Molecular recognition of RhlB and RNase D in the Caulobacter crescentus RNA degradosome.
The endoribonuclease RNase E is a key enzyme in RNA metabolism for many bacterial species. In Escherichia coli, RNase E contributes to the majority of RNA turnover and processing events, and the enzyme has been extensively characterized as the central component of the RNA degradosome assembly. A similar RNA degradosome assembly has been described in the α-proteobacterium Caulobacter crescentus, with the interacting partners of RNase E identified as the Kreb's cycle enzyme aconitase, a DEAD-box RNA helicase RhlB and the exoribonuclease polynucleotide phosphorylase. Here we report that an additional degradosome component is the essential exoribonuclease RNase D, and its recognition site within RNase E is identified. We show that, unlike its E. coli counterpart, C. crescentus RhlB interacts directly with a segment of the N-terminal catalytic domain of RNase E. The crystal structure of a portion of C. crescentus RNase E encompassing the helicase-binding region is reported. This structure reveals that an inserted segment in the S1 domain adopts an α-helical conformation, despite being predicted to be natively unstructured. We discuss the implications of these findings for the organization and mechanisms of the RNA degradosome.
Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK.
Jarrod E
JE
Voss
Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK.
Ben F
BF
Luisi
Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK swh32@cam.ac.uk.
Steven W
SW
Hardwick
D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D001665:Binding Sites; D020134:Catalytic Domain; D016935:Caulobacter crescentus / Q000201:enzymology*; D053487:DEAD-box RNA Helicases / Q000737:chemistry / Q000378:metabolism*; D004722:Endoribonucleases / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D009097:Multienzyme Complexes / Q000737:chemistry* / Q000378:metabolism; D011117:Polyribonucleotide Nucleotidyltransferase / Q000737:chemistry* / Q000378:metabolism; D054730:Protein Interaction Domains and Motifs; D020365:RNA Helicases / Q000737:chemistry* / Q000378:metabolism; D012329:RNA, Bacterial / Q000378:metabolism; D043244:Ribonuclease III / Q000737:chemistry / Q000378:metabolism*
D001426:Bacterial Proteins; D009097:Multienzyme Complexes; D012329:RNA, Bacterial; C111244:degradosome; D011117:Polyribonucleotide Nucleotidyltransferase; D004722:Endoribonucleases; D043244:Ribonuclease III; C022537:ribonuclease E; D053487:DEAD-box RNA Helicases; D020365:RNA Helicases