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Nucleic Acids Research, 2004, Vol. 32, Database issue D104-D108
© 2004 Oxford University Press

The tmRNA website: reductive evolution of tmRNA in plastids and other endosymbionts

Pulcherie Gueneau de Novoa and Kelly P. Williams*,1

Centro de Biofisica y Bioquimica, Instituto Venezolano de Investigaciones Cientificas, Altos de Pipe, MI, Venezuela and 1 Department of Biology, Indiana University, Bloomington, IN 47405, USA

*To whom correspondence should be addressed at 1001 E. Third Street, Bloomington, IN 47405, USA. Tel: +1 812 856 5697; Fax: +1 812 855 6705; Email: kellwill{at}indiana.edu
+AY313266–AY313270, AF169625, AF169626 and AF550350–AF550357

tmRNA combines tRNA- and mRNA-like properties and ameliorates problems arising from stalled ribosomes. Research on the mechanism, structure and biology of tmRNA is served by the tmRNA website (http://www.indiana.edu/~tmrna), a collection of sequences, alignments, secondary structures and other information. Because many of these sequences are not in GenBank, a BLAST server has been added; another new feature is an abbreviated alignment for the tRNA-like domain only. Many tmRNA sequences from plastids have been added, five found in public sequence data and another 10 generated by direct sequencing; detection in early-branching members of the green plastid lineage brings coverage to all three primary plastid lineages. The new sequences include the shortest known tmRNA sequence. While bacterial tmRNAs usually have a lone pseudoknot upstream of the mRNA segment and a string of three or four pseudoknots downstream, plastid tmRNAs collectively show loss of pseudoknots at both postions. The pseudoknot-string region is also too short to contain the usual pseudoknot number in another new entry, the tmRNA sequence from a bacterial endosymbiont of insect cells, Tremblaya princeps. Pseudoknots may optimize tmRNA function in free-living bacteria, yet become dispensible when the endosymbiotic lifestyle relaxes selective pressure for fast growth.


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