Quantitative Proteomic and Microarray Analysis of the Archaeon Methanosarcina acetivorans Grown with Acetate versus Methanol

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• 作者：Lingyun Li ; Qingbo Li ; Lars Rohlin ; UnMi Kim ; Kirsty Salmon ; Tomas Rejtar ; Robert P. Gunsalus ; Barry L. Karger ; James G. Ferry
• 刊名：Journal of Proteome Research
• 出版年：2007
• 出版时间：February 2007
• 年：2007
• 卷：6
• 期：2
• 页码：759 - 771
• 全文大小：300K
• 年卷期：v.6,no.2(February 2007)
• ISSN：1535-3907

文摘

Methanosarcina acetivorans strain C2A is an acetate- and methanol-utilizing methane-producingorganism for which the genome, the largest yet sequenced among the Archaea, reveals extensivephysiological diversity. LC linear ion trap-FTICR mass spectrometry was employed to analyze acetate-vs methanol-grown cells metabolically labeled with ¹⁴N vs ¹⁵N, respectively, to obtain quantitative proteinabundance ratios. DNA microarray analyses of acetate- vs methanol-grown cells was also performedto determine gene expression ratios. The combined approaches were highly complementary, extendingthe physiological understanding of growth and methanogenesis. Of the 1081 proteins detected, 255were ges/entities/ge.gif">3-fold differentially abundant. DNA microarray analysis revealed 410 genes that were ges/entities/ge.gif">2.5-folddifferentially expressed of 1972 genes with detected expression. The ratios of differentially abundantproteins were in good agreement with expression ratios of the encoding genes. Taken together, theresults suggest several novel roles for electron transport components specific to acetate-grown cells,including two flavodoxins each specific for growth on acetate or methanol. Protein abundance ratiosindicated that duplicate CO dehydrogenase/acetyl-CoA complexes function in the conversion of acetateto methane. Surprisingly, the protein abundance and gene expression ratios indicated a general stressresponse in acetate- vs methanol-grown cells that included enzymes specific for polyphosphateaccumulation and oxidative stress. The microarray analysis identified transcripts of several genesencoding regulatory proteins with identity to the PhoU, MarR, GlnK, and TetR families commonly foundin the Bacteria domain. An analysis of neighboring genes suggested roles in controlling phosphatemetabolism (PhoU), ammonia assimilation (GlnK), and molybdopterin cofactor biosynthesis (TetR).Finally, the proteomic and microarray results suggested roles for two-component regulatory systemsspecific for each growth substrate.