Substrate recognition by class I lysyl-tRNA synthetases:: A molecular basis for gene displacement

Lysyl-tRNA synthetases (LysRSs) are unique amongst the aminoacyl-tRNA synthetases in being composed of unrelated class I and class II enzymes, To allow direct comparison between the two types of LysRS, substrate recognition by class I LysRSs was examined. Genes encoding both an archaeal and a bacterial class I enzyme were able to rescue an Escherichia coli strain deficient in LysRS, indicating their ability to functionally substitute for a class LI LysRS in vivo, In vitro characterization showed lysine activation and recognition to be tRNA-dependent, an attribute of several class I, but not class II, aminoacyl-tRNA synthetases, Examination of tRNA recognition showed that class I LysRSs recognize the same elements in tRNA(Lys) as their class II counterparts, namely the discriminator base (N73) and the anticodon, This sequence-specific recognition of the same nucleotides in tRNA(Lys) by the two unrelated types of enzyme suggests that tRNA(Lys) predates at least one of the LysRSs in the evolution of the translational apparatus, The only observed variation in recognition was that the G2.U71 wobble pair of spirochete tRNA(Lys) acts as antideterminant for class II LysRS but does not alter class I enzyme recognition. This difference in tRNA recognition strongly favors the use of a class I-type enzyme to aminoacylate particular tRNA(Lys) species and provides a molecular basis for the observed displacement of class II by class I LysRSs in certain bacteria.