PhytoMetaSyn Project Summary

            Plants can be considered the world's best chemists in terms of their ability to produce an immense diversity of molecules based on a myriad of skeletal structures and functional group combinations. The unparalleled biosynthetic capacity of plants has long been exploited through the use of many plants as traditional medicines and later the medical and commercial application of pure plant metabolites including pharmaceuticals (e.g. codeine, vinblastine, taxol), flavours (humulone, nootkatone, carvone), fragrances (jasmine, rose oil), pigments (carotenoids, anthocyanins, betalains), insecticides (pyrethrins), and other fine chemicals. Terpenoids, alkaloids and polyketides are three major categories of plant natural products and are represented by tens of thousands of known compounds, with many more still undiscovered. The metabolic diversity of these compounds reflects the fundamental mechanisms that drive the evolution of plant natural products. Plants interact with their environment mainly through chemical means and metabolites play diverse physiological roles from pathogen defence to pollinator attraction. An important feature of plant natural product metabolism is the ability of enzymes to acquire novel functions through random mutation. The number of enzymes involved in creating metabolic diversity in plants is staggering. Approximately one-fifth of the genes in the model plant Arabidopsis thaliana are thought to participate in the biosynthesis of secondary metabolites, or compounds that are not considered necessary for normal plant growth and development. Remarkably, this catalytic diversity has remained largely untapped for the industrial production of high-value bioproducts. Large-scale and ultra-high throughput DNA sequencing provides a means to accelerate the discovery of unique enzymes for the biosynthesis of complex plant metabolites, enabling their production in microbial hosts under controlled conditions.  For example, the recent production of the antimalarial drug artemisinin, a plant natural product, using engineered yeast cells highlights the innovative potential that arises from interdisciplinary and applied research in plant genomics, microbial engineering and synthetic biology.

            Synthetic biology is an emerging field, which we define for the purpose of this application, as the reduction of biological systems to their basic functional components (a "parts catalogue"), and the engineering of new biological processes for specific industrial applications through the assembly of individual parts in desirable combinations. In the context of combinatorial biochemistry, which involves the mixing and matching of biosynthetic genes between organisms to create combinations not necessarily found in nature, we propose to establish (1) a novel functional genomics pipeline and (2) a process engineering technology based on the massive identification, characterization and cataloguing of novel plant enzymes (the “parts”) coupled with their deployment in yeast strains optimized to support high flux to the metabolites required by the reconstituted plant biosynthetic pathways. This integrated and novel combination of genomics, metabolomics and synthetic biology will provide cutting-edge Canadian leadership in the plant metabolism and synthetic biology fields, and accelerate the industrial-scale development of enzymes and microorganisms for a wide variety of applications in the bioproducts sector. We will use massively parallel DNA sequencing to probe the genes expressed in 75 plants producing bioactive natural products. Each plant DNA sequence dataset will be supported with targeted metabolomics based on mass spectrometric analysis. The development of robust bioinformatics tools will promote the rational selection of unknown genes, which will be expressed in engineered microbial strains. The key deliverables of this project are: (1) A public resource of genomic and metabolomic information for 75 plants producing bioactive natural products; (2) engineered yeast strains that produce high-value plant natural products; (3) the extensive cataloguing of new enzymes for use as biocatalysts in plug-and-play synthetic biology applications; (4) the invention of efficient functional genomics approaches for elucidating novel metabolic pathways and identifying unknown biosynthetic genes from non-model plants; and (5) a thorough analysis of related regulatory, ethical, and economic issues, including consultations with the public, which will help to ensure that technology development is not just scientifically sound, but is also socially robust.