BER Research Highlights

Search Date: March 23, 2017

51 Records match the search term(s):


December 14, 2012

Metabolic Imaging: Watching Sugars Move in Plants

Fluorine-18 is a radioactive isotope that emits positrons. Using positron emission tomography (PET), scientists can image the movement and localization, in living organisms, of molecules that contain fluorine-18. Fluorine-18-labeled-fluorosugars, that is, natural sugars into which fluorine-18 atoms have been incorporated, enable study of the mechanisms by which living organisms use and process these biomolecules and offer opportunities to observe sugar distribution and metabolism in real time. Fluorine-18 fluoro-deoxyglucose (FDG) has already been established as an important PET imaging agent in human medicine. It is well known that vascular plants transport the bulk of their carbohydrate load in the form of sucrose. Now, U.S. Department of Energy scientists at the University of Missouri—Columbia have synthesized fluorine-18-fluoro-deoxy-sucrose (FDS) and used it to obtain the first images of corn plant leaves that demonstrate realtime transport of the sugar. Their results will enable investigators to image sucrose metabolism in living plants and, from these images, gain insight into metabolic pathways in plants with potential value for biofuel production.

Reference: Gaddam, V., and M. Harmata. 2013. “Synthesis of 6′-Deoxy-6′-Fluorosucrose,” Carbohydrate Research 369, 38–41. DOI: 10.1016/j.carres.2012.12.001. (Reference link)

Contact: Prem Srivastava, SC-23.2, (301) 903-4071
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


December 09, 2012

Using Synchrotron Spectroscopy to Understand How a Protein Evolves

A major challenge in research to enable large-scale production of biofuels is developing enzymes that are highly efficient in converting biomass components into usable fuels. Enzymes are proteins that are configured to catalyze such conversions. Many protein structures are known, including those of many valuable enzymes. Much less is known about how small changes in a protein’s composition can change its three-dimensional structure and control its catalytic efficiency, or even convert a protein with no catalytic function into one that is an efficient catalyst. New research shows the structural basis for conversion by directed evolution of a non-catalytic small protein into an enzyme that is an effective catalyst for linking RNA molecules. The scientists used an Extended X-ray Absorption Fine Structure (EXAFS) station at the Stanford Synchrotron Radiation Lightsource (SSRL) to determine the active-site structure of the newly synthesized enzyme. The EXAFS experiments were able to show the exact chemical environment of each zinc atom in the new enzyme, leading to an explanation of why it had developed the catalytic activity. The research was carried out by a team of scientists from the University of Minnesota and SSRL and is published in Nature Chemical Biology.

Reference: Chao, F.-A., et al., 2013. “Structure and Dynamics of a Primordial Catalytic Fold Generated by In Vitro Evolution,” Nature Chemical Biology 9, 81–83. DOI: 10.1038/nchembio.1138. (Reference link)

Contact: Roland F. Hirsch, SC-23.2, (301) 903-9009
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


December 07, 2012

Finding a Steady-State Solution in Dynamical Biological Networks

Cellular biochemical networks govern biological function and are strongly influenced by the exchange of molecules between the cell and its environment. Modeling this exchange process and its impact on cellular networks for whole microbial cells will be a key step in developing biology-based applications in bioenergy and other Department of Energy (DOE) mission areas. However, it has been a problem to represent nutrient exchange with the environment for genome-scale kinetic models, in a manner consistent with the existence of a steady state. New research has developed a mathematical model that establishes sufficient conditions for a non-equilibrium steady-state for cellular biochemical networks. The research proves the theorem that reactions conserving mass and kinetic rate laws are sufficient conditions for the existence of a non-equilibrium steady state. The new study demonstrates how to mathematically model the exchange of molecules between any cell and its environment. The results of this DOE Scientific Discovery through Advanced Computing (SciDAC) research by Fleming and Thiele of the University of Iceland are foundational for future efforts to computationally model non-equilibrium steady states as part of  whole cell microbial models.

Reference: Fleming, R. M. T., and I. Thiele. 2012. “Mass Conserved Elementary Kinetics Is Sufficient for the Existence of a Non-Equilibrium Steady State Concentration,” Journal of Theoretical Biology 314, 173–81. DOI: 10.1016/j.jtbi.2012.08.021. (Reference link)

Contact: Christine Chalk, SC-21.1, (301) 903-5152, Susan Gregurick, SC-23.2, (301) 903-7672
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Division: SC-23.2 Biological Systems Science Division, BER


December 07, 2012

Increased Nitrogen Deposition Slows Carbon Decomposition in Forest Soils

Global production of agricultural fertilizers has vastly increased the amount of nitrogen compounds entering natural terrestrial ecosystems. Although it is clear that increased nitrogen availability boosts primary productivity (i.e., plant growth) in ecosystems, the impacts of this nitrogen influx on the decomposition of dead plant material by soil microbes remain poorly understood. A collaborative team of U.S. Department of Energy researchers at the Universities of Michigan and Oklahoma examined carbon decomposition by soil fungi and bacteria at an experimental forest site in Michigan. GeoChip 4.0, a DNA microarray containing probes for thousands of functional genes, was used to measure expression of genes involved in degradation of complex carbon compounds in soil samples from sites that have been exposed to elevated nitrogen input for the past 18 years. Compared to nearby control plots, sites with elevated nitrogen showed significant decreases in the diversity and overall expression levels of fungal and actinobacterial genes involved in deconstruction of cellulose, lignin, and other plant compounds. This finding correlates with a long-term observation of decreased carbon decomposition rates in soils at the nitrogen-elevated sites and points to the specific mechanism underlying this shift. These findings shed new light on poorly understood processes occurring in forest soils and improve our ability to better predict how ecosystems will respond to changing environmental variables.

Reference: Eisenlord, S. D., Z. Freedman, D. R. Zak, K. Xue, Z. He, and J. Zhou. 2013. "Microbial Mechanisms Mediating Increased Soil Carbon Storage under Elevated Atmospheric Nitrogen Deposition," Applied Environmental Microbiology 79, 1191–99. DOI: 10.1128/AEM.03156-12. (Reference link)

Contact: Joseph Graber, SC-23.2, (301) 903-1239
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


November 23, 2012

Watching Plant Biomass Breakdown to Improve Biofuel Production

Sustainable and cost-effective production of biofuels from plant biomass is hindered by the cost of pretreatment and low sugar yields after enzymatic hydrolysis of plant cell wall polysaccharides. Many studies have looked at enzymatic action on individual biomass components, but in nature, the plant cell wall is a complex, networked structure that interacts concertedly with pretreatment enzymes. To fully understand the mechanisms of enzymatic plant cell wall deconstruction for optimal production of bioenergy from biomass, it is imperative to understand the whole system. Scientists at the U. S. Department of Energy’s (DOE) BioEnergy Science Center (BESC) and DOE National Renewable Energy Laboratory (NREL) have addressed this problem by using a combination of advanced microscopic imaging methods in a correlative, real-time manner to examine both fungal and bacterial enzyme systems. With this new technology, they are able to localize the enzymatic sites of action without compromising the cell wall’s structural integrity. The results suggest that an optimal strategy for enhancing fermentable sugar yield from enzymatic deconstruction is to modify lignins to be more amenable to removal through pretreatment while maintaining polysaccharide integrity, improving accessibility to enzyme action.

Reference: Ding, S.-Y., Y.-S. Liu, Y. Zeng, M. E. Himmel, J. O. Baker, and E. A. Bayer. 2012. “How Does Plant Cell Wall Nanoscale Architecture Correlate with Enzymatic Digestibility?” Science 338(6110), 1055–60. DOI: 10.1126/science.1227491. (Reference link).

Contact: Cathy Ronning, SC-23.2, (301) 903-9549
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Division: SC-23.2 Biological Systems Science Division, BER


November 22, 2012

Biochemistry of a Mysterious Microbial Community

Subsurface microbial communities are highly diverse and comprise an enormous fraction of Earth’s biomass, but lack of knowledge related to their ecological function makes understanding their ongoing biogeochemical processes difficult. Using synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectromicroscopy to probe biofilm samples from a cold subsurface sulfur spring, researchers recently determined how bacteria and archaea work together to influence global sulfur and carbon cycles. By revealing the bright spectral signals of akylic and methyl groups, together with sulfur functional groups, SR-FTIR unambiguously identified the bacteria’s sulfur-oxidizing metabolic activity. Archaeal cells, which were the dominant population in this biofilm, showed no such activity, suggesting a thriving mutual metabolism of archaea and bacteria. The research was conducted using resources at the Advanced Light Source at Lawrence Berkeley National Laboratory.

Reference: Probst, A. J., et al. 2012. “Tackling the Minority: Sulfate-Reducing Bacteria in an Archaea-Dominated Subsurface Biofilm,” The ISME Journal 7, 635–51. (Reference link)

Contact: Roland F. Hirsch, SC-23.2, (301) 903-9009
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


November 12, 2012

Engineering Secondary Cell Walls in Plants

The polysaccharide polymers of plant cell walls provide a carbon and energy source for biofuel production, but they are embedded in lignin, which gives plants their required rigidity but is also primarily responsible for the recalcitrance of plant biomass to enzymatic hydrolysis. Previous attempts to engineer reduced lignin content in plants were imprecise and resulted in unacceptable negative impacts on plant growth because of vessel integrity loss. In this work, researchers engineered lignin and polysaccharide biosynthesis in a cell-type specific manner such that lignin was greatly reduced in the normally lignin-rich fiber cells, and the amount of polysaccharide polymers was much greater in vessel cells. The resulting plants were viable and grew normally. When biomass from these engineered plants was subjected to enzymatic digestion, more sugars were released than from wild-type plants, a desirable trait for biofuels production.

Reference: Yang, F., P. Mitra, L. Zhang, L. Prak, Y. Verhertbruggen, J.-S. Kim, L. Sun, K. Zheng, K. Tang, M. Auer, H. V. Scheller, and D. Loque. 2013. “Engineering Secondary Cell Wall Deposition in Plants,” Plant Biotechnology Journal 11, 325–335. DOI: 10.1111/pbi.12016. (Reference link)

Contact: Kent Peters, SC-23.2, (301) 903-5549
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Division: SC-23.2 Biological Systems Science Division, BER


November 12, 2012

Soil Microbes Eat Nitrous Oxide, a Potent Greenhouse Gas

The use of large amounts of nitrogen fertilizer in modern agriculture has resulted in massive releases of nitrous oxide (N2O) into the atmosphere. Although shorter lived than CO2, N2O is over 300 times more potent as a greenhouse gas, so understanding its role and behavior in global climate change is important. Soil microbes naturally consume ammonia in fertilizers, converting it into N2O or dinitrogen gas (N2), a harmless component of the atmosphere. Previous attempts to estimate the abundance of microbes that perform these processes have significantly overestimated N2O production, suggesting that a large, but undetected group of microbes is converting ammonia to N2. In a new study, researchers have used a comparative genomics approach to identify new gene sequences involved in conversion of ammonia to N2 and demonstrated that this genetic pathway is present in several abundant groups of soil microbes not previously thought to be involved in nitrogen conversion. Preliminary experiments suggest that these organisms are capable of this form of metabolism in the laboratory and that the relevant genes are present in soil samples. These results have revealed an important missing piece in our understanding of the terrestrial nitrogen cycle. Further research on the physiology of these organisms and determination of their environmental abundance should improve model predictions for release of greenhouse gasses from soils of bioenergy landscapes or other agricultural systems.

Reference: Sanford, R. A., D. D. Wagner, Q. Wu, J. C. Chee-Sanford, S. H. Thomas, C. Cruz-García, G. Rodríguez, A. Massol-Deyá, K. K. Krishnani, K. M. Ritalahti, S. Nissen, K. T. Konstantinidis, and F. E. Löffler. 2012. “Unexpected Nondenitrifier Nitrous Oxide Reductase Gene Diversity and Abundance in Soils,” Proceedings of the National Academy of Sciences USA 109(48), 19709–714. DOI: 10.1073/pnas.1211238109. (Reference link).

Contact: Joseph Graber, SC-23.2, (301) 903-1239
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


November 06, 2012

Identifying the Best Biofuel-Producing Microbes

To use a microbe as a factory to make a desired product, a bacterial strain that already produces the compound is treated to generate many mutants, some of which may produce more of the product. From all these new variants, the challenge is to identify those microbes that make the largest amounts of the desired compound. This is particularly difficult when the target compound (e.g., a biofuel) does not confer any selective advantage to the microbe. To solve this problem, researchers at the U.S. Department of Energy’s (DOE) Lawrence Berkeley National Laboratory and DOE Joint BioEnergy Institute designed a “biosensor”—a genetic regulator that “senses” the presence of the desired product (e.g., butanol). The expression of a gene that confers an advantage to the microbe, such as resistance to the antibiotic tetracycline, is then induced by the presence of the biosensor. Butanol biosensor-containing Escherichia coli cells, for example, grow in the presence of the antibiotic only if the medium also contains butanol. Finally, plasmids capable of synthesizing various amounts of butanol were introduced into E. coli containing the butanol biosensor and growing in tetracycline-containing medium. High butanol-producing cells could readily be identified by their faster growth rates. This approach will facilitate the selection of microbial strains that produce large quantities of any small molecule, an important step toward the development of renewable biofuels.

Reference: Dietrich, J. A., D. L. Shis, A. Alikhani, and J. D. Keasling. 2012. “Transcription Factor-Based Screens and Synthetic Selections for Microbial Small-Molecule Biosynthesis,” ACS Synthetic Biology, DOI: 10.1021/sb300091d. (Reference link).

Contact: Pablo Rabinowicz, SC-23.2 (301) 903-0379
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


November 01, 2012

Impacts of Elevated CO2 on Photosynthetic Microbes in Arid Ecosystems

In many harsh desert environments, microbial “biocrust” communities dominated by photosynthetic bacterial species (cyanobacteria) cover up to 70% of the land surface and play important roles in nutrient cycling, water retention, and stabilizing soil against erosion. These communities are highly adapted to the specific environmental conditions of arid ecosystems, and it is unclear what impacts climate change processes may have on them. Operating in collaboration with DOE’s long-term Free-Air CO2 Enrichment (FACE) program, researchers at Los Alamos National Laboratory have published new findings on the effects of 10 years of controlled elevated CO2 exposure on cyanobacterial biocrusts using environmental metagenomics. Natural biocrusts exposed to elevated CO2 (550 ppmv) were shown to have significantly reduced abundance of cyanobacteria relative to plots exposed to ambient CO2 concentrations (360 ppmv). These findings were correlated with an observed loss of biocrust coverage in the elevated CO2 plots, although curiously, total soil biomass measurements did not change significantly. Loss of cyanobacterial abundance appears to be at partially related to increased damage from oxidative stress, with genes involved in resistance to this kind of stress appearing more frequently in the elevated CO2 samples. Although more study is needed, these results present preliminary evidence suggesting that increasing atmospheric CO2 concentrations have a deleterious impact on desert biocrusts and may result in decreased performance by these communities.

Reference: Steven, B., L. Gallegos-Graves, C. M. Yeager, J. Belnap, R. D. Evans, and C. R. Kuske. 2012. “Dryland Biological Soil Crust Cyanobacteria Show Unexpected Decreases in Abundance Under Long-Term Elevated CO2,” Environmental Microbiology, DOI: 10.1111/1462-2920.12011. (Reference link)

Contact: Joseph Graber, SC-23.2, (301) 903-1239
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


October 19, 2012

Marine Ecosystems More Complex Than Previously Thought

The tiny cyanobacterium Prochlorococcus is among the most abundant and important in the oceans, and distinct variants (“ecotypes”) exist at different water depths. An estimated 100 million cells of this unicellular organism can be found in a single liter of seawater. These cyanobacteria help remove some 10 billion tons of carbon from the atmosphere each year. New research addresses a long-held assumption that the size of a microbial population in the marine community corresponds to its level of activity in terms of carbon uptake and growth rate, thus determining its impact on global biogeochemical cycles. Researchers, including scientists at the U.S. Department of Energy’s Joint Genome Institute, studied the activity levels of several Prochlorococcus ecotypes at several locations in the Pacific and Atlantic oceans. The results suggest that the theory does not fully explain the link between abundance levels and activity. In their article, the authors state: “Our results suggest that low abundance microbes may be disproportionately active in certain environments and that some of the most abundant may have low metabolic activity.” “We observed uncoupling of abundance and specific activity of Prochlorococcus in the Sargasso Sea depth profile, which highlights deficiencies in our understanding of marine microbial ecology and population structure.” They conclude that marine ecosystem functioning is likely to be more complex and dynamic than previously thought. This finding has significant implications for understanding the role of the oceans in the global carbon cycle.

Reference: Hunt, D. E., Y. Lin, M. J. Church, D. M. Karl, S. G. Tringe, L. K. Izzo, and Z. I. Johnson. 2012. “The Relationship Between Abundance and Specific Activity of Two Bacterioplankton in Open Ocean Surface Waters,” Applied Environmental Microbiology, DOI: 10.1128/AEM.02155-12. (Reference link).

Contact: Dan Drell, SC-23.2, (301) 903-4742
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


October 16, 2012

Proteome Atlas for the Poplar Tree

Populus, a fast-growing perennial tree, holds potential as a bioenergy crop due to its ability to produce large amounts of biomass on non-agricultural land. For woody perennial plants such as poplar, there is a tight coupling between growth and photosynthesis during the plant's lifetime. To understand this process, researchers at the U.S. Department of Energy's BioEnergy Science Center (BESC) have measured more than 11,000 proteins in different tissues of poplar, including mature leaves, young leaves, roots, and stems. They have developed a poplar proteome atlas that shows which proteins are present in the various tissue types at a given point in time. By mapping the proteins back to tissue-specific metabolic pathways, the BESC scientists demonstrated that the same organ can participate in two different growth stages. Their findings confirm prior hypotheses that mature leaves appear to function primarily in the generation of energy via photosynthesis while young leaves partition resources between growth and photosynthesis. This study illustrates that a comprehensive systems approach to proteomics can yield valuable information on the lifecycle of bioenergy-related plants. The paper is the cover article for the latest issue of Molecular and Cellular Proteomics.

Reference: Abraham, P., R. J. Giannone, R. M. Adams, U. Kalluri, G. A. Tuskan, and R. L. Hettich. 2013. "Putting the Pieces Together: High-Performance LC-MS/MS Provides Network-, Pathway-, and Protein-Level Perspectives in Populus, "Molecular and Cellular Proteomics 12, 106–119. DOI: 10.1074/mcp.M112.022996. (Reference link)

Contact: Susan Gregurick, SC-23.2, (301) 903-7672
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Division: SC-23.2 Biological Systems Science Division, BER


September 10, 2012

Rapid Mapping of All Atoms in Biochemical Reactions

In the design and bioengineering of metabolic pathways for clean bioenergy and other applications, it is important to understand and eventually manipulate the movement of atoms in these biochemical reactions. For example, assessing how a reactant compound is transformed into a targeted product allows researchers to optimize for efficiency in the pathways. A new computational system (Minimum Weighted Edit-Distance or MWED) allows mapping of all the non-hydrogen atoms in biochemical reactions from the initial reactants to the final products. MWED relies on predicting the propensity of forming or breaking chemical bonds during a biochemical reaction. It then calculates and optimizes all possible solutions to the reaction of interest. Because it also uses a mixed-integer linear programming technique, it is three-fold faster than other, similar techniques. The MWED all atom pathway mapping was benchmarked on 2,446 manually curated biochemical reactions from the KEGG database. The researchers found that only 22 MWED-predicted reactions were in error (error rate of 0.9%) due mainly to difficulties in representing stereochemistry in the reactions. MWED offers research scientists an extremely fast and highly accurate method to model all atoms in biochemical reactions, both for novel bioengineering as well as for tracking isotopically labeled atoms in metabolic experiments.

Reference: Latendresse, M., J. P. Malerich, M. Travers, and P. D. Karp. 2012. “Accurate Atom-Mapping Computation for Biochemical Reactions,” Journal of Chemical Information and Modeling, DOI: 10.1021/ci3002217. (Reference link)

Contact: Susan Gregurick, SC-23.2, (301) 903-7672
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


September 04, 2012

Locating Hydrogen Atoms in a Protein Using Neutron Crystallography

Hydrogen atoms are notoriously difficult to locate in proteins, yet they are key atoms in many of the chemical reactions of life and comprise one-half of a protein's atoms. X-ray crystallography has been used to determine the atomic structure of many proteins and macromolecular complexes, but only a small fraction of the hydrogen atoms in these molecules can be located using this technique. In contrast, neutrons are scattered by hydrogen atoms, enabling determination of the position of these atoms in a protein molecule, though usually only to a medium resolution of about 2Å. Now, scientists at the Los Alamos Neutron Science Center have used the Protein Crystallography Station to determine the structure of a protein with the positions of its hydrogen atoms defined to an ultrahigh resolution of 1.1Å, the highest resolution ever for a neutron structure of a protein. They were able not only to locate nearly 95% of the hydrogen atoms in the protein at this resolution, but could determine the location of the hydrogen bonds that help determine the three-dimensional structure of the folded protein, and in some cases see how individual hydrogen atoms vibrate about their position in the protein. This new capability will improve understanding of the activity of many proteins, as well as guide computational modeling of systems such as protein-substrate and protein-drug complexes. The research was a collaboration of scientists at the University of Toledo, Los Alamos National Laboratory, and Oak Ridge National Laboratory.

Reference: Chen, J. C.-H., B.L. Hanson, S.Z. Fisher, P. Langan, and A.Y. Kovalevsky. 2012. "Direct Observation of Hydrogen Atom Dynamics and Interactions by Ultrahigh Resolution Neutron Protein Crystallography," Proceedings of the National Academy of Sciences (USA) 109(38), 15301–306. DOI: 10.1073/pnas.1208341109. (Reference link)

Contact: Roland F. Hirsch, SC-23.2, (301) 903-9009
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


September 04, 2012

Structural Patterning in Bacteria May Improve Their Bioenergy Uses

In comparison to multicellular plants and animals, bacteria are relatively simple, typically existing as single cells. However, some bacteria cooperate to form surprisingly sophisticated structures. The photosynthetic microbe Nostoc punctiforme forms long filaments of connected cells. At regular spacing along these filaments, individual cells differentiate to form heterocysts, non-photosynthetic cells that convert nitrogen gas into biologically useful nitrogen compounds. This patterning allows these microbes to separately perform both photosynthesis (which produces O2 as byproduct) and "fix" nitrogen using enzymes that are poisoned by oxygen, cooperatively exchanging the resulting nutrients between the cell types. In a new study, U.S. Department of Energy (DOE) researchers at the University of California, Davis, describe genetic mechanisms responsible for the establishment and maintenance of this distinctive pattern in growing filaments. When the expression of a series of regulatory genes (the "pat system") was experimentally manipulated, filaments formed with abnormal distributions of heterocysts. By analyzing these patterns and tracking the distribution of related proteins in dividing cells, the investigators were able to develop a new model describing the regulatory interactions resulting in the pattern that allows optimal photosynthesis and nitrogen fixation in the filaments. The results of this study provide valuable new insights into the mechanisms used by microbes to tune their functional attributes through the use of structural patterns and could lead to the development of new tools for optimizing processes in biological systems engineered for bioenergy applications.

Reference: Risser, D. D., F. C. Y. Wong, and J. C. Meeks. 2012. "Biased Inheritance of the Protein PatN Frees Vegetative Cells To Initiate Patterned Heterocyst Differentiation," Proceedings of the National Academy of Sciences (USA) 109, 15342-347. DOI: 10.1073/pnas.1207530109. (Reference link)

Contact: Joseph Graber, SC-23.2, (301) 903-1239
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


August 31, 2012

New Computational Method To Simulate Behavior of Cellulose Fibers

Cellulose fibers provide the structural framework for plant cell walls and are critical for plant growth, stability, and normal function. These same properties of cellulose fibers are also the main obstacle for efficient conversion of biomass to biofuels. Molecular dynamic simulations can aid in understanding cellulose fiber crystallinity and its resilience to deconstruction; however, since the fibers are very large, realistic molecular simulations require extensive run times on leadership-class supercomputers. Recently Scientific Discovery through Advanced Computing (SciDAC) supported researchers at Oak Ridge National Laboratory, in collaboration with RIKEN National Lab in Japan, developed a coarse-grained simulation method termed REACH (Realistic Extension Algorithm via Covariance Hessian) that will enable more efficient simulation of large cellulose fibers. The REACH method reduces the complexity of the simulation (coarse graining) and directly relates molecular force parameters from the more complex all-atom simulation to the faster REACH simulation. Using this method, the researchers simulated the behavior of a cellulose fiber of 36 chains and 40 to 160 degrees of polymerization with a speed of up to 24 nanoseconds per day of computation. The REACH simulations are in agreement with previous findings that the hydrophobic face of the cellulose fiber is more easily deconstructed than the hydrophilic face. An extension of REACH is now being developed that will account for larger amplitude strand separation motions of the fibers thought to precede subsequent deconstruction.

Reference: Glass, D. C., K. Moritsugu, X. Cheng, and J. C. Smith. 2012. "REACH Coarse-Grained Simulation of a Cellulose Fiber," Biomacromolecules 13(9), 2634-44. DOI: 10.1021/bm300460f. (Reference link)

Contact: Susan Gregurick, SC-23.2, (301) 903-7672
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


August 31, 2012

Understanding Enzyme Specificity Through Systems-Level Metabolic Modeling

In biology, some enzymes are highly specialized and catalyze specific reactions with a few or only one substrate, while other enzymes are promiscuous and can catalyze reactions using a variety of substrates. This phenomenon also has been observed experimentally for microbes involved in bioenergy-related processes. What is not understood, however, is why, within an organism, some enzymes are highly specialized while others remain generalists. Recently, researchers addressed this question using whole genome metabolic reconstructions and analysis, including dynamical simulations of environmental changes to understand microbial responses. Their findings indicate that enzymes with very specialized function maintain a higher flux, or processing rate, and require more regulation of their activities. This higher flux and higher regulation allows these enzymes to be more responsive and adaptive to environmental surroundings and changes then their less specialized counterparts. This work also illustrates that understanding environmental cellular physiology is greatly enhanced when using a systems biology approach rather than approaches that are focused on single enzyme simulations. These new results offer a means of translating genomic information into functional capabilities, with particular relevance for microbes involved in biofuel production.

Reference: Nam, H., N. E. Lewis, J. A. Lerman, D.-H. Lee, R. L. Chang, D. Kim, and B. O. Palsson. 2012. "Network Context and Selection in the Evolution to Enzyme Specificity," Science 337(6098), 1101-04. DOI: 10.1126/science.1216861. (Reference link)

Contact: Susan Gregurick, SC-23.2, (301) 903-7672
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


August 24, 2012

Understanding How Microbial Membrane Transporters Work

Membrane transport proteins play a key role in controlling the movement of a wide variety of carbon sources into microbial cells, including complex sugars and plant structural polymers derived from lignin. The transporter profile also influences the composition and structure of microbial communities in soils. However, the functioning of these proteins has not been adequately characterized. Researchers at Argonne National Laboratory have studied a specific type of transporter called the ATP-binding cassette (ABC) proteins. Using a combination of functional characterization (ligand-binding thermal screens), analytical tools for structural analysis (x-ray crystallography), and a computational framework, the functions of ABC transporters have been identified and better defined. The binding strength of various ABC transporters to aromatic products of lignin degradation was determined, and a set of ABC microbial transporters not previously identified with aromatic product transport was found. High-resolution crystal structures were produced for seven of the strongly bound molecular complexes, providing insights into the molecular basis for the observed strong binding. They revealed essential details about the modes of molecular interactions (e.g., hydrogen bonds) and the physical configuration of the active binding site. Knowledge derived from these experiments creates a foundation for developing a sequence-based computational method to predict what molecules will bind similar, but uncharacterized transporters in other microbes.

Reference: Michalska, K., C. Chang, J. C. Mack, S. Zerbs, A. Joachimiak, and F. R. Collart. 2012. “Characterization of Transport Proteins for Aromatic Compounds Derived from Lignin: Benzoate Derivative Binding Proteins,” Journal of Molecular Biology 423(4), 555–75. DOI: 10.1016/j.jmb.2012.08.017. (Reference link)

Contact: Arthur Katz, SC-23.2, (301) 903-4932
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Division: SC-23.2 Biological Systems Science Division, BER


August 22, 2012

New Genetic Tools for Engineering a Biomass-Degrading Microbe

Achieving efficient and cost-effective breakdown of cellulosic plant biomass remains a significant barrier to the development of economically competitive biofuels that do not compete with food supplies. The hot spring bacterium Caldicellulosiruptor has been shown to efficiently degrade biomass (e.g., switch grass and corn stover) at temperatures over 160° Fahrenheit, but further characterization and engineering of this organism for biofuel production has proven challenging due to a lack of tools for genetic manipulation. Researchers at the DOE BioEnergy Science Center (BESC) have now developed the first system allowing the stable introduction of foreign DNA elements into this microbe. This breakthrough is based on the identification of a Caldicellulosiruptor "immune system" that normally protects the bacterium from viral infection, destroying outside DNA before it can be integrated into the host genome. The BESC team was able develop a set of targeted nucleic acid modifications that protects DNA from the host immune system and allows the introduction of new genes and regulatory elements into the organism. Now that Caldicellulosiruptor is a step closer to the model status of an easily manipulated microbe like E. coli, the team can more effectively study the organism's unique cellulose-degrading properties and engineer new metabolic pathways that would allow direct conversion of plant biomass into next-generation biofuels.

Reference: Chung, D., J. Farkas, J. R. Huddleston, E. Olivar, and J. Westpheling. 2012. "Methylation by a Unique a-class N4-Cytosine Methyltransferase Is Required for DNA Transformation of Caldicellulosiruptor bescii DSM6725," PLoS ONE 7(8), e43844. DOI: 10.1371/journal.pone.0043844. (Reference link)

Contact: Joseph Graber, SC-23.2, (301) 903-1239
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


August 22, 2012

Regulation of Wood Formation Characterized in Populus

Poplar is a promising bioenergy feedstock due to its rapid growth and large biomass, and because sugars extracted from the lignocellulosic biomass (wood) of these native trees can be fermented to form renewable biofuels. These sugars are embedded within lignin, a complex, rigid structure that is critical to the overall health of the plant but that also impedes extraction of the sugars. New U.S. Department of Energy research is providing insight into how the lignocellulosic material forms in poplar. The process involves the expression of a cascade of genes whose regulation is poorly understood. The researchers at North Carolina State University report their discovery of a single protein ("controller" protein) that regulates this cascade on multiple levels to ensure normal growth, doing so in a way never before seen in plants. The controller protein was found outside the cell nucleus. In the presence of one of four other related proteins, it is carried into the nucleus where the two proteins bind. The newly formed molecule then suppresses expression of the regulatory gene cascade. This discovery helps define how wood formation occurs at the molecular level, furthering our understanding of a process critical to plant growth. The results will help guide research to optimize bioenergy production from biomass.

Reference: Li, Q., Y.-C. Lin, Y.-H. Sun, J. Song, H. Chen, X.-H. Zhang, R. R. Sederoff, and V. L. Chiang. 2012. "Splice Variant of the SND1 Transcription Factor Is a Dominant Negative of SND1 Members and Their Regulation in Populus trichocarpa," Proceedings of the National Academy of Sciences (USA) 109(36), 14699-704. DOI: 10.1073/pnas.1212977109. (Reference link)

Contact: Cathy Ronning, SC-23.2, (301) 903-9549
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER



Poplar Trees provided by North Carolina State University



August 14, 2012

New Method for Delivering Biologically Active Molecules into Algae Cells

Algae can produce a wide variety of biofuels, chemical building blocks, nutrients, and proteins using sunlight as an energy source and carbon dioxide or other simple carbon compounds. DOE scientists at Lawrence Berkeley Lab have developed a new method to deliver radioactive or fluorescently labeled small molecules or protein probes into algal cells to monitor cellular messengers such as mRNA, gene expression or to develop biosensors. A molecular probe's ability to pass through the cell membrane is often restricted by its water and lipid solubility. The new method overcomes these restrictions, enabling transport of molecules across the cell wall and membrane barriers. The transporter technology is broadly applicable and can be used for the delivery of labeled probes into algal cells for the development of sensitive biological assays for dynamic imaging of gene expression. The technique is being further developed to transport genetic materials and for probing changes in the carbon metabolism of these cells. These advances will enable scientists to improve algae as a tool for a wide variety of applications.

Reference: Hyman, J. M., E. I. Geihe, B. M. Trantow, B. Parvin, and P. A. Wender. 2012 "A Molecular Method for the Delivery of Small Molecules and Proteins Across the Cell Wall of Algae Using Molecular Transporters," Proceedings of the National Academy of Sciences (USA) 109(33), 13,225-230. DOI: 10.1073/pnas.1202509109. (Reference link)

Contact: Prem Srivastava, SC-23.2, (301) 903-4071
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


August 07, 2012

Bacterium with Improved Hydrogen Production from Sunlight

One challenge to the commercialization of microbial production of hydrogen using sunlight is that the oxygen produced by photosynthesis decreases hydrogen production. Various biological mechanisms have evolved to separate the two reactions and scientists have been looking for engineering solutions, but the challenge is not yet solved. Scientists at the Pacific National Northwest Laboratory now have shown for the first time that a single-celled cyanobacterium, Cyanothece, is able to produce hydrogen and oxygen simultaneously without interruption for at least 100 hours. The bacteria produce hydrogen at relatively high rates without high cell density or inducing circadian rhythms, as required in studies by other researchers. Furthermore, there is little photo-damage and decay of the photosynthesis apparatus, perhaps enabled by the removal of excess electrons by the hydrogen production. These results and the improved understanding of the underlying cyanobacterial physiology will help advance the biotechnology of microbial hydrogen production.

Reference: Melnicki, M. R., et al. 2012. "Sustained H2 Production Driven by Photosynthetic Water Splitting in a Unicellular Cyanobacterium," mBio 3(4), e00197-12. DOI:10.1128/mBio.00197-12. (Reference link)

Contact: John Houghton, SC-23.2, (301) 903-8288, John Houghton, SC-23.2, (301) 903-8288
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER



Marine Cyanobacterium Cyanothece
The single-celled marine cyanobacterium Cyanothece 51142, captured by a light microscope. Source: Washington University, St. Louis



August 03, 2012

Resequencing Poplar To Improve Its Use as a Bioenergy Feedstock

The fast-growing black cottonwood (Populus trichocarpa), a fast-growing tree that inhabits stream and river banks across a long north-south range of western North America, has been identified as a promising bioenergy crop. Many genetic and genomic resources for Populus have been developed and are being used to study the molecular basis of desirable traits such as biomass yield, cell wall characteristics, and environmental adaptation. To develop superior Populus cultivars for bioenergy feedstocks, it is necessary to understand the genetic and genomic structure of the Populus population to reliably detect phenotype-genotype associations, which informs suitable breeding approaches. Researchers at the DOE BioEnergy Research Center (BESC), together with the DOE Joint Genome Institute (DOE JGI), sequenced the genomes of 16 different black cottonwood varieties, broadly spanning north to south of the species' native range, and determined the population structure and genetic variation on a geographic scale. They found that significant genetic differentiation existed and was strongly correlated with latitudinal location of the sampled trees, suggesting that this species may have survived the past glaciation in multiple locations along the northwest of North America. The study demonstrates that advanced population genetics approaches should be more feasible in Populus than previously thought, increasing the potential for genetic improvement of Populus as a biofuel feedstock.

Reference: Slavov, G. T., S. P. DiFazio, J. Martin, W. Schackwitz, W. Muchero, E. Rodgers-Melnick, M. F. Lipphardt, C. P. Pennacchio, U. Hellsten, L. A. Pennacchio, T. C. Mockler, M. Freitag, A. Geraldes, Y. A. El-Kassaby, S. D. Mansfield, Q. C. B. Cronk, C. J. Douglas, S. H. Strauss, D. Rokhsar, and G. A. Tuskan. 2012. "Genome Resequencing Reveals Multiscale Geographic Structure and Extensive Linkage Disequilibrium in the Forest Tree Populus trichocarpa," New Phytologist, DOI: 10.1111/j.1469-8137.2012.04258.x. (Reference link)

Contact: Cathy Ronning, SC-23.2, (301) 903-9549
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


July 26, 2012

Switchgrass Chromosome Structure Revealed

Switchgrass is considered to be a promising biofuel feedstock because of its ability to produce high biomass yields on marginal lands with minimal inputs. Several efforts to improve switchgrass as a dedicated bioenergy crop have been initiated, but breeding efforts are hampered by the outbred, tetraploid nature of this species and by limited knowledge of its chromosome architecture. Researchers at the USDA-Agricultural Research Service have used sophisticated molecular, cytological, and imaging techniques to tease apart and unambiguously identify the nine relatively small and otherwise undistinguishable base chromosomes of a dihaploid switchgrass line, producing the first karyotype (systematized arrangement of the total chromosome complement) of this bioenergy crop. The scientists were able to distinguish the two switchgrass ecotypes as well as the two basic subgenomes using this resource. This new capability will greatly facilitate identification of specific gene pools (e.g., regionally adapted cultivars) for switchgrass improvement toward the goal of making it a productive biomass crop. The research was supported in part by the joint USDA-DOE Plant Feedstocks Genomics for Bioenergy Program.

Reference: Young, H. A., G. Sarath, and C. M. Tobias. 2012. "Karyotype Variation Is Indicative of Subgenomic and Ecotypic Differentiation in Switchgrass," BMC Plant Biology 12, 117. DOI: 10.1186/1471-2229-12-117. (Reference link)

Contact: Cathy Ronning, SC-23.2, (301) 903-9549
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


July 02, 2012

How a Surface Protein Enables Metabolism of a Methane-Generating Microbe

Methanogenic microbes known as Archaea carry out many chemical transformations essential for anaerobic carbon recycling in virtually all environments. However, little is known about how raw materials for, and products of, these transformations are transported between an Archaeal cell and its environment. Research now has determined the structure of a key surface-layer protein of a methane-generating microbe, Methanosarcina acetivorans, enabling new insights into how this microbe communicates with its surroundings. The new information enables construction of a diagram of the cell envelope's surface layer, showing the pores through which chemical species move back and forth. Three types of pores with distinctly different sizes and shapes were identified. All of them are small and highly negatively charged, which means that they are highly selective about which substances can pass through the layer into the cell. DNA sequencing of several related species of Methanosarcinales suggests that the structures of their surface layer proteins are similar to the one in M. acetivorans. These results provide valuable information for understanding the role of these microbes in producing methane in natural environments, a potentially major factor in global carbon cycling. The research was led by Robert Gunsalus of the UCLA-DOE Institute of Genomics and Proteomics.

Reference: Arbing, M. A., et al. 2012. "Structure of the Surface Layer of the Methanogenic Archaean Methanosarcina acetivorans," Proceedings of the National Academy of Sciences of the USA 109(89), 11,812-817. DOI: 10.1073/pnas.1120595109. (Reference link)

Contact: Roland F. Hirsch, SC-23.2, (301) 903-9009
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


June 29, 2012

Fungal End to Coal and the Carboniferous Period: A Possible Solution for Biofuels?

Much of the world's coal was generated 300-360 million years ago during the Carboniferous period. Wood (a major pool of organic carbon that is highly resistant to decay largely due to its lignin content) was deposited, transformed to peat, and eventually transformed to coal. But coal formation may also have declined from an unlikely source: fungi. These fungi had enzymes (ligninases) capable of degrading lignin, a category of enzyme important for the Department of Energy's bioenergy mission, since lignin in plant biomass hinders biomass conversion to biofuels. An international team of scientists from Clark University and DOE's Joint Genome Institute has proposed that a species of fungus, first appearing at about the end of the Carboniferous period, could more efficiently break down dead plant matter, possibly leading to the decline in coal formation. By comparing the genomic sequences of 31 fungi, including 12 sequenced for this study, the researchers showed that genes able to degrade lignin first appeared at the end of this period. Instead of becoming coal, the plant biomass decayed and the carbon was released into the atmosphere as carbon dioxide. This research provides insights into the origin of ligninases that can be used to develop processes for converting plant and tree biomass into bioenergy products.

Reference: Floudas, D., et.al. 2012. "The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes," Science 336, 1715-19. DOI: 10.1126/science.1221748. (Reference link)

Contact: Dan Drell, SC-23.2, (301) 903-4742
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER



Amanita muscaria of the Class Agaricomycetes
Source: Lawrence Berkeley National Laboratory



June 28, 2012

Understanding How microbes Work Together: Methane Production by Partnered Microbes

Methanogenic archaea and sulfate-reducing bacteria (SRBs) both play important roles in the carbon cycle of soils, wetlands, and other environments with limited oxygen availability. SRBs are versatile consumers of a variety of organic compounds, while methanogens primarily convert hydrogen and CO2 into methane. Neither of these organisms is capable of independent growth on lactate, a small organic compound that is an important intermediate in food webs, but can consume it when working together in a partnership called syntrophy. Researchers at the University of Washington and Lawrence Berkeley National Laboratory have published a new study that helps explain how this partnership works. They carried out a high-resolution transcriptomic study of changes in gene expression of the methanogen Methaococcus maripaludis during syntrophic growth on lactate with the SRB Desulfovibrio vulgaris as a partner. The methanogen shows a substantial shift in genes associated with conversion of hydrogen to methane, switching over to a parallel set of enzymes that may be better adapted to low rates of hydrogen production and other conditions associated with syntrophy. These results advance our understanding of microbial production of a potent greenhouse gas and highlight the important role of subtle interactions between organisms that influence environmental processes.

Reference: Walker, C. B., A. M. Redding-Johanson, E. E. Baidoo, L. Rajeev, Z. He, E. L. Hendrickson, M. P. Joachimiak, S. Stolyar, A. P. Arkin, J. A. Leigh, J. Zhou, J. D. Keasling, A. Mukhopadhyay, and D. A. Stahl. 2012. "Functional Responses of Methanogenic Archaea to Syntrophic Growth," The ISME Journal 6, 2045-2055. DOI: 10.1038/ismej.2012.60. (Reference link)

Contact: Joseph Graber, SC-23.2, (301) 903-1239
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


June 18, 2012

Genomic Encyclopedia of Bacteria and Archaea Finds More Cellulases

The biotechnology and biofuels industries are particularly interested in cellulases, enzymes that break down cellulose, the most abundant organic compound on Earth and the component that makes up 33 percent of all plant matter. Cellulases from a group of aerobic bacteria called Actinobacteria are of special interest as sources of enzymes useful for biofuel production from lignocellulosic biomass. They have distinct features and cellular organization when contrasted to those in anaerobic bacteria (such as the Clostridia). The DOE Joint Genome Institute (JGI) has sequenced the genomes of 11 diverse strains of these bacteria. Comparative analysis using the JGI's Integrated Microbial Genomes system followed by experimental verification identified eight cellulolytic Actinobacterial species that were not previously known to degrade cellulose. Of seven organisms tested, six showed activity in assays for cellulases. One organism, Catenulispora acidiphilia, previously unknown to break down cellulose, has 15 predicted cellulases and may be used in future biofuel production. This work, conducted under the umbrella of the JGI's Genomic Encyclopedia of Bacteria and Archaea (GEBA) project, broadens the repertoire of useful enzymes beyond those previously recognized.

Reference: Anderson, I., B. Abt, A. Lykidis, H.-P. Klenk, N. Kyrpides, and N. Ivanova. 2012. "Genomics of Aerobic Cellulose Utilization Systems in Actinobacteria," PLoS ONE 7(6), e39331. DOI: 10.1371/journal.pone.0039331. (Reference link)

Contact: Dan Drell, SC-23.2, (301) 903-4742
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


June 08, 2012

Watching Carbon Dioxide Move in Plant Leaves

U.S. Department of Energy (DOE) plant biology research seeks to optimize plant productivity, both for biofuel development and for carbon sequestration in biomass. Taking a lesson from medical technology, plant biologists are now using sophisticated imaging technology to learn more about nutrient utilization in plants by watching the movement of those nutrients in real time. Positron emission tomography (PET) imaging has been used to study carbon transport in live plants using 11CO2, but because plants typically have very thin leaves, littlemedium is availablefor the emitted positronsto undergo an annihilation event within the plant leaf resulting in limited sensitivity for PET imaging.To address this problem DOE’s Thomas Jefferson Laboratory has developed a compact beta-positive, beta-minus particle imager (PhytoBeta imager) for 11CO2 leaf imaging. The detector is equipped with a flexible arm to allow its placement on or under a leaf while maintaining its original orientation. The detector has been used to generate dynamic images of carbon translocation in a leaf of the spicebush (Lindera benzoin) under two transient light conditions. The PhytoBeta detector system and methodology opens new possibilities for short-lived radioisotope use in plant biology research,especially for problems relatedto carbon utilization, transport, and sequestration.

Reference: Weisenberger, A. G., B. Kross, S. Lee, J. McKisson, J. E. McKisson, W. Xi, C. Zorn, C. D. Reid, C. R. Howell, A. S. Crowell, L. Cumberbatch, B. Fallin, A. Stolin, and M. F. Smith. 2012. “PhytoBeta Imager: A Positron Imager for Plant Biology,” Physics in Medicine and Biology 57(13), 4195–210. DOI: 10.1088/0031-9155/57/13/4195. (Reference link)

Contact: Dean Cole, SC 23.2, (301) 903-3268
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


June 07, 2012

Improving the Reliability of Metagenomic Sequencing Data

Natural microbial communities usually are made up of a large variety of species. Knowing the community's composition is important for addressing DOE energy and environmental missions. Sequencing of the community's combined genome (the ‘metagenome') is now the best way to characterize these communities, but to make sense of the data, it is important to accurately account for all of the experimental and instrumental errors in the process. Up to now, the instrumental errors have been routinely estimated, but not the sample collection and preparation errors. As part of the DOE Systems Biology Knowledgebase project, researchers at Argonne National Laboratory have developed an open-source program called DRISEE (duplicate read inferred sequencing error estimation) to account for both types of errors. DRISEE identifies errors that could be due to sample collection, intermediary DNA processing techniques, or to the instruments themselves. Using DRISEE, the authors reproduce known error rates from a given set of standard data. They then apply this method to show that many factors can contribute to errors in sequencing including read length and sample preparation. Although this method so far only applies to 454 and Illumina sequencing, it will provide valuable assistance to scientists trying to assemble genomes from metagenomic data by helping them determine if the sequence data has a true error and should be disregarded or if it is a natural sequence variation and should be included.

Reference: Keegan, K. P., W. L. Trimble, J. Wilkening, A. Wilke, T. Harrison, M. D'Souze, and F. Meyer. 2012. "A Platform-Independent Method for Detecting Errors in Metagenomic Sequencing Data: DRISSE," PLoS Computational Biology 8(6), e1002541. DOI: 10.1371/journal.pcbi.1002451. (Reference link)

Contact: Susan Gregurick, SC-23.2, (301) 903-7672
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


May 25, 2012

New Clues to Cold Tolerance and Lipid Production for Biofuels in Polar Alga

Algae are of major interest to researchers who are developing alternative energy sources. For example, lipids making up algal membranes can be transformed into biodiesel. One photosynthetic alga, Coccomyxa subellipsoidea C-169, was recently isolated in Antarctica and now is the first alga from a polar region to have its genome sequenced. Surprisingly, the alga thrives at temperatures close to 20°C, though it is tolerant of the cold temperatures in the Antarctic. C. subellipsoidea was sequenced by the DOE Joint Genome Institute, and its predicted protein families were compared with those from several other sequenced green algae. The researchers found that the polar alga had more enzymes involved in lipid metabolism, such as those that desaturate fatty acids. This greater versatility of lipid metabolism is thought to have contributed to its adaptation to cold. The research will provide insights on novel enzymes that may prove useful to researchers working to harness algae for biodiesel production.

Reference: Blanc, G., et al. 2012. "The Genome of the Polar Eukaryotic Microalga Coccomyxa subellipsoidea Reveals Traits of Cold Adaptation," Genome Biology 13, R39. DOI: 10.1186/gb-2012-13-5-r39. (Reference link)

Contact: Dan Drell, SC-23.2, (301) 903-4742
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


May 24, 2012

Understanding Plant Hormones

Plants respond to developmental cues and environmental stresses by controlling both the level and activity of various hormones. A highly adaptable scaffold enables the evolution of promiscuous activity within the auxin-responsive GH3 enzyme family, leading to diversification of substrate specificity and evolution of metabolic control systems. Newly reported crystal structures provide a glimpse into substrate recognition and control of hormones involved in plant growth, development, and defense, enabling deeper understanding of plant metabolism intricacies. The research was conducted using resources at the Advanced Photon Source at Argonne National Laboratory.

Reference: Westfall, C. S., et al. 2012. “Structural Basis for Prereceptor Modulation of Plant Hormones by GH3 Proteins,” Science 336, 1708–11. (Reference link)

Contact: Roland F. Hirsch, SC-23.2, (301) 903-9009
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER



Comparison of GH3 Protein Binding Sites. In plants, GH3 proteins act as molecular on/off switches that control bioactive plant hormone formation by catalyzing the addition of specific amino acids to jasmonic acid, auxin, and benzoates. X-ray structures of GH3 proteins reveal a common three-dimensional fold but variability in the hormone binding site. This figure shows the variation in the jasmonic acid binding site of Arabidopsis thaliana GH3.11/JAR1 (gold) and the salicylic acid binding site of A. thaliana GH3.12/PBS3 (green). more...

Image credit: Argonne National Laboratory



May 14, 2012

Ionic Liquids: Degrading Biomass but Not Biofuel-Producing Microbes

A major hurdle to the development of economically competitive biofuels remains the difficulty of separating long sugar chains from plant biomass (cellulose and hemicellulose) from the tough network of lignin that gives strength and resilience. Pretreatment of plant material by ionic liquids (ILs), a class of salts that are molten at room temperature, is highly effective in disrupting biomass structure and liberating cellulose chains for subsequent conversion to biofuel compounds by fermentative microbes. However, residual IL molecules are highly toxic to biofuel-producing microbes and must be fully removed from the cellulose fraction prior to conversion, an expensive and time-consuming process. To understand this IL toxicity and enable development of resistant strains of microbes, researchers at the Joint Bioenergy Institute (JBEI) examined shifts in gene expression of a novel biomass-degrading bacterium when exposed to an IL. Enterobacter lignolyticus was surprisingly resistant to IL exposure, altering its cell membrane composition, activating a series of pumps to remove IL from the cell interior, and balancing osmotic pressure across the cell membrane. Many of the response mechanisms were specific to IL exposure and were not triggered by exposure to standard salts. These findings provide new insights into the mechanisms used by microbes to tolerate exposure to ionic liquids and may lead to the improvement of IL tolerance in biofuel-producing microbes through targeted genetic engineering.

Reference: Khudyakov, J. I., P. D'haeseleer, S. E. Borglin, K. M. DeAngelis, H. Woo, E. A. Lindquist, T. C. Hazen, B. A. Simmons, and M. P. Thelen. 2012. "Global Transcriptome Response to Ionic Liquid by a Tropical Rain Forest Soil Bacterium, Enterobacter lignolyticus," Proceedings of the National Academy of Sciences of the USA 109(32), E2173-E2182. DOI: 10.1073/pnas.1112750109. (Reference link)

Contact: Joseph Graber, SC-23.2, (301) 903-1239
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


May 10, 2012

Insights into Transport of Lignin-Degradation Compounds in Biofuel-Producing Microbes

Understanding how lignin degradation compounds are transported into microbial cells for further processing into biofuels and for other biotechnology purposes is essential. Using the bacterium Rhodopseudomonas palustris as a model to study the transport of these compounds, researchers from Argonne and Brookhaven national laboratories have applied high-throughput genomic and biophysical approaches to determine the characteristics of the proteins that bind the lignin-degradation products. These binding proteins are part of a large complex, the ABC transporter, that moves chemical compounds through the cell membrane into the cell. The researchers found that the proteins bind aromatic compounds with high affinity and tested the physical configuration of these binding proteins with and without the aromatic degradation products present. The results suggested that the shape of the proteins does not change, but that local changes do occur in the tertiary structure where degradation compounds bind. This molecular reconfiguration could position the aromatic compounds to be more easily transported through the cell membrane. The combination of theoretical models validated by these studies and experimental approaches should be applicable to other organisms relevant to biofuels research.

Reference: Pietri, R., S. Zerbs, D. Corgliano, M. Allaire, F. Collart, and L. Miller. 2012. "Biophysical and Structural Characterization of a Sequence-Diverse Set of Solute-Binding Proteins for Aromatic Compounds," Journal of Biological Chemistry 287, 23748-56. DOI: 10.1074/jbc.M112.352385. (Reference link)

Contact: Arthur Katz, SC-23.2, (301) 903-4932
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


April 16, 2012

New Method to Compare Organism Functionality

Systems biology approaches to bioenergy and environmental research are enabled by reliable models of processes in living cells. Advances in genome sequencing and computational modeling have led to the development of over 100 genome-scale network reconstructions (constraint-based models). Rapid increases in this number are expected, so methods that use algorithms to compare functional characteristics between organisms will be increasingly important. Scientists at the University of Wisconsin have reported a novel approach that embeds two constraint-based models into an optimization model. This combination identifies those genes and reaction pathways that contribute most to differences in metabolic functionality. The authors identified several differences in metabolism in two cyanobacteria that have potential for biofuel production, Synechococcus and Cyanothece. For example, they demonstrated the necessity for a particular protein (plastocyanin) for photosynthesis in Cyanothece, but not in Synechococcus. The new approach also aids the curation of constraint-base models by identifying pathways that are coded by the organism, but that are missing from the model.

Reference: Hamilton, J. J., and J. L. Reed. 2012. "Identification of Functional Differences in Metabolic Networks Using Comparative Genomics and Constraint-Based Models," PLoS ONE 7(4), e34670. DOI:10.1371/journal.pone.0034670. (Reference link)

Contact: John Houghton, SC-23.2, (301) 903-8288
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


April 12, 2012

Switchgrass Sequencing Provides Insight into Genome Structure and Organization

Perennial switchgrass (Panicum virgatum L.) is capable of producing high biomass yields with low inputs on marginal lands, making it one of the most promising candidate bioenergy feedstocks. Breeding programs are underway to enhance and improve switchgrass as a viable agricultural crop, but these efforts are hampered by the limited genetic and genomic information currently available. The switchgrass genome is now being sequenced, but its highly complex structure makes assembly difficult. Researchers at the DOE Joint Genome Institute (JGI) and the DOE Joint BioEnergy Institute (JBEI) report on the construction, sequencing, and analysis of two "Bacterial Artificial Chromosome" (BAC) libraries from switchgrass. These libraries contain relatively large DNA segments and represent essentially a random sampling of the genome, allowing the researchers to analyze structure and function at a genome-wide scale. Comparisons with sequences from other bioenergy-relevant grasses reveal that switchgrass is closely related to sorghum, indicating that the fully sequenced sorghum genome would serve as a good reference for assembling switchgrass gene space. The resources generated here will have utility for a number of applications, including identification of switchgrass gene functions relevant to bioenergy production.

Reference: Sharma, M. K., R. Sharma, P. Cao, J. Jenkins, L. E. Bartley, M. Qualls, J. Grimwood, J. Schmutz, D. Rokhsar, and P. C. Ronald. 2012. "A Genome-Wide Survey of Switchgrass Genome Structure and Organization," PLoS ONE 7(4), e33892, DOI: 10.1371/journal.pone.0033892. (Reference link)

Contact: Cathy Ronning, SC-23.2, (301) 903-9549
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


April 05, 2012

Understanding How Bacteria Use Sunlight

Cyanobacteria are prime candidates for the biological production of biofuels, especially hydrogen. They photosynthesize in sunlight, have relatively fast growth rates, are tolerant to extreme environments, and can accumulate high amounts of intracellular compounds and produce large quantities of H2. New research has combined a new genome-scale, constraint-based model of the cyanobacterium Cyanothece with experiments in a novel photobioreactor. The model and experiments provide new insights into the effect of light quality on metabolism and the bacteria's mechanisms for balancing reductant and electron flows. The model differs from similar models of other cyanobacteria in its detailed treatment of the photosynthesis and respiratory systems. The photobioreactor features dual sources of monochromatic light that can vary photon flux with wavelengths that are tuned to the two bacterial photosynthesis systems. The results will guide development of genome-scale metabolic models for other cyanobacteria and may help with the genetic manipulation of photosynthetic microorganisms to improve biofuel production. These findings were presented by a team of DOE scientists led by Pacific Northwest National Laboratory and the University of Wisconsin.

Reference: Vu, T. T, et al. 2012. "Genome-Scale Modeling of Light-Driven Reductant Partitioning and Carbon Fluxes in Diazotrophic Unicellular Cyanobacterium Cyanothece sp. ATCC 51142," PLoS Computational Biology 8(4), e1002460, DOI:10.1371/journal.pcbi.1002460. (Reference link)

Contact: John Houghton, SC-23.2, (301) 903-8288
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER



Pacific Northwest National Laboratory Photobioreactor



March 27, 2012

Using Systems Biology to Understand Complex Microbial Communities

The ability to effectively model and predict integrated functional properties across complex groups of microbes is critical to understanding major environmental processes. Advances in this area would also facilitate development of novel bioengineering approaches utilizing the unique functional compartmentalization that enables microbial communities to efficiently perform complex cooperative processes. In a new perspective essay, DOE researchers Karsten Zengler and Bernhard Palsson of the University of California San Diego describe a conceptual approach to extend systems biology tools developed to understand metabolic functions of single organisms to more complex multispecies communities. This is a considerable challenge since detailed physiological information is only available for the small fraction of microbes that can be cultivated. Cultivation independent approaches such as metagenomics provide a snapshot of overall functional potential but little information on dynamic processes or interactions between members. Building on preliminary successes with modeling interactions in simple two member partnerships, the authors suggest that a combination of these "bottom up" and "top down" approaches that incorporates efficient targeting of organisms performing processes of interest, high-resolution imaging of spatial process relationships, and more refined environmental 'omics techniques could yield predictive computational models of microbial community function.

Reference: Zengler, K., and B.O. Palsson. 2012. "A Roadmap for the Development of Community Systems (CoSys) Biology," Nature Reviews Microbiology, DOI:10.1038/nrmicro2763. (Reference link)

Contact: Joseph Graber, SC-23.2, (301) 903-1239
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


March 20, 2012

White Rot Fungus Sequence Provides New Understanding of Lignin Degradation

Lignin is a key building block in plant cell walls and one of the two most abundant biopolymers on Earth. It is also highly resistant to breakdown, complicating efforts to use plant biomass for producing biofuels. No animals and few fungi or bacteria are able to degrade lignin. However, the white rot fungus Ceriporiopisis subvermispora not only degrades lignin but leaves the cellulose in biomass intact. An international team of scientists has sequenced and annotated (assigned possible functions to genes) the genome of this fungus to learn more about its mechanisms of lignin degradation. Using experiments and a comparison with the sequence of its more studied relative Phanaerochaete chrysosporium, the scientists identified differences in the degradation genes between the two fungi and developed new hypotheses about the mechanisms that enable these fungi to target lignin but not cellulose. These results may assist in the development of improved pathways for the conversion of biomass to biofuels as well as provide improvements in deconstruction of wood for the pulp and paper industry. The study included researchers at the DOE's Joint Genome Institute (DOE-JGI).

Reference: Fernandez-Fueyo, E., et al. 2012. "Comparative Genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium Provide Insight into Selective Ligninolysis," Proceedings of the National Academy of Sciences of the United States of America 109(14), 5458-63. DOI:10.1073/pnas.1119912109. (Reference link)

Contact: Dan Drell, SC-23.2, (301) 903-4742
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


March 11, 2012

Understanding the Roles Played by Hydrosulphide Membrane Channel and Its Relatives in Living Systems

The hydrosulphide ion (HS–), a critical element in the origin of life on Earth, is important in physiology and cellular signaling. The HS– species is also the terminal product when an anaerobic bacterium derives its oxidative power from sulphate instead of oxygen. A recent study conducted on beamlines at the National Synchrotron Light Source revealed the structure of the hydrosulphide ion channel (HSC), a membrane-pore molecule, elucidating how HS– is able to escape from pathogenic Clostridium difficile cells. In the same protein family, the formate channel (FocA), which has a fold similar to HSC, has been shown to play two other roles related to bioenergy and environmental science. In the first case, hydrogen gas production in Escherichia coli depends on the selective decomposition of formate, whose concentration depends on FocA. In the second, when Euglena experiences long-term chronic exposure to cadmium ions, it overexpresses a FocA protein. This protein has been proposed as a marker for long-lasting cadmium pollution in water.

Reference: Czyzewski, B. K., and D.-N. Wang. 2012. “Identification and Characterization of a Bacterial Hydrosulphide Ion Channel,” Nature 483, 494–97. (Reference link)

Contact: Roland F. Hirsch, SC-23.2, (301) 903-9009
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


March 02, 2012

Microbes Stress Out During Conversion of Pretreated Biomass to Biofuels

Chemical pretreatment of plant biomass prior to enzymatic breakdown significantly improves the release of sugar molecules, which are subsequently converted to biofuel compounds by fermentative microbes. However, pretreatment also introduces a variety of stress factors that can interfere with these fermentative organisms, including residual chemicals, toxins released from the biomass, high concentrations of sugars, and production of biofuels themselves. Researchers at the DOE Great Lakes Bioenergy Research Center (GLBRC) describe the integration of gene expression and physiological stress responses in an ethanol-producing strain of Escherichia coli during growth on corn stover that had been pretreated using ammonia fiber expansion (AFEX) and enzymatic digestion. Their results indicate that osmotic pressure resulting from high sugar concentrations and toxicity due to ethanol production were the two most important stressors to E. coli under these conditions, and that the cells activated a cascade of carefully timed stress tolerance pathways in response to these factors. Identification of these pathways provides new targets for metabolic engineering to improve stress tolerances of biofuel-producing microbes, leading to the development of more sophisticated approaches to leverage microbes' natural abilities to sense and respond to environmental stress.

Reference: Swalbach, M. S., et al. 2012. "Complex Physiology and Compound Stress Responses during Fermentation of Alkali-Pretreated Corn Stover Hydrolysate by an Escherichia coli Ethanologen," Applied and Environmental Microbiology 78, 3442-57, DOI: 10.1128/AEM.07329-11. (Reference link)

Contact: Joseph Graber, SC-23.2, (301) 903-1239
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


March 01, 2012

Microbial Communities Help Solve Environmental Contamination

Microbes are very effective at carrying out a wide range of chemical reactions, even ones that involve substances toxic to higher life forms. Many groundwater sites contaminated with compounds such as trichloroethene (TCE), a pervasive groundwater pollutant often used by industry as cleansers or degreasers, are decontaminated by microbes. Dehalococcoides are the only family of bacteria known to break down TCE to ethene, a harmless chemical compound often used to help ripen fruits. A team of researchers has conducted a metagenomic analysis of a stable dechlorinating community derived from sediment collected at the Alameda Naval Air Station (ANAS) in California. The team identified the other members of this microbial community, since microbes such as Dehalococcoides are known to dechlorinate chemicals more effectively in the presence of other microorganisms. This study showed that all of the genes that code for enzymes involved in dechlorination were associated with Dehalococcoides, emphasizing its importance as the dominant dechlorinating microbe in the ANAS microbial community. Understanding the composition and functioning of communities such as this one will contribute to similar remediation efforts on a variety of cleanup challenges that DOE faces, as well as other processes (e.g., plant nutrition, carbon processing) that microbial communities carry out. The research was based on sequencing carried out by the DOE Joint Genome Institute (JGI).

Reference: Brisson, V. L. et al. 2012. "Metagenomic Analysis of a Stable Trichloroethene-Degrading Microbial Community," The ISME Journal, 1–13. DOI:10.1038/ismej.2012.15. (Reference link)

Contact: Dan Drell, SC-23.2, (301) 903-4742
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


February 16, 2012

Using High-Performance Computing to Study the Hydration of Cellobiose

Cellobiose, the two glucose basic repeat unit of cellulose, is formed during enzymatic or acidic hydrolysis of plant biomass, an early step in the production of biofuels. DOE researchers at the University of California, Irvine, have investigated the stability of cellobiose in water using high-level quantum molecular dynamics at DOE's NERSC high-performance computing facility. The results from these simulations suggest that water dynamics play a leading role in stabilizing cellobiose in particular low energy states. The findings also indicate that long-range interactions between the water molecules and the sugar give rise to collective motions that could impact downstream enzymatic functions in the production of biofuels. These results provide new insight into a key step in the conversion of biomass to fuel molecules.

Reference: Pincu, M., and R. B. Gerber. 2012. "Hydration of Cellobiose: Structure and Dynamics of Cellobiose-(H2O)n, n=5 to 25," Chemical Physics Letters 531, 52–58, DOI: 10.1016/jcplett.2012.02.019. (Reference link)

Contact: Susan Gregurick, SC-23.2, (301) 903-7672
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


February 09, 2012

Understanding How Plants Sense Ultraviolet Light

Sunlight is essential for plant development and growth, yet many details of the mechanisms by which plants respond to sunlight are poorly understood. A recent study published in Science provides new information about the molecular changes initiated by exposure to the UV-B portion of sunlight. The research used small-angle x-ray scattering (SAXS) experiments to characterize how the plant photoreceptor UVR8 changes shape when exposed to UV-B radiation. Two UVR8 molecules are complexed together as a dimer in plant cells and break apart on exposure to UV-B. The separate molecules then interact with a series of proteins in the cell to signal the presence of solar radiation. A specific mutation in UVR8 was found to "retune" the molecule's response from UV-B to UV-C radiation. The results will be useful in understanding how to optimize biomass crop growth. The SAXS studies were carried out at the SIBYLS experimental station at the Advanced Light Source at the Berkeley Lab. The study was led by Elizabeth Getzoff of the Scripps Research Institute.

Reference: Christie, J. M., et al. 2012. "Plant UVR8 Photoreceptor Senses UV-B by Tryptophan-Mediated Disruption of Cross-Dimer Salt Bridges," Science 335, 1492&ndash96. DOI: 10.1126/science.1218091. (Reference link)

Contact: Roland F. Hirsch, SC-23.2, (301) 903-9009
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


February 08, 2012

New Approach for Converting Plant Biomass to Ethanol

The conversion of plant biomass to liquid transportation fuel using consolidated bioprocessing (CBP) technology is a promising, cost-efficient strategy to develop energy from renewable sources. CBP takes advantage of the ability of certain microbes to convert sugars contained within the plant cell wall to high-energy chemicals such as ethanol or butanol, but the efficiency can be hampered by the recalcitrance of certain plant materials to deconstruction. While plant cell wall composition and corresponding resistance to breakdown varies considerably within plant species, this genetic diversity can potentially be exploited if plant material is efficiently screened for such properties. Researchers at the U.S. Department of Energy’s (DOE) BioEnergy Science Center (BESC), together with scientists funded by the U.S. Department of Agriculture-DOE Plant Feedstocks Genomics for Bioenergy program, report the development of a robust assay for biomass digestibility and conversion using the anaerobic bacterium Clostridium phytofermentans. This bacterium is capable of directly converting a wide array of fermentable biomass components to ethanol without the addition of costly, exogenous, deconstruction enzymes. The assay, which measures ethanol production under the influence of different variables, was tested on both herbaceous grasses and woody plants. Significant differences in ethanol production within individual plant species were found, indicating detection of subtle genetic differences. This method provides a means of assessing feedstock quality for digestibility and ethanol production that will facilitate genetic analysis of energy crops for amenability to biological conversion.

Reference: Lee, S. J., et al. 2012. “Biological Conversion Assay Using Clostridium phytofermentans to Estimate Plant Feedstock Quality,” Biotech for Biofuels 5:5, DOI: 10.1186/1754-6834-5-5. (Reference link)

Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


January 25, 2012

Miscanthus Genetic Map Provides Resource for Crop Improvement

Perennial grasses are a potential source of feedstocks for "second-generation" cellulosic bioethanol because they efficiently accumulate large amounts of biomass and can be grown on marginal lands not suitable for conventional agricultural food crops. Among these grasses, Miscanthus is one of the most promising bioenergy crops in the Midwest because of its extremely high biomass yields, in particular the species Miscanthus x giganteus. However, efforts to breed improved varieties of Miscanthus are hampered by its complicated genome structure and lack of genetic tools. With support from the Joint USDA-DOE Plant Feedstocks Genomics for Bioenergy program, researchers report the first genetic linkage maps of Miscanthus using molecular markers derived from the closely related sugarcane grass. Genetic similarity between Miscanthus, sorghum, and sugarcane allowed comparative studies between the three species, revealing information into the genomic relationships among them and also allowing the first genetic map length estimate of Miscanthus. These resources provide a framework that will significantly enhance Miscanthus improvement efforts by facilitating identification of biomass-relevant genes and marker-assisted selection in this important bioenergy crop.

Reference: Kim, C., D. Zhang, S. A. Auckland, L. K. Rainville, K. Jakob, B. Kronmiller, E. J. Sacks, M. Deuter, and A. H. Paterson. 2012. "SSR-Based Genetic Maps of Miscanthus sinensis and M. sacchariflorus and Their Comparison to Sorghum," Theoretical and Applied Genetics, DOI:10.1007/s00122-012-1790-1. (Reference link)

Contact: Cathy Ronning, SC-23.2, (301) 903-9549
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


January 17, 2012

New Type of Lignin Discovered in Vanilla Plant

Found within the plant cell wall, lignin is a complex polymeric compound that provides the plant with both mechanical support and protection from pests and pathogens. However, the structural rigidity of this compound also inhibits efficient conversion of the sugars within plant cell walls into biofuels, making lignin a major obstacle to the efficient production of biofuels from cellulosic feedstocks. Three types of lignin are usually found in nature: H-, G-, and S-lignins. They are synthesized by polymerization of their respective monolignol units. However, lignin biosynthesis can be relatively flexible, sometimes allowing different and more unusual monolignols to be incorporated. Researchers at the DOE BioEnergy Science Center (BESC) and DOE Great Lakes Bioenergy Research Center (GLBRC) report the identification and characterization of a new type of polymer, C-lignin, composed almost exclusively of caffeyl units. Detected in the Vanilla orchid, a few related orchids, and some cactus species, this unique new lignin was found only in the seed coats, with more conventional lignins observed in other plant tissues. These results may lead to a greater understanding of the lignin biosynthetic pathway, as well as new approaches for engineering biomass that can be more easily and efficiently digested for conversion into biofuels.

Reference: Chen, F., Y. Tobimatsu, D. Havkin-Frenkeld, R. A. Dixon, and J. Ralph. 2012. "A Polymer of Caffeyl Alcohol in Plant Seeds," Proceedings of the National Academy of Sciences of the United States of America 109(5), 1772-77. DOI: 10.1073/pnas.1120992109. (Reference link)

Contact: Cathy Ronning, SC-23.2, (301) 903-9549
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


January 15, 2012

Bioenergy Plants Database

Plant feedstocks for next-generation biofuels (e.g., lignocellulosic biomass) will come from many different sources depending on the geographic region and will likely include high biomass-producing species such as switchgrass, pine, poplar, and sorghum. Genome-enabled tools promise to facilitate breeding efforts to maximize biomass quality and yield in these plants; however, most of these species lack a complete genome sequence and many have only limited genetic tools available. To enable genome-based improvement of lignocellulosic biofuel feedstock species, researchers at Michigan State University, with support from the joint USDA-DOE Plant Feedstocks Genomics for Bioenergy program, have developed the Biofuel Feedstock Genomics Resource (BFGR). This web-based portal and database contains data from 54 bioenergy-relevant plant species, together with annotation and tools that allow identification and analysis of genes important for improvement of bioenergy traits, molecular marker analysis, and mapping to specific biochemical and metabolic pathways. Importantly, the database provides comparative analysis tools to allow scientists investigating species that lack a genome sequence to identify critical genes and develop experimentation to determine gene function. The BFGR will provide a valuable resource for plant breeders to use in improving bioenergy feedstocks for biofuel production.

Reference: Childs, K. L., K. Konganti, and C. R. Buell. 2012. "The Biofuel Feedstock Genomics Resource: A Web-Based Portal and Database To Enable Functional Genomics of Plant Biofuel Feedstock Species," Database, DOI:10.1093/database/bar061. (Reference link)

Contact: Cathy Ronning, SC-23.2, (301) 903-9549
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


January 11, 2012

Helping Researchers Find Bioenergy-Related Data

A systems biology approach to biological research requires ready access to information from many investigators conducting a wide variety of experiments. DOE's BioEnergy Science Center (BESC) is undertaking large experimental campaigns to understand the biosynthesis and biodegradation of biomass and to develop biofuel solutions. BESC is generating large volumes of diverse data, including genome sequences, omics data, and diverse assay results. To assist the community of bioenergy researchers, BESC has developed a public Knowledgebase repository (besckb.ornl.gov) that they describe in the journal Bioinformatics. The BESC Knowledgebase serves as a central repository for experimentally generated data and provides an integrated, interactive, and user-friendly analysis framework. The Knowledgebase portal makes tools available for visualization, integration, and analysis of data produced by BESC or obtained from external resources. The aim of this database is to provide a resource for a systems-level understanding of cellular processes involved in plant formation, degradation, and biofuel production. The BESC Knowledgebase fits within the scope of a larger Knowledgebase activity across the DOE Genomic Science Program (http://genomicscience.energy.gov/compbio/).

Reference: Syed, M. H., T. V. Karpinets, M. Parang, M. R. Leuze, B. H. Park, D. Hyatt, S. D. Brown, S. Moulton, M. D. Galloway, and E. C. Uberbacher. 2012. "BESC Knowledgebase Public Portal," Bioinformatics, DOI: 10.1093/bioinformatics/bts016. (Reference link)

Contact: Susan Gregurick, SC-23.2, (301) 903-7672
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


January 08, 2012

Combining Crystallography and Visible Spectroscopy to Understand Enzymes

Structure and function are intimately linked but do not necessarily predict the other. For example, X-ray crystallography provides 3-D atomic structural information about biological macromolecules but does not define important details about metal ions. However, the oxidation state of metal ions at an enzyme's active site has a critical effect on enzyme behavior. Thus, an enzyme's catalytic function derives from the electronic structure of those atoms influencing or directly participating in the reaction, information not revealed by the scattering methods used in X-ray crystallography. A new technology has been developed that simultaneously carries out crystallography and UV-visible and Raman spectroscopy to determine the atomic structure of the entire protein, and electronic and vibrational structures of the metal ions or cofactors within. The combined instrumentation has been used to study the process of demethylation of an organic substrate molecule by an enzyme whose active site includes an iron-sulfur cluster. The authors used spectroscopy to follow the change in the oxidation state of the cluster during the crystallography data collection and to formulate a mechanism for the process. The results provide insight into an important class of phenomena that control cellular behavior. The technology was developed by scientists at the Protein Crystallography Research Resource at the National Synchrotron Light Source at Brookhaven National Laboratory. The new study was led by Allen M. Orville of Brookhaven and Pinghua Liu and Karen N. Allen of Boston University and is published in the Journal of the American Chemical Society.

Reference: Daughtry, K. D., et al. 2012. "Quaternary Ammonium Oxidative Demethylation: X-Ray Crystallographic, Resonance Raman, and UV-Visible Spectroscopic Analysis of a Rieske-Type Demethylase," Journal of the American Chemical Society 134(5), 2823-2834. DOI: 10.1021/ja2111898. (Reference link)

Contact: Roland F. Hirsch, SC-23.2, (301) 903-9009
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER


January 05, 2012

Nanowire pH Sensor for Biological Applications

A cell's internal and external pH plays a critical role in influencing many cellular chemical reactions and functions. Yet measuring pH without the appearance of artifacts in these challenging cellular and extracellular nanoscale environments is very difficult. New silicon nanowire (SiNW) pH sensors that possess long-term stability in these difficult environments have been developed by scientists at Lawrence Berkeley National Laboratory and their collaborators. The sensors were produced using a top-down fabrication process combining electron beam lithography (EBL) with conventional photolithography. A passivation layer (silicon nitride applied using plasma enhanced chemical vapor deposition) is coated on the SiNW's surface to enhance electrical insulation and ion-blocking properties. This study shows that the application of these techniques results in improved stability of the sensor and enhances its performance. The paper explains how to achieve reliable performance in biological systems and discusses the trade-off between stability and pH sensitivity of the sensor response.

Reference: Choi, S., I. Park, Z. Hao, H.-Y. Holman, and A. P. Pisano. 2012. "Quantitative Studies of Long-Term Stable, Top-Down Fabricated Silicon Nanowire pH Sensors," Applied Physics A: Materials Science & Processing, DOI: 10.1007/s00339-011-6754-9. (Reference link)

Contact: Arthur Katz, SC-23.2, (301) 903-4932
Topic Areas:

Division: SC-23.2 Biological Systems Science Division, BER