-Omics study of Sulfolobus solfataricus species under different carbon sources

The acidic thermophilic archaeon Sulfolobus solfataricus has been widely used as a model organism in archaeal research and it can utilise different compounds (tryptone or glucose) as carbon sources. However, the understanding of this archaeon in responding to these carbon sources (at quantitative proteome level, metabolome level) and its regulation (at phospho proteome level) has not been well studied yet. Therefore, I would like to investigate the effects of different carbon sources (tryptone and glucose) to different S. solfataricus strains (P2, PBL2025 and PBL2073). Furthermore, a P-peptide (phospho peptide) enrichment protocol was optimised. Quantitative phosphoproteomic analysis was performed for S. solfataricus P2 using optimised P-peptide enrichment and iTRAQ strategy. In order to achieve these goals, firstly, the growth effect on different S. solfatarcius strains from different carbon sources was monitored to determine the sampling times. Sample preparation and technical optimisation for quantitative proteomic and phosphoproteomic studies were then performed. Secondly, both proteomic (iTRAQ) and metabolomic (GC-MS) tools were applied to determine the global proteomic and metabolomic changes of three different S. solfatarcius strains in responding to two carbon sources (glucose and tryptone). Thirdly, MOAC (metal oxide affinity chromatography)-TiO2, IMAC (immobilized metal ion affinity chromatography)-Fe and combination of these two (SIMAC) were tested for P-peptide enrichment of tryptic digested protein of S. solfataricus grown on standard media. This thesis reports the quantitative proteomic and metabolomic changes in three different S. solfataricus strains in responding to different carbon sources. An optimised P-peptide enrichment strategy was also established, which may be applied for other achaeal studies. Furthermore, quantitative phosphoproteomic study was performed for S. solfataricus P2, and this was recognised as the first global quantitative phosphoproteomic study in this archaeon.