Data from: Sign epistasis limits evolutionary trade-offs at the confluence of single- and multi-carbon metabolism in Methylobacterium extorquens AM1

Adaptation of one set of traits is often accompanied by attenuation of traits important in other selective environments, leading to fitness trade-offs. The mechanisms that either promote or prevent the emergence of trade-offs remain largely unknown, and are difficult to discern in most systems. Here, we investigate the basis of trade-offs that emerged during experimental evolution of Methylobacterium extorquens AM1 to distinct growth substrates. After 1500 generations of adaptation to a multi-carbon substrate, succinate (S), many lineages had lost the ability to use one-carbon compounds such as methanol (M), generating a mixture of M+ and M− evolved phenotypes. We show that trade-offs in M− strains consistently arise via antagonistic pleiotropy through recurrent selection for loss-of-function mutations to ftfL (formate-tetrahydrofolate ligase), which improved growth on S while simultaneously eliminating growth on M. But if loss of FtfL was beneficial, why were M trade-offs not found in all populations? We discovered that eliminating FtfL was not universally beneficial on S, as it was neutral or even deleterious in certain evolved lineages that remained M+. This suggests that sign epistasis with earlier arising mutations prevented the emergence of mutations that drove trade-offs through antagonistic pleiotropy, limiting the evolution of metabolic specialists in some populations.

单一性状集的适应往往伴随其他选择环境中重要性状的衰减，进而引发适合度权衡（fitness trade-offs）。目前，促进或阻止权衡出现的分子机制仍尚未完全明确，且在多数研究系统中难以被解析。本研究聚焦扭脱甲基杆菌AM1（Methylobacterium extorquens AM1）在适应不同生长底物的实验进化（experimental evolution）过程中所产生的权衡现象的内在机制。在适应多碳底物琥珀酸盐（succinate，S）1500代后，多个进化谱系丧失了利用甲醇（methanol，M）等一碳化合物（one-carbon compounds）的能力，形成了包含M+（保留甲醇利用能力）与M−（丧失甲醇利用能力）两类进化表型的混合种群。研究表明，M−菌株的权衡现象始终通过拮抗多效性（antagonistic pleiotropy）产生：反复的选择压力作用于ftfL（甲酰四氢叶酸连接酶，formate-tetrahydrofolate ligase）的功能丧失突变（loss-of-function mutations），该突变可提升菌株在琥珀酸盐培养基中的生长性能，同时完全消除其利用甲醇的能力。但倘若丧失FtfL功能具有适应性优势，为何并非所有种群都出现了与甲醇利用相关的权衡？我们的研究发现，在琥珀酸盐培养基中，丧失FtfL功能并非普遍具有适应性优势：在部分仍保留M+表型的进化谱系中，该突变呈中性甚至有害。这提示，与早期出现的突变之间的符号上位性（sign epistasis）阻断了通过拮抗多效性引发权衡的突变的出现，进而限制了部分种群中代谢特化型菌株的演化。