Toward a Complete Genetic Description of the Yeast Actin Cytoskeleton

酵母肌动蛋白细胞骨架的完整遗传描述

• 批准号: 7348313
• 负责人: DAVID C AMBERG
• 金额: $ 32.71万
• 依托单位: UPSTATE MEDICAL UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-02-01 至 2011-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7348313
• 关键词: Actin-Binding Protein; Actins; Affect; Alanine; Alleles; Back; Binding; Binding Sites; Biochemical; Bioinformatics; Biological; Biological Process; Categories; Cell physiology; Cells; Classification; Cluster Analysis; Collection; Communities; Complement; Complex; Cytoskeletal Filaments; Cytoskeleton; Data; Data Analyses; Data Set; Databases; Defect; Development; Diploidy; Essential Genes; Eukaryotic Cell; Gene Deletion; Genes; Genetic; Genetic Screening; Genetic Structures; Genome; Genomics; Growth; Hereditary Disease; Housing; Human; Imagery; Individual; Investigation; Knock-out; Knowledge; Link; Malignant Neoplasms; Maps; Mediating; Methods; Microfilaments; Modeling; Nature; Online Systems; Organism; Other Genetics; Pattern; Phenocopy; Phenotype; Prevalence; Proteins; Range; Reagent; Regulation; Research; Research Personnel; Saccharomyces; Saccharomyces cerevisiae; Scanning; Screening procedure; Site; Structure; Surface; System; Systems Biology; Technology; Testing; Yeasts; base; computer based statistical methods; data integration; data mining; design; functional group; gene function; genetic analysis; genome database; human disease; insight; interest; loss of function mutation; mutant; novel; programs; protein protein interaction; spatial relationship; stoichiometry; technology development; three dimensional structure; tool; web-accessible; yeast genetics

DESCRIPTION: S. cerevsiae has served as a proving ground for new genomics technologies, application of these technologies and the development of the bioinformatics tools required to analyze these datasets. In addition, focused biological investigations by a large research community has resulted detailed understandings of how individual genes contribute to basic cellular functions. We propose to harness the genetic power of yeast to unify existing knowledge with the functions of the actin cytoskeleton, a major integrator of cellular systems. Actin filaments are constructed of a single protein but diversity in actin function is mediated by a large battery of accessory proteins. Investigations on the yeast actin cytoskeleton have led to the development of powerful tools and reagents to study how interactions with the actin cytoskeleton contribute to its regulation and utilization by cellular systems, but many of these tools and reagents have not been utilized to their fullest extent to realize a complete picture of the yeast actin cytoskeleton or the cellular systems it affects. Notable among these reagents is a large collection of mutants in the single essential actin gene ACT1 that were specifically designed to disrupt protein-protein interactions. We propose to use these reagents and the power of yeast genetics and genomics to uncover a complete or at least nearly complete genetic description of those genes that impact, or whose functions are impacted by, the actin cytoskeleton. Complex haploinsufficiency screens will be performed with a null allele of actin against the entire ordered array of yeast gene knock-outs to try and uncover genes sensitive to reductions in actin stoichiometry. This sub- network of genes will then be retested against the large collection of mutant actin alleles to determine which of the genetic interactions can be attributed to reductions in subsets of actin functions. To complete the "actin interactome", this analysis will be complemented by synthetic lethal screening with the set of viable actin alanine scan mutants. All interactions will be correlated back to the loss or reduction in specific subsets of actin functions as defined by the actin mutants. To bring further coherence to the data, genes of the actin interactome will also be examined for genetic interactions with the genes for all known actin-binding proteins. Analysis of this highly integrated data set will be used to arrange both the actin alleles and their interacting genes into groups that we hypothesize will reflect shared defects such as the loss of binding between actin and specific actin binding proteins. Bayesian data integration with other datasets will be used for function prediction and to uncover novel relationships between gene sets and cluster analysis will be used to correlate these patterns back to the structure of actin. Visualization of the network will be facilitated by the development of a three-dimensional version of the network display tool Osprey that will connect nodes of the network back to the structure of actin. All data and data analysis resulting from this proposal will be maintained in a free access, Web-based format within the Toronto GRID database, the SGD, and PIXIE.Princeton.edu.

描述：S. cerevsiae已成为新的基因组学技术、这些技术的应用和分析这些数据集所需的生物信息学工具的开发的试验场。此外，一个大型研究团体的集中生物学研究已经详细了解了单个基因如何促进基本细胞功能。我们建议利用酵母的遗传力量，将现有的知识与肌动蛋白细胞骨架的功能统一起来，肌动蛋白细胞骨架是细胞系统的主要集成商。肌动蛋白丝由单一蛋白质构成，但肌动蛋白功能的多样性由大量辅助蛋白介导。对酵母肌动蛋白细胞骨架的研究已经导致开发了强大的工具和试剂来研究与肌动蛋白细胞骨架的相互作用如何有助于细胞系统对其的调节和利用，但是这些工具和试剂中的许多还没有被充分利用来实现酵母肌动蛋白细胞骨架或其影响的细胞系统的全貌。在这些试剂中值得注意的是一个单一的必需肌动蛋白基因ACT 1的突变体，专门设计破坏蛋白质-蛋白质相互作用的大集合。我们建议使用这些试剂和酵母遗传学和基因组学的力量，以揭示一个完整的或至少接近完整的遗传描述的那些基因的影响，或其功能受到影响，肌动蛋白细胞骨架。将用肌动蛋白的无效等位基因对酵母基因敲除的整个有序阵列进行复杂的单倍不足筛选，以尝试并揭示对肌动蛋白化学计量减少敏感的基因。然后将针对大量突变肌动蛋白等位基因的集合重新测试基因的子网络，以确定哪些遗传相互作用可以归因于肌动蛋白功能子集的减少。为了完成“肌动蛋白相互作用组”，该分析将通过用一组可行的肌动蛋白丙氨酸扫描突变体进行合成致死筛选来补充。所有的相互作用都与肌动蛋白突变体所定义的肌动蛋白功能的特定子集的丧失或减少相关。为了使数据进一步一致，肌动蛋白相互作用组的基因也将被检查与所有已知的肌动蛋白结合蛋白的基因的遗传相互作用。这个高度集成的数据集的分析将被用来安排肌动蛋白等位基因和它们的相互作用的基因成组，我们假设将反映共同的缺陷，如肌动蛋白和特定的肌动蛋白结合蛋白之间的结合损失。贝叶斯数据集成与其他数据集将用于功能预测，并揭示新的基因集和聚类分析之间的关系将被用来关联这些模式回肌动蛋白的结构。网络的可视化将通过网络显示工具Osprey的三维版本的开发来促进，该工具将网络的节点连接回肌动蛋白的结构。本提案产生的所有数据和数据分析将以免费访问、基于Web的格式保存在多伦多全球资源信息数据库、SGD和PIXIE.tageton.edu中。