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RNA. 2005 May;11(5):567-77. Epub 2005 Apr 5.

Co-evolution of tRNA 3' trailer sequences with 3' processing enzymes in bacteria.

Author information

  • 1Department of Biomedical Sciences, Florida Atlantic University, 777 Glades Road, BC71, Boca Raton, FL 33431, USA. zli@fau.edu

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 alpha-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.

PMID:
15811923
[PubMed - indexed for MEDLINE]
PMCID:
PMC1370745
Free PMC Article

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