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Scaletti ER, Pettersson P, Patrick J, Shilling PJ, Westergren RG, Daley DO, Mäler L, Widmalm G, Stenmark P. Structural and functional insights into the Pseudomonas aeruginosa glycosyltransferase WaaG and the implications for lipopolysaccharide biosynthesis. J Biol Chem 2023; 299:105256. [PMID: 37716703 PMCID: PMC10579960 DOI: 10.1016/j.jbc.2023.105256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/31/2023] [Accepted: 09/10/2023] [Indexed: 09/18/2023] Open
Abstract
The glycosyltransferase WaaG in Pseudomonas aeruginosa (PaWaaG) is involved in the synthesis of the core region of lipopolysaccharides. It is a promising target for developing adjuvants that could help in the uptake of antibiotics. Herein, we have determined structures of PaWaaG in complex with the nucleotide-sugars UDP-glucose, UDP-galactose, and UDP-GalNAc. Structural comparison with the homolog from Escherichia coli (EcWaaG) revealed five key differences in the sugar-binding pocket. Solution-state NMR analysis showed that WT PaWaaG specifically hydrolyzes UDP-GalNAc and unlike EcWaaG, does not hydrolyze UDP-glucose. Furthermore, we found that a PaWaaG mutant (Y97F/T208R/N282A/T283A/T285I) designed to resemble the EcWaaG sugar binding site, only hydrolyzed UDP-glucose, underscoring the importance of the identified amino acids in substrate specificity. However, neither WT PaWaaG nor the PaWaaG mutant capable of hydrolyzing UDP-glucose was able to complement an E. coli ΔwaaG strain, indicating that more remains to be uncovered about the function of PaWaaG in vivo. This structural and biochemical information will guide future structure-based drug design efforts targeting PaWaaG.
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Affiliation(s)
- Emma R Scaletti
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Pontus Pettersson
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Joan Patrick
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Patrick J Shilling
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | | | - Daniel O Daley
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Lena Mäler
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
| | - Pål Stenmark
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
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2
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The Basis for Natural Multiresistance to Phage in Pseudomonas aeruginosa. Antibiotics (Basel) 2020; 9:antibiotics9060339. [PMID: 32570896 PMCID: PMC7344871 DOI: 10.3390/antibiotics9060339] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/01/2020] [Accepted: 06/16/2020] [Indexed: 01/21/2023] Open
Abstract
Pseudomonas aeruginosa is responsible for long-term infections and is particularly resistant to treatments when hiding inside the extracellular matrix or biofilms. Phage therapy might represent an alternative to antibiotic treatment, but up to 10% of clinical strains appear to resist multiple phages. We investigated the characteristics of P. aeruginosa clinical strains naturally resistant to phages and compared them to highly susceptible strains. The phage-resistant strains were defective in lipopolysaccharide (LPS) biosynthesis, were nonmotile and displayed an important degree of autolysis, releasing phages and pyocins. Complete genome sequencing of three resistant strains showed the existence of a large accessory genome made of multiple insertion elements, genomic islands, pyocins and prophages, including two phages performing lateral transduction. Mutations were found in genes responsible for the synthesis of LPS and/or type IV pilus, the major receptors for most phages. CRISPR-Cas systems appeared to be absent or inactive in phage-resistant strains, confirming that they do not play a role in the resistance to lytic phages but control the insertion of exogenous sequences. We show that, despite their apparent weakness, the multiphage-resistant strains described in this study displayed selective advantages through the possession of various functions, including weapons to eliminate other strains of the same or closely related species.
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3
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Khandekar S, Liebens V, Fauvart M, Tulkens PM, Michiels J, Van Bambeke F. The Putative De- N-acetylase DnpA Contributes to Intracellular and Biofilm-Associated Persistence of Pseudomonas aeruginosa Exposed to Fluoroquinolones. Front Microbiol 2018; 9:1455. [PMID: 30042739 PMCID: PMC6048251 DOI: 10.3389/fmicb.2018.01455] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 06/12/2018] [Indexed: 11/30/2022] Open
Abstract
Persisters are the fraction of antibiotic-exposed bacteria transiently refractory to killing and are recognized as a cause of antibiotic treatment failure. The putative de-N-acetylase DnpA increases persister levels in Pseudomonas aeruginosa upon exposure to fluoroquinolones in broth. In this study the wild-type PAO1 and its dnpA insertion mutant (dnpA::Tn) were used in parallel and compared for their capacity to generate persisters in broth (surviving fraction after exposure to high antibiotic concentrations) and their susceptibility to antibiotics in models of intracellular infection of THP-1 monocytes and of biofilms grown in microtiter plates. Multiplication in monocytes was evaluated by fluorescence dilution of GFP (expressed under the control of an inducible promoter) using flow cytometry. Gene expression was measured by quantitative RT-PCR. When exposed to fluoroquinolones (ciprofloxacin or levofloxacin) but not to meropenem or amikacin, the dnpA::Tn mutant showed a 3- to 10-fold lower persister fraction in broth. In infected monocytes, fluoroquinolones (but not the other antibiotics) were more effective (difference in Emax: 1.5 log cfu) against the dnpA::Tn mutant than against the wild-type PAO1. Dividing intracellular bacteria were more frequently seen (1.5 to 1.9-fold) with the fluoroquinolone-exposed dnpA::Tn mutant than with its parental strain. Fluoroquinolones (but not the other antibiotics) were also 3-fold more potent to prevent biofilm formation by the dnpA::Tn mutant than by PAO1 as well as to act upon biofilms (1–3 days of maturity) formed by the mutant than by the parental strain. Fluoroquinolones induced the expression of gyrA (4.5–7 fold) and mexX (3.6–5.4 fold) in the parental strain but to a lower extent (3–4-fold for gyrA and 1.8–2.8-fold for mexX, respectively) in the dnpA::Tn mutant. Thus, our data show that a dnpA insertion mutant of P. aeruginosa is more receptive to fluoroquinolone antibacterial effects than its parental strain in infected monocytes or in biofilms. The mechanism of this higher responsiveness could involve a reduced overexpression of the fluoroquinolone target.
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Affiliation(s)
- Shaunak Khandekar
- Pharmacologie Cellulaire et Moléculaire, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
| | - Veerle Liebens
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Maarten Fauvart
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium.,Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium.,imec, Leuven, Belgium
| | - Paul M Tulkens
- Pharmacologie Cellulaire et Moléculaire, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium.,Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
| | - Françoise Van Bambeke
- Pharmacologie Cellulaire et Moléculaire, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
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4
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Defraine V, Liebens V, Loos E, Swings T, Weytjens B, Fierro C, Marchal K, Sharkey L, O'Neill AJ, Corbau R, Marchand A, Chaltin P, Fauvart M, Michiels J. 1-((2,4-Dichlorophenethyl)Amino)-3-Phenoxypropan-2-ol Kills Pseudomonas aeruginosa through Extensive Membrane Damage. Front Microbiol 2018; 9:129. [PMID: 29472905 PMCID: PMC5809444 DOI: 10.3389/fmicb.2018.00129] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 01/18/2018] [Indexed: 12/31/2022] Open
Abstract
The ever increasing multidrug-resistance of clinically important pathogens and the lack of novel antibiotics have resulted in a true antibiotic crisis where many antibiotics are no longer effective. Further complicating the treatment of bacterial infections are antibiotic-tolerant persister cells. Besides being responsible for the recalcitrant nature of chronic infections, persister cells greatly contribute to the observed antibiotic tolerance in biofilms and even facilitate the emergence of antibiotic resistance. Evidently, eradication of these persister cells could greatly improve patient outcomes and targeting persistence may provide an alternative approach in combatting chronic infections. We recently characterized 1-((2,4-dichlorophenethyl)amino)-3-phenoxypropan-2-ol (SPI009), a novel anti-persister molecule capable of directly killing persisters from both Gram-negative and Gram-positive pathogens. SPI009 potentiates antibiotic activity in several in vitro and in vivo infection models and possesses promising anti-biofilm activity. Strikingly, SPI009 restores antibiotic sensitivity even in resistant strains. In this study, we investigated the mode of action of this novel compound using several parallel approaches. Genetic analyses and a macromolecular synthesis assays suggest that SPI009 acts by causing extensive membrane damage. This hypothesis was confirmed by liposome leakage assay and membrane permeability studies, demonstrating that SPI009 rapidly impairs the bacterial outer and inner membranes. Evaluation of SPI009-resistant mutants, which only could be generated under severe selection pressure, suggested a possible role for the MexCD-OprJ efflux pump. Overall, our results demonstrate the extensive membrane-damaging activity of SPI009 and confirm its clinical potential in the development of novel anti-persister therapies.
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Affiliation(s)
- Valerie Defraine
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium.,Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
| | - Veerle Liebens
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Evelien Loos
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Toon Swings
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium.,Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
| | - Bram Weytjens
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Carolina Fierro
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Kathleen Marchal
- Data Integration and Biological Networks, Ghent University, Ghent, Belgium
| | - Liam Sharkey
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Alex J O'Neill
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | | | | | - Patrick Chaltin
- CISTIM Leuven vzw, Leuven, Belgium.,Centre for Drug Design and Discovery, Leuven, Belgium
| | - Maarten Fauvart
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium.,Smart Electronics Unit, Department of Life Sciences and Imaging, imec, Leuven, Belgium
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium.,Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
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Identification of 1-((2,4-Dichlorophenethyl)Amino)-3-Phenoxypropan-2-ol, a Novel Antibacterial Compound Active against Persisters of Pseudomonas aeruginosa. Antimicrob Agents Chemother 2017. [PMID: 28630188 DOI: 10.1128/aac.00836-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Antibiotics typically fail to completely eradicate a bacterial population, leaving a small fraction of transiently antibiotic-tolerant persister cells intact. Persisters are therefore seen to be a major cause of treatment failure and greatly contribute to the recalcitrant nature of chronic infections. The current study focused on Pseudomonas aeruginosa, a Gram-negative pathogen belonging to the notorious ESKAPE group of pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) and, due to increasing resistance against most conventional antibiotics, posing a serious threat to human health. Greatly contributing to the difficult treatment of P. aeruginosa infections is the presence of persister cells, and elimination of these cells would therefore significantly improve patient outcomes. In this study, a small-molecule library was screened for compounds that, in combination with the fluoroquinolone antibiotic ofloxacin, reduced the number of P. aeruginosa persisters compared to the number achieved with treatment with the antibiotic alone. Based on the early structure-activity relationship, 1-((2,4-dichlorophenethyl)amino)-3-phenoxypropan-2-ol (SPI009) was selected for further characterization. Combination of SPI009 with mechanistically distinct classes of antibiotics reduced the number of persisters up to 106-fold in both lab strains and clinical isolates of P. aeruginosa Further characterization of the compound revealed a direct and efficient killing of persister cells. SPI009 caused no erythrocyte damage and demonstrated minor cytotoxicity. In conclusion, we identified a novel antipersister compound active against P. aeruginosa with promising applications for the design of novel, case-specific combination therapies in the fight against chronic infections.
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6
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Latino L, Caroff M, Pourcel C. Fine structure analysis of lipopolysaccharides in bacteriophage-resistant Pseudomonas aeruginosa PAO1 mutants. Microbiology (Reading) 2017; 163:848-855. [DOI: 10.1099/mic.0.000476] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Libera Latino
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Martine Caroff
- LPS-BioSciences, Bât 409, I2BC, Université Paris-Sud, 91405 Orsay, France
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
| | - Christine Pourcel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France
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7
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Light Modulates Metabolic Pathways and Other Novel Physiological Traits in the Human Pathogen Acinetobacter baumannii. J Bacteriol 2017; 199:JB.00011-17. [PMID: 28289081 DOI: 10.1128/jb.00011-17] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 03/02/2017] [Indexed: 02/03/2023] Open
Abstract
Light sensing in chemotrophic bacteria has been relatively recently ascertained. In the human pathogen Acinetobacter baumannii, light modulates motility, biofilm formation, and virulence through the blue-light-sensing-using flavin (BLUF) photoreceptor BlsA. In addition, light can induce a reduction in susceptibility to certain antibiotics, such as minocycline and tigecycline, in a photoreceptor-independent manner. In this work, we identified new traits whose expression levels are modulated by light in this pathogen, which comprise not only important determinants related to pathogenicity and antibiotic resistance but also metabolic pathways, which represents a novel concept for chemotrophic bacteria. Indeed, the phenylacetic acid catabolic pathway and trehalose biosynthesis were modulated by light, responses that completely depend on BlsA. We further show that tolerance to some antibiotics and modulation of antioxidant enzyme levels are also influenced by light, likely contributing to bacterial persistence in adverse environments. Also, we present evidence indicating that surfactant production is modulated by light. Finally, the expression of whole pathways and gene clusters, such as genes involved in lipid metabolism and genes encoding components of the type VI secretion system, as well as efflux pumps related to antibiotic resistance, was differentially induced by light. Overall, our results indicate that light modulates global features of the A. baumannii lifestyle.IMPORTANCE The discovery that nonphototrophic bacteria respond to light constituted a novel concept in microbiology. In this context, we demonstrated that light could modulate aspects related to bacterial virulence, persistence, and resistance to antibiotics in the human pathogen Acinetobacter baumannii In this work, we present the novel finding that light directly regulates metabolism in this chemotrophic bacterium. Insights into the mechanism show the involvement of the photoreceptor BlsA. In addition, tolerance to antibiotics and catalase levels are also influenced by light, likely contributing to bacterial persistence in adverse environments, as is the expression of the type VI secretion system and efflux pumps. Overall, a profound influence of light on the lifestyle of A. baumannii is suggested to occur.
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8
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Gerits E, Spincemaille P, De Cremer K, De Brucker K, Beullens S, Thevissen K, Cammue BPA, Vandamme K, Fauvart M, Verstraeten N, Michiels J. Repurposing AM404 for the treatment of oral infections by Porphyromonas gingivalis. Clin Exp Dent Res 2017; 3:69-76. [PMID: 29744181 PMCID: PMC5719815 DOI: 10.1002/cre2.65] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 03/04/2017] [Accepted: 03/14/2017] [Indexed: 01/21/2023] Open
Abstract
Porphyromonas gingivalis is a major pathogen involved in oral diseases such as periodontitis and peri‐implantitis. Management of these diseases typically includes mechanical debridement of the colonized surfaces followed by application of antiseptics or antibiotics. Disadvantages associated with the use of antiseptics and the growing worldwide problem of antibiotic resistance have necessitated the search for alternative agents. In this study, the antibacterial and antibiofilm properties of AM404, an active metabolite of paracetamol, were tested against P. gingivalis and other bacterial pathogens. The activity of AM404 was tested against 10 bacteria, including both oral and nonoral human pathogens. The minimal inhibitory concentration (MIC) of AM404 was determined by measuring optical density (OD) values. The minimum biofilm inhibitory concentration (MBIC) was detected by crystal violet staining. The activity of structural analogs of AM404 was tested by MIC determinations. The effect of AM404 on P. gingivalis biofilms formed on titanium disks as a model for dental implants was evaluated by colony forming unit counting. Potential cytotoxicity of AM404 towards HEK‐293 (human embryonic kidney cells), HepG2 (human hepatoma cells), IEC‐6 (rat intestinal cells), and Panc‐1 cells (pancreatic cancer cells) was assessed by 3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyltetrazolium bromide assays. To get more insight in the mode of action of AM404, we used the fluorescent dyes N‐phenyl‐1‐napthylamine and SYTOX green to investigate outer and inner membrane damage of P. gingivalis induced by AM404, respectively. Of all tested pathogens, AM404 only inhibited growth and biofilm formation of P. gingivalis. Moreover, it showed potent activity against P. gingivalis biofilms formed on titanium surfaces. A structure–activity analysis demonstrated that the unsaturated carbon chain is essential for its antibacterial activity. Importantly, AM404 was not toxic towards the tested mammalian cells up to concentrations approaching 4× the MIC. Membrane damage assays using fluorescent probes N‐phenyl‐1‐napthylamine and SYTOX green revealed that membrane permeabilization presumably is the primary antibacterial mode of action of AM404. Collectively, our results suggest that AM404 has the potential to be used for the development of new drugs specifically targeting P. gingivalis‐related infections.
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Affiliation(s)
- Evelien Gerits
- Department of Microbial and Molecular Systems KU Leuven, Centre of Microbial and Plant Genetics Leuven Belgium
| | - Pieter Spincemaille
- Department of Laboratory Medicine University Hospitals Leuven Leuven Belgium
| | - Kaat De Cremer
- Department of Microbial and Molecular Systems KU Leuven, Centre of Microbial and Plant Genetics Leuven Belgium.,Department of Plant Systems Biology VIB Ghent Belgium
| | - Katrijn De Brucker
- Department of Microbial and Molecular Systems KU Leuven, Centre of Microbial and Plant Genetics Leuven Belgium
| | - Serge Beullens
- Department of Microbial and Molecular Systems KU Leuven, Centre of Microbial and Plant Genetics Leuven Belgium
| | - Karin Thevissen
- Department of Microbial and Molecular Systems KU Leuven, Centre of Microbial and Plant Genetics Leuven Belgium
| | - Bruno P A Cammue
- Department of Microbial and Molecular Systems KU Leuven, Centre of Microbial and Plant Genetics Leuven Belgium.,Department of Plant Systems Biology VIB Ghent Belgium
| | - Katleen Vandamme
- Department of Oral Health Sciences UZ Leuven, Restorative Dentistry-KU Leuven, BIOMAT Leuven Belgium
| | - Maarten Fauvart
- Department of Microbial and Molecular Systems KU Leuven, Centre of Microbial and Plant Genetics Leuven Belgium.,Department of Life Science Technologies imec, Smart Systems and Emerging Technologies Unit Belgium
| | - Natalie Verstraeten
- Department of Microbial and Molecular Systems KU Leuven, Centre of Microbial and Plant Genetics Leuven Belgium
| | - Jan Michiels
- Department of Microbial and Molecular Systems KU Leuven, Centre of Microbial and Plant Genetics Leuven Belgium
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9
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Repurposing Toremifene for Treatment of Oral Bacterial Infections. Antimicrob Agents Chemother 2017; 61:AAC.01846-16. [PMID: 27993858 DOI: 10.1128/aac.01846-16] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 12/11/2016] [Indexed: 12/24/2022] Open
Abstract
The spread of antibiotic resistance and the challenges associated with antiseptics such as chlorhexidine have necessitated a search for new antibacterial agents against oral bacterial pathogens. As a result of failing traditional approaches, drug repurposing has emerged as a novel paradigm to find new antibacterial agents. In this study, we examined the effects of the FDA-approved anticancer agent toremifene against the oral bacteria Porphyromonas gingivalis and Streptococcus mutans We found that the drug was able to inhibit the growth of both pathogens, as well as prevent biofilm formation, at concentrations ranging from 12.5 to 25 μM. Moreover, toremifene was shown to eradicate preformed biofilms at concentrations ranging from 25 to 50 μM. In addition, we found that toremifene prevents P. gingivalis and S. mutans biofilm formation on titanium surfaces. A time-kill study indicated that toremifene is bactericidal against S. mutans Macromolecular synthesis assays revealed that treatment with toremifene does not cause preferential inhibition of DNA, RNA, or protein synthesis pathways, indicating membrane-damaging activity. Biophysical studies using fluorescent probes and fluorescence microscopy further confirmed the membrane-damaging mode of action. Taken together, our results suggest that the anticancer agent toremifene is a suitable candidate for further investigation for the development of new treatment strategies for oral bacterial infections.
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10
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Van den Bergh B, Fauvart M, Michiels J. Formation, physiology, ecology, evolution and clinical importance of bacterial persisters. FEMS Microbiol Rev 2017; 41:219-251. [DOI: 10.1093/femsre/fux001] [Citation(s) in RCA: 217] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 01/12/2017] [Indexed: 12/19/2022] Open
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11
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Liebens V, Frangipani E, Van der Leyden A, Fauvart M, Visca P, Michiels J. Membrane localization and topology of the DnpA protein control fluoroquinolone tolerance in Pseudomonas aeruginosa. FEMS Microbiol Lett 2016; 363:fnw184. [PMID: 27481702 DOI: 10.1093/femsle/fnw184] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2016] [Indexed: 12/31/2022] Open
Abstract
DnpA, a putative de-N-acetylase of the PIG-L superfamily, is required for antibiotic tolerance in Pseudomonas aeruginosa Exactly how dnpA (gene locus PA5002) directs the formation of antibiotic-tolerant persister cells is currently unknown. Previous research provided evidence for a role in surface-associated process(es), possibly in lipopolysaccharide biosynthesis. In silico sequence analysis of DnpA predicts a single transmembrane domain and Nin/Cout orientation of DnpA. In contrast, we here show that DnpA is an integral inner membrane protein containing two transmembrane domains, with the major C-terminal part located at the cytoplasmic face. Correct insertion into the inner membrane is necessary for DnpA to promote fluoroquinolone tolerance. The membrane localization of DnpA further supports its role in cell envelope-associated process(es). In addition to shedding light on the biological role of DnpA, this study highlights the risks of overreliance on the predictive value of bioinformatics tools and the importance of rigorous experimental validation of in silico predictions.
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Affiliation(s)
- Veerle Liebens
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
| | | | | | - Maarten Fauvart
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium imec, Smart Systems and Emerging Technologies Unit, Department of Life Science Technologies, 3001 Leuven, Belgium
| | - Paolo Visca
- Department of Sciences, Roma Tre University, Rome 00146, Italy
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
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12
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Experimental Evolution of Escherichia coli Persister Levels Using Cyclic Antibiotic Treatments. Methods Mol Biol 2016; 1333:131-43. [PMID: 26468106 DOI: 10.1007/978-1-4939-2854-5_12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Persister cells are difficult to study owing to their transient nature and their usually small number in bacterial populations. In the past, numerous attempts have been made to elucidate persistence mechanisms. However, because of the challenges involved in studying persisters and the clear redundancy in mechanisms underlying their generation, our knowledge of molecular pathways to persistence remains incomplete. Here, we describe how to use experimental evolution with cyclic antibiotic treatments to generate mutants with an increased persister level in stationary phase, ranging from the initial ancestral level up to 100 %. This method will help to unravel molecular pathways to persistence, and opens up a myriad of new possibilities in persister research, such as the convenient study of nearly pure persister cultures and the possibility to investigate the role of time and environmental aspects in the evolution of persistence.
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13
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Efficacy of Artilysin Art-175 against Resistant and Persistent Acinetobacter baumannii. Antimicrob Agents Chemother 2016; 60:3480-8. [PMID: 27021321 DOI: 10.1128/aac.00285-16] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 03/17/2016] [Indexed: 01/21/2023] Open
Abstract
Bacteriophage-encoded endolysins have shown promise as a novel class of antibacterials with a unique mode of action, i.e., peptidoglycan degradation. However, Gram-negative pathogens are generally not susceptible due to their protective outer membrane. Artilysins overcome this barrier. Artilysins are optimized, engineered fusions of selected endolysins with specific outer membrane-destabilizing peptides. Artilysin Art-175 comprises a modified variant of endolysin KZ144 with an N-terminal fusion to SMAP-29. Previously, we have shown the high susceptibility of Pseudomonas aeruginosa to Art-175. Here, we report that Art-175 is highly bactericidal against stationary-phase cells of multidrug-resistant Acinetobacter baumannii, even resulting in a complete elimination of large inocula (≥10(8) CFU/ml). Besides actively dividing cells, Art-175 also kills persisters. Instantaneous killing of A. baumannii upon contact with Art-175 could be visualized after immobilization of the bacteria in a microfluidic flow cell. Effective killing of a cell takes place through osmotic lysis after peptidoglycan degradation. The killing rate is enhanced by the addition of 0.5 mM EDTA. No development of resistance to Art-175 under selection pressure and no cross-resistance with existing resistance mechanisms could be observed. In conclusion, Art-175 represents a highly active Artilysin against both A. baumannii and P. aeruginosa, two of the most life-threatening pathogens of the order Pseudomonadales.
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Gerits E, Blommaert E, Lippell A, O’Neill AJ, Weytjens B, De Maeyer D, Fierro AC, Marchal K, Marchand A, Chaltin P, Spincemaille P, De Brucker K, Thevissen K, Cammue BPA, Swings T, Liebens V, Fauvart M, Verstraeten N, Michiels J. Elucidation of the Mode of Action of a New Antibacterial Compound Active against Staphylococcus aureus and Pseudomonas aeruginosa. PLoS One 2016; 11:e0155139. [PMID: 27167126 PMCID: PMC4864301 DOI: 10.1371/journal.pone.0155139] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 04/25/2016] [Indexed: 01/29/2023] Open
Abstract
Nosocomial and community-acquired infections caused by multidrug resistant bacteria represent a major human health problem. Thus, there is an urgent need for the development of antibiotics with new modes of action. In this study, we investigated the antibacterial characteristics and mode of action of a new antimicrobial compound, SPI031 (N-alkylated 3, 6-dihalogenocarbazol 1-(sec-butylamino)-3-(3,6-dichloro-9H-carbazol-9-yl)propan-2-ol), which was previously identified in our group. This compound exhibits broad-spectrum antibacterial activity, including activity against the human pathogens Staphylococcus aureus and Pseudomonas aeruginosa. We found that SPI031 has rapid bactericidal activity (7-log reduction within 30 min at 4x MIC) and that the frequency of resistance development against SPI031 is low. To elucidate the mode of action of SPI031, we performed a macromolecular synthesis assay, which showed that SPI031 causes non-specific inhibition of macromolecular biosynthesis pathways. Liposome leakage and membrane permeability studies revealed that SPI031 rapidly exerts membrane damage, which is likely the primary cause of its antibacterial activity. These findings were supported by a mutational analysis of SPI031-resistant mutants, a transcriptome analysis and the identification of transposon mutants with altered sensitivity to the compound. In conclusion, our results show that SPI031 exerts its antimicrobial activity by causing membrane damage, making it an interesting starting point for the development of new antibacterial therapies.
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Affiliation(s)
- Evelien Gerits
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Eline Blommaert
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Anna Lippell
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Alex J. O’Neill
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Bram Weytjens
- Department of Information Technology (INTEC, iMINDS), U.Ghent, Ghent, Belgium
| | - Dries De Maeyer
- Department of Information Technology (INTEC, iMINDS), U.Ghent, Ghent, Belgium
| | - Ana Carolina Fierro
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
- Department of Information Technology (INTEC, iMINDS), U.Ghent, Ghent, Belgium
| | - Kathleen Marchal
- Department of Information Technology (INTEC, iMINDS), U.Ghent, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, U.Ghent, Ghent, Belgium
| | - Arnaud Marchand
- CISTIM Leuven vzw, Bio-Incubator, KU Leuven, Leuven, Belgium
| | - Patrick Chaltin
- CISTIM Leuven vzw, Bio-Incubator, KU Leuven, Leuven, Belgium
- Centre for Drug Design and Discovery (CD3), Research and Development, KU Leuven, Leuven, Belgium
| | - Pieter Spincemaille
- Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
| | | | - Karin Thevissen
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Bruno P. A. Cammue
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
- Department of Plant Systems Biology, VIB, Ghent, Belgium
| | - Toon Swings
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Veerle Liebens
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Maarten Fauvart
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
- imec, Smart Systems and Emerging Technologies Unit, Department of Life Science Technologies, Leuven, Belgium
| | | | - Jan Michiels
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
- * E-mail:
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15
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Latino L, Midoux C, Hauck Y, Vergnaud G, Pourcel C. Pseudolysogeny and sequential mutations build multiresistance to virulent bacteriophages in Pseudomonas aeruginosa. MICROBIOLOGY-SGM 2016; 162:748-763. [PMID: 26921273 DOI: 10.1099/mic.0.000263] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Coevolution between bacteriophages (phages) and their prey is the result of mutualistic interactions. Here, we show that pseudolysogeny is a frequent outcome of infection by virulent phages of Pseudomonas aeruginosa and that selection of resistant bacterial mutants is favoured by continuous production of phages. We investigated the frequency and characteristics of P. aeruginosa strain PAO1 variants resisting infection by different combinations of virulent phages belonging to four genera. The frequency of resistant bacteria was 10- 5 for single phage infection and 10- 6 for infections with combinations of two or four phages. The genome of 27 variants was sequenced and the comparison with the genome of the parental PAO1 strain allowed the identification of point mutations or small indels. Four additional variants were characterized by a candidate gene approach. In total, 27 independent mutations were observed affecting 14 genes and a regulatory region. The mutations affected genes involved in biosynthesis of type IV pilus, alginate, LPS and O-antigen. Half of the variants possessed changes in homopolymer tracts responsible for frameshift mutations and these phase variation mutants were shown to be unstable. Eleven double mutants were detected. The presence of free phage DNA was observed in association with exclusion of superinfection in half of the variants and no chromosomal mutation could be found in three of them. Upon further growth of these pseudolysogens, some variants with new chromosomal mutations were recovered, presumably due to continuous evolutionary pressure.
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Affiliation(s)
- Libera Latino
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay,91198 Gif-sur-Yvette cedex,France
| | - Cédric Midoux
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay,91198 Gif-sur-Yvette cedex,France
| | - Yolande Hauck
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay,91198 Gif-sur-Yvette cedex,France
| | - Gilles Vergnaud
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay,91198 Gif-sur-Yvette cedex,France
| | - Christine Pourcel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay,91198 Gif-sur-Yvette cedex,France
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16
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Liebens V, Gerits E, Knapen WJ, Swings T, Beullens S, Steenackers HP, Robijns S, Lippell A, O'Neill AJ, Veber M, Fröhlich M, Krona A, Lövenklev M, Corbau R, Marchand A, Chaltin P, De Brucker K, Thevissen K, Cammue BP, Fauvart M, Verstraeten N, Michiels J. Identification and characterization of an anti-pseudomonal dichlorocarbazol derivative displaying anti-biofilm activity. Bioorg Med Chem Lett 2015; 24:5404-8. [PMID: 25453797 DOI: 10.1016/j.bmcl.2014.10.039] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 10/08/2014] [Accepted: 10/14/2014] [Indexed: 12/31/2022]
Abstract
Pseudomonas aeruginosa strains resistant towards all currently available antibiotics are increasingly encountered, raising the need for new anti-pseudomonal drugs. We therefore conducted a medium-throughput screen of a small-molecule collection resulting in the identification of the N-alkylated 3,6-dihalogenocarbazol 1-(sec-butylamino)-3-(3,6-dichloro-9H-carbazol-9-yl)propan-2-ol (MIC = 18.5 μg mL⁻¹). This compound, compound 1, is bacteriostatic towards a broad spectrum of Gram-positive and Gram-negative pathogens, including P. aeruginosa. Importantly, 1 also eradicates mature biofilms of P. aeruginosa. 1 displays no cytotoxicity against various human cell types, pointing to its potential for further development as a novel antibacterial drug.
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17
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Verstraeten N, Knapen W, Kint C, Liebens V, Van den Bergh B, Dewachter L, Michiels J, Fu Q, David C, Fierro A, Marchal K, Beirlant J, Versées W, Hofkens J, Jansen M, Fauvart M, Michiels J. Obg and Membrane Depolarization Are Part of a Microbial Bet-Hedging Strategy that Leads to Antibiotic Tolerance. Mol Cell 2015; 59:9-21. [DOI: 10.1016/j.molcel.2015.05.011] [Citation(s) in RCA: 170] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 03/20/2015] [Accepted: 05/01/2015] [Indexed: 10/25/2022]
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18
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Stepanyan K, Wenseleers T, Duéñez-Guzmán EA, Muratori F, Van den Bergh B, Verstraeten N, De Meester L, Verstrepen KJ, Fauvart M, Michiels J. Fitness trade-offs explain low levels of persister cells in the opportunistic pathogen Pseudomonas aeruginosa. Mol Ecol 2015; 24:1572-83. [PMID: 25721227 DOI: 10.1111/mec.13127] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2014] [Revised: 01/09/2015] [Accepted: 02/13/2015] [Indexed: 02/03/2023]
Abstract
Microbial populations often contain a fraction of slow-growing persister cells that withstand antibiotics and other stress factors. Current theoretical models predict that persistence levels should reflect a stable state in which the survival advantage of persisters under adverse conditions is balanced with the direct growth cost impaired under favourable growth conditions, caused by the nonreplication of persister cells. Based on this direct growth cost alone, however, it remains challenging to explain the observed low levels of persistence (<<1%) seen in the populations of many species. Here, we present data from the opportunistic human pathogen Pseudomonas aeruginosa that can explain this discrepancy by revealing various previously unknown costs of persistence. In particular, we show that in the absence of antibiotic stress, increased persistence is traded off against a lengthened lag phase as well as a reduced survival ability during stationary phase. We argue that these pleiotropic costs contribute to the very low proportions of persister cells observed among natural P. aeruginosa isolates (3 × 10(-8) -3 × 10(-4)) and that they can explain why strains with higher proportions of persister cells lose out very quickly in competition assays under favourable growth conditions, despite a negligible difference in maximal growth rate. We discuss how incorporating these trade-offs could lead to models that can better explain the evolution of persistence in nature and facilitate the rational design of alternative therapeutic strategies for treating infectious diseases.
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Affiliation(s)
- Kristine Stepanyan
- Centre of Microbial and Plant Genetics, KU Leuven - University of Leuven, Kasteelpark Arenberg 20 bus 2460, 3001 Leuven, Belgium
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