THE COMPLETE GENOME SEQUENCE AND ANALYSIS OF M SMEGMATIS

耻垢分枝杆菌全基因组序列及分析

• 批准号: 6031166
• 负责人: ROBERT D FLEISCHMANN
• 金额: $ 78.82万
• 依托单位: INSTITUTE FOR GENOMIC RESEARCH
• 依托单位国家: 美国
• 财政年份: 2000
• 资助国家: 美国
• 起止时间: 2000-04-01 至 2003-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6031166
• 关键词: Internet; Mycobacterium smegmatis; computer assisted sequence analysis; cooperative study; genetic library; genetic models; genetic strain; genome; microorganism resource /registry; molecular biology information system; nucleic acid sequence; open reading frames; polymerase chain reaction; transfer RNA

The completion and annotation of the DNA sequence from two strains of M. tuberculosis, the laboratory strain H37Rv and the virulent clinical isolate CDC1551 will provide the mycobacteria and tuberculosis research communities with an unprecedented resource for investigating the infectivity, virulence, colonization, pathogenicity, and the mechanisms of drug- sensitivity and resistance of M. tuberculosis. Despite the abundance of information provided by the genomic sequence, the exceedingly slow growth rate and highly virulent nature of the organism make working with M. tuberculosis and its genetic manipulation formidable tasks. A great deal of effort has gone into developing M. smegmatis, a fast-growing non-pathogen, as a genetic surrogate for M. tuberculosis. Through these efforts, it is possible for the mycobacterial researcher to utilize M. smegmatis in much the same manner as E. coli is used in the greater microbiological community. Obtaining the complete genome sequence of M. smegmatis will represent a milestone in mycobacterial research. In addition to providing invaluable information for continuing its development as a genetic system for recombinant methodologies, the organism provides a valuable model for studying unique aspects of mycobacterial biology, including cell wall biosynthesis, regulation of growth-rate, drug-sensitivity, protein secretion, gene regulation, etc. The Institute for Genomic Research has developed a cost effective and efficient approach to microbial genome sequencing that has been used to sequence and assemble seven microbial genomes. The genome of M. smegmatis strain mc2155 will be sequenced using this whole genome shotgun strategy. Small and large insert random libraries will be prepared and a sufficient number of random shotgun sequences to reach 8-fold coverage will be obtained. Assembly of the genome will be done using the version 2.0 of the TIGR Assembly software and closure will be obtained with a variety of PCR based techniques developed at The Institute. Annotation of the genome will employ a variety of computer techniques for identifying open reading frames and identifying proteins of known function through similarity searches against curated databases. Additional analyses will identify features such as exported proteins, tRNA and rRNA genes, repeated sequences, promoter sequences and ribosome binding sites. The data will be made available to the research community through the TIGR Microbial Database on the World Wide Web (www.tigr.org).

结核分枝杆菌实验室株H37Rv和临床分离株CDC1551 DNA序列的完成和注释的完成，将为分枝杆菌和结核病研究界研究结核分枝杆菌的感染性、毒力、定植、致病性以及耐药和耐药机制提供前所未有的资源。尽管基因组序列提供了丰富的信息，但这种生物极其缓慢的生长速度和高度毒力的性质使得研究结核分枝杆菌及其遗传操作的任务艰巨。为了开发一种快速生长的非病原体污垢分枝杆菌，作为结核分枝杆菌的基因替代品，人们付出了大量的努力。通过这些努力，分枝杆菌研究人员有可能利用耻垢分枝杆菌，就像在更大的微生物群落中使用大肠杆菌一样。获得耻垢分枝杆菌的完整基因组序列将是分枝杆菌研究的一个里程碑。除了为继续发展成为重组方法学的遗传系统提供宝贵的信息外，该生物还为研究分枝杆菌生物学的独特方面提供了一个宝贵的模型，包括细胞壁生物合成、生长速度调节、药物敏感性、蛋白质分泌、基因调节等。基因组研究所开发了一种具有成本效益和效率的微生物基因组测序方法，已用于对7个微生物基因组进行测序和组装。耻垢分枝杆菌菌株mc2155的基因组将使用这种全基因组鸟枪法进行测序。将准备小的和大的插入随机文库，并将获得足够数量的随机散弹枪序列以达到8倍的覆盖率。基因组的组装将使用TIGR组装软件的2.0版进行，并将通过研究所开发的各种基于聚合酶链式反应的技术获得闭合。基因组的注释将使用各种计算机技术来识别开放阅读框架，并通过对精心挑选的数据库进行相似性搜索来识别已知功能的蛋白质。其他分析将确定输出蛋白质、tRNA和rRNA基因、重复序列、启动子序列和核糖体结合位点等特征。这些数据将通过TIGR万维网微生物数据库(www.tigr.org)提供给研究界。