Organisation and regulation of bacterial enhancer-binding proteins

细菌增强子结合蛋白的组织和调节

• 批准号: BB/R018499/1
• 负责人: Xiaodong Zhang
• 金额: $ 131.07万
• 依托单位: Imperial College London
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2018
• 资助国家: 英国
• 起止时间: 2018 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FR018499%2F1
• 关键词: Organisation; regulation; bacterial; enhancer; binding

RNA polymerase (RNAP) is a fundamental cellular machinery responsible for converting genetic information stored in DNA to another genetic molecule, called RNA, that can then be converted to protein or act in another regulatory or structural capacity. Accessing information in DNA occurs in a complex, highly controlled process called gene transcription and the core molecular machinery, the RNAP enzyme, is conserved from bacteria to humans. DNA is normally organised in chromosomes which organise DNA into higher order structures. Gene transcription is a highly regulated event in development and a major response to growth and environmental stimuli in all known living systems. Although significant advance has been made towards understanding how RNAP functions as an enzyme, including the work recognised by the Nobel Prize in Chemistry in 2006, how it is controlled by factors that signal special cellular states and events, is still poorly understood. We are studying a unique system in bacteria that responds to bacterial stress and affects the ability of bacteria to respond to environmental changes, therefore affecting its ability to infect as a pathogen or propagate in a biotechnological setting. The key unique transcription factor, called sigma54, binds to RNAP and normally inhibits RNAP to prevent gene expression. Following a set of complex transactions with special control proteins that utilise the energy currency of the cell, a molecule called ATP, this system is then activated in a remodeling event to allow the RNAP to transcribe key genes in response to e.g. changes in the environment. These controlling activator proteins respond to a wide range of signals and are organised remotely on the DNA from RNAP. Therefore how these components are brought together to productively interact with each other and how the DNA is organised in this system as well as how signals regulate this system are extremely important to understand. In this current proposed research, we plan to utilise the latest developments in life sciences technologies, especially using electron microscopy, to study these complex protein-DNA assemblies and how they change upon environmental signals to allow a regulated gene expression event. Such work is likely to shed light onto how RNAP in humans, plants and animals is activated. Furthermore, our approach of looking at large complex assemblies in transcription will bring us one step closer to studying these systems in the context of a complete chromosome and in intact cells. Furthermore, we want to exploit the structural features of these highly regulated states in order to design novel antibiotics that inhibit gene transcription for drug therapies as this system, although important for responding to stress, is not essential for normal bacterial growth under a range of conditions, but is important for many adaptations in hostile environments such as the host. The bacteria therefore will be under less pressure to develop resistance. This approach is especially effective when combined with other antibiotics. Inhibiting bacterial RNAP, and hence gene transcription, is a validated antibiotic strategy e.g. in controlling TB infections, so our work should provide novel avenues for effective antibiotic development at a time when it is crucial to have new reagents to control dangerous pathogenic bacteria of humans and animals.

RNA聚合酶（RNAP）是一种基本的细胞机制，负责将储存在DNA中的遗传信息转化为另一种称为RNA的遗传分子，然后可以转化为蛋白质或以另一种调节或结构能力发挥作用。DNA中的核糖核酸信息发生在一个复杂的、高度受控的过程中，称为基因转录，核心分子机制RNAP酶从细菌到人类都是保守的。DNA通常组织在染色体中，染色体将DNA组织成更高级的结构。基因转录是发育过程中高度调控的事件，是所有已知生命系统对生长和环境刺激的主要反应。尽管在理解RNAP作为酶的功能方面取得了重大进展，包括2006年诺贝尔化学奖认可的工作，但它如何受到信号特殊细胞状态和事件的因素的控制，仍然知之甚少。我们正在研究细菌中一种独特的系统，该系统对细菌压力做出反应，并影响细菌对环境变化做出反应的能力，从而影响其作为病原体感染或在生物技术环境中繁殖的能力。关键的独特转录因子，称为sigma 54，与RNAP结合，通常抑制RNAP以阻止基因表达。在与利用细胞能量货币的特殊控制蛋白（一种称为ATP的分子）进行一系列复杂的交易之后，该系统在重塑事件中被激活，以允许RNAP转录关键基因以响应例如环境的变化。这些控制激活蛋白对广泛的信号做出反应，并在RNAP的DNA上远程组织。因此，这些组件如何聚集在一起以产生相互作用，DNA如何在这个系统中组织以及信号如何调节这个系统是非常重要的。在目前拟议的研究中，我们计划利用生命科学技术的最新发展，特别是使用电子显微镜，研究这些复杂的蛋白质-DNA组装体以及它们如何根据环境信号发生变化，以允许调节基因表达事件。这项工作可能会揭示人类，植物和动物中RNAP是如何激活的。此外，我们在转录中观察大型复杂组装的方法将使我们更接近在完整染色体和完整细胞的背景下研究这些系统。此外，我们希望利用这些高度调节状态的结构特征，以设计抑制基因转录的新型抗生素用于药物治疗，因为该系统虽然对于应对压力很重要，但对于一系列条件下的正常细菌生长并不重要，但对于宿主等恶劣环境中的许多适应性很重要。因此，细菌产生耐药性的压力较小。这种方法在与其他抗生素联合使用时特别有效。抑制细菌RNAP，从而抑制基因转录，是一种经过验证的抗生素策略，例如在控制结核感染中，因此我们的工作应该为有效的抗生素开发提供新的途径，因为有新的试剂来控制人类和动物的危险病原菌至关重要。

项目成果

Mechanisms of DNA opening revealed in AAA+ transcription complex structures.

• DOI: 10.1126/sciadv.add3479
• 发表时间: 2022-12-21
• 期刊: Science advances
• 影响因子: 13.6

Structures of Class I and Class II Transcription Complexes Reveal the Molecular Basis of RamA-Dependent Transcription Activation.

• DOI: 10.1002/advs.202103669
• 发表时间: 2022-03
• 期刊: Advanced science (Weinheim, Baden-Wurttemberg, Germany)
• 作者: Hao M;Ye F;Jovanovic M;Kotta-Loizou I;Xu Q;Qin X;Buck M;Zhang X;Wang M
• 通讯作者: Wang M

Structures of Bacterial RNA Polymerase Complexes Reveal the Mechanism of DNA Loading and Transcription Initiation.

• DOI: 10.1016/j.molcel.2018.05.021
• 发表时间: 2018-06-21
• 期刊: Molecular cell
• 影响因子: 16
• 作者: Glyde R;Ye F;Jovanovic M;Kotta-Loizou I;Buck M;Zhang X
• 通讯作者: Zhang X

Structural basis of transcription inhibition by the DNA mimic protein Ocr of bacteriophage T7

噬菌体 T7 的 DNA 模拟蛋白 Ocr 转录抑制的结构基础

• DOI: 10.7554/elife.52125
• 发表时间: 2020
• 期刊: eLife
• 影响因子: 7.7
• 作者: Ye F