title: Concurrent neutral evolution of mRNA secondary structures and encoded proteins.
abstract: Messenger RNA sequences often have to preserve functional secondary structure elements in addition to coding for proteins. We present a statistical analysis of retroviral mRNA which supports the hypothesis that the natural genetic code is adapted to such complementary coding. These sequences are still able to explore efficiently the space of possible proteins by point mutations. This is borne out by the observation that, in stem regions of retroviral mRNA foldings, silent mutations on one strand are preferentially accompanied by conservative mutations on the other. Distances between amino acids based on physicochemical properties are used to quantify the conservation of protein function under the constraint of maintained RNA secondary structure. We find that preservation of RNA secondary structure by compensatory mutations is evolutionary compatible with the efficient search for new variants on the protein level.
authors.affiliation: Theorectical Chemistry, Tech University Munich, Lichtenbergstr. 4, D 85747 Garching, Germany.
authors.forename: J
authors.initials: J
authors.lastname: Konecny
authors.forename: M
authors.initials: M
authors.lastname: Schöniger
authors.forename: I
authors.initials: I
authors.lastname: Hofacker
authors.forename: M D
authors.initials: MD
authors.lastname: Weitze
authors.forename: G L
authors.initials: GL
authors.lastname: Hofacker
mesh_terms: D001483:Base Sequence; D019143:Evolution, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics*; D015302:Simian Immunodeficiency Virus / Q000235:genetics; D014764:Viral Proteins / Q000235:genetics
chemical_list: D012333:RNA, Messenger; D014764:Viral Proteins