Our project is organized into three specific aims that form our discovery pipeline. The first aim is focused on developing and applying new bioinformatic tools for identifying gene clusters encoding natural product pathways in plant genomes. The second aim is focused on developing and applying new synthetic biology tools for designing and building reconstructed plant gene clusters that are more amenable to high-throughput screening and functional validation. The third aim is focused on developing and applying a high-throughput chemical characterization and identification platform by combining novel synthetic biology measurement tools with analytical chemistry validation. The tools underlying our discovery pipeline will be made available to the GNPN and broader research community as they are developed, and will have transformative impacts on natural products discovery beyond our center’s efforts. The specific aims include:
Aim 1. Identify gene clusters involved in specialized metabolism in plant genomes
We will build a dedicated bioinformatics platform for rapid prediction of metabolic gene clusters in any sequenced plant genome.
Aim 2. Design and build reconstructed natural product gene clusters for functional expression in platform hosts
We will develop new synthetic biology tools and general paradigms for building and expressing minimal plant gene clusters in yeast or tobacco, with a focus on systems amenable to high-throughput screening.
Aim 3. Characterize novel natural products produced from reconstructed plant gene clusters
We will develop a high-throughput chemical characterization and identification platform by combining novel synthetic biology measurement tools with analytical chemistry validation. We will design metabolite sensors to test natural product gene clusters and develop data-rich mass spectrometry methods for product identification.
Major goals of the project:
(1) Find new natural products, novel enzymes and pathways in plants. Our algorithm will predict gene clusters for specialized metabolism in >70 sequenced plant genomes. We plan to test 100 distinct gene clusters/year from among these candidates in tobacco and yeast platform hosts (not including rebuilt cluster variants). These clusters will be prioritized to maximize chemical diversity. We predict that our proposed throughput will generate ample new natural products and a wealth of insight into plant biosynthetic pathways.
(2) Change the way plant natural products are discovered. The enormity of specialized metabolic genes in sequenced plants supports the fact that plants are incredible sources of novel natural products. Yet these compounds remain underutilized due to our lack of knowledge of biosynthetic pathways. We suggest that the phenomenon of plant gene clusters represents an unprecedented opportunity to redefine and accelerate the discovery process in plants.
(3) Develop a suite of broadly applicable synthetic biology tools that will accelerate natural product discovery regardless of the source organism. We propose a diverse set of new tools that not only will be critical for our discovery pipeline in plants, but will also be applicable to metabolism in any organism.
Our project will develop a new, systematic, high-throughput, broadly applicable discovery pipeline that will drastically change the way natural product pathways are discovered in plants. One of the most exciting aspects of a gene cluster-based discovery approach in plants is that it allows for discovery of both novel metabolites and new metabolic enzymes. Underlying our innovative discovery pipeline is a set of novel bioinformatic, synthetic biology, and measurement/characterization tools that will serve as enabling resources for the broader natural products research community. Our future work will continue to improve the throughput, speed, and success rate of our discovery pipeline, with the continual iteration and integration of new tools enabled by continuing advances in synthetic biology, bioinformatics, genomics, natural product chemistry, and plant specialized metabolism. As a separate future effort, the synthetic biology tools developed through this center and the newly-discovered natural products and associated pathways will feed directly into drug discovery and biomanufacturing strategies.