PNNL's Genomics:GTL Research
Protein interaction network for several important cellular processes in Shewanella oneidensis. View highlight (PDF, 142K).
The U.S. Department of Energy Office of Science Genomics:GTL (Genomes to Life) program is focused on building a systems-level understanding of microbes and microbial communities. This understanding is necessary to address critical problems regarding energy production, environmental remediation, and global climate change.
GTL Overview
Today, scientists know the complete DNA sequences of many organisms – from microbes to plants to humans. DOE's GTL program is using this genomic information in combination with high-throughput technologies to explore the diverse capabilities of microbes. The specific goals of the program include (1) identifying and understanding, at the molecular level, the interactions of proteins and other cellular components that drive cellular processes; (2) characterizing the gene regulatory networks and pathways by which cells carry out critical functions; and (3) studying the complex processes that microbial communities perform in their natural environments. The overall goal of the program is to create realistic and ultimately predictive models of complex biological systems. To support the program's ambitious goals, four core scientific facilities have been proposed to be built to provide the necessary research infrastructure. These include:
- GTL Facility for the Production and Characterization of Proteins and Molecular Tags
- GTL Facility for Whole Proteome Analysis
- GTL Facility for Characterization and Imaging of Molecular Machines
- GTL Facility for Analysis and Modeling of Cellular Systems and Microbial Community Dynamics.
PNNL's Contribution
Pacific Northwest National Laboratory (PNNL) has assisted DOE in the GTL planning process and is a key participant in the GTL program. Our scientists serve as technical leaders for a variety of DOE GTL research goals.
Shewanella Federation - PNNL leads the Microbial Cell Project's Shewanella Federation, which is focused on understanding how metal-reducing bacteria sense and respond to their environment. Microbial metal reduction has potential application as a remediation strategy to immobilize radionuclides and metals in the environment.
Genomics:GTL Center for Molecular and Cellular Systems (CMCS) - PNNL and Oak Ridge National Laboratory lead the Genomics:GTL CMCS research team. The CMCS team seeks to understand biochemical functions at the molecular level. Integrating a variety of existing molecular biology, microbiology, analytical, and computational tools, the CMCS team is working to produce, identify, and characterize protein complexes. The project also supports the development of new capabilities to isolate, identify, and characterize protein complexes as well as the development of novel bioinformatic and computational tools. Initially, CMCS efforts are focused on two microbial systems, Rhodopseudomonas palustris (R. palustris) and Shewanella oneidensis (S. oneidensis). These two organisms are common to the DOE GTL Microbial Cell Program.
Development and Application of New Technologies for Comprehensive and Quantitative High-Throughput Microbial Proteomics - As part of DOE GTL's Technology Development and Use, Proteomics and Metabolomics research, a team led by PNNL scientist Richard Smith is working to improve the quality of global proteome measurements, speed up data generation, and supply the computational infrastructure and tools needed to manage this data. The computational element of this project is imperative for extracting biological knowledge from large and complex data sets.
Development of Multipurpose Tags and Affinity Reagents for Rapid Isolation and Visualization of Protein Complexes - As part of the DOE GTL's Technology Development and Use, Protein Production and Molecular Tags research, PNNL scientist Thomas Squier and his team are developing high-throughput methods to rapidly isolate and characterize protein complexes. Their method uses a small genetically encoded protein tag with an 8 amino-acid sequence containing a tetracysteine motif. This protein tag can be used to capture proteins and protein complexes using affinity reagents, manipulated with fluorescent dyes for imaging experiments to locate proteins or protein complexes in living cells, and applied to kinetic studies to characterize cell signaling complexes. By studying protein complexes, we can learn what molecules are working together to perform cellular functions.
Some material for this webpage was taken directly from the U.S. Department of Energy Office of Science Genomics:GTL website. Please refer to this website for more detailed information about DOE's GTL program.