Structure/Function of Transcription Complex Regulation

转录复合物调控的结构/功能

• 批准号: 10734994
• 负责人: Robert Landick
• 金额: $ 75.68万
• 依托单位: UNIVERSITY OF WISCONSIN-MADISON
• 依托单位国家: 美国
• 财政年份: 1987
• 资助国家: 美国
• 起止时间: 1987-07-01 至 2027-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10734994
• 关键词: Abbreviations; Actinobacteria class; Affect; Amino Acids; Antibiotics; Antisense RNA; Bacillus subtilis; Bacteria; Bacterial Chromosomes; Bacterial RNA; Bacteroides fragilis; Behavior; Biochemical; Biogenesis; Biological Assay; Biotechnology; C-terminal; Catalysis; Chromatin; Chromatin Structure; Chromosome Structures; Clostridium difficile; Closure by clamp; Complement; Complex; Consensus; Coupled; Coupling; Cryoelectron Microscopy; DNA; DNA Insertion Elements; DNA-Directed RNA Polymerase; Disease; Elements; Escherichia coli; Eukaryota; Family; Filament; Firmicutes; Gene Expression Regulation; Gene Silencing; Genetic Transcription; Goals; Growth; Health; Hi-C; Human; In Vitro; Interferometry; Knowledge; Link; Mediating; Medicine; Methods; Microbe; Modeling; Molecular; Molecular Biology; Molecular Chaperones; Molecular Conformation; Molecular Structure; Mycobacterium tuberculosis; N-terminal; Nucleoproteins; Nucleotides; Positioning Attribute; Prokaryotic Cells; Proteobacteria; RNA; RNA Folding; RNA chemical synthesis; Regulation; Reporter; Research; Ribosomes; Role; Rotation; Signal Transduction; Spectrum Analysis; Structure; System; Transcription Elongation; Transcriptional Regulation; Translations; Triplet Multiple Birth; Work; Y protein; antimicrobial; ds-DNA; gene therapy; genetic approach; genome-wide; improved; in vivo; insight; microbial community; mycobacterial; paralogous gene; pathogenic microbe; premature; recruit; single molecule; transcription factor; virtual

Project Summary/Abstract The long-term goal of this project is to define the interactions within transcription elongation complexes and with regulators that cause and control pausing and termination by RNA polymerase. Pausing and premature termination underlie many aspects of gene regulation in diverse prokaryotes and eukaryotes, including transcription through chromatin and linkages to RNA maturation and translation. Both the basic mechanisms of pausing and termination and the mechanisms by which regulators control pausing and termination depend on poorly understood changes to interactions within the elongation complex. Many of these interactions modulate conformational changes in RNA polymerase involving mobile modules including the clamp, trigger loop, and lineage-specific insertions that must achieve particular conformations for efficient transcription. Understanding how regulators promote or inhibit these different conformations in diverse bacteria will provide key basic knowledge essential to guide the rational manipulation of regulators for antimicrobials or genetic therapies. Knowledge gained about diverse bacterial systems also helps define highly conserved mechanisms of transcription in humans. Additionally, bacterial RNA polymerases are known target of antibiotics, and knowledge about their functional mechanisms will aid in identifying and characterizing new antibiotics. A combination of structural, biochemical, and genetic approaches will be used to characterize the interac- tions in the elongation complex that mediate regulation. New methods for transcription assay by cryo-electron microscopy, for single-molecule assay of RNA polymerase interactions with RNA structures, regulators, and ribosomes, and for genome-scale analysis of chromatin structure and elongation complex regulation will be developed. This combination of approaches will be used to understand connections among progress of the elongation complex during transcription, the structure of bacterial chromatin, RNA folding, and RNA translation. The work builds on recent discoveries of the structural basis by which RNA polymerase pauses, of the role of H-NS family nucleoprotein filaments in stimulating pausing and termination during transcriptional silencing, and of the different actions of the only universal transcription elongation regulator, NusG. The specific aims of the project are to (i) integrate models of pausing and termination mechanisms across diverse bacterial lineages; (ii) elucidate the molecular basis of pro- vs. anti-pausing and recruitment for NusGs and paralogs; and (iii) link genome-scale regulation in vivo to the molecular basis of elongation complex structural changes. This integrated research will help build a new understanding of transcriptional regulation by defining how pause and termination signals change elongation complex structure and activity dynamically across evolutionarily diverse microbes. The impact of these studies will be an improved understanding of elongation complex regulation, with broad applications to biotechnology, human medicine, and both prokaryotic and eukaryotic molecular biology.

项目摘要/摘要 该项目的长期目标是定义转录伸长络合物中的相互作用和 与导致和控制RNA聚合酶暂停和终止的调节剂。暂停和过早 终止是基因调节的许多方面，包括多种原核生物和真核生物，包括 通过染色质转录以及与RNA成熟和翻译的联系。两种基本机制 暂停和终止以及监管机构控制暂停和终止的机制取决于 关于伸长复合物中相互作用的变化不足。这些互动中的许多 调节涉及移动模块在内的RNA聚合酶的构象变化，包括夹具，触发器 循环和谱系特异性插入必须实现有效转录的特殊构象。 了解监管机构如何促进或抑制各种细菌中的这些不同构象 关键基本知识是指导对抗菌或遗传的调节剂的合理操纵的必不可少的必不可少的 疗法。对各种细菌系统获得的知识也有助于定义高度保守的机制 人类的转录。另外，细菌RNA聚合酶是已知的抗生素靶标，并且 有关其功能机制的知识将有助于识别和表征新的抗生素。 结构，生化和遗传方法的结合将用于表征 介导调节的延伸络合物中的tions。通过冷冻电子转录测定的新方法 显微镜，用于与RNA聚合酶相互作用与RNA结构，调节剂和 核糖体，以及用于染色质结构和伸长复合物调控的基因组规模分析 发达。这种方法的组合将用于了解 转录过程中的伸长复合物，细菌染色质，RNA折叠和RNA的结构 翻译。这项工作建立在最新的结构基础上，RNA聚合酶暂停， H-NS家族核蛋白丝在转录过程中刺激暂停和终止的作用 沉默，以及唯一的通用转录伸长调节剂NUSG的不同作用。这 该项目的具体目的是（i）整合暂停和终止机制的模型 细菌谱系； （ii）阐明nusg和抗pa和抗pa和募集的分子基础 旁系同居； （iii）将体内的基因组规模调节与伸长络合物结构的分子基础联系起来 更改。这项综合研究将有助于通过定义转录调节的新理解 暂停和终止信号如何在跨越伸长的复杂结构和活动跨越 进化上的微生物。这些研究的影响将是对伸长率的改进的理解 复杂的监管，对生物技术，人类医学以及原核生物的广泛应用和 真核分子生物学。

项目成果

Genome-scale analysis of escherichia coli FNR reveals complex features of transcription factor binding.

• DOI: 10.1371/journal.pgen.1003565
• 发表时间: 2013-06
• 期刊: PLoS genetics
• 影响因子: 4.5
• 作者: Myers KS;Yan H;Ong IM;Chung D;Liang K;Tran F;Keleş S;Landick R;Kiley PJ
• 通讯作者: Kiley PJ

Single-molecule kinetic studies on DNA transcription and transcriptional regulation.

DNA转录和转录调控的单分子动力学研究。

• 发表时间: 1995
• 期刊: Biophysical journal.
• 作者: Gelles,J;Yin,H;Finzi,L;Wong,OK;Landick,R
• 通讯作者: Landick,R

Tethering of the large subunits of Escherichia coli RNA polymerase.

大肠杆菌 RNA 聚合酶大亚基的束缚。

• DOI: 10.1074/jbc.272.39.24137
• 发表时间: 1997
• 期刊: The Journal of biological chemistry
• 作者: Severinov,K;Mooney,R;Darst,SA;Landick,R
• 通讯作者: Landick,R

Termination-altering amino acid substitutions in the beta' subunit of Escherichia coli RNA polymerase identify regions involved in RNA chain elongation.

大肠杆菌 RNA 聚合酶 β 亚基中终止改变的氨基酸取代可识别参与 RNA 链延长的区域。

• DOI: 10.1101/gad.8.23.2913
• 发表时间: 1994
• 期刊: Genes & development
• 影响因子: 10.5
• 作者: Weilbaecher,R;Hebron,C;Feng,G;Landick,R
• 通讯作者: Landick,R

Structure of microcin J25, a peptide inhibitor of bacterial RNA polymerase, is a lassoed tail.

• DOI: 10.1021/ja036756q
• 发表时间: 2003-09
• 期刊: Journal of the American Chemical Society
• 影响因子: 15
• 作者: K. Wilson;M. Kalkum;J. Ottesen;J. Yuzenkova;B. Chait;R. Landick;T. Muir;K. Severinov;S. Darst