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Riboswitch Dynamics at Atomic Resolution

原子分辨率下的核糖开关动力学

基本信息

批准号：
10588135
负责人：
Qi Zhang
金额：
$ 33.94万
依托单位：
UNIV OF NORTH CAROLINA CHAPEL HILL
依托单位国家：
美国
项目类别：
财政年份：
2015
资助国家：
美国
起止时间：
2015-05-01 至 2025-01-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10588135
关键词：
3-Dimensional Adopted Anabolism Antibiotic Resistance Antibiotics Bacillus cereus Bacteria Binding Biochemical Biological Assay Biological Process Cells Chemicals Code Communication Complex Computer Models Coupled Deltaproteobacteria Development Engineering Flavin Mononucleotide Fluorides Funding Gene Expression Regulation Genetic Transcription Goals Individual Kinetics Ligand Binding Ligands Maps Mediating Modeling Molecular Molecular Conformation Mutagenesis Mutation Pathway interactions Play Process Property RNA RNA Conformation Regulation Regulator Genes Research Resolution Riboflavin Ribosomes Role Spectrum Analysis Structural Models Structure System Techniques Testing Therapeutic Thermodynamics Time Transcriptional Activation Transcriptional Regulation Translational Regulation Translations Untranslated RNA Work antimicrobial aptamer conformational conversion insight novel pathogenic bacteria protein expression public health relevance small molecule synthetic biology technological innovation tool

项目摘要

Conformational dynamics play essential roles in the regulatory functions of coding and non-coding RNAs. Many regulatory RNAs undergo these functionally important conformational dynamics as they are being transcribed, a process referred to as ‘co-transcriptional folding’. While intrinsic RNA conformational dynamics and co-transcriptional folding can be coupled to elicit biological functions, the underlying mechanisms remain poorly understood due to difficulties in characterizing and examining RNA conformational dynamics in the context of co-transcriptional folding. Towards our long-term goal of elucidating how regulatory RNAs function, the overall objective of this proposal is to integrate breakthrough techniques of solution NMR, computational modeling, and time-resolved chemical probing to uncover principles of regulation via co-transcriptional RNA dynamics with specific applications to riboswitches, a class of non-coding RNAs that serve as ligand- dependent gene regulators and are emerging targets for developing novel antibiotics. During the prior funding period, we have challenged the conventional working model of riboswitches by showing that, under solution conditions, the sensing aptamer domain of the fluoride riboswitch adopts the same conformation in the presence or absence of the ligand. We found that the ligand-free sensing aptamer undergoes distinct conformational dynamics involving a low-populated and short-lived excited state (ES), where the ES- mediated conformational transition works in coordination with co-transcriptional folding to regulate ligand- dependent transcription activation. The present proposal represents a continuum of our conceptual and technological innovations towards understanding riboswitch functions, in which we aim to establish co- transcriptional RNA dynamics based regulatory mechanisms, to advance new paradigms for transcriptional and translational riboswitches, and to perform biochemical assays and mutagenesis to reengineer individual regulatory steps to test predictions. To accomplish the overall objective, the proposed research details three specific objectives that feature a gradual increase in the complexity: (1) characterize co-transcriptional RNA dynamics of the transcriptional fluoride riboswitch, (2) characterize co-transcriptional RNA dynamics of the translational fluoride riboswitch, and (3) characterize co-transcriptional RNA dynamics of the FMN riboswitches. Results will be used to test the central hypothesis of this proposal that RNA structures have evolved to encode distinct co-transcriptional conformational dynamics to facilitate regulatory structural changes along specific functional pathways. By developing a deep mechanistic understanding of transcriptional and translational riboswitches, the proposed studies will illuminate fundamental properties of co-transcriptional RNA dynamics and its role in gene regulation. The conceptual framework and experimental tools developed in the proposal can further assist the development of RNA-targeted antimicrobial therapeutics and advance the molecular understanding of co-transcriptional regulation of functional RNAs.

构象动力学在编码rna和非编码rna的调控功能中起着重要作用。