MFB: RNA modifications of frameshifting stimulators: cellular platforms to engineer gene expression by computational mutation predictions and functional experiments

MFB：移码刺激器的RNA修饰：通过计算突变预测和功能实验来设计基因表达的细胞平台

• 批准号: 2330628
• 负责人: Tamar Schlick
• 金额: $ 150万
• 依托单位: New York University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2024
• 资助国家: 美国
• 起止时间: 2024-03-01 至 2027-02-28
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2330628&HistoricalAwards=false
• 关键词: MFB; RNA; modifications; frameshifting; stimulators

In this Molecular Foundations for Biotechnology (MFB) project, Dr. Tamar Schlick from New York University and Dr. Alain Laederach from the University of North Carolina will develop advanced computational tools to predict and control how viral protein synthesis is affected when the cell’s machinery (the ribosome) shifts and thus changes how the three-letter code in messenger RNA (mRNA) is read. This frameshifting in translating the mRNA triplet code has been found to be preprogrammed in viruses and human cells to modify the expression of gene products and to regulate biochemical processes. This study aims to computationally predict and experimentally test how introducing mutations to mRNA affects its three-dimensional structure and, consequently, programmed frameshifting in prototypical viral genomes. Revealing the specific structural and sequence requirements for frameshifting in prototype viruses will facilitate the design of novel efficient frameshifting elements, with potential applications to viral packaging of genes. This project will provide interdisciplinary training to students in mathematics, computer science, biology, physics, chemistry, and engineering, with particular emphasis on enhancing minority participation in STEM activities. Public outreach efforts will be included to reach general audiences and highlight the intersection of mathematics, biology, computing, and biotechnologies that have implications in human health. Programmed ribosomal frameshifting (PRF) is a widespread mechanism for modifying the gene expressed by altering the mRNA triplet-nucleotide transcript to generate an alternate gene product. Indispensable to many viruses including HIV and SARS-associated coronaviruses for translating overlapping mRNA reading frames, PRF is also a mechanism in endogenous human, eukaryotic and prokaryotic genes. Because PRF has been shown to dramatically influence viral viability or the biochemical regulation of human processes, the modulation of frameshifting defines a platform for engineering gene expression. However, the complex aspects of frameshifting and the structural plasticity of the RNA frameshifting element (FSE) must be understood before engineering and therapeutic strategies can succeed. In this synergistic biological, chemical, mathematical, and computational research program, graph-theory-based tools will be developed to predict FSE mutations for prototype viral systems aimed at substantially lowering frameshifting efficiency as a novel biotechnological strategy against viral infections and related human diseases associated with PRF. The effect of these mutations will be assessed by Luciferase assay measurements, and the resulting FSE structural landscapes analyzed by techniques suitable for RNAs with multiple conformations. Besides an improved understanding of the mechanisms of frameshifting and computational tools for predicting FSE-landscape-altering mutations, this project will produce new biotechnological, RNA modifying tools as potential therapeutic agents against RNA viruses or applicable to human and other genes that employ frameshifting. Applications to viral packaging/drug delivery also arise, as frameshifting is a compact mechanism to store gene coding information and can be exploited to overcome genomic size limitations.This project is jointly funded by the Division of Chemistry (CHE), the Division of Mathematical Sciences (DMS), and the Division of Physics (PHY) in the Directorate for Mathematical and Physical Sciences (MPS).This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

在这个生物技术分子基础（MFB）项目中，纽约大学的Tamar Schlick博士和北卡罗来纳大学的Alain Laederach博士将开发出高级计算工具，以预测和控制病毒蛋白合成时，当细胞机械（核糖体）的转移和因此如何改变了三个封闭式的serveenger insermender rna（MRNA）时，病毒蛋白合成如何受到影响。已经发现，在翻译mRNA三胞胎代码的转换中，已在病毒和人类细胞中制备，以改变基因产物的表达并调节生化过程。这项研究的目的是在计算上预测和实验测试mRNA引入突变如何影响其三维结构，从而在原型病毒基因组中进行了编程的Frameshifting。揭示了原型病毒中帧外观的特定结构和序列要求，将有助于设计新型有效的帧速率元素，并潜在地应用于基因的病毒包装。该项目将为数学，计算机科学，生物学，物理，化学和工程学的学生提供跨学科的培训，并特别强调增强少数群体参与STEM活动。将包括公众推广工作，以吸引一般受众并强调对人类健康具有影响的数学，生物学，计算和生物技术的交集。编程的核糖体框架（PRF）是一种通过改变mRNA三胞胎核苷酸转录物来改变基因表达基因表达的宽度机制，以生成替代基因产物。对于许多病毒，包括HIV和与SARS相关的冠状病毒，用于翻译重叠的mRNA读帧的必不可少，PRF也是内源性人，真核和原核基因的一种机制。由于PRF已被证明会极大地影响人类过程的病毒生存力或生化调节，因此帧速率的调节定义了工程基因表达的平台。但是，在工程和治疗策略可以成功之前，必须理解框架的复杂方面和RNA帧速率元件（FSE）的结构可塑性（FSE）。在这个合成的生物学，化学，数学和计算研究计划中，将开发基于图理论的工具，以预测原型病毒系统的FSE突变，旨在实质上降低范围效率，作为针对病毒感染和与PRF相关的相关人类疾病的新型生物技术策略。这些突变的效果将通过荧光素酶评估测量值评估，以及由适合有多个考虑因素的RNA分析的最终的FSE结构景观。除了对预测FSE-LAN​​DSCAPE-SCAPE-SCAPE-ORTERTERITS突变的框架和计算工具的机制有了深入的了解外，该项目还将生成新的生物技术，RNA修饰工具，作为针对RNA病毒或适用于人类和其他采用Frameshifting的人类和其他基因的潜在治疗剂。在病毒包装/药物输送中的应用也将到来，因为框架是存储基因编码信息的紧凑机制，可以探索克服基因组大小的限制。该项目由化学（CHE）共同资助，由数学科学（DMS）和奖项（DMS）和物理（PHY）（PHY）（PHY）（PHY）（PHY）（PHY）（PHY）（MR）（MR）（MR）授予MATHISISS（PHY）（M.法定使命，并使用基金会的知识分子优点和更广泛的影响标准通过评估被认为是宝贵的支持。