Systems-level analysis and mechanistic dissection of metabolic pathways in bacteria:
Metabolism provides energy, creates building blocks, and regulates macromolecular processes. Integrating metabolism with other cellular responses provides the robustness enabling bacterial survival in diverse nutrient and toxic environments, key to their success as commensals, pathogens and industrial workhorses. Bacterial metabolism has been extensively studied, primarily in E. coli, the model system for establishing metabolic networks. Metabolic processes have often been probed by qualitative, non-saturating genetic techniques that may miss players and connections, thereby leading to a focus on the identification/characterization of individual components rather than considering metabolism as a cellular system. Thus even in E. coli, our knowledge of metabolism is far from complete: not all metabolic pathways have a comprehensive description of component parts, interconnections between metabolic pathways are not well-established and integration of metabolism with other cellular processes is poorly understood.
A major obstacle impeding systems-level analysis of metabolism has been the lack of a comprehensive, quantitative, functional-genomics approach that provides an entire parts list and hints of connections. In this direction, my lab utilizes high-throughput quantitative methodologies, chemical-genomics (response of every gene deletion/overexpression strain to chemical perturbations,∼ 4000 genes) and double-mutant analysis, to identify novel players and networks in metabolism. The information extracted from these genomic approaches is then integrated with knowledge from other high-throughput datasets like phenotype microarray analysis, transcriptional profiling and proteome analysis to generate testable hypotheses about the function of novel genes, the process they participate in, and interconnections between pathways. As a complement, we also perform detailed molecular studies of important targets to establish their functional roles.
Our research mainly focuses on the metabolic processes that govern utilization of carbon sources implicated in pathogenesis and those providing tolerance to toxic agents important in biofuel production. Overall, this study will identify novel transporters, metabolic enzymes and regulators required for the degradation of carbon sources and toxic agents; cross-talk between metabolic pathways; and stress response pathways important for survival in toxic conditions. Thus, the combined use of a functional-genomics approach and mechanistic analysis will expand our knowledge of metabolism beyond a mere description of parts and will provide new metabolic information that can be harnessed to design novel antibacterials and create strains with superior toxicity tolerance. .
- Oh, E., Becker, A. H., Sandikci, A., Huber, D., Chaba, R., Gloge, F., Nichols, R. J., Typas, A., Gross, C. A., Kramer, G., Weissman, J. S. and Bukau, B. (2011). Selective ribosome profiling reveals the co-translational chaperone action of trigger factor in vivo. Cell 147(6):1295-1308. (Faculty of 1000: factor 8).
- Chaba, R.*, Alba, B.M., Guo, M., Sohn, J., Ahuja, N., Sauer, R. T. and Gross, C. A.* (2011). Signal integration by DegS and RseB governs the δE-mediated envelope stress response in Escherichia coli. PNAS 108(5): 2106-2111. *co-corresponding authors (Faculty of 1000: factor 8).
- Nichols, R. J., Choo, Y. J., Sen, S., Beltrao, P., Zietek, M., Chaba, R., Lee, S., Kazmierczak, K. M., Lee, K. J., Wong, A., Shales, M., Lovett, S., Winkler, M. E., Krogan, N. J., Typas, A. and Gross, C. A. (2011). Phenotypic Landscape of a Bacterial Cell. Cell 144(1):143-156. (Faculty of 1000: factor 13)
- Chaba, R., Grigorova, I. L., Flynn, J. M., Baker, T. A. and Gross, C. A. (2007). Design principles of the proteolytic cascade governing the δE-mediated envelope stress response in Escherichia coli: keys to graded, buffered, and rapid signal transduction. Genes Dev. 21(1): 124-136. *This article was highlighted in the perspective in Genes and Development. Hasenbein, S., Merdanovic, M. and Ehrmann, M. (2007). Determinants of regulated proteolysis in signal transduction. Genes Dev. 21(1): 6-10.
- Grigorova, I. L.,Chaba, R., Zhong, H. J., Alba, B. M., Rhodius, V., Herman, C. and Gross, C. A. (2004). Fine-tuning of the Escherichia coli δE envelope stress response relies on multiple mechanisms to inhibit signal-independent proteolysis of the transmembrane anti-sigma factor, RseA. Genes Dev. 18(21): 2686-2697.