Quantitative single cell mass spectrometry reveals the dynamics of plant natural product biosynthesis

Abstract

Plants produce an extraordinary array of complex natural products (specialized metabolites). Since the biosynthetic genes that are responsible for synthesis of these molecules are often localized to rare or distinct cell types, recently developed single cell RNA-sequencing (scRNA-seq) approaches have tremendous potential to resolve these complex pathways. In contrast, detection, identification, and quantification of metabolites in single cells has remained challenging. Here, we report a robust method for single cell mass spectrometry in which we rigorously characterize and quantify the concentrations of four classes of natural products in individual cells of leaf, root, and petal of the medicinal plant Catharanthus roseus. These single cell mass spectrometry datasets reveal information about the biosynthetic processes that cannot be determined from the corresponding scRNA-seq data alone, providing a highly resolved picture of natural product biosynthesis at cell-specific resolution.