Research abstract

Article abstract

Nature Biotechnology 20, 1118 - 1123 (2002)
Published online: 7 October 2002 | doi:10.1038/nbt749

Genome sequence of the dissimilatory metal ion–reducing bacterium Shewanella oneidensis

John F. Heidelberg1,2, Ian T. Paulsen1,3, Karen E. Nelson1, Eric J. Gaidos4,5, William C. Nelson1, Timothy D. Read1, Jonathan A. Eisen1,3, Rekha Seshadri1, Naomi Ward1,2, Barbara Methe1, Rebecca A. Clayton1, Terry Meyer6, Alexandre Tsapin4, James Scott7, Maureen Beanan1, Lauren Brinkac1, Sean Daugherty1, Robert T. DeBoy1, Robert J. Dodson1, A. Scott Durkin1, Daniel H. Haft1, James F. Kolonay1, Ramana Madupu1, Jeremy D. Peterson1, Lowell A. Umayam1, Owen White1, Alex M. Wolf1, Jessica Vamathevan1, Janice Weidman1, Marjorie Impraim1, Kathy Lee1, Kristy Berry1, Chris Lee1, Jacob Mueller1, Hoda Khouri1, John Gill1, Terry R. Utterback1, Lisa A. McDonald1, Tamara V. Feldblyum1, Hamilton O. Smith1,8, J. Craig Venter1,9, Kenneth H. Nealson4,10 & Claire M. Fraser1,11

This article is distributed under the terms of the Creative Commons Attribution-Non-Commercial-Share Alike license (, which permits distribution, and reproduction in any medium, provided the original author and source are credited. This license does not permit commercial exploitation, and derivative works must be licensed under the same or similar license.

Shewanella oneidensis is an important model organism for bioremediation studies because of its diverse respiratory capabilities, conferred in part by multicomponent, branched electron transport systems. Here we report the sequencing of the S. oneidensis genome, which consists of a 4,969,803–base pair circular chromosome with 4,758 predicted protein-encoding open reading frames (CDS) and a 161,613–base pair plasmid with 173 CDSs. We identified the first Shewanella lambda-like phage, providing a potential tool for further genome engineering. Genome analysis revealed 39 c-type cytochromes, including 32 previously unidentified in S. oneidensis, and a novel periplasmic [Fe] hydrogenase, which are integral members of the electron transport system. This genome sequence represents a critical step in the elucidation of the pathways for reduction (and bioremediation) of pollutants such as uranium (U) and chromium (Cr), and offers a starting point for defining this organism's complex electron transport systems and metal ion–reducing capabilities.

  1. The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850.
  2. The Center for Marine Biotechnology, 701 East Pratt Street, Baltimore, MD 21202.
  3. Johns Hopkins University, Charles and 34th Streets, Baltimore, MD 21218.
  4. Jet Propulsion Laboratory, 4800 Oak Grove Drive, Pasadena, CA 91109.
  5. Current address: Department of Geology and Geophysics, University of Hawaii, Honolulu, HI 96822.
  6. Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721.
  7. Carnegie Institution of Washington, Geophysical Laboratory, 5251 Broad Branch Rd. NW, Washington, DC 20015.
  8. Current address: Celera Genomics, 45 West Gude Drive, Rockville, MD 20850.
  9. Current address: The Center for the Advancement of Genomics, 1901 Research Boulevard, Rockville, MD 20850.
  10. Current address: Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089.
  11. George Washington University Medical Center, 2300 Eye Street NW, Washington, DC 20037.

Correspondence to: Claire M. Fraser1,11 e-mail:

These links to content published by NPG are automatically generated

Semantides and Modern Bacterial Systematics
Nature Encyclopaedia of Life Sciences
 See all 2 matches for Reference

Shewanella—the environmentally versatile genome
Nature Biotechnology Research News (01 Nov 2002)
Iron acquisition: straight up and on the rocks?
Nature Structural Biology News and Views (01 Apr 2003)

Identification of co-regulated genes through Bayesian clustering of predicted regulatory binding sites
Nature Biotechnology Research (01 Apr 2003)
A novel protein–mineral interface
Nature Structural Biology Article (01 Apr 2003)
 See all 4 matches for Research