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Nucleic Acids Research, 2001, Vol. 29, No. 7 1602-1607
© 2001 Oxford University Press

Phylogenetic analysis of tmRNA genes within a bacterial subgroup reveals a specific structural signature

Brice Felden1,2,*, Christian Massire3, Eric Westhof3, John F. Atkins1 and Raymond F. Gesteland1

1Department of Human Genetics, University of Utah, 15N 2030E Room 6250, Salt Lake City, UT 84112-5330, USA, 2Laboratoire de Biochimie Pharmaceutique, Faculté de Pharmacie, Université de Rennes I, UPRES Jeune Equipe 2311, IFR 97, 2 avenue du Prof. Léon Bernard, F-35043 Rennes, France and 3Unité Propre de Recherche 9002 du CNRS, Institut de Biologie Moléculaire et Cellulaire, 15 rue Descartes, F-67084 Strasbourg, France

Bacterial tmRNA mediates a trans-translation reaction, which permits the recycling of stalled ribosomes and probably also contributes to the regulated expression of a subset of genes. Its action results in the addition of a small number of C-terminal amino acids to protein whose synthesis had stalled and these constitute a proteolytic recognition tag for the degradation of these incompletely synthesized proteins. Previous work has identified pseudoknots and stem–loops that are widely conserved in divergent bacteria. In the present work an alignment of tmRNA gene sequences within 13 ß-proteobacteria reveals an additional sub-structure specific for this bacterial group. This sub-structure is in pseudoknot Pk2, and consists of one to two additional stem–loop(s) capped by stable GNRA tetraloop(s). Three-dimensional models of tmRNA pseudoknot 2 (Pk2) containing various topological versions of the additional sub-structure suggest that the sub-structures likely point away from the core of the RNA, containing both the tRNA and the mRNA domains. A putative tertiary interaction has also been identified.

* To whom correspondence should be addressed at: Laboratorie de Biochimie Moléculaire et Structurale, Faculté de Pharmacie, Université de Rennes, 2 Avenue du Prof. Léon Bernard, 35043 Rennes Cedex, France. Tel: +33 2 99 33 68 95; Fax: +33 2 99 33 62 08; Email: bfelden{at}univ-rennes1.fr Present address: Christian Massire, Ibis Therapeutics division of Isis Pharmaceuticals, 2292 Faraday Avenue, Carlsbad, CA 92008, USA


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