Recognition and cooperation between the ATP-dependent RNA helicase RhlB and ribonuclease RNase E.
The Escherichia coli protein RhlB is an ATP-dependent motor that unfolds structured RNA for destruction by partner ribonucleases. In E. coli, and probably many other related gamma-proteobacteria, RhlB associates with the essential endoribonuclease RNase E as part of the multi-enzyme RNA degradosome assembly. The interaction with RNase E boosts RhlB's ATPase activity by an order of magnitude. Here, we examine the origins and implications of this effect. The location of the interaction sites on both RNase E and RhlB are refined and analysed using limited protease digestion, domain cross-linking and homology modelling. These data indicate that RhlB's carboxy-terminal RecA-like domain engages a segment of RNase E that is no greater than 64 residues. The interaction between RhlB and RNase E has two important consequences: first, the interaction itself stimulates the unwinding and ATPase activities of RhlB; second, RhlB gains proximity to two RNA-binding sites on RNase E, with which it cooperates to unwind RNA. Our homology model identifies a pattern of residues in RhlB that may be key for recognition of RNase E and which may communicate the activating effects. Our data also suggest that the association with RNase E may partially repress the RNA-binding activity of RhlB. This repression may in fact permit the interplay of the helicase and adjacent RNA binding segments as part of a process that steers substrates to either processing or destruction, depending on context, within the RNA degradosome assembly.
Chandran
Vidya
V
Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK.
Poljak
Leonora
L
Vanzo
Nathalie F
NF
Leroy
Anne
A
Miguel
Ricardo Núñez
RN
Fernandez-Recio
Juan
J
Parkinson
James
J
Burns
Christopher
C
Carpousis
Agamemnon J
AJ
Luisi
Ben F
BF
D000251:Adenosine Triphosphatases / Q000378:metabolism; D000255:Adenosine Triphosphate / Q000378:metabolism*; D053487:DEAD-box RNA Helicases / Q000378:metabolism*; D004722:Endoribonucleases / Q000378:metabolism*; D004926:Escherichia coli / Q000201:enzymology* / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000378:metabolism*; D009097:Multienzyme Complexes / Q000378:metabolism; D009691:Nucleic Acid Denaturation; D011117:Polyribonucleotide Nucleotidyltransferase / Q000378:metabolism; D012313:RNA / Q000378:metabolism; D020365:RNA Helicases / Q000378:metabolism
D029968:Escherichia coli Proteins; D009097:Multienzyme Complexes; C111244:degradosome; D012313:RNA; D000255:Adenosine Triphosphate; D011117:Polyribonucleotide Nucleotidyltransferase; D004722:Endoribonucleases; C022537:ribonuclease E; D000251:Adenosine Triphosphatases; C502431:RhlB protein, E coli; D053487:DEAD-box RNA Helicases; D020365:RNA Helicases