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Regulation of elongation by RNA polymerase and ribosome via intrinsic signals and transcription-translation coupling

RNA聚合酶和核糖体通过内在信号和转录-翻译耦合调节延伸

基本信息

批准号：
BB/J006378/1
负责人：
Nikolay Zenkin
金额：
$ 69.1万
依托单位：
Newcastle University
依托单位国家：
英国
项目类别：
Research Grant
财政年份：
2012
资助国家：
英国
起止时间：
2012 至无数据
项目状态：
已结题

来源：
https://gtr.ukri.org/projects?ref=BB%2FJ006378%2F1
关键词：
Regulation elongation RNA polymerase ribosome

项目摘要

Understanding the molecular mechanisms governing the expression of genes in the cell is an essential part of developing strategies for intelligent manipulation of harmful and useful organisms, development of new antimicrobial and antifungal agents, and, importantly, for understanding emergence and evolution of Life.In bacteria, both steps of gene expression, copying genes into RNA (transcription) and production of proteins on RNA (translation), are coupled. This implies tight interactions and mutual regulation of these two molecular machineries, which determine the overall rate of gene expression, which, in turn, is important for all cellular processes. This regulation and mechanisms determining the rates of transcription and translation are poorly understood. We are the first laboratory who developed a unique experimental system where both steps of gene expression can be assembled from purified components and investigated simultaneously in the test tube. We also possess some unique biochemical techniques, which allowed us for example to describe the mechanism involved in regulation of the development of HIV-1, and to uncover mode of action of antibiotic Tagetitoxin. In this proposal, by using these techniques, we will investigate what factors determine rates of both steps of gene expression: (i) we will apply a systematic approach to understand the signals in the DNA that may influence the rate of transcription; (ii) we will investigate the interactions and mutual regulation of transcription and translation. Sophisticated regulation of transcription and translation are the major factors for survival of pathogenic bacteria. Understanding of relations between these two steps of gene expression will improve our knowledge of these bacteria, and thus provide new tools for fighting infectious diseases. We collaborate with a bio-tech company on applying experimental tools developed in our research to elucidation of modes of action of new antibiotics, inhibitors of RNA polymerase. Being at the interface of transcription and translation, the proposed study will be valuable for both of these vast fields of molecular biology. We collaborate with the leading UK laboratories who will use the tools designed in this study to investigate mechanisms of gene expression by biophysical methods, such as single-molecule techniques, crystallography, cryo-electron microscopy. Furthermore, simultaneous assembly of the two major cellular machineries in the test tube may become the first step for production of artificially assembled living organisms.

了解基因在细胞中表达的分子机制，是开发有害和有益生物智能操纵策略，开发新的抗菌剂和抗真菌剂的重要组成部分，更重要的是，了解生命的出现和进化。在细菌中，基因表达的两个步骤，将基因复制到RNA中，蛋白质的合成（转录）和在RNA上的蛋白质的产生（翻译）是偶联的。这意味着这两种分子机制的紧密相互作用和相互调节，决定了基因表达的总体速率，而基因表达反过来对所有细胞过程都很重要。这种调节和机制决定转录和翻译的速率知之甚少。我们是第一个开发出独特的实验系统的实验室，在该系统中，基因表达的两个步骤可以从纯化的组分中组装，并在试管中同时进行研究。我们还拥有一些独特的生物化学技术，例如，这使我们能够描述HIV-1发展的调节机制，并揭示抗生素Tagetitoxin的作用模式。在本提案中，通过使用这些技术，我们将研究哪些因素决定基因表达的两个步骤的速率：（i）我们将应用系统的方法来理解DNA中可能影响转录速率的信号;（ii）我们将研究转录和翻译的相互作用和相互调节。复杂的转录和翻译调控是致病菌生存的主要因素。了解这两个基因表达步骤之间的关系将提高我们对这些细菌的认识，从而为对抗传染病提供新的工具。我们与一家生物技术公司合作，将我们研究中开发的实验工具应用于阐明新抗生素（RNA聚合酶抑制剂）的作用模式。作为转录和翻译的界面，所提出的研究将对这两个广阔的分子生物学领域都有价值。我们与英国领先的实验室合作，他们将使用本研究中设计的工具，通过生物物理方法（如单分子技术，晶体学，冷冻电子显微镜）研究基因表达的机制。此外，在试管中同时组装两种主要的细胞机器可能成为生产人工组装的活生物体的第一步。

项目成果

期刊论文数量（10）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

A link between transcription fidelity and pausing in vivo.

DOI：
10.1080/21541264.2016.1274812
发表时间：
2017-03-15
期刊：
Transcription
影响因子：
0
作者：
Gamba P;James K;Zenkin N
通讯作者：
Zenkin N

In vitro experimental system for analysis of transcription-translation coupling.

DOI：
10.1093/nar/gkr1262
发表时间：
2012-03
期刊：
Nucleic acids research
影响因子：
14.9
作者：
Castro-Roa D;Zenkin N
通讯作者：
Zenkin N

Misincorporation by RNA polymerase is a major source of transcription pausing in vivo.

DOI：
10.1093/nar/gkw969
发表时间：
2017-02-17
期刊：
Nucleic acids research
影响因子：
14.9
作者：
James K;Gamba P;Cockell SJ;Zenkin N
通讯作者：
Zenkin N

The Fic protein Doc uses an inverted substrate to phosphorylate and inactivate EF-Tu.

FIC蛋白DOC使用倒立的底物磷酸化和失活的EF-TU。

DOI：
10.1038/nchembio.1364
发表时间：
2013-12
期刊：
NATURE CHEMICAL BIOLOGY
影响因子：
14.8
作者：
Castro-Roa, Daniel;Garcia-Pino, Abel;De Gieter, Steven;van Nuland, Nico A. J.;Loris, Remy;Zenkin, Nikolay
通讯作者：
Zenkin, Nikolay

Single-peptide DNA-dependent RNA polymerase homologous to multi-subunit RNA polymerase.