Exoribonuclease R interacts with endoribonuclease E and an RNA helicase in the psychrotrophic bacterium Pseudomonas syringae Lz4W

J Biol Chem. 2005 Apr 15;280(15):14572-8. doi: 10.1074/jbc.M413507200. Epub 2005 Feb 10.

Abstract

Endoribonuclease E, a key enzyme involved in RNA decay and processing in bacteria, organizes a protein complex called degradosome. In Escherichia coli, Rhodobacter capsulatus, and Streptomyces coelicolor, RNase E interacts with the phosphate-dependent exoribonuclease polynucleotide phosphorylase, DEAD-box helicase(s), and additional factors in an RNA-degrading complex. To characterize the degradosome of the psychrotrophic bacterium Pseudomonas syringae Lz4W, RNase E was enriched by cation exchange chromatography and fractionation in a glycerol density gradient. Most surprisingly, the hydrolytic exoribonuclease RNase R was found to co-purify with RNase E. Co-immunoprecipitation and Ni(2+)-affinity pull-down experiments confirmed the specific interaction between RNase R and RNase E. Additionally, the DEAD-box helicase RhlE was identified as part of this protein complex. Fractions comprising the three proteins showed RNase E and RNase R activity and efficiently degraded a synthetic stem-loop containing RNA in the presence of ATP. The unexpected association of RNase R with RNase E and RhlE in an RNA-degrading complex indicates that the cold-adapted P. syringae has a degradosome of novel structure. The identification of RNase R instead of polynucleotide phosphorylase in this complex underlines the importance of the interaction between endo- and exoribonucleases for the bacterial RNA metabolism. The physical association of RNase E with an exoribonuclease and an RNA helicase apparently is a common theme in the composition of bacterial RNA-degrading complexes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Triphosphate / chemistry
  • Blotting, Western
  • Centrifugation, Density Gradient
  • Chromatography, Ion Exchange
  • Electrophoresis, Polyacrylamide Gel
  • Endoribonucleases / chemistry
  • Endoribonucleases / metabolism*
  • Endoribonucleases / physiology*
  • Exoribonucleases / metabolism*
  • Glycerol / pharmacology
  • Immunoprecipitation
  • Protein Binding
  • Pseudomonas syringae / enzymology*
  • RNA / chemistry
  • RNA / metabolism
  • RNA Helicases / metabolism*
  • Recombinant Proteins / chemistry
  • Ribonucleases / chemistry
  • Time Factors
  • Transcription, Genetic

Substances

  • Recombinant Proteins
  • RNA
  • Adenosine Triphosphate
  • Endoribonucleases
  • Exoribonucleases
  • Ribonucleases
  • ribonuclease R
  • ribonuclease E
  • RNA Helicases
  • Glycerol