Systems Microbiology
Microbial Interactions. Understanding microbial interactions—those that occur between different microbes as well as between microbes and their extracellular environment—has the potential for high scientific impact in areas as diverse as gene function discovery to microbial ecology.
PNNL scientists are conducting research to acquire a predictive understanding of how microbial interactions impart stability, fitness, and functional efficiency to microbial systems. In particular, we are investigating those systems that are involved in the fate and transport of subsurface pollutants and terrestrial primary production, or that are being harnessed for applications in engineered systems such as next-generation biorefineries.
Cryo-transmission electron microscope image of Shewanella oneidensis MR-1Our approach is the study of critical microbial properties and processes on three systems levels—molecular, cellular, and community. We do this through fundamental research and technology development that underpins all microbial and plant research in DOE's Genomics: GTL program.
Biofuels and Bioenergy. Our scientists perform genome-enabled studies of phototrophic metabolism for bioenergy applications through application of metabolic modeling and synthetic biology tools. The scientific focus includes:
- Metabolic reconstruction of "model" cyanobacterial organisms (emphasis on hydrogen; longer-term targets may include lipids and hydrocarbons)
- Exploring the potential of autotroph-heterotroph associations (AHAs) for biofuel production (initial emphasis on hydrogen production in binary cultures of Shewanella and model cyanobacteria; long term: extension to new/engineered strains and biofuels)
- Exploratory studies (bioprospecting) of halotolerant/halophilic photosynthetic organisms to elucidate metabolic properties directly related to the production of relevant metabolites either as axenic or mixed cultures.
Systems Biology of Shewanella. PNNL has led an international consortium that has used a systems biology approach to studying Shewanella oneidensis, a metabolically versatile bacterium that can reduce a wide range of organic compounds, metal ions, and radionuclides. S. oneidensis is of particular interest to DOE for its use in reducing the mobilization of radionuclides at DOE sites.
We are applying knowledge and resources from our studies of Shewanella to biogeochemistry and energy issues, such as contaminant fate and transport, electron transfer to minerals, and hydrogen production.
Research highlights
At Pacific Northwest National Laboratory, scientists work to advance the knowledge and understanding of the evolution of bacterium, such as Shewanella oneidensis, shown here, that are important in the fate and transport of contaminants, particularly metals.- S. oneidensis genome annotation curation. In collaboration with Gretta Serres at Woods Hole Marine Sciences Laboratory, we have used both bioinformatics tools and experimental data and literature mining to develop a robust curation of the annotation for the genome sequence of S. oneidensis MR-1. Data produced by PNNL's high-throughput accurate mass time and tag proteomics capability has been used extensively to improve the gene model.
- Mapping Mobile Elements. PNNL scientists have mapped nearly 300 mobile elements within the genome of S. oneidensis MR-1 and identified over 200 pseudogenes (genes with mutations predicted to prevent production of functional proteins), thereby advancing our knowledge and understanding of the evolution of the bacterium.
Related publications
- Gupta, N., J. Benhamida, V. Bhargava, D. Goodman, E. Kain, I. Kerman, N. Nguyen, N. Ollikainen, J. Rodriguez, J. Wang, M. S. Lipton, M. Romine, V. Bafna, R. D. Smith, P. A. Pevzner. 2008. "Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes." Genome Res. 18(7):1133-1142.
- Gupta, N., S. Tanner, J. Navdeep, J. Adkins, M. Lipton, R. Edwards, M. Romine, A. Osterman, V. Bafna, R. D. Smith, and P. Pevzner. 2007. "Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation." Genome Res. 17(9):1362-1377.
- Lipton, M. S., M. F. Romine, M. E. Monroe, D. A. Elias, L. Pasa-Tolic, G. A. Anderson, D. J. Anderson, J. K. Fredrickson, K. K. Hixson, C. D. Masselon, H. M. Mottaz, N. Tolic, and R. D. Smith. 2006. "The AMT tag approach to proteomic characterization of Deinococcus radiodurans and Shewanella oneidensis." In Microbial Proteomics, Methods of Biochemical Analysis 49:113-134. John Wiley & Sons, Inc., Hoboken, NJ.
- Elias, D. A., M. E. Monroe, M. J. Marshall, M. F. Romine, A. S. Beliaev, J. K. Fredrickson, G. A. Anderson, R. D. Smith, and M. S. Lipton. 2005. "Detection and characterization of hypothetical proteins in Shewanella oneidensis MR-1 using mass spectrometry proteomics." Proteomics 5(12):3120-3130.
Respiration of Shewanella. Using top-down and bottom-up approaches to characterize regulatory genes and networks, we've discovered that Shewanella is "wired" differently—primary regulatory control of respiration is mediated by Crp rather than Fnr.
Publication
- Fredrickson, J. K., M. F. Romine, A. S. Beliaev, J. M. Auchtung, M. E. Driscoll, T. S. Gardner, K. H. Nealson, A. L. Osterman , G. Pinchuk, J. L. Reed, D. A. Rodionov, J. L. Rodrigues, D. A. Saffarini, M. H. Serres, A. M. Spormann, I. B. Zhulin, and J. M. Tiedje. 2008. "Towards environmental systems biology of Shewanella." Nat. Rev. Microbiol. 6(8):592-603.
Novel catabolic pathways. In collaboration with Andrei Osterman at the Burnham Institute we have used comparative genomics strategies to discover a new pathway for degradation of N-acetyl glucosamine (a breakdown product of chitin) and a novel gene that enables Shewanellae to use lactate as a sole source of carbon and energy. See Discovery Fleshes Out Metabolism of Key Environmental and Energy Bacteria
Related Publications
- Pinchuk GE, DA Rodionov, C Yang, X Li, AL Osterman, E Dervyn, OV Geydebrekht, SB Reed, MF Romine, FR Collart, J Scott, JK Fredrickson, and AS Beliaev. 2008. "Genomic reconstruction of Shewanella oneidensis MR-1 metabolism reveals previously uncharacterized machinery for lactate utilization." PNAS 106:2874-2879.
- Yang, C., D. A. Rodionov, X. Li, O. N. Laikova, M. S. Gelfand, O. P. Zagnitko, M. F. Romine, A. Obraztsova, K. H. Nealson, and A. L. Osterman. 2006. "Comparative genomics and experimental characterization of N-acetylglucosamine utilization pathways of Shewanella oneidensis." J. Biol. Chem. 281(40):29872-29885.
Researchers
Jim Fredrickson, Margaret Romine, Alex Beliaev, and Grigoriy Pinchuk.