Project number 15

Using a highly-evolvable synthetic yeast chromosome to optimize second-generation biofuel production

1. Biological question
Yeast cells are used for production of green chemicals, drugs and biofuels.  In many cases, this requires introduction of new biosynthetic genes and pathways.  For example, in second-generation biofuel production, genes for xylose metabolism derived from bacteria or fungi are inserted in the yeast genome, allowing conversion of cheap substrates like plant waste into bio-ethanol. However, many of these foreign genes do not function optimally in yeast, which reduces the production efficiency.
Here, we will use the latest molecular biology techniques to design and synthesize an entire synthetic chromosome that contains multiple copies of the xylose pathway.  In addition, we will also insert cre-lox sequences that allow controlled rearrangement of the chromosome, as well as sequences that allow attraction of error-prone DNA polymerases.  Together, this results in a controllable elevated mutation rate in the synthetic chromosome, which allows to use experimental evolution to obtain optimized variants of the xylose pathway that yield increased bioethanol production efficiency

2. Goals
1. Design a completely artificial and evolvable yeast chromosome that encodes multiple copies of bacterial and fungal xylose fermentation genes
2. Produce the designed chromosome using the latest synthetic biology
3. Use experimental evolution to optimize the production of ethanol from plant waste
4. Investigate which mutations occurred during experimental evolution and how these result in more optimal function

3.   Incorporation into different VIB labs
Work will be carried out in the VIB groups of Yves Van de Peer (50%, bioinformatics, design of the chromosome and analysis of mutations) and Kevin Verstrepen (50% wet-lab work). 

Keywords
synthetic biology, evolution, green chemistry, biotechnology, biofuel

Supervisors
Kevin J. Verstrepen, VIB Lab of Systems Biology, KU Leuven, Leuven
Yves Van de Peer, VIB Dept. of Plant Systems Biology, UGent, Gent