title: DsrA regulatory RNA represses both hns and rbsD mRNAs through distinct mechanisms in Escherichia coli.
abstract: The 87 nucleotide long DsrA sRNA has been mostly studied for its translational activation of the transcriptional regulator RpoS. However, it also represses hns mRNA, which encodes H-NS, a major regulator that affects expression of nearly 5% of Escherichia coli genes. A speculative model previously suggested that DsrA would block hns mRNA translation by binding simultaneously to start and stop codon regions of hns mRNA (coaxial model). Here, we show that DsrA efficiently blocked translation of hns mRNA by base-pairing immediately downstream of the start codon. In addition, DsrA induced hns mRNA degradation by actively recruiting the RNA degradosome complex. Data presented here led to a model of DsrA action on hns mRNA, which supports a canonical mechanism of sRNA-induced mRNA degradation by binding to the translation initiation region. Furthermore, using MS2-affinity purification coupled with RNA sequencing technology (MAPS), we also demonstrated that DsrA targets rbsD mRNA, involved in ribose utilization. Surprisingly, DsrA base pairs far downstream of rbsD start codon and induces rapid degradation of the transcript. Thus, our study enables us to draw an extended DsrA targetome.
authors.affiliation: Université de Sherbrooke, Faculty of Medicine and Health Sciences, Department of Biochemistry, RNA Group, Sherbrooke, Québec, Canada.
authors.forename: David
authors.initials: D
authors.lastname: Lalaouna
authors.affiliation: Université de Sherbrooke, Faculty of Medicine and Health Sciences, Department of Biochemistry, RNA Group, Sherbrooke, Québec, Canada.
authors.forename: Audrey
authors.initials: A
authors.lastname: Morissette
authors.affiliation: Université de Sherbrooke, Faculty of Medicine and Health Sciences, Department of Biochemistry, RNA Group, Sherbrooke, Québec, Canada.
authors.forename: Marie-Claude
authors.initials: MC
authors.lastname: Carrier
authors.affiliation: Université de Sherbrooke, Faculty of Medicine and Health Sciences, Department of Biochemistry, RNA Group, Sherbrooke, Québec, Canada.
authors.forename: Eric
authors.initials: E
authors.lastname: Massé
mesh_terms: D001483:Base Sequence; D004722:Endoribonucleases; D004926:Escherichia coli / Q000235:genetics*; D015964:Gene Expression Regulation, Bacterial; D008969:Molecular Sequence Data; D009097:Multienzyme Complexes; D011117:Polyribonucleotide Nucleotidyltransferase; D014176:Protein Biosynthesis; D020365:RNA Helicases; D020871:RNA Stability; D012329:RNA, Bacterial / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism*; D058727:RNA, Small Untranslated / Q000235:genetics / Q000378:metabolism*; D038621:Regulatory Sequences, Ribonucleic Acid; D017423:Sequence Analysis, RNA / Q000379:methods
chemical_list: D009097:Multienzyme Complexes; D012329:RNA, Bacterial; D012333:RNA, Messenger; D058727:RNA, Small Untranslated; D038621:Regulatory Sequences, Ribonucleic Acid; C111244:degradosome; D011117:Polyribonucleotide Nucleotidyltransferase; D004722:Endoribonucleases; D020365:RNA Helicases