Genomes to Life Contractor-Grantee Workshop III
February 6-9, 2005, Washington, D.C.
Genomics:GTL Program Projects
Shewanella Federation
35
Global Profiling of Shewanella oneidensis MR-1: Expression of ‘Hypothetical’ Genes and Improved Functional Annotations
Eugene Kolker*1 (ekolker@biatech.org), Alex F. Picone1, Michael Y. Galperin2, Margaret F. Romine3, Roger Higdon1, Kira S. Makarova2, Natali Kolker1, Gordon A. Anderson3, Xiaoyun Qiu4, Kenneth J. Auberry3, Gyorgy Babnigg5, Alex S. Beliaev3, Paul Edlefsen1, Dwayne A. Elias3, Yuri Gorby3, Ted Holzman1, Joel Klappenbach4, Konstantinos T. Konstantinidis4, Miriam L. Land6, Mary S. Lipton3, Lee-Ann McCue7, Matthew Monroe3, Ljiljana Pasa-Tolic3, Grigoriy Pinchuk3, Samuel Purvine1,3, Margaret Serres8, Sasha Tsapin9, Brian A. Zakrajsek3, Wenhong Zhu10, Jizhong Zhou6, Frank W. Larimer6, Charles Lawrence7, Monica Riley8, Frank R. Collart5, John R. Yates, III10, Richard D. Smith3, Carol Giometti5, Kenneth Nealson9, James K. Fredrickson3, and James M. Tiedje4
1BIATECH, Bothell, WA; 2National Institutes of Health, Bethesda, MD; 3Pacific Northwest National Laboratory, Richland, WA; 4Michigan State University, East Lansing, MI;5Argonne National Laboratory, Argonne, IL; 6Oak Ridge National Laboratory, Oak Ridge, TN; 7Wadsworth Center, Albany, NY; 8Marine Biological Laboratory, Woods Hole, MA; 9University of Southern California, Los Angeles, CA; and 10Scripps Research Institute, La Jolla, CA
The γ-proteobacterium Shewanella oneidensis strain MR-1 is a metabolically versatile organism that can reduce a wide range of organic compounds, metal ions, and radionuclides. Similar to most other sequenced organisms, approximately 40% of the predicted ORFs in the S. oneidensis genome were annotated as uncharacterized ‘hypothetical’ genes. We implemented an integrative approach using experimental and computational analyses to provide more detailed insight into gene function. Global expression profiles were determined for cells following UV irradiation and under aerobic and suboxic growth conditions. Transcriptomic and proteomic analyses confidently identified 538 ‘hypothetical’ genes as expressed in S. oneidensis cells both as mRNAs and proteins (33% of all predicted ‘hypothetical’ proteins). Publicly available analysis tools and databases and the expression data were applied to improve the annotation of these genes. The annotation results were scored using a seven-category schema that ranked both confidence and precision of the functional assignment. We were able to identify homologs for nearly all of these ‘hypothetical’ proteins (97%), but could confidently assign exact biochemical functions for only 16 proteins (category 1; 3%). Altogether, computational and experimental evidence provided functional assignments or insights for 240 more genes (categories 2-5; 45%). These functional annotations advance our understanding of genes involved in vital cellular processes including energy conversion, ion transport, secondary metabolism, and signal transduction. We propose that this integrative approach offers a valuable means to undertake the enormous challenge of characterizing the rapidly growing number of ‘hypothetical’ proteins with each newly sequenced genome.
This work was carried out by the Shewanella Federation supported by the Genomics: GTL program of the Department of Energy’s Offices of Biological and Environmental Research and Advanced Scientific Computing Research (Grants DE-FG02-03ER63527, DE-FG02-02ER63427, and DE-FG02-02ER63342). Argonne, Oak Ridge, and Pacific Northwest National Laboratories are managed for the Department of Energy by University of Chicago (Contract W-31-109-ENG-38), University of Tennessee-Battelle LLC (Contract DE-AC05-00OR22725), and Battelle Memorial Institute (Contract DE-ACO6-76RLO1830), respectively.
* Presenting author
