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Defining Adaptors for mRNA Degradation in Bacteria

定义细菌中 mRNA 降解的接头

基本信息

批准号：
10556098
负责人：
Matthew Tien
金额：
$ 1.76万
依托单位：
MASSACHUSETTS INSTITUTE OF TECHNOLOGY
依托单位国家：
美国
项目类别：
财政年份：
2020
资助国家：
美国
起止时间：
2020-04-01 至 2022-06-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10556098
关键词：
Adaptor Signaling Protein Address Affect Affinity Chromatography Animal Model Bacillus subtilis Bacteria Bacterial Model Behavior Binding Biochemical Biological Assay Categories Cells Complex DNA-Directed RNA Polymerase Dependence Development Dose Endoribonucleases Environment Event Fellowship Fostering Foundations Future Gene Expression Gene Expression Regulation Genes Genetic Genetic Transcription Gram-Positive Bacteria Individual Infection Institutes Invaded Knowledge Massachusetts Measures Mediating Mentors Mentorship Messenger RNA Methodology Methods Microbial Biofilms Modeling Molecular Molecular Biology Mutagenesis Nucleic Acid Biochemistry Organism Pathway interactions Play Positioning Attribute Post-Transcriptional Regulation Protein Isoforms Proteins RNA RNA Degradation Regulation Research Research Personnel Resolution Ribonucleases Role Shapes Site Small RNA Specific qualifier value Specificity Staphylococcus aureus Streptococcus pyogenes Techniques Technology Testing Titrations Toxin Training Transcript Transcriptional Regulation Virulence complement system crosslink design endonuclease experience experimental study falls forward genetics genetic approach genome-wide in vivo in vivo monitoring mRNA Decay mRNA Transcript Degradation mutant next generation sequencing novel nuclease overexpression pathogen pathogenic bacteria professor response tool transcription factor transcriptome transcriptome sequencing

项目摘要

PROJECT SUMMARY/ABSTRACT Transcription and RNA turnover shape the pool of transcripts in the cell. Regulation of RNA degradation, however, remains elusive when compared to the enumerable mechanisms of transcriptional control. In bacteria, mRNA decay is thought to be initiated by a few endoribonucleases that have promiscuous activities, yet mRNA half-lives vary greatly. Here I propose to globally define the set of adaptors for endoribonucleases that instruct mRNA decay, akin to transcription factors modulating the activity of RNA polymerase. Only a few adaptors of degradation have been discovered in bacteria, and they were all found serendipitously. To provide a far more comprehensive view, I will develop several general methodologies that will be translatable to other organisms. My first approach will identify classes of RNAs potentially targeted by the same adaptor, using their dependence on nuclease levels as a classifier. Demonstration of this top-down method utilizes the central endonuclease RNase Y from the gram-positive bacterium Bacillus subtilis. Completion of the first part of this aim will be the first high-resolution study of RNA degradation in B. subtilis and demonstrates a general strategy to define the direct targets of promiscuous central endonucleases. Secondly, to complement the systems-wide approach, I have designed both genetic and biochemical approaches to identify the molecular constituents of adaptors of degradation. Discoveries of novel adaptors for mRNA decay will expand our understanding of gene regulation and provide transformative tools for molecular biology. Together, this set of top-down and bottom-up approaches will transform our understanding of endonuclease specificity in bacteria and provide a general strategy for studying the post-transcriptional control of gene expression. The fellowship training plan leverages complementary expertise and experiences of two mentors, Dr. Gene- Wei Li and Dr. Alan Grossman. Technical training within the research strategy consists of (1) quantitative modeling and next-generation sequencing techniques from my sponsor Dr. Li and (2) methodologies in forward genetics assays and nucleic acid biochemistry from my co-sponsor Dr. Grossman. Dr. Li is a trained physicist and has a record of developing cutting-edge approaches to address his unique perspective on gene regulation. Dr. Grossman is a renowned bacterial geneticist and has thirty years of mentorship experience as a professor with many postdoctoral trainees obtaining independent research positions. The combined environment fostered by these two individuals at the Massachusetts Institute of Technology serves to address the aims of the research proposed and to aid in my development as an independent researcher.

项目总结/文摘