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: 7591810
• 负责人: DAVID C AMBERG
• 金额: $ 36.52万
• 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/7591810
• 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 Genetics; 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; 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已成为新基因组技术，这些技术的应用以及开发分析这些数据集所需的生物信息学工具的验证基础。此外，大型研究界的重点生物学研究对单个基因如何促进基本细胞功能有了详细的理解。我们建议利用酵母的遗传能力将现有知识与肌动蛋白细胞骨架的功能（细胞系统的主要集成剂）的功能统一。肌动蛋白丝是由单个蛋白质构造的，但肌动蛋白功能的多样性是由大量辅助蛋白介导的。对酵母肌动蛋白细胞骨架的调查导致了强大的工具和试剂的开发，以研究与肌动蛋白细胞骨架的相互作用如何有助于其通过细胞系统的调节和利用，但是许多这些工具和试剂尚未充分利用其全面，以实现对酵母菌肌动蛋白细胞骨骼或细胞骨骼系统的完整图像。在这些试剂中，值得注意的是单个必需肌动蛋白基因ACT1中的大量突变体，这些突变体是专门设计用于破坏蛋白质蛋白相互作用的。我们建议使用这些试剂以及酵母遗传学和基因组学的力量，以发现影响肌动蛋白细胞骨架的那些基因或受其功能影响的那些基因的完整或几乎完整的遗传描述。复杂的单倍不足屏幕将使用肌动蛋白的无效等位基因对整个酵母基因敲除阵列进行，以尝试发现对肌动蛋白化学计量的减少敏感的基因。然后，将对大量突变肌动蛋白等位基因收集的基因网络进行重新测试，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”，将通过与可行的肌动蛋白丙氨酸扫描突变体组合进行合成致命筛选来补充。所有相互作用都将与肌动蛋白突变体定义的肌动蛋白功能的特定子集的损失或减少相关。为了使数据进一步连贯，还将检查肌动蛋白相互作用组的基因与所有已知的肌动蛋白结合蛋白的遗传相互作用。对此高度集成数据集的分析将用于将肌动蛋白等位基因及其相互作用的基因排列为我们假设的组将反映共享缺陷，例如肌动蛋白和特定肌动蛋白结合蛋白之间的结合丧失。贝叶斯数据集成与其他数据集将用于功能预测，并发现基因集和群集分析之间的新型关系将用于将这些模式与肌动蛋白的结构相关联。通过开发三维版本的网络显示工具鱼鹰，将促进网络的可视化，该版本将将网络的节点连接回肌动蛋白的结构。该提案产生的所有数据和数据分析都将在多伦多电网数据库，SGD和Pixie.princeton.edu的自由访问，基于Web的格式中维护。