Virus-host interactions and microbial ecology

 描述(申请人提供)：病毒-宿主相互作用和微生物生态学。这项提议包含了两个截然不同的微生物系统。虽然这两个系统旨在了解基本的生物现象，但它们也与微生物的毒性和人类健康密切相关。它们是：(1)DNA转座事件和细菌基因组组织的修复，以转座噬菌体Mu为模型；(2)鞭毛运动的感官能力和群内细菌的生存策略，以群为模型。(1)可转座噬菌体Mu在阐明所有可移动元件的转座机制中发挥了核心作用。当发现HIV DNA整合的机制与Mu相似时，模仿Mu的高通量整合分析导致了HIV整合酶抑制剂Raltegravir的开发和销售。我们目前关注的是转座的最后一步，它涉及链后转移修复仍然存在的缺口 留在目标中，这个过程仍然是一个黑匣子。我们最近开发的体内修复试验揭示了大肠杆菌复制体在修复中的一个重要作用。这项工作对于将复制体-转座体界面作为药物设计的新靶点具有重要意义。此外，我们最近对靶点选择蛋白Mub性质的洞察，结合DNA测序的进展，为利用Mu作为探针研究大肠杆菌的类核组织开辟了新的基础，其细节仍不清楚。(2)在大量鞭毛细菌中，鞭毛马达感知到一个“表面”信号，告知细菌其环境生态位。作为回应，细菌可以决定生长更多的鞭毛来聚集在表面，或者分泌多糖并在表面附着的生物膜中过着静止的生活。这些反应在细菌感染、表面定植、持久性和致病机制中起着重要作用。来自不同细菌的结果现在明确地表明，马达不仅调控转录，而且还调控转录后途径。然而，感觉机制仍然是未知的，可能是因为我们还没有完全了解运动功能。到目前为止，我们已经积累了关于蜂群的知识，以及我们最近发现的信号分子c-di-GMP在马达上起到刹车的作用，这让我们能够理解鞭毛马达如何充当表面传感器。细菌成群的另一个奇怪的方面是它们对抗生素的较高耐受性。我们最近的发现是，这些细菌通过一种完全不同的策略移动，这种策略被称为‘Lévy Walk’，这为研究这种行为及其与抗生素耐药性的相关性提供了一种新的途径。众所周知，在资源稀缺的时期，鸟类、鱼类甚至人类等大型动物都会使用L的步态策略。L步法被认为在没有记忆的情况下优化了对稀疏分布目标的搜索。有趣的是，细菌在游泳时使用基于记忆的随机行走策略，但在成群时不使用。

 DESCRIPTION (provided by applicant): Virus-host interactions and microbial ecology. This proposal encompasses two very different microbial systems. While directed at understanding fundamental biological phenomena, both systems are also acutely relevant to microbial virulence and to human health. These are: (1) Repair of DNA transposition events and bacterial genome organization, using transposable phage Mu as our model, and (2) Sensory prowess of the flagella motor and survival strategies of bacteria within a group, using swarming as our model. (1) Transposable phage Mu has played a central role in elucidating the transposition mechanism of all mobile elements. When the mechanism of HIV DNA integration was discovered to be similar to that of Mu, high-throughput integration assays modeled after Mu, led to the development and marketing of the HIV integrase inhibitor Raltegravir. We are currently focused on the last step of transposition, which involves post-strand transfer repair of gaps still remaining in the target, a process that is still a black box. The in vivo repair assays we have developed have recently revealed an essential role of the E. coli replisome in repair. The work has implications for the replisome-transpososome interface as a new target for drug design. In addition, our recent insights into properties of the target-site selection protein MuB, combined with the advances in DNA sequencing, open up new ground for exploiting Mu as a probe for the nucleoid organization of E. coli, whose details are still foggy. (2) In a large number of flagellatd bacteria, the flagellar motor perceives a `surface' signal that informs the bacterium of its environmental niche. In response, the bacteria can decide to grow more flagella to swarm over the surface, or secrete polysaccharides and live a sedentary life in surface-adherent biofilms. These responses play important roles in bacterial infection, surface colonization, persistence and pathogenesis. Results from different bacteria have now unequivocally implicated the motor in regulating not only transcription, but also post-transcriptional pathways. However, the sensing mechanism is still in the dark, likely because we don't completely understand motor function. The knowledge of swarming we have amassed thus far, as well as our more recent discovery of the signaling molecule c-di-GMP acting as a brake on the motor, has placed us in a position to understand how the flagellar motor might act as a surface sensor. Another curious aspect of swarming bacteria is their higher tolerance to antibiotics. Our recent finding that these bacteria move by an entirely different strategy called `Lévy walk', offers a new avenue of investigation into this behavior and its relevance to antibiotic tolerance. The Lévy-walk strategy is known to be used by large animals such as birds, fish and even humans in times of scarcity. The Lévy walk is thought to optimize search of sparsely distributed targets in the absence of memory. Interestingly, bacteria use a memory-based random walk strategy during swimming, but not during swarming.