Comparative Proteomics Study of Salt Tolerance between a Nonsequenced Extremely Halotolerant Cyanobacterium and Its Mildly Halotolerant Relative Using in vivo Metabolic Labeling and in vitro Isobaric Labeling

Euhalothece sp. BAA001 is an extremely halotolerant cyanobacterium, and recent proteomic investigations have revealed many shared survival strategies with its well-studied and moderately halotolerant relative Synechocystis sp. PCC6803. We exploit the shared tryptic peptides between these organisms and directly compare the relative protein abundance in cells grown in the exact same salt conditions. This comparison is made with added salt (NaCl) concentrations of 0, 3, and 6% (w/v), where significant abundance differences are explained in terms of prioritization of essential cellular processes in relation to salinity tolerance. Implementation of N-15 in vivo metabolic labeling in conjunction with conventional search software, Mascot, and quantification software MSQUANT allowed 243 unique proteins to be quantified. The characteristic stress response that Euhalothece displays in 0% salt is observed through higher abundance of stress associated proteins, including a putative DNA binding stress protein and antioxidative enzymes. In contrast, Synechocystis expresses a greater number of stress proteins in 3% and 6% salt. In addition to in vivo metabolic labeling, an experiment using in vitro isobaric labeling (iTRAQ) was also carried out, which successfully demonstrated its applicability in cross-species proteomics.