Seeking Better Biofuels

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October 26, 2015

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by Melody M. Bomgardner (Chemical & Engineering News) Researchers at the Joint BioEnergy Institute transform biomass into energy-rich fuel molecules -- .. JBEI researchers are zeroing in on concepts that others have decided are too difficult or would take too long to prove. Can you engineer a plant’s cell walls to release its sugar building blocks? Is there a new chemistry that can break cell walls down? Can you identify a new fuel candidate by its chemical structure and then engineer a microbe capable of producing it from sugar?

At almost every turn, synthetic biology promises answers to these questions. Keasling (Jay Keasling, the principal investigator and chief executive officer of the Joint BioEnergy Institute at Lawrence Berkeley National Laboratory), who is also a professor at the University of California, Berkeley, is a native of that burgeoning field. He founded Amyris and LS9, two of the earliest biobased chemical firms that use engineered microbes. JBEI scientists say Keasling has given the institute an entrepreneurial vibe; several have started their own companies.

JBEI is one of three Department of Energy-funded Bioenergy research centers established in 2007 by the Office of Science to accelerate research breakthroughs related to advanced biofuels. The other two are at Oak Ridge National Laboratory and the University of Wisconsin, Madison.

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Early this month, JBEI hit two milestones—it filed its 100th patent application and published its 500th paper. But its future is uncertain. At the end of 2017 it will reach the end of its second funding cycle. Keasling has plans to set up a new version of the institute that will apply the science it is developing to problems beyond fuels.

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Combinations of heat, acids, bases, and enzymes can be used in many ways to extract sugars from biomass. Yet no technique is efficient, quick, and cheap. After many years of effort, the people who work with biomass still have the same complaint: Plant cell walls are recalcitrant and don’t want to release their valuable sugar molecules.

And that’s no accident. Plants have evolved clever ways to protect their valuable tissues from insect and microbial pests, and those methods work equally well against humans who wish to make renewable fuels and chemicals. Most of a plant’s sugar is bound up in cellulose and hemicellulose—complex polysaccharides that give cell walls their structure. The polysaccharides are cross-linked by lignin, a phenolic polymer that is resistant to water.

To make economical use of biomass, scientists need a better understanding of the underlying biology of the plant cell wall, according to Jennifer C. Mortimer, JBEI’s director of plant systems biology. “We have very, very limited knowledge to help answer questions such as, ‘Why are plant cell walls so hard to break down?’ ” she says.

Mortimer’s group studies the molecular architecture of cell walls, in particular the shapes of various forms of cellulose, hemicellulose, and lignin and how they are arranged relative to each other.

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But she’d also like to know how plants make sugars, transport them to cells, and assemble them into cellulose and other macromolecules. “If we understand how plants are made, we can use synthetic biology to reroute certain pathways to make simpler versions of the polymers with fewer types of bonds,” she suggests.

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Pinene, usually extracted from pinewood, has a ring structure that makes it a potential precursor to high-energy fuels for jets and rockets (ACS Synth. Biol. 2014, DOI: 10.1021/sb4001382).

Bisabolane has a similarly handy carbon ring. Lee says it has promise as a biosynthetic alternative to diesel. His team has been manufacturing the precursor bisabolene by engineering the mevalonate pathway in microbes. The pathway is responsible for the C₅ starting materials for isoprenoids. It also has been engineered to produce the biobased chemical intermediate farnesene and the antimalarial drug artemisinin (Nat. Commun. 2011, DOI: 10.1038/ncomms1494). Amyris, the start-up founded by Keasling, developed the artemisinin pathway and is commercializing farnesene.

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“Fuels are chemicals. We go to all this trouble to make a beautiful molecule just to burn it up in your car,” says Leonard Katz, a JBEI collaborator and director of research in synthetic biology at UC Berkeley. Katz’s expertise is harnessing a family of multienzyme complexes called polyketide synthases, or PKSs, to make useful chemicals.

PKSs are responsible for making polyketide drugs including the antibiotic tetracycline. They work like modular assembly factories. “By repurposing PKS, we make fuels and chemicals where the intermediates don’t flow freely but are tied to the enzymes,” Katz says. By linking PKS modules so that each performs a transformation, it is possible to make chemicals such as adipic acid and customized polymers with advanced properties.

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In one set of experiments, researchers used the device to evaluate the effect of four different ionic liquids at four concentrations on the growth rates and ethanol production of yeast (Lab Chip 2015, DOI: 10.1039/c4lc00794h). READ MORE Abstract (Biochemistry) Abstract (Proceedings of the National Academy of Sciences) Abstract (Microbiome) Abstract (Applied and Environmental Microbiology)