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Loss of a Universal tRNA Feature

Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061

Received 2 August 2006/ Accepted 5 December 2006

tRNA^His has thus far always been found with one of the most distinctive of tRNA features, an extra 5' nucleotide that is usually a guanylate. tRNA^His genes in a disjoint alphaproteobacterial group comprising the Rhizobiales, Rhodobacterales, Caulobacterales, Parvularculales, and Pelagibacter generally fail to encode this extra guanylate, unlike those of other alphaproteobacteria and bacteria in general. Rather than adding an extra 5' guanylate posttranscriptionally as eukaryotes do, evidence is presented here that two of these species, Sinorhizobium meliloti and Caulobacter crescentus, simply lack any extra nucleotide on tRNA^His. This loss correlates with changes at the 3' end sequence of tRNA^His and at many sites in histidyl-tRNA synthetase that might be expected to affect tRNA^His recognition, in the flipping loop, the insertion domain, the anticodon-binding domain, and the motif 2 loop. The altered tRNA charging system may have affected other tRNA charging systems in these bacteria; for example, a site in tRNA^Glu sequences was found to covary with tRNA^His among alphaproteobacteria.

Published ahead of print on 15 December 2006.