内切酶通常位于内含子和 I 组内含子内，这可能有助于它们移动到保守区域。在这些保守位置插入会降低被消除的机会，并减缓元件的删除，因为元件的删除必须精确，以免破坏蛋白质的功能。此外，靶向位点的功能限制使得宿主更难对归巢内切酶产生免疫力。因此，这些元件将作为分子寄生虫更好地在保守位点中生存和传播。相比之下，剪接体内含子和 II 组内含子则没有显示出对保守位点的显著偏好，并且似乎已经采用了不同的策略来逃避丢失。
