Effect of host defenses on symbiont adaptations and genome erosion in a protective mutualism

在共生关系的进化过程中，共生伙伴之间的相互依赖往往越来越密切，从而在与共生生活方式相关的稳定条件下，对可有可无的基因的选择压力减轻。再加上在传播过程中由于种群瓶颈造成的强烈遗传漂变，这通常会导致遗传物质的损失和AT含量的增加，这一过程称为基因组侵蚀。虽然这一过程的结果在昆虫共生体中得到了充分的记录，但基因组侵蚀的早期阶段和加速它的机制因素仍然知之甚少。在本项目中，我们的目标是重建防御性狼-链霉菌共生关系中的基因组侵蚀，以了解共生微生物基因组衰变的原因和后果。我们的关键假设是，暴露于宿主产生的一氧化氮（NO）对共生体基因组造成了很高的突变压力，特别是对DNA修复机制的破坏，在基因组侵蚀中起着关键作用。为了验证这一假设，并概述了狼-链霉菌共生中的基因组侵蚀，我们将(i)对15个密切相关的共生菌株在基因组衰变的不同阶段的基因组进行测序和比较，以重建假原化事件的序列并评估选择的特征；（ii）在体外和体内研究使狼共生体能够应对极端亚硝化胁迫的基因组和/或基因调节适应。（iii）使用体外实验和实验进化来测试NO暴露和DNA修复机制的故障是否在触发或加速退化性基因组进化中起关键作用。由于一氧化氮是一种广泛存在的信号和防御分子，在拮抗和互惠关联中，拟议项目的结果不仅将阐明加速基因组侵蚀的因素，而且将增强我们对分子宿主-微生物相互作用控制共生特异性和维持的一般理解。

During the evolution of mutualistic associations, the symbiotic partners often evolve increasingly intimate interdependence, resulting in relaxed selective pressures on dispensable genes under the stable conditions associated with the symbiotic lifestyle. Together with strong genetic drift due to population bottlenecks during transmission, this commonly results in the loss of genetic material and an increase in AT content, a process called genome erosion. While the results of this process are well-documented in insect symbionts, the early stages of genome erosion and the mechanistic factors accelerating it are still poorly understood. In the proposed project, we aim to reconstruct genome erosion in the defensive beewolf-Streptomyces mutualism in order to understand the causes and consequences of genomic decay in symbiotic microorganisms. Our key hypothesis is that exposure to host-produced nitric oxide (NO) inflicts a high mutational pressure on the symbiont genome and - particularly upon damage of the DNA repair machinery - plays a key role in genome erosion. In order to test this hypothesis and recapitulate genome erosion in the beewolf-Streptomyces symbiosis, we will (i) sequence and compare the genomes of 15 closely related symbiont strains in different stages of genomic decay to reconstruct the sequence of pseudogenization events and assess signatures of selection, (ii) investigate in vitro and in vivo the genomic and/or gene regulatory adaptations that allow the beewolf symbionts to cope with the extreme nitrosative stress, and (iii) use in vitro experiments and experimental evolution to test whether NO exposure and malfunctions of the DNA repair machinery play key roles in triggering or accelerating degenerative genome evolution. As nitric oxide is a widely occurring signaling and defense molecule in antagonistic and mutualistic associations, the results of the proposed project will not only shed light on the factors accelerating genome erosion, but will also enhance our general understanding of molecular host-microbe interactions governing symbiosis specificity and maintenance.