title: Contribution of silent mutations to thermal adaptation of RNA bacteriophage Qβ.
abstract: Changes in protein function and other biological properties, such as RNA structure, are crucial for adaptation of organisms to novel or inhibitory environments. To investigate how mutations that do not alter amino acid sequence may be positively selected, we performed a thermal adaptation experiment using the single-stranded RNA bacteriophage Qβ in which the culture temperature was increased from 37.2°C to 41.2°C and finally to an inhibitory temperature of 43.6°C in a stepwise manner in three independent lines. Whole-genome analysis revealed 31 mutations, including 14 mutations that did not result in amino acid sequence alterations, in this thermal adaptation. Eight of the 31 mutations were observed in all three lines. Reconstruction and fitness analyses of Qβ strains containing only mutations observed in all three lines indicated that five mutations that did not result in amino acid sequence changes but increased the amplification ratio appeared in the course of adaptation to growth at 41.2°C. Moreover, these mutations provided a suitable genetic background for subsequent mutations, altering the fitness contribution from deleterious to beneficial. These results clearly showed that mutations that do not alter the amino acid sequence play important roles in adaptation of this single-stranded RNA virus to elevated temperature.
  
  
  OBJECTIVE
  Recent studies using whole-genome analysis technology suggested the importance of mutations that do not alter the amino acid sequence for adaptation of organisms to novel environmental conditions. It is necessary to investigate how these mutations may be positively selected and to determine to what degree such mutations that do not alter amino acid sequences contribute to adaptive evolution. Here, we report the roles of these silent mutations in thermal adaptation of RNA bacteriophage Qβ based on experimental evolution during which Qβ showed adaptation to growth at an inhibitory temperature. Intriguingly, four synonymous mutations and one mutation in the untranslated region that spread widely in the Qβ population during the adaptation process at moderately high temperature provided a suitable genetic background to alter the fitness contribution of subsequent mutations from deleterious to beneficial at a higher temperature.
authors: Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori, Japan.
authors: Akiko
authors: A
authors: Kashiwagi
authors: Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori, Japan.
authors: Ryu
authors: R
authors: Sugawara
authors: Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori, Japan.
authors: Fumie
authors: F
authors: Sano Tsushima
authors: Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori, Japan.
authors: Tomofumi
authors: T
authors: Kumagai
authors: Graduate School of Information Science and Technology, Osaka University, Osaka, Japan Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan Dynamical Micro-scale Reaction Environment Project, Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Osaka, Japan yomo@ist.osaka-u.ac.jp.
authors: Tetsuya
authors: T
authors: Yomo
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D005075:Biological Evolution; D003090:Coliphages / Q000235:genetics*; D004926:Escherichia coli / Q000821:virology; D056084:Genetic Fitness; D006358:Hot Temperature; D009154:Mutation; D009690:Nucleic Acid Conformation; D012317:RNA Phages / Q000235:genetics*; D012367:RNA, Viral / Q000235:genetics*
chemical_list: C028696:Qbeta ribonucleic acid; D012367:RNA, Viral