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J. Biol. Chem., Vol. 279, Issue 49, 51554-51560, December 3, 2004

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Quantitative Proteomic Analysis of Metabolic Regulation by Copper Ions in Methylococcus capsulatus (Bath)^*

Wei-Chun Kao, Yet-Ran Chen, Eugene C. Yi¶, Hookeun Lee¶, Qiang Tian¶, Keh-Ming Wu||**, Shih-Feng Tsai||**, Steve S.-F. Yu, Yu-Ju Chen, Ruedi Aebersold¶, and Sunney I. Chan

From the Department of Chemistry, National Taiwan University, Taipei 106, Taiwan, the Institute of Chemistry, Academia Sinica, Nankang, Taipei 115, Taiwan, the ^¶Institute for Systems Biology, Seattle, Washington 98103-8904, the ^||Institute of Genetics and Genome Research Center, National Yang-Ming University, Taipei 112, Taiwan, and the ^**Division of Molecular and Genomics Medicine, National Health Research Institute, Taipei 115, Taiwan

Copper ions switch the oxidation of methane by soluble methane monooxygenase to particulate methane monooxygenase in Methylococcus capsulatus (Bath). Toward understanding the change in cellular metabolism related to this transcriptional and metabolic switch, we have undertaken genomic sequencing and quantitative comparative analysis of the proteome in M. capsulatus (Bath) grown under different copper-to-biomass ratios by cleavable isotope-coded affinity tag technology. Of the 682 proteins identified, the expressions of 60 proteins were stimulated by at least 2-fold by copper ions; 68 proteins were down-regulated by 2-fold or more. The 60 proteins overexpressed included the methane and carbohydrate metabolic enzymes, while the 68 proteins suppressed were mainly responsible for cellular signaling processes, indicating a role of copper ions in the expression of the genes associated with the metabolism of the organism downstream of methane oxidation. The study has also provided a complete map of the C₁ metabolism pathways in this methanotroph and clarified the interrelationships between them.

Received for publication, July 15, 2004 , and in revised form, September 22, 2004.

^* This work was supported by Academia Sinica and grants from the National Science Council of Taiwan (NSC 91-2113-M-001-045 and 92-2113-M-001-057). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

The on-line version of this article (available at http://www.jbc.org) contains supplemental Tables 1-3.

To whom correspondence should be addressed: Inst. of Chemistry, Academia Sinica, 128 Academia Rd. Section 2, Nangkang 115, Taipei, Taiwan. Tel./Fax: 886-2-2789-8654; E-mail: chans{at}chem.sinica.edu.tw.

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