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 DNA 中存储的遗传信息转化为另一种称为 RNA 的遗传分子，然后 RNA 可以转化为蛋白质或发挥另一种调节或结构能力。获取 DNA 中的信息发生在一个复杂的、高度受控的过程中，称为基因转录，而核心分子机制 RNAP 酶从细菌到人类都是保守的。 DNA 通常在染色体中组织，染色体将 DNA 组织成更高阶的结构。基因转录是发育过程中高度调控的事件，也是所有已知生命系统中对生长和环境刺激的主要反应。尽管在理解 RNAP 作为酶如何发挥作用方面已经取得了重大进展，包括 2006 年诺贝尔化学奖认可的工作，但人们对它如何受到发出特殊细胞状态和事件信号的因素的控制仍然知之甚少。我们正在研究细菌中的一种独特系统，该系统对细菌应激做出反应，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传播的能力。关键的独特转录因子 sigma54 与 RNAP 结合，通常会抑制 RNAP 以阻止基因表达。在与利用细胞能量货币（一种称为 ATP 的分子）的特殊控制蛋白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多种信号作出反应，并在来自 RNAP 的 DNA 上远程组织。因此，了解这些组件如何组合在一起以有效地相互作用、DNA 在该系统中如何组织以及信号如何调节该系统非常重要。在当前提出的研究中，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，来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实现受调控的基因表达事件。此类工作可能会揭示人类、植物和动物体内 RNAP 的激活方式。此外，我们观察转录中大型复杂组装体的方法将使我们更接近在完整染色体和完整细胞中研究这些系统。此外，我们希望利用这些高度调控状态的结构特征来设计抑制药物治疗基因转录的新型抗生素，因为该系统虽然对于应对应激很重要，但对于一系列条件下的正常细菌生长并不是必需的，但对于宿主等恶劣环境中的许多适应很重要。因此，细菌产生耐药性的压力较小。这种方法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，例如因此，当拥有新试剂来控制人类和动物的危险致病菌至关重要时，我们的工作应该为有效的抗生素开发提供新的途径。

项目成果

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

I 类和 II 类转录复合物的结构揭示了 RamA 依赖性转录激活的分子基础。

• DOI: http://dx.10.1002/advs.202103669
• 发表时间: 2022
• 期刊: Advanced science (Weinheim, Baden-Wurttemberg, Germany)
• 作者: Hao M

Structural basis of s 54 displacement and promoter escape in bacterial transcription

细菌转录中 s 54 置换和启动子逃逸的结构基础

• DOI: http://dx.10.1073/pnas.2309670120
• 发表时间: 2024
• 期刊: Proceedings of the National Academy of Sciences
• 作者: Gao F

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: http://dx.10.1101/822460
• 发表时间: 2019
• 作者: Ye F

Bacterial Enhancer Binding Proteins-AAA+ Proteins in Transcription Activation.

转录激活中的细菌增强子结合蛋白 - AAA 蛋白。

• DOI: http://dx.10.3390/biom10030351
• 发表时间: 2020
• 期刊: Biomolecules
• 影响因子: 5.5
• 作者: Gao F

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

细菌 RNA 聚合酶复合物的结构揭示了 DNA 加载和转录起始的机制。

• DOI: http://dx.10.1016/j.molcel.2018.05.021
• 发表时间: 2018
• 期刊: Molecular cell
• 影响因子: 16
• 作者: Glyde R