Recoding of the selenocysteine UGA codon by cysteine in the presence of a non-canonical tRNACys and elongation factor SelB

In many organisms, the UGA stop codon is recoded to insert selenocysteine (Sec) into proteins. Sec incorporation in bacteria is directed by an mRNA element, known as the Sec-insertion sequence (SECIS), located downstream of the Sec codon. Unlike other aminoacyl-tRNAs, Sec-tRNA(Sec) is delivered to the ribosome by a dedicated elongation factor, SelB. We recently identified a series of tRNA(Sec)-like tRNA genes distributed across Bacteria that also encode a canonical tRNA(Sec). These tRNAs contain sequence elements generally recognized by cysteinyl-tRNA synthetase (CysRS). While some of these tRNAs contain a UCA Sec anticodon, most have a GCA Cys anticodon. tRNA(Sec) with GCA anticodons are known to recode UGA codons. Here we investigate the clostridial Desulfotomaculum nigrificans tRNA(Sec)-like tRNA(Cys), and show that this tRNA is acylated by CysRS, recognized by SelB, and capable of UGA recoding with Cys in Escherichia coli. We named this non-canonical group of tRNA(Cys) as tRNA(ReC)' (Recoding with Cys). We performed a comprehensive survey of tRNA(ReC) genes to establish their phylogenetic distribution, and found that, in a particular lineage of clostridial Pelotomaculum, the Cys identity elements of tRNA(ReC) had mutated. This novel tRNA, which contains a UCA anticodon, is capable of Sec incorporation in E. coli, albeit with lower efficiency relative to Pelotomaculum tRNA(Sec). We renamed this unusual tRNA(Sec) derived from tRNA(ReC) as tRNA(ReU)' (Recoding with Sec). Together, our results suggest that tRNA(ReC) and tRNA(ReU) may serve as safeguards in the production of selenoproteins and - to our knowledge - they provide the first example of programmed codon-anticodon mispairing in bacteria.