Context-dependent anticodon recognition by class I lysyl-tRNA synthetases

Lysyl-tRNA synthesis is catalyzed by two unrelated families of aminoacyl-tR NA synthetases. In most bacteria and all eukarya, the known lysyl-tRNA synt hetases (LysRSs) are subclass IIb-type aminoacyl-tRNA synthetases, whereas many archaea and a scattering of bacteria contain an unrelated class I-type LysRS. Examination of the recognition of partially modified tRNA(Lys) anti codon variants by a bacterial (from Borrelia burgdorferi) and an archaeal ( from Methanococcus maripaludis) class I lysyl-tRNA synthetase revealed diff erences in the pattern of anticodon recognition between the two enzymes. U3 5 and U36 were both important for recognition by the B. burgdorferi enzyme, whereas only U36 played a role in recognition by M. maripaludis LysRS. Exa mination of the phylogenetic distribution of class I LysRSs suggested a cor relation between recognition of U35 and U36 and the presence of asparaginyl -tRNA synthetase (AsnRS), which also recognizes U35 and U36 in the anticodo n of tRNA(Asn). However, the class II LysRS of Helicobacter pylori, an orga nism that lacks AsnRS, also recognizes both U35 and U36, indicating that th e presence of AsnRS has solely influenced the phylogenetic distribution of class I LysRSs. These data suggest that competition between unrelated amino acyl-tRNA synthetases for overlapping anticodon sequences is a determinant of the phylogenetic distribution of extant synthetase families. Such patter ns of competition also provide a basis for the two separate horizontal gene transfer events hypothesized in the evolution of the class I lysyl-tRNA sy nthetases.