Dynamics of co-transcriptional riboswitch folding through single-molecule microscopy

通过单分子显微镜观察共转录核糖开关折叠的动力学

• 批准号: 10367950
• 负责人: Catherine Scull
• 金额: $ 1.24万
• 依托单位: UNIVERSITY OF MICHIGAN AT ANN ARBOR
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-01-27 至 2022-03-11
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10367950
• 关键词: 5' Untranslated Regions; Active Sites; Anti-Bacterial Agents; Archaea; Arts; Bacteria; Bacterial RNA; Biogenesis; Biological Assay; Biological Sciences; Biology; Biophysics; Cell Survival; Cells; Chemistry; Collection; Complex; DNA-Directed RNA Polymerase; Development; Educational workshop; Elements; Elongation Factor; Equilibrium; Escherichia coli; Eukaryota; Fellowship; Future; Gene Expression; Genetic Transcription; Genome; Grant; Institutes; Life; Ligand Binding; Literature; Maintenance; Measurement; Measures; Mediating; Mentors; Mentorship; Messenger RNA; Methodology; Michigan; Microscopy; Modification; Molecular Conformation; Mutate; Nucleotides; Pathway interactions; Point Mutation; Polymerase; Positioning Attribute; Postdoctoral Fellow; Prokaryotic Cells; RNA; RNA Binding; RNA Folding; RNA Polymerase I; RNA Polymerase II; RNA Splicing; Research; Ribosomal RNA; Ribosomes; Science; Scientist; Signal Transduction; Structure; Talents; Techniques; Technology; Testing; Time; Training; Transcription Elongation; Transcriptional Elongation Factors; Translation Initiation; Translations; Universities; Work; cell growth; college; experimental study; gain of function; graduate student; in vivo; mutant; negative elongation factor; novel; programs; single molecule; single-molecule FRET; skills; tool; transcription factor; transcription termination; undergraduate student

Project Abstract and Summary: RNA elements known as riboswitches are critical for proper genome expression and maintenance in many prokaryotes. Riboswitches are generally found upstream, in the 5’ untranslated region of an mRNA, and fold co-transcriptionally to structurally impede mRNA transcription and/or translation. In the presence of specific RNA binding ligands, riboswitches undergo alterations in secondary structure that either: 1) disallow translation initiation, or 2) result in altered transcription termination. Riboswitches are rarely found in eukaryotes, and thus present a novel vulnerability that can be targeted for anti-bacterial therapies. It has been clearly demonstrated in the literature that nascent RNA structure influences transcriptional activity of the transcribing polymerase in bulk assays, but little work has been done on how the transcribing polymerase itself influences nascent RNA structure in return. Further, RNA structure has been shown to impact active site conformations of the polymerase, but never in the context of the riboswitch. In this study we will comprehensively examine the mechanisms by which riboswitches influence the transcribing RNAP, and vice versa, using cutting edge single-molecule techniques. In addition to the novel science proposed in this application, this fellowship will further enhance my training, and strengthen me as an independent scientist. I will participate in seminars, workshops, mentoring and teach opportunities, as well as professional development and networking opportunities afforded to me by the diverse collection of programs offered at the University of Michigan (including programs organized by: the College of Literature, Sciences, and the Arts, the Life Sciences Institute, the Department of Chemistry, the Center for RNA Biomedicine, the Michigan Life Sciences Fellowship, the Office of Graduate Student and Postdoctoral Affairs, and the University of Michigan Postdoctoral Association). Further, Dr. Nils Walter has already demonstrated excellent mentorship skills, and his lab is comprised of a large, diverse group of postdoctoral fellows and graduate students with whom I can find support and guidance. Our lab also includes a large number of talented undergraduates which will provide me with many opportunities for collaborating with younger mentees. Overall, the research planned in this proposal, and the support granted to me by this program, will enrich both me and the field of riboswitch RNA biology.

项目摘要和总结： RNA元件被称为核糖开关，对于许多基因组的正确表达和维持至关重要。 原核生物核糖开关通常存在于mRNA的5'非翻译区的上游，并且折叠在mRNA的5'非翻译区中。 共转录以在结构上阻碍mRNA转录和/或翻译。存在特异 RNA结合配体，核糖开关经历二级结构的改变，要么：1）不允许翻译 起始，或2）导致改变的转录终止。核糖开关很少在真核生物中发现，因此 提出了一种新的弱点，可以针对抗菌治疗。已经清楚地表明， 在文献中，新生RNA结构影响转录聚合酶的转录活性， 大量实验，但很少有工作已经做了转录聚合酶本身如何影响新生RNA 结构作为回报。此外，RNA结构已显示影响RNA的活性位点构象。 聚合酶，但从来没有在核糖开关的情况下。在这项研究中，我们将全面审查 核糖开关影响转录RNAP的机制，反之亦然，使用切割 尖端的单分子技术。 除了在这个应用程序中提出的新科学，这个奖学金将进一步加强我的训练， 并加强我作为一个独立科学家的能力我将参加研讨会，讲习班，指导和教学 机会，以及专业发展和网络机会提供给我的各种 密歇根大学提供的一系列课程（包括由以下机构组织的课程： 文学、科学和艺术，生命科学研究所，化学系， RNA生物医学，密歇根生命科学奖学金，研究生和博士后办公室 事务，和密歇根大学博士后协会）。此外，尼尔斯·沃尔特博士已经 表现出出色的指导技能，他的实验室由一个庞大的，多样化的博士后团队组成， 研究员和研究生，我可以找到支持和指导。我们的实验室还包括一个大型的 许多有才华的本科生，这将为我提供许多合作的机会， 年轻的学员。总的来说，这项研究计划，并给予我的支持，这一点， 程序，将丰富我和核糖开关RNA生物学领域。