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Free keywords:
SWATH; archaea; mass spectrometry; proteome; stress response
Abstract:
We performed an in-depth proteome analysis of the haloarchaeal model organism Haloferax volcanii under standard, low/high salt and low/high temperature conditions using label-free mass spectrometry. Qualitative analysis of protein identification data from high-pH/reversed phase fractionated samples indicated 61.1% proteome coverage (2,509 proteins), which is close to the maximum recorded values in archaea. Identified proteins matched to the predicted proteome in their physicochemical properties, with only a small bias against low-molecular-weight and membrane-associated proteins. Cells grown under low and high salt stress as well as low and high temperature stress were quantitatively compared to standard cultures by SWATH mass spectrometry. 2,244 proteins, or 54.7% of the predicted proteome, were quantified across all conditions at high reproducibility, which allowed for global analysis of protein expression changes under these stresses. Of these, 2,034 were significantly regulated under at least one stress condition. KEGG pathway enrichment analysis showed that several major cellular pathways are part of H. volcanii's universal stress response. In addition, specific pathways (purine, cobalamin, tryptophan) were affected by temperature stress. The most strongly down-regulated proteins under all stress conditions, zinc finger protein HVO_2753 and ribosomal protein S14, were found oppositely regulated to their immediate genetic neighbors from the same operon.
