title: Toxins MazF and MqsR cleave Escherichia coli rRNA precursors at multiple sites.
abstract: The endoribonuclease toxins of the E. coli toxin-antitoxin systems arrest bacterial growth and protein synthesis by targeting cellular mRNAs. As an exception, E. coli MazF was reported to cleave also 16S rRNA at a single site and separate an anti-Shine-Dalgarno sequence-containing RNA fragment from the ribosome. We noticed extensive rRNA fragmentation in response to induction of the toxins MazF and MqsR, which suggested that these toxins can cleave rRNA at multiple sites. We adapted differential RNA-sequencing to map the toxin-cleaved 5'- and 3'-ends. Our results show that the MazF and MqsR cleavage sites are located within structured rRNA regions and, therefore, are not accessible in assembled ribosomes. Most of the rRNA fragments are located in the aberrant ribosomal subunits that accumulate in response to toxin induction and contain unprocessed rRNA precursors. We did not detect MazF- or MqsR-cleaved rRNA in stationary phase bacteria and in assembled ribosomes. Thus, we conclude that MazF and MqsR cleave rRNA precursors before the ribosomes are assembled and potentially facilitate the decay of surplus rRNA transcripts during stress.
authors.affiliation: a Institute of Technology, University of Tartu , Tartu , Estonia.
authors.forename: Toomas
authors.initials: T
authors.lastname: Mets
authors.affiliation: a Institute of Technology, University of Tartu , Tartu , Estonia.
authors.forename: Markus
authors.initials: M
authors.lastname: Lippus
authors.affiliation: a Institute of Technology, University of Tartu , Tartu , Estonia.
authors.forename: David
authors.initials: D
authors.lastname: Schryer
authors.affiliation: b Institute of Molecular and Cell Biology, University of Tartu , Tartu , Estonia.
authors.forename: Aivar
authors.initials: A
authors.lastname: Liiv
authors.affiliation: a Institute of Technology, University of Tartu , Tartu , Estonia.
authors.forename: Villu
authors.initials: V
authors.lastname: Kasari
authors.affiliation: a Institute of Technology, University of Tartu , Tartu , Estonia.
authors.forename: Anton
authors.initials: A
authors.lastname: Paier
authors.affiliation: a Institute of Technology, University of Tartu , Tartu , Estonia.
authors.forename: Ülo
authors.initials: Ü
authors.lastname: Maiväli
authors.affiliation: b Institute of Molecular and Cell Biology, University of Tartu , Tartu , Estonia.
authors.forename: Jaanus
authors.initials: J
authors.lastname: Remme
authors.affiliation: a Institute of Technology, University of Tartu , Tartu , Estonia.
authors.forename: Tanel
authors.initials: T
authors.lastname: Tenson
authors.affiliation: a Institute of Technology, University of Tartu , Tartu , Estonia.
authors.forename: Niilo
authors.initials: N
authors.lastname: Kaldalu
mesh_terms: D001427:Bacterial Toxins / Q000378:metabolism; D001665:Binding Sites; D004268:DNA-Binding Proteins / Q000378:metabolism*; D004722:Endoribonucleases / Q000378:metabolism*; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000378:metabolism*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D010766:Phosphorylation; D011485:Protein Binding; D011487:Protein Conformation; D059367:RNA Cleavage; D012322:RNA Precursors / Q000235:genetics / Q000378:metabolism; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012335:RNA, Ribosomal / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D017423:Sequence Analysis, RNA; D013312:Stress, Physiological / Q000235:genetics
chemical_list: D001427:Bacterial Toxins; D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; C422955:MazF protein, E coli; C508571:MqsR protein, E coli; D012322:RNA Precursors; D012329:RNA, Bacterial; D012335:RNA, Ribosomal; D004722:Endoribonucleases
keywords: Differential RNA sequencing; MazF; MqsR; Toxin-Antitoxin systems; rRNA precursors; ribosome