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 ␣-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.

The RNase E/G-type endoribonuclease of higher plants is located in the chloroplast and cleaves RNA similarly to the E. coli enzyme

“…Homologs of RNase E exist in most bacteria, some archaea, as well as in some algae and higher plants ( Lee and Cohen 2003;Li et al 2005;Bollenbach et al 2007;Horie et al 2007). Several Gram-negative bacteria contain two proteins of this family, for example, RNase E and RNase G in E. coli, while others such as cyanobacteria contain only one (Kaberdin et al 1998;Lee and Cohen 2003).…”

Exoribonuclease R in Mycoplasma genitalium can carry out both RNA processing and degradative functions and is sensitive to RNA ribose methylation

“…RNase R is more widespread in eubacteria than is RNase II (Zuo and Deutscher 2001;Li et al 2005). Interestingly, only one putative exoribonuclease has been identified in Mycoplasma genitalium based on extensive sequence analysis.…”

“…All conserved regions of EcR are present in MgR. Based on exhaustive data mining, including PHI-BLAST, multiple sequence alignment and motif identification, no other exoribonuclease is identifiable in Mycoplasma (Zuo and Deutscher 2001;Li et al 2005). Although it is possible that other exoribonuclease(s) may exist without significant sequence similarity to previously characterized nucleases, it is clear that homologs of most exoribonucleases are not encoded in the small genomes of Mycoplasma, and that RNase R likely functions in multiple aspects of RNA metabolism in this organism.…”

Novel One-step Mechanism for tRNA 3′-End Maturation by the Exoribonuclease RNase R of Mycoplasma genitalium

“…It is unknown how this organism carries out RNA metabolism, a process usually requiring the action of numerous RNases in other bacteria. Surprisingly, none of the RNases listed above for tRNA 3Ј-maturation was identified in M. genitalium and related species (2,9,10). Recently, we demonstrated that purified RNase R of M. genitalium exhibits 3Ј 3 5Ј exoribonuclease activity that is somewhat different from the activities of its E. coli homologues RNases R and II (11).…”

“…The 5Ј-leader sequences in tRNA precursors are removed ubiquitously by RNase P. At the 3Ј-end, the extra sequences are removed by a variety of different mechanisms. In bacteria, tRNA 3Ј-processing may be accomplished by the actions of endo-or exoribonucleases or both (1,2). In Escherichia coli, the primary tRNA transcript undergoes an initial cleavage by RNase E in its 3Ј-trailer downstream of the CCA sequence (3,4), followed by stepwise trimming reactions of the extra residues by multiple exoribonucleases, including RNases T, PH, D, II, and BN and polynucleotide phosphorylase (5,6).…”