A multidisciplinary approach to elucidating gene function in a model Gram-positiv

阐明革兰氏阳性模型中基因功能的多学科方法

• 批准号: 7942971
• 负责人: DAVID Z RUDNER
• 金额: $ 103.49万
• 依托单位: HARVARD MEDICAL SCHOOL
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-09-30 至 2012-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7942971
• 关键词: Animal Model; Antibiotic Resistance; Antibiotics; Bacillus subtilis; Bacteria; Bar Codes; Bioinformatics; C-terminal; Cell Size; Cell division; Cellular biology; Chemicals; Chromosomes; Collaborations; Collection; Communities; Competence; DNA biosynthesis; Data; Data Analyses; Data Set; Databases; Development; Ensure; Epitopes; Escherichia coli; Essential Genes; Experimental Designs; Expression Library; Fluorescence Microscopy; Funding; Future; Gene Expression; Genes; Genetic; Genome; Genomics; Goals; Gram-Positive Bacteria; Growth; Health; Housing; Human; Institutes; Internet; Lead; Letters; Libraries; Literature; Maps; Measures; Metabolism; Methodology; Methods; Microbial Biofilms; Microbial Genetics; Microbiology; Modeling; Molecular; Molecular Genetics; Molecular Profiling; Noise; Online Systems; Ontology; Organism; Participant; Pathogenicity; Pathway interactions; Phenotype; Protocols documentation; Publishing; RNA Degradation; Research; Research Infrastructure; Research Personnel; Resolution; Resources; Site; Specialist; Texas; abstracting; base; cell motility; chemical genetics; comparative; detection of nutrient; drug sensitivity; experience; functional genomics; gene function; genetic profiling; genome database; genome-wide; interdisciplinary approach; interest; killings; knockout gene; member; multidisciplinary; mutant; overexpression; pathogen; pathogenic bacteria; promoter; research study; software development; text searching; tool; trait; transcription factor; web site; wiki

DESCRIPTION (provided by applicant): Because of the diversity of niches they inhabit, their versatility, and the threat their members pose to human health, Gram-positive bacteria are of paramount importance to multiple facets of microbiology. Nonetheless, there has been no systematic effort to elucidate gene functions and relationships on a genome-wide scale in any Gram-positive bacterium. Bacillus subtilis is the premier model organism for studies of Gram-positive bacteria because it offers powerful classical and molecular genetics, high-resolution cell biology, as well as a large and vibrant community of researchers. Evidence from other model organisms demonstrates that genome-wide approaches accelerate functional discovery. The opportunity for GO funding has catalyzed a broad-based community of researchers to pool their expertise to create a focused, coordinated, multidisciplinary effort to develop the genomic resources necessary to implement a comprehensive gene function effort. This initiative will serve as the blueprint for similar efforts in other model and pathogenic bacteria in the future. We will: 1. Construct genome-scale tools for global phenotypic analysis. These will include two bar-coded null mutant libraries, an ordered over-expression library, 300 promoter fusions to yfp and a C-terminal epitope- tagged library for all essential genes. 2. Develop and provide proof-of-principle experiments for key phenotyping methods. These will include high-throughput genetic interaction analysis and chemical genetic profiling; global cytological phenotyping; and transcriptional profiling. 3. Integrate and analyze the data across species. Each global phenotyping dataset will be analyzed in collaboration with bioinformaticists. This analysis will generate probabilistic functional interaction maps and transcriptional networks that will provide key information about gene functions and relationships. These will be used for comparative analysis among Gram-positive organisms and between Gram-positives and Gram- negatives. 4. Develop a B. subtilis database (subtilisHUB). We will build a web-based data resource to support ongoing functional annotation. This site will document the construction of all the genomic tools, house protocols and datasets, and provide infrastructure to enable Gene Ontology assignments, literature mining, and community discussion. 5. Engage the community of microbiologists in the genomic resources and approaches. A broad community of research specialists will launch genome-scale projects taking advantage of the tools, methodologies, and resources. PUBLIC HEALTH RELEVANCE: This proposal is aimed at elucidating the function of all the genes in Bacillus subtilis, the major model organism for an important class of bacteria, Gram-positive bacteria. The project will generate genome-scale tools; pioneer the development of global phenotypic analysis for bacteria; and establish a web resource that will ensure continuity beyond the funding term. The concerted, community-based effort we propose will have far-reaching impact on research in bacteria in general, and on many Gram-positive pathogens.

描述（由申请人提供）：由于革兰氏阳性菌栖息环境的多样性、多功能性及其成员对人类健康构成的威胁，革兰氏阳性菌对于微生物学的多个方面都至关重要。尽管如此，还没有系统性的努力来阐明任何革兰氏阳性细菌在全基因组范围内的基因功能和关系。枯草芽孢杆菌是研究革兰氏阳性菌的首要模型生物，因为它提供了强大的经典和分子遗传学、高分辨率的细胞生物学以及庞大而充满活力的研究人员群体。来自其他模式生物的证据表明，全基因组方法加速了功能发现。 GO 资助的机会促使基础广泛的研究人员群体汇集他们的专业知识，创建一个有重点、协调一致的多学科工作，以开发实施全面基因功能工作所需的基因组资源。这一举措将为未来在其他模型和病原细菌方面的类似努力提供蓝图。我们将： 1. 构建用于全球表型分析的基因组规模工具。这些将包括两个条形码无效突变文库、一个有序过表达文库、300 个与 yfp 融合的启动子以及一个针对所有必需基因的 C 端表位标记文库。 2. 开发并提供关键表型分析方法的原理验证实验。这些将包括高通量遗传相互作用分析和化学遗传分析；整体细胞学表型分析；和转录分析。 3. 整合和分析跨物种的数据。每个全球表型数据集将与生物信息学家合作进行分析。该分析将生成概率功能相互作用图和转录网络，提供有关基因功能和关系的关键信息。这些将用于革兰氏阳性生物之间以及革兰氏阳性生物和革兰氏阴性生物之间的比较分析。 4. 开发枯草芽孢杆菌数据库（subtilisHUB）。我们将构建一个基于网络的数据资源来支持正在进行的功能注释。该站点将记录所有基因组工具、内部协议和数据集的构建，并提供基础设施以实现基因本体作业、文献挖掘和社区讨论。 5. 让微生物学家群体参与基因组资源和方法。广泛的研究专家群体将利用这些工具、方法和资源启动基因组规模的项目。 公共健康相关性：该提案旨在阐明枯草芽孢杆菌中所有基因的功能，枯草芽孢杆菌是一类重要细菌（革兰氏阳性菌）的主要模式生物。该项目将生成基因组规模的工具；引领细菌全球表型分析的发展；并建立一个网络资源，以确保资助期限后的连续性。我们提出的基于社区的协调一致的努力将对一般细菌和许多革兰氏阳性病原体的研究产生深远的影响。