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

Picrophilus torridus is a thermoacidophilic archaeon which 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 extreme acidic and moderate thermal environment. 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 chromatography mass spectrometry (LC-MS/MS). 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. 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. Majority of the cytosolic proteins were observed to be multi-functional and involved in activities related to microbial metabolism. Comparison with an earlier study which 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 information discerned in this study might add to the knowledge-base of P. torridus proteome and provide a useful basis for further proteomic studies on other thermoacidophilic archaea.