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J. Biol. Chem., Vol. 280, Issue 15, 14572-14578, April 15, 2005

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Exoribonuclease R Interacts with Endoribonuclease E and an RNA Helicase in the Psychrotrophic Bacterium Pseudomonas syringae Lz4W^*

Rajyaguru Ichchhashankar Purusharth, Franziska Klein¶, Shaheen Sulthana||, Stephanie Jäger¶, Medicharla Venkata Jagannadham, Elena Evguenieva-Hackenberg¶, Malay Kumar Ray**, and Gabriele Klug¶

From the ^¶Institut für Mikrobiologie und Molekularbiologie der Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany and the Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India

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 Ni²⁺-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.

Received for publication, December 1, 2004 , and in revised form, February 4, 2005.

^* This work was supported in part by the Volkswagen Foundation. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

Recipient of a senior research fellowship from Council of Scientific and Industrial Research (CSIR), India.

^|| Recipient of a junior research fellowship from CSIR, India.

^** To whom correspondence may be addressed: Centre for Cellular and Molecular Biology, Hyderabad 500007, India. Tel.: 91-40-27192512; Fax: 91-40-27160591; E-mail: malay{at}ccmb.res.in. To whom correspondence may be addressed: Institut für Mikrobiologie und Molekularbiologie, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany. Tel.: 49-641-99-35542; Fax: 49-641-99-35549; E-mail: Gabriele.Klug{at}mikro.bio.uni-giessen.de.

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