Targeted Gene Evolution via Replication-Transcription Conflicts

描述（由申请人提供）：通过复制-转录冲突的靶向基因进化微生物非常好地适应环境的快速变化，这在很大程度上是由于它们的快速进化能力。阐明驱动微生物进化的机制对传染病的治疗至关重要，特别是在耐药病原体出现的情况下。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增加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基因中有害突变的发生率，这些基因处于强烈的负向选择下，以防止变异。虽然细菌可能从变异正选择下基因诱变率的增加中获益良多，但细胞选择性地使这些基因突变的机制却知之甚少，如果有的话。在这里，我提出了一个特定基因通过复制和转录之间的定向依赖遭遇的靶向进化模型。最近，我发现了染色体周围的内源性区域，在那里复制和转录机制发生了冲突。这些发现表明，复制和转录之间的冲突远比以前认为的要突出得多，并且这些冲突经常发生的热点地区。自我最初的发现以来，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。我提出了一项研究计划，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，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必要基因，这些基因可能是复制-转录冲突诱导诱变的主要目标。我的研究计划旨在研究这些基因在选择条件下的适应功能，以及冲突对其变异的影响。这一建议有可能揭示细菌，以及可能包括真核生物在内的其他生物，如何以受控的方式改变特定基因的功能以快速适应。这项工作可以为细菌有机体的生物学和进化提供深远的见解，特别是人类病原体。

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.