The Role of Proteomics in Bacterial Response to Antibiotics
Abstract
:1. Introduction
1.1. Multidrug Resistance (MDR), Priority Pathogens and Antibiotic Tolerant Persister Phenotype
1.2. Proteomics by Mass Spectrometry as A Tool and Common Data Acquisition Strategies
1.3. Applications of Proteomic Data Acquisition in Studies of Bacteria
2. The Role of Proteomic Analysis in Generating New Insight about The Mechanism of Action of Antibiotics and Antibiotic Resistance
2.1. Cell Wall Synthesis Inhibitors
2.2. Inhibitors of Protein Translation
2.2.1. Aminoglycosides
2.2.2. Macrolides
2.3. Inhibitors of DNA Synthesis
2.4. Cyclic Lipopeptides That are Used as Last Resort Drugs in Treatment of Bacterial Infections
2.4.1. Polymyxins and Colistin
2.4.2. Daptomycin
2.5. Promising Drug Candidates: Antimicrobial Peptides
3. Discussion and Conclusions
Author Contributions
Funding
Conflicts of Interest
References
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Pathogen | Resistance | Priority | Gram +/− |
---|---|---|---|
Acinetobacter baumannii | carbapenem-resistant | Critical | − |
Pseudomonas aeruginosa | carbapenem-resistant | Critical | − |
* Enterobacteriaceae | carbapenem-resistant, extended-spectrum β lactamase (ESBL)-producing | Critical | − |
Enterococcus faecium | vancomycin-resistant | High | + |
Staphylococcus aureus | methicillin-resistant,vancomycin-intermediate and resistant | High | + |
Helicobacter pylori | clarithromycin-resistant | High | − |
Campylobacter spp. | fluoroquinolone-resistant | High | − |
Salmonellae | fluoroquinolone-resistant | High | − |
Neisseria gonorrhoeae | cephalosporin-resistant, fluoroquinolone-resistant | High | − |
Streptococcus pneumoniae | penicillin-non-susceptible | Medium | + |
Haemophilus influenzae | ampicillin-resistant | Medium | − |
Shigella spp. | fluoroquinolone-resistant | Medium | − |
Drug | Bacterial Strain | Primary MOA | Phenotypic Investigation, Target | Time of Exposure | Concentration | Proteomic Approach and Method | Proteome Coverage (%) * | Results, Selected DEPs | Reference |
---|---|---|---|---|---|---|---|---|---|
PMB | E. coli | Outer membrane | Planktonic, Adaptive responses, (tolerance) | 30 growth cycles 31 × 16 h | 1 µg/mL 5 µg/mL 10 µg/ml | iTRAQ labeling (TMT) LC-MS/MS | 4,558 (pr. sample) | 1 µg/mL: (66 ↑, 22 ↓) 10 µg/mL: (232 ↑, 82 ↓) | [46] |
LL-37 | Strep. pneumoniae | Bacterial membrane, DNA | Planktonic, resistance | 1–2 h | 2.5 µg/ml | Label-free, DDA | 68%, 1,293/195 | 23-↑ 29-↓ | [61] |
CIP | E. coli | DNA gyrase | Persisters | 3 h, cyclic antibiotic exposure | 5 µg/mL (100 × MIC) | Label-free, DDA | 739 | 23 ↑ 12 ↓ | [62] |
RIF AMP | E. coli | RNA synthesis, cell wall | Persisters | 30 min RIF 3 h AMP | 100 µg/mL RIF, 100 µg/mL AMP | Label-free, DDA | 1,160 | 70 ↓ 35 ↑(persisters) | [59] |
CST PMB | E. coli | Outer membrane | mcr-1 colistin-resistance | NS | 0, 0.5–1 μg/mL | Label-free, DDA (TOF-MS/MS) DIA | 64.3%, 2,784 | No drug: 26 ↑, 31 ↓ CST 0.5: 75 ↑, 311 ↓ CST 1: 69 ↑, 237 ↓ PMB 0.5: 35 ↑, 219 ↓ PMB 1: 16 ↑, 147 ↓ | [43] |
TOB | P. aeruginosa | Protein synthesis | Outer membrane vesicles | 24 h | 1 µg/mL (sub-MIC) | Label-free, iBAQ, | 757 | 165 ↓,17 ↑ | [42] |
- | E. coli (ESBL-ST131) | Cell wall biosynthesis | Characterization of clinical isolates | No exposure | - | MALDI-TOF MS, LC-MS/MS | 10 | - | [62] |
AgNPs | P. aeruginosa | Cell membrane, ROS generation | Planktonic | 24 h | 0.1–50 µg/mL | Labeling, iTRAQ | ND | 3-↑,5-supressed | [49] |
AMP CTX CFP | E. coli | Cell wall biosynthesis | Outer membrane vesicles, β-lactam resistance | 12–84 h | AMP: 30 µg/mL CTX: 4 µg/mL CFP: 1.25 µg/mL | SDS-PAGE, MALDI-TOF-MS | 1,639 (273 mapped) 260 (OMVs resistant) 270 (OMVs susceptible) | 83 ↑, 49 ↓ (resistant) | [63] |
MEM CIP | E. coli(NDM, KPC or IMP) | Cell wall biosynthesis, DNA gyrase | Planktonic, β-lactam resistance | 4 h | sub-MIC 0.3–24 µg/mL MEM 32 µg/mL CIP | DIA | 457 | OmpA: (all strains-CIP) ↓ and (IMP-MEM)↑ HU DNA-bp: (NDM and KPC-MEM) ↑ GroEL/GroES and GrpE: (all strains-MEM) ↑ | [64] |
DAP | S. aureus | Lipoteichoic acid biosynthesis | Planktonic, biofilm, resistant | 4 months (Daily passages) | 0–31 µg/mL | Labeling | 60%, 1,709 | 349 DEPs, 105 ↑ 80 ↓ | [47] |
CIP | P. aeruginosa | DNA gyrase | Biofilms- antibiotic tolerant subpopulation | 1.5, 5.5, 14.5 h | 60 µg/Ml (Supra-MIC) | Label (BONCAT enrichment) | > 1,200 | 1.5h: 73 (41 unique) 5.5 h: 187 (80 unique) 14.5: 204 (90 unique) | [39] |
CIP | P. aeruginosa | DNA gyrase | Planktonic, adaptive resistance | 48 h | 0.125–8 µg/mL | Label-free, DDA | 57.6% 3,251 | mu0125_l: 57 ↑,76 ↓ mu0125_h:62 ↑,92 ↓ mu05_l: 43 ↑, 26 ↓ mu05_h: 48 ↑, 68 ↓ | [40] |
DAP | S. aureus | Lipoteichoic acidbiosynthesis | Planktonic, resistant and sensitive population | 18 h | 0.25–2 × MIC | Labeling, iTRAQ | 872 | 34 ↑ 17 ↓ | [48] |
CST | A. baumannii MDR-ZJ06 | Outer membrane | Planktonic, resistance in MDR strains | ON cultures | 8 × MIC 64 × MIC 200 × MIC | Labeling, iTRAQ | 1,582 | 31 ↑ 51 ↓ | [65] |
CIP BC | P. aeruginosa | DNA gyrase, outer membrane | Outer membrane proteins, Biofilms, adaptive resistance | 12 days | CIP: 6 µg/mL BC: 324 µg/mL | 2-DE SDS-PAGE | 10 proteins/600 spots | 9 ↓ 1 ↑ | [38] |
CST | P. aeruginosa | Outer membrane | Biofilms, Tolerance | 2-32 h, 8 h | 10 µg/mL-(10 × MIC) | Label - Pulsed-SILAC | 4,250 | 256 ↑ 140 ↓ | [66] |
OFX | M. tuberculosis | DNA gyrase | Planktonic, Mono-resistance | 36 h | 2 µg/mL (sub-MIC) | 2-DE, MALDI-TOF MS | 14 | 14 ↑ | [67] |
KAN | E. coli | Protein synthesis | Outer membrane Resistance | 10 sequential subcultures | 6.25 µg/mL (1/2 MIC) | 2-DE, MALDI-TOF MS | 11 | 6 ↑ 5 ↓ | [68] |
TOB | P. aeruginosa | Protein synthesis | Planktonic, adaptive resistance | DDE: 60 min TCE: 15, 60, 120, 360 min | DDE: 0.1, 0.5, 1µg/mL TCE: 1 µg/mL | DDA | > 1000 (TOB) | 96 ↑ | [41] |
OXA | MRSA, MSSA | Cell wall biosynthesis | Planktonic | NS | sub-MIC 1/8 × MIC 8 µg/mL 0.125 µg/mL | Label-free, DDA | MRSA: 1,071, (41%) MSSA: 1,034 (40%) | MRSA: 65 ↑,16 ↓ MSSA: 162 ↑, 63 ↓ | [69] |
SM GEN CEF TET NA | E. coli | Protein synthesis, cell wall synthesis, DNA gyrase | Effect of low abundance of NarG and NarH on resistance | 10 sequential subcultures | 1/2 MIC | 2-DE, MALDI-TOF MS | 94 | CAZ-R: 7↓ 6↑ SM-R: 5 ↓ 1↑ TET-R:7 ↓ 1↑ GEN-R: 9 ↓ 1↑ NA-R: 10 ↓ | [70] |
ERY | E. coli | Protein synthesis | Planktonic, resistance | 0, 43, 68, 103 h | sub-MIC 10 µg/mL (sub-MIC) | 2-DE, MALDI-TOF/TOF | 35/91 sp. | 43 h: 14 ↑, 3 ↓ 68 h: 6 ↓ 103h: 14 ↑, 1 ↓ | [71] |
CIP | P. aeruginosa | DNA gyrase | Planktonic, adaptive resistance | 0–48 h | PAO1: 0–8 × MIC (0–4 µg/mL) PAK: 1/2 MIC (0.125 µg/mL) | 2-DE, MALDI-TOF/TOF | 3/650 sp. | 2 proteins with higher phosphorylated/total protein ratio 1 ↑ | [37] |
β-lactams | E. coli (TEM-52 and CMY-2) | Cell wall biosynthesis | β-lactam resistance mediated | No exposure | - | 2-DE, IEF, MALDI-TOF/TOF | C583 strain: 64 sp. C580 strain: 91 sp. | - | [72] |
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Tsakou, F.; Jersie-Christensen, R.; Jenssen, H.; Mojsoska, B. The Role of Proteomics in Bacterial Response to Antibiotics. Pharmaceuticals 2020, 13, 214. https://doi.org/10.3390/ph13090214
Tsakou F, Jersie-Christensen R, Jenssen H, Mojsoska B. The Role of Proteomics in Bacterial Response to Antibiotics. Pharmaceuticals. 2020; 13(9):214. https://doi.org/10.3390/ph13090214
Chicago/Turabian StyleTsakou, Foteini, Rosa Jersie-Christensen, Håvard Jenssen, and Biljana Mojsoska. 2020. "The Role of Proteomics in Bacterial Response to Antibiotics" Pharmaceuticals 13, no. 9: 214. https://doi.org/10.3390/ph13090214
APA StyleTsakou, F., Jersie-Christensen, R., Jenssen, H., & Mojsoska, B. (2020). The Role of Proteomics in Bacterial Response to Antibiotics. Pharmaceuticals, 13(9), 214. https://doi.org/10.3390/ph13090214