Genetic code expansion enables plant-directed control of bacterial activity

Microorganisms have the potential to deliver growth-promoting benefits to plants and crops; however, to be useful in a field setting, their gene expression should be programmable and restricted to specific plant hosts and conditions. Here, using O-methyl-L-tyrosine (OMY) as a model compound, we establish noncanonical amino acids (ncAAs) as a tool for plant-based control of associated microbial activity. We use genetic code expansion to engineer OMY-dependent control of protein synthesis in the soil bacterium Bacillus subtilis. Engineered B. subtilis strains express an orthogonal aminoacyl-tRNA synthetase and tRNA pair that, upon provision of OMY, results in suppression of in-frame amber stop codons in target transcripts. We engineer Arabidopsis, tomato and poplar to biosynthesize OMY, showing that plant-derived OMY can stimulate gene expression in both model and wild soil bacteria. This demonstrates that inducible and tissue-specific expression of a single biosynthetic enzyme by the plant enables on-demand control over microbial activity, establishing ncAAs as a tool for programming plant-microorganism partnerships.