Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland.
Swiss Institute of Bioinformatics, Lausanne, Switzerland.
Nat Ecol Evol. 2019 Aug;3(8):1184-1196. doi: 10.1038/s41559-019-0939-6. Epub 2019 Jul 22.
Microbes are exposed to changing environments, to which they can respond by adopting various lifestyles such as swimming, colony formation or dormancy. These lifestyles are often studied in isolation, thereby giving a fragmented view of the life cycle as a whole. Here, we study lifestyles in the context of this whole. We first use machine learning to reconstruct the expression changes underlying life cycle progression in the bacterium Bacillus subtilis, based on hundreds of previously acquired expression profiles. This yields a timeline that reveals the modular organization of the life cycle. By analysing over 380 Bacillales genomes, we then show that life cycle modularity gives rise to mosaic evolution in which life stages such as motility and sporulation are conserved and lost as discrete units. We postulate that this mosaic conservation pattern results from habitat changes that make these life stages obsolete or detrimental. Indeed, when evolving eight distinct Bacillales strains and species under laboratory conditions that favour colony growth, we observe rapid and parallel losses of the sporulation life stage across species, induced by mutations that affect the same global regulator. We conclude that a life cycle perspective is pivotal to understanding the causes and consequences of modularity in both regulation and evolution.
微生物处于不断变化的环境中，它们可以通过各种生活方式来应对，如游泳、群体形成或休眠。这些生活方式通常是孤立地研究的，从而对整个生命周期的全貌产生了碎片化的认识。在这里，我们在整体的背景下研究生活方式。我们首先使用机器学习，根据数百个之前获得的表达谱，重建细菌枯草芽孢杆菌中与生命周期进展相关的表达变化。这产生了一个时间线，揭示了生命周期的模块化组织。通过分析超过 380 个芽孢杆菌目基因组，我们表明，生命周期的模块化导致镶嵌进化，其中运动和孢子形成等生命阶段作为离散单元被保守和丢失。我们假设这种镶嵌保守模式是由使这些生命阶段变得过时或有害的栖息地变化引起的。事实上，当我们在有利于菌落生长的实验室条件下进化八个不同的芽孢杆菌菌株和物种时，我们观察到在物种中，由于影响相同全局调节剂的突变，孢子形成生命阶段迅速而平行地丢失。我们得出的结论是，从生命周期的角度来看，对于理解调节和进化中模块化的原因和后果至关重要。
