(7bi) Synthetic Biology for Next-Generation Plant Natural Product Discovery and Biosynthesis

Plant natural products are chemicals of great pharmaceutical and agrochemical significance due to their structural complexity and chemical diversity. Comprehensive study of their biosynthesis lays the groundwork for studies to not only further our understanding of plant secondary metabolism, but also advance the biomanufacturing of natural product based novel bioactive compounds. Yeast has been proven as a versatile platform host for the production of various complex plant natural products, while increasingly, efforts have been made to leverage yeast as a heterologous host for plant natural product discovery. I am interested in developing synthetic biology platforms to enable the systematic discovery and production of plant natural product compounds, ultimately transforming our ability to understand how nature achieves complex compound biosynthesis. My future research will integrate plant functional genomics, synthetic biology, and metabolic engineering to develop and advance engineering approaches for putative plant biosynthetic pathway prediction and reconstruction, cellular information sensing, and metabolite production optimization. In the short term, I will develop synthetic biology technologies by discovering and engineering novel natural products derived from model plants (e.g., Arabidopsis and tomato) in yeast, which will contribute new synthetic biology toolkits, transcriptomics and metabolomics analysis methods, and reconstructed pathways that will be of great use to the broader research community. In the long term, my research agenda will expand to study and engineer less studied plant systems, thus drastically empowering plant natural product exploration. This research program will advance the development of scalable complex natural product manufacturing platforms, and will foster a variety of interdisciplinary collaborations and applications (e.g., plant biology, bioinformatics, biomass conversion, bioprocessing, and crop protection).

Research Experience:

(1) Discovery and biosynthesis of complex plant natural product in yeast utilizing synthetic biology approaches (Advisor: Professor Christina D. Smolke, Stanford University)

I have dedicated my postdoctoral research to develop cutting-edge synthetic biology technologies for the discovery and biosynthesis of complex compounds. To demonstrate the potential of yeast as a discovery platform, my research has been focused on the development of an integrated plant cluster discovery pipeline spanning multiple research fields (i.e., bioinformatics, plant biology, natural product biochemistry, and synthetic biology). The multidisciplinary approach allows us to predict novel gene clusters directly from plant genome sequences, which led to the discovery of novel tomato natural products. To leverage the versatility of yeast as a production platform, I have developed a 31-gene plant benzylisoquinoline alkaloid (BIA) biosynthetic pathway in yeast, and enhanced the titer of the anticancer BIA, noscapine, from 20 ng/L to 2 mg/L by protein engineering, metabolic engineering, and fermentation optimization.

(2) Development of synthetic biology approaches for efficient yeast engineering (Advisor: Professor Huimin Zhao, UIUC)

My graduate research focused on developing synthetic biology approaches to engineer Saccharomyces cerevisiae for enhanced bioethanol production using protein evolution, pathway reconstruction, and genome editing tools. To facilitate metabolite sensing and screening, I developed the first transcription factor based malonyl-CoA biosensor in yeast that enables genome-wide, high-throughput screening. I also developed a workflow for flux analysis of primary metabolism in yeast, and employed transcriptomics analysis to identify novel gene targets for further strain optimization. By leveraging these engineering and analytical methods at the protein, pathway, and genome levels, I established a highly efficient yeast strain that converts multiple carbon sources to bioethanol and enhanced the overall titer of bioethanol by three-fold, leading to direct implementation of this technology in pilot scale production.

Teaching Interests:

Teaching experience

Serving as a teaching assistant at UIUC, I taught two graduate-level courses, “Mass Transfer” and “Biomolecular Engineering”. During the three years’ TA experience, I have established my teaching principles: 1) inspire interests in advanced scientific research and frontier technologies; 2) enable the students to understand the concepts behind the teaching materials; 3) help students to develop critical thinking skills; 4) provide opportunities for teamwork and leadership; and 5) provide constructive feedbacks and follow-up suggestions.

Mentoring experience

I obtained extensive mentoring experience by mentoring students at both undergraduate and graduate levels. I was the formal laboratorial mentor of an undergraduate student at UIUC. I also served as the mentor of rotation students at Stanford University. My objective during mentoring is to both provide fundamental scientific and laboratorial training and to encourage academic independency. The projects were designed to provide adequate technical training and to ensure the mentees develop the skills they need to be independent researchers. I worked with the mentees to provide feedback throughout the learning process to ensure that they continue to sharpen and hone their research skills. Specifically, I insist on encouraging my students to utilize available resources and supports from experts, and to think broadly and explore their preliminary ideas, thus enabling the establishment of their own scientific vision and research goals.

Teaching philosophy

My goal of teaching and mentoring is to create a learning environment that interfaces critical thinking with solid understanding of state-of-the-art scientific knowledge. I anticipate the students to obtain the awareness of scientific and engineering principles, an interdisciplinary knowledge background, and the capability of maintaining their curiosities and interests, which will serve them regardless of their eventual career paths. To achieve this goal, I would like to motivate the students by showing the applications of the concepts taught in class, thus they are inspired to pursue the knowledge after class. I will define the scope and goals of the courses, pose questions in the beginning of the lectures, and expect the students to find the answers during the lecture. Homework will be designed to clarify the central topics of the course, normally comprise of one or two much more comprehensive problems to ensure students can learn and understand on their own. I would also emphasize written evaluations including projects and exams. In addition, students are always encouraged to discuss with peer, TA and me on any related topics to extend their vision.

Selected Publications:

1. Y. Li*, S. Li* (equal contribution) and C. D. Smolke, “Complete biosynthesis and optimization of the anticancer noscapine in yeast” (in preparation)
2. S. Li*, Y. Li* (equal contribution) and C. D. Smolke, “Microbial synthesis of high-value phytochemicals”, Nature Chemistry (in review)
3. M. Wang, S. Li and H. Zhao, “Design and engineering of intracellular-metabolite-sensing/regulation gene circuits in eukaryotes”, Biotechnology and Bioengineering, 2016, 113, 206-215
4. S. Li, T. Si and H. Zhao, “Development of a synthetic malonyl-CoA sensor in Saccharomyces cerevisiae for intracellular metabolite monitoring and genome-wide screening”, ACS Synthetic Biology, 2015, 4, 1308-1315
5. S. Li*, S. Ha*(equal contribution), H. Kim, J. M. Galazka, J. H. D. Cate, Y. Jin and H. Zhao, “Investigation of the functional role of aldose 1-epimerase in engineered cellobiose utilization”, Journal of Biotechnology, 2013, 10, 1-6
6. S. Li, J. Du, J. Sun, J. M. Galazka, N. L. Glass, J. H. D. Cate, X. Yang and H. Zhao, “Overcoming glucose repression in mixed sugar fermentation by co-expressing a cellobiose transporter and a β-glucosidase in Saccharomyces cerevisiae”, Molecular Biosystems, 2010, 6, 2129-2213
7. J. Du, S. Li and H. Zhao, “Discovery and characterization of novel D-xylose-specific transporters from Neurospora crassa and Pichia stipitis”, Molecular Biosystems, 2010, 6, 2150-2156