Parallel evolution of plant alkaloid biosynthesis from bacterial-like decarboxylases

The basic amino acids lysine and ornithine are precursors to bioactive alkaloids including nicotine, hyoscyamine, and securinine. The amino acids can be incorporated into alkaloids in a symmetric or nonsymmetric manner. Here, we report the discovery of enzymes responsible for the nonsymmetric pathway. We used transcriptomics and enzyme characterisation, including mutagenesis and isotope labelling, to identify the enzyme catalysing the nonsymmetric lysine incorporation step of securinine biosynthesis in Flueggea suffruticosa. We then used phylogenetics to expand the investigation across plants and identified orthologs from Nicotiana tabacum and Artemisia annua. We report the ornithine/lysine/arginine decarboxy-oxidases (OLADOs), pyridoxal phosphate (PLP)-dependent enzymes responsible for the nonsymmetric pathway, catalysing the single-step decarboxylative oxidative deamination of lysine, ornithine, or arginine. These enzymes are part of the group III ornithine/lysine/arginine decarboxylase-like family (OLADLs), previously associated with prokaryotes. We show that OLADLs are widespread in plants and that OLADOs have repeatedly emerged from OLADLs through parallel evolution. This investigation introduces a new class of eukaryotic decarboxylases and describes enzymes involved in multiple alkaloid biosynthesis pathways. It furthermore demonstrates how the principle of parallel evolution at a genomic and enzymatic level can be leveraged for gene discovery across multiple lineages.