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J. Biol. Chem., Vol. 279, Issue 47, 48780-48786, November 19, 2004

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Differential Modes of Transfer RNA^Ser Recognition in Methanosarcina barkeri^*

Dragana Korencic, Carla Polycarpo, Ivana Weygand-Durasevic¶, and Dieter Söll||**

From the Molecular Biophysics and Biochemistry and ^||Chemistry, Yale University, New Haven, Connecticut 06520–8114, the Department of Chemistry, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia, and ^¶Rudjer Boskovic Institute, 10000 Zagreb, Croatia

Two dissimilar seryl-transfer RNA (tRNA) synthetases (SerRSs) exist in Methanosarcina barkeri, one of bacterial type and the other resembling SerRSs present only in some methanogenic archaea. To investigate the requirements of these enzymes for tRNA^Ser recognition, serylation of variant transcripts of M. barkeri tRNA^Ser was kinetically analyzed in vitro with pure enzyme preparations. Characteristically for the serine system, the length of the variable arm was shown to be crucial for both enzymes, as was the identity of the discriminator base (G73). Moreover, a novel determinant for the specific tRNA^Ser recognition was identified as the anticodon stem base pair G30:C40; its contribution to the efficiency of serylation was remarkable for both SerRSs. However, despite these similarities, the two SerRSs do not possess a uniform mode of tRNA^Ser recognition, and additional determinants are necessary for serylation specificity by the methanogenic enzyme. In particular, the methanogenic SerRS relies on G1:C72 identity and on the number of unpaired nucleotides at the base of the variable stem for tRNA^Ser recognition, unlike its bacterial type counterpart. We propose that such a distinction between the two enzymes in tRNA^Ser identity determinants reflects their evolutionary pathways, hence attesting to their diversity.

Received for publication, August 2, 2004 , and in revised form, September 13, 2004.

^* This work was supported by grants from NIGMS, National Institutes of Health, the U.S. Department of Energy, and the National Aeronautics and Space Administration. 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.

^** To whom correspondence should be addressed: Dept. of Molecular Biophysics and Biochemistry, Yale University, P. O. Box 208114, 266 Whitney Ave., New Haven, CT 06520–8114. Tel.: 203-432-6200; Fax: 203-432-6202; E-mail: soll{at}trna.chem.yale.edu.

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