Transcription termination and its regulation in E. Coli

大肠杆菌中的转录终止及其调控

基本信息

批准号：
8672454
负责人：
EVGENY A NUDLER
金额：
$ 16.95万
依托单位：
NEW YORK UNIVERSITY SCHOOL OF MEDICINE
依托单位国家：
美国
项目类别：
财政年份：
2014
资助国家：
美国
起止时间：
2014-01-01 至 2014-12-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8672454
关键词：
Address Amino Acids Antibiotics Bacterial Genes Bacterial RNA Bacteriophages Binding Sites Biochemical Carbon Cell Survival Cells ChIP-on-chip Chemicals Complex Consensus Coupled DNA DNA-Directed RNA Polymerase Elongation Factor Enterobacter Escherichia coli Essential Genes Future Gene Expression Gene Expression Regulation Genes Genetic Transcription Genomics Goals Grant Growth Health Human Intrinsic factor Kinetics Maps Microarray Analysis Modeling Molecular Mutation Nutrient Pathway interactions Pattern Pharmaceutical Preparations Phenotype Physiological Process Protein Inhibition Proteins RNA RNA Binding Regulation Research Resistance Rho Factor Role Signal Transduction Site Source Structure Testing Thermodynamics Transcript Translations Vitamins Work antimicrobial antitermination bicozamycin chromatin immunoprecipitation design dietary supplements environmental change genome-wide in vivo inhibitor/antagonist insight multidisciplinary novel protein protein interaction research study response rho small molecule termination factor transcription termination

项目摘要

DESCRIPTION (provided by applicant): Transcription termination is a process whereby the elongation complex (EC) dissociates into RNA transcript, DNA template, and RNA polymerase (RNAP) in response to intrinsic signals or specific factors. Rho termination factor is essential in regulating gene expression in Enterobacter and is a target for specific antibiotics. Rho has been intensively studied in the last three decades, however, the actual termination process, i.e. the mechanism by which Rho disrupts the EC, remains unknown. Moreover, the identity of most Rho termination sites in vivo and the role of Rho in cell's adaptation to environmental changes remain unknown. The long-term objective of the proposed work is to provide a comprehensive physiological and mechanistic description of Rho-dependent termination in Escherichia coli and the mechanism of its regulation by particular host and phage proteins. Specifically we propose to: 1) Determine conformational changes in RNAP that accompany the termination process, and the role of certain RNAP domains in Rho termination. 2) Determine how E.coli S4 and phage l N proteins modify the EC rendering it resistant to Rho termination. 3) Determine the physiological role and mechanism of novel anti-Rho factors that we have identified in preliminary studies. 4) Establish the role of Rho in gene regulation on a genomic scale. The significance of proposed research for human health is several-fold. Complete structural understanding of termination/antitermination processes would allow for designing small molecule mimics and inhibitors that change the pattern of bacterial gene expression or interrupt transcription of essential genes prematurely, and thus serve as novel antimicrobials. Examples of antibiotics that specifically target Rho have been already described. Furthermore, better understanding the mechanisms of antitermination would suggest the optimal strategies for constructing bacterial strains that overproduce essential dietary supplements and other biologically active compounds. Finally, since eukaryotic RNAPs share basic sequence and structural homologies with bacterial RNAP, the fundamental mechanism of the EC stabilization and destabilization must be similar. Therefore, proposed experiments will also provide insight to the basic mechanisms of eukaryotic transcription termination. We will explore the mechanism of Rho termination and antitermination in E.coli. The significance of proposed research for human health is several-fold. Complete structural understanding of termination/antitermination processes would allow designing small molecule mimics and inhibitors of the termination process that change the pattern of bacterial gene expression or interrupt transcription of essential genes prematurely, and thus serve as novel antimicrobials. Furthermore, better understanding the mechanisms of antitermination would suggest optimal strategies for constructing bacterial strains that overproduce essential dietary supplements (vitamins, amino acids, etc.) and other important biologically active compounds. Finally, the proposed experiments will also provide insight to the basic mechanisms of eukaryotic transcription termination.

描述（由申请人提供）：转录终止是延伸复合物（EC）响应内在信号或特定因素而解离成RNA转录物、DNA模板和RNA聚合酶（RNAP）的过程。 Rho 终止因子对于调节肠杆菌基因表达至关重要，并且是特定抗生素的靶标。在过去的三十年里，Rho 得到了深入的研究，然而，实际的终止过程，即 Rho 破坏 EC 的机制仍然未知。此外，体内大多数Rho终止位点的身份以及Rho在细胞适应环境变化中的作用仍然未知。这项工作的长期目标是对大肠杆菌中 Rho 依赖性终止及其特定宿主和噬菌体蛋白的调节机制提供全面的生理和机制描述。具体来说，我们建议：1）确定伴随终止过程的RNAP构象变化，以及某些RNAP结构域在Rho终止中的作用。 2)确定大肠杆菌S4和噬菌体lN蛋白如何修饰EC使其抵抗Rho终止。 3）确定我们在初步研究中确定的新型抗Rho因子的生理作用和机制。 4) 确定 Rho 在基因组规模的基因调控中的作用。拟议的研究对人类健康具有多重意义。对终止/反终止过程的完整结构理解将允许设计小分子模拟物和抑制剂，这些小分子模拟物和抑制剂可以改变细菌基因表达模式或过早中断必需基因的转录，从而充当新型抗菌剂。已经描述了专门针对 Rho 的抗生素的例子。此外，更好地理解抗终止机制将为构建过量生产必需膳食补充剂和其他生物活性化合物的细菌菌株提供最佳策略。最后，由于真核 RNAP 与细菌 RNAP 具有基本序列和结构同源性，因此 EC 稳定和去稳定的基本机制必须相似。因此，所提出的实验也将为真核转录终止的基本机制提供见解。我们将探讨大肠杆菌中 Rho 终止和抗终止的机制。拟议的研究对人类健康具有多重意义。对终止/反终止过程的完整结构理解将允许设计终止过程的小分子模拟物和抑制剂，从而改变细菌基因表达模式或过早中断必需基因的转录，从而充当新型抗菌剂。此外，更好地了解抗终止机制将为构建过量生产必需膳食补充剂（维生素、氨基酸等）和其他重要生物活性化合物的细菌菌株提供最佳策略。最后，所提出的实验还将深入了解真核转录终止的基本机制。

项目成果

期刊论文数量（29）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

UvrD helicase: an old dog with a new trick: how one step backward leads to many steps forward.

UvrD解旋酶：一只老狗有了新把戏：如何后退一步导致前进许多步。

DOI：
发表时间：
2015-01
期刊：
影响因子：
0
作者：
Epshtein; Vitaliy
通讯作者：
Vitaliy

Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria.

通过新生 RNA 感知小分子：控制细菌转录的机制。

DOI：
发表时间：
2002-11-27
期刊：
影响因子：
64.5
作者：
Mironov, Alexander S;Gusarov, Ivan;Rafikov, Ruslan;Lopez, Lubov Errais;Shatalin, Konstantin;Kreneva, Rimma A;Perumov, Daniel A;Nudler, Evgeny
通讯作者：
Nudler, Evgeny

Extensive functional overlap between sigma factors in Escherichia coli.

大肠杆菌中 sigma 因子之间存在广泛的功能重叠。

DOI：
发表时间：
2006-09
期刊：
影响因子：
16.8
作者：
Wade, Joseph T;Castro Roa, Daniel;Grainger, David C;Hurd, Douglas;Busby, Stephen J W;Struhl, Kevin;Nudler, Evgeny
通讯作者：
Nudler, Evgeny

RNA polymerase backtracking in gene regulation and genome instability.

RNA聚合酶在基因调控和基因组不稳定性中的回溯。