Westphal Lacey L, Lau Jasmine, Negro Zuly, Moreno Ivan J, Ismail Mohammed Wazim, Lee Heewook, Tang Haixu, Finkel Steven E, Kram Karin E
Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, RRI 303, 1050 Child's Way, Los Angeles, CA, 90089-2910, USA.
Department of Biology, California State University, Dominguez Hills, NSM A-137, 1000 E. Victoria Street, Carson, CA, 90747, USA.
Res Microbiol. 2018 Apr;169(3):145-156. doi: 10.1016/j.resmic.2018.01.003. Epub 2018 Feb 15.
Experimental evolution studies have characterized the genetic strategies microbes utilize to adapt to their environments, mainly focusing on how microbes adapt to constant and/or defined environments. Using a system that incubates Escherichia coli in different complex media in long-term batch culture, we have focused on how heterogeneity and environment affects adaptive landscapes. In this system, there is no passaging of cells, and therefore genetic diversity is lost only through negative selection, without the experimentally-imposed bottlenecking common in other platforms. In contrast with other experimental evolution systems, because of cycling of nutrients and waste products, this is a heterogeneous environment, where selective pressures change over time, similar to natural environments. We determined that incubation in each environment leads to different adaptations by observing the growth advantage in stationary phase (GASP) phenotype. Re-sequencing whole genomes of populations identified both mutant alleles in a conserved set of genes and differences in evolutionary trajectories between environments. Reconstructing identified mutations in the parental strain background confirmed the adaptive advantage of some alleles, but also identified a surprising number of neutral or even deleterious mutations. This result indicates that complex epistatic interactions may be under positive selection within these heterogeneous environments.
实验进化研究已经描述了微生物用于适应其环境的遗传策略，主要聚焦于微生物如何适应恒定和/或特定环境。通过一个在长期分批培养中于不同复杂培养基中培养大肠杆菌的系统，我们关注了异质性和环境如何影响适应性景观。在这个系统中，细胞没有传代，因此遗传多样性仅通过负选择丧失，而没有其他平台中常见的实验性瓶颈效应。与其他实验进化系统不同，由于营养物质和代谢产物的循环，这是一个异质环境，其中选择压力随时间变化，类似于自然环境。通过观察稳定期生长优势（GASP）表型，我们确定在每个环境中的培养会导致不同的适应性。对群体的全基因组重测序确定了一组保守基因中的突变等位基因以及不同环境之间进化轨迹的差异。在亲本菌株背景中重建已鉴定的突变证实了一些等位基因的适应性优势，但也发现了数量惊人的中性甚至有害突变。这一结果表明，在这些异质环境中，复杂的上位相互作用可能受到正选择。
