How to Cope With Heavy Metal Ions: Cellular and Proteome-Level Stress Response to Divalent Copper and Nickel in Halobacterium salinarum R1 Planktonic and Biofilm Cells

Abstract

Halobacterium salinarum R1 is an extremely halophilic archaeon capable of adhesion and forming biofilms, allowing it to adjust to a range of growth conditions. We have recently shown that living in biofilms facilitates its survival under Cu 2+ and Ni 2+ stress, with specific rearrangements of the biofilm architecture observed following exposition. In this study, quantitative analyses were performed by SWATH mass spectrometry to determine the respective proteomes of planktonic and biofilm cells after exposition to Cu 2+ and Ni 2+ .Quantitative data for 1180 proteins were obtained, corresponding to 46% of the predicted proteome. In planktonic cells, 234 of 1180 proteins showed significant abundance changes after metal ion treatment, of which 47% occurred in Cu 2+ and Ni 2+ treated samples. In biofilms, significant changes were detected for 52 proteins. Only three proteins changed under both conditions, suggesting metal-specific stress responses in biofilms. Deletion strains were generated to assess the potential role of selected target genes. Strongest effects were observed for OE5245F and OE2816F strains which exhibited increased and decreased biofilm mass after Ni 2+ exposure, respectively. Moreover, EPS obviously plays a crucial role in H. salinarum metal ion resistance. Further efforts are required to elucidate the molecular basis and interplay of additional resistance mechanisms.

Toxic heavy metal/oxyanion tolerance in haloarchaea from some saline and hypersaline ecosystems

“…The results demonstrated a relatively high susceptibility to zinc, and only 35% of haloarchaeal isolates could grow in the presence of 1 mM Zn 2+ . This result was in accordance with previously published [19, 33, 36, 37]. In addition, Baati et al reported that all 22 haloarchaeal strains in their study were resistant to 0.5 mM of zinc though only 22.7% were resistant to 1 mM of Zn 2+ [38].…”

A genome-scale atlas reveals complex interplay of transcription and translation in an archaeon

“…Notably, of the 32 non-redundant IS element-encoded proteins (Table S3) with above-average mRNA levels, only four were detected by SWATH-MS in this study, suggesting they were all post-transcriptionally repressed. By analyzing proteomics data from PeptideAtlas (76, 77) and PRIDE (78), including PXD003667 (79) and PXD015192 (80), we confirmed that 50% of the 32 transposases have been previously detected, depending on techniques and biological conditions. In addition, except for VNG_0051a, we established that these proteins bear the features required for detection by SWATH-MS. With that reasoning, we posit that the lack of detection of transposases in this study is due to their low abundance or complete absence.…”

A Genome-Scale Atlas Reveals Complex Interplay of Transcription and Translation in an Archaeon

“…Notably, of the 33 nonredundant mobilome proteins (see Table S3 at https://doi.org/10.6084/m9.figshare.21936396.v2 ) with above-average mRNA levels, only 4 were detected by SWATH-MS in this study, suggesting that they were all post-transcriptionally repressed. By analyzing proteomics data from PeptideAtlas ( 77 , 78 ) and PRIDE ( 79 ), including data under ProteomeXchange identifiers PXD003667 ( 80 ) and PXD015192 ( 81 ), we confirmed that 50% of the 33 mobilome proteins have been previously detected, depending on the techniques and biological conditions. In addition, except for VNG_0051a, we established that these proteins bear the features required for detection by SWATH-MS. With that reasoning, we posit that the lack of detection of transposases in this study is due to their low abundance or complete absence.…”