Connecting genes to metabolites by a systems biology approach

Abstract

Plants are of pivotal importance to sustain life on Earth because they supply oxygen, food, energy, and many valuable metabolites. All plant constituents, including secondary metabolites, some of which are used as flavors, fragrances, colorants, or pharmaceuticals, are ultimately derived from primary products of photosynthesis through multiple enzymatic steps encoded by the genome of each plant. However, our knowledge of how both primary and secondary metabolites are synthesized and which genes are involved is far from complete. A better understanding of metabolite synthesis and the regulation thereof will be increasingly important for improving the sustainability and efficiency of useful plant production. Recently, the availability of entire genome sequences of Arabidopsis thaliana and rice and the development of functional genomics tools have allowed the elucidation of metabolite syntheses by a systems biology approach (1–3). The mining and exploitation of the data obtained from genomics and the related research areas of genomewide transcriptomics, proteomics, and metabolomics will bring us into a new era of understanding of biological systems (Fig. 1). Fig. 1. A schematic representation of a plant metabolomics platform using a systems biology approach. The platform is divided into multiple analytical approaches aimed at increased coverage of the metabolome. Data processing methods enable us to track both known and unknown metabolites, which can then be integrated from across multiple platforms. Multivariate analyses are used to find trends in data and select most relevant unknown compounds for further identification. Sulfur is one of the essential nutrients for all plants, required to synthesize the key amino acids cysteine and methionine, which in turn are needed to produce functional proteins and many secondary metabolites (4). Approximately 90% of the reduced S is bound through these amino …