Genomes to Life Contractor-Grantee Workshop III
February 6-9, 2005, Washington, D.C.
Genomics:GTL Program Projects
Shewanella Federation
39
Reverse-Engineering Microbial Networks in Escherichia coli and Shewanella oneidensis MR-1 via Large-Scale Perturbation Studies
G. Cottarel, M.E. Driscoll, J. Faith, M.K. Kohanski, J. Wierzbowski, C.B. Cantor, J.J. Collins, and T.S. Gardner* (tgardner@bu.edu)
Boston University, Boston, MA
The impressive capabilities of microbes, ranging from energy transduction to signal processing, rival those of any engineered system. Functions of respiration, growth, and environmental sensing are principally regulated by transcriptional gene networks. Identifying the large-scale structure and dynamics of such networks is an important first step towards engineering microbes for applications in bioremediation and energy production.
Towards this goal, we have recently completed a pilot study validating an approach for rapid cell-wide reverse-engineering of transcriptional gene networks. In an extended study of the DNA-damage response network of Escherichia coli, we generated genome expression profiles of cells under 65 experimental conditions, encompassing both time-series profiles and genetic perturbations, in a background of antibiotic-induced DNA damage.
We succeeded in reconstructing a network map comprising over one hundred genes using an inference algorithm developed previously in our lab [1,2]. This network provides a comprehensive picture of a major stress-response system in prokaryotes, buttressing and unifying evidence from previous studies. In addition, we have also identified several novel regulators in the network, for which we are pursuing further experimental validation. Our results establish the feasibility and scalability of our reverse-engineering approach, and have laid the groundwork for a similar study in Shewanella oneidensis MR-1.
S. oneidensis is a gram-negative microbe whose ability to reduce heavy-metals and other organic toxins has made it a promising candidate for use in environmental remediation. Using our reverse-engineering methods, we are conducting a broad series of growth-condition perturbations to reconstruct the transcriptional networks governing Shewanella’s respiratory system.To facilitate these studies, we have designed the first high-density Affymetrix oligonucleotide microarray for S. oneidensis. Beyond its use for genome-wide expression profiling, this microarray can also be used in chromatin immunoprecipitation studies, which will complement our expression-based inference techniques.
The knowledge we are deriving from our work both in E. coli and S. oneidensis has a variety of applications, including the improvement of antibiotics, environmental remediation, and the prospect of biologically-derived energy sources.
References
- Gardner TS, di Bernardo D, Lorenz D, Collins JJ. Inferring genetic networks and identifying compound mode of action via expression profiling. Science. 2003 Jul 4;301(5629):102-5.
- Tegner J, Yeung MK, Hasty J, Collins JJ. Reverse engineering gene networks: Integrating genetic perturbations with dynamical modeling. Proc Natl Acad Sci U S A. 2003 May 13;100(10):5944-9.
* Presenting author
