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Molecular & Cellular Proteomics 5:987-997, 2006.
© 2006 by The American Society for Biochemistry and Molecular Biology, Inc.

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Research

Proteome Analysis of Halobacterium sp. NRC-1 Facilitated by the Biomodule Analysis Tool BMSorter^*,S

Rueichi R. Gan, Eugene C. Yi^,¶, Yulun Chiu, Hookeun Lee^||, Yu-chieh P. Kao^**, Timothy H. Wu^**, Ruedi Aebersold^,||, David R. Goodlett and Wailap Victor Ng^{**,,¶¶,||||}

From the Institute of Biochemistry, ^** Institute of Bioinformatics, Institute of Biotechnology in Medicine, and ^¶¶ Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming University, ^* Taipei City Hospital, Taipei 112, Taiwan, Republic of China, Institute for Systems Biology, Seattle, Washington 98103, ^¶ Zymogenetics, Inc., Seattle, Washington 98012, ^|| Institute for Molecular Systems Biology, ETH Hönggerberg and Faculty of Natural Sciences, University of Zurich, Zurich CH-8093, Switzerland, and Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195

To better understand the extremely halophilic archaeon Halobacterium species NRC-1, we analyzed its soluble proteome by two-dimensional liquid chromatography coupled to electrospray ionization tandem mass spectrometry. A total of 888 unique proteins were identified with a ProteinProphet probability (P) between 0.9 and 1.0. To evaluate the biochemical activities of the organism, the proteomic data were subjected to a biological network analysis using our BMSorter software. This allowed us to examine the proteins expressed in different biomodules and study the interactions between pertinent biomodules. Interestingly an integrated analysis of the enzymes in the amino acid metabolism and citrate cycle networks suggested that up to eight amino acids may be converted to oxaloacetate, fumarate, or oxoglutarate in the citrate cycle for energy production. In addition, glutamate and aspartate may be interconverted from other amino acids or synthesized from citrate cycle intermediates to meet the high demand for the acidic amino acids that are required to build the highly acidic proteome of the organism. Thus this study demonstrated that proteome analysis can provide useful information and help systems analyses of organisms.

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