Background: Picrophilus torridus is a thermoacidophilic archaeon that thrives in an extremely low pH (0-1) and high temperatures (50-60°C). Thus, it is a suitable organism to study microbial genetics and metabolic adaptations to the extremely acidic and moderate thermal environment. Objective: In the present study we have conducted a global proteome analysis of P. torridus and discerned the cytosolic proteome of P. torridus using gel-free, liquid chromatographymass spectrometry (LC-MS/MS). Methods: The cytosolic proteins of P. torridus were extracted and identified using gel-free, LCMS/ MS. Gene Ontology-based pathway analysis and protein-protein interaction studies were performed to understand the role of various cytosolic proteins in sustaining the thermoacidophilic environment. Also, domain analysis of hypothetical/uncharacterized proteins was performed. Results: Using gel-free LC-MS/MS, 408 cytosolic proteins of P. torridus were identified, including 36 hypothetical/uncharacterized proteins. Thus, we could identify 26.58 % of the theoretical proteome of P. torridus. The majority of the cytosolic proteins were observed to be multi-functional and involved in activities related to microbial metabolism. Conclusion: Comparison with an earlier study that used gel-based LC-MS analysis to identify cytosolic proteins of P. torridus revealed that gel-free LC-MS was better in identifying more number of proteins and also, higher/lower molecular weight proteins. The findings of this study may contribute to our understanding of the P. torridus proteome and serve as a foundation for future proteomic research on other thermoacidophilic archaea.

中文翻译：

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嗜热嗜酸菌 Picrophilus torridus 的胞质蛋白质组的蛋白质组学和计算分析

背景：Picrophilus torridus 是一种嗜热嗜酸古菌，可在极低的 pH (0-1) 和高温 (50-60°C) 下繁衍生息。因此，它是研究微生物遗传学和代谢适应极端酸性和适度热环境的合适生物体。目标：在本研究中，我们对 P. torridus 进行了全球蛋白质组分析，并使用无凝胶液相色谱质谱法 (LC-MS/MS) 识别了 P. torridus 的胞质蛋白质组。方法：使用无凝胶、LCMS/MS 提取和鉴定 P. torridus 的胞质蛋白。进行了基于基因本体论的通路分析和蛋白质-蛋白质相互作用研究，以了解各种胞质蛋白在维持嗜热嗜酸环境中的作用。还，对假设/未表征的蛋白质进行了域分析。结果：使用无凝胶 LC-MS/MS，鉴定了 P. torridus 的 408 种胞质蛋白，包括 36 种假设/未表征的蛋白质。因此，我们可以确定 26.58% 的 P. torridus 理论蛋白质组。观察到大多数胞质蛋白具有多功能性，并参与与微生物代谢相关的活动。结论：与使用基于凝胶的 LC-MS 分析鉴定 P. torridus 胞质蛋白的早期研究相比，无凝胶 LC-MS 在鉴定更多蛋白质以及更高/更低分子量蛋白质方面表现更好。这项研究的结果可能有助于我们了解 P.