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: 8403075
• 负责人: Charles W. Carter
• 金额: $ 28.35万
• 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/8403075
• 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".

描述（由申请人提供）：研究功能的演变对于研究的挑战是挑战性的，因为它需要重建灭绝祖先节点的合理模型。我们建议生成实验测试的模型，以研究进化如何在与健身性增加相关的蛋白质水平上引入和修改功能关系。我们以类似但更自由基的程序为基础，基于鉴定共同的核心高等教育结构来重建酶的基因结构和功能，比从基于系统发生序列的方法访问的酶更古老的基因结构和功能，以类似但更激进的程序来补充建立的统计推断。我们专注于祖先氨基酰基-TRNA合成酶的非常古老的模型，其进化下降是密码子指导蛋白质合成及其基因表达的起源的关键。 AARS并非都是同源的，而是出现在两个不同的超家族中。该项目是最深刻的动机，渴望了解与两个超家族相关的深刻对称性。我们希望测试的几种假设中，I类和II类AARS的祖先形式最初是在相同的感觉/反义开放式阅读框架的相对方面编码的。我们介绍了Urzymology一词（从Ur =原始，原始，早期 +酶）来描述这种祖先蛋白的创建和实验研究，这些蛋白质超出了祖先基因复活的范围。 Urzymology带来了在时间上操纵生物学对象的能力。 Urzymes与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可以测试明确模型，以实现催化，特异性和变构的演变。许多明显意外事件的原则证明提供了变革性研究的强大组合。 AIM 1将记录I类和II类氨基酰基-TRNA合成酶Urzymes的相对氨基酸特异性，并在Urzymes和现代AARS之间建立详细的机械差异。 AIM 2致力于对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对链上。 AIM 3将增强计算设计过程，并建立遗传系统，以选择和表征较少的细胞毒性构建体，以最终用于选择具有改善酶促功能的Urzymes。通过在此处提出的实验绘制功能适应的记录将通过提供实验工具访问和表征可能进化中间体的实验工具来补充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，这些范式通过对模块如何在蛋白质中相互作用的新了解，以补充药物设计以及新蛋白质试剂的工程和设计。通过识别同时出现的蛋白质超家族，增强“同源性”的含义，验证感觉/反义基因编码将丰富对蛋白质组的理解。