Proteome analysis of Halobacterium sp. NRC-1 facilitated by the biomodule analysis tool BMSorter

Rueichi R. Gan, Eugene C. Yi, Yulun Chiu, Hookeun Lee, Yu Chieh P. Kao, Timothy H. Wu, Ruedi Aebersold, David R. Goodlett, Wailap Victor Ng*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

14 Scopus citations


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 Protein-Prophet 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.

Original languageEnglish
Pages (from-to)987-997
Number of pages11
JournalMolecular and Cellular Proteomics
Issue number6
StatePublished - Jun 2006


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