A systems analysis of novel essential cell cycle components in Caulobacter

柄杆菌中新型重要细胞周期成分的系统分析

• 批准号: 8814110
• 负责人: Dante Ricci
• 金额: $ 5.03万
• 依托单位: STANFORD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-03-01 至 2016-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8814110
• 关键词: Animal Model; Anti-Bacterial Agents; Antibiotics; Bacteria; Bacterial Infections; Binding; Biochemical; Bioinformatics; Biological Models; Categories; Caulobacter; Caulobacter crescentus; Cell Cycle; Cell Cycle Progression; Cell Cycle Regulation; Cells; ChIP-on-chip; Chromosomes; Clinical Treatment; Clinical Trials; Computing Methodologies; Consensus; DNA; DNA Sequence Rearrangement; Development; Elements; Ensure; Event; Gene Expression; Gene Expression Profiling; Genes; Genetic; Genetic Programming; Genome; Genomics; Goals; Growth; Growth and Development function; Health; Human; Indium; Intercistronic Region; Intergenic Sequence; Investigation; Knowledge; Lead; Length; Logic; Malignant Neoplasms; Microarray Analysis; Modality; Molecular; Nature; Nucleic Acid Regulatory Sequences; Open Reading Frames; Organism; Pharmaceutical Preparations; Positioning Attribute; Protein Binding; Proteins; Proteome; Regulatory Pathway; Regulon; Resolution; Ribosomes; Role; Sampling; System; Systems Analysis; Untranslated RNA; antimicrobial; base; cell growth; cellular development; crosslink; design; genetic analysis; genetic element; insight; novel; programs; research study; small molecule; transcription factor

DESCRIPTION (provided by applicant): The core regulatory circuitry that drives and paces cell cycle progression in the bacterium Caulobacter crescentus constitutes a highly integrated system designed to ensure that multiple events take place in a spatiotemporally regulated manner. Although identification and characterization of various master regulators has offered extraordinary insight into the molecular basis of cell cycle control, the recent identification of novel, essential transcription factors and non-coding genetic elements in the Caulobacter genome strongly suggest an incomplete regulatory circuit and novel, undescribed regulatory modalities. The central goal of this project is to determine the roles of novel essential regulator elements in cell cycle control. Specifically, I propose to identify the regulatory functions of two novel cell-cycle-regulated Caulobacter transcription factors by using microarray analysis to identify genes regulated by each. I will employ ChIP-chip and bioinformatic analysis to experimentally and computationally identify the binding motif(s) for each transcription factor. In addition, I will conduct genetic and biochemical analysis to determine the requirement for essential non-coding chromosomal elements in cell cycle progression. Among the intergenic, non-coding "essential gap" sequences recently identified in the Caulobacter genome, over 60% lie immediately adjacent to cell-cycle-regulated genes, suggesting a role for these sequences in cell cycle control. Therefore, I will divide this subset into five categories based on the points during the cell cycle at which adjacent ORFs are induced and characterize representative sequences from each set through deletion, complementation, inversion, and transposition analysis. This will allow me to probe the essential nature of these sequences by manipulating various parameters such as length, position, and orientation. As preliminary evidence suggests that proteins may bind some of these sequences, I will use DNA sampling in order to crosslink and purify proteins that bind each sequence specifically. This broad approach will enable me to determine how the new essential elements of the Caulobacter genome are integrated into the core genetic circuit that controls cell growth and development.

描述（由申请人提供）：驱动和加速新月柄杆菌细菌细胞周期进程的核心调节电路构成了一个高度集成的系统，旨在确保多个事件以时空调节的方式发生。虽然鉴定和表征的各种主调节器提供了非凡的洞察细胞周期控制的分子基础，最近鉴定的新的，必需的转录因子和非编码基因元件的柄杆菌基因组中强烈建议一个不完整的监管电路和新的，未描述的监管模式。该项目的中心目标是确定新的必需调节元件在细胞周期控制中的作用。具体而言，我建议确定两个机构的监管职能 新的细胞周期调控柄杆菌转录因子，通过使用微阵列分析，以确定每个调控基因。我将采用ChIP芯片和生物信息学分析，以实验和计算确定每个转录因子的结合基序。此外，我将进行遗传和生化分析，以确定细胞周期进程中对基本非编码染色体元件的需求。在最近在柄杆菌基因组中鉴定的基因间非编码“必需间隙”序列中，超过60%紧邻细胞周期调控基因，表明这些序列在细胞周期控制中的作用。因此，我将根据细胞周期中相邻ORF被诱导的时间点将该子集分为五类，并通过缺失、互补、倒位和转座分析来表征每组的代表性序列。这将允许我通过操纵各种参数，如长度，位置和方向，来探测这些序列的本质。初步证据表明，蛋白质可能会结合这些序列中的一些，我将使用DNA采样，以交联和纯化蛋白质，结合每个序列特异性。这种广泛的方法将使我能够确定柄杆菌基因组的新的基本元素是如何整合到控制细胞生长和发育的核心遗传电路中的。