Natural diversity of group II introns

II 组内含子的自然多样性

• 批准号: RGPIN-2017-05871
• 负责人: Zimmerly, Steven
• 金额: $ 3.64万
• 依托单位: University of Calgary
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Individual
• 财政年份: 2020
• 资助国家: 加拿大
• 起止时间: 2020-01-01 至 2021-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=711442
• 关键词: Natural; diversity; group; II; introns

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.

移动DNA是自私的遗传因素，它们在没有立即受益的宿主受益的情况下扩散。但是，随着时间的流逝，它们一直是许多有用的进化发明（例如端粒酶）的来源。移动DNA是诱变药物的动力学，但也是适应性的动力。 II组内含子是细菌中一种可移动DNA，具有催化RNA和恢复元素的特性。内含子的序列编码两个组成部分：1）催化RNA成分，可进行自裂反应； 2）一种内含子编码的逆转录酶，可促进剪接反应并允许内含子整合到新的基因组位置。 II组内含子具有特殊的用途，已经演变为许多变体形式，最重要的是真核剪接体内含子和非LTR逆转座盆，分别占人类基因组的约25％和约20％。 Zimmerly Lab的过去研究有助于确立自然界中存在的II组内含子的广度。在这里，我们将进一步研究II组内含子如何分化和进化以获得新的特征和生物学影响，并具有三个目标。 1）我们将使用生物信息学工具来策划GenBank的II组内含子。除了生成更新的人口普查外，还可以识别新的内含子变体。对累积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演变。 2）我们将研究二元剪接的现象，该现象由II组内含子的子集进行。虽然大多数II组内含子通过单个外显子结合基序识别其5'外显子，但子集可以或者可以或两个外显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，我们假设这是不寻常剪接特性的生物学功能。 3）我们将检查C.Te.I1内含子TETANI替代剪接的前所未有的反应。在这里，一个内含子可能扮演了可能有益的作用，可以将单个5'外显子连接到四个下游外显子之一，从而产生来自单个遗传基因座的五种蛋白质变体。为了解决该反应的生物学后果，我们将研究三个甲状腺梭菌患者分离株中的内含子，并将数据与参考菌株进行比较。这三种菌株的基因组将进行测序，RNA-seq将用于检测剪接和转录特性。这三种方法共同阐明了II组内含子的功能变异和适应性，并有助于我们理解移动DNA和核酶如何在进化时代适应和多样化，有时会变得驯化以在其细菌宿主中扮演有用的作用。