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Genetics, Vol. 179, 113-123, May 2008, Copyright © 2008
doi:10.1534/genetics.107.085688
On the Evolution and Expression of Chlamydomonas reinhardtii Nucleus-Encoded Transfer RNA Genes
Valérie Cognat*,
Jean-Marc Deragon
,
Elizaveta Vinogradova*,1,
Thalia Salinas*,
Claire Remacle
and
Laurence Maréchal-Drouard*,2
* Institut de Biologie Moléculaire des Plantes, Unité Propre de Recherche 2357, Conventionnée avec l'Université Louis Pasteur (Strasbourg 1), Centre National de la Recherche Scientifique, 67084 Strasbourg Cedex, France, Université de Perpignan Via Domitia, CNRS UMR5096 Laboratoire Génome et Développement des Plantes, 66860 Perpignan Cedex, France and Génétique des Microorganismes, Département des Sciences de la Vie, Institut de Botanique, Université de Liège, B-4000 Liège, Belgium
2 Corresponding author: Institut de Biologie Moléculaire des Plantes du CNRS, UPR2357 du CNRS, 12 rue du Général Zimmer, 67084 Strasbourg Cedex, France.
E-mail: laurence.drouard{at}ibmp-ulp.u-strasbg.fr
In Chlamydomonas reinhardtii, 259 tRNA genes were identified and classified into 49 tRNA isoaccepting families. By constructing phylogenetic trees, we determined the evolutionary history for each tRNA gene family. The majority of the tRNA sequences are more closely related to their plant counterparts than to animals ones. Northern experiments also permitted us to show that at least one member of each tRNA isoacceptor family is transcribed and correctly processed in vivo. A short stretch of T residues known to be a signal for termination of polymerase III transcription was found downstream of most tRNA genes. It allowed us to propose that the vast majority of the tRNA genes are expressed and to confirm that numerous tRNA genes separated by short spacers are indeed cotranscribed. Interestingly, in silico analyses and hybridization experiments show that the cellular tRNA abundance is correlated with the number of tRNA genes and is adjusted to the codon usage to optimize translation efficiency. Finally, we studied the origin of SINEs, short interspersed elements related to tRNAs, whose presence in Chlamydomonas is exceptional. Phylogenetic analysis strongly suggests that tRNAAsp-related SINEs originate from a prokaryotic-type tRNA either horizontally transferred from a bacterium or originally present in mitochondria or chloroplasts.
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