title: Widespread selection for local RNA secondary structure in coding regions of bacterial genes.
abstract: Redundancy of the genetic code dictates that a given protein can be encoded by a large collection of distinct mRNA species, potentially allowing mRNAs to simultaneously optimize desirable RNA structural features in addition to their protein-coding function. To determine whether natural mRNAs exhibit biases related to local RNA secondary structure, a new randomization procedure was developed, DicodonShuffle, which randomizes mRNA sequences while preserving the same encoded protein sequence, the same codon usage, and the same dinucleotide composition as the native message. Genes from 10 of 14 eubacterial species studied and one eukaryote, the yeast Saccharomyces cerevisiae, exhibited statistically significant biases in favor of local RNA structure as measured by folding free energy. Several significant associations suggest functional roles for mRNA structure, including stronger secondary structure bias in the coding regions of intron-containing yeast genes than in intronless genes, and significantly higher folding potential in polycistronic messages than in monocistronic messages in Escherichia coli. Potential secondary structure generally increased in genes from the 5' to the 3' end of E. coli operons, and secondary structure potential was conserved in homologous Salmonella typhi operons. These results are interpreted in terms of possible roles of RNA structures in RNA processing, regulation of mRNA stability, and translational control.
authors.affiliation: Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
authors.forename: Luba
authors.initials: L
authors.lastname: Katz
authors.forename: Christopher B
authors.initials: CB
authors.lastname: Burge
mesh_terms: D019295:Computational Biology / Q000379:methods / Q000706:statistics & numerical data; D015964:Gene Expression Regulation, Bacterial; D015966:Gene Expression Regulation, Fungal; D005798:Genes, Bacterial; D005800:Genes, Fungal; D007438:Introns / Q000235:genetics; D009690:Nucleic Acid Conformation; D016366:Open Reading Frames; D009876:Operon / Q000235:genetics; D012313:RNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D020871:RNA Stability / Q000235:genetics; D012329:RNA, Bacterial / Q000096:biosynthesis / Q000737:chemistry* / Q000235:genetics*; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D000077278:RNA, Mitochondrial; D012441:Saccharomyces cerevisiae / Q000235:genetics; D013816:Thermodynamics
chemical_list: D012329:RNA, Bacterial; D012333:RNA, Messenger; D000077278:RNA, Mitochondrial; D012313:RNA