Targeted Gene Evolution via Replication-Transcription Conflicts

描述(由申请人提供)：通过复制-转录冲突进行定向基因进化微生物非常好地适应其环境的快速变化，这在很大程度上是由于它们快速进化的能力。阐明推动微生物进化的机制对于传染病的治疗至关重要，特别是在出现耐药病原体的情况下。适应性进化的速度直接取决于基因变异出现的速度。已知有几种机制可以提高整个基因组的突变率，然而，这些机制有一个内在的问题：它们也增加了高度保守的基因中有害突变的发生速度，这些基因处于针对变异的强烈负选择之下。尽管细菌在对变异进行正向选择的情况下，基因突变率的提高可能会显著受益，但细胞选择性突变这些基因的机制，即使有的话，也是知之甚少。在这里，我提出了一个模型，通过复制和转录之间的定向相遇，特定基因的靶向进化。最近，我确定了复制和转录机制在染色体周围发生碰撞的内源性区域。这些发现表明，复制和转录之间的冲突比以前认识到的要突出得多，而且在一些热点地区，这些冲突经常发生。自从我最初发现以来，我一直在继续研究这个话题，最近获得的证据表明，复制-转录冲突可能是靶向基因进化的基本机制。我提出了一个研究计划，通过研究复制-转录冲突、适应性突变和细菌进化之间的关系来加深我们对这些关键事件的理解。此外，我已经确定了快速进化的基本基因，这些基因可能是复制-转录冲突诱导突变的主要目标。我的研究项目旨在研究这些基因在选择性条件下适应过程中的功能，以及冲突对它们变异的影响。这一提议有可能揭开细菌，可能还有其他生物，包括真核生物，如何以受控的方式改变特定基因的功能，以实现快速适应。这项工作可以提供对细菌生物体，特别是人类病原体的生物学和进化的深远见解。

DESCRIPTION (provided by applicant): Targeted Gene Evolution via Replication-Transcription Conflicts Microorganisms adapt to rapid changes in their environment exceptionally well, in large part due to their ability to evolve quickly. Elucidating the mechanism driving microbial evolution is critical for treatment of infectious diseases, especially in light o the emergence of drug-resistant pathogens. The rate of adaptive evolution directly depends on the rate of at which genetic variants arise. Several mechanisms are known to increase the rate of mutagenesis across the entire genome, however, these mechanisms have an intrinsic problem: they also increase the rate at which deleterious mutations arise in highly conserved genes that are under strong negative selection against variation. Though bacteria may benefit significantly from an increased rate of mutagenesis in the genes under positive selection for variation, the mechanisms by which cells could selectively mutate these genes are understood poorly, if at all. Here, I present a model for the targeted evolution of specific genes through orientation-dependent encounters between replication and transcription. Recently, I identified endogenous regions around the chromosome where the replication and transcription machineries collide. These findings indicated that conflicts between replication and transcription are far more prominent than previously appreciated and that there are hotspots where these encounters take place frequently. I have continued to research this topic since my initial discovery, and recently obtained evidence suggesting that replication- transcription conflicts may be a basic mechanism for targeted gene evolution. I propose a research program that deepens our understanding of these critical events by investigating the relationship between replication-transcription conflicts adaptive mutagenesis, and the evolution of bacteria. In addition, I have identified fast evolving essential genes that are likely the major targets of replication-transcription conflict induced mutagenesis. My research program is designed to investigate the function of these genes during adaptation under selective conditions, and the impact of conflicts on their variation. This proposal has the potential to unravel how bacteria, and possibly other organisms, including eukaryotes, vary the function of specific genes in a controlled manner for rapid adaptation. This work could provide far-reaching insights into the biology and evolution of bacterial organisms, in general, and in particular human pathogens.