The Response of Haloferax volcanii to Salt and Temperature Stress: A Proteome Study by Label‐Free Mass Spectrometry

Abstract

In-depth proteome analysis of the haloarchaeal model organism Haloferax volcanii has been performed 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 indicates 61.1% proteome coverage (2509 proteins), which is close to the maximum recorded values in archaea. Identified proteins match 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 are quantitatively compared to standard cultures by sequential window acquisition of all theoretical mass spectra (SWATH-MS). A total of 2244 proteins, or 54.7% of the predicted proteome, are quantified across all conditions at high reproducibility, which allowed for global analysis of protein expression changes under these stresses. Of these, 2034 are significantly regulated under at least one stress condition. KEGG pathway enrichment analysis shows that several major cellular pathways are part of H. volcanii's universal stress response. In addition, specific pathways (purine, cobalamin, and tryptophan) are affected by temperature stress. The most strongly downregulated proteins under all stress conditions, zinc finger protein HVO_2753 and ribosomal protein S14, are found oppositely regulated to their immediate genetic neighbors from the same operon.

Ribosome Profiling in Archaea Reveals Leaderless Translation, Novel Translational Initiation Sites, and Ribosome Pausing at Single Codon Resolution

“…We also identified potential protein-coding sequences in contexts that are often missed (71), such as TSS on extremely small ORFs or those that are within ORFs or antisense to known ORFs. We found hundreds of alternative TSS in Hv including initiation sites 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 altering translation efficiency of the annotated protein, as proposed in Bacteria and Eukarya (26,42).…”

Uncovering chemical signatures of salinity gradients through compositional analysis of protein sequences

“…(e, g) Tables S2 and S3 of Lin et al (2017). (g, h) Supporting Table 1C of Jevtić et al (2019). Only proteins with at least 2-fold expression difference and marked as significant were included.…”

Distinct trends in chemical composition of proteins from metagenomes in redox and salinity gradients

“…differentially expressed proteins reported in 13 studies on non-halophilic bacterial and eukaryotic cells were summarized in a previous publication 17 . We augmented that compilation with data from an additional seven studies on bacteria and archaea [57][58][59][60][61][62][63] , including four halophiles ( Table 2). The reported significantly differentially expressed genes or proteins were mapped to UniProt accession numbers 66 ;…”

“…For each of the wild-type and ∆sigB mutant, only proteins that were identified in extracellular vesicles in a single condition (0.5 M salt stress or without salt stress) were included. (L, M)Supporting Table 1Cof ref 63…”