Bio production
5th of October - Patrick Boyle (Ginkgo Bioworks)
class slides
Recordings
How do you tailor the metabolism of a microbe to make a product? People have been tweaking microbial metabolism since the advent of fermented foods like beer, bread, and cheese. Over the last century, new tools have been transforming this process into an engineering discipline. In this class, we will explore the latest tools and approaches to designing microbial metabolism.
How does engineering in biology differ from engineering in other fields? What design principles can be applied to microbes, which are products of evolution? How do we find good biological parts? How do we know if an engineered microbe is performing as expected? We will review Design, Build, and Test strategies appropriate for engineering the metabolism of microbes.
Background reading
PDFs available if requested
General review of synthetic biology tools and methods for metabolic engineering
Bonus Background reading
Recent publication on the production of opiods in yeast
Engineering yeast to produce the anti-malarial drug artemisinin
Publication on the use of DNA synthesis and bioinformatics to discover novel enzymes
Review article on common pathways that are engineered in microbes to produce plant natural products
Software (not required for assignment)
Assignment
Design a biosynthetic route to produce a small molecule in an organism. See the class slides for tools and examples. Choose a target compound and answer the following questions:
1. What chassis and pathway will you use? 2. How will you measure product formation? 3. What chassis enzymes would you modify?
