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Magalhães S, Aroso M, Roxo I, Ferreira S, Cerveira F, Ramalheira E, Ferreira R, Vitorino R. Proteomic profile of susceptible and multidrug-resistant clinical isolates of Escherichia coli and Klebsiella pneumoniae using label-free and immunoproteomic strategies. Res Microbiol 2016; 168:222-233. [PMID: 28040467 DOI: 10.1016/j.resmic.2016.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 11/12/2016] [Accepted: 12/18/2016] [Indexed: 01/13/2023]
Abstract
Infectious diseases caused by multidrug-resistant (MDR) Enterobacteriaceae have exponentially increased in the past decade, and are a major concern in hospitals. In the first part of the work, we compared the proteome profile of MDR and susceptible clinical isolates of Escherichia coli and Klebsiella pneumoniae in order to identify possible biological processes associated with drug resistance and susceptible phenotypes, using a label-free approach. In the second part, we used an immunoproteomics approach to identify immunoreactive proteins in the same isolates. A total of 388 and 377 proteins were identified in MDR and susceptible E. coli, respectively, evidencing that biological processes related to translation are upregulated in E. coli MDR, while there is an upregulation of processes related to catalytic activity in K. pneumoniae MDR. Both MDR strains show downregulation of processes related to amino acid activation and tRNA amino-acylation. Our data also suggest that MDR strains have higher immunoreactivity than the susceptible strains. The application of high-throughput mass spectrometry (MS) and bioinformatics to the study of modulation of biological processes might shed light on the characterization of multidrug resistance in bacteria.
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Affiliation(s)
- Sandra Magalhães
- QOPNA, Mass Spectrometry Center, Department of Chemistry, University of Aveiro, Aveiro, Portugal; iBiMED - Institute for Biomedicine, University of Aveiro, Aveiro, Portugal
| | - Miguel Aroso
- iBiMED - Institute for Biomedicine, University of Aveiro, Aveiro, Portugal
| | - Inês Roxo
- Clinical Pathology, Centro Hospitalar do Baixo Vouga, Oliveira do Bairro, Portugal
| | - Sónia Ferreira
- Clinical Pathology, Centro Hospitalar do Baixo Vouga, Oliveira do Bairro, Portugal; Institute of Education and Citizenship, Oliveira do Bairro, Portugal
| | - Frederico Cerveira
- Clinical Pathology, Centro Hospitalar do Baixo Vouga, Oliveira do Bairro, Portugal
| | - Elmano Ramalheira
- Clinical Pathology, Centro Hospitalar do Baixo Vouga, Oliveira do Bairro, Portugal
| | - Rita Ferreira
- QOPNA, Mass Spectrometry Center, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Rui Vitorino
- iBiMED - Institute for Biomedicine, University of Aveiro, Aveiro, Portugal; Department of Physiology and Cardiothoracic Surgery, Faculty of Medicine, University of Porto, Porto, Portugal.
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Rao AA, Patkari M, Reddy PJ, Srivastava R, Pendharkar N, Rapole S, Mehra S, Srivastava S. Proteomic analysis of Streptomyces coelicolor in response to Ciprofloxacin challenge. J Proteomics 2013; 97:222-34. [PMID: 23994098 DOI: 10.1016/j.jprot.2013.08.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 07/17/2013] [Accepted: 08/10/2013] [Indexed: 11/19/2022]
Abstract
UNLABELLED Multi-drug tolerance is an important phenotypic property that complicates treatment of infectious diseases and reshapes drug discovery. Hence a systematic study of the origins and mechanisms of resistance shown by microorganisms is imperative. Since soil-dwelling bacteria are constantly challenged with a myriad of antibiotics, they are potential reservoirs of resistance determinants that can be mobilized into pathogens over a period of time. Elucidating the resistance mechanisms in such bacteria could help future antibiotic discoveries. This research is a preliminary study conducted to determine the effects of ciprofloxacin (CIP) on the intrinsically resistant Gram-positive soil bacterium Streptomyces coelicolor. The effect was investigated by performing 2-DE on total protein extracts of cells exposed to sub-lethal concentrations of ciprofloxacin as compared to the controls. Protein identification by MALDI-TOF/TOF revealed 24 unique differentially expressed proteins, which were statistically significant. The down-regulation of proteins involved in carbohydrate metabolism indicated a shift in the cell physiology towards a state of metabolic shutdown. Furthermore, the observed decline in protein levels involved in transcription and translation machinery, along with depletion of enzymes involved in amino acid biosynthesis and protein folding could be a cellular response to DNA damage caused by CIP, thereby minimizing the effect of defective and energetically wasteful metabolic processes. This could be crucial for the initial survival of the cells before gene level changes could come into play to ensure survival under prolonged adverse conditions. These results are a first attempt towards profiling the proteome of S. coelicolor in response to antibiotic stress. This article is part of a Special Issue entitled: Trends in Microbial Proteomics. BIOLOGICAL SIGNIFICANCE Soil-dwelling bacteria could serve as a reservoir of resistance determinants for clinically important bacteria. In this work, we investigated, for the first time, the differential proteomic profile of S. coelicolor cells in response to sub-inhibitory concentrations of Ciprofloxacin using 2-DE. Results indicate a shift in the cell physiology towards a state of metabolic shutdown, possibly to counter the DNA damage by ciprofloxacin. Further, up-regulation of GAPDH, RNA pol mRNA and Translation IF2 protein indicates a reprogramming of the cell for long-term survival. This study could serve as a basis for further investigations to elucidate the general mechanism by which soil bacteria exhibit resistance to fluroquinolones. This may help in developing new drug protocols and inventing novel drugs to counter resistance to this class of antibiotics in pathogenic bacteria.
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Affiliation(s)
- Aishwarya Anand Rao
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Minal Patkari
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Panga Jaipal Reddy
- Wadhwani Research Center for Biosciences and Bioengineering, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Rajneesh Srivastava
- Wadhwani Research Center for Biosciences and Bioengineering, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Namita Pendharkar
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, Maharashtra, India
| | - Srikanth Rapole
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, Maharashtra, India
| | - Sarika Mehra
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Sanjeeva Srivastava
- Wadhwani Research Center for Biosciences and Bioengineering, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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Otvos L, de Olivier Inacio V, Wade JD, Cudic P. Prior antibacterial peptide-mediated inhibition of protein folding in bacteria mutes resistance enzymes. Antimicrob Agents Chemother 2006; 50:3146-9. [PMID: 16940114 PMCID: PMC1563543 DOI: 10.1128/aac.00205-06] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2006] [Revised: 04/12/2006] [Accepted: 06/09/2006] [Indexed: 11/20/2022] Open
Abstract
The antimicrobial activity of amoxicillin against TEM-1-expressing strains could be fully recovered when bacteria were preincubated with sublethal doses of an antibacterial peptide derivative. Assays with the simultaneous administration of antibiotics or synergy assays with kanamycin or ciprofloxacin, where resistance development does not involve properly folded proteins, failed to yield similar results.
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Affiliation(s)
- Laszlo Otvos
- Sbarro Institute for Cancer Research and Molecular Medicine, Temple University, Philadelphia, PA 19122, USA.
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Hennequin C, Collignon A, Karjalainen T. Analysis of expression of GroEL (Hsp60) of Clostridium difficile in response to stress. Microb Pathog 2001; 31:255-60. [PMID: 11710845 DOI: 10.1006/mpat.2001.0468] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Our laboratory has previously shown that adherence of Clostridium difficile to tissue culture cells is augmented by various stresses and that GroEL, a heat shock protein, serves an adhesive function in this bacterium. In this communication, RT-PCR, SDS-PAGE and immunoblotting were used to study the stress response in C. difficile following heat, acid or osmotic shock, iron deprivation or presence of a subinhibitory concentration of ampicillin in the culture medium. All these stresses increased transcription of groEL and production of GroEL to various degrees. Furthermore, the protein was found in membrane fractions and in the extracellular space after heat stress.
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Affiliation(s)
- C Hennequin
- Universite de Paris-Sud, Faculte de Pharmacie, Department de Microbiologie, 5 Rue JB Clement, F-92296 Chatenay-Malabry Cedex, France
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Bisognano C, Vaudaux P, Rohner P, Lew DP, Hooper DC. Induction of fibronectin-binding proteins and increased adhesion of quinolone-resistant Staphylococcus aureus by subinhibitory levels of ciprofloxacin. Antimicrob Agents Chemother 2000; 44:1428-37. [PMID: 10817688 PMCID: PMC89892 DOI: 10.1128/aac.44.6.1428-1437.2000] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We recently reported that strain EN1252a, a fluoroquinolone-resistant derivative of Staphylococcus aureus NCTC8325 with mutations in grlA and gyrA, expressed increased levels of fibronectin-binding proteins (FnBPs) and showed a significantly higher attachment to fibronectin-coated polymer surfaces after growth in the presence of subinhibitory concentrations of ciprofloxacin. The present study evaluated the occurrence and frequency of fluoroquinolone-induced FnBP-mediated adhesion in clinical isolates of fluoroquinolone-resistant methicillin-resistant S. aureus (MRSA) and methicillin-susceptible S. aureus (MSSA). Eight of ten MRSA isolates and four of six MSSA isolates with grlA and gyrA mutations exhibited significant increases in attachment to fibronectin-coated surfaces after growth in the presence of one-quarter the MIC of ciprofloxacin. Fluoroquinolone-induced FnBP-mediated adhesion of one clinical MRSA strain and the double mutant strain EN1252a also occurred on coverslips removed from the subcutaneous space of guinea pigs. For strain EN1252a, the regulation of fnb transcription by sub-MICs of ciprofloxacin was studied on reporter plasmids carrying fnb-luxAB fusions. One-quarter of the MIC of ciprofloxacin significantly increased fnbB, but not fnbA, promoter activity of the fluoroquinolone-resistant mutant but not its fluoroquinolone-susceptible parent ISP794. This response was abolished by pretreatment with rifampin, indicating an effect at the level of transcription. Activation of the fnbB promoter was not due to an indirect effect of ciprofloxacin on growth rate and still occurred in an agr mutant of strain EN1252a. These data suggest that sub-MIC levels of ciprofloxacin activate the fnbB promoter of some laboratory and clinical isolates, thus contributing to increased production of FnBP(s) and leading to higher levels of bacterial attachment to fibronectin-coated or subcutaneously implanted coverslips.
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Affiliation(s)
- C Bisognano
- Division of Infectious Diseases, University Hospital, CH-1211 Geneva 14, Switzerland
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Mizushima T, Tsutsumi S, Rokutan K, Tsuchiya T. Suppression of ethanol-induced apoptotic DNA fragmentation by geranylgeranylacetone in cultured guinea pig gastric mucosal cells. Dig Dis Sci 1999; 44:510-4. [PMID: 10080142 DOI: 10.1023/a:1026692920848] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The purpose of this study was to elucidate the molecular mechanism of action of geranylgeranylacetone, an antiulcer drug. Treatment with ethanol for 8 hr at the optimum concentration (7.5%) caused apoptotic DNA fragmentation in cultured guinea pig gastric mucosal cells. Pretreatment of cells with geranylgeranylacetone suppressed the DNA fragmentation in a dose-dependent manner. The maximum effect was achieved at 10(-6) M, at which concentration the drug was previously shown to induce heat-shock proteins. The suppression required an incubation period longer than 1 hr. Pretreatment of cells with low concentrations of ethanol also prevented DNA fragmentation.
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Affiliation(s)
- T Mizushima
- Faculty of Pharmaceutical Sciences, Okayama University, Japan
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Kim SJ, Kim S. Abnormal proteins enhance stress-induced cell death. Biochem Biophys Res Commun 1998; 243:153-7. [PMID: 9473497 DOI: 10.1006/bbrc.1997.7956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The effect of abnormal proteins on cell viability was studied using artificially cleaved polypeptides. Escherichia coli methionyl-tRNA synthetase (MetRS) consists of two distinct domains and its activity is essential for cell viability. The polypeptide chain was split by linker insertion and expressed as two fragments. Two pairs of polypeptides, one split within the N-terminal domain and another at the junction of the two domains retained aminoacylation activity. The in vitro activities of these split mutants were enhanced by the presence of chaperonin, GroESL. However, cells containing these split polypeptides became sensitive to conditions that induce GroESL. The results of this work suggest that an abnormally generated protein can cause cell death under stressful conditions.
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Affiliation(s)
- S J Kim
- Department of Biology, Sung Kyun Kwan University, Kyunggido, Korea
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