title: Sequence features of E. coli mRNAs affect their degradation.
abstract: Degradation of mRNA in bacteria is a regulatory mechanism, providing an efficient way to fine-tune protein abundance in response to environmental changes. While the mechanisms responsible for initiation and subsequent propagation of mRNA degradation are well studied, the mRNA features that affect its stability are yet to be elucidated. We calculated three properties for each mRNA in the E. coli transcriptome: G+C content, tRNA adaptation index (tAI) and folding energy. Each of these properties were then correlated with the experimental transcript half life measured for each transcript and detected significant correlations. A sliding window analysis identified the regions that displayed the maximal signal. The correlation between transcript half life and both G+C content and folding energy was strongest at the 5' termini of the mRNAs. Partial correlations showed that each of the parameters contributes separately to mRNA half life. Notably, mRNAs of recently-acquired genes in the E. coli genome, which have a distinct nucleotide composition, tend to be highly stable. This high stability may aid the evolutionary fixation of horizontally acquired genes.
authors.affiliation: Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel.
authors.forename: Gal
authors.initials: G
authors.lastname: Lenz
authors.forename: Adi
authors.initials: A
authors.lastname: Doron-Faigenboim
authors.forename: Eliora Z
authors.initials: EZ
authors.lastname: Ron
authors.forename: Tamir
authors.initials: T
authors.lastname: Tuller
authors.forename: Uri
authors.initials: U
authors.lastname: Gophna
mesh_terms: D001482:Base Composition; D003062:Codon; D019295:Computational Biology / Q000379:methods; D004926:Escherichia coli / Q000235:genetics*; D019143:Evolution, Molecular; D005798:Genes, Bacterial; D016678:Genome; D008957:Models, Genetic; D015233:Models, Statistical; D014176:Protein Biosynthesis; D012313:RNA / Q000378:metabolism; D020871:RNA Stability / Q000235:genetics*; D012333:RNA, Messenger / Q000378:metabolism*; D014158:Transcription, Genetic; D059467:Transcriptome
chemical_list: D003062:Codon; D012333:RNA, Messenger; D012313:RNA