Genomes to Life Contractor-Grantee Workshop III
February 6-9, 2005, Washington, D.C.
Genomics:GTL Program Projects
Shewanella Federation
34
The Shewanella Federation: Functional Genomic Investigations of Dissimilatory Metal-Reducing Shewanella
James K. Fredrickson*1(jim.fredrickson@pnl.gov), Carol S. Giometti2, Eugene Kolker3*, Kenneth H. Nealson4, James M. Tiedje5, Jizhong Zhou6, Monica Riley7, Shimon Weiss8, James J. Collins9, Frank Larimer6, Frank Collart2, Lee Ann McCue10, Chip Lawrence10, and Timothy S. Gardner9
1Pacific Northwest National Laboratory, Richland, WA; 2Argonne National Laboratory, Argonne, IL; 3BIATECH, Bothell, WA; 4University of Southern California, Los Angeles, CA; 5Michigan State University, East Lansing, MI; 6Oak Ridge National Laboratory, Oak Ridge, TN; 7Marine Biological Laboratory, Woods Hole, MA; 8University of California, Los Angeles, and 9Boston University, Boston, MA; and 10Wadsworth Center, Troy, NY
Shewanella oneidensis MR-1 is a motile, facultative γ-Proteobacterium with remarkable metabolic versatility in regards to electron acceptor utilization; it can utilize O2, nitrate, fumarate, TMAO, DMSO, Mn, Fe, and S0 as terminal electron acceptors during anaerobic respiration. The ability to effectively reduce nitrate, polyvalent metals including solid phase Fe and Mn oxides and radionuclides such as uranium and technetium has generated considerable interest in the potential role of this organism in metal biogeochemical cycling and bioremediation. The Shewanella Federation (SF), a collaborative scientific team assembled by DOE, is applying these approaches to achieve a system-level understanding of how Shewanella regulates energy and material flow and to utilize its versatile electron transport system to reduce metals and nitrate. The SF has developed an integrated approach to Shewanella functional genomics that capitalizes on the relative strengths, capabilities, and expertise of each group. SF members share information and resources and collaborate on projects that range from a few investigators focused on a defined topic to more complex “Federation-level” efforts. These intend to utilize combined SF capabilities in addressing more general scientific questions.
The SF is organized into various working groups that are engaged in a series of Shewanella-based collaborative sub-projects. The ongoing investigations include: (i) generation of deletion mutants in each of the 40 predicted c-type cytochromes in the MR-1 genome and characterization of their phenotype; (ii) global expression profiling using whole genome microarray and proteomic analyses and network modeling of steady-state and transitions between growth on various electron acceptors; and (iii) analyses of global regulatory mutants involved in carbon and energy metabolism; and development of common standards and statistical models for numerous SF-wide studies. In addition, coordinate work is underway to revise the annotation of MR-1 based on new information generated by the SF and available in public databases. Supported by the database development, this re-annotation effort will provide the foundation for further functional experimentation, analysis, and modeling of MR-1. Additionally, it will facilitate comparative genomic of analyses of seven new strains of Shewanella recently completed by DOE’s Joint Genome Institute. These include S. amazonensis, S. putrefaciens strains CN32 and 200, S. denitrificans OS217T, S. baltica OS155, S. frigidimarina 400, S. sp. str. PV-4. In parallel, detailed physiological analyses are also being conducted with the sequenced strains to provide a basis for genomic comparisons and predictions. The overall goal of this collaborative effort is to develop an evolutionary model for speciation in Shewanella as well as providing additional insights into electron transport and carbon metabolism.
* Presenting author
