Experimental evolution of Tobacco etch virus carrying exogenous sequences

Here we explore experimentally the evolutionary fate of viruses with a simulated HGT event, using the plant RNA virus Tobacco etch virus (TEV), by separately introducing two functional, exogenous sequences to its genome. One of the events simulates the acquisition of a new function though HGT of a conserved AlkB domain, responsible for the repair of alkylation or methylation damage in many organisms. The other event simulates the acquisition of a sequence that duplicates an existing function, through HGT of the 2b RNA silencing suppressor from Cucumber mosaic virus (CMV). We then evolved these two viruses, tracked the maintenance of the horizontally transferred sequences over time, and for the final virus populations, sequenced their genome and measured viral fitness. We found that the AlkB domain was rapidly purged from the TEV genome, restoring fitness to wild-type levels. Conversely, the 2b gene was stably maintained and did not have a major impact on viral fitness. Moreover, we found that 2b is functional in TEV, as it provides a replicative advantage when the functional domain of HC-Pro related to RNA silencing suppression is mutated. These observations therefore suggest a potentially interesting role for HGT of short functional sequences in ameliorating evolutionary constraints.

本研究以植物RNA病毒烟草蚀刻病毒（Tobacco etch virus, TEV）为实验材料，通过模拟水平基因转移（Horizontal Gene Transfer, HGT）事件，探究病毒的演化命运。我们分别向其基因组引入两段具备功能的外源性序列：其一为通过水平基因转移获取的保守AlkB结构域（AlkB domain），该结构域在众多生物中负责修复烷基化或甲基化损伤，以此模拟新功能的获得；其二为从黄瓜花叶病毒（Cucumber mosaic virus, CMV）中水平基因转移获取的2b RNA沉默抑制子序列，以此模拟通过序列复制实现现有功能的强化。随后我们对这两种重组病毒进行传代演化，实时追踪水平转移序列随时间的维持情况，并对最终的病毒种群开展基因组测序，同时测定病毒的适合度。研究发现，AlkB结构域会被快速从TEV基因组中清除，使病毒适合度恢复至野生型水平；与之相反，2b基因能够稳定维持，且对病毒适合度无显著影响。此外，我们证实2b在TEV中具备功能：当HC-Pro（辅助成分蛋白酶）中与RNA沉默抑制相关的功能结构域发生突变时，2b可赋予病毒复制优势。综上，上述结果表明，短功能序列的水平基因转移在缓解演化约束方面可能具有潜在的重要作用。