Qiu Wen, Pham Trong Khoa, Zou Xin, Ow Saw Yen, Wright Phillip C
ChELSI Institute, Department of Chemical and Biological Engineering, the University of Sheffield , Mappin Street, Sheffield, S1 3JD, United Kingdom.
State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University , Hangzhou, 310058, China.
J Proteome Res. 2017 Jul 7;16(7):2370-2383. doi: 10.1021/acs.jproteome.6b00920. Epub 2017 Jun 9.
The thermoacidophilic crenarchaeon Sulfolobus solfataricus has been widely used as a model organism for archaeal systems biology research. Investigation using its spontaneous mutant PBL2025 provides an effective metabolic baseline to study subsequent mutagenesis-induced functional process shifts as well as changes in feedback inhibitions. Here, an untargeted metabolic investigation using quantitative proteomics and metabolomics was performed to correlate changes in S. solfataricus strains P2 against PBL2025 and under both glucose and tryptone. The study is combined with pathway enrichment analysis to identify prominent proteins with differential stoichiometry. Proteome level quantification reveals that over 20% of the observed overlapping proteome is differentially expressed under these conditions. Metabolic-induced differential expressions are observed along the central carbon metabolism, along with 12 other significantly regulated pathways. Current findings suggest that PBL2025 is able to compensate through the induction of carbon metabolism, as well as other anabolic pathways such as Val, Leu and iso-Leu biosynthesis. Studying protein abundance changes after changes in carbon sources also reveals distinct differences in metabolic strategies employed by both strains, whereby a clear down-regulation of carbohydrate and nucleotide metabolism is observed for P2, while a mixed response through down-regulation of energy formation and up-regulation of glycolysis is observed for PBL2025. This study contributes, to date, the most comprehensive network of changes in carbohydrate and amino acid pathways using the complementary systems biology observations at the protein and metabolite levels. Current findings provide a unique insight into molecular processing changes through natural (spontaneous) metabolic rewiring, as well as a systems biology understanding of the metabolic elasticity of thermoacidophiles to environmental carbon source change, potentially guiding more efficient directed mutagenesis in archaea.
嗜热嗜酸泉古菌嗜热栖热菌已被广泛用作古菌系统生物学研究的模式生物。利用其自发突变体PBL2025进行的研究提供了一个有效的代谢基线，以研究随后诱变诱导的功能过程转变以及反馈抑制的变化。在此，进行了一项非靶向代谢研究，使用定量蛋白质组学和代谢组学来关联嗜热栖热菌菌株P2与PBL2025在葡萄糖和胰蛋白胨条件下的变化。该研究结合了通路富集分析，以识别具有不同化学计量的突出蛋白质。蛋白质组水平的定量分析表明，在这些条件下，超过20%的观察到的重叠蛋白质组存在差异表达。沿着中心碳代谢以及其他12条显著调控的通路观察到了代谢诱导的差异表达。目前的研究结果表明，PBL2025能够通过诱导碳代谢以及其他合成代谢途径（如缬氨酸、亮氨酸和异亮氨酸生物合成）来进行补偿。研究碳源变化后蛋白质丰度的变化还揭示了两种菌株所采用的代谢策略的明显差异，即观察到P2的碳水化合物和核苷酸代谢明显下调，而PBL2025则通过下调能量生成和上调糖酵解表现出混合反应。迄今为止，本研究利用蛋白质和代谢物水平的互补系统生物学观察结果，构建了碳水化合物和氨基酸途径变化的最全面网络。目前的研究结果为通过自然（自发）代谢重排引起的分子加工变化提供了独特的见解，以及对嗜热嗜酸菌对环境碳源变化的代谢弹性的系统生物学理解，可能指导古菌中更有效的定向诱变。
