Proteomics and Computational Analysis of Cytosolic Proteome of a Thermoacidophilic Euryarchaeon, Picrophilus torridus

Background: Picrophilus torridus is a thermoacidophilic archaeon that thrives in an extremely low pH (0-1) and high temperatures (50-60 degrees 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, LC-MS/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.

Automated summary

Through gel-free LC-MS/MS, 408 cytosolic proteins of P. torridus were identified, with most being multifunctional and involved in microbial metabolism activities. In comparison with gel-based LC-MS analysis, gel-free method proved to be better in identifying a greater number of proteins, including those with higher/lower molecular weights.