John DueberView all speakers
John Dueber received his B.S. in Biochemistry from the University of Delaware in 1999 and Ph.D. at UCSF in 2005 under the mentorship of Prof. Wendell Lim. He then was a QB3 Distinguished Fellow with Profs. Jay Keasling and Adam Arkin until 2010.
Currently he is an Assistant Professor at U.C. Berkeley in the Bioengineering department and a member of the Energy Biosciences Institute. The Dueber lab’s research interests mainly focus on engineering strategies for increasing control and improving performance of multi-enzyme pathways – both signaling and metabolic.
Engineering high-flux metabolic pathways often results in undesired crosstalk with cellular factors of the production host. These could be losses of metabolites to competing pathways, accumulation of toxic intermediates, allosteric regulation, protein degradation, and non-optimal enzyme activity at cytosolic pH or redox state. We are following lessons from eukaryotic evolution to build a synthetic organelle capable of segregating engineered metabolism from the native biochemistry in the cytosol. Towards this, we are repurposing the peroxisome as this organelle is not required for S. cerevisiae viability provided fatty acids are not used as a sole carbon source. This organelle varies dramatically across fungi species with the majority of the cellular volume being occupied by the peroxisome in yeasts such as Hansenula polymorpha and methanol-induced Pichia pastoris, suggesting that higher capacity peroxisomes can be genetically engineered. We have been able to improve the efficiency of a seldom-used targeting sequence that allows us to clear out the majority of the native luminal protein while importing multiple heterologous enzymes in the folded state. Additionally, we have successfully implemented a strategy for redirecting plasma membrane transporters to the peroxisome membrane. We are currently in the process of demonstrating that flux can be controlled through a branched pathway to control which product is synthesized. Ultimately, we endeavor to alter the environment of this organelle (e.g., redox state, pH, etc.). to enable biochemistry that would not be feasible in the cytosol.