title: 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 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.
authors.affiliation: Department of Biomedical Sciences, Florida Atlantic University, 777 Glades Road, BC71, Boca Raton, FL 33431, USA. zli@fau.edu
authors.forename: Zhongwei
authors.initials: Z
authors.lastname: Li
authors.forename: Xin
authors.initials: X
authors.lastname: Gong
authors.forename: Vedang H
authors.initials: VH
authors.lastname: Joshi
authors.forename: Muxin
authors.initials: M
authors.lastname: Li
mesh_terms: D001419:Bacteria / Q000201:enzymology* / Q000235:genetics; D001482:Base Composition; D001483:Base Sequence; D019295:Computational Biology; D017124:Conserved Sequence / Q000235:genetics*; D004722:Endoribonucleases / Q000378:metabolism*; D004926:Escherichia coli / Q000201:enzymology / Q000235:genetics; D019143:Evolution, Molecular; D005798:Genes, Bacterial / Q000235:genetics; D016680:Genome, Bacterial; D008969:Molecular Sequence Data; D012322:RNA Precursors / Q000235:genetics / Q000378:metabolism; D012329:RNA, Bacterial / Q000235:genetics / Q000378:metabolism*; D012343:RNA, Transfer / Q000235:genetics* / Q000378:metabolism*; D013379:Substrate Specificity
chemical_list: D012322:RNA Precursors; D012329:RNA, Bacterial; D012343:RNA, Transfer; D004722:Endoribonucleases; C022537:ribonuclease E