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GSP PI Meeting 2011 Abstracts DOE/SC-0140 Joint Meeting 2011 Genomic Science Awardee Meeting IX and USDA-DOE Plant Feedstock Genomics for Bioenergy Awardee Meeting [Revised: April 14, 2011] Crystal City, Virginia April 10-13, 2011 Prepared for the Prepared by U.S. Department of Energy Biological and Environmental Research Information System Office of Science Oak Ridge National Laboratory Office of Biological and Environmental Research Oak Ridge, TN 37830 Germantown, MD 20874-1290 Managed by UT-Battelle, LLC For the U.S. Department of Energy http://genomicscience.energy.gov Under contract DE-AC05-00OR22725 Systems Biology Strategies and Technologies for Understanding Microbes, Plants, and Communities biological experts for a number of different microbes and Analytical Strategies for the Study plants. In our poster, we highlight the ability to use pan- omics data for, characterization of microbial communities, of Plants, Microbes, and Microbial elucidation of phenotypic and genotyptic relationships, Communities advances in the characterization of protein modification state, and the determination of protein localization in stem, root and leaf tissues of Arabidopsis. Microbes do not live in isolation; therefore, understanding the function of a microbe in the environment and the effect Proteomics183 and Pan-omics Driven Analysis of of the environment upon the microbe requires the character- ization of the community as a whole. Research on individual Microbial Communities, Comparative Biology microbes takes on a larger significance if the findings about and Environmental Symbiosis an organism in cell culture can be extrapolated to the activi- 1 ties of the organism within the natural community in the Mary S. Lipton * ([email protected]), Stephen J. environment. SAR11, also known as Pelagibacter ubique, is 1 1 1 Callister, Kristin E. Burnum, Roslyn N. Brown, Kim K. the dominant heterotrophic bacterial clade in the oceans, Hixson,2 Janani Shutthanandan,1 Samuel O. Purvine,2 where roughly 25% of the 16S rRNA gene sequences Angela D. Norbeck,1 Matthew E. Monroe,1 Carrie D. retrieved from uncultured marine bacteria belong to the Nicora,1 Gordon A. Anderson,1 and Richard D. Smith1 SAR11 group. Evolutionary selection to minimize genome (PI) size in large, nutrient-limited ocean populations, known as Collaborators: Steve Giovannoni,3 Cameron Currie,4 genome streamlining, has been implicated as an important Michael Kahn,5 Donald Bryant,6 Norman Lewis,5 and factor in the evolution of SAR11. These cells have dispensed David Kramer7 with many pathways and transporters that are typically present in bacteria with more complex genomes. We have 1Biological Sciences Division; Pacific Northwest investigated how Pelagibacter respond to iron limitation by National Laboratory; 2Environmental Molecular Sciences applying differential measurements using our new pan- Laboratory; Pacific Northwest National Laboratory; omics platform to Pelagibacter cell cultures. 3Oregon State University; 4University of Wisconsin; 5 6 The fungus-growing ant– microbe symbiosis is a paradig- Washington State University; Pennsylvania State 7 matic example of organic complexity generated through University; and Michigan State University symbiotic association and, over the last decade, it has Project Goals: This project employs comprehensive global become a model system for studying symbiosis. We have and directed pan-omics analyses and novel informatics demonstrated an in-depth profiling of the fungal garden approaches (developed in parallel in this program) of complete with bacteria (fungus alone, isolated bacteria, and microbes, plants and microbial communities to enhance fungal garden intact) to understand the relationship between scientific understanding through elucidation of pheno- the fungus and the bacterial protectors. Proteomics and typic relationships between environmentally important metabolomic studies of the secreted proteins from the bac- microorganisms, characterization of higher organisms, teria have been characterized in an effort to understand the characterization of the metabolic activities within micro- relationship between the ants and the fungus. These studies bial communities, and identification of post-translation- demonstrate, the ability to use pan-omics measurements ally modified proteins. on an ecosystem level, spanning bacteria to multi-cellular organisms. Inherent to exploiting microbial function for carbon cycling, bioremediation or biofuel production or utilizing plants as The genotype of an organism is the full hereditary genome, energy precursors is the detailed understanding of the physi- while the phenotype is the actual observed biochemical ology of the cell. Cellular functions are dictated by the pro- characteristics of an organism. Although the genome of teins expressed in the cell, their resident lifetime in the cell, an organism influences its phenotype, phylogenetically their localization and their modification state. Additionally, diverse organisms can share a common phenotype. As these processes mitigate the metabolites in the cell that serve such, genome-based comparisons are limited in describing as energy and carbon currency. This project exploits the these common mechanisms in diverse organisms. We have technological and informatics advances of the pan-omics developed a number of proteomics databases for each of measurement pipeline at PNNL (as described in the poster the six bacterial phyla known to contain chlorophyll-based by Anderson et al and Metz et al) to address organism- phototrophs, including the recently discovered Candidatus specific scientific objectives developed in conjunction with Chloroacidobacteria thermophilum, which is currently the only * Presenting author ‡Poster Number Not in Sequence 145 Systems Biology Strategies and Technologies known phototroph within the phylum Acidobacteria. Using needed to elucidate interacting networks of genes, pro- these databases, to investigate diverse bacteria that share teins, and biochemical reactions in biological systems. a similar photosynthetic phenotype while having vastly different genotypes. With a better understanding of the The goal of BER’s Genome Science Program (GSP) is to photosynthetic pathways, and especially the pathways occur- achieve a predictive systems level understanding of plants, ring within cyanobacteria and chloroplasts, systems biology microbes and biological communities via the integration of approaches will be poised to determine how these organisms fundamental science and technology developments to enable can be used to create alternative fuels, as well as their role in biological solutions to challenges in energy, environment the carbon cycle. and climate. Achieving this goal requires comprehensive proteomics, metabolomics, lipidomics, and glycomics, i.e. Symbiosis is the long-term interaction between different pan-omics, measurement capabilities and the integration biological species. One sort of symbiosis is nitrogen fixation of data generated by these approaches. This project aims to occurring in specialized symbiotic interactions between facilitate understandings of biological systems by providing plants and bacteria is a major source of useful nitrogen. We pan-omics molecular measurement capabilities that will have used Pan-omics measurements to elucidate the interac- be applied in biology-driven collaborative projects led by tion between Medicago truncatula and Sinorhizobium meliloti, investigators actively engaged in developing systems biology mapping proteins expressed in both the plant and the sym- approaches in support of BER’s research agenda. Our strat- biont with preliminary understanding of their interaction. egy benefits from advances in high resolution nano-liquid chromatography (LC) separations combined with high mass Additional information and supplementary material can accuracy mass spectrometry (MS) measurements and other be found at the PNNL proteomics website at http://ober- developments that afford large gains in performance and proteomics.pnl.gov/ throughput. These efforts also include the automation of key Acknowledgements: This research is supported by the Office of Biological steps in proteomics sample processing; fractionation of pro- and Environmental Research of the U.S. Department of Energy. Portions tein samples based on surface membrane protein enrichment of this research were performed in the Environmental Molecular Sciences and subcellular fractionation methods using differential gra- Laboratory, a national scientific user facility sponsored by the DOE’s dient centrifugation; and implementation of novel methods Office of Biological and Environmental Research Pacific Northwest for protein extraction from environmental (e.g. soil) samples. National Laboratory is operated for the U.S. Department of Energy by Battelle Memorial Institute through Contract No. DE-AC05-76RLO Additional advancements involve the implementation of 1830. targeted proteomics methods (e.g. activity-based protein profiling and multiple reaction monitoring) and approaches for the elucidation of protein isoforms (e.g. integrated top- down and bottom-up proteomics) and post-translational modifications (e.g. phosphoproteomics and characterization of protein glycosites). Proteomics184 and Pan-omics Measurements for Comprehensive Systems Characterization of To facilitate these goals, this project includes efforts to develop and apply new measurement platforms and inte- Biological Systems grated analytical strategies implemented in concert with the Thomas O. Metz* ([email protected]),
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