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Nucleic Acids Research, 2002, Vol. 30, No. 9 2018-2024
© 2002 Oxford University Press

Two-piece tmRNA in cyanobacteria and its structural analysis

Cyril Gaudin, Xiong Zhou1, Kelly P. Williams1 and Brice Felden*

Laboratoire de Biochimie Pharmaceutique, Faculté de Pharmacie, Université de Rennes I, UPRES Jeune Equipe 2311, IFR 97, 2 avenue du Pr Léon Bernard, 35043 Rennes cedex, France and 1Department of Biology, Indiana University, 1001 East Third Street, Bloomington, IN 47405, USA

tmRNA acts to rescue stalled bacterial ribosomes while encoding a peptide tag added trans-translationally to the nascent peptide, targeting it for proteolysis. The permuted gene structure found in a group of cyanobacteria is shown to produce a two-piece mature tmRNA, as had been observed previously for the independently permuted gene of {alpha}-proteobacteria. The pieces have been mapped onto the gene sequence and aligned for the permuted cyanobacterial tmRNA sequences, including four novel sequences. Structural probing and base pair co-variations support a secondary structure model in which two pairings in the tRNA-like domain hold the two pieces together, and the coding piece bearing the tag reading frame additionally contains a single transient pseudoknot and three other stem–loops. This represents a dramatic reduction in pseudoknot number from the five present in one-piece cyanobacterial tmRNA.

* To whom correspondence should be addressed. Tel: +33 2 23 23 48 51; Fax: +33 2 23 23 44 56; Email: brice.felden{at}univ-rennes1.fr + AY082654 and AY082655


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