Lon Protease Is Important for Growth under Stressful Conditions and Pathogenicity of the Phytopathogen, Bacterium Dickeya solani
Abstract
:1. Introduction
2. Results
2.1. Construction of the D. solani IPO 2222 Δlon and the Complemented D. solani IPO 2222 Δlon/lon Strains
2.2. The Expression of the lon Gene is Upregulated under Certain Stressful Conditions
2.3. Lon Protease Plays a Protective Role under Ionic and High-Temperature Stresses
2.4. Deletion of the lon Gene Delays the Onset of the Infection Symptoms
2.5. The Deletion of lon Affects the Activity of Secreted Pectate Lyases
2.6. Lon Protease is Essential for Efficient Motility
2.7. Comparison of Proteomic Profiles of the D. solani Δlon and WT Cells under Physiological and Stressful Conditions
3. Discussion
4. Materials and Methods
4.1. Materials
4.2. Bacterial Growth Conditions
4.3. Construction of the lon Deletion Strain
4.4. Single-Copy Complementation
4.5. Plasmid and Genomic DNA Purification
4.6. Preparation of Electrocompetent Cells and Electroporation
4.7. In Vivo Infection of the Potato Plants
4.8. Pathogenicity on Potato Tubers, Chicory and Chinese Cabbage Leaves.
4.9. Determination of Motility
4.10. Determination of Secreted PCWDE Activity
4.11. Siderophore Activity Assay
4.12. RNA Extraction
4.13. Reverse Transcription
4.14. Quantitative Real-Time PCR (qPCR)
4.15. Protein Electrophoresis and Immunodetection
4.16. Sample Preparation for Mass Spectrometry
4.17. Protein Digestion
4.18. Liquid Chromatography and Mass Spectrometry
4.19. SWATH Mass Spectrometry Experiments
4.20. Data Analysis
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
CAS | casamino acids |
CFU | colony forming units |
CMC | carboxymethyl cellulose |
Cq | quantification cycle |
DAP | diaminopimelic acid |
LA | Luria Agar |
MFD | Mu-free donor |
OD | optical density |
PGA | polygalacturonic acid |
PCWDE | plant cell wall degrading enzymes |
PQCS | protein quality control system |
SRP | soft rot Pectobacteriaceae |
SWATH-MS | Sequential Window Acquisition of All Theoretical Mass Spectra |
T1SS | type I secretion system |
T2SS | type II secretion system |
T3SS | type III secretion system |
WT | wild-type |
References
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Protein | 30 °C | 40 °C | |||
---|---|---|---|---|---|
Accession Number | Name | x-Fold | Log2x-Fold | x-Fold | Log2x-Fold |
Motility | |||||
• Downregulated | |||||
A0A2K8VVE7_9GAMM | Flagellin | 0.35 | −0.46 | ||
A0A2K8VVK5_9GAMM | Protein phosphatase CheZ | 0.41 | −0.39 | ||
A0A2K8W5V2_9GAMM | Methyl-accepting chemotaxis protein I (Serine chemoreceptor protein) | 0.24 | −0.63 | 0.21 | −0.67 |
A0A2K8VVH9_9GAMM | Signal transduction histidine kinase CheA | 0.34 | −0.46 | ||
A0A2K8VXS1_9GAMM | Methyl-accepting chemotaxis protein I (Serine chemoreceptor protein) | 0.43 | −0.37 | ||
A0A2K8W5V2_9GAMM | Methyl-accepting chemotaxis protein I (Serine chemoreceptor protein) | 0.24 | −0.63 | ||
A0A2K8VVG7_9GAMM | Flagellar motor switch protein FliG | 0.46 | −0.34 | ||
A0A2K8VVJ6_9GAMM | Positive regulator of CheA protein activity (CheW) | 0.35 | −0.45 | ||
Iron metabolism | |||||
• Downregulated | |||||
A0A2K8VW36_9GAMM | Ferrichrome-iron receptor | 0.50 | −0.30 | 0.27 | −0.56 |
A0A2K8VW52_9GAMM | 2,3-dihydroxybenzoate-AMP ligase enterobactinsiderophore | 0.30 | -0.52 | 0.15 | -0.82 |
A0A2K8W494_9GAMM | Nonspecific DNA-binding protein Dps/Iron-binding ferritin-like antioxidant protein/Ferroxidase | 0.47 | −0.32 | ||
A0A2K8VUB7_9GAMM | Ferrous iron transport protein B | 0.45 | −0.34 | ||
A0A2K8VW26_9GAMM | Isochorismatase enterobactin siderophore/Apo-aryl carrier domain of EntB | 0.4 | −0.34 | ||
A0A2K8VW34_9GAMM | Isochorismate synthase enterobactin siderophore | 0.48 | −0.32 | ||
A0A2K8VW22_9GAMM | Enterobactin synthetase component F, serine activating enzyme | 0.36 | −0.44 | ||
• Upregulated | |||||
A0A2K8W4W8_9GAMM | Achromobactin biosynthesis protein AcsASiderophoresynthetase superfamily, group B | 7.58 | 0.88 | 3.044 | 0.48 |
A0A2K8VWX6_9GAMM | Iron-sulfur cluster insertion protein ErpA | 4.90 | 0.69 | ||
A0A2K8W3W2_9GAMM | Ferric uptake regulation protein | 9.87 | 0.99 | ||
A0A2K8VWQ7_9GAMM | Iron-sulfur cluster assembly scaffold protein IscU | 3.67 | 0.56 | ||
A0A2K8W4W2_9GAMM | Achromobactin biosynthesis protein AcsD Siderophore synthetase superfamily, group A | 2.77 | 0.44 | ||
Stress-Related | |||||
• Downregulated | |||||
A0A2K8VUY7_9GAMM | Phage shock protein A | 0.31 | −0.51 | 0.35 | −0.45 |
A0A2K8VZS1_9GAMM | Small heat shock protein IbpA | 0.45 | −0.35 | ||
A0A2K8VZU2_9GAMM | Universal stress protein | 0.49 | −0.31 | ||
A0A2K8VUY1_9GAMM | Phage shock protein B OS=Dickeya solani | 0.38 | −0.41 | ||
• Upregulated | |||||
A0A2K8VTF5_9GAMM | Protease II | 4.44 | 0.65 | 2.94 | 0.47 |
A0A2K8VX21_9GAMM | Protein RecA | 2.65 | 0.42 | ||
A0A2K8W3I9_9GAMM | ATP-dependent Clp protease proteolytic subunit | 2.00 | 0.30 | ||
A0A2K8W3U6_9GAMM | Cold shock protein CspE | 2.91 | 0.46 | ||
A0A2K8VZ71_9GAMM | Cold shock protein CspG | 17.27 | 1.24 | ||
A0A2K8W1Q0 | Osmotically inducible protein OsmY | 2.50 | 0.40 | ||
A0A2K8VUA2_9GAMM | Protease HtpX | 2.22 | 0.35 | ||
• Differentially expressed | |||||
A0A2K8W260_9GAMM | Periplasmic protein related to spheroplast formation | 0.40 | −0.40 | 2.79 | 0.45 |
Transport | |||||
• Downregulated | |||||
A0A2K8W052_9GAMM | Phosphate-binding protein PstS | 0.48 | −0.32 | ||
A0A2K8VVW1_9GAMM | Histidine ABC transporter, histidine-binding periplasmic protein HisJ | 0.47 | −0.33 | ||
A0A2K8VU80_9GAMM | N-acetylneuraminic acid outer membrane channel protein NanC | 0.27 | −0.56 | ||
A0A2K8VTK7_9GAMM | Oligopeptide ABC transporter, periplasmic oligopeptide-binding protein OppA | 0.46 | −0.34 | ||
A0A2K8VWQ4_9GAMM | Periplasmic substrate-binding transport protein | 0.49 | −0.31 | ||
A0A2K8W2K3_9GAMM | Inositol transport system sugar-binding protein | 0.41 | −0.39 | ||
A0A2K8W3K7_9GAMM | Efflux pump membrane transporter | 0.37 | −0.43 | ||
A0A2K8VZR0_9GAMM | Dipeptide-binding ABC transporter, periplasmic substrate-binding component | 0.39 | −0.41 | ||
A0A2K8W417_9GAMM | Cobalt/zinc/cadmium efflux RND transporter, membrane fusion protein, CzcB family | 0.47 | −0.337 | ||
A0A2K8VSS7_9GAMM | Methionine ABC transporter substrate-binding protein | 0.44 | −0.36 | ||
• Upregulated | |||||
A0A2K8W0I4_9GAMM | Xylose ABC transporter, periplasmic xylose-binding protein XylF | 3.06 | 0.49 | 2.85 | 0.45 |
A0A2K8VXC1_9GAMM | L-proline glycine betaine binding ABC transporter protein ProX | 2.25 | 0.35 | 2.46 | 0.39 |
A0A2K8W3M0_9GAMM | Lead, cadmium, zinc and mercury transporting ATPase | 3.14 | 0.50 | ||
Metabolism | |||||
• Downregulated | |||||
A0A2K8W021_9GAMM | ATP synthase subunit delta | 0.47 | −0.33 | ||
A0A2K8W4F2_9GAMM | Glutamate-1-semialdehydeaminotransferase | 0.10 | −1.01 | 0.16 | −0.806 |
A0A2K8W580_9GAMM | Enoyl-acyl-carrier-protein reductase NADPH | 0.38 | −0.42 | ||
A0A2K8W1R7_9GAMM | Alkyl hydroperoxide reductase protein C | 0.40 | −0.40 | ||
A0A2K8VTW6_9GAMM | NAD(P) transhydrogenase subunit alpha | 0.47 | −0.33 | ||
A0A2K8W040_9GAMM | ATP synthase epsilon chain | 0.23 | −0.64 | ||
A0A2K8W444_9GAMM | 6-phosphogluconolactonase | 0.40 | −0.40 | ||
A0A2K8VVU5_9GAMM | NADH-quinone oxidoreductase | 0.46 | −0.33 | ||
A0A2K8VV27_9GAMM | Endo-1,4-beta-xylanase A | 0.230 | −0.53 | 0.13 | −0.89 |
A0A2K8VXQ3_9GAMM | PTS system, cellobiose-specific IIB component | 0.45 | −0.35 | ||
A0A2K8W121_9GAMM | Biotin carboxyl carrier protein of acetyl-CoA carboxylase | 0.41 | −0.39 | ||
A0A2K8W3J3_9GAMM | Cytochrome O ubiquinol oxidase subunit I | 0.47 | −0.32 | ||
A0A2K8VTY0_9GAMM | Superoxide dismutase [Cu-Zn] | 0.38 | −0.42 | ||
A0A2K8VU81_9GAMM | Sugar-binding protein | 0.47 | −0.33 | 0.37 | −0.43 |
A0A2K8W4J6_9GAMM | Putative l-lactate dehydrogenase, Iron-sulfur cluster-binding subunit YkgF | 0.36 | −0.44 | ||
A0A2K8VWF7_9GAMM | Peptidyl-prolyl cis-trans isomerase | 2.31 | 0.36 | ||
A0A2K8VT63_9GAMM | ATP phosphoribosyltransferase | 0.45 | −0.35 | ||
A0A2K8VVY8_9GAMM | Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta | 0.42 | −0.38 | ||
A0A2K8VX73_9GAMM | Phosphoheptose isomerase | 0.28 | −0.55 | ||
A0A2K8W077_9GAMM | Bifunctional polymyxin resistance protein ArnA | 0.20 | −0.71 | ||
• Upregulated | |||||
A0A2K8VTR1_9GAMM | 3-hydroxypropionate dehydrogenase | 4.17 | 0.62 | 4.24 | 0.63 |
A0A2K8VV57_9GAMM | Thioredoxin/glutathione peroxidase BtuE | 3.29 | 0.52 | 5.75 | 0.76 |
A0A2K8VXQ4_9GAMM | Putative phosphatase/kinase | 6.94 | 0.84 | 10.73 | 1.03 |
A0A2K8VTR5_9GAMM | SAM-dependent methyltransferase YafE (UbiE-like protein) | 4.13 | 0.62 | 4.38 | 0.64 |
A0A2K8W193_9GAMM | Glyoxalase | 2.42 | 0.38 | ||
A0A2K8VYC9_9GAMM | Fructose-bisphosphate aldolase class II | 2.80 | 0.45 | ||
A0A2K8W3S4_9GAMM | Thiol peroxidase, Bcp-type | 2.57 | 0.41 | ||
A0A2K8VV22_9GAMM | Glutaredoxin | 2.77 | 0.44 | ||
A0A2K8W3N7_9GAMM | Stomatin/prohibitin-family membrane protease subunit YbbK | 2.66 | 0.43 | ||
A0A2K8VXG5_9GAMM | Adenylate cyclase | 2.37 | 0.38 | ||
A0A2K8W3S1_9GAMM | Glycoprotein/polysaccharide metabolism | 14.75 | 1.17 | 3.187 | 0.507 |
A0A2K8VVX6_9GAMM | Phosphatase YfbT | 2.04 | 0.31 | ||
A0A2K8VYD6_9GAMM | Biosynthetic arginine decarboxylase | 3.62 | 0.56 | ||
A0A2K8VSW1_9GAMM | Soluble aldose sugar dehydrogenase, PQQ-dependent PE = 4 SV = 1 | 2.38 | 0.38 | ||
A0A2K8VXS7_9GAMM | Aminotransferase | 2.36 | 0.37 | ||
A0A2K8VXE7_9GAMM | Sulfite reductase [NADPH] flavoprotein alpha-component | 2.03 | 0.31 | ||
A0A2K8VY35_9GAMM | 3-isopropylmalate dehydratase large subunit | 2.21 | 0.34 | ||
A0A2K8W254_9GAMM | Phosphopentomutase | 2.60 | 0.41 | ||
A0A2K8VT52_9GAMM | Phosphoserine aminotransferase | 2.47 | 0.39 | ||
A0A2K8W0R3_9GAMM | ADP-l-glycero-d-manno-heptose-6-epimerase | 4.45 | 0.65 | 5.20 | 0.72 |
A0A2K8VY36_9GAMM | 3-isopropylmalate dehydratase small subunit | 2.51 | 0.40 | ||
A0A2K8VWH1_9GAMM | Methylglyoxal synthase | 2.27 | 0.36 | 2.85 | 0.45 |
• Differentially expressed | |||||
A0A2K8W2T8_9GAMM | Phosphotransferase system, phosphocarrier protein HPr | 0.49 | −0.31 | 2.66 | 0.42 |
A0A2K8VYF1_9GAMM | Epimerase domain-containing protein | 2.34 | 0.37 | 0.18 | −0.75 |
A0A2K8W293_9GAMM | Thiol:disulfide interchange protein | 0.46 | −0.34 | 2.13 | 0.33 |
Virulence | |||||
• Upregulated | |||||
A0A2K8VU37_9GAMM | Various polyols ABC transporter, permease component 2 | 2.75 | 0.44 | ||
A0A2K8VUF2_9GAMM | Harpin hrpN (Harpin-Ech) | 2.28 | 0.36 | ||
A0A2K8VUE5_9GAMM | Hrp pili protein hrpA (TTSS pilin hrpA) | 10.64 | 1.03 | ||
Transcription/Translation | |||||
• Downregulated | |||||
A0A2K8VT33_9GAMM | Serine-tRNA ligase | 0.47 | −0.33 | ||
A0A2K8VW75_9GAMM | JmjC domain-containing protein | 0.48 | −0.32 | ||
• Upregulated | |||||
A0A2K8VZG3_9GAMM | Transcriptional (Co)regulator CytR | 3.47 | 0.54 | ||
A0A2K8VZY6_9GAMM | DNA-directed RNA polymerase subunit omega | 2.45 | 0.39 | ||
A0A2K8W0W8_9GAMM | 50S ribosomal protein L7/L12 | 2.11 | 0.32 | ||
A0A2K8VUA3_9GAMM | Translation initiation factor 3 | 2.69 | 0.43 | ||
A0A2K8VX20_9GAMM | Ribosome hibernation protein YfiA | 13.75 | 1.14 | ||
A0A2K8W224_9GAMM | 50S ribosomal protein L27 | 2.03 | 0.31 | ||
A0A2K8W3J6_9GAMM | 50S ribosomal protein L31 type B | 3.42 | 0.53 | ||
A0A2K8VWY3_9GAMM | RNA polymerase-binding transcription factor DksA | 2.07 | 0.32 | ||
A0A2K8VY97_9GAMM | ABC transporter, ATP-binding protein | 2.45 | 0.39 | 2.04 | 0.31 |
A0A2K8VYE8_9GAMM | RNA-binding protein Hfq | 2.70 | 0.43 | ||
A0A2K8VYF1_9GAMM | Epimerase domain-containing protein | 2.34 | 0.37 | 0.18 | −0.75 |
Others | |||||
• Downregulated | |||||
A0A2K8W376_9GAMM | UPF0325 protein D083_3591 | 0.36 | −0.45 | ||
A0A2K8W2W2_9GAMM | IncI1 plasmid conjugative transfer protein TraF | 0.30 | −0.53 | 0.26 | −0.58 |
A0A2K8W4R1_9GAMM | Uncharacterized protein | 0.45 | −0.34 | 0.33 | −0.48 |
A0A2K8VTN2_9GAMM | Uncharacterized protein | 0.41 | −0.38 | ||
A0A2K8VV11_9GAMM | Major outer membrane lipoprotein | 0.50 | −0.30 | ||
• Upregulated | |||||
A0A2K8W3L1_9GAMM | Putative membrane protein OS=Dickeya solani | 175.34 | 2.24 | 117.58 | 2.07 |
A0A2K8VWZ4_9GAMM | S-ribosylhomocysteinelyase | 2.03 | 0.31 | ||
A0A2K8VZT1_9GAMM | Putative membrane protein | 7.12 | 0.85 | ||
A0A2K8VTR0_9GAMM | Putative secreted protein | 5.63 | 0.75 | ||
A0A2K8VT84_9GAMM | Uncharacterized protein | 5.23 | 0.72 | 6.61 | 0.82 |
• Differentially expressed | |||||
A0A2K8W4I6_9GAMM | Uncharacterized protein | 4.19 | 0.62 | 0.33 | −0.48 |
Strain | Genotype | Reference or Source |
Escherichia coli DH5α | F– φ80lacZΔM15 Δ(lacZYA-argF)U169 recA1 endA1 hsdR17(rK–, mK+) phoA supE44 λ– thi-1 gyrA96 relA1 | [58] |
Escherichia coli DH5α pir | sup E44 ΔlacU169 (ΦlacZΔM15) recA1 endA1 hsdR17 thi-1 gyrA96, relA1 λpir phage lysogen | [59] |
Escherichia coli MFD pir | MG1655 RP4-2-Tc::[ΔMu1::aac(3)IV-ΔaphA-Δnic35-ΔMu2::zeo] ΔdapA::(erm-pir) ΔrecA | [60] |
Dickeya solani IPO 2222 | WT | [61] |
D. solani IPO 2222 Δlon | Δlon | This work |
D. solani IPO 2222 Δlon/lon | Δlon/lon | This work |
Plasmids | Feature | Reference or Source |
pDOC-C | pEX100T, Sce1 -Sce1 sacB AmpR | [62] |
pDOC-K | pEX100T, Sce1-KanR -Sce1 sacB AmpR | [62] |
pACBSCE | I-Sce1 λ-Red CmR | [62] |
pDFDOC-C-lon | pDOC-C Sce1-KanR-Sce1 | This work |
pRE112 | pRE107 cmR sacB | [63] |
pmScarlet | pMB1 ori mScarlet AmpR | [64] |
pLonScar | pRE112 lon mScarlet | This work |
Primer | Primer Sequence 5′-3′ | Amplified DNA |
---|---|---|
lonkan L | CAGGGTACCTTCCCTTAACCTGGCGGAAACGAAACTAAGAGAGAGCTCTGACCGGTCAATTGGCTGGAG | kanamycin resistance gene with added sequences flanking the D. solani lon gene amplified from pDOC-K |
lonkan R | GCACACTCGAGCCAGCCTTTTT TTCTCAGTGGTTTTTGCGATAGGTCACTAATATCCTCCTTAGTTCC | |
lonsolani L | CGATTACCTATAGGCGAAACC | lon and kanamycin resistance gene amplified from D. solani and D. solani Δ lon gDNA, respectively |
lonsolani R | CAGGCTCAACAGTGCTCTAAC | |
1 L | AGTGAACTGCATGAATTCCCGTTGATCCAGATCTTGCGCGA | 500 bp upstream from the start codon of lon gene amplified from D. solani gDNA |
1 R | GTTCGGAACGCTCAGGGTTCATAGAGCTCTCTCTTAGTTTCGTTTCC | |
2 lon L | ATGAACCCTGAGCGTTCCGAA | lon gene amplified from D. solani gDNA |
2 lon R | CACGTTTCACTTTCCGGGTTCCTATTTTTTGGCTACCGACTTCAC | |
3 scarlet L | GAGACCCGGAAAGTGAAAACGTG | mScarlet gene amplified from pmScarlet |
3 scarlet R | TTACCGCCTTTGAGTGAGCTG | |
4 L | CAGCTCACTCAAAGGCGGTAATGACCTATCGCAAAAACCAC | 500 bp downstream from the stop codon of lon gene amplified from D. solani gDNA |
4 R | ATGCGATATCGAGCTCTCCCAAAACCGTCCCACCTCAGATT |
FWD Primer Sequence (5′-3′) | REV Primer Sequence (5′-3′) | Amplicon Length [bp] | PCR Efficiency | R2 | Concentration [µM] | |
---|---|---|---|---|---|---|
lon | TGGTCATTCCGTTGTTTGTTGGTC | CATCCGTTGAGGCTTCTTTCTGTG | 111 | 1.97 | 1.0 | 0.3 |
16S rRNA | GCTCGTGTTGTGAAATGTTGGGTT | GCAGTCTCCCTTGAGTTCCCAC | 94 | 1.96 | 1.0 | 0.225 |
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Figaj, D.; Czaplewska, P.; Przepióra, T.; Ambroziak, P.; Potrykus, M.; Skorko-Glonek, J. Lon Protease Is Important for Growth under Stressful Conditions and Pathogenicity of the Phytopathogen, Bacterium Dickeya solani. Int. J. Mol. Sci. 2020, 21, 3687. https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21103687
Figaj D, Czaplewska P, Przepióra T, Ambroziak P, Potrykus M, Skorko-Glonek J. Lon Protease Is Important for Growth under Stressful Conditions and Pathogenicity of the Phytopathogen, Bacterium Dickeya solani. International Journal of Molecular Sciences. 2020; 21(10):3687. https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21103687
Chicago/Turabian StyleFigaj, Donata, Paulina Czaplewska, Tomasz Przepióra, Patrycja Ambroziak, Marta Potrykus, and Joanna Skorko-Glonek. 2020. "Lon Protease Is Important for Growth under Stressful Conditions and Pathogenicity of the Phytopathogen, Bacterium Dickeya solani" International Journal of Molecular Sciences 21, no. 10: 3687. https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21103687