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Directed Evolution for Biofuels

by Devin Trudeau

A popular topic in the news these days is America’s fossil fuel dependence, and ways we can get around it. Caltech is on the forefront of alternative energy research, with groups investigating solar power, wind power, and biofuels. In particular, next-generation biofuels offers the potential for a cheap, abundant, and environmentally friendly energy source.

Next-generation biofuels production involves degrading lignocellulosic biomass from plants into glucose, which is then fermented by micro-organisms into the fuel of interest, such as ethanol or isobutanol. A major obstacle to this process is the conversion of lignocellulose into glucose. In essentially all biofuel production plants, enzymes known as cellulases are used to break down the cellulose. However, this process is expensive and inefficient since cellulases are rather slow enzymes, and degrade over time.

An alternative approach is to use chemical methods, such as acid hydrolysis, to break down lignocellulose. The main problem here is that chemical byproducts, mainly aromatic aldehydes, are produced, which inhibit subsequent fermentation. Since chemical degradation methods are theoretically cheaper and more efficient than enzymatic methods, solving this problem would be a big step forward for clean energy.

A conceptually simple solution is to develop strains of micro-organisms that have resistance to the toxic byproducts in lignocellulose hydrolysate. To do this, I am using directed evolution to engineer enzymes that can convert a broad spectrum of aromatic aldehydes into less-toxic analogues (alcohols and acids) inside yeast cells.

Directed evolution is a method of protein engineering that involves building large libraries of mutants of a protein of interest, then screening or selecting them for a property of interest. It is arguably the best method for creating proteins with useful functions, as little knowledge is needed to begin with, but a lot of knowledge is gained from the study of the mutant proteins that are eventually found. For this project, we will learn both how to improve micro-organism survival under chemical stress, and how enzymes evolve to react on different aromatic aldehyde substrates.

Devin Trudeau

PhD candidate

Laboratory of Professor Frances H. Arnold