title: Coevolution in RNA molecules driven by selective constraints: evidence from 5S rRNA.
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 positions. Breaking these pairs would directly increase the size of the adjoining loop or bulge, causing a partial or total structural rearrangement. In conclusion, our results indicate that sequence coevolution is a direct result of maintaining optimal structural and functional integrity.
authors.affiliation: StateKey Laboratory of Crop Stress Biology in Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, People's Republic of China.
authors.forename: Nan
authors.initials: N
authors.lastname: Cheng
authors.forename: Yuanhui
authors.initials: Y
authors.lastname: Mao
authors.forename: Youyi
authors.initials: Y
authors.lastname: Shi
authors.forename: Shiheng
authors.initials: S
authors.lastname: Tao
mesh_terms: D020029:Base Pairing / Q000235:genetics*; D001499:Bayes Theorem; D019295:Computational Biology; D003198:Computer Simulation; D019143:Evolution, Molecular; D008957:Models, Genetic; D009154:Mutation / Q000235:genetics; D010802:Phylogeny; D012341:RNA, Ribosomal, 5S / Q000235:genetics* / Q000378:metabolism*; D012641:Selection, Genetic
chemical_list: D012341:RNA, Ribosomal, 5S