Annotation of the Mycoplasma alligatoris genome

描述(申请人提供)：支原体是一种重要的病原体，通常具有严格的自然寄主取向和鲜为人知的毒力机制。这项工作的广泛目标是通过比较支原体基因组的保守和可变特征来增加对支原体宿主范围和毒力决定因素的理解。比较基因组学是阐明支原体病遗传基础的一种新的分子生物学工具。鳄支原体在这项工作中值得优先考虑，因为在一些宿主中，它会导致超急性致命疾病，但在其他宿主中，它只是共生的。其具体目的是通过与密切相关的肺支原体的基因组比对来组装鳄鱼支原体基因组的草图，并识别与宿主嗜性和毒力有关的候选基因。工作草案将使用自动化的高通量序列组装方法进行组装。序列比对将通过比较同步性和基于PCR的缺口闭合来验证。编码序列将通过用支原体序列训练的内插马尔可夫模型来识别，并根据它们的公共数据库匹配来分类。候选宿主范围基因可以通过与已知粘附素的总体相似性或签名配体结合基序来识别。毒力因子可能包括其他软体动物细胞表面或分泌的水解酶的同系物，或存在于其他细菌中的致病决定因素。已知的生物学作用或预测的特性与宿主细胞表面配体结合或鳄鱼分枝杆菌致病作用一致的同系物的序列将被详细描述。这些数据将被整合到鳄鱼黏附、运输和代谢途径的补充表示中，并通过生物学上记录良好的软体动物代谢图进行验证。基于聚合酶链式反应的克隆的简便性和生物信息学软件的可访问性使这一项目成为吸引本科生进行创新生物医学研究的理想项目。

DESCRIPTION (provided by applicant): Mycoplasmas are important pathogens with usually strict natural host tropism and poorly understood virulence mechanisms. The broad objective of this work is increased understanding of mycoplasmal host-range and virulence determinants through comparison of conserved and variable features of mycoplasmal genomes. Comparative genomics is a new alternative to the usual tools of molecular biology to elucidate the genetic bases of mycoplasmosis. Mycoplasma alligatoris merits priority in that effort because in some hosts it causes hyperacute lethal disease, but it is merely commensal in others. The specific aims are to assemble a draft map of the M. alligatoris genome by alignment with that of closely-related Mycoplasma pulmonis, and to identify candidate genes involved in host tropism and virulence. The working draft will be assembled by using automated high-throughput sequence assembly methods. Sequence alignments will be validated by comparative synteny and PCR-based gap closure. Coding sequences will be identified by interpolated Markov models trained with mycoplasmal sequences and cataloged according to their public database matches. Candidate host-range genes may be recognized by overall similarity to known adhesins or by signature ligand-binding motifs. Virulence factors may include homologs to cell-surface or secreted hydrolytic enzymes of other mollicutes, or to pathogenic determinants present in other bacteria. The sequences of homologs whose known biological roles or predicted properties are consistent with host cell-surface ligand-binding or the pathogenic effects of M. alligatoris will be characterized in detail. The data will be integrated in a representation of the complement of adhesion, transport, and metabolic pathways of M. alligatoris validated by the biologically well-documented metabolic map of the mollicutes. The ease of PCR-based cloning and the accessibility of bioinformatics software make this an ideal project to engage undergraduate students in innovative biomedical research.