title: Recognition of the 70S ribosome and polysome by the RNA degradosome in Escherichia coli.
abstract: The RNA degradosome is a multi-enzyme assembly that contributes to key processes of RNA metabolism, and it engages numerous partners in serving its varied functional roles. Small domains within the assembly recognize collectively a diverse range of macromolecules, including the core protein components, the cytoplasmic lipid membrane, mRNAs, non-coding regulatory RNAs and precursors of structured RNAs. We present evidence that the degradosome can form a stable complex with the 70S ribosome and polysomes, and we demonstrate the proximity in vivo of ribosomal proteins and the scaffold of the degradosome, RNase E. The principal interactions are mapped to two, independent, RNA-binding domains from RNase E. RhlB, the RNA helicase component of the degradosome, also contributes to ribosome binding, and this is favoured through an activating interaction with RNase E. The catalytic activity of RNase E for processing 9S RNA (the ribosomal 5S RNA precursor) is repressed in the presence of the ribosome, whereas there is little affect on the cleavage of single-stranded substrates mediated by non-coding RNA, suggestings that the enzyme retains capacity to cleave unstructured substrates when associated with the ribosome. We propose that polysomes may act as antennae that enhance the rates of capture of the limited number of degradosomes, so that they become recruited to sites of active translation to act on mRNAs as they become exposed or tagged for degradation.
authors.affiliation: Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK.
authors.forename: Yi-Chun
authors.initials: YC
authors.lastname: Tsai
authors.forename: Dijun
authors.initials: D
authors.lastname: Du
authors.forename: Lilianha
authors.initials: L
authors.lastname: Domínguez-Malfavón
authors.forename: Daniela
authors.initials: D
authors.lastname: Dimastrogiovanni
authors.forename: Jonathan
authors.initials: J
authors.lastname: Cross
authors.forename: Anastasia J
authors.initials: AJ
authors.lastname: Callaghan
authors.forename: Jaime
authors.initials: J
authors.lastname: García-Mena
authors.forename: Ben F
authors.initials: BF
authors.lastname: Luisi
mesh_terms: D001665:Binding Sites; D003432:Cross-Linking Reagents; D053487:DEAD-box RNA Helicases / Q000378:metabolism; D004722:Endoribonucleases / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism*; D004926:Escherichia coli / Q000201:enzymology*; D029968:Escherichia coli Proteins / Q000378:metabolism; D031541:Fluorescence Resonance Energy Transfer; D009097:Multienzyme Complexes / Q000378:metabolism*; D011117:Polyribonucleotide Nucleotidyltransferase / Q000378:metabolism*; D011132:Polyribosomes / Q000378:metabolism*; D054730:Protein Interaction Domains and Motifs; D012313:RNA / Q000378:metabolism; D020365:RNA Helicases / Q000378:metabolism*; D012323:RNA Processing, Post-Transcriptional; D058727:RNA, Small Untranslated / Q000378:metabolism; D012269:Ribosomal Proteins / Q000378:metabolism; D054681:Ribosome Subunits, Large, Bacterial / Q000378:metabolism; D054680:Ribosome Subunits, Small, Bacterial / Q000378:metabolism; D012270:Ribosomes / Q000378:metabolism*
chemical_list: D003432:Cross-Linking Reagents; D029968:Escherichia coli Proteins; D009097:Multienzyme Complexes; D058727:RNA, Small Untranslated; D012269:Ribosomal Proteins; C111244:degradosome; D012313:RNA; D011117:Polyribonucleotide Nucleotidyltransferase; D004722:Endoribonucleases; C022537:ribonuclease E; C502431:RhlB protein, E coli; D053487:DEAD-box RNA Helicases; D020365:RNA Helicases