The dtd gene from Bacillus amyloliquefaciens encodes a putative d-tyrosyl-tRNATyr deacylase and is a selectable marker for Bacillus subtilis

Genetically engineered microbes are of high practical importance due to their cost-effective production of valuable metabolites and enzymes, and the search for new selectable markers for genetic manipulation is of particular interest. Here, we revealed that the soil bacterium Bacillus amyloliquefaciens A50 is tolerant to the non-canonical amino acid d-tyrosine (d-Tyr), in contrast to the closely related Bacillus strain B. subtilis 168, which is a widely used “domesticated” laboratory strain. The gene responsible for resistance to d-Tyr was identified. The resistance was associated with the activity of a potential d-tyrosyl-tRNATyr deacylase. Orthologs of this enzyme are capable of hydrolyzing the ester bond and recycling misacetylated d-aminoacyl-tRNA molecules into free tRNAs and d-amino acids. This gene, yrvI (dtd), is applicable as a convenient, small selectable marker for non-antibiotic resistance selection in experiments aimed at genome editing of d-Tyr-sensitive microorganisms.