Genomics:GTL

Research Highlights for Milestone 2: Cell and Community Function, Regulation, and Dynamics

• Platforms deploying advanced high-throughput separations and spectrometric instrumentation coupled with appropriate computational infrastructure are being developed by multiple projects for global proteomic analyses to identify and quantify large sets of proteins more comprehensively, including quantitative modalities for analyzing small samples (e.g., Measuring Differential Expression of Cytochromes in the Metal-Reducing Bacterium Geobacter).
• Some projects are focusing on uncultured microbes and microbial communities and the use of microfluidics and miniaturization with the goal of eventually reducing sample sizes to single or a few microbes.
• Functional imaging technologies are being improved to study the biochemistry of key microbial functions at the cellular and subcellular levels.
• Novel analysis approaches are being undertaken by several projects that are assessing the metabolome as a means of analyzing gene function.
• Projects investigating biological mechanisms having potential for alternative fuel production include investigations of the role of cellulose-binding modules in cellulolytic activity and large-scale analysis of the genes and metabolic pathways involved in photolytic hydrogen production.
• R. palustris, a common soil and water bacterium, is one of the most metabolically versatile organisms because it can make its living by converting sunlight into cellular energy, producing hydrogen as it degrades and recycles cellulose and lignins, and living off other substrates. Research goals are to use metabolic modeling to help optimize carbon sequestration and hydrogen evolution. One team of scientists has taken global approaches to ascertain mechanisms of metabolic regulation of carbon dioxide, hydrogen, nitrogen, aromatic acid, sulfur pathways, and other processes. A coordinated application of gene-expression profiling, proteomics, carbon-flux analysis, and computing approaches has been combined with more traditional studies of mutation analysis and cellular characterizations.
• Research on gene regulation in Caulobacter crescentus is focusing on the importance of master regulators (see Genetic Regulation in Bacteria).
• A goal for studies of environmental microbial systems biology is facile viewing of life processes—in real time. The molecules of life’s complex choreography must be observed as its components carry out their specified activities inside and among cells interacting in dynamic microbial communities. A number of more in-depth systems biology projects are being undertaken on four organisms. These projects focus on integrating the results of the analyses of cellular proteomes, biochemistry, and imaging; they also model pathways.
  • The first two projects study cyanobacteria at the foundation of ocean food chains responsible for about half the photosynthesis (CO₂ fixation) on earth.
    • Accomplishments of Synechococcus research include the Synechococcus Encyclopedia, which provides integrated access to genomics and proteomics databases to aid studies into the behavior of these abundant marine organisms important to global carbon fixation (see Synechococcus Encyclopedia). Other research efforts have given insight into the specificity of RuBisCO, an enzyme central to photosynthetic carbon fixation (see New Imaging and Computational Tools Enable Investigations of Carbon Cycling in Marine Cyanobacteria).
    • Accomplishments regarding Prochlorococcus include explorations into gene expression in day-night cycles of this photosynthetic organism and gene transfer between it and phages (see Transfer of Photosynthetic Genes Between Bacteria and Phages).
  • The second two projects study organisms with capabilities to remove or detoxify metals from contaminated environments. Remediation projects are making an array of microbial-system measurements, including gene expression and qualitative and quantitative proteomics with modeling and simulation experiments on metal-reducing bacteria. The aim is to understand gene and operon regulation under natural environmental conditions that may affect the outcomes of metal-reduction and immobilization processes mediated by bacteria including Geobacter sulfurreducens and S. oneidensis:
    • Some accomplishments of the Shewanella Federation include identifying global stress-response patterns to radiation, nitrate, and oxygen; identifying gene-expression patterns that are electron- acceptor specific; determining the role of selected global regulators in anaerobic respiration; demonstrating expression of hypothetical genes and enhanced genome annotation; and elucidating mechanisms of electron transfer to metals and metal oxides (see The Shewanella Federation).
    • Some accomplishments of Geobacter research include creating in silico models of Geobacter to predict responses to environmental conditions and aid in optimizing bioremediation and energy harvesting; demonstrating that Geobacter can generate electricity from a wide variety of organic wastes and renewable biomass; and determining that growth and activity of metal-reducing organisms in natural environments are enhanced by feeding microbes carbon sources such as acetate (see Geobacter; Harvesting Electricity from Aquatic Sediments with Microbial Fuel Cells).