Co-evolution of tRNA 3′ trailer sequences with 3′ processing enzymes in bacteria
Abstract
Maturation of the tRNA 3′ terminus is a complicated process in bacteria. Usually, it is initiated by an endonucleolytic cleavage carried out by RNase E and Z in different bacteria. In Escherichia coli, RNase E cleaves AU-rich sequences downstream of tRNA, producing processing intermediates with a few extra residues at the 3′ end; these are then removed by exoribonuclease trimming to generate the mature 3′ end. Here we show that essentially all E. coli tRNA precursors contain a potential RNase E cleavage site, the AU-rich sequence element (AUE), in the 3′ trailer. This suggests that RNase E cleavage and exonucleolytic trimming is a general pathway for tRNA maturation in this organism. Remarkably, the AUE immediately downstream of each tRNA is selectively conserved in bacteria having RNase E and tRNA-specific exoribonucleases, suggesting that this pathway for tRNA processing is also commonly used in these bacteria. Two types of RNase E-like proteins are identified in actinobacteria and the α-subdivision of proteobacteria. The tRNA 3′ proximal AUE is conserved in bacteria with only one type of E-like protein. Selective conservation of the AUE is usually not observed in bacteria without RNase E. These results demonstrate a novel example of co-evolution of RNA sequences with processing activities.
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Footnotes
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↵3 Present addresses: Bioinformatics Program, Georgia Institute of Technology, Atlanta, GA 30332, USA;
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↵4 Methacton High School, Norristown, PA 19403, USA.
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Article published online ahead of print. Article and publication date are at http://www.rnajournal.org/cgi/doi/10.1261/rna.7287505.
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- Accepted January 23, 2005.
- Received December 23, 2004.
- Copyright 2005 by RNA Society