Sense/Antisense Genetic Coding and the Origins of Translation

正义/反义遗传编码和翻译的起源

• 批准号: 8209141
• 负责人: Charles W. Carter
• 金额: $ 29.38万
• 依托单位: UNIV OF NORTH CAROLINA CHAPEL HILL
• 依托单位国家: 美国
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-08-01 至 2014-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8209141
• 关键词: Acylation; Amino Acids; Amino Acids Activation; Amino Acyl-tRNA Synthetases; Anticodon; Base Sequence; Binding; Binding Sites; Biological; Biological Assay; Biological Process; Boxing; C-terminal; Catalysis; Code; Codon Nucleotides; Complement; Databases; Development; Drug Design; Enzymes; Escherichia coli; Evolution; Experimental Models; Gene Expression; Gene Structure; Genes; Genetic; Genetic Code; Genetic Screening; Genomics; Homologous Gene; Ions; Ligase; Measurable; Measures; Methods; Modeling; Mutagenesis; N-terminal; Nature; Open Reading Frames; Peptides; Phylogenetic Analysis; Phylogeny; Plasmids; Procedures; Process; Property; Protein Biosynthesis; Protein Engineering; Proteins; Proteome; Publishing; Reagent; Relative (related person); Research; Secure; Sequence Alignment; Solubility; Specificity; Structure; Study models; System; Testing; Time; Transfer RNA; Translations; Validation; Work; base; catalyst; cytotoxic; cytotoxicity; design; engineering design; fitness; gene function; improved; insight; markov model; mutant; pressure; public health relevance; research study; structural genomics; tool

DESCRIPTION (provided by applicant): The evolution of function is challenging to study, because it requires reconstructing reasonable models for extinct ancestral nodes. We propose to generate experimentally testable models for studying how evolution has introduced and modified functional relationships at the protein level associated with increased fitness. We complement the established statistical inference from sequence phylogenies (ancestral gene resurrection) with an analogous, but more radical procedure based on identifying common, core tertiary structures to reconstruct gene structure and function of enzymes far more ancient (albeit less secure) than those accessible from phylogenetic sequence-based methods. We focus on very ancient models for ancestral aminoacyl-tRNA synthetases, whose evolutionary descent was key to the origins of codon-directed protein synthesis and hence gene expression. The aaRS are not all homologous, but instead occur in two distinct superfamilies. This project is most deeply motivated by a desire to understand the profound symmetries that relate the two superfamilies. Among several hypotheses we hope to test is that the ancestral forms of class I and class II AARS were initially encoded on opposite strands of the same sense/antisense open reading frame. We introduce the term Urzymology (from Ur = primitive, original, early + enzyme) to describe the creation and experimental study of such ancestral proteins, which lie beyond the reach of ancestral gene resurrection. Urzymology brings with it the ability to manipulate biological objects across time. Complementation between Urzymes and subsequently acquired functional modules and parallel mutagenesis of Urzymes and contemporary enzymes make it possible to test explicit models for the evolution of catalysis, specificity, and allostery. Published proofs-of-principle for many obvious contingencies provide an exceptionally strong combination of transformative research. Aim 1 will document the relative amino acid specificities of Class I and II aminoacyl-tRNA synthetase Urzymes, and establish detailed mechanistic differences between the Urzymes and contemporary aaRS. Aim 2 is devoted to experimental study of the Rodin-Ohno hypothesis that the two aaRS classes arose on opposite strands of the same ancestral gene. Aim 3 will enhance the computational design process and establish genetic systems to select and characterize less cytotoxic constructs for eventual use in selecting Urzymes with improved enzymatic function. Charting the record of functional adaptation with experiments like those proposed here will complement the growing genomic sequence database by providing experimental tools to access and characterize likely evolutionary intermediates. Outlining the evolutionary record of functional adaptation will supplement intuitive use of sequence databases with experimental paradigms that complement drug design and the engineering and design of new protein reagents by explicit new understanding of how modules interact in proteins. Validating sense/antisense genetic coding would enrich understanding of the proteome, by identifying pairs of protein superfamilies that arose simultaneously, enhancing the meaning of "homology". PUBLIC HEALTH RELEVANCE: To examine how catalysis and specificity evolve, we recreate extinct proteins predicted by evolutionary analysis to be critical for protein synthesis. Examining functional evolutionary branch points experimentally in this manner will generate and test entirely new insights. Central to the effort is the increasing evidence that genes for the two aminoacyl-tRNA synthetase Classes were originally encoded sense and antisense, on opposite strands of the same ancestral gene. The sense/antisense coding hypothesis simplifies what appear to be irreducible complexities associated with the origins of translation. Experimental validation would significantly change the way we understand the proteome and provide new explanations for the existence, complexity, and elegance of the specific genes and systems that drive both normal and pathological biological processes.

描述（由申请人提供）：功能演化的研究具有挑战性，因为它需要为灭绝的祖先节点重建合理的模型。我们建议生成可通过实验测试的模型，用于研究进化如何在与增强适应性相关的蛋白质水平上引入和修改功能关系。我们用一种类似但更激进的程序来补充序列系统发生（祖先基因复活）中已建立的统计推论，该程序基于识别常见的核心三级结构来重建比可访问的酶更古老（尽管不太安全）的基因结构和酶功能。基于系统发育序列的方法。我们专注于非常古老的祖先氨酰-tRNA 合成酶模型，其进化血统是密码子指导的蛋白质合成和基因表达起源的关键。 aaRS并不全是同源的，而是出现在两个不同的超家族中。这个项目的最深层动机是希望了解两个超家族之间的深刻对称性。我们希望测试的几个假设之一是，I 类和 II 类 AARS 的祖先形式最初是在同一有义/反义开放阅读框的相反链上编码的。我们引入了 Urzymology 一词（来自 Ur = 原始、原始、早期 + 酶）来描述此类祖先蛋白质的创造和实验研究，这些蛋白质超出了祖先基因复活的范围。酶学带来了跨时间操纵生物物体的能力。 Urzymes 和随后获得的功能模块之间的互补以及 Urzymes 和当代酶的平行诱变使得测试催化、特异性和变构进化的明确模型成为可能。已发布的针对许多明显意外情况的原理证明提供了变革性研究的异常强大的组合。目标 1 将记录 I 类和 II 类氨酰基-tRNA 合成酶 Urzyme 的相对氨基酸特异性，并建立 Urzyme 和当代 aaRS 之间的详细机制差异。目标 2 致力于 Rodin-Ohno 假设的实验研究，即两个 aaRS 类别出现在同一祖先基因的相反链上。目标 3 将增强计算设计过程并建立遗传系统来选择和表征细胞毒性较小的构建体，最终用于选择具有改进酶功能的 Urzyme。通过像这里提出的那些实验来绘制功能适应的记录，将通过提供实验工具来访问和表征可能的进化中间体，从而补充不断增长的基因组序列数据库。概述功能适应的进化记录将通过实验范式补充序列数据库的直观使用，通过对模块如何在蛋白质中相互作用的明确新理解来补充药物设计以及新蛋白质试剂的工程和设计。验证有义/反义遗传编码将通过识别同时出现的成对蛋白质超家族来丰富对蛋白质组的理解，从而增强“同源性”的含义。 公共健康相关性：为了研究催化作用和特异性如何进化，我们重新创建了进化分析预测对蛋白质合成至关重要的已灭绝蛋白质。以这种方式通过实验检查功能进化分支点将产生并测试全新的见解。这项工作的核心是越来越多的证据表明，两种氨酰基-tRNA 合成酶类的基因最初是在同一祖先基因的相反链上编码有义和反义的。有义/反义编码假说简化了与翻译起源相关的看似不可简化的复杂性。实验验证将显着改变我们理解蛋白质组的方式，并为驱动正常和病理生物过程的特定基因和系统的存在、复杂性和优雅提供新的解释。