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. 2020 Apr 10;30:105466. doi: 10.1016/j.dib.2020.105466

Dataset on phenotypic characterization, on protein and genome analysis of three fluorescent Pseudomonas strains from mid-mountain water

Elodie Dussert 1, Mélissa Tourret 1, Barbara Deracinois 1, Matthieu Duban 1, Valérie Leclère 1, Benoit Cudennec 1, Rozenn Ravallec 1, Josette Behra-Miellet 1,⁎
PMCID: PMC7168345  PMID: 32322618

Abstract

The identification of non-fermentative Gram negative bacilli from run-off and spring water, including fluorescent Pseudomonas is very complex and investigations are needed to contribute to the systematic of these bacteria. In this dataset, the phenotypical profiles of three strains isolated from Vosges mountains first identified as Pseudomonas fluorescens were determined using APIⓇ 50 CH galleries. Then, the identification of their proteins released directly into water was carried out using tandem/mass spectrometry after separating proteins on native two-dimensional polyacrylamide gels. Finally, genotypic analysis data is presented, that illustrates biodiversity in this fluorescent bacterial group.

This data is referred by a research article entitled “Fluorescent Pseudomonas strains from mid-mountain water able to release antioxidant proteins directly into water”.

Keywords: Bacterial identification, Fluorescent Pseudomonas, Proteomics, Genome sequencing

Abbreviations: ANI, average nucleotide identity; MALDI, matrix assisted laser desorption ionization; MS, mass spectrometry; MS/MS, tandem mass spectrometry; MW, molecular weight; Nb, number of experimental peptides recognized; NCBI, National Center for Biotechnology Information; NR, not reviewed; P., Pseudomonas; PFF, peptide fragment fingerprinting; PMF, peptide mass fingerprinting; ppm, parts per million; R, reviewed; Spot no., spot number; TCS, tetra correlation search; TOF/TOF, time-of-flight/time-of-flight

Specifications table

Subject Microbiology
Specific subject area Identification of three fluorescent Pseudomonas strains isolated from mid-mountain run-off water (France)
Type of data Table
Figure
How data were acquired APIⓇ 50 CH galleries (bioMérieux Diagnostics, Marcy-l'Etoile, France). Average nucleotide identity (ANI) and tetra correlation search (TCS) analyzes with JSpecies software (Ribocon GmbH).
Alignment of the 3 bacterial draft genome sequences versus the complete genomes of the nearest bacterial species was performed using MAUVE algorithm.
Protein identification by mass spectrometry (MS) and/or tandem mass spectrometry (MS/MS) using an Autoflex SpeedTM matrix assisted laser desorption ionization (MALDI) time-of-flight/time-of-flight (TOF/TOF) mass spectrometer (Bruker, Bremen, Germany). Molecular mass measurement was performed in automatic mode using FlexControlTM 3.4 software in reflectron mode for MALDI-TOF peptide mass fingerprinting (PMF, MS mode) or LIFT mode for MALDI-TOF/TOF peptide fragment fingerprinting (PFF, MS/MS mode). Peak lists were generated from MS and MS/MS spectra using FlexAnalysisTM 3.4 software. Database search using PMF or PFF datasets was performed in the UniProt/SwissProt and National center for biotechnology information (NCBI) databases via Mascot 2.2 (Matrix Science Ltd, London, UK)] or PEAKS Studio 7.0 (Bioinformatics Solutions).
Data format Raw
Analyzed
Parameters for data collection Three strains of fluorescent Pseudomonas were collected from water and first identified as Pseudomonas fluorescens using optical microscopy, oxidase test and micro gallery APIⓇ 20 NE (bioMérieux) before to be tested. They were stored at −32 °C before to be aerobically cultured at 25 °C, either in broth medium and then recovered after spinning and placed into distilled water to produce the proteins analyzed, or on plate count agar to analyze their genomes. Total deoxyribonucleic acid (DNA) was extracted using the Wizard genomic purification DNA kit (Promega Corp., Madison, WI, USA) and sequenced at MicrobesNG
(http://www.microbesng.uk) using Illumina MiSeq and HiSeq 2500 technology platforms.
Description of data collection APIⓇ 50 CH galleries were inoculated with Fl4BN1, Fl4BN2 and Fl5BN2 fluorescent strains and positive characters were collected and compared. Genome was extracted using the Wizard genomic purification DNA kit before to be sequenced and analyzed using TCS and ANI indices. An alignment of the sequences was performed that compared the three draft genomes with the genomes of the nearest bacterial species. The proteins released directly into distilled water by the three strains were then separated in native 2D-gels after washing and desalting using filter with 10-kDa cut-off. Trypsin hydrolysis was then performed on the proteins contained in the spots of interest in the colored gels, before to be analyzed for their mass using MS and MS/MS and database search above mentioned.
Data source location Charles Viollette Institute
Lille, France
North latitude 50°36′ and east longitude 3°8′
Data accessibility 1. With the article
2. Accession numbers of the three genomes deposited in NCBI database: (SUBID BioProject BioSample Accession Organism) - SUB6805363 PRJNA601118 SAMN13831441 JAAARL000000000 Pseudomonas sp. Fl5BN2 https://www.ncbi.nlm.nih.gov/nuccore/JAAARL000000000
__ https://www.ncbi.nlm.nih.gov/Traces/wgs/JAAARL01?display=contigs
- SUB6805363 PRJNA601118 SAMN13831440 JAAARM000000000 Pseudomonas sp. Fl4BN1
https://www.ncbi.nlm.nih.gov/nuccore/JAAARM000000000
__ https://www.ncbi.nlm.nih.gov/Traces/wgs/JAAARM01?display=contigs - SUB6805363 PRJNA601118 SAMN13831439 JAAARN000000000 Pseudomonas sp. Fl4BN2
https://www.ncbi.nlm.nih.gov/nuccore/JAAARN000000000__ https://www.ncbi.nlm.nih.gov/Traces/wgs/JAAARN01?display=contigs
3. Repository name : Mendeley Data
Data identification number : DOI: 10.17632/p5kt4dvmxt.1
Direct URL to Data : https://data.mendeley.com/datasets/p5kt4dvmxt/1
Related research article Elodie Dussert1, Mélissa Tourret1, Barbara Deracinois1, Matthieu Duban1, Valérie Leclère1, Benoit Cudennec1, Rozenn Ravallec1, Josette Behra-Miellet1.
Fluorescent Pseudomonas strains from mid-mountain water able to release antioxidant proteins directly into water
Journal: Microbiological Research
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Value of the data

  • •

    The data shows the complexity of the identification of fluorescent Pseudomonas strains, isolated from water.

  • •

    The data could be valuable for researchers working on the systematics of non-pathogenic bacteria from water, especially to compare Pseudomonas genomes with TCS and ANI.

  • •

    The data could be useful for researches on antioxidant proteins released into water by non-pathogenic bacteria.

  • •

    The data could contribute to the bacterial systematics of non-fermentative fluorescent Gram-negative bacilli.

1. Data description

Table 1 shows the data related to APIⓇ 50 CH micro galleries for the three strains studied: Fl4BN1, Fl4BN2 and Fl5BN2. For each substrate, oxidation and assimilation are specified. Table 2 describes TCS or tetra-nucleotide signature data for Fl4BN1, Fl4BN2 and Fl5BN2. Draft genomes of Fl4BN1 and Fl5BN2 were found very close to Pseudomonas batumici UCM B-321 strain and Pseudomonas protegens Cab57 strain, with Z-scores of 0.98989 and 0.98953 for Fl4BN1 and 0.98945 and 0.98938 for Fl5BN2, respectively whereas Fl4BN2 was identified as Pseudomonas fragi P121 and Pseudomonas sp. Lz4W with Z-scores of 0.99969 and 0.99949, respectively. Pairwise genome comparison was performed using JSpecies to measure the probability that genomes belonged to the same species with their ANI: data are described in Tables 3 and 4 for ANIb and ANIm respectively. ANIb and ANIm analyzes of Fl4BN2 genome sequence versus 12 strains defined as having the genomes closest to those of Fl4BN1, Fl4BN2 and Fl5BN2 using TCS test revealed that this strain could belong to Pseudomonas fragi or Pseudomonas sp. Lz4W species with ANI higher than 98%. Both analyzes showed that Fl4BN1 and Fl5BN2 belonged to the same species with 99.28% ANIm (Table 4) and an ANIb higher than 98.94% (Table 3). Fig. 1 shows alignments of the bacterial draft genomes with the complete genomes of the nearest species determined by average nucleotide identity (JSpecies) (Pseudomonas sp. Lz4W and P. fragi P121 for Fl4BN2 and Pseudomonas protegens CHA0 for Fl4BN1 and Fl5BN2), performed using the Progressive MAUVE algorithm. Table 5, Table 6, Table 7, Table 8, Table 9, Table 10, Table 11 summarize the raw data obtained from proteomic searches and available in Mendeley Data (deposited as Raw data of the article: “Dataset on phenotypic characterization, on protein and genome analysis of three fluorescent Pseudomonas strains from mid-mountain water”). Table 5 is related to the raw data contained in folder “MS” of Mendeley Data and describes identification of the proteins released by the three strains. They migrated in a gel with an isoelectric point gradient from 3 to 10 and were identified by the technique of peptide mapping by the mass through the “Mascot” search algorithm. These proteins were classified in three families: “Proteins counteracting oxidative stress and/or ensuring redox balance”, “Chaperonin proteins” and “Other proteins involved in stress response”. For each protein, sequence coverage (%), theoretical isoelectric point, theoretical molecular weight, number of experimental peptides recognized, rank, probability MOWSE score, maximum difference between theoretical peptide masses and experimental ones, score (−10 lgP) and database leading to the identification were presented. Only the significant data are described. Tables 6, 8 and 10 are related to folder “MS-MS”/subfolder “NCBI” of Mendeley Data and contain the identification data of the proteins released by Fl4BN1, Fl4BN2 and Fl5BN2, respectively, by the technique of mapping by mass through the “PEAKS studio” search algorithm with NCBI database. Tables 7, 9 and 11 are related to folder “MS-MS”/subfolder “SwissProt” of Mendeley Data and include the identification data of the proteins produced by Fl4BN1, Fl4BN2 and Fl5BN2, respectively, by the technique of mapping by mass through the “PEAKS studio” search algorithm with SwissProt database. Only significant data (with score greater than the peptide hit threshold (30) obtained with “PEAKS studio” search algorithm was presented and classified in three families: “Proteins counteracting oxidative stress and/or ensuring redox balance”, “Chaperonin proteins” and “Other proteins involved in stress response”. Moreover, database research was carried out using different databases: bacteria database not reviewed (_NR), bacteria database reviewed (_R), and Pseudomonas protegens database (NCBI and SwissProt).

Table 1.

Data obtained using APIⓇ 50 CH micro gallery.

Test (active ingredients) Fl4BN1 Fl4BN2 Fl5BN2
Glycerol A- O+/A+ A-
Erythritol – – –
D-arabinose – A- –
L-arabinose – A- –
D-ribose A- A- A-
D-xylose O+ A- O+
L-xylose – – –
D-adonitol – – –
Methyl-βD-xylopyranoside – – –
D-galactose O+ O+/A- O+
D-glucose A- O-/A- A+
D-fructose A- O+/A+ A-
D-mannose – O+ A-
L-sorbose – – –
L-rhamnose – – –
Dulcitol – – –
Inositol A+ A+ A-
D-mannitol A+ – A+
D-sorbitol – – –
Methyl-αD-mannopyranoside – – –
Methyl-αD-glucopyranoside – – –
N-acetylglucosamine A+ – A-
Amygdalin – – –
Arbutin – – –
Esculin (ferric citrate) – – –
Salicin – – –
D-cellobiose – – –
D-maltose – – –
D-lactose (bovine origin) – – –
D-melibiose – – –
D-saccharose (sucrose) – – –
D-trehalose A+ A+ A-
Inuline – – –
D-melezitose – – –
D-raffinose – – –
Amidon (starch) – – –
Glycogen – – A-
Xylitol – – –
Gentiobiose – – –
D-turanose – – –
D-lyxose – – –
D-tagatose – – –
D-fucose F+ O+ F-
L-fucose – A+ –
D-arabitol A+ A+ A-
L-arabitol – – –
Potassium gluconate A+ A+ A+
Potassium 2-ketogluconate A+ A+ A+
Potassium 5-ketogluconate – – –
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F+ = strong fermentation, F- = weak fermentation, O+ = strong oxidation, O- = weak oxidation, A+ = strong assimilation (strong growth of microorganism when the substrate used is the only source of carbon), A- = weak assimilation (weak growth of microorganism when the substrate used is the only source of carbon).

Table 2.

TCS data for Fl4BN1, Fl4BN2 and Fl5BN2. ** above cut-off (> 0.999), * in range (> 0.989), below cut-off (< 0.989).

Pos. Species Strain Domain Phylum Class Order Family Z-Score
Fl4BN1 1 Pseudomonas batumici UCM B-321 UCM B-321 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.98989 *
2 Pseudomonas protegens Cab57 null Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.98953 *
3 Pseudomonas protegens Pf-5 Pf-5 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.9888
4 Pseudomonas protegens CHA0 CHA0 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.98873
5 Pseudomonas sp. Os17 Os17 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.98751
6 Pseudomonas sp. GM17 GM17 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.98536
7 Pseudomonas chlororaphis subsp. piscium PCL1391 PCL1391 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.98517
8 Pseudomonas chlororaphis O6 O6 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.98456
9 Pseudomonas putida (GCA_001006135) CBB5 CBB5 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.9845
10 Pseudomonas chlororaphis subsp. aurantiaca str. JD37 JD37 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.9844
11 Pseudomonas chlororaphis subsp. aureofaciens 30–84 30–84 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.98435
12 Pseudomonas chlororaphis PA23 PA23 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.9842
13 Pseudomonas sp. GM78 GM78 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.98399
14 Pseudomonas sp. CF161 CF161 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.98383
15 Pseudomonas chlororaphis subsp. aurantiaca PB-St2 PB-St2 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.98265
16 Pseudomonas sp. G5(2012) G5 G5 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.98165
17 Pseudomonas sp. ABAC61 ABAC61 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.98138
18 Pseudomonas fluorescens (GCA_000836415) UM270 UM270 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.98084
19 Pseudomonas fuscovaginae IRRI 6609 IRRI 6609 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.98083
20 Pseudomonas putida (GCA_000729805) MC4-5222 MC4-5222 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.98053
Fl4BN2 1 Pseudomonas fragi P121 P121 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.99969 **
2 Pseudomonas sp. Lz4W Lz4W Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.99949 **
3 Pseudomonas sp. L10.10 L10.10 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.9944 *
4 Pseudomonas deceptionensis DSM 26,521 DSM 26,521 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.97569
5 Pseudomonas taetrolens DSM 21,104 DSM 21,104 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.97146
6 Pseudomonas sp. CF149 CF149 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.967
7 Pseudomonas psychrophila DSM 17,535 DSM 17,535 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.96683
8 Pseudomonas fluorescens str. S613 S613 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.95446
9 Pseudomonas sp. GM55 GM55 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.95355
10 Pseudomonas sp. GM48 GM48 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.95245
11 Pseudomonas sp. UW4 UW4 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.95237
12 Pseudomonas sp. Leaf48 Leaf48 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.95231
13 Pseudomonas sp. GM49 GM49 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.95209
14 Pseudomonas sp. GM74 GM74 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.94993
15 Pseudomonas sp. GM33 GM33 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.94968
16 Pseudomonas alkylphenolia KL28 KL28 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.94814
17 Pseudomonas sp. Root71 Root71 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.94767
18 Pseudomonas sp. Root68 Root68 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.94755
19 Pseudomonas fluorescens (GCA_000967965) C8 C8 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.94607
20 Pseudomonas sp. StFLB209 StFLB209 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.94582
Fl5BN2 1 Pseudomonas batumici UCM B-321 UCM B-321 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.98945 *
2 Pseudomonas protegens Cab57 null Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.98938 *
3 Pseudomonas protegens Pf-5 Pf-5 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.98866
4 Pseudomonas protegens CHA0 CHA0 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.98857
5 Pseudomonas sp. Os17 Os17 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.98698
6 Pseudomonas sp. GM17 GM17 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.98467
7 Pseudomonas chlororaphis subsp. piscium PCL1391 PCL1391 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.98443
8 Pseudomonas putida (GCA_001006135) CBB5 CBB5 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.98435
9 Pseudomonas chlororaphis O6 O6 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.98381
10 Pseudomonas sp. GM78 GM78 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.98373
11 Pseudomonas chlororaphis subsp. aurantiaca str. JD37 JD37 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.98369
12 Pseudomonas chlororaphis subsp. aureofaciens 30–84 30–84 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.98367
13 Pseudomonas chlororaphis PA23 PA23 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.98345
14 Pseudomonas sp. CF161 CF161 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.98329
15 Pseudomonas chlororaphis subsp. aurantiaca PB-St2 PB-St2 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.98191
16 Pseudomonas sp. G5(2012) G5 G5 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.98152
17 Pseudomonas sp. ABAC61 ABAC61 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.98117
18 Pseudomonas putida (GCA_000729805) MC4-5222 MC4-5222 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.98042
19 Pseudomonas fluorescens (GCA_000836415) UM270 UM270 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.98028
20 Pseudomonas fuscovaginae IRRI 6609 IRRI 6609 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae 0.98026
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Table 3.

ANIb data for Fl4BN1, Fl4BN2 and Fl5BN2. The values represent scores (%). In bold values > 95%: identification of species.

Fl4BN1_92_ctg.fas Fl4BN2_181ctg.fas Fl5BN2_59_ctg.fas Pseudomonas batumici UCM B-321 Pseudomonas protegens Cab57 Pseudomonas protegens CHA0 Pseudomonas protegens Pf-5 Pseudomonas sp. Os17 Pseudomonas sp. GM17 Pseudomonas fragi P121 Pseudomonas sp. Lz4W Pseudomonas sp. L10.10 Pseudomonas deceptionensis DSM 26,521 Pseudomonas taetrolens DSM 21,104 Pseudomonas sp. CF149
Fl4BN1_92_ctg.fas * 77.48 98.94 79.62 87.50 87.55 87.48 87.11 82.62 77.44 77.49 77.22 77.82 77.15 77.23
Fl4BN2_181ctg.fas 78.38 * 78.40 78.70 78.56 78.56 78.51 78.58 78.93 98.95 99.00 90.53 84.80 83.06 83.93
Fl5BN2_59_ctg.fas 99.03 77.56 * 79.78 87.53 87.60 87.54 87.07 82.58 77.49 77.50 77.30 77.78 77.11 77.24
Pseudomonas batumici UCM B-321 80.06 78.21 80.12 * 80.67 80.71 80.63 80.67 81.22 78.16 78.21 77.95 78.48 77.71 77.77
Pseudomonas protegens Cab57 87.64 77.91 87.61 80.45 * 98.36 98.06 89.15 83.53 77.88 77.88 77.40 78.04 77.47 77.55
Pseudomonas protegens CHA0 87.69 77.79 87.70 80.58 98.40 * 98.65 89.11 83.57 77.75 77.80 77.46 78.09 77.49 77.51
Pseudomonas protegens Pf-5 87.62 77.88 87.61 80.41 98.03 98.55 * 88.89 83.48 77.90 77.90 77.48 78.14 77.52 77.48
Pseudomonas sp. Os17 87.40 78.11 87.39 80.68 89.43 89.30 89.18 * 83.62 78.09 78.15 77.67 78.25 77.75 77.59
Pseudomonas sp. GM17 82.98 78.28 82.97 81.02 83.75 83.79 83.75 83.59 * 78.32 78.36 78.07 78.66 78.01 78.05
Pseudomonas fragi P121 78.39 99.19 78.40 78.85 78.71 78.66 78.65 78.70 79.09 * 99.14 90.71 85.00 83.22 84.37
Pseudomonas sp. Lz4W 78.30 99.25 78.30 78.79 78.67 78.62 78.63 78.66 79.02 99.21 * 90.76 84.99 83.24 84.22
Pseudomonas sp. L10.10 78.14 90.67 78.17 78.40 78.31 78.31 78.27 78.30 78.80 90.69 90.65 * 84.75 83.08 83.92
Pseudomonas deceptionensis DSM 26,521 78.38 84.93 78.39 78.89 78.69 78.76 78.76 78.71 79.16 84.98 84.91 84.63 * 83.68 87.99
Pseudomonas taetrolens DSM 21,104 77.77 83.11 77.74 78.30 78.03 78.08 78.04 78.15 78.58 83.10 83.16 82.94 83.57 * 83.02
Pseudomonas sp. CF149 77.81 84.09 77.82 78.07 78.07 78.08 78.08 78.11 78.49 84.29 84.15 83.80 87.97 83.03 *
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Table 4.

ANIm data for Fl4BN1, Fl4BN2 and Fl5BN2. The values represent scores (%). In bold, values > 95%: identification of species.

Fl4Bn1_92_ctg.fas Fl4Bn2_181ctg.fas Fl5Bn2_59_ctg.fas Pseudomonas batumici UCM B-321 Pseudomonas protegens Cab57 Pseudomonas protegens CHA0 Pseudomonas protegens Pf-5 Pseudomonas sp. Os17 Pseudomonas sp. GM17 Pseudomonas fragi P121 Pseudomonas sp. Lz4W Pseudomonas sp. L10.10 Pseudomonas deceptionensis DSM 26,521 Pseudomonas taetrolens DSM 21,104 Pseudomonas sp. CF149
Fl4Bn1_92_ctg.fas * 84.79 99.28 85.96 89.17 89.24 89.20 89.05 86.89 84.74 84.73 84.67 84.75 84.61 84.53
Fl4Bn2_181ctg.fas 84.79 * 84.80 84.80 84.86 84.83 84.82 84.81 84.93 99.15 99.30 91.37 87.06 86.24 86.54
Fl5Bn2_59_ctg.fas 99.28 84.80 * 85.93 89.16 89.24 89.19 89.06 86.89 84.77 84.75 84.66 84.71 84.63 84.54
Pseudomonas batumici UCM B-321 85.95 84.80 85.93 * 86.24 86.27 86.25 86.26 86.57 84.89 84.84 84.84 84.82 84.84 84.69
Pseudomonas protegens Cab57 89.16 84.86 89.16 86.24 * 98.58 98.38 90.66 87.40 84.93 84.88 84.87 84.85 84.68 84.68
Pseudomonas protegens CHA0 89.24 84.84 89.24 86.27 98.60 * 98.87 90.64 87.45 84.96 84.84 84.78 84.85 84.72 84.68
Pseudomonas protegens Pf-5 89.21 84.83 89.19 86.25 98.38 98.87 * 90.53 87.49 84.89 84.83 84.77 84.82 84.76 84.65
Pseudomonas sp. Os17 89.05 84.80 89.06 86.25 90.66 90.64 90.53 * 87.42 84.88 84.86 84.69 84.92 84.78 84.66
Pseudomonas sp. GM17 86.88 84.91 86.88 86.57 87.40 87.44 87.48 87.42 * 84.96 84.97 84.79 84.96 84.92 84.77
Pseudomonas fragi P121 84.74 99.14 84.76 84.89 84.93 84.95 84.88 84.88 84.97 * 99.28 91.35 87.05 86.23 86.77
Pseudomonas sp. Lz4W 84.74 99.30 84.75 84.84 84.87 84.84 84.82 84.87 84.98 99.29 * 91.36 87.07 86.27 86.62
Pseudomonas sp. L10.10 84.67 91.37 84.66 84.84 84.87 84.77 84.77 84.70 84.79 91.35 91.36 * 87.00 86.16 86.53
Pseudomonas deceptionensis DSM 26,521 84.75 87.06 84.71 84.82 84.85 84.86 84.83 84.92 84.96 87.04 87.07 87.00 * 86.46 89.41
Pseudomonas taetrolens DSM 21,104 84.61 86.24 84.62 84.83 84.69 84.73 84.77 84.78 84.92 86.23 86.27 86.16 86.46 * 86.12
Pseudomonas sp. CF149 84.54 86.53 84.55 84.69 84.68 84.68 84.66 84.66 84.77 86.76 86.62 86.53 89.40 86.11 *
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Fig. 1.

Fig. 1

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Alignments of the bacterial draft genomes of Fl4BN1, Fl5BN2 and Fl4BN2 with the complete genomes of the nearest species determined by average nucleotide identity (JSpecies) performed using the Progressive MAUVE algorithm. a. Alignment of Fl4BN1 draft genome versus Pseudomonas protegens CHA0 genome (NCBI accession number: NC_021237). b. Alignment of Fl5BN2 draft genome versus P. protegens CHA0 genome (NCBI accession number: NC_021237). c. Alignment of Fl4BN2 draft genome versus Pseudomonas sp. Lz4W genome (NCBI accession number: CP017432.1). d. Alignment of Fl4BN2 draft genome versus Pseudomonas fragi P121 genome (NCBI accession number: NZ_CP013861).

Table 5.

Identification of the proteins released by Fl4BN1, Fl4BN2 and Fl5BN2. They migrated in a gel with an isoelectric point gradient from 3 to 10 and were identified by the technique of peptide mapping by mass through the “Mascot” search algorithm. (http://www.matrixscience.com/cgi/search_form.pl?FORMVER=2&SEARCH=PMF). In the algorithm Mascot with the SwissProt and NCBI "National Center for Biotechnology Information" databases, protein identification was “significant” if the probability MOWSE score was greater than the signification threshold where P was the probability that the observed match was a random event. (Spot no.) spot number. (MW) molecular weight. (Nb) number of experimental peptides recognized. Maximum ≠ between theoretical/experimental masses = maximum difference between theoretical peptide masses and experimental ones, expressed in ppm (parts per million).

Strain Protein family Spot no. Data Research algorithm: Mascot
Definition Sequence coverage (%) Theoretical pI Theoretical MW (kDa) Nb Rank Probability MOWSE score (signification threshold) ppm −10lgP Database
Fl4BN1 Proteins counteracting oxidative stress and/or ensuring redox balance o3 ILVC_PSEF5, Ketol-acid reductoisomerase (NADP(+)) OS=Pseudomonas fluorescens (strain ATCC BAA-477/NRRL B-23,932/Pf-5) GN=ilvC 34 5.48 36.441 10 1 81 (68) 44.5 0.0029 SwissProt
o4 WP_003212997.1, MULTISPECIES: superoxide dismutase [Pseudomonas] 46 5.56 22.078 8 1 107 (93) 43.4 0.0021 NCBIprot
SODF_PSEPK, Superoxide dismutase [Fe] OS=Pseudomonas putida (strain ATCC 47,054/DSM 6125/NCIMB 11,950/KT2440) GN=sodB 36 5.55 22.096 6 1 76 (68) 31.8 0.0086 SwissProt
Chaperonin proteins c2 HTPG_PSEPF, Chaperone protein HtpG OS=Pseudomonas fluorescens (strain Pf0-1) GN=htpG 27 5.13 71.241 17 1 90 (68) 48.9 0.00033 SwissProt
c4 WP_025126505.1, trigger factor [Pseudomonas sp. PH1b] 46 4.82 48.500 18 1 117 (93) 37.5 0.00021 NCBIprot
WP_015636350.1, trigger factor [Pseudomonas protegens] 40 4.81 48.481 16 2 94 (93) 32.8 0.039 NCBIprot
WP_047337326.1, trigger factor [Pseudomonas fluorescens] 40 4.78 48.567 16 2 94 (93) 32.8 0.039 NCBIprot
WP_011062275.1, MULTISPECIES: trigger factor [Pseudomonas] 40 4.78 48.539 16 2 94 (93) 32.8 0.039 NCBIprot
TIG_PSEF5, Trigger factor OS=Pseudomonas fluorescens (strain ATCC BAA-477/NRRL B-23,932/Pf-5) GN=tig 40 4,78 48.539 16 1 102 (68) 32.8 2.1E-05 SwissProt
c5 SURA_PSEF5, Chaperone SurA OS=Pseudomonas fluorescens (strain ATCC BAA-477/NRRL B-23,932/Pf-5) GN=surA 34 5,3 47.375 15 1 85 (68) 22.8 0.0011 SwissProt
c7 WP_047301678.1, MULTISPECIES: nucleotide exchange factor GrpE [Pseudomonas] 52 4.67 20.853 14 1 116 (93) 32 0.00026 NCBIprot
WP_047283881.1, nucleotide exchange factor GrpE [Pseudomonas fluorescens] 52 4.65 20.782 14 1 116 (93) 32 0.00026 NCBIprot
WP_011059187.1, MULTISPECIES: nucleotide exchange factor GrpE [Pseudomonas] 52 4.65 20.810 14 1 116 (93) 32 0.00026 NCBIprot
GRPE_PSEF5, Protein GrpE OS=Pseudomonas fluorescens (strain ATCC BAA-477/NRRL B-23,932/Pf-5) GN=grpE 52 5.5 20.810 14 1 116 (68) 32 8.4E-07 SwissProt
Other proteins involved in stress response p2 CAPB_PSEFR, Cold shock protein CapB OS=Pseudomonas fragi GN=capB 69 6.54 7.722 6 1 77 (68) 56.5 0.0071 SwissProt
Fl4BN2 Chaperonin proteins c1 WP_019410411.1, molecular chaperone DnaK [Pseudomonas psychrophila] 34 4.84 68.449 19 1 124 (93) 39.5 4.1E-05 NCBIprot
DNAK_PSEA7, Chaperone protein DnaK OS=Pseudomonas aeruginosa (strain PA7) GN=dnaK 28 4.81 68.405 14 1 91 (68) 49.9 0.00026 SwissProt
c2 WP_003439583.1, MULTISPECIES: molecular chaperone DnaK [Pseudomonas] 38 4.84 68.265 21 1 150 (93) 32.3 1,0E-07 NCBIprot
c3 WP_019410411.1, molecular chaperone DnaK [Pseudomonas psychrophila] 36 4.84 68.449 17 1 109 (93) 39.8 0.0013 NCBIprot
c4 WP_003439583.1, MULTISPECIES: molecular chaperone DnaK [Pseudomonas] 44 4.84 68.265 22 1 135 (93) 47.9 3.3E-06 NCBIprot
c5 WP_003439583.1, MULTISPECIES: molecular chaperone DnaK [Pseudomonas] 42 4.84 68.265 24 1 170 (93) 36.7 1,0E-09 NCBIprot
DNAK_PSEA7, Chaperone protein DnaK OS=Pseudomonas aeruginosa (strain PA7) GN=dnaK 28 4.81 68.405 16 1 115 (68) 38.7 1.1E-06 SwissProt
c6 WP_003439583.1, MULTISPECIES: molecular chaperone DnaK [Pseudomonas] 40 4.84 68.265 20 1 133 (93) 48 5.2E-06 NCBIprot
DNAK_PSEA7, Chaperone protein DnaK OS=Pseudomonas aeruginosa (strain PA7) GN=dnaK 30 4.81 68.405 15 1 93 (68) 48 0.00017 SwissProt
c7 WP_003446928.1, MULTISPECIES: molecular chaperone HtpG [Pseudomonas] 45 5.18 71.200 23 1 153 (93) 49.9 5.2E-08 NCBIprot
c9 WP_010655838.1, trigger factor [Pseudomonas fragi] 47 4.77 48.560 17 1 175 (93) 49.5 3.3E-10 NCBIprot
c10 WP_010655838.1, trigger factor [Pseudomonas fragi] 40 4.77 48.560 14 1 126 (93) 47.5 2.6E-05 NCBIprot
c11 WP_003441361.1, trigger factor [Pseudomonas sp. Lz4W] 57 4.77 48.530 22 1 164 (93) 48.1 4.1E-09 NCBIprot
Other proteins involved in stress response p2 WP_074811207.1, cold-shock protein [Pseudomonas syringae] 81 6.54 7.836 8 1 100 (93) 23.6 0.011 NCBIprot
CAPB_PSEFR, Cold shock protein CapB OS=Pseudomonas fragi GN=capB 66 6.54 7.722 6 1 83 (68) 18.1 0.0017 SwissProt
Fl5BN2 Proteins counteracting oxidative stress and/or ensuring redox balance o3 WP_057397981.1, dihydrolipoyl dehydrogenase [Pseudomonas fluorescens] 36 5.93 50.091 12 1 98 (93) 23.3 0.016 NCBIprot
o4 WP_008049689.1, dihydrolipoyl dehydrogenase [Pseudomonas sp. GM74] 35 6.03 50.104 12 1 103 (93) 48.7 0.0052 NCBIprot
o5 WP_016966196.1, MULTISPECIES: superoxide dismutase [Pseudomonas] 53 5.55 22.089 11 1 104 (93) 49.4 0.0041 NCBIprot
Chaperonin proteins c2 WP_041119683.1, chaperonin GroEL [Pseudomonas protegens] 46 4.99 56.841 17 1 116 (93) 42.6 0.00026 NCBIprot
CH60_PSEF5, 60 kDa chaperonin OS=Pseudomonas fluorescens (strain ATCC BAA-477/NRRL B-23,932/Pf-5) GN=groL 46 4.99 57.086 17 1 115 (68) 42.6 1.1e-06 SwissProt
c4 WP_025126505.1, trigger factor [Pseudomonas sp. PH1b] 63 4.82 48.500 21 1 199 (93) 41.7 1.3E-12 NCBIprot
TIG_PSEF5, Trigger factor OS=Pseudomonas fluorescens (strain ATCC BAA-477/NRRL B-23,932/Pf-5) GN=tig 57 4.78 48.539 16 1 164 (68) 41.7 1.3E-11 SwissProt
c5 WP_011063825.1, MULTISPECIES: molecular chaperone SurA [Pseudomonas] 53 5.30 47.375 22 1 174 (93) 48.2 4.1E-10 NCBIprot
SURA_PSEF5, Chaperone SurA OS=Pseudomonas fluorescens (strain ATCC BAA-477/NRRL B-23,932/Pf-5) GN=surA 53 5.30 47.375 22 1 174 (68) 48.2 1.3E-12 SwissProt
Other proteins involved in stress response p1 SEB63063.1, C-terminal processing peptidase-1. Serine peptidase. MEROPS family S41A [Pseudomonas saponiphila] 29 5.97 77.543 18 1 114 (93) 45 0.00041 NCBIprot
p4 WP_074811207.1, cold-shock protein [Pseudomonas syringae] 85 6.54 7.836 8 1 109 (93) 43.1 0.0013 NCBIprot
CAPB_PSEFR, Cold shock protein CapB OS=Pseudomonas fragi GN=capB 71 6.54 7.722 7 1 91 (68) 43.1 0.00028 SwissProt
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Table 6.

Identification of the proteins released by Fl4BN1. They migrated in a gel with an isoelectric point gradient from 3 to 10 and were identified by the technique of peptide mapping by mass through the “PEAKS studio” search algorithm, NCBI database. In the algorithm of PEAKS studio with the SwissProt and NCBI “National Center for Biotechnology Information” databases, protein identification was “significant” if the (−10lgP) score was greater than the peptide hit threshold (30.0). P was the probability that the observed match was a random event. (Spot no.) spot number. (MW) molecular weight. (R) reviewed. (NR) not reviewed. (P. protegens) Pseudomonas protegens.

Protein family Spot no. Data
 Research algorithm: PEAKS
Definition Accession number: NCBI reference sequence (version) Theoretical MW (kDa) Sequence coverage (%) −10lgP Database
Proteins counteracting oxidative stress and/or ensuring redox balance o1 dihydrolipoyl dehydrogenase [Pseudomonas protegens] gi|1332918899 49.831 5 61.76 NCBI_P. protegens
o2 MULTISPECIES: peroxiredoxin [Pseudomonas] gi|499375533 21.787 6 96.79 NCBI_P. protegens
MULTISPECIES: peroxiredoxin [Pseudomonas] gi|495197643 21.773 6 96.79 NCBI_P. protegens
MULTISPECIES: peroxiredoxin [Pseudomonas] WP_003178707.1 21.856 6 65.14 NCBI_Bacteria_NR
MULTISPECIES: peroxiredoxin [Pseudomonas] WP_003231418.1 21.938 6 65.14 NCBI_Bacteria_NR
MULTISPECIES: peroxiredoxin [Pseudomonas] WP_003188979.1 21.947 6 65.14 NCBI_Bacteria_NR
MULTISPECIES: peroxiredoxin [Pseudomonas] WP_003254945.1 21.730 6 65.14 NCBI_Bacteria_NR
peroxiredoxin [Pseudomonas putida KT2440] NP_743245.1 21.730 6 65.14 NCBI_Bacteria_NR
MULTISPECIES: peroxiredoxin [Pseudomonas] WP_003172097.1 21.933 6 65.14 NCBI_Bacteria_NR
MULTISPECIES: peroxiredoxin [Pseudomonas] WP_003204949.1 21.929 6 65.14 NCBI_Bacteria_NR
MULTISPECIES: peroxiredoxin [Pseudomonas] WP_003227723.1 21.765 6 65.14 NCBI_Bacteria_NR
Chaperonin proteins c1 MULTISPECIES: molecular chaperone DnaK [Pseudomonas] gi|499371610 68.476 7 45.69 NCBI_P. protegens
c2 MULTISPECIES: molecular chaperone HtpG [Pseudomonas] gi|499372481 71.349 5 63.50 NCBI_P. protegens
molecular chaperone HtpG [Pseudomonas protegens] gi|1332903508 71.349 5 63.50 NCBI_P. protegens
molecular chaperone HtpG [Pseudomonas protegens] gi|1332919100 71.336 5 63.50 NCBI_P. protegens
c3 chaperonin GroEL [Pseudomonas protegens] gi|751652819 56.819 17 139.15 NCBI_P. protegens
MULTISPECIES: molecular chaperone GroEL [Pseudomonas] gi|499375514 57.065 17 139.15 NCBI_P. protegens
chaperonin GroEL [Beggiatoa alba] WP_002686219.1 57.692 3 35.32 NCBI_Bacteria_NR
60 kDa chaperonin GroEL [Shewanella oneidensis MR-1] NP_716,337.1 57.080 3 35.32 NCBI_Bacteria_NR
chaperonin GroEL [Thauera linaloolentis] WP_004339041.1 56.684 3 35.32 NCBI_Bacteria_NR
MULTISPECIES: molecular chaperone GroEL [Bordetella] WP_003808619.1 57.483 3 35.32 NCBI_Bacteria_NR
molecular chaperone GroEL [Bordetella pertussis Tohama I] NP_882014.1 57.482 3 35.32 NCBI_Bacteria_NR
MULTISPECIES: chaperonin GroEL [Pseudomonas] WP_003238874.1 56.883 3 35.32 NCBI_Bacteria_NR
chaperonin GroEL [Pseudomonas fluorescens] WP_003175873.1 56.927 3 35.32 NCBI_Bacteria_NR
MULTISPECIES: chaperonin GroEL [Pseudomonas] WP_003178748.1 56.843 3 35.32 NCBI_Bacteria_NR
MULTISPECIES: chaperonin GroEL [Pseudomonas] WP_003227683.1 56.905 3 35.32 NCBI_Bacteria_NR
chaperonin GroEL [Pseudomonas fluorescens] WP_003193939.1 56.882 3 35.32 NCBI_Bacteria_NR
chaperonin GroEL [Cystobacter fuscus] WP_002624037.1 58.167 3 35.32 NCBI_Bacteria_NR
molecular chaperone GroEL [Coxiella burnetii RSA 493] NP_820699.1 58.284 3 35.32 NCBI_Bacteria_NR
molecular chaperone GroEL [Nitrosococcus oceani] WP_002813030.1 58.284 3 35.32 NCBI_Bacteria_NR
c6 chaperonin GroEL [Pseudomonas protegens] gi|751652819 56.819 17 139.15 NCBI_P. protegens
MULTISPECIES: molecular chaperone GroEL [Pseudomonas] gi|499375514 57.065 17 139.15 NCBI_P. protegens
Other proteins involved in stress response p1 tail-specific protease [Pseudomonas protegens] gi|499375085 79.065 2 66.15 NCBI_P. protegens
peptidase S41 [Pseudomonas protegens] gi|1043219129 79.051 2 66.15 NCBI_P. protegens
MULTISPECIES: tail-specific protease [Pseudomonas] gi|829054598 79.040 2 66.15 NCBI_P. protegens
tail-specific protease [Pseudomonas protegens] gi|505449515 79.066 2 66.15 NCBI_P. protegens
tail-specific protease [Pseudomonas protegens] gi|751652595 79.024 2 66.15 NCBI_P. protegens
MULTISPECIES: tail-specific protease [Pseudomonas fluorescens group] gi|517923405 79.026 2 66.15 NCBI_P. protegens
tail-specific protease [Pseudomonas protegens] gi|1332920536 79.022 2 66.15 NCBI_P. protegens
tail-specific protease [Pseudomonas protegens] gi|1332900179 79.008 2 66.15 NCBI_P. protegens
MULTISPECIES: tail-specific protease [Pseudomonas] WP_003179086.1 78.994 2 45.61 NCBI_Bacteria_NR
MULTISPECIES: tail-specific protease [Pseudomonas] WP_003204565.1 79.144 2 45.61 NCBI_Bacteria_NR
peptidase S41 [Pseudomonas fluorescens] WP_003172944.1 79.122 2 45.61 NCBI_Bacteria_NR
MULTISPECIES: peptidase S41 [Pseudomonas] WP_003190141.1 79.102 2 45.61 NCBI_Bacteria_NR
MULTISPECIES: peptidase S41 [Pseudomonas] WP_003211110.1 79.101 2 45.61 NCBI_Bacteria_NR
MULTISPECIES: tail-specific protease [Pseudomonas] WP_003231887.1 79.074 2 45.61 NCBI_Bacteria_NR
tail-specific protease Prc [Pseudomonas putida KT2440] NP_743876.1 79.097 2 45.61 NCBI_Bacteria_NR
S41 family peptidase [Pseudomonas sp. Lz4W] WP_003446856.1 79.047 2 45.61 NCBI_Bacteria_NR
p3 MULTISPECIES: cold-shock protein [Pseudomonas] gi|495252543 7.736 14 43.15 NCBI_P. protegens
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Table 7.

Identification of the proteins released by Fl4BN1. They migrated in a gel with an isoelectric point gradient from 3 to 10 and were identified by the technique of peptide mapping by mass through the “PEAKS studio” search algorithm, SwissProt database. In the algorithm of PEAKS studio with the SwissProt and NCBI "National Center for Biotechnology Information" databases, protein identification was "significant" if the (−10lgP) score was greater than the peptide hit threshold (30.0). P was the probability that the observed match was a random event. (Spot no.) spot number. (MW) molecular weight. (R) reviewed. (NR) not reviewed. (P. protegens) Pseudomonas protegens.

Protein family Spot no. Data
 Research algorithm: PEAKS
Definition Accession number: SwissProt reference sequence (version) Theoretical MW (kDa) Sequence coverage (%) −10lgP Database
Proteins counteracting oxidative stress and/or ensuring redox balance o1 Dihydrolipoyl dehydrogenase OS=Pseudomonas protegens (strain DSM 19,095/LMG 27,888 / CHA0) GN=lpdG A0A2C9EIR1_PSEPH 49.874 5 47.56 SwissP_P. protegens
o2 Putative peroxiredoxin TsaA OS=Pseudomonas protegens (strain DSM 19,095/LMG 27,888 / CHA0) GN=tsaA A0A2C9ESU7_PSEPH 21.787 6 80.76 SwissP_P. protegens
Antioxidant, AhpC/TSA family OS=Pseudomonas fluorescens (strain ATCC BAA-477/NRRL B-23,932 / Pf-5) OX=220,664 GN=PFL_4857 Q4K745_PSEF5 21.787 6 80.76 SwissP_P. protegens
Alkyl hydroperoxide reductase OS=Pseudomonas protegens OX=380,021 GN=A1395_15,140 A0A2J7U847_9PSED 21.773 6 80,76 SwissP_P. protegens
Chaperonin proteins c1 Chaperone protein DnaK OS=Pseudomonas fluorescens (strain SBW25) GN=dnaK DNAK_PSEFS 68.200 11 90.38 SwissP_Bacteria_R
Chaperone protein DnaK OS=Pseudomonas protegens (strain DSM 19,095 / LMG 27,888 / CHA0) GN=dnaK A0A2C9EG81_PSEPH 68.476 3 28.43 SwissP_P. protegens
Chaperone protein DnaK OS=Pseudomonas protegens OX=380,021 GN=dnaK A0A2T6GM17_9PSED 68.433 3 28.43 SwissP_P. protegens
Chaperone protein DnaK OS=Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23,932 / Pf-5) GN=dnaK DNAK_PSEF5 68.476 3 28.43 SwissP_P. protegens
c2 Chaperone protein HtpG OS=Pseudomonas protegens OX=380,021 GN=htpG A0A2T6GQG4_9PSED 71.363 5 82.38 SwissP_P. protegens
Chaperone protein HtpG OS=Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23,932 / Pf-5) GN=htpG HTPG_PSEF5 71.349 5 82.38 SwissP_P. protegens
Chaperone protein DnaK OS=Pseudomonas protegens (strain DSM 19,095 / LMG 27,888 / CHA0) OX=1,124,983 GN=dnaK A0A2J7UMP6_9PSED 68.476 3 82.43 SwissP_P. protegens
Chaperone protein HtpG OS=Pseudomonas protegens (strain DSM 19,095 / LMG 27,888 / CHA0) OX=1,124,983 GN=htpG A0A2C9EIV4_PSEPH 71.581 5 82.38 SwissP_P. protegens
c3 60 kDa chaperonin OS=Pseudomonas protegens (strain DSM 19,095 / LMG 27,888 / CHA0) OX=1,124,983 GN=groL A0A2C9ESJ4_PSEPH 57.065 15 165.11 SwissP_P. protegens
60 kDa chaperonin OS=Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23,932 / Pf-5) GN=groL CH60_PSEF5 57.065 15 117.99 SwissP_Bacteria_R
c4 Trigger factor OS=Pseudomonas protegens OX=380,021 GN=tig PE=3 SV=1 A0A2T6GBS8_9PSED 48.484 2 31.70 SwissP_P. protegens
Trigger factor OS=Pseudomonas mendocina (strain ymp) GN=tig TIG_PSEMY 48.330 2 24.02 SwissP_Bacteria_R
Trigger factor OS=Pseudomonas fluorescens (strain Pf0-1) GN=tig TIG_PSEPF 48.485 2 24.02 SwissP_Bacteria_R
c5 Elongation factor Tu OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700,928 / UPEC) GN=tufA EFTU_ECOL6 43.314 2 25.24 SwissP_Bacteria_R
Other proteins involved in stress response p1 Peptidase, S41 family OS=Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23,932 / Pf-5) OX=220,664 GN=prc Q4K8E7_PSEF5 79.065 2 70.45 SwissP_P. protegens
Tail-specific protease Prc OS=Pseudomonas protegens (strain DSM 19,095 / LMG 27,888 / CHA0) OX=1,124,983 GN=prc A0A2C9ERC3_PSEPH 79.066 2 70.45 SwissP_P. protegens
p3 Temperature acclimation protein B OS=Pseudomonas protegens (strain DSM 19,095 / LMG 27,888 / CHA0) OX=1,124,983 GN=tapB A0A2C9ES32_PSEPH 7.736 40 34.43 SwissP_P. protegens
/Temperature acclimation protein B OS=Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23,932 / Pf-5) OX=220,664 GN=tapB Q4K7Q5_PSEF5 7.736 40 34.43 SwissP_P. protegens
Cold-shock protein OS=Pseudomonas protegens OX=380,021 GN=A1395_14,565 A0A2K4M1K2_9PSED 7.736 40 34.43 SwissP_P. protegens
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Table 8.

Identification of the proteins released by Fl4BN2 culture. They migrated in a gel with an isoelectric point gradient from 3 to 10 and were identified by the technique of peptide mapping by mass through the “PEAKS studio” search algorithm, NCBI database. In the algorithm of PEAKS studio with the SwissProt and NCBI "National Center for Biotechnology Information" databases, protein identification was "significant" if the (−10lgP) score was greater than the peptide hit threshold (30.0). P was the probability that the observed match was a random event. (Spot no.) spot number. (MW) molecular weight. (R) reviewed. (NR) not reviewed. (P. protegens) Pseudomonas protegens.

Protein family Spot no. Data
 Research algorithm: PEAKS
Definition Accession number: NCBI reference sequence (version) Theoretical MW (kDa) Sequence coverage (%) −10lgP Database
Proteins counteracting oxidative stress and/or ensuring redox balance o1 MULTISPECIES: monothiol glutaredoxin, Grx4 family [Pseudomonas] gi|1125808736 12.108 12 136.77 NCBI_P. protegens
MULTISPECIES: monothiol glutaredoxin, Grx4 family [Pseudomonas] gi|499375536 12.050 12 136.77 NCBI_P. protegens
MULTISPECIES: Grx4 family monothiol glutaredoxin [Pseudomonas] WP_003246056.1 11.793 12 94.59 NCBI_Bacteria_NR
Grx4 family monothiol glutaredoxin [Pseudomonas aeruginosa] WP_003110008.1 11.871 12 94.59 NCBI_Bacteria_NR
MULTISPECIES: Grx4 family monothiol glutaredoxin [Pseudomonas] WP_003188975.1 11.545 12 94.59 NCBI_Bacteria_NR
Grx4 family monothiol glutaredoxin [Pseudomonas syringae] WP_003405440.1 11.649 12 94.59 NCBI_Bacteria_NR
MULTISPECIES: Grx4 family monothiol glutaredoxin [Pseudomonas] WP_002554852.1 11.677 12 94.59 NCBI_Bacteria_NR
MULTISPECIES: Grx4 family monothiol glutaredoxin [Pseudomonas] WP_003092082.1 11.843 12 94.59 NCBI_Bacteria_NR
MULTISPECIES: Grx4 family monothiol glutaredoxin [Pseudomonas] WP_004396490.1 11.650 12 94.59 NCBI_Bacteria_NR
Grx4 family monothiol glutaredoxin [Pseudomonas aeruginosa] WP_003130081.1 11.843 12 94.59 NCBI_Bacteria_NR
Grx4 family monothiol glutaredoxin [Pseudomonas stutzeri] WP_003295894.1 11.820 12 94.59 NCBI_Bacteria_NR
hypothetical protein PA3533 [Pseudomonas aeruginosa PAO1] NP_252223.1 11.843 12 94.59 NCBI_Bacteria_NR
MULTISPECIES: Grx4 family monothiol glutaredoxin [Pseudomonas] WP_003299217.1 11.817 12 94.59 NCBI_Bacteria_NR
MULTISPECIES: Grx4 family monothiol glutaredoxin [Pseudomonas] WP_003453456.1 11.819 12 94.59 NCBI_Bacteria_NR
Grx4 family monothiol glutaredoxin [Pseudomonas stutzeri] WP_003289286.1 11.833 12 94.59 NCBI_Bacteria_NR
Grx4 family monothiol glutaredoxin [Pseudomonas syringae] WP_004393736.1 11.676 12 94.59 NCBI_Bacteria_NR
glutaredoxin-like protein [[Pseudomonas syringae] pv. tomato str. DC3000] NP_793922.1 11.650 12 94.59 NCBI_Bacteria_NR
MULTISPECIES: Grx4 family monothiol glutaredoxin [Pseudomonas] WP_003284603.1 11.857 12 94.59 NCBI_Bacteria_NR
monothiol glutaredoxin [Pseudomonas putida KT2440] NP_743242.1 12.123 12 94.59 NCBI_Bacteria_NR
MULTISPECIES: Grx4 family monothiol glutaredoxin [Pseudomonas] WP_003254949.1 12.137 12 94.59 NCBI_Bacteria_NR
Grx4 family monothiol glutaredoxin [Pseudomonas fluorescens] WP_003178700.1 12.050 12 94.59 NCBI_Bacteria_NR
MULTISPECIES: Grx4 family monothiol glutaredoxin [Pseudomonas] WP_003208710.1 12.000 12 94.59 NCBI_Bacteria_NR
MULTISPECIES: Grx4 family monothiol glutaredoxin [Pseudomonas] WP_003231422.1 11.874 12 94.59 NCBI_Bacteria_NR
Grx4 family monothiol glutaredoxin [Pseudomonas fluorescens] WP_003172092.1 12.015 12 94.59 NCBI_Bacteria_NR
MULTISPECIES: Grx4 family monothiol glutaredoxin [Pseudomonas] WP_003204956.1 12.135 12 94.59 NCBI_Bacteria_NR
MULTISPECIES: Grx4 family monothiol glutaredoxin [Pseudomonas] WP_003443184.1 12.080 12 94.59 NCBI_Bacteria_NR
MULTISPECIES: Grx4 family monothiol glutaredoxin [Pseudomonas] WP_003227729.1 12.109 12 94.59 NCBI_Bacteria_NR
Chaperonin proteins c1 MULTISPECIES: molecular chaperone DnaK [Pseudomonas] WP_003439583.1 68.193 20 351.06 NCBI_Bacteria_NR
molecular chaperone DnaK [Pseudomonas stutzeri] WP_003298038.1 68.696 7 262.60 NCBI_Bacteria_NR
molecular chaperone DnaK [Pseudomonas stutzeri] WP_003293240.1 68.628 7 262.60 NCBI_Bacteria_NR
c3 molecular chaperone DnaK [Pseudomonas protegens] gi|1332900475 68.460 18 237.39 NCBI_P. protegens
molecular chaperone DnaK [Pseudomonas protegens] gi|1332918337 68.430 18 237.39 NCBI_P. protegens
MULTISPECIES: molecular chaperone DnaK [Pseudomonas] gi|499371610 68.476 17 204.77 NCBI_P. protegens
molecular chaperone DnaK [Pseudomonas stutzeri] WP_003293240.1 68.628 7 262.60 NCBI_Bacteria_NR
MULTISPECIES: molecular chaperone DnaK [Pseudomonas] WP_003439583.1 68.193 20 351.06 NCBI_Bacteria_NR
molecular chaperone DnaK [Pseudomonas stutzeri] WP_003298038.1 68.696 7 262.60 NCBI_Bacteria_NR
c4 molecular chaperone DnaK [Pseudomonas protegens] gi|1332900475 68.460 18 237.39 NCBI_P. protegens
molecular chaperone DnaK [Pseudomonas protegens] gi|1332918337 68.430 18 237.39 NCBI_P. protegens
MULTISPECIES: molecular chaperone DnaK [Pseudomonas] gi|499371610 68.476 17 204.77 NCBI_P. protegens
MULTISPECIES: molecular chaperone DnaK [Pseudomonas] WP_003439583.1 68.193 20 351.06 NCBI_Bacteria_NR
c5 molecular chaperone DnaK [Pseudomonas protegens] gi|1332900475 68.460 18 237.39 NCBI_P. protegens
molecular chaperone DnaK [Pseudomonas protegens] gi|1332918337 68.430 18 237.39 NCBI_P. protegens
MULTISPECIES: molecular chaperone DnaK [Pseudomonas] gi|499371610 68.476 17 204.77 NCBI_P. protegens
c6 MULTISPECIES: molecular chaperone DnaK [Pseudomonas] WP_003439583.1 68.193 20 351.06 NCBI_Bacteria_NR
c8 MULTISPECIES: molecular chaperone HtpG [Pseudomonas] gi|499372481 71.349 13 153.49 NCBI_P. protegens
molecular chaperone HtpG [Pseudomonas protegens] gi|1332903508 71.349 13 153.49 NCBI_P. protegens
molecular chaperone HtpG [Pseudomonas protegens] gi|1332919100 71.336 13 153.49 NCBI_P. protegens
MULTISPECIES: molecular chaperone HtpG [Pseudomonas] WP_003446928.1 71.244 13 190.80 NCBI_Bacteria_NR
c9 MULTISPECIES: trigger factor [Pseudomonas] gi|499374697 48.569 22 165.79 NCBI_P. protegens
c10 MULTISPECIES: trigger factor [Pseudomonas] gi|499374697 48.569 22 165.79 NCBI_P. protegens
c11 MULTISPECIES: trigger factor [Pseudomonas] gi|499374697 48.569 22 165.79 NCBI_P. protegens
c12 nucleotide exchange factor GrpE [Pseudomonas protegens] gi|1332900474 20.837 25 116.18 NCBI_P. protegens
MULTISPECIES: nucleotide exchange factor GrpE [Pseudomonas] WP_003439582.1 20.897 21 86.11 NCBI_Bacteria_NR
c13 nucleotide exchange factor GrpE [Pseudomonas protegens] gi|1332900474 20.837 25 116.18 NCBI_P. protegens
MULTISPECIES: nucleotide exchange factor GrpE [Pseudomonas] WP_003439582.1 20.897 21 86.11 NCBI_Bacteria_NR
heat shock protein GrpE [Pseudomonas putida KT2440] NP_746836.1 20.531 9 35.12 NCBI_Bacteria_NR
MULTISPECIES: nucleotide exchange factor GrpE [Pseudomonas] WP_003249927.1 20.501 9 35.12 NCBI_Bacteria_NR
c14 MULTISPECIES: cyclophilin [Pseudomonas] gi|515532580 18.283 7 44.00 NCBI_P. protegens
MULTISPECIES: cyclophilin [Pseudomonas] gi|499374623 18.269 7 44.00 NCBI_P. protegens
Other proteins involved in stress response p1 MULTISPECIES: cold-shock protein CapB [Pseudomonas] gi|488617988 7.727 46 157.27 NCBI_P. protegens
MULTISPECIES: nucleoid-associated protein, YbaB/EbfC family [Pseudomonas] gi|505447677 12.131 12 85.20 NCBI_P. protegens
p2 MULTISPECIES: cold-shock protein CapB [Pseudomonas] gi|488617988 7.727 46 157.27 NCBI_P. protegens
cold shock protein CapB [[Pseudomonas syringae] pv. tomato str. DC3000] NP_793906.1 7.727 46 116.65 NCBI_Bacteria_NR
MULTISPECIES: cold-shock protein CapB [Pseudomonas] WP_002554837.1 7.727 46 116.65 NCBI_Bacteria_NR
Open in a new tab

Table 9.

Identification of the proteins released by Fl4BN2. They migrated in a gel with an isoelectric point gradient from 3 to 10 and were identified by the technique of peptide mapping by mass through the “PEAKS studio” search algorithm, SwissProt database. In the algorithm of PEAKS studio with the SwissProt and NCBI “National Center for Biotechnology Information” databases, protein identification was “significant” if the (−10lgP) score was greater than the peptide hit threshold (30.0). P was the probability that the observed match was a random event. (Spot no.) spot number. (MW) molecular weight. (R) reviewed. (NR) not reviewed. (P. protegens) Pseudomonas protegens.

Protein family Spot no. Data
 Research algorithm: PEAKS
Definition Accession number: SwissProt reference sequence (version) Theoretical MW (kDa) Sequence coverage (%) −10lgP Database
Proteins counteracting oxidative stress and/or ensuring redox balance o1 Glutaredoxin OS=Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23,932 / Pf-5) OX=220,664 GN=grxD Q4K742_PSEF5 12.050 12 127.54 SwissP_P. protegens
Glutaredoxin OS=Pseudomonas protegens OX=380,021 GN=grxD A0A2T6GIP8_9PSED 12.050 12 127.54 SwissP_P. protegens
Glutaredoxin OS=Pseudomonas protegens OX=380,021 GN=A1395_15,155 A0A2J7U865_9PSED 12.108 12 127.54 SwissP_P. protegens
Glutaredoxin OS=Pseudomonas protegens (strain DSM 19,095 / LMG 27,888 / CHA0) OX=1,124,983 GN=grxD A0A2C9ESK9_PSEPH 12.050 12 127.54 SwissP_P. protegens
Chaperonin proteins c1 Chaperone protein DnaK OS=Pseudomonas protegens OX=380,021 GN=dnaK A0A2J7UJG0_9PSED 68.430 18 242.89 SwissP_P. protegens
Chaperone protein DnaK OS=Pseudomonas protegens (strain DSM 19,095 / LMG 27,888 / CHA0) OX=1,124,983 GN=dnaK A0A2C9EG81_PSEPH 68.476 17 208.95 SwissP_P. protegens
c2 Chaperone protein DnaK OS=Pseudomonas protegens OX=380,021 GN=dnaK A0A2J7UJG0_9PSED 68.430 18 242.89 SwissP_P. protegens
Chaperone protein DnaK OS=Pseudomonas protegens (strain DSM 19,095 / LMG 27,888 / CHA0) OX=1,124,983 GN=dnaK A0A2C9EG81_PSEPH 68.476 17 208.95 SwissP_P. protegens
c3 Chaperone protein DnaK OS=Pseudomonas mendocina (strain ymp) GN=dnaK DNAK_PSEMY 68.746 11 285.87 SwissP_Bacteria_R
Chaperone protein DnaK OS=Pseudomonas protegens OX=380,021 GN=dnaK A0A2J7UJG0_9PSED 68.430 18 242.89 SwissP_P. protegens
Chaperone protein DnaK OS=Pseudomonas protegens (strain DSM 19,095 / LMG 27,888 / CHA0) OX=1,124,983 GN=dnaK A0A2C9EG81_PSEPH 68.476 17 208.95 SwissP_P. protegens
Chaperone protein DnaK OS=Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23,932 / Pf-5) GN=dnaK DNAK_PSEF5 68.476 12 171.05 SwissP_Bacteria_R
c4 Chaperone protein DnaK OS=Pseudomonas protegens OX=380,021 GN=dnaK A0A2J7UJG0_9PSED 68.430 18 242.89 SwissP_P. protegens
Chaperone protein DnaK OS=Pseudomonas protegens (strain DSM 19,095 / LMG 27,888 / CHA0) OX=1,124,983 GN=dnaK A0A2C9EG81_PSEPH 68.476 17 208.95 SwissP_P. protegens
Chaperone protein DnaK OS=Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23,932 / Pf-5) GN=dnaK DNAK_PSEF5 68.476 12 171.05 SwissP_Bacteria_R
c6 Chaperone protein DnaK OS=Pseudomonas mendocina (strain ymp) GN=dnaK DNAK_PSEMY 68.476 11 285.87 SwissP_Bacteria_R
Chaperone protein DnaK OS=Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23,932 / Pf-5) GN=dnaK DNAK_PSEF5 68.476 12 171.05 SwissP_Bacteria_R
c8 Chaperone protein HtpG OS=Pseudomonas protegens OX=380,021 GN=htpG A0A2T6GQG4_9PSED 71.363 13 142.20 SwissP_P. protegens
Chaperone protein HtpG OS=Pseudomonas protegens OX=380,021 GN=htpG A0A2J7UMP6_9PSED 71.336 13 142.20 SwissP_P. protegens
Chaperone protein HtpG OS=Pseudomonas protegens (strain DSM 19,095 / LMG 27,888 / CHA0) OX=1,124,983 GN=htpG A0A2C9EIV4_PSEPH 71.581 13 142.20 SwissP_P. protegens
Chaperone protein HtpG OS=Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23,932 / Pf-5) GN=htpG HTPG_PSEF5 71.349 13 137.93 SwissP_Bacteria_R
c9 Trigger factor OS=Pseudomonas protegens OX=380,021 GN=tig A0A2J7U087_9PSED 48.516 18 165.99 SwissP_P. protegens
Trigger factor OS=Pseudomonas protegens (strain DSM 19,095 / LMG 27,888 / CHA0) GN=tig A0A2C9EQ79_PSEPH 48.511 17 165.98 SwissP_P. protegens
Trigger factor OS=Pseudomonas aeruginosa (strain LESB58) GN=tig TIG_PSEA8 48.582 12 94.71 SwissP_Bacteria_R
Trigger factor OS=Pseudomonas aeruginosa (strain ATCC 15,692 / DSM 22,644 / CIP 104,116 / JCM 14,847 / LMG 12,228 / 1C / PRS 101 / PAO1) GN=tig TIG_PSEAE 48.582 12 94.71 SwissP_Bacteria_R
Trigger factor OS=Pseudomonas aeruginosa (strain PA7) GN=tig TIG_PSEA7 48.548 12 94.71 SwissP_Bacteria_R
Trigger factor OS=Pseudomonas aeruginosa (strain UCBPP-PA14) GN=tig TIG_PSEAB 48.582 12 94.71 SwissP_Bacteria_R
c11 Trigger factor OS=Pseudomonas protegens OX=380,021 GN=tig A0A2J7U087_9PSED 48.516 18 165.99 SwissP_P. protegens
Trigger factor OS=Pseudomonas protegens (strain DSM 19,095 / LMG 27,888 / CHA0) GN=tig A0A2C9EQ79_PSEPH 48.511 17 165.98 SwissP_P. protegens
c12 Protein GrpE OS=Pseudomonas protegens OX=380,021 GN=grpE A0A2J7UA71_9PSED 20.837 25 153.06 SwissP_P. protegens
Protein GrpE OS=Pseudomonas protegens OX=380,021 GN=grpE A0A2T6GLZ5_9PSED 10.865 25 153.06 SwissP_P. protegens
Protein GrpE OS=Pseudomonas protegens (strain DSM 19,095 / LMG 27,888 / CHA0) OX=1,124,983 GN=grpE A0A2C9EG73_PSEPH 20.823 25 153.06 SwissP_P. protegens
Protein GrpE OS=Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23,932 / Pf-5) GN=grpE GRPE_PSEF5 20.823 25 88.28 SwissP_Bacteria_R
c13 Protein GrpE OS=Pseudomonas protegens OX=380,021 GN=grpE A0A2J7UA71_9PSED 20.837 25 153.06 SwissP_P. protegens
Protein GrpE OS=Pseudomonas protegens OX=380,021 GN=grpE A0A2T6GLZ5_9PSED 10.865 25 153.06 SwissP_P. protegens
Protein GrpE OS=Pseudomonas protegens (strain DSM 19,095 / LMG 27,888 / CHA0) OX=1,124,983 GN=grpE A0A2C9EG73_PSEPH 20.823 25 153.06 SwissP_P. protegens
Protein GrpE OS=Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23,932 / Pf-5) GN=grpE GRPE_PSEF5 20.823 25 88.28 SwissP_Bacteria_R
Other proteins involved in stress response p1 Cold shock protein CapB OS=Pseudomonas protegens (strain DSM 19,095 / LMG 27,888 / CHA0) OX=1,124,983 GN=capB A0A2C9EHH8_PSEPH 7.727 46 271.99 SwissP_P. protegens
Cold shock protein CapB OS=Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23,932 / Pf-5) OX=220,664 GN=capB Q4KH94_PSEF5 7.727 46 271.99 SwissP_P. protegens
Cold-shock protein OS=Pseudomonas protegens OX=380,021 GN=A1395_02635 A0A2J7UBE2_9PSED 7.727 46 271.99 SwissP_P. protegens
Nucleoid-associated protein PFL_1905 OS=Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23,932 / Pf-5) OX=220,664 GN=PFL_1905 Y1905_PSEF5 12 12 75.61 SwissP_P. protegens
Nucleoid-associated protein A1395_05835 OS=Pseudomonas protegens OX=380,021 GN=A1395_05835 A0A2K4M432_9PSED 12.131 12 75.61 SwissP_P. protegens
Nucleoid-associated protein PFLCHA0_c19450 OS=Pseudomonas protegens (strain DSM 19,095 / LMG 27,888 / CHA0) OX=1,124,983 GN=PFLCHA0_c19450 A0A2C9EJ97_PSEPH 12.131 12 75.61 SwissP_P. protegens
Nucleoid-associated protein PFL_1905 OS=Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23,932 / Pf-5) GN=PFL_1905 Y1905_PSEF5 12.000 12 84.97 SwissP_Bacteria_R
p2 Cold shock protein CapB OS=Pseudomonas protegens (strain DSM 19,095 / LMG 27,888 / CHA0) OX=1,124,983 GN=capB A0A2C9EHH8_PSEPH 7.727 46 271.99 SwissP_P. protegens
Cold shock protein CapB OS=Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23,932 / Pf-5) OX=220,664 GN=capB Q4KH94_PSEF5 7.727 46 271.99 SwissP_P. protegens
Cold-shock protein OS=Pseudomonas protegens OX=380,021 GN=A1395_02635 A0A2J7UBE2_9PSED 7.727 46 271.99 SwissP_P. protegens
Cold shock protein CapB OS=Pseudomonas syringae pv. tomato (strain ATCC BAA-871 / DC3000) GN=capB CAPB_PSESM 7.727 46 135.90 SwissP_Bacteria_R
p3 Cold shock protein CapB OS=Pseudomonas syringae pv. tomato (strain ATCC BAA-871 / DC3000) GN=capB CAPB_PSESM 7.727 46 135.90 SwissP_Bacteria_R
Open in a new tab

Table 10.

Identification of the proteins released by Fl5BN2. They migrated in a gel with an isoelectric point gradient from 3 to 10 and were identified by the technique of peptide mapping by mass through the “PEAKS studio” search algorithm, NCBI database. In the algorithm of PEAKS studio with the SwissProt and NCBI "National Center for Biotechnology Information" databases, protein identification was "significant" if the (−10lgP) score was greater than the peptide hit threshold (30.0). P was the probability that the observed match was a random event. (Spot no.) spot number. (MW) molecular weight. (R) reviewed. (NR) not reviewed. (P. protegens) Pseudomonas protegens.

Protein family Spot no. Data
 Research algorithm: PEAKS
Definition Accession number: NCBI reference sequence (version) Theoretical MW (kDa) Sequence coverage (%) −10lgP Database
Proteins counteracting oxidative stress and/or ensuring redox balance o2 Chain B, 1 Dihydrolipoyl Dehydrogenase Pseudomonas putida KT2440 gi|1258501321 50.185 8 108.72 NCBI_Bacteria_R
Chain A, 1 Dihydrolipoyl Dehydrogenase Pseudomonas putida KT2440 gi|1101274917 50.185 8 108.72 NCBI_Bacteria_R
Chain B, 1 Dihydrolipoyl Dehydrogenase Pseudomonas putida KT2440 gi|1101274918 50.185 8 108.72 NCBI_Bacteria_R
Chain A, 1 Dihydrolipoyl Dehydrogenase Pseudomonas putida KT2440 gi|1258501320 50.185 8 108.72 NCBI_Bacteria_R
dihydrolipoyl dehydrogenase [Pseudomonas protegens] gi|1332903368 49.797 9 86.94 NCBI_P. protegens
dihydrolipoyl dehydrogenase [Pseudomonas protegens] gi|1332918899 49.831 9 86.94 NCBI_P. protegens
MULTISPECIES: dihydrolipoyl dehydrogenase [Pseudomonas] gi|499372476 49.874 9 86.94 NCBI_P. protegens
dihydrolipoyl dehydrogenase [Pseudomonas protegens] gi|1332903368 49.797 9 86.94 NCBI_P. protegens
MULTISPECIES: dihydrolipoyl dehydrogenase [Pseudomonas] WP_003223013.1 49.812 9 130.96 NCBI_Bacteria_NR
o3 dihydrolipoyl dehydrogenase [Pseudomonas protegens] gi|1332903368 49.797 9 86.94 NCBI_P. protegens
dihydrolipoyl dehydrogenase [Pseudomonas protegens] gi|1332918899 49.831 9 86.94 NCBI_P. protegens
MULTISPECIES: dihydrolipoyl dehydrogenase [Pseudomonas] gi|499372476 49.874 9 86.94 NCBI_P. protegens
MULTISPECIES: dihydrolipoyl dehydrogenase [Pseudomonas] WP_003223013.1 49.812 9 130.96 NCBI_Bacteria_NR
o5 MULTISPECIES: superoxide dismutase [Pseudomonas] gi|499375502 22.003 29 155.45 NCBI_P. protegens
Chain B, 1 Iron Superoxide Dismutase Pseudomonas putida gi|349943 21.530 14 138.13 NCBI_Bacteria_R
Chain A, 1 Iron Superoxide Dismutase Pseudomonas putida gi|349942 21.530 14 138.13 NCBI_Bacteria_R
Chain B, 1 SUPEROXIDE DISMUTASE Pseudomonas putida gi|12084343 21.890 14 138.13 NCBI_Bacteria_R
Chain C, 1 SUPEROXIDE DISMUTASE Pseudomonas putida gi|12084344 21.890 14 138.13 NCBI_Bacteria_R
Chain A, 1 SUPEROXIDE DISMUTASE Pseudomonas putida gi|12084342 21.890 14 138.13 NCBI_Bacteria_R
superoxide dismutase [Pseudomonas putida KT2440] NP_743076.1 21.939 25 116.36 NCBI_Bacteria_NR
MULTISPECIES: superoxide dismutase [Fe] [Pseudomonas] WP_003255187.1 21.939 25 116.36 NCBI_Bacteria_NR
MULTISPECIES: superoxide dismutase [Pseudomonas] WP_003212997.1 21.978 25 116.36 NCBI_Bacteria_NR
MULTISPECIES: superoxide dismutase [Pseudomonas] WP_003175739.1 22.005 25 116.36 NCBI_Bacteria_NR
Chaperonin proteins c2 chaperonin GroEL [Pseudomonas protegens] gi|751652819 56.819 20 136.41 NCBI_P. protegens
MULTISPECIES: molecular chaperone GroEL [Pseudomonas] gi|499375514 57.065 20 136.41 NCBI_P. protegens
MULTISPECIES: chaperonin GroEL [Pseudomonas] WP_003238874.1 56.883 3 81.74 NCBI_Bacteria_NR
chaperonin GroEL [Pseudomonas fluorescens] WP_003175873.1 56.927 3 81.74 NCBI_Bacteria_NR
MULTISPECIES: chaperonin GroEL [Pseudomonas] WP_003178748.1 56.843 3 81.74 NCBI_Bacteria_NR
MULTISPECIES: chaperonin GroEL [Pseudomonas] WP_003227683.1 56.905 3 81.74 NCBI_Bacteria_NR
chaperonin GroEL [Pseudomonas fluorescens] WP_003193939.1 56.882 3 81.74 NCBI_Bacteria_NR
c3 chaperonin GroEL [Pseudomonas protegens] gi|751652819 56.819 11 131.03 NCBI_P. protegens
MULTISPECIES: molecular chaperone GroEL [Pseudomonas] gi|499375514 57.065 11 131.03 NCBI_P. protegens
MULTISPECIES: chaperonin GroEL [Pseudomonas] WP_003238874.1 56.883 7 77.38 NCBI_Bacteria_NR
chaperonin GroEL [Pseudomonas fluorescens] WP_003193939.1 56.882 7 77.38 NCBI_Bacteria_NR
c6 MULTISPECIES: molecular chaperone DnaK [Pseudomonas] gi|499371610 68.476 8 107.62 NCBI_P. protegens
MULTISPECIES: molecular chaperone DnaK [Pseudomonas] WP_003212222.1 68.330 8 103.78 NCBI_Bacteria_NR
c7 MULTISPECIES: molecular chaperone DnaK [Pseudomonas] gi|499371610 68.476 8 107.62 NCBI_P. protegens
MULTISPECIES: molecular chaperone DnaK [Pseudomonas] WP_003212222.1 68.330 8 103.78 NCBI_Bacteria_NR
c8 MULTISPECIES: FKBP-type peptidyl-prolyl cis-trans isomerase [Pseudomonas] gi|495199965 21.678 18 217.97 NCBI_P. protegens
MULTISPECIES: FKBP-type peptidyl-prolyl cis-trans isomerase [Pseudomonas] WP_003194089.1 21.675 9 124.62 NCBI_Bacteria_NR
MULTISPECIES: FKBP-type peptidyl-prolyl cis-trans isomerase [Pseudomonas] WP_003230860.1 21.718 9 124.62 NCBI_Bacteria_NR
MULTISPECIES: FKBP-type peptidyl-prolyl cis-trans isomerase [Pseudomonas] WP_003176055.1 21.689 9 124.62 NCBI_Bacteria_NR
c9 MULTISPECIES: cyclophilin [Pseudomonas] gi|515532580 18.283 14 60.40 NCBI_P. protegens
MULTISPECIES: cyclophilin [Pseudomonas] gi|499374623 18.269 14 60.40 NCBI_P. protegens
peptidyl-prolyl cis-trans isomerase [Pseudomonas savastanoi] WP_004664345.1 18.176 7 20.50 NCBI_Bacteria_NR
peptidyl-prolyl cis-trans isomerase [Pseudomonas syringae] WP_003390678.1 18.315 7 20.50 NCBI_Bacteria_NR
peptidyl-prolyl cis-trans isomerase [Pseudomonas syringae] WP_004418527.1 18.328 7 20.50 NCBI_Bacteria_NR
MULTISPECIES: peptidyl-prolyl cis-trans isomerase [Pseudomonas] WP_003404493.1 18.300 7 20.50 NCBI_Bacteria_NR
MULTISPECIES: peptidyl-prolyl cis-trans isomerase [Pseudomonas syringae group] WP_004661308.1 18.218 7 20.50 NCBI_Bacteria_NR
MULTISPECIES: peptidyl-prolyl cis-trans isomerase [Pseudomonas] WP_003441354.1 18.288 7 20.50 NCBI_Bacteria_NR
peptidyl-prolyl cis-trans isomerase [Pseudomonas syringae] WP_003423206.1 18.332 7 20.50 NCBI_Bacteria_NR
Other proteins involved in stress response p4 MULTISPECIES: cold-shock protein [Pseudomonas] gi|489272243 7.697 20 38.71 NCBI_P. protegens
p5 MULTISPECIES: cold-shock protein CapB [Pseudomonas] gi|488617988 7.727 46 140.69 NCBI_P. protegens
cold shock protein CapB [[Pseudomonas syringae] pv. tomato str. DC3000] NP_793906.1 7.727 46 81.81 NCBI_Bacteria_NR
MULTISPECIES: cold-shock protein CapB [Pseudomonas] WP_002554837.1 7.727 46 81.81 NCBI_Bacteria_NR
Open in a new tab

Table 11.

Identification of the proteins released by Fl5BN2. They migrated in a gel with an isoelectric point gradient from 3 to 10 and were identified by the technique of peptide mapping by mass through the “PEAKS studio” search algorithm, SwissProt database. In the algorithm of PEAKS studio with the SwissProt and NCBI "National Center for Biotechnology Information" databases, protein identification was "significant" if the (−10lgP) score was greater than the peptide hit threshold (30.0). P was the probability that the observed match was a random event. (Spot no.) spot number. (MW) molecular weight. (R) reviewed. (NR) not reviewed. (P. protegens) Pseudomonas protegens.

Protein family Spot no. Data
 Research algorithm: PEAKS
Definition Accession number: SwissProt reference sequence (version) Theoretical MW (kDa) Sequence coverage (%) −10lgP Database
Proteins counteracting oxidative stress and/or ensuring redox balance o1 Dihydrolipoyl dehydrogenase OS=Pseudomonas fluorescens GN=lpd DLDH_PSEFL 50.151 4 88.73 SwissP_Bacteria_R
Dihydrolipoyl dehydrogenase OS=Pseudomonas aeruginosa (strain ATCC 15,692 / DSM 22,644 / CIP 104,116 / JCM 14,847 / LMG 12,228 / 1C / PRS 101 / PAO1) GN=lpdG DLDH2_PSEAE 50.165 4 88.73 SwissP_Bacteria_R
Dihydrolipoyl dehydrogenase OS=Pseudomonas putida GN=lpdG DLDH2_PSEPU 49.896 4 88.73 SwissP_Bacteria_R
o2 Dihydrolipoyl dehydrogenase OS=Pseudomonas protegens OX=380,021 GN=lpdA A0A2T6GPH9_9PSED 49.810 9 95.34 SwissP_P. protegens
Dihydrolipoyl dehydrogenase OS=Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23,932 / Pf-5) OX=220,664 GN=lpdA_1 Q4KFY7_PSEF5 49.874 9 95.34 SwissP_P. protegens
Dihydrolipoyl dehydrogenase OS=Pseudomonas protegens (strain DSM 19,095 / LMG 27,888 / CHA0) OX=1,124,983 GN=lpdG A0A2C9EIR1_PSEPH 49.874 9 95.34 SwissP_P. protegens
Dihydrolipoyl dehydrogenase OS=Pseudomonas protegens OX=380,021 GN=A1395_04885 A0A2J7ULV5_9PSED 49.831 9 95.34 SwissP_P. protegens
Dihydrolipoyl dehydrogenase OS=Pseudomonas fluorescens GN=lpd DLDH_PSEFL 50.151 4 88.73 SwissP_Bacteria_R
Dihydrolipoyl dehydrogenase OS=Pseudomonas aeruginosa (strain ATCC 15,692 / DSM 22,644 / CIP 104,116 / JCM 14,847 / LMG 12,228 / 1C / PRS 101 / PAO1) GN=lpdG DLDH2_PSEAE 50.165 4 88.73 SwissP_Bacteria_R
Dihydrolipoyl dehydrogenase OS=Pseudomonas putida GN=lpdG DLDH2_PSEPU 49.896 4 88.73 SwissP_Bacteria_R
Dihydrolipoyl dehydrogenase OS=Pseudomonas sp. RIT-PI-r OX=1,699,620 GN=AK821_18,310 A0A0P6RYG8_9PSED 49.840 4 63.95 SwissP_Bacteria_NR
o3 Dihydrolipoyl dehydrogenase OS=Pseudomonas protegens OX=380,021 GN=lpdA A0A2T6GPH9_9PSED 49.810 9 95.34 SwissP_P. protegens
Dihydrolipoyl dehydrogenase OS=Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23,932 / Pf-5) OX=220,664 GN=lpdA_1 Q4KFY7_PSEF5 49.874 9 95.34 SwissP_P. protegens
Dihydrolipoyl dehydrogenase OS=Pseudomonas protegens (strain DSM 19,095 / LMG 27,888 / CHA0) OX=1,124,983 GN=lpdG A0A2C9EIR1_PSEPH 49.874 9 95.34 SwissP_P. protegens
Dihydrolipoyl dehydrogenase OS=Pseudomonas protegens OX=380,021 GN=A1395_04885 A0A2J7ULV5_9PSED 49.831 9 95.34 SwissP_P. protegens
o5 Superoxide dismutase OS=Pseudomonas protegens (strain DSM 19,095 / LMG 27,888 / CHA0) OX=1,124,983 GN=sodB A0A2C9ESB6_PSEPH 22.003 25 122.57 SwissP_P. protegens
Superoxide dismutase OS=Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23,932 / Pf-5) OX=220,664 GN=sodB Q4K776_PSEF5 22.003 25 122.57 SwissP_P. protegens
Superoxide dismutase OS=Pseudomonas protegens OX=380,021 GN=A1395_14,980 A0A2J7U822_9PSED 22.003 25 122.57 SwissP_P. protegens
Superoxide dismutase OS=Pseudomonas putida OX=303 GN=A3L25_01085 A0A166M6 × 6_PSEPU 21.937 25 151.90 SwissP_Bacteria_NR
Superoxide dismutase OS=Pseudomonas putida OX=303 GN=QV12_13,665 A0A0D1LV26_PSEPU 21.994 25 151.90 SwissP_Bacteria_NR
Superoxide dismutase OS=Pseudomonas putida OX=303 GN=sodB A0A1B2F769_PSEPU 21.969 25 151.90 SwissP_Bacteria_NR
Superoxide dismutase OS=Pseudomonas putida OX=303 GN=A3K88_05175 A0A177YS39_PSEPU 21.909 25 151.90 SwissP_Bacteria_NR
Superoxide dismutase OS=Pseudomonas putida B6-2 OX=1,081,940 GN=KKK_27,785 A0A168XBM6_PSEPU 21.939 25 151.90 SwissP_Bacteria_NR
Superoxide dismutase OS=Pseudomonas fluorescens OX=294 GN=sodB_1 A0A0D0RQL4_PSEFL 21.948 25 151.90 SwissP_Bacteria_NR
Superoxide dismutase OS=Pseudomonas sp. RIT-PI-r OX=1,699,620 GN=AK821_22,885 A0A0P6S377_9PSED 21.992 25 151.90 SwissP_Bacteria_NR
Superoxide dismutase OS=Pseudomonas fluorescens OX=294 GN=sodB_1 A0A109L2F9_PSEFL 22.005 25 151.90 SwissP_Bacteria_NR
Superoxide dismutase OS=Pseudomonas putida OX=303 GN=AYO28_24,560 A0A177SFW3_PSEPU 22.019 25 151.90 SwissP_Bacteria_NR
Superoxide dismutase OS=Pseudomonas sp. GM67 OX=1,144,335 GN=PMI33_04148 J2UAB6_9PSED 22.021 25 151.90 SwissP_Bacteria_NR
Superoxide dismutase OS=Pseudomonas putida OX=303 GN=AO269_03685 A0A0W0Q2E4_PSEPU 22.007 25 151.90 SwissP_Bacteria_NR
Superoxide dismutase OS=Pseudomonas sp. GM21 OX=1,144,325 GN=PMI22_04575 J3EKI1_9PSED 21.978 25 151.90 SwissP_Bacteria_NR
Superoxide dismutase OS=Pseudomonas fluorescens WH6 OX=746,360 GN=sodB E2XX94_PSEFL 22.005 25 151.90 SwissP_Bacteria_NR
Superoxide dismutase OS=Pseudomonas plecoglossicida NB2011 OX=1,330,531 GN=L321_24,006 S2JST8_9PSED 21.952 25 151.90 SwissP_Bacteria_NR
Superoxide dismutase OS=Pseudomonas fluorescens BRIP34879 OX=1,205,750 GN=A986_21,285 L7H2T0_PSEFL 21.950 25 151.90 SwissP_Bacteria_NR
Superoxide dismutase OS=Pseudomonas trivialis OX=200,450 GN=TU79_05835 A0A0R2ZL85_9PSED 21.950 25 151.90 SwissP_Bacteria_NR
Superoxide dismutase OS=Pseudomonas sp. 22 E 5 OX=1,844,093 GN=sodB_1 A0A1B5EYJ2_9PSED 22.005 25 151.90 SwissP_Bacteria_NR
Superoxide dismutase OS=Pseudomonas monteilii OX=76,759 GN=BC89_13,580 A0A136QIN6_9PSED 21.937 25 151.90 SwissP_Bacteria_NR
Superoxide dismutase OS=Pseudomonas sp. Leaf58 OX=1,736,226 GN=ASF02_16,300 A0A0Q4N799_9PSED 21.937 25 151.90 SwissP_Bacteria_NR
Superoxide dismutase OS=Pseudomonas sp. CMAA1215 OX=1,387,231 GN=P308_25,440 U7A3I6_9PSED 21.989 25 151.90 SwissP_Bacteria_NR
Superoxide dismutase [Fe] OS=Pseudomonas putida (strain ATCC 47,054 / DSM 6125 / NCIMB 11,950 / KT2440) GN=sodB SODF_PSEPK 21.939 25 113.96 SwissP_Bacteria_R
Chaperonin proteins c1 Chaperone protein HtpG OS=Pseudomonas fluorescens (strain SBW25) GN=htpG HTPG_PSEFS 71.633 2 36.92 SwissP_Bacteria_R
c2 60 kDa chaperonin OS=Pseudomonas protegens (strain DSM 19,095 / LMG 27,888 / CHA0) OX=1,124,983 GN=groL A0A2C9ESJ4_PSEPH 57.065 15 155.61 SwissP_P. protegens
60 kDa chaperonin OS=Pseudomonas sp. GM18 OX=1,144,324 GN=groL J2NZ80_9PSED 57.053 7 135.04 SwissP_Bacteria_NR
60 kDa chaperonin OS=Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23,932 / Pf-5) GN=groL CH60_PSEF5 57.065 15 123.35 SwissP_Bacteria_R
c3 60 kDa chaperonin OS=Pseudomonas protegens (strain DSM 19,095 / LMG 27,888 / CHA0) OX=1,124,983 GN=groL A0A2C9ESJ4_PSEPH 57.065 11 130.43 SwissP_P. protegens
60 kDa chaperonin OS=Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23,932 / Pf-5) GN=groL CH60_PSEF5 57.065 11 113.92 SwissP_Bacteria_R
c6 Chaperone protein DnaK OS=Pseudomonas protegens (strain DSM 19,095 / LMG 27,888 / CHA0) OX=1,124,983 GN=dnaK A0A2C9EG81_PSEPH 68.476 8 146.02 SwissP_P. protegens
Chaperone protein DnaK OS=Pseudomonas protegens OX=380,021 GN=dnaK A0A2J7UJG0_9PSED 68.430 10 138.77 SwissP_P. protegens
Chaperone protein DnaK OS=Pseudomonas fluorescens (strain SBW25) GN=dnaK DNAK_PSEFS 68.200 6 95.25 SwissP_Bacteria_R
Chaperone protein DnaK OS=Pseudomonas sp. ES3-33 OX=1,628,833 GN=dnaK A0A0D9A6C8_9PSED 68.415 6 92.03 SwissP_Bacteria_NR
c7 Chaperone protein DnaK OS=Pseudomonas protegens (strain DSM 19,095 / LMG 27,888 / CHA0) OX=1,124,983 GN=dnaK A0A2C9EG81_PSEPH 68.476 8 146.02 SwissP_P. protegens
Chaperone protein DnaK OS=Pseudomonas protegens OX=380,021 GN=dnaK A0A2J7UJG0_9PSED 68.430 10 138.77 SwissP_P. protegens
Chaperone protein DnaK OS=Pseudomonas fluorescens (strain SBW25) GN=dnaK DNAK_PSEFS 68.200 6 95.25 SwissP_Bacteria_R
Chaperone protein DnaK OS=Pseudomonas sp. ES3-33 OX=1,628,833 GN=dnaK A0A0D9A6C8_9PSED 68.415 6 92.03 SwissP_Bacteria_NR
c8 Peptidyl-prolyl cis-trans isomerase OS=Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23,932 / Pf-5) OX=220,664 GN=fklB Q4K5T2_PSEF5 21.678 18 214.28 SwissP_P. protegens
Peptidyl-prolyl cis-trans isomerase OS=Pseudomonas protegens (strain DSM 19,095 / LMG 27,888 / CHA0) OX=1,124,983 GN=fklB A0A2C9ETR2_PSEPH 21.678 18 214.28 SwissP_P. protegens
Peptidyl-prolyl cis-trans isomerase OS=Pseudomonas protegens OX=380,021 GN=A1395_26,505 A0A2J7TS41_9PSED 21.664 18 214.28 SwissP_P. protegens
Peptidyl-prolyl cis-trans isomerase OS=Pseudomonas fluorescens OX=294 GN=fklB_1 A0A0D0SQ47_PSEFL 21.675 18 209.04 SwissP_Bacteria_NR
Peptidyl-prolyl cis-trans isomerase OS=Pseudomonas batumici OX=226,910 GN=UCMB321_4721 A0A0C2E6G3_9PSED 21.586 18 209.04 SwissP_Bacteria_NR
Peptidyl-prolyl cis-trans isomerase OS=Pseudomonas synxantha BG33R OX=96,901 GN=fklB I4LAD2_9PSED 21.645 18 209.04 SwissP_Bacteria_NR
Peptidyl-prolyl cis-trans isomerase OS=Pseudomonas sp. CMAA1215 OX=1,387,231 GN=P308_28,130 U7A1W8_9PSED 21.708 18 209.04 SwissP_Bacteria_NR
Peptidyl-prolyl cis-trans isomerase OS=Pseudomonas fluorescens OX=294 GN=A7317_24,270 A0A0W0HKF0_PSEFL 21.689 18 209.04 SwissP_Bacteria_NR
Peptidyl-prolyl cis-trans isomerase OS=Pseudomonas fluorescens BRIP34879 OX=1,205,750 GN=A986_02186 L7HNG1_PSEFL 21.718 18 209.04 SwissP_Bacteria_NR
Peptidyl-prolyl cis-trans isomerase OS=Pseudomonas fluorescens WH6 OX=746,360 GN=fkpA E2XY02_PSEFL 21.689 18 209.04 SwissP_Bacteria_NR
Peptidyl-prolyl cis-trans isomerase OS=Pseudomonas sp. 37 R 15 OX=1,844,104 GN=fklB_2 A0A1B5DMV2_9PSED 21.675 18 209.04 SwissP_Bacteria_NR
Peptidyl-prolyl cis-trans isomerase OS=Pseudomonas sp. 22 E 5 OX=1,844,093 GN=fklB_3 A0A1B5ESY5_9PSED 21.675 18 209.04 SwissP_Bacteria_NR
Peptidyl-prolyl cis-trans isomerase OS=Pseudomonas sp. 24 E 1 OX=1,844,094 GN=fklB_1 A0A1B5D261_9PSED 21.689 18 209.04 SwissP_Bacteria_NR
Peptidyl-prolyl cis-trans isomerase OS=Pseudomonas sp. RIT357 OX=1,470,593 GN=BW43_01525 A0A031J4K3_9PSED 21.648 18 209.04 SwissP_Bacteria_NR
Peptidyl-prolyl cis-trans isomerase OS=Pseudomonas trivialis OX=200,450 GN=TU79_07195 A0A0R2ZUP9_9PSED 21.746 18 209.04 SwissP_Bacteria_NR
c9 Peptidyl-prolyl cis-trans isomerase OS=Pseudomonas protegens OX=380,021 GN=C5U62_23,620 A0A2T6GHH3_9PSED 18.267 7 46.63 SwissP_P. protegens
Peptidyl-prolyl cis-trans isomerase OS=Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23,932 / Pf-5) OX=220,664 GN=ppiB Q4K9R9_PSEF5 18.269 7 46.63 SwissP_P. protegens
Peptidyl-prolyl cis-trans isomerase OS=Pseudomonas protegens OX=380,021 GN=A1395_23,035 A0A2J7U033_9PSED 18.283 7 46.63 SwissP_P. protegens
Peptidyl-prolyl cis-trans isomerase OS=Pseudomonas protegens (strain DSM 19,095 / LMG 27,888 / CHA0) OX=1,124,983 GN=cyp A0A2C9EQ49_PSEPH 18.269 7 46.63 SwissP_P. protegens
Other proteins involved in stress response p2 Nucleoid protein HU beta subunit OS=Pseudomonas amygdali pv. lachrymans str. M302278 OX=629,267 GN=PLA106_24,593 F3IQ72_PSEAV 9.106 23 72.47 SwissP_Bacteria_NR
DNA-binding protein HU, beta subunit OS=Pseudomonas fluorescens WH6 OX=746,360 GN=hupB E2XUJ9_PSEFL 9.062 23 72.47 SwissP_Bacteria_NR
Nucleoid protein HU beta subunit OS=Pseudomonas syringae pv. papulans OX=83,963 GN=ALO65_02562 A0A0P9ZVJ6_PSESX 9.106 23 72.47 SwissP_Bacteria_NR
DNA-binding protein HU, beta subunit OS=Pseudomonas fluorescens BRIP34879 OX=1,205,750 GN=A986_22,410 L7GXR8_PSEFL 9.062 23 72.47 SwissP_Bacteria_NR
Transcriptional regulator OS=Pseudomonas sp. CMAA1215 OX=1,387,231 GN=P308_20,875 U7A634_9PSED 9.091 23 72.47 SwissP_Bacteria_NR
DNA-binding protein HU, beta subunit OS=Pseudomonas coronafaciens pv. zizaniae OX=251,700 GN=ALO38_02514 A0A0Q0HEI0_9PSED 9.076 23 72.47 SwissP_Bacteria_NR
DNA-binding protein HU OS=Pseudomonas sp. Root68 OX=1,736,585 GN=ASD91_22,695 A0A0Q8J0C7_9PSED 9.106 23 72.47 SwissP_Bacteria_NR
Nucleoid protein HU beta subunit OS=Pseudomonas syringae pv. aceris OX=199,198 GN=ALO91_03094 A0A0L8IW02_PSESX 9.106 23 72.47 SwissP_Bacteria_NR
Nucleoid protein HU beta subunit OS=Pseudomonas savastanoi pv. phaseolicola OX=319 GN=ALO55_00346 A0A0P9 × 6 × 9_PSESH 9.106 23 72.47 SwissP_Bacteria_NR
DNA-binding protein HU-beta OS=Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23,932 / Pf-5) GN=hupB DBHB_PSEF5 9.106 23 65.89 SwissP_Bacteria_R
p3 DNA-binding protein HU-beta OS=Pseudomonas protegens (strain DSM 19,095 / LMG 27,888 / CHA0) OX=1,124,983 GN=hupB A0A2C9EQC3_PSEPH 9.106 23 80.95 SwissP_P. protegens
DNA-binding protein HU-beta OS=Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23,932 / Pf-5) OX=220,664 GN=hupB Q9KHS6|DBHB_PSEF5 9.106 23 80.95 SwissP_P. protegens
DNA-binding protein HU OS=Pseudomonas protegens OX=380,021 GN Created by potrace 1.16, written by Peter Selinger 2001-2019 C5U62_31,250 A0A2T6GBS6_9PSED 9.106 23 80.95 SwissP_P. protegens
p4 Cold shock protein CapB OS=Pseudomonas protegens (strain DSM 19,095 / LMG 27,888 / CHA0) OX=1,124,983 GN=capB A0A2C9EHH8_PSEPH 7.727 46 146.74 SwissP_P. protegens
Cold shock protein CapB OS=Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23,932 / Pf-5) OX=220,664 GN=capB Q4KH94_PSEF5 7.727 46 146.74 SwissP_P. protegens
Cold-shock protein OS=Pseudomonas protegens OX=380,021 GN=A1395_02635 A0A2J7UBE2_9PSED 7.727 46 146.74 SwissP_P. protegens
Cold shock protein CapB OS=Pseudomonas syringae pv. tomato (strain ATCC BAA-871 / DC3000) GN=capB CAPB_PSESM 7.727 46 127.60 SwissP_Bacteria_R
Cold shock protein CapB OS=Pseudomonas fragi GN=capB CAPB_PSEFR 7.727 46 127.60 SwissP_Bacteria_R
Cold shock protein OS=Pseudomonas sp. GM49 OX=1,144,331 GN=PMI29_02448 J2SK38_9PSED 7.727 46 123.98 SwissP_Bacteria_NR
Cold-shock DNA-binding protein family OS=Pseudomonas deceptionensis OX=882,211 GN=SAMN04489800_1852 A0A0J6GIW5_9PSED 7.727 46 123.98 SwissP_Bacteria_NR
Cold-shock protein OS=Pseudomonas syringae pv. cerasicola OX=264,451 GN=ALO50_03241 A0A0P9NMB0_PSESX 7.727 46 123.98 SwissP_Bacteria_NR
CapB_2 protein OS=Pseudomonas fluorescens OX=294 GN=capB_2 A0A075PGX5_PSEFL 7.727 46 123.98 SwissP_Bacteria_NR
Cold-shock protein OS=Pseudomonas tremae OX=200,454 GN=ALO43_00013 A0A0Q0CHU5_9PSED 7.727 46 123.98 SwissP_Bacteria_NR
Cold shock protein CapB OS=Pseudomonas fluorescens BRIP34879 OX=1,205,750 GN=A986_0300 L7HLD3_PSEFL 7.727 46 123.98 SwissP_Bacteria_NR
Cold acclimation protein B OS=Pseudomonas sp. 22 E 5 OX=1,844,093 GN=capB_2 A0A1B5EK52_9PSED 7.727 46 123.98 SwissP_Bacteria_NR
Cold-shock protein OS=Pseudomonas putida OX=303 GN=AO269_03090 A0A0W0P7R9_PSEPU 7.697 46 123.98 SwissP_Bacteria_NR
Cold-shock protein OS=Pseudomonas brassicacearum OX=930,166 GN Created by potrace 1.16, written by Peter Selinger 2001-2019 CD58_06475 W8PFF4_9PSED 7.727 46 123.98 SwissP_Bacteria_NR
Cold-shock protein OS=Pseudomonas amygdali pv. eriobotryae OX=129,137 GN=AL052_06405 A0A0P9QTI2_PSEA0 7.727 46 123.98 SwissP_Bacteria_NR
Cold-shock protein OS=Pseudomonas azotoformans OX=47,878 GN=AYR47_13,715 A0A127HXU4_PSEAZ 7.727 46 123.98 SwissP_Bacteria_NR
Cold shock protein OS=Pseudomonas fluorescens (strain SBW25) OX=216,595 GN=capB C3K709_PSEFS 7.727 46 123.98 SwissP_Bacteria_NR
Cold-shock protein OS=Pseudomonas amygdali pv. morsprunorum OX=129,138 GN=AC509_2282 A0A0N0GLZ4_PSEA0 7.727 46 123.98 SwissP_Bacteria_NR
Cold-shock protein OS=Pseudomonas sp. RIT-PI-r OX=1,699,620 GN=AK821_27,805 A0A0P6S0W4_9PSED 7.727 46 123.98 SwissP_Bacteria_NR
Uncharacterized protein OS=Pseudomonas syringae pv. aceris OX=199,198 GN=ALO91_01408 A0A0L8ITA8_PSESX 7.727 46 123.98 SwissP_Bacteria_NR
Cold-shock protein OS=Pseudomonas sp. Root68 OX=1,736,585 GN=ASD91_00740 A0A0Q8J556_9PSED 7.727 46 123.98 SwissP_Bacteria_NR
Cold-shock protein OS=Pseudomonas syringae pv. syringae OX=321 GN=AL062_19,410 A0A0M9H959_PSESY 7.727 46 123.98 SwissP_Bacteria_NR
Cold-shock DNA-binding protein family OS=Pseudomonas fragi OX=296 GN=AV641_05125 A0A0 × 8EWR3_PSEFR 7.727 46 123.98 SwissP_Bacteria_NR
Cold-shock protein OS=Pseudomonas weihenstephanensis OX=1,608,994 GN=TU86_02400 A0A0J6IW85_9PSED 7.727 46 123.98 SwissP_Bacteria_NR
Cold-shock protein OS=Pseudomonas amygdali pv. ciccaronei OX=264,452 GN=ALO78_01383 A0A0P9Q5F3_PSEA0 7.727 46 123.98 SwissP_Bacteria_NR
Cold shock protein OS=Pseudomonas sp. GM18 OX=1,144,324 GN=PMI21_04449 J2NQX1_9PSED 7.727 46 123.98 SwissP_Bacteria_NR
Cold shock protein OS=Pseudomonas amygdali pv. lachrymans str. M302278 OX=629,267 GN=PLA106_06845 F3IF92_PSEAV 7.727 46 123.98 SwissP_Bacteria_NR
Cold shock protein CapB OS=Pseudomonas antarctica OX=219,572 GN=A7J50_1439 A0A172YYL9_9PSED 7.727 46 123.98 SwissP_Bacteria_NR
Cold-shock protein OS=Pseudomonas coronafaciens pv. zizaniae OX=251,700 GN=ALO38_04720 A0A0Q0F3Z6_9PSED 7.727 46 123.98 SwissP_Bacteria_NR
Cold-shock DNA-binding protein family OS=Pseudomonas kilonensis OX=132,476 GN=SAMN04490188_3222 A0A0F4XHM9_9PSED 7.727 46 123.98 SwissP_Bacteria_NR
Cold shock protein OS=Pseudomonas sp. GM21 OX=1,144,325 GN=PMI22_04135 J2NCS9_9PSED 7.727 46 123.98 SwissP_Bacteria_NR
Cold shock protein OS=Pseudomonas sp. GM67 OX=1,144,335 GN=PMI33_02223 J2UA47_9PSED 7.727 46 123.98 SwissP_Bacteria_NR
Cold-shock DNA-binding protein family OS=Pseudomonas lini OX=163,011 GN=SAMN04490191_5956 A0A0J6KCW5_9PSED 7.727 46 123.98 SwissP_Bacteria_NR
Cold-shock protein OS=Pseudomonas amygdali pv. ulmi OX=251,720 GN=AL065_17,960 A0A0Q0E2H2_PSEA0 7.727 46 123.98 SwissP_Bacteria_NR
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2. Experimental design, materials, and methods

2.1. Phenotypic identification of bacterial strains

Pseudomonas strains were isolated from water (of pH 5.5) taken on the granite soil of the Vosges mountains (France) using spraying water on plate count agar (PCA, Biokar Diagnostics, Beauvais, France). Colony forming units (CFUs) were first selected on the ultraviolet ray fluorescence criterion. They were then identified as P. fluorescens using phenotypic and biochemical tests such as bacillus morphology with Gram negative staining and oxidase and catalase research, followed by inoculating APIⓇ 50CH micro galleries (bioMérieux Diagnostics, Marcy-l'Etoile, France). The three strains to be analyzed were named Fl4BN1, Fl4BN2 and Fl5BN2.

2.2. Whole genome analysis

Total deoxyribonucleic acid (DNA) was extracted using the Wizard genomic purification DNA kit (Promega Corp., Madison, WI, USA) and sequenced at MicrobesNG (http://www.microbesng.uk) using Illumina MiSeq and HiSeq 2500 technology platforms, with 2 × 250-bp paired-end reads. The closest existing reference genome was determined using Kraken [1], and the reads were mapped using the Burrows-Wheeler aligner (BWA) MEM algorithm (http://bio-bwa.sourceforge.net) to assess data quality. The reads were assembled by de novo assembly using SPAdes (http://cab.spbu.ru/ software/spades/). Gene function prediction was performed by the rapid annotations using subsystems technology (RAST) server (http://rast.nmpdr.org) [2] followed by an annotation using the SEED database [3]. The alignments of the bacterial draft genomes with the complete genomes of the nearest species determined by average nucleotide identity (JSpecies) (Pseudomonas sp. Lz4W and P. fragi P121 for Fl4BN2 and Pseudomonas protegens CHA0 for Fl4BN1 and Fl5BN2) were also performed using the Progressive MAUVE algorithm [4].

2.3. Average nucleotide identity and tetra correlation search analyzes

Bacteria draft genomes deposited in NCBI database were compared with indices based on the analysis of whole-genome sequences that had for species delineation, such as TCS based on the previously algorithm described [5] and ANI, as previously reported [6] using the JSpecies software (Ribocon GmbH) (http://jspecies.ribohost.com/jspeciesws/) [7]. TCS was performed between each assembled genome in the cart against the entire genomes reference database GenomesDB. Data is provided as a hit list (only the first 20/100 hits were presented in this dataset for each strain) for fast insights into the relationships of our organisms of interest (internal reference database GenomesDB: 47,489 entries, release date: 2018-03-14). The ANI was calculated based on the BLAST algorithm (ANIb) [6,8] and the MUMmer ultra-rapid aligning tool (ANIm) [9], between pairwise genomic comparisons with the 12 species frequently found for the three strains. The recommended species cut-off was 95% for the ANIb and ANIm indices, and higher than 0.99 for tetra-nucleotide signature analysis.

2.4. Proteomic characterization of the bacteria

The proteins directly produced into distilled water (DW) by the three strains, separated by two-dimensional polyacrylamide gel electrophoresis were analyzed for their mass after in-gel-trypsin-digestion, concentration and elution. The AnchorChipTM MALDI target plate was used to deposit the extracted peptides eluted from ZipTip C18 by an 80% acetonitrile (ACN), 0.1% trifluoroacetic acid (TFA) (vol/vol) solution and mixed with α-cyano-4-hydroxy-cinnamic acid matrix (5 mg.ml−1 in ACN:TFA, 85:0.1 vol/vol). The molecular mass measurements were performed in automatic mode using FlexControlTM 3.4 software in reflectron mode for MALDI-TOF peptide mass fingerprinting (PMF, MS mode) or LIFT mode for MALDI-TOF/TOF peptide fragment fingerprinting (PFF, MS/MS mode). External calibration was performed using a method previously described [10]. A maximum of ten precursor ions per sample were chosen for MS/MS analysis. Peak lists were generated from MS and MS/MS spectra using FlexAnalysisTM 3.4 software. Database search using PMF or PFF datasets was performed in the UniProt/SwissProt and NCBI databases via Mascot 2.2 (Matrix Science Ltd, London, UK)] or PEAKS Studio 7.0 (Bioinformatics Solutions). A mass tolerance of 50 parts per million (ppm) and 1 missing cleavage site were generally admitted for PMF. All sequence recovery percentages were higher than 27%. A MS/MS tolerance of 150 ppm and 3 missing cleavage sites for MS/MS searching were allowed. Variable cysteine carbamidomethylation and methionine oxidation were also considered. The relevance of protein identities was judged according to their score in the research software (p value of 0.05 (p < 0.05), False Discovery Rate < 1%).

Acknowledgments

Acknowledgments

The authors thank all the bodies that contributed to the funding of this research. The REALCAT platform is benefiting from a state subsidy administrated by the French National Research Agency (ANR) within the frame of the ‘future Investments’ program (PIA), with the contractual reference ‘ANR-11-EQPX-0037′. The European Union, through the ERDF funding administered by the Hauts-de-France Region, has co-financed the platform. Centrale Lille, the CNRS, and Lille University as well as the Centrale Initiative Foundation, are thanked for their financial contribution to the acquisition and implementation of the equipment of the REALCAT platform. The Hauts-de-France Region attributed the thesis Region Contract N°17007747 to Elodie Dussert for her studies that were also performed thanks to the ‘Contrats de Plan ETAT-REGION’ CPER PO 2015–2020 ALIBIOTECH.

Conflict of Interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

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