Safina Ksenia R, Mironov Andrey A, Bazykin Georgii A
Sector for Molecular Evolution, Institute of Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences, Moscow, Russia.
Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia.
Genome Biol Evol. 2017 Feb 1;9(2):340-349. doi: 10.1093/gbe/evw295.
Many RNA molecules possess complicated secondary structure critical to their function. Mutations in double-helical regions of RNA may disrupt Watson-Crick (WC) interactions causing structure destabilization or even complete loss of function. Such disruption can be compensated by another mutation restoring base pairing, as has been shown for mRNA, rRNA and tRNA. Here, we investigate the evolution of intrinsic transcription terminators between closely related strains of Bacillus cereus. While the terminator structure is maintained by strong natural selection, as evidenced by the low frequency of disrupting mutations, we observe multiple instances of pairs of disrupting-compensating mutations in RNA structure stems. Such two-step switches between different WC pairs occur very fast, consistent with the low fitness conferred by the intermediate non-WC variant. Still, they are not instantaneous, and probably involve transient fixation of the intermediate variant. The GU wobble pair is the most frequent intermediate, and remains fixed longer than other intermediates, consistent with its less disruptive effect on the RNA structure. Double switches involving non-GU intermediates are more frequent at the ends of RNA stems, probably because they are associated with smaller fitness loss. Together, these results show that the fitness landscape of bacterial transcription terminators is rather rugged, but that the fitness valleys associated with unpaired stem nucleotides are rather shallow, facilitating evolution.
许多RNA分子具有对其功能至关重要的复杂二级结构。RNA双螺旋区域的突变可能会破坏沃森-克里克（WC）相互作用，导致结构不稳定甚至功能完全丧失。正如在mRNA、rRNA和tRNA中所显示的那样，这种破坏可以通过另一个恢复碱基配对的突变来补偿。在这里，我们研究了蜡样芽孢杆菌密切相关菌株之间内在转录终止子的进化。虽然终止子结构通过强烈的自然选择得以维持，这从破坏突变的低频率可以看出，但我们在RNA结构茎中观察到多对破坏-补偿突变的实例。不同WC碱基对之间的这种两步转换发生得非常快，这与中间非WC变体所赋予的低适应性一致。然而，它们并非瞬间完成，可能涉及中间变体的短暂固定。GU摆动碱基对是最常见的中间体，并且比其他中间体保持固定的时间更长，这与其对RNA结构的破坏作用较小一致。涉及非GU中间体的双重转换在RNA茎的末端更为频繁，可能是因为它们与较小的适应性损失相关。总之，这些结果表明细菌转录终止子的适应性景观相当崎岖，但与未配对茎核苷酸相关的适应性低谷相当浅，这有利于进化。
