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    • 2018-03-26 10:30:16
    • Article ID: 691666

    Sewage Sludge Leads to Biofuels Breakthrough

    JBEI enzyme discovery enables first-time microbial production of an aromatic biofuel

    • Credit: (Credit: Chickmarkley)

      This lake in Berkeley, California was one source of the toluene-producing enzyme (phenylacetate decarboxylase) discovered in the JBEI study.

    Researchers at the U.S. Department of Energy Joint BioEnergy Institute (JBEI) and Lawrence Berkeley National Laboratory (Berkeley Lab) have discovered a new enzyme that will enable microbial production of a renewable alternative to petroleum-based toluene, a widely used octane booster in gasoline that has a global market of 29 million tons per year.

    Results from a study led by Harry Beller, Berkeley Lab senior scientist and scientific lead at JBEI, were published Monday in the journal Nature Chemical Biology. The other lead co-authors are Andria Rodrigues and Kamrun Zargar of JBEI.

    A major focus of research at JBEI, and in the broader community of biofuel researchers, is the production of industrially and commercially relevant fuels and chemicals from renewable resources, such as lignocellulosic biomass, rather than from petroleum. The enzyme discovered in this study will enable the first-time microbial production of bio-based toluene, and in fact, the first microbial production of any aromatic hydrocarbon biofuel.

    The enzyme discovery resulted from the intensive study of two very different microbial communities that produced toluene. One community contained microbes from lake sediment, and the other from sewage sludge. Since microbes in the environment are a reservoir of enzymes that catalyze an extraordinarily diverse set of chemical reactions, it’s not unusual for scientists working in biotechnology to source enzymes from nature.

    Beller was motivated to investigate bio-based toluene after reading literature reports from the 1980s that revealed microbial toluene biosynthesis in anoxic lake sediments. Despite a number of reports of bacterial toluene production since that time, the identity of the enzyme catalyzing this biochemically challenging reaction has been a mystery for decades.

    The radical nature of GREs allows them to catalyze chemically challenging reactions, such as anaerobic decarboxylation of phenylacetate to generate toluene. Beyond their potential biotechnological applications, a number of known GREs are relevant to human health and occur within the human gut microbiome.

    The process of enzyme discovery for this project was both challenging and unconventional. The researchers first started working with a bacterial species reported to make toluene, but when those reports appeared to be irreproducible, the scientists turned to the environment for toluene-producing cultures – specifically to municipal sewage and anoxic lake sediment.

    “All enzyme discovery projects are challenging. But moving from discovery in a single bacterial species, to discovery in a complex microbial community from sewage sludge or lake sediments, was more difficult by orders of magnitude,” says Beller. “This study became a needle-in-a-haystack search for the toluene-producing enzyme in a candidate pool of hundreds of thousands of enzymes.” 

    In fact, metagenome analyses revealed that these microbial communities each contained more than 300,000 genes – the equivalent of more than 50 bacterial genomes. Another challenge was that the anaerobic microbial communities and many of their enzymes were sensitive to oxygen, forcing the scientists to manipulate cultures and enzymes under strictly anaerobic conditions.

    The discovery process combined protein purification techniques used by biochemists for decades, such as fast protein liquid chromatography, with modern metagenomic, metaproteomic, and associated bioinformatic analyses, some of which were carried out in collaboration with the Joint Genome Institute, a DOE Office of Science User Facility. An important component of the discovery process was to validate the researchers’ predictions of the toluene biosynthesis enzyme with experiments using highly controlled assays involving purified proteins.

    An intriguing question arising from this research is: why would a bacterium produce toluene? The researchers don’t have the definitive answer but present two hypotheses in the paper. One possibility is that the bacterium is producing toluene as a toxin to outcompete other microbes in its environment. Another hypothesis is that the phenylacetate decarboxylase (toluene-producing) reaction provides a strategy for the bacterium to regulate its internal pH in a somewhat acidic, fermentative environment.

    Beller and his colleagues believe that their study results have implications for fundamental and applied science. From a biochemical perspective, the study expands the known catalytic range of GREs, and from a biotechnological perspective, it will enable first-time biochemical synthesis of an aromatic fuel hydrocarbon from renewable resources.

    “We have so much to learn about the extraordinary metabolic diversity of bacteria,” Beller said. “Through eons of evolution, nature has devised enzymes that can catalyze difficult chemical reactions, and as we discover these, we can harness them for biotechnology.”

    JBEI is a DOE Bioenergy Research Center funded by DOE’s Office of Science. The other co-authors of the paper, “Discovery of enzymes for toluene synthesis from anoxic microbial communities,” are Yu-Wei Wu, Avneesh K. Saini, Renee M. Saville, Jose H. Pereira, Paul D. Adams, Susannah G. Tringe, Christopher J. Petzold, and Jay D. Keasling.

     # # #

    Lawrence Berkeley National Laboratory addresses the world’s most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Lab’s scientific expertise has been recognized with 13 Nobel Prizes. The University of California manages Berkeley Lab for the U.S. Department of Energy’s Office of Science. For more, visit www.lbl.gov.

    DOE’s Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.

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    Stronger, lighter, greener

    A new award-winning magnet technology invented at the U.S. Department of Energy's Argonne National Laboratory could help drive the nation's transition from gas-powered vehicles to electric and hybrid power more rapidly, at lower cost, and in a more environmentally friendly way.

    Science Up-Close: Developing a Cookbook for Efficient Fusion Energy

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    Peering into the Mist: How Water Vapor Changes Metal at the Atomic Level

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    Neutron science publications reach new highs at ORNL's flagship facilities

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    Fiery sighting: A new physics of eruptions that damage fusion experiments

    Feature describes first direct sighting of a trigger for bursts of heat that can disrupt fusion reactions.

    Microbial Types May Prove Key to Gas Releases from Thawing Permafrost

    Scientists discover key types of microbes that degrade organic matter and release carbon dioxide and methane into the atmosphere.

    An effect that Einstein helped discover 100 years ago offers new insight into a puzzling magnetic phenomenon

    Experiments at the Department of Energy's SLAC National Accelerator Laboratory have seen for the first time what happens when magnetic materials are demagnetized at ultrafast speeds of millionths of a billionth of a second: The atoms on the surface of the material move, much like the iron bar did. The work, done at SLAC's Linac Coherent Light Source (LCLS) X-ray laser, was published in Nature earlier this month.

    Found: A precise method for determining how waves and particles affect fusion reactions

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    Discovery adapts natural membrane to make hydrogen fuel from water

    In a recent study from the U.S. Department of Energy's (DOE) Argonne National Laboratory, scientists have combined two membrane-bound protein complexes to perform a complete conversion of water molecules to hydrogen and oxygen.

    How Plants Regulate Sugar Deposition in Cell Walls

    Identified genes involved in plant cell wall polysaccharide production and restructuring could aid in engineering bioenergy crops.


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    Top 10 Discoveries of 2018

    Every year, the U.S. Department of Energy's (DOE) Brookhaven National Laboratory compiles a list of the biggest advances made by the Lab's staff scientists, engineers, and visiting researchers. From uncovering mysteries of the universe to building better batteries, here, in no particular order, are our picks for the top 10 discoveries of 2018.

    U.S. Department of Energy Announces $33 Million for Small Business Research and Development Grants

    The U.S. Department of Energy announced it will award 189 grants totaling $33 million to 149 small businesses in 32 states.

    DOE to Provide $16 Million for New Research into Atmospheric and Terrestrial Processes

    The U.S. Department of Energy (DOE) announced a plan to provide $16 million for new observational research aimed at improving the accuracy of today's climate and earth system models.

    Machine learning award powers Argonne leadership in engine design

    When attempting to design engines to be more fuel-efficient and emissions-free, automotive manufacturers have to take into account all the complexity inherent in the combustion process.

    ORNL partners with industry to address multiple nuclear technology challenges

    The Department of Energy's Oak Ridge National Laboratory is collaborating with industry on six new projects focused on advancing commercial nuclear energy technologies that offer potential improvements to current nuclear reactors and move new reactor designs closer to deployment.

    Lithium earns honors for three physicists working to bring the energy that powers the sun to Earth

    Feature describes research of three PPPL physicists who have won the laboratory's 2018 outstanding research awards

    DOE approves technical plan and cost estimate to upgrade Argonne facility; Project will create X-rays that illuminate the atomic scale, in 3D

    The U.S. Department of Energy has approved the technical scope, cost estimate and plan of work for an upgrade of the Advanced Photon Source, a major storage-ring X-ray source at Argonne.

    Costas Soukoulis elected to National Academy of Inventors

    Costas Soukoulis, Ames Laboratory senior scientist and Iowa State University Frances M. Craig Endowed Chair and Distinguished Professor, has been named as a 2018 National Academy of Inventors (NAI) Fellow.

    Biophysicist F. William Studier Elected Fellow of the National Academy of Inventors

    F. William Studier, a Senior Biophysicist Emeritus at the U.S. Department of Energy's Brookhaven National Laboratory and Adjunct Professor of Biochemistry at Stony Brook University, has been elected as a Fellow of the National Academy of Inventors (NAI). He is among 148 renowned academic inventors being recognized by NAI for 2018.

    Blast to the future

    A grant from DOE's Technology Commercialization Fund will help researchers at Argonne and industry partners seek improvements to U.S. manufacturing by making discovery and design of new materials more efficient.


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    Rapid Lake Draining on Ice Sheets Changes How Water Moves in Unexpected Ways

    Widespread fracturing during lake drainage triggers vertical shafts to form that affect the Greenland Ice Sheet.

    New Historical Emissions Trends Estimated with the Community Emissions Data System

    The data system will allow for more detailed, consistent, and up-to-date global emissions trends that will aid in understanding aerosol effects.

    Peering into the Mist: How Water Vapor Changes Metal at the Atomic Level

    New insights into molecular-level processes could help prevent corrosion and improve catalytic conversion.

    Microbial Types May Prove Key to Gas Releases from Thawing Permafrost

    Scientists discover key types of microbes that degrade organic matter and release carbon dioxide and methane into the atmosphere.

    New Method Knocks Out Yeast Genes with Single-Point Precision

    Researchers can precisely study how different genes affect key properties in a yeast used industrially to produce fuel and chemicals.

    How Plants Regulate Sugar Deposition in Cell Walls

    Identified genes involved in plant cell wall polysaccharide production and restructuring could aid in engineering bioenergy crops.

    Scientists Identify Gene Cluster in Budding Yeasts with Major Implications for Renewable Energy

    How yeast partition carbon into a metabolite may offer insights into boosting production for biofuels.

    More Designer Peptides, More Possibilities

    A combined experimental and modeling approach contributes to understanding small proteins with potential use in industrial, therapeutic applications.

    Deep Learning for Electron Microscopy

    Artificial intelligence on Summit to discover atomic-scale structures.

    Clarifying Rates of Methylmercury Production

    New model provides more accurate estimates of how fast microbes produce a mercury-based neurotoxin.


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