title: Avoidance of stochastic RNA interactions can be harnessed to control protein expression levels in bacteria and archaea.
abstract: A critical assumption of gene expression analysis is that mRNA abundances broadly correlate with protein abundance, but these two are often imperfectly correlated. Some of the discrepancy can be accounted for by two important mRNA features: codon usage and mRNA secondary structure. We present a new global factor, called mRNA:ncRNA avoidance, and provide evidence that avoidance increases translational efficiency. We also demonstrate a strong selection for the avoidance of stochastic mRNA:ncRNA interactions across prokaryotes, and that these have a greater impact on protein abundance than mRNA structure or codon usage. By generating synonymously variant green fluorescent protein (GFP) mRNAs with different potential for mRNA:ncRNA interactions, we demonstrate that GFP levels correlate well with interaction avoidance. Therefore, taking stochastic mRNA:ncRNA interactions into account enables precise modulation of protein abundance.
authors.affiliation: School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.|Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.
authors.forename: Sinan Uğur
authors.identifier: 0000-0001-8081-7819
authors.initials: SU
authors.lastname: Umu
authors.affiliation: School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.|Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.
authors.forename: Anthony M
authors.initials: AM
authors.lastname: Poole
authors.affiliation: School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.|Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.|Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Australia.
authors.forename: Renwick Cj
authors.initials: RC
authors.lastname: Dobson
authors.affiliation: School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.|Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.|BioProtection Research Centre, University of Canterbury, Christchurch, New Zealand.
authors.forename: Paul P
authors.identifier: 0000-0002-7808-1213
authors.initials: PP
authors.lastname: Gardner
mesh_terms: D001105:Archaea / Q000235:genetics* / Q000378:metabolism*; D001419:Bacteria / Q000235:genetics* / Q000378:metabolism*; D017930:Genes, Reporter; D049452:Green Fluorescent Proteins / Q000032:analysis / Q000235:genetics; D014176:Protein Biosynthesis; D012333:RNA, Messenger / Q000378:metabolism*; D022661:RNA, Untranslated / Q000378:metabolism*
chemical_list: D012333:RNA, Messenger; D022661:RNA, Untranslated; D049452:Green Fluorescent Proteins
keywords: Archaea; E. coli; bacteria; bioinformatics; computational biology; evolutionary biology; gene expression; genomics; ncRNA; systems biology