Natural diversity of group II introns

移动DNA是自私的遗传元素，它们在没有立即给宿主带来好处的情况下繁殖；然而，随着时间的推移，它们已经成为许多有用的进化发明的来源，例如端粒酶。移动DNA是诱变剂，但也是适应的促进者，其动态还不是很清楚。第二组内含子是细菌中一种可移动的DNA，既具有催化RNA的性质，又具有逆转录元件的性质。内含子序列编码两个组分：1)执行自剪接反应的催化RNA组分；2)内含子编码的逆转录酶，促进剪接反应并允许内含子整合到新的基因组位置。第二类内含子具有非常广泛的功能，已经进化成许多变异形式，其中最重要的是真核剪接体内含子和非LTR反转录转座子，它们分别占人类基因组的25%和20%。齐默利实验室过去的研究帮助确定了自然界中存在的第二类内含子的广度。在这里，我们将进一步研究第二组内含子如何分化和进化以获得新的特征和生物学影响，目的有三个。1)我们将使用生物信息学工具来管理GenBank中的第二组内含子。除了产生最新的普查，预计这将发现新的内含子变异。对累积的序列数据的系统发育分析将允许重建内含子的主要谱系的进化。2)我们将研究二元剪接现象，这是由第二组内含子的子集实现的。虽然大多数第二类内含子通过单个外显子结合基序识别其5‘外显子，但一个子集可以交替使用两个外显子结合基序中的任何一个。我们将剖析二元剪接的机制，并确定其对内含子迁移率的影响，我们假设这是异常剪接性质的生物学功能。3)我们将研究破伤风杆菌中C.te.I1内含子的选择性剪接的前所未有的反应。在这里，一个内含子可能起到了有益的作用，允许一个5‘外显子连接到四个下游外显子中的一个，从一个遗传位点产生五个蛋白质变体。为了解决这一反应的生物学后果，我们将调查破伤风弧菌三个患者分离株的内含子，并将数据与参考菌株进行比较。这三个菌株的基因组将被测序，RNA-Seq将用于检测剪接和转录特性。这三种方法结合起来将有助于阐明第二组内含子的功能变异和适应，并有助于我们理解移动DNA和核酶如何随着进化时间的推移适应和多样化，有时会被驯化以在细菌宿主中发挥有用的作用。

Mobile DNAs are selfish genetic elements that proliferate without immediate benefits to their hosts; however, over time they have been the source of many useful evolutionary inventions such as telomerase. The dynamics by which mobile DNAs are agents of mutagenesis, yet also enablers of adaptation, are not well understood. Group II introns are a type of mobile DNA in bacteria that possesses properties of both catalytic RNAs and retroelements. The sequence of the introns encodes two components: 1) a catalytic RNA component that carries out a self-splicing reaction; and 2) an intron-encoded reverse transcriptase that facilitates the splicing reaction and allows the introns to integrate into new genomic locations. Group II introns are exceptionally versatile, having evolved into many variant forms, with the most important arguably being eukaryotic spliceosomal introns and non-LTR retrotransposons, which make up ~25% and ~20% of the human genome, respectively. Past research in the Zimmerly lab has helped to establish the breadth of group II introns that exist in nature. Here we will further investigate how group II introns have differentiated and evolved to acquire new characteristics and biological impacts, with three aims. 1) We will use bioinformatic tools to curate group II introns in GenBank. In addition to generating an updated census, this is expected to identify new intron variants. Phylogenetic analysis of the accumulated sequence data will allow reconstruction of the evolution of a major lineage of the introns. 2) We will investigate the phenomenon of binary splicing, which is carried out by a subset of group II introns. While most group II introns recognize their 5' exon by a single exon-binding motif, a subset can alternately use either of two exon-binding motifs. We will dissect the mechanism for binary splicing and determine its effect on intron mobility, which we hypothesize to be the biological function of the unusual splicing property. 3) We will examine the unprecedented reaction of alternative splicing of the C.te.I1 intron in Clostridium tetani. Here an intron has taken on a presumably beneficial role, allowing a single 5' exon to be ligated to one of four downstream exons, producing five protein variants from a single genetic locus. To address the biological consequences of this reaction, we will investigate the intron in three patient isolates of C. tetani and compare data to a reference strain. The genomes of the three strains will be sequenced, and RNA-Seq will be used to detect splicing and transcription properties. Together these three approaches will help illuminate the functional variants and adaptations of group II introns, and contribute to our understanding of how mobile DNAs and ribozymes adapt and diversify over evolutionary time, sometimes becoming domesticated to take on useful roles within their bacterial hosts.