Proteomics data for characterizing Microbacterium oleivorans A9, an uranium-tolerant actinobacterium isolated near the Chernobyl nuclear power plant

Abstract

Microbacterium oleivorans A9 cells were exposed or not to 10 µM uranyl nitrate as resting cells in sodium chloride solution. Bacteria exposed to U(VI) and controls were harvested after 0.5, 4, and 24 h of toxicant exposure. Bacteria were subjected to high-throughput proteomics analysis using a Q-Exactive HF high resolution tandem mass spectrometer incorporating an ultra-high-field orbitrap analyzer. MS/MS spectra were assigned with a protein sequence database derived from a draft genome obtained by Illumina sequencing and systematic six-reading frame translation of all the contigs. Proteins identified in bacteria exposed to U(VI) and controls at the three time points allow defining the proteome dynamics upon uranium stress. The data reported here are related to a published study regarding the proteome dynamics of M. oleivorans A9 upon uranium stress by Gallois et al. (in press) entitled “Proteogenomic insights into uranium tolerance of a Chernobyl׳s Microbacterium bacterial isolate”. The data accompanying the manuscript describing the database searches and comparative analysis have been deposited to the ProteomeXchange with identifier PXD005794.

Specifications table

Subject area	Environmental microbiology
More specific subject area	Actinobacteria comparative proteogenomics
Type of data	Figure, mass spectrometry raw files, Excel tables
How data was acquired	Data-dependent acquisition of tandem mass spectra using a Q-Exactive HF tandem mass spectrometer (Thermo).
Data format	Raw and processed
Experimental factors	Cells, at the exponential growth phase, were harvested and the resulting cell pellets were resuspended in NaCl solution with 0 (control) or 10 µM uranyl nitrate. For each of the three sampling time points, 0.5, 4 and 24 h, four biological replicates were performed.
Experimental features	The 24 proteomes were briefly run on SDS-PAGE, followed by trypsin proteolysis. Tryptic peptides were analyzed by nanoLC-MS/MS and spectra were assigned with a draft genome-derived protein sequence database.
Data source location	CEA-Marcoule, DRF-Li2D, Laboratory “Innovative technologies for Detection and Diagnostics”, BP 17171, F-30200 Bagnols-sur-Cèze, France
Data accessibility	Data are within this article and deposited to the ProteomeXchange via the PRIDE repository with identifier PRIDE: PXD005794.

Value of the data

• •The data are an interesting resource regarding the proteome content of a soil bacterium with extreme tolerance to heavy metals.
• •The proteogenomics strategy described here allows a quick identification of proteins based on a draft genome of this high GC content organism.
• •The data have been used to define the proteome changes in response to uranium stress in an Actinobacteria isolate from the trench T22 located near the Chernobyl nuclear power plant. As described in detail in the accompanying manuscript [1], the uranyl stress perturbed the phosphate and iron metabolic pathways.

1. Data

This report contains the complete list of peptide-to-spectrum assignments for the control (not treated) samples and Uranium-treated samples of Microbacterium oleivorans A9 in the first round of the proteogenomics cascade search (Supplementary Table S1), in the second round of the cascade search (Supplementary Table S2). A total of 746,092 MS/MS spectra were assigned in the first search round and 747,621 MS/MS spectra were interpreted in the second search round. All the tandem mass spectrometry characteristics (measured mass, charge, protease cleavage, post-translational modifications, and retention time) are indicated.

Fig. 1 shows the schematic flowchart of experiments, data processing and results that were obtained and formatted in.xls tables. The proteome data from four independent biological replicates per time point (0.5, 4 and 24 h) upon uranium exposure or control, i.e. from 24 samples, were assigned to tryptic peptides against the M. oleivorans A9 ORF database described by Gallois et al. [1] following a proteogenomic approach [2], [3], [4]. The deposited data comprised the 24 raw files and the interpreted files. Supplementary Tables S1 and S2 list the peptide-to-spectrum matches with all the tandem mass spectrometry characteristics in the first query round against the large proteogenomics database and second query round against the reduced ORF database, respectively.

Fig. 1.

Flowchart of experiments, data processing and refined data tables.

2. Experimental design, materials and methods

2.1. Preparation of Microbacterium oleivorans A9 samples

M. oleivorans A9 cells were isolated from Chernobyl trench T22 soil [5] and exposed as described [1]. Briefly, cells were harvested and the cell pellets were resuspended in 0.1 M NaCl pH 5.0 with 0 (control) or 10 µM uranyl nitrate. Four independent biological replicates were performed for statistical purpose. Fractions of 1 ml of cell suspension were taken after 0.5, 4, and 24 h for each condition. After centrifugation, the resulting supernatants were removed and the pellets were conserved at -80 °C until proteomic analysis. Proteogenomics were carried out as previously described [1], [6] taking into account the recent draft genome of the strain.

2.2. Protein extracts and tandem mass spectrometry

The 24 peptide mixtures were performed using a Q-Exactive HF mass spectrometer (ThermoFisher) coupled to an UltiMate 3000 LC system (Dionex-LC Packings) in similar conditions as those previously described. Peptide mixtures (10 μl) were loaded and desalted on-line on a reverse phase precolumn (Acclaim PepMap 100 C18) from LC Packings. Peptides were then resolved onto a reverse phase Acclaim PepMap 100 C18 column and injected into the Q-Exactive HF mass spectrometer. The Q-Exactive HF instrument was operated according to a Top20 data-dependent acquisition method as previously described [7].

2.3. Protein sequence database for proteogenomic MS/MS assignment

The recorded MS/MS spectra for the 24 samples were searched against our home-made ORF database with the parameters described previously [1]. This database contains 30,853 polypeptide sequences, for a total of 4,903,573 amino acids with an average of 159 amino acids per polypeptide. The number of MS/MS spectra per protein (spectral counts) was determined for the four replicates of each of the three time points for both conditions. The statistical protein variation was compared for each time point between the uranyl exposure and the control conditions using the T-Fold option of PatternLab 2.0 software [8].

Transparency document. Supplementary material

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Appendix A. Supplementary material

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