Mechanisms of the tRNA wobble cytidine modification essential for AUA codon decoding in prokaryotes

Bacteria and archaea have 2-lysylcytidine (L or lysidine) and 2-agmatinylcytidine (agm (agm²C or agmatidine), respectively, at the first (wobble) position of the anticodon of the AUA codon-specific tRNA^Ile. These lysine- or agmatine-conjugated cytidine derivatives are crucial for the precise decoding of the genetic code. L is synthesized by tRNA tRNA^elI-lysidine synthetase (TilS), which uses L-lysine and ATP as substrates. Agm²C formation is catalyzed by tRNA^elI-agm²C synthetase (TiaS), which uses agmatine and ATP for the reaction. Despite the fact that TilS and TiaS synthesize structurally similar cytidine derivatives, these enzymes belong to nonrelated protein families. Therefore, these enzymes modify the wobble cytidine by distinct catalytic mechanisms, in which TilS activates the C2 carbon of the wobble cytidine by adenylation, while TiaS activates it by phosphorylation. In contrast, TilS and TiaS share similar tRNA recognition mechanisms, in which the enzymes recognize the tRNA acceptor stem to discriminate tRNA^Ile and tRNA^Met.