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J. Biol. Chem., Vol. 282, Issue 22, 16267-16277, June 1, 2007

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Exoribonuclease R in Pseudomonas syringae Is Essential for Growth at Low Temperature and Plays a Novel Role in the 3' End Processing of 16 and 5 S Ribosomal RNA^*

From the Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India

The (3' 5') exoribonuclease RNase R interacts with the endoribonuclease RNase E in the degradosome of the cold-adapted bacterium Pseudomonas syringae Lz4W. We now present evidence that the RNase R is essential for growth of the organism at low temperature (4 °C). Mutants of P. syringae with inactivated rnr gene (encoding RNase R) are cold-sensitive and die upon incubation at 4 °C, a phenotype that can be complemented by expressing RNase R in trans. Overexpressing polyribonucleotide phosphorylase in the rnr mutant does not rescue the cold sensitivity. This is different from the situation in Escherichia coli, where rnr mutants show normal growth, but pnp (encoding polyribonucleotide phosphorylase) and rnr double mutants are nonviable. Interestingly, RNase R is not cold-inducible in P. syringae. Remarkably, however, rnr mutants of P. syringae at low temperature (4 °C) accumulate 16 and 5 S ribosomal RNA (rRNA) that contain untrimmed extra ribonucleotide residues at the 3' ends. This suggests a novel role for RNase R in the rRNA 3' end processing. Unprocessed 16 S rRNA accumulates in the polysome population, which correlates with the inefficient protein synthesis ability of mutant. An additional role of RNase R in the turnover of transfer-messenger RNA was identified from our observation that the rnr mutant accumulates transfer-messenger RNA fragments in the bacterium at 4 °C. Taken together our results establish that the processive RNase R is crucial for RNA metabolism at low temperature in the cold-adapted Antarctic P. syringae.

Received for publication, June 12, 2006 , and in revised form, April 2, 2007.

^* This work was supported by the Volkswagen Foundation, by the Council of Scientific and Industrial Research (to M. K. R.), by a Council of Scientific and Industrial Research senior research fellowship (to R. I. P.), and by a Department of Biotechnology, Government of India postdoctoral fellowship (to M. B.). 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.

The on-line version of this article (available at http://www.jbc.org) contains supplemental Table S1 and supplemental Figs. S1–S3.

¹ To whom correspondence should be addressed: Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India. Tel.: 91-4027192512; Fax: 91-4017160591; E-mail: malay{at}ccmb.res.in.

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