RNA modification: Mechanism and links to other metabolic pathways

RNA 修饰：机制以及与其他代谢途径的联系

基本信息

批准号：
10618350
负责人：
MANAL A SWAIRJO
金额：
$ 41.06万
依托单位：
SAN DIEGO STATE UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2014
资助国家：
美国
起止时间：
2014-09-15 至 2025-05-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10618350
关键词：
ATP Hydrolysis ATP phosphohydrolase Active Sites Address Amino Acyl-tRNA Synthetases Anabolism Anti-Bacterial Agents Anticodon Bacteria Biochemical Bioinformatics Cell Cycle Regulation Cell Wall Cell division Cell physiology Chemicals Chemistry Codon Nucleotides Collaborations Comparative Genomic Analysis Complex Data Defect Development Elements Enzymatic Biochemistry Enzymes Foundations Funding Genetic Genome Goals Gram-Negative Bacteria Indiana Initiator Codon Institution Kinetics Laboratories Life Link Measures Metabolic Metabolic Pathway Metabolism Methods Microbial Genetics Modification Molecular Molecular Target Mutagenesis Nucleotides Organism Outcome Pathway interactions Peptidoglycan Phenotype Phosphorylation Phosphotransferases Physiological Play Positioning Attribute Process Productivity Protein Dephosphorylation Proteins Pseudomonas putida RNA RNA Sequences Recycling Regulation Regulatory Pathway Reporting Research Ribosomal Frameshifting Role Specificity Streptococcus pneumoniae Structural Biochemistry System Therapeutic Intervention Transfer RNA Translations Work combat experimental study genetic information human disease insight microbial disease multidisciplinary mutant novel posttranscriptional prevent programs stem structural biology virtual

项目摘要

Summary Transfer-RNAs (tRNA) are key molecules of translation, and their ability to accurately and efficiently decode genetic information is dependent on post-transcriptional modification of nucleotides, particularly in the critical anticodon stem loop (ASL). Deficiencies in these modifications can be lethal, and have been linked to a variety of pleiotropic phenotypes and human disease states. The long-term goals of this research program are to develop a detailed understanding of the biosynthetic pathways to complex tRNA modifications, the roles these modifications play in cellular physiology, and to identify novel targets in their pathways for therapeutic intervention. This application specifically focuses on elucidating the molecular mechanisms of formation and specificity of the universal ASL modification threonylcarbamoyladenosine (t6A) in bacteria, and elucidating the regulatory pathways that link it to bacterial cell wall synthesis. t6A is a complex modification found in the ASLs of tRNAs decoding ANN codons, and is critical for tRNA function by preventing ribosomal frameshifting, promoting cognate codon recognition, facilitating tRNA translocation, and serving as a recognition determinant for aminoacyl-tRNA synthetases. In the previous funding period we arrived at the first mechanistic proposal for the t6A biosynthesis cycle in which the proteins TsaC2, TsaB and TsaD function together to install threonylcarbamoyl on A37 of substrate tRNA, while TsaE provides an unexpected ATPase activity required for turnover of the cycle. We also discovered that TsaE is a novel bacterial S/T/Y kinase, and our bioinformatic analyses suggested a linkage of t6A biosynthesis to cell wall metabolism, which raises new questions about the widely reported cell wall synthesis phenotypes associated with t6A deficiency. In the current application we propose 4 specific aims that will allow us to elucidate 1) the tRNA specificity of the bacterial t6A system, 2) the mechanism of TC-AMP transfer in t6A biosynthesis, 3) the mechanism of ATP-hydrolysis driven turnover of the t6A cycle, and 4) the links between TsaE and cell-wall synthesis and/or cell division. This work will be accomplished through a combination of biochemical, structural, genetic, and physiologic approaches.

概括转移RNA（tRNA）是翻译的关键分子，其准确和准确的能力有效地解码遗传信息取决于转录后修饰核苷酸，尤其是在临界反密码子茎环（ASL）中。这些缺陷修饰可能是致命的，并且与多种多效性表型和人类疾病状态。该研究计划的长期目标是开发详细的了解复杂tRNA修饰的生物合成途径，这些作用修饰在细胞生理学中发挥作用，并在其途径中识别新目标治疗干预。该应用特别着重于阐明形成的分子机制通用ASL修饰的特异性threonylcarbamoyladenosine（T6a）在细菌中，并阐明将其与细菌细胞壁合成联系起来的调节途径。 T6a是一个复杂的在TRNA解码ANN密码子的ASL中发现的修改，对于TRNA功能至关重要通过防止核糖体帧汇总，促进同源密码子识别，促进tRNA 易位，作为氨基酰基-TRNA合成酶的识别决定因素。在上一个资金期间，我们提出了T6A的第一个机械提案蛋白质TSAC2，TSAB和TSAD功能一起安装的生物合成周期 Threonylcarbamoyl在底物tRNA的A37上，而TSAE提供了意外的ATPase活性周期营业额所需。我们还发现TSAE是一种新型细菌S/T/Y激酶，我们的生物信息学分析表明，T6a生物合成与细胞壁代谢有联系，这提出了有关广泛报道的细胞壁合成表型相关的新问题缺乏T6a。在当前的应用程序中，我们提出了4个具体目标，这将使我们能够阐明1）细菌T6A系统的tRNA特异性，2）T6a中TC-AMP转移的机理生物合成，3）ATP-Hydrolssy驱动T6A周期营业额的机制，4）在TSAE和细胞壁合成和/或细胞分裂之间。这项工作将通过生化，结构，遗传和生理方法的结合。

项目成果

期刊论文数量（14）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Mechanism and catalytic strategy of the prokaryotic-specific GTP cyclohydrolase-IB.

原核生物特异性GTP环化水解酶-IB的机制和催化策略。

DOI：
10.1042/bcj20161025
发表时间：
2017
期刊：
The Biochemical journal
影响因子：
0
作者：
Paranagama,Naduni;Bonnett,ShilahA;Alvarez,Jonathan;Luthra,Amit;Stec,Boguslaw;Gustafson,Andrew;Iwata-Reuyl,Dirk;Swairjo,ManalA
通讯作者：
Swairjo,ManalA

Structure-based design of guanosine analogue inhibitors targeting GTP cyclohydrolase IB towards a new class of antibiotics.

针对 GTP 环水解酶 IB 的鸟苷类似物抑制剂的基于结构的设计，成为一类新型抗生素。

DOI：
10.1016/j.bmcl.2019.126818
发表时间：
2020
期刊：
Bioorganic & medicinal chemistry letters
影响因子：
2.7
作者：
Samaan,GeorgeN;Paranagama,Naduni;Haque,Ayesha;Hecht,DavidA;Swairjo,ManalA;Purse,ByronW
通讯作者：
Purse,ByronW

Crystal structure of the archaeosine synthase QueF-like-Insights into amidino transfer and tRNA recognition by the tunnel fold.

DOI：
10.1002/prot.25202
发表时间：
2017-01
期刊：
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
影响因子：
2.9
作者：
Mei, Xianghan;Alvarez, Jonathan;Bon Ramos, Adriana;Samanta, Uttamkumar;Iwata-Reuyl, Dirk;Swairjo, Manal A.
通讯作者：
Swairjo, Manal A.

The Importance of Being Modified: The Role of RNA Modifications in Translational Fidelity.