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: 7854281
• 负责人: DAVID Z RUDNER
• 金额: $ 96.51万
• 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 2011-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7854281
• 关键词: Animal Model; Antibiotic Resistance; Antibiotics; Bacillus subtilis; Bacteria; Bar Codes; Bioinformatics; C-terminal; Cell Size; Cell division; Cellular biology; Chemicals; Chromosomes; Classification; 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; 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; public health relevance; 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）：由于它们栖息的生态位的多样性，它们的多功能性以及它们的成员对人类健康构成的威胁，革兰氏阳性菌对微生物学的多个方面至关重要。尽管如此，一直没有系统的努力，以阐明基因组范围内的任何革兰氏阳性细菌的基因功能和关系。枯草芽孢杆菌是研究革兰氏阳性菌的首要模式生物，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，以及一个庞大而充满活力的研究人员社区。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资助的机会已经催化了一个基础广泛的研究人员社区，汇集他们的专业知识，以创建一个集中的，协调的，多学科的努力，以开发必要的基因组资源，以实现全面的基因功能的努力。这一举措将成为未来在其他模式和病原菌中进行类似努力的蓝图。我们将：1.构建基因组规模的全球表型分析工具。这些将包括两个条形码无效突变库，有序过表达库，300个启动子融合到yfp和C-末端表位标记的所有必需基因的库。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特征分析;全球细胞学表型分析;以及转录特征分析。3.整合和分析跨物种的数据。将与生物信息学家合作分析每个全球表型数据集。这种分析将产生概率功能相互作用图和转录网络，这将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微生物之间以及革兰氏阳性菌和革兰氏阴性菌之间的比较分析。4.发展一个B。枯草杆菌数据库（subtilisHUB）。我们将建立一个基于Web的数据资源，以支持正在进行的功能注释。该网站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，使基因本体分配，文献挖掘和社区讨论。5.让微生物学家社区参与基因组资源和方法。广泛的研究专家社区将利用工具、方法和资源启动基因组规模的项目。 公共卫生关系：该建议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。该项目将产生基因组规模的工具;开创细菌全球表型分析的发展;并建立一个网络资源，以确保资金期限后的连续性。我们提出的协调一致的、以社区为基础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。