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J. Biol. Chem., Vol. 282, Issue 45, 32902-32911, November 9, 2007

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A Multifunctional RNA Recognition Motif in Poly(A)-specific Ribonuclease with Cap and Poly(A) Binding Properties^*

Per Nilsson, Niklas Henriksson, Anna Niedzwiecka^¶, Nikolaos A. A. Balatsos¹, Kyriakos Kokkoris, Jens Eriksson, and Anders Virtanen²

From the Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden, the Biological Physics Group, Institute of Physics, Polish Academy of Sciences, 02-668, Warsaw, Poland, and the ^¶Department of Biophysics, Institute of Experimental Physics, Warsaw University, 02-089 Warsaw, Poland

Poly(A)-specific ribonuclease (PARN) is an oligomeric, processive and cap-interacting 3' exoribonuclease that efficiently degrades mRNA poly(A) tails. Here we show that the RNA recognition motif (RRM) of PARN harbors both poly(A) and cap binding properties, suggesting that the RRM plays an important role for the two critical and unique properties that are tightly associated with PARN activity, i.e. recognition and dependence on both the cap structure and poly(A) tail during poly(A) hydrolysis. We show that PARN and its RRM have micromolar affinity to the cap structure by using fluorescence spectroscopy and nanomolar affinity for poly(A) by using filter binding assay. We have identified one tryptophan residue within the RRM that is essential for cap binding but not required for poly(A) binding, suggesting that the cap- and poly(A)-binding sites associated with the RRM are both structurally and functionally separate from each other. RRM is one of the most commonly occurring RNA-binding domains identified so far, suggesting that other RRMs may have both cap and RNA binding properties just as the RRM of PARN.

Received for publication, March 20, 2007 , and in revised form, August 21, 2007.

^* This work was supported by Polish Ministry of Science and Higher Education Grant 2 P04A 033 28 and by the Swedish Strategic Research Foundation, the Swedish Research Council, the Wallenberg Consortium North, and Linneus Support from the Swedish Research Council to the Uppsala RNA Research Centre. 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 Fig. S1 and supplemental Table S1.

¹ Present address: Dept. of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, Ploutonos 26, 412 21 Larissa, Greece and Institute of Biomedical, Research and Technology, Papanastasiou 51, 412 22 Larissa, Greece.

² To whom correspondence should be addressed: Dept. of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden. Tel.: 46-18-4714908; Fax: 46-18-530396; E-mail: Anders.Virtanen{at}icm.uu.se.

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