coevolution in rna molecules driven by selective constraints evidence from 5s rrna共同进化的rna分子的选择性限制从5 s rrna的证据.pdf

Coevolution in RNA Molecules Driven by Selective Constraints: Evidence from 5S rRNA 1,2 1 3 1,2 Nan Cheng , Yuanhui Mao , Youyi Shi , Shiheng Tao * 1 StateKey Laboratory of Crop Stress Biology in Arid Areas and College of Life Sciences, Northwest AF University, Yangling, People’s Republic of China, 2 Bioinformatics Center, Northwest AF University, Yangling, People’s Republic of China, 3 College of Science, Northwest AF University, Yangling, People’s Republic of China Abstract Understanding intra-molecular coevolution helps to elucidate various structural and functional constraints acting on molecules and might have practical applications in predicting molecular structure and interactions. In this study, we used 5S rRNA as a template to investigate how selective constraints have shaped the RNA evolution. We have observed the nonrandom occurrence of paired differences along the phylogenetic trees, the high rate of compensatory evolution, and the high TIR scores (the ratio of the numbers of terminal to intermediate states), all of which indicate that significant positive selection has driven the evolution of 5S rRNA. We found three mechanisms of compensatory evolution: Watson-Crick interaction (the primary one), complex interactions between multiple sites within a stem, and interplay of stems and loops. Coevolutionary interactions between sites were observed to be highly dependent on the structural and functional environment in which they occurred. Coevolution occurred mostly in those sites closest to loops or bulges within structurally or functionally important helices, which may be under weaker selective constraints than other stem posit