Dataset Information

Haloferax volcanii lysine acetylation

ABSTRACT: Oxidative stress adaptation strategies are important to cell function and are linked to cardiac, neurodegenerative disease and cancer. Representatives of the domain Archaea are used as model organisms based on their extreme tolerance to oxidants and close evolutionary relationship with eukaryotes. Study of the halophilic archaeon Haloferax volcanii reveals lysine acetylation to be associated with oxidative stress responses. The strong oxidant hypochlorite: i) stimulates an increase in lysine acetyltransferase HvPat2 to HvPat1 abundance ratios and ii) selects for lysine deacetylase sir2 mutants. Here we report the dynamic occupancy of the lysine acetylome of glycerol-grown H. volcanii as it shifts in profile in response to hypochlorite. These findings are revealed by the: 1) quantitative multiplex LC-MS/MS analysis of the SILAC-compatible parent and Δsir2 mutant strains and 2) label free LC-MS/MS analysis of H26 ‘wild type’ cells. The results show that lysine acetylation is associated with key biological processes including DNA topology, central metabolism, cobalamin biosynthesis and translation. Lysine acetylation targets are found conserved across species. Moreover, lysine residues modified by acetylation and ubiquitin-like sampylation are identified suggesting post-translational modification (PTM) crosstalk. Overall, the results of this study expand the current knowledge of lysine acetylation in Archaea, with the long-term goal to provide a balanced evolutionary perspective of PTM systems in living organisms.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Haloferax Volcanii Ds2

SUBMITTER: Ricardo Couto-Rodriguez

LAB HEAD: Julie Maupin-Furlow

PROVIDER: PXD041799 | Pride | 2023-07-20

REPOSITORIES: Pride

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Publications

Insights into the Lysine Acetylome of the Haloarchaeon Haloferax volcanii during Oxidative Stress by Quantitative SILAC-Based Proteomics.

Couto-Rodríguez Ricardo L RL Koh Jin J Chen Sixue S Maupin-Furlow Julie A JA

Antioxidants (Basel, Switzerland) 20230601 6

Oxidative stress adaptation strategies are important to cell function and are linked to cardiac, neurodegenerative disease, and cancer. Representatives of the Archaea domain are used as model organisms based on their extreme tolerance to oxidants and close evolutionary relationship with eukaryotes. A study of the halophilic archaeon Haloferax volcanii reveals lysine acetylation to be associated with oxidative stress responses. The strong oxidant hypochlorite: (i) stimulates an incr ...[more]

PMID: 37371933

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Project description:Among multiple interconnected pathways for L-Lysine (L-Lys) catabolism in pseudomonads, Pseudomonas aeruginosa PAO1 employed the decarboxylase and the transaminase pathways. However, up till now several genes involved in the operation and regulation of these pathways were still missing. Transcriptome analyses coupled with promoter activity measurements and mutant growth phenotype analysis lead us to identify several new members of the L-Lys and D-Lys catabolic pathways and their regulatory elements, including argR to trigger lysine decarboxylation into cadaverine, PauR for the Î³-glutamylation pathway of polyamine catabolism into 5-aminovalerate, gcdR-gcdHG for glutarate utilization, dpkA, amaR-amaAB and PA2035 for D-Lys catabolism, lysR-lysXE for L-Lys efflux, and lysP for L-Lys uptake. Gene expression microarray, including probe preparation, hybridization, fluidics run and chip scan, was performed by Georgia State University DNA/Protein Core Facility. P. aeruginosa PAO1 was grown aerobically in minimal medium P with 350 rpm shaking at 37C, in the presence of 10mM L-glutamate supplemented with 10 mM L-lysine, cadaverine, 5-amino valerate, glutaric acid, D-lysine or 5mM L-pipecolate. Cells were harvested when the optical density at 600 nm reached 0.5~0.6 by centrifugation for 5 minutes at 4C. Total RNA samples were isolated by RNeasy purification kit following instructions of the manufacturer (Qiagen). Reverse transcription for cDNA synthesis, fragmentation by DNase I treatment, cDNA probe labeling and hybridization were performed according to the instructions of GeneChip manufacturer (Affymetrix). Data were processed by Microarray Suite 5.0 software normalizing the absolute expression signal values of all chips to a target intensity of 500. GeneSpring software (Silicon Genetics) was used for expression pattern analysis and comparison. Data collection was carried out using GCOS 1.4 software (Affymetrix). Probe intensity values were normalized to a target value of 500 with normalization factor equal to 1. Data analysis was performed using GeneSpring GX 11 Software (Aglient, Palo Alto,CA). Related Research Papers: 1. Indurthi SM, Chou HT, Lu CD. Molecular Characterization of lysR-lysXE, gcdR-gcdHG, and amaR-amaAB Operons for Lysine Export and Catabolism: A Comprehensive Lysine Catabolic Network in Pseudomonas aeruginosa PAO1. Microbiology. 2015 Submitted [EMID:04803de65c782] 2. Chou HT, Li J, and Lu CD. Functional Characterization of the agtABCD and agtSR Operons for Î³-Aminobutyrate and Î´-Aminovalerate Uptake and Regulation in Pseudomonas aeruginosa PAO1. Curr. Microbiology. 2014 Jan;68(1):59-63. 3. Chou HT, Li JY, Peng YC, Lu CD. Molecular characterization of PauR and its role in control of putrescine and cadaverine catabolism through the Î³-glutamylation pathway in Pseudomonas aeruginosa PAO1. J Bacteriol. 2013 Sep; 195(17):3906-13. 4. Chou HT, Hegazy M, Lu CD. L-lysine Catabolism is Controlled by Arginine/ArgR in Pseudomonas aeruginosa PAO1. J Bacteriol. 2010 Nov;192(22):5874-80

Project description:Specific histone modifications play important roles in chromatin functions such as activation or repression of gene transcription. These participation must occur as a dynamic process, however, most of histone modification state maps reported to date only provide static pictures linking certain modification with active or silenced states. This study focused on the global histone modification variation that occurs in response to transcriptional reprogramming produced by a physiological perturbation in yeast. We have performed genome-wide chromatin immunoprecipitation analysis for eight specific histone modifications before and after of a saline stress. The most striking change is a quick deacetylation of lysines 9 and 14 of H3 and lysine 8 of H4 associated to repression of genes. Genes that are activated increase the acetylation levels at these same sites, but this acetylation process of activated genes seems minor quantitatively to that of the deacetylation of repressed genes. The observed changes in tri-methylation of lysines 4, 36 and 79 of H3 and also di-methylation of lysine 79 of H3 are much more moderate than those of acetylation. Additionally, we have produced new genome-wide maps for six histone modifications at more than five times higher resolution of previous available data and analyzed for the first time in S. cerevisiae genome wide profiles of two more, acetylation of lysine 8 of H4 and di-methylation of lysine 79 of H3. In this research we have shown that dynamic of acetylation state of histones during activation or repression of transcription is a process much quicker than methylation and therefore the changes produced in the acetylation may affect methylation but the reverse path is not possible. The experiments described in this study compare ChIP with a histone modification antibody to a control ChIP with a core histone antibody. Budding yeast samples were analyzed in exponential growing conditions (YPD) or after 10 minutes of 0.4M NaCl stress. For each experiment 1 or 2 biological replicates were performed.

Dataset Information

Haloferax volcanii lysine acetylation

Publications

Insights into the Lysine Acetylome of the Haloarchaeon <i>Haloferax volcanii</i> during Oxidative Stress by Quantitative SILAC-Based Proteomics.

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