U.S. Department of Energy

Pacific Northwest National Laboratory

Systems Biology

PNNL has been recognized as a leader in systems biology within the DOE national laboratory system since the establishment of the Biological Systems Initiative in 2001. The Integrated Omics technical group excels at generating the high content proteomic and metabolomic datasets required for computational modeling and simulation of complex biological processes. Working closely with colleagues in the Computational Biology technical group, staff in the Integrated Omics group have made essential contributions to systems biology programs in microbial communities, biofuels, viral pathogenesis, host-pathogen interactions, and biodefense.

Photosynthetic microbes for biofuel production

The transformation of sunlight and CO2 into fuels, or their precursors, is an inherent property of photoautotrophic organisms. However, significant advances in efficiency are necessary to attain environmental and economic sustainability. Currently, productivities of photosynthetic organisms are limited by a set of well recognized shortcomings, which include deficiencies in: (a) efficiently coupling light capture to photosynthetic processes, (b) managing the absorption of excess excitation energy, (c) understanding and manipulating CO2 availability, trafficking and reduction, and (d) regulation/integration of metabolic networks and the impact of nutrient levels on the sustained synthesis of biofuel relevant products. To overcome existing economic hurdles, biofuels research efforts must focus on the core issues of efficient light capture and utilization, ensuring that CO2 levels are not limiting, and reprogramming metabolic networks that were selected during evolution to enable cell proliferation and survival in the presence of organisms competing for limited resources. We are using proteomics and redox-based chemoproteomics to facilitate the understanding of photosynthetic autotrophs to maximize their biodesign potential for biofuels production.

Lignocellulose degradation for biofuel production

In nature, an important service provided by fungal, bacterial, and archael microbes and communities is the breakdown of cellulosic biomass, comprised mainly of cellulose, hemicellulose, and lignin. In all, roughly 70% of plant biomass is composed of 5- and 6-carbon sugars, making it a primary substrate for the development of second generation biofuels generated from non-edible crops. However, the unlocking of these sugars by industrial bioconversion is currently inefficient, requiring extensive chemical and physical pre-treatment of recalcitrant cellulosic biomass to make it amenable to glycoside hydrolase enzymes that must posses a high degree of catalytic activity and thermal stability. We are using proteomics and chemoproteomics to identify novel glysocide hydrolases, including those that are thermotolerant and acid-stable, from diverse microbes. We are also working with complex mixtures of lignocellulose degrading enzymes obtained from highly efficient microbial communities, such as the cow rumen.

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