Synthetic strategies for optically controlling gene expression may enable the precise spatiotemporal control of genes in any combination of cells that cannot be targeted with specific promoters. We develop an improved genetic code expansion system in C. elegans and use it to create a photo-activatable Cre recombinase. We laser-activate Cre in single neurons within a bilaterally symmetric pair to selectively switch on expression of a loxP controlled optogenetic channel in the targeted neuron. We use the system to dissect, in freely moving animals, the individual contributions of the mechanosensory neurons PLML/PLMR to the C. elegans touch response circuit, revealing distinct and synergistic roles for these neurons. We thus demonstrate how genetic code expansion and optical targeting can be combined to break the symmetry of neuron pairs and dissect behavioural outputs of individual neurons that cannot be genetically targeted.

Two thirds of the 302 neurons in C. elegans form bilaterally symmetric pairs in its physical connectome, and similar gross morphological symmetries are seen in the nervous systems of many other animals. A central question is whether and how this morphological symmetry is broken to produce functional asymmetry. Addressing this question, in all but two cases, has been impossible because no promoters are known that can direct gene expression to a single cell within a symmetric pair. Here we develop an efficient genetic code expansion system in C. elegans and use this system to create a photoactivatable version of Cre recombinase. Using this system, we target single neurons within a bilaterally symmetric pair (PLMR and PLML) with a laser. This turns on Cre and thereby switches on expression of an optogenetic channel in a single cell. We hereby overcome the limitation that these neurons cannot be targeted by genetic means. Our approach enables the generation of large numbers of animals for downstream experiments. By globally illuminating groups of freely moving animals to stimulate the targeted neurons that express an optogenetic channel we dissect the individual contributions of PLMR and PLML to the C. elegans touch response. Our results reveal that the individual neurons make asymmetric contributions to this behaviour, and suggest distinct roles for PLMR and PLML in the habituation to repeated stimulation. Our results demonstrate how genetic code expansion and optical targeting can be combined to break the symmetry of neuron pairs in C. elegans and thereby dissect the contributions of individual neurons to behaviour.

Genetic code expansion in multicellular organisms is currently limited to the use of repurposed amber stop codons. Here, we introduce a system for the use of quadruplet codons to direct incorporation of non-canonical amino acids in vivo in an animal, the nematode worm Caenorhabditis elegans. We develop hybrid pyrrolysyl tRNA variants to incorporate non-canonical amino acids in response to the quadruplet codon UAGA. We demonstrate the efficiency of the quadruplet decoding system by incorporating photocaged amino acids into two proteins widely used as genetic tools. We use photocaged lysine to express photocaged Cre recombinase for the optical control of gene expression and photocaged cysteine to express photo-activatable caspase for light inducible cell ablation. Our approach will facilitate the routine adoption of quadruplet decoding for genetic code expansion in eukaryotic cells and multicellular organisms.