Metabolic Capabilities and Systems Fluctuations in Haloarcula marismortui Revealed by Integrative Genomics and Proteomics Analyses

• Published in: Journal of proteome research 2011-07, Vol.10 (7), p.3261-3273
• Main Authors: Chu, Lichieh Julie, Yang, Hanyin, Shih, Peiyin, Kao, Yuchieh, Tsai, Yihsuan Shannon, Chen, Jinzhi, Huang, Gueitang, Weng, Rueyhung Roc, Ting, Ying Sonia, Fang, Xuefeng, von Haller, Priska D, Goodlett, David R, Ng, Wailap Victor
• Format: Article
• Language: English
• Subjects: Archaeal Proteins - genetics; Archaeal Proteins - metabolism; Data Mining; Gene Expression Profiling; Haloarcula marismortui - genetics; Haloarcula marismortui - metabolism; Metabolic Networks and Pathways - genetics; Models, Biological; Peptide Fragments - analysis; Peptide Fragments - chemistry; Protein Interaction Mapping; Proteome - genetics; Proteome - metabolism; Proteomics - methods; Signal Transduction; Stress, Physiological; Tandem Mass Spectrometry; Trypsin - metabolism
• ISSN: 1535-3893; 1535-3907
• DOI: 10.1021/pr200290x

The 1310 Haloarcula marismortui proteins identified from mid-log and late-log phase soluble and membrane proteomes were analyzed in metabolic and cellular process networks to predict the available systems and systems fluctuations upon environmental stresses. When the connected metabolic reactions with identified proteins were examined, the availability of a number of metabolic pathways and a highly connected amino acid metabolic network were revealed. Quantitative spectral count analyses suggested 300 or more proteins might have expression changes in late-log phase. Among these, integrative network analyses indicated approximately 106 were metabolic proteins that might have growth-phase dependent changes. Interestingly, a large proportion of proteins in affected biomodules had the same trend of changes in spectral counts. Disregard the magnitude of changes, we had successfully predicted and validated the expression changes of nine genes including the rimK, gltCP, rrnAC0132, and argC in lysine biosynthesis pathway which were downregulated in late-log phase. This study had not only revealed the expressed proteins but also the availability of biological systems in two growth phases, systems level changes in response to the stresses in late-log phase, cellular locations of identified proteins, and the likely regulated genes to facilitate further analyses in the postgenomic era.