U.S. Department of Energy Office of Science
Genomic Science Program
Systems Biology for Energy and Environment
DOE Joint BioEnergy Institute (JBEI)
Project Description: Research at the DOE Joint BioEnergy Institute (JBEI) is using the tools of synthetic biology to produce the next generation of biofuels. JBEI is engineering microbes and enzymes to process the complex sugars of cellulosic biomass into biofuels that can directly replace gasoline. By developing new bioenergy crops, JBEI will transform lignin into a source of valuable new products. A six-institution partnership led by Lawrence Berkeley National Laboratory, JBEI is based in the San Francisco Bay Area, which is fast becoming a hub of renewable energy research and development. JBEI is headquartered in a new laboratory in Emeryville, California, centrally situated among the partner institutions. JBEI’s research strategy revolves around four interdependent efforts that focus on (1) developing new bioenergy crops, (2) enhancing biomass deconstruction, (3) producing new biofuels through synthetic biology, and (4) creating technologies that advance biofuel research.
Research Strategy:
1. Developing New Bioenergy Crops
To increase our understanding of genes and enzymes involved in the synthesis and modification of plant cell walls, JBEI researchers are using well-characterized genomes and genetic-engineering tools established for rice and Arabidopsis (a small flowering plant related to mustard). These two model systems are ideal research subjects because they go from seed to mature plant in weeks or months, rather than the year or more required for energy crops such as switchgrass and poplar. Genetic insights from rice (a model for grasses) and Arabidopsis (a model for trees) will accelerate the development of new energy crops. In addition, JBEI researchers are investigating metabolic pathways involved in lignin biosynthesis. The research may lead to development of plants that can be deconstructed more easily. This unique basic research program could help to transform lignin into a valuable source of chemicals and polymers, while also improving the economics of converting cellulosic biomass into fuels.2. Enhancing Biomass Deconstruction
JBEI researchers are developing new pretreatments and enzymes that enhance cellulose conversion to sugars and minimize toxic by-products. As part of this effort, they are exploring a broad range of biomass environments, from rainforests to compost, to discover and isolate new enzymes that more efficiently degrade cellulose and lignin. Their studies of the mechanisms of biomass deconstruction at the molecular level will enable new insights and approaches for the efficient conversion of all plant components to useful products.
Synthetic Biology
Building Novel Biological Systems for Useful Purposes
Synthetic biologists design and build novel organisms to generate products not made by natural systems. This process may involve constructing entirely new biological systems from a set of standard parts—genes, proteins, and metabolic pathways— or redesigning existing biological systems. The tools of synthetic biology also can be used to study the interior of living cells at the molecular level, providing critical new information and insight into the machinery of life and the natural world. Synthetic biology holds promise for advances in many areas, including the development of renewable, carbon-neutral energy sources, nonpolluting biological routes for the production of chemicals, safer and more effective pharmaceuticals, and better environmental remediation technologies.
At JBEI, researchers will use synthetic biology to develop new platform hosts for producing enzymes and fuels and to create biomolecular parts and devices for constructing new fuel-generating organisms and improved plants. Among other advances, such goals will be achieved through the improved capabilities of fermentative organisms to tolerate processing conditions and inhibit unwanted by-products. Capabilities also will be engineered into fuel-producing organisms to convert five-carbon sugars into fuel and make use of lignin monomers. Following the strategy that biological systems can be revamped more effectively or built from scratch if standardized parts are employed, investigators will assemble a catalog of well-characterized biosynthetic components to help in designing, testing, optimizing, and implementing integrated large-scale biosynthetic units. These tools and principles, used by JBEI Chief Executive Jay Keasling to develop a relatively inexpensive synthetic biology alternative for producing the antimalarial drug artemisinin, will aid in developing the next generation of biofuels.
3. Producing New Biofuels Through Synthetic Biology
JBEI researchers are applying synthetic biology approaches to engineer microorganisms that convert the sugars released from biomass deconstruction into ethanol and other, more advanced biofuels such as longer alcohols and alkanes.
These next-generation biofuels will yield almost as much energy per volume as gasoline and will be transportable through existing fuel pipelines. Biologically produced alkanes and other oil-like hydrocarbons could replace gasoline in today’s cars on a gallon-for-gallon basis.
Mathematical models of metabolism and gene regulation, developed from detailed understanding of Escherichia coli and Saccharomyces cerevisiae (yeast) biology, will guide the design and construction of new microbes for biofuel synthesis.
4. Creating Technologies that Advance Biofuel Research
JBEI researchers are creating new, broadly applicable technologies to advance research that will speed the development of biofuels. Among these technologies is a novel chip-based system that can be used to identify new enzymes with cellulose- and lignin-degrading activities. In addition, JBEI researchers are constructing automated microfluidic platforms that can simultaneously screen hundreds of enzymatic reactions to help identify the best enzymes for biomass deconstruction. Technologies also are being developed for rapid high-resolution imaging to visualize and characterize the effects of pretreatment protocols on plant biomass. These and other enabling technologies are expected to generate large volumes of data that will be collected and catalogued in a centralized database, then analyzed using new bioinformatics tools. Industry Partnerships To promote the transfer of JBEI inventions to private industry for commercial development that can benefit the nation, JBEI is establishing collaborations with companies that have relevant scientific and marketing capabilities in energy, agribusiness, and biotechnology. The JBEI Industry Partnership Program provides companies with opportunities to contribute to JBEI and become part of the JBEI community. To further help ensure that its science will ultimately be able to serve national needs, JBEI has established an advisory committee with representation from the entire spectrum of the biofuel industry.
Education and Outreach
Educational efforts at JBEI build on strong undergraduate, graduate, and postdoctoral training programs, established technical training and seminar programs, and nationally recognized K–12 and community-college science outreach programs already in place at JBEI’s member institutions. In addition to starting a new student fellowship program, JBEI will collaborate with U.C. Berkeley’s Management of Technology Program to enable young scientists and engineers to develop biofuel-related business plans.
Lead Institution: Lawrence Berkeley National Laboratory, Berkeley, California
Principal Investigator: Jay Keasling
Partnering Institutions:
- DOE’s Lawrence Berkeley National Laboratory (LBNL), Berkeley, California (lead institution): LBNL, a multidisciplinary national laboratory, is home to the Advanced Light Source, the Molecular Foundry, the National Center for Electron Microscopy, and the National Energy Research Scientific Computing Center. LBNL also is a founding partner of the DOE Joint Genome Institute, one of the world’s largest and most productive DNA sequencing centers. LBNL provides expertise in bioinformatics, data management and biological modeling, in addition to being a world leader in advanced imaging, nanoscale biology, applied mathematics, and biochemical design.
- DOE’s Sandia National Laboratories (SNL), Albuquerque, New Mexico, and Livermore, California: SNL is a multidisciplinary national laboratory that hosts DOE’s Combustion Research Facility, a premier center for combustion science, and is a partner in DOE’s Sun Lab, a virtual laboratory for the study of solar-power technologies. Sandia provides expertise in systems engineering and integration function, microfluidics, computation, and robotics and materials development, as well as experience in manufacturing technologies.
- DOE’s Lawrence Livermore National Laboratory (LLNL), Livermore, California: LLNL, a multidisciplinary national laboratory, is home to the Center for Accelerator Mass Spectrometry and the world’s fastest supercomputer, the BlueGene/L. LLNL also is one of the DOE Joint Genome Institute’s founding partners and provides expertise in genomics, bioinformatics, experimental protein production, advanced measurement technologies, and high-performance scientific computing.
- University of California, Berkeley: This university is ranked first by the National Research Council for distinguished scholarship and is home to the Synthetic Biology Engineering Research Center and the Energy Biosciences Institute and provides expertise in molecular and cellular biology, molecular genetics, proteomics, and environmental sciences.
- University of California, Davis: U.C. Davis oversees the California Biomass Collaborative and is home to the Northern California Nanotechnology Center, the Western Regional Center of the National Institute for Global Environmental Change, and the U.C. Davis Genome Center. The university provides expertise in plant and environmental sciences, genetics, plant physiology, evolutionary biology, and environmental science.
- Carnegie Institution (CI) Department of Plant Biology, Palo Alto, California: CI is a private, nonprofit organization. Its Department of Plant Biology at Stanford University maintains TAIR, a comprehensive database on Arabidopsis thaliana, the model organism for plant molecular genetics. The institution provides expertise in photosynthesis, bioinformatics, and growth and developmental processes that enable plants to survive disease and environmental stress.
Location of Center: San Francisco Bay (East), California
Funds / Support From Other Sources: Extensively leveraged.