title: Functional interaction between RNase III and the Escherichia coli ribosome.
abstract: BACKGROUND
  RNase III is a dsRNA specific endoribonuclease which is involved in the primary processing of rRNA and several mRNA species in bacteria. Both primary structural elements and the secondary structure of the substrate RNA play a role in cleavage specificity.
  
  
  RESULTS
  We have analyzed RNase III cleavage sites around both ends of pre-23 S rRNA in the ribosome and in the protein-free pre-rRNA. It was found that in the protein-free pre-23 S rRNA the main cleavage site is at position (-7) in respect of the mature 5' end. When pre-23 S rRNA was in 70 S ribosomes or in 50 S subunits, the RNase III cleavage occurred at position (-3). We have demonstrated that RNase III interacts with both ribosomal subunits and with even higher affinity with 70 S ribosomes. Association of RNase III with 70 S ribosomes cannot be dissociated by poly(U) RNA indicating that the binding is specific.
  
  
  CONCLUSIONS
  In addition to the primary and secondary structural elements in RNA, protein binding to substrate RNA can be a determinant of the RNase III cleavage site.
authors.affiliation: Institute of Molecular and Cell Biology, Tartu University, Riia 23, 51010 Tartu, Estonia. snoopy@ut.ee
authors.forename: Ular
authors.initials: U
authors.lastname: Allas
authors.forename: Aivar
authors.initials: A
authors.lastname: Liiv
authors.forename: Jaanus
authors.initials: J
authors.lastname: Remme
mesh_terms: D001482:Base Composition / Q000235:genetics; D001483:Base Sequence / Q000235:genetics; D001665:Binding Sites / Q000235:genetics / Q000502:physiology; D004722:Endoribonucleases / Q000378:metabolism / Q000502:physiology*; D004926:Escherichia coli / Q000201:enzymology* / Q000235:genetics*; D029968:Escherichia coli Proteins / Q000378:metabolism; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009694:Nucleic Acid Precursors / Q000235:genetics / Q000378:metabolism / Q000502:physiology; D012323:RNA Processing, Post-Transcriptional / Q000235:genetics / Q000502:physiology; D012329:RNA, Bacterial / Q000235:genetics / Q000378:metabolism / Q000502:physiology; D012338:RNA, Ribosomal, 23S / Q000235:genetics / Q000378:metabolism / Q000502:physiology; D016601:RNA-Binding Proteins / Q000378:metabolism / Q000502:physiology; D043244:Ribonuclease III; D012269:Ribosomal Proteins / Q000378:metabolism; D012270:Ribosomes / Q000378:metabolism / Q000502:physiology*
chemical_list: D029968:Escherichia coli Proteins; D009694:Nucleic Acid Precursors; D012329:RNA, Bacterial; D012338:RNA, Ribosomal, 23S; D016601:RNA-Binding Proteins; D012269:Ribosomal Proteins; D004722:Endoribonucleases; D043244:Ribonuclease III; C468366:ribonuclease III, E coli