Trna methyltransferase

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Nucleic Acids Research Advance Access published June 4, 2010
Nucleic Acids Research, 2010, 1–11 doi:10.1093/nar/gkq451

New archaeal methyltransferases forming 1-methyladenosine or 1-methyladenosine and 1-methylguanosine at position 9 of tRNA
Morgane Kempenaers1, Martine Roovers2, Yamina Oudjama2, Karolina L. Tkaczuk3,4, Janusz M. Bujnicki3,5 and Louis Droogmans1,*
´ Laboratoire deMicrobiologie, Universite Libre de Bruxelles (ULB), 2Institut de Recherches Microbiologiques Jean-Marie Wiame, Avenue E. Gryson 1, B-1070 Bruxelles, Belgium, 3International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4 St., PL-02-109 Warsaw, 4Institute of Technical Biochemistry, Technical University of Lodz, B. Stefanowskiego 4/10, PL-90-924 Lodz and 5Institute of Molecular Biology andBiotechnology, Faculty of Biology, Adam Mickiewicz University, PL-61-614 Poznan, Poland
Received February 22, 2010; Revised May 9, 2010; Accepted May 10, 2010

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ABSTRACT Two archaeal tRNA methyltransferases belonging to the SPOUT superfamily and displaying unexpectedactivities are identified. These enzymes are orthologous to the yeast Trm10p methyltransferase, which catalyses the formation of 1-methylguanosine at position 9 of tRNA. In contrast, the Trm10p orthologue from the crenarchaeon Sulfolobus acidocaldarius forms 1-methyladenosine at the same position. Even more surprisingly, the Trm10p orthologue from the euryarchaeon Thermococcus kodakaraensis methylates theN1-atom of either adenosine or guanosine at position 9 in different tRNAs. This is to our knowledge the first example of a tRNA methyltransferase with a broadened nucleoside recognition capability. The evolution of tRNA methyltransferases methylating the N1 atom of a purine residue is discussed. INTRODUCTION Cellular RNAs possess numerous chemically modified nucleosides, but the largest number andthe greatest variety are found in transfer RNA (tRNA). These modifications are introduced by many different enzymes during the complex process of RNA maturation. The functions of these modified nucleosides are not well known, but it seems that modifications in the anticodon region play a direct role in increasing translational efficiency and fidelity, while modifications outside the anticodon regionare typically involved in the maintenance of the structural integrity of tRNA. Among naturally occurring nucleoside modifications, base and ribose methylations are by far the most frequently encountered (1,2). These methylations are catalysed by tRNA methyltransferases (MTases) that use S-adenosyl-L-methionine (AdoMet) as the methyl donor, with a single exception of a recently identified enzyme,which uses a folate as the methyl donor (3). AdoMet-dependent MTases belong to at least seven evolutionarily and structurally unrelated classes/ superfamilies (4–6). Most of the known RNA MTases belong to class I. They possess a fold similar to the Rossmann fold, and are therefore called Rossmann fold MTases (RFM). The structure comprises a seven-stranded b sheet with a central topologicalswitch-point and a characteristic reversed b hairpin at the carboxyl end of the sheet (6"7#5"4"1"2"3"). This b sheet is flanked by a helices to form an aba sandwich (4). RFM enzymes are typically monomeric although di-tri- or tetrameric structures have been reported. Class IV MTases, also named the SPOUT class MTases, a nomenclature coming from the first two members of this class, SpoU and TrmD, act also onRNA, but are structurally different from the class I MTases (7). They possess a five-stranded b sheet core (5"3"4"1"2") flanked by seven a helices. The most characteristic feature of these enzymes is the presence of a deep topological knot in the C-terminal part of the sheet. This knot is responsible for AdoMet binding. All known SPOUT MTases are dimers, with the catalytic site formed at the...
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