title: Quantitative proteomic analysis of metabolic regulation by copper ions in Methylococcus capsulatus (Bath).
abstract: 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.
authors.affiliation: Department of Chemistry, National Taiwan University, Taipei 106, Taiwan.
authors.forename: Wei-Chun
authors.initials: WC
authors.lastname: Kao
authors.forename: Yet-Ran
authors.initials: YR
authors.lastname: Chen
authors.forename: Eugene C
authors.initials: EC
authors.lastname: Yi
authors.forename: Hookeun
authors.initials: H
authors.lastname: Lee
authors.forename: Qiang
authors.initials: Q
authors.lastname: Tian
authors.forename: Keh-Ming
authors.initials: KM
authors.lastname: Wu
authors.forename: Shih-Feng
authors.initials: SF
authors.lastname: Tsai
authors.forename: Steve S-F
authors.initials: SS
authors.lastname: Yu
authors.forename: Yu-Ju
authors.initials: YJ
authors.lastname: Chen
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
authors.forename: Sunney I
authors.initials: SI
authors.lastname: Chan
mesh_terms: D001426:Bacterial Proteins; D001669:Biochemical Phenomena; D001671:Biochemistry; D002241:Carbohydrates / Q000737:chemistry; D019295:Computational Biology / Q000379:methods; D003300:Copper / Q000737:chemistry / Q000378:metabolism*; D019992:Databases as Topic; D015536:Down-Regulation; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial; D007477:Ions; D008697:Methane / Q000737:chemistry; D020619:Methylococcus capsulatus / Q000378:metabolism*; D008954:Models, Biological; D010100:Oxygen / Q000737:chemistry; D010455:Peptides / Q000737:chemistry; D020543:Proteome; D040901:Proteomics / Q000379:methods; D015398:Signal Transduction; D014158:Transcription, Genetic
chemical_list: D001426:Bacterial Proteins; D002241:Carbohydrates; D007477:Ions; D010455:Peptides; D020543:Proteome; D003300:Copper; D008697:Methane; D010100:Oxygen