2001 DOE Genome Research in Support of the Genomic Science Program

In Fiscal Year 2001, the U.S. Department of Energy Office of Biological and Environmental Research (BER) and Office of Advanced Scientific Computing Research (ASCR) called for new research that was to become the predecessor of the Genomic Science Program. The following projects were funded from these solicitations and are part of the Genomic Science Program. These research solicitations, Microbial Cell Project and Advanced Modeling and Simulation of Biological Systems, called for research that would use experimentation and computation to lead to a more comprehensive understanding of the functioning of microbes as complete biological systems. The following projects were funded from these solicitations and are part of the Genomic Science program.

Jim Fredrickson (PNNL), Jizhong Zhou (ORNL), and Eugene Kolker (BIATECH) for Environmental Sensing, Metabolic Response and Regulatory Networks in the Respiratory Versitile Bacterium Shewanella to initiate the Shewanella Federation, a multi-investigator and multi-lab consortium to characterize the biology of the fully sequenced bacterium Shewanella oneidensis MR-1. This microbe is widespread in the environment and has metabolic capacities allowing it to “handle” (reduce or oxidize) many of the metals of major concern to DOE due to their presence at contaminated DOE sites. The research will use innovative technologies to: 1) analyze the proteome and transcriptome (using Mass Spec and microarray methods); 2) localize the proteins in the cell envelope (using various microscope approaches); 3) characterize the biochemistry and physiology, using optical methods to examine protein/protein interactions (in collaboration with Shimon Weiss at UCLA); and 4) model cell networks (in collaboration with Bernhard Palsson, UCSD).

Harley McAdams (Stanford) for Global Characterization of Genetic Regulatory Circuitry Controlling Adaptive Metabolic Pathways, to study Caulobacter crescentus, an important organism for bioremediation. The 5 main thrusts are: 1) to identify genome circuits involved in growth; 2) to study the physiology of cells in biofilms; 3) to study signal transduction networks; 4) to combine these experiments with computational programs to predict metabolic and regulatory pathways and operons and to construct a regulatory map to identify networks that control growth cell cycle, biofilm formation and response to stress; and 5) to model, using this vast array of information generated about the biology of C. crescentus, its biology. DOEs Office of Basic Energy Sciences is also helping to fund this project.

Derek Lovley (U Mass Amherst) for a Conceptual and In Silico Model of the Dissimilatory Metal-Reducing Microorganism, Geobacter sulfurreducens, to study the energetics and metabolism of Geobacter sulfurreducens, a model organism for various Geobacter species and other iron-reducing microbes. Geobacter species dominate subsurface sites in which iron reduction occurs. The project will model central metabolism, electron transport, growth under nutrient-limiting conditions, regulatory mechanisms, and environmental responses in G. sulfurreducens. The long term goal is to develop a predictive in silico model of these processes.

Michael Daly (Uniformed Services University of the Health Sciences) for the Dynamics of Cellular Processes in Deinococcus radiodurans, to study the multiple cellular components of the responses of the highly radiation-resistant microbe, Deinococcus radiodurans, to acute and chronic radiation exposure. This project will use computational and experimental approaches including whole cell mass spectrometry (MS) and DNA arrays. The organism focused on, Deinococcus radiodurans is capable of resisting enormous doses of radiation and the mechanisms behind this ability are as yet uncharacterized.

Robert Tabita (Ohio State) for the Rhodopseudomonas palustris Microbial Cell Project, to study Rhodopseudomonas palustris, a model purple nonsulfur photosynthetic bacterium. This bacterium is remarkably versatile in the ways in which it can grow. The genome sequence is complete and the annotation is nearing completion. A genetic system is available. This group will carry out research to characterize the biochemical and physiological processes as well as functional proteomic analyses using expression profiling with transcriptional micro-array analysis, intracellular localization and computational cell process modeling. The combination of genomics, proteomics, DNA array technology, bacterial “two hybrid” systems, and directed and random mutagenesis constitutes a global approach to the biology of R. palustris.

Timothy Donohue (University of Wisconsin-Madison) for the Molecular Basis for Metabolic and Energetic Diversity, to analyze and model the flux of carbon, nitrogen and “reducing power” of the versatile microorganism, the alpha proteobacterium Rhodobacter sphaeroides strain 2.4.1. A main goal is to understand the complex regulation system in this versatile bacterium and the expected complexity of the genome.

John Leigh (University of Washington) for Global Regulation in the Methane Producing Archaeon Methanococcus maripaludis, to study Methanococcus maripaludis, a methane producing microbe of considerable promise for understanding biomass conversion. The focus will be on understanding its physiology (using microarrays) and its regulatory systems (using mutagenesis of candidate regulatory genes), especially those pertinent to methane production. Funding for this project is provided by DOEs Office of Basic Energy Sciences.

Willem Vermaas (Arizona State University) for An Integrative Approach to Energy, Carbon, and Redox Metabolism in the Cyanobacterium Synechococcus, to study Synechocystis sp. PCC 6803, the first photosynthetic organism whose genome was completely sequenced. The main approach will be to exploit the library of targeted gene deletion mutants that are available (with more becoming available) to study photosynthesis and electron transport pathways. This will be combined with other proteomic, metabolic, and intracellular localization information to build a metabolic model. Funding for this project is provided by DOEs Office of Basic Energy Sciences.

Norman Dovichi (University of Washington) for the Single-Cell Proteome Project: Ultrasensitive Proteome Analysis of Deinococcus radiodurans, to develop capillary analysis technologies to permit the monitoring of changes in protein expression in single cells using fluorescence and pushing the resolution by an order of magnitude over what it presently is; in short, to build a “better microscope” for tracking gene expression in single cells following environmental challenges (e.g., exposure to radiation).

Kenneth Downing (LBNL) for Electron Tomography of Microbial Cells, to study the use of electron tomography to image the inside of a microbial cell by freezing intact microbial cells in a way that preserves one layer of liquid water molecules above their membranes (permitting survival and viability). EM images and computer reconstruction are then be used to derive 3D images of internal cell constituents.

Gary Andersen (LLNL) for Pangenomic Analysis Using RDA, to pursue advanced protein-protein interaction systems for use to characterize the protein machines within Caulobacter crescentus (in collaboration with Harley McAdams, Stanford). This project will build a cellular protein interaction map using a protein-fragment complementation assay that offers advantages over the yeast two-hybrid system.

David Case (Scripps Research Institute) for Biomolecular Simulation Using Amber and CHARMM, to build on the existing CHARMM and Amber simulation packages, adapting them in novel ways to massively parallel architectures and high-performance CPUs.

Peter Ortoleva (Indiana University) for Cyber Cell: Automated Physico-Chemical Cell Model Development Through Information Technology, to integrate the comprehensive reaction-transport-genetic cell simulator, Cyber-Cell, with experimental data, resulting in an automated model development methodology. The model will be developed and tested using data on E. coli.

Andrey Rzhetsky (Columbia University) for Computational Analysis and Simulation of Bacterial Molecular Networks, to enhance our ability to predict and control bacterial phenotypic behavior by proper manipulation of genomic information and environmental stimuli. Such bacterial phenotypic behavior can be steered towards DOE-relevant activities such as environmental remediation and restoration of contaminated environments.

Albert Laszio Barabasi (University of Notre Dame) for Organization of Complex Metabolic Networks, to develop semi-quantitative models that capture the structure and function of the E. coli metabolism. The investigators plan to complement the purely topologic, pathway based methodologies with dynamical information quantifying how the different components of E. coli metabolism work together under varying conditions. The approach emphasizes topological characterization of the networks, and statistical characterization of the fluctuation of metabolites, leading to experimentally testable predictions. The modeling approach will combine stoichiometric and regulatory information.

Julie Mitchell, (University of California, San Diego) for Parallel Protein Docking and Interaction Dynamics with Adaptive Meash Solutions to the Poisson-Boltzmann Equation, to improve tools for determination of the structures of protein complexes through docking with an energy function of high quality. Particular emphasis is given to electrostatic interactions, and much of the work involves needed improvements to approaches in current use through application of accurate solutions to the Poisson-Boltzmann equation.

Michael Colvin (Lawrence Livermore National Laboratory) for Advanced Molecular Simulations of E. coli Polymerase III, to use advanced molecular simulation methods on terascale computers to improve understanding of bacterial multicomponent protein machines. The research will involve performing dynamical simulations of E. coli DNA polymerase III biochemical processes using classical and quantum mechanical force fields and object-oriented implementations of these algorithms that efficiently use massively parallel computers.

Haluk Resat (Pacific Northwest National Laboratory) for Computational Approaches and Framework for Microbial Cell Simulations, to develop a wide-ranging set of computational tools in support of intracellular model building. These tools will be applied to build computable representations of the core energy and material pathways in Rhodobacter sphaeroides genome sequenced and being assembled at present. R. sphaeroides is of interest and relevant for applying and validating newly developed biological modeling tools as (1) the structure, function and regulation of its photosynthetic systems are among the best characterized (2) it provides, in a single organism, access to the entire range of metabolic lifestyles, their coupling and regulation.

T.P. Straatsma (Pacific Northwest National Laboratory) for Molecular Modeling of Complex Enzymatic reactions: The Respiratory Enzyme Flavocytochrome c3 Fumarate Reductase of Shewanella frigidimarina, to carry out highly detailed simulations of complex reaction mechanisms in bacterial enzymes such as a flavocytochrome. Research involves ongoing development of a program that permits such simulations, and specific application to the study of metal ion reduction through an electron transfer process. The tools developed will be useful to many researchers.

Christopher Schilling (Genomatica, Inc.) for Development of the Next Generation of Genome-scale Constraints-Based Cellular Models, to carry out a top-down approach to metabolic modeling, that begins with a stoichiometric network model and successively constrains the set of admissible solutions with conditions that are derived, for instance, from thermodynamics resulting, ideally, in a unique solution that is the true solution.

Eugene Kolker (BIATECH) for Interdisciplinary Study of Shewanella putrefaciens MR-1’s Metabolism and Metal Reduction, to study S. putrefaciens MR-1 in an attempt to delineate the organisms response to environmental perturbation. MR-1 is a suitable organism for this study because it can function in aerobic conditions, reduces metals, has a well-defined biochemistry and a sequenced genome.