Genomic Comparison of A. actinomycetemcomitans Strains

A. actinomycetemcomitans 菌株的基因组比较

• 批准号: 7881117
• 负责人: Casey CHEN
• 金额: $ 7.9万
• 依托单位: UNIVERSITY OF SOUTHERN CALIFORNIA
• 依托单位国家: 美国
• 财政年份: 1999
• 资助国家: 美国
• 起止时间: 1999-01-01 至 2011-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7881117
• 关键词: Actinobacillus actinomycetemcomitans; Bacillus (bacterium); Bacteria; Bacterial Genome; Cataloging; Catalogs; Cloning; DNA; DNA Microarray Chip; Disease; Disease Association; Disease Outcome; Elements; Exhibits; Gene Expression; Gene Pool; Gene Silencing; Genes; Genetic; Genome; Genomic Instability; Genomic Islands; Genomic Islet; Genomics; Horizontal Gene Transfer; Human; Individual; Inherited; Laboratories; Lead; Life Style; Maps; Molecular Profiling; Pathogenesis; Pathogenicity; Pattern; Periodontal Diseases; Periodontitis; Phenotype; Relative (related person); Research; Testing; Time; Variant; Virulence; Virulence Factors; base; fitness; flexibility; genetic element; improved; inhibitor/antagonist; islet; mutant; pathogen; pathogenic bacteria

DESCRIPTION (provided by applicant): It is hypothesized that the genomes of bacterial pathogens are comprised of a core gene pool and a flexible gene pool. The stable core gene pool is inherited clonally and is found in virtually every strain of a species. In contrast, the flexible pool contains genetic elements that are acquired by horizontal gene transfer (HGT). Individual bacterial strains have different constellations of flexible genes that are tailored to their specific life style. Genomic islands (GEIs) are large DNA blocks (10-100kbp) acquired by bacteria via HGT en bloc and constitute important components of the flexible gene pool of bacterial genome. The distinctions between pathogenic and non-pathogenic bacteria in some species have been explained by the acquisition of GEIs by pathogenic strains. Bacteria may also increase their virulence by genomic deletions. In some instances, genomic deletions eliminate inhibitors of virulence factors and allow a full expression of pathogenicity. The Gram-negative facultative bacillus Actinobacillus actinomycetemcomitans (Aa) is a major pathogen in human periodontitis. Individual clones of Aa appear to exhibit differing degrees of pathogenicity and might even employ different virulence mechanisms. Our laboratory has obtained preliminary evidence for the presence of GEIs and smaller genomic islets (of unknown functions) in diverse Aa strains. The insertions of GEIs and slets have lead to truncation and/or inactivation of genes in some Aa strains. Here we test the hypothesis that both GEIs/islets and genomic deletions are common in Aa strains. Furthermore, the gain and loss of genes may change the phenotypes and virulence of Aa. 4 Specific Aims are identified: I) Perform genomic comparison of Aa isolates by DNA microarrays based on the sequenced Aa strain HK1651, II) identify non-HK1651 GEIs/islets in Aa by PCR genomic mapping followed by cloning and sequencing, III) Examine the expression of Aa GEIs/islets and their impact to the gene expression profiles of Aa, IV) Assess the stability of Aa genome over time by arrays. The research plan is expected to (i) generate a thorough catalogue of GEIs/islets and large DNA deletions in the genomes of diverse Aa strains, (ii) obtain evidence for the expression (and possibly the functions) of GEIs/islets, (iii) examine the gene expression profiles of Aa with or without the presence of GEIs/islets, (iv) obtain evidence for the genomic instability of Aa over short periods of time (years), (v) identify new candidate virulence factors of Aa and (vi) elucidate the genetic basis of the phenotype and virulence variations of Aa. The results are likely to further the progress in the field of periodontal disease pathogenesis.

描述（由申请人提供）：假设细菌病原体的基因组由一个核心基因库和一个灵活基因库组成。稳定的核心基因库是克隆遗传的，几乎在一个物种的每一个品系中都能找到。相比之下，柔性池包含通过水平基因转移（HGT）获得的遗传元素。每个细菌菌株都有不同的灵活基因群，以适应它们特定的生活方式。基因组岛（Genomic islands, GEIs）是细菌通过HGT群体获得的10-100kbp的大DNA片段，是细菌基因组灵活基因库的重要组成部分。致病菌和非致病菌在某些物种中的区别可以通过致病菌株获得gei来解释。细菌也可能通过基因缺失来增加它们的毒力。在某些情况下，基因组缺失消除了毒力因子的抑制剂，并允许充分表达致病性。革兰氏阴性兼性放线菌杆菌（Aa）是人类牙周炎的主要病原体。Aa的单个克隆似乎表现出不同程度的致病性，甚至可能采用不同的毒力机制。我们的实验室已经获得了在不同Aa菌株中存在gei和较小的基因组岛（功能未知）的初步证据。在一些Aa菌株中，gei和slets的插入导致了基因的截断和/或失活。在这里，我们验证了gei /胰岛和基因组缺失在Aa菌株中普遍存在的假设。此外，基因的获得和丢失可能会改变Aa的表型和毒力。4确定了特定目的：1)基于测序的Aa菌株HK1651，通过DNA微阵列对Aa分离物进行基因组比较；2)通过PCR基因组定位，克隆和测序鉴定Aa中非HK1651的GEIs/胰岛；3)检测Aa GEIs/胰岛的表达及其对Aa基因表达谱的影响；4)通过阵列评估Aa基因组随时间的稳定性。该研究计划预计将(i)在不同Aa菌株的基因组中生成gei /胰岛和大DNA缺失的完整目录，（ii）获得gei /胰岛表达（可能还有功能）的证据，（iii）检查有或没有gei /胰岛存在的Aa基因表达谱，（iv）获得短时间（年）内Aa基因组不稳定性的证据。(v)确定新的Aa候选毒力因子；（vi）阐明Aa表型和毒力变异的遗传基础。该研究结果有望进一步推动牙周病发病机制研究领域的进展。