WHOLE GENOME SHOTGUN SEQUENCING OF STREPTOCOCCUS MITIS

MITIS 链球菌的全基因组鸟枪法测序

• 批准号: 6229914
• 负责人: Herve S TETTELIN
• 金额: $ 20.35万
• 依托单位: INSTITUTE FOR GENOMIC RESEARCH
• 依托单位国家: 美国
• 财政年份: 2001
• 资助国家: 美国
• 起止时间: 2001-09-01 至 2003-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6229914
• 关键词: DNA; Streptococcus mitis; bacteria infection mechanism; bacterial cytopathogenic effect; computer assisted sequence analysis; cooperative study; genetic library; genetic mapping; genetic strain; genome; molecular biology information system; nucleic acid sequence; oral bacteria; polymerase chain reaction; pulsed field gel electrophoresis; tooth surface

DESCRIPTION (Adapted from the Investigator?s Abstract): The goal is to determine the complete genome sequence of the type strain of Streptococcus mitis, the predominant pioneer colonizer of tooth surfaces, and thus an initiator of dental plaque formation relevant to caries and periodontal disease. These pioneer streptococci facilitate or inhibit the establishment of late colonizers and oral pathogens. The predominance of IgA1 protease producing S. mitis variants in the pharynx is associated with allergic disease. S. mitis is a causative agent of endocarditits. It is an emerging source of septicemia in cancer patients, and the first vancomycin-resistant S. mitis isolate was reported in one such case. Phylogenetically, S. mitis and the overt pathogen S. pneumoniae, the causative agent of otitis, pneumoniae, septicemia and meningitis, are nearest neighbors. There is clear demonstration that the S. mitis type strain constitutes a reservoir of genetic determinants that contribute to penicillin resistance in pathogenic S. pneumoniae. The fear is that resistance to vancomycin will be transferred in a similar manner. The approach is a whole genome random sequencing strategy used successfully at TIGR to sequence twelve prokaryotic genomes. The yearlong project will consists of four phases: 1) Construction of small, medium and large insert size genomic libraries from S. mitis type strain, NCTC 12261. 2) Sequencing both ends of a sufficient number of small insert clones to provide 8-fold sequence coverage of the genome. Medium and large insert clones will be sequenced to 6-fold and 10-fold clone coverage, respectively. This will provide a sequence scaffold that will aid in verifying genome architecture. Further, 10-fold clone coverage from the large (50 kb) insert library will ensure a predicted sequence hit every 5,000 bp of the 2.2 Mb S. mitis genome. 3) Assembling the genome sequence from the collection of sequence reads, and closing remaining gaps. 4) Annotation of the genome sequence to identify all open reading frames, assignment of gene names and functional roles based on database similarity searches. Accomplishing this goal will provide a unique opportunity to compare the repertoire of genes in the commensal S. mitis to that of other streptococci, such as the highly virulent, type-4 S. pneumoniae strain, nearing completion at TIGR, allowing the identification of virulence-associated genes.

描述（改编自研究者？s摘要）：目标是 确定链球菌模式菌株的全基因组序列 轻症，牙齿表面的主要先驱殖民者，因此， 与龋齿和牙周病相关牙菌斑形成引发剂 疾病这些先锋链球菌促进或抑制 晚期定居者和口腔病原体。IgA1蛋白酶的优势 S.咽部的轻症变体与过敏性疾病有关。S.缓症 是心内膜炎的病原体。它是一种新兴的败血症来源 在癌症患者中，第一个万古霉素耐药的S.缓解分离株为 在一个这样的案例中。系统发育上，S. mitis和显性病原体S. 肺炎，耳炎、肺炎、败血症和 脑膜炎，是最近的邻居。有明确的证据表明，S。 缓症型菌株构成遗传决定子的储存库， 有助于致病性S.肺炎。令人担心的是 对万古霉素的耐药性也会以类似的方式转移。 该方法是一种全基因组随机测序策略，已成功用于 TIGR对12个原核基因组进行测序。为期一年的项目将包括 分四个阶段进行：1）小、中、大插入片段基因组的构建 从S.缓症型菌株，NCTC 12261。2)测序一个 足够数量的小插入克隆，以提供8倍的序列覆盖率， 基因组中等和大插入克隆将被测序至6倍， 10-倍克隆覆盖率。这将提供一个序列支架 这将有助于验证基因组结构。此外，10倍克隆覆盖率 将确保预测的序列命中 2.2Mb S. mitis基因组。3)组装基因组序列 从序列读段的集合中，并关闭剩余的缺口。四、 对基因组序列进行注释以鉴定所有开放阅读框， 基于数据库相似性的基因名称和功能角色的分配 搜索.实现这一目标将提供一个独特的比较机会 基因库在大肠杆菌S.对其他人的宽容 链球菌，如高毒力的4型S.肺炎菌株，接近 在TIGR完成，允许鉴定毒力相关基因。