Berkeley Lab

History: 2002-2011

In 2009, Department of Energy Office of Biological and Environmental Research (OBER) merged four separate programs: The Environmental Stress Pathway Project (ESPP), the Protein Complex Analysis Project (PCAP), Molecular assemblies, genes, and genomics integrated efficiently (MAGGIE), and a MAGGIE-allied program Genemap-MS into a single SFA with integrated and aligned aims and goals.

ESPP was established in 2002 to understand the microbial processes and interactions driving metal-reduction/remediation in radionuclide contaminated sites.  Environmental metagenomic studies were carried out to identify community differences in both taxonomic and gene functional structure associated with different contaminant geochemistries before and after stimulation. From these, key cellular processes were selected to to examine in the laboratory.  A key laboratory model system, capable of performing metal reduction and establishing syntrophic interactions, was used to hone the ability to map the cellular metabolic and stress response networks that might be deployed during the metal reduction process. A sulfate-reducing bacterium (SRB), Desulfovibrio vulgaris Hildenborough (DvH) and an unnatural syntrophic partner, the methanogen Methanococcus maripaludis (Mm) served as a focal point for these studies and models for the key processes thought to be important during stimulated metal reduction at the environmental sites.

PCAP was established in 2005 to develop high-throughput and high resolution technologies to discover spatio-temporal interactions of proteins within bacteria. Its approach combined novel mass-spectrometry and both optical and cryo-EM imaging. The core strategy of the alliance was to vastly improve the ability to map the cellular networks and to get to structure-function faster than was then possible. With this increase in capability, new mechanisms would be easier to uncover and predictive models of cellular networks better informed.

MAGGIE was established in 2007 to understand the dynamics of protein and metabolic networks by comparing specifically chosen phylogenetically diverse pathways and proteins involved in key ubiquitous stress responses involved in DNA damage, salt tolerance, and carbon stress. The project deployed advanced structural biological techniques such as small-angle X-RAY scattering, high-throughput metabolomics, and high-controlled RNA analysis to discover key mechanisms of these stress responses. With its allied program, Genemap-MS, it also deployed advanced mass-spectrometry to  map proteins to their metabolic functions. They also developed a data integration framework to integrate physiological data to predict models of cellular transcriptional responses to environmental change. To understand  and predict cellular behaviors, excellent technologies for molecular measurement were rigorously integrated in a clean mathematical framework.

Our initial field site was Hanford, WA on the Columbia River. Due to a variety of factors, Hanford was closed to us for research. In 2011 in consultation with BER leadership, after careful assessment of several field sites, within the constraints of DOE mission, cost and geographic proximity to team members, we chose the Oak Ridge Reservation Field Research Center (FRC) as our new field site.

Environmental Stress Pathway Project (ESPP2)

ESPP logoAdam Arkin, co-Principal Investigator (LBNL, Physical Biosciences Division)
Terry Hazen, co-Principal Investigator (LBNL, Earth Sciences Division)

formerly known as Rapid Deduction of Stress Response Pathways in Metal/Radiomuclide Reducing Bacteria
ESPP2 is developing computational models that describe and predict the behavior of gene regulatory networks in microbes in response to the environmental conditions found in DOE waste sites. The research takes place within the Virtual Institute for Microbial Stress and Survival (VIMSS).

Protein Complex Analysis Project (PCAP)

dvulgarisMark Biggin, Principal Investigator (LBNL, Life Sciences Division)

This project aims to characterize microbes under stress response to conditions commonly found in U.S. Department of Energy (DOE) metal and radiomuclide contaminated sites, with an emphasis on high-throughput analysis of microbial multi-protein complexes. The project integrates microbiology (production of tagged protein expression strains and biomass production), multi-protein complex isolation and identification by mass spectrometry, imaging multi-protein complexes by electron microscopy, and computational analysis and modeling that seeks to understand how these complexes control a microorganisms;s ability to survive in relevant contaminated environments while reducing metals and radiomuclides. Data production and analysis methods will be automated to establish a pipeline that can analyze the majority of stable multi-protein complexes in a amicrobe as well as a number of unstable complexes. The project, awarded in october 2005, will build on the research and infrastructure of an on-going Genomics:GTL project “Rapid deduction of stress response pathways in metal and radiomuclide bacteria” that established the Virtual Institute for Microbial Stress and Survival (VIMSS).

Molecular Assemblies, Genes and Genomics Integrated Efficiently (MAGGIE)

maggieJohn Tainer, Principal Investigator (LBNL, Life Sciences Division)

MAGGIE will provide robust GTL technologies and comprehensive characterizations to efficiently couple gene sequences and genomic analyses with protein interactions and thereby elucidate functional relationships and pathways. The operational principle guiding MAGGIE objectives can be succinctly stated: protein functional relationships involve interaction mosaics that self-assemble from independent protein pieces that are tuned by modifications and metabolites. MAGGIE builds strong synergies among the Components to address long term and immediate GTL objectives by combining the advantages of specific microbial systems with those advanced technologies, The objective for the proposed 5-year MAGGIE Program is therefore to comprehensively characterize the Protein Complexes (PCs) and Modified Proteins (MPs) underlying microbial cell biology. A compelling overall goal is to help reduce the immense complexity of protein interactions to interpretable patterns through an interplay among experimental efforts of MAGGIE Program members in molecular biology, biochemistry, biophysics, mathematics, computational science, and informatics. MAGGIE will address immediate GTL missions by accomplishing three specific goals: 1) Provide a comprehensive, hierarchical map of prototypical microbial PCs and MPs by combining native biomass and tagged protein characterizations from hyperthermophiles (temperature-trapping otherwise reversible protein interactions) with comprehensive systems biology characterizations of a non-thermophilic model organism, 2) Develop and apply advanced mass spectroscopy and SAXS technologies for high throughput characterizations of PCs and MPs, and 3) Create and test powerful computational descriptions for protein functional interactions. In concert, MAGGIE investigators will characterize microbial metabolic modularity and provide the informed basis to design functional islands suitable to transform microbes for specific DOE missions.

Genemap-MS

Genemap-MSTrent Northen, Principal Investigator (LBNL, Life Sciences Division)

The utility of genetic information being derived from sequencing efforts is diminished by the incomplete/incorrect annotations associated with “completed” genomes. Homology-based protein function predictions are limited by evolutionary processes that result in conserved domains and sequence being shared by enzymes of widely diverse functions. Therefore, additional experimental datasets directed at validating and improving genome annotations are required. Project Genemap-MS uses integrated approach of universally applicable high-throughput (HT) methods for validating genome annotation using mass spectrometry (MS) based proteomics, metabolomics, and our developing technologies for detecting biochemical activities on arrayed metabolite substrates. Overall, Genemap-MS provides a balance of mature and robust MS technologies with MS technology development which are directed at addressing specific DOE needs for exploiting microbial processes for bioenergy production, carbon sequestration, and environmental remediation.