Rationale for the evolutionary retention of two unrelated LYSYL-tRNA synthetases

by Ataide, Sandro Fernandes

Lysine insertion during coded protein synthesis requires lysyl-tRNALys, which is synthesized by lysyl-tRNA synthetase (LysRS). Two unrelated forms of LysRS are known: LysRS2, which is found in eukaryotes, most bacteria and a few archaea, and LysRS1, which is found in most archaea and a few bacteria. A detailed comparison of the amino acid recognition strategies of LysRS1 (Borrelia burgdorferi) and LysRS2 (Escherichia coli) was undertaken by studying the effects of lysine analogues on the aminoacylation reaction in vitro and in vivo. Also, based on comparisons of crystal structures and discrimination of lysine analogues by both LysRSs, the roles of the key residues in the active site of LysRS2 (lysS encoded) from E. coli were determined in vitro and in vivo. The differences in resistance to naturally occurring non-cognate amino acids suggest the distribution of LysRS1 and LysRS2 contributes to quality control during protein synthesis.

LysRS1 and LysRS2 are not normally found together within one organism. In the pathogen Bacillus cereus both forms of LysRS are encoded; to investigate what role these two LysRSs might play in B. cereus, their RNA substrate specificities were investigated. It was found that in B. cereus the two different LysRSs together aminoacylate a small RNA of unknown function named tRNAOther. Aminoacylation of tRNAOther was found to be confined to stationary phase, suggesting a role for this non-canonical tRNA in growth phase-specific protein synthesis. Analysis of the non-canonical Watson-Crick base pairs and a bulge in the predicted secondary structure of tRNAOther indicate the importance of these identity elements in recognition by the LysRS1:LysRS2 complex. The role of tRNAOther in B. cereus was also investigated by the construction of a deletion strain, indicating that tRNAOther is not an essential gene. The results implicate tRNAOther in multiple regulatory functions that remain, as yet, uncharacterized.