1
|
Krin E, Carvalho A, Lang M, Babosan A, Mazel D, Baharoglu Z. RavA-ViaA antibiotic response is linked to Cpx and Zra2 envelope stress systems in Vibrio cholerae. Microbiol Spectr 2023; 11:e0173023. [PMID: 37861314 PMCID: PMC10848872 DOI: 10.1128/spectrum.01730-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 09/08/2023] [Indexed: 10/21/2023] Open
Abstract
IMPORTANCE The RavA-ViaA complex was previously found to sensitize Escherichia coli to aminoglycosides (AGs) in anaerobic conditions, but the mechanism is unknown. AGs are antibiotics known for their high efficiency against Gram-negative bacteria. In order to elucidate how the expression of the ravA-viaA genes increases bacterial susceptibility to aminoglycosides, we aimed at identifying partner functions necessary for increased tolerance in the absence of RavA-ViaA, in Vibrio cholerae. We show that membrane stress response systems Cpx and Zra2 are required in the absence of RavA-ViaA, for the tolerance to AGs and for outer membrane integrity. In the absence of these systems, the ∆ravvia strain's membrane becomes permeable to external agents such as the antibiotic vancomycin.
Collapse
Affiliation(s)
- Evelyne Krin
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Paris, France
| | - André Carvalho
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Paris, France
- Sorbonne Université, Collège doctoral, Paris, France
| | - Manon Lang
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Paris, France
- Sorbonne Université, Collège doctoral, Paris, France
| | - Anamaria Babosan
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Paris, France
| | - Didier Mazel
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Paris, France
| | - Zeynep Baharoglu
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Paris, France
| |
Collapse
|
2
|
Babosan A, Fruchard L, Krin E, Carvalho A, Mazel D, Baharoglu Z. Nonessential tRNA and rRNA modifications impact the bacterial response to sub-MIC antibiotic stress. Microlife 2022; 3:uqac019. [PMID: 37223353 PMCID: PMC10117853 DOI: 10.1093/femsml/uqac019] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 09/12/2022] [Indexed: 05/25/2023]
Abstract
Antimicrobial resistance develops as a major problem in infectious diseases treatment. While antibiotic resistance mechanisms are usually studied using lethal antibiotic doses, lower doses allowing bacterial growth are now considered as factors influencing the development and selection of resistance. Starting with a high-density Tn insertion library in Vibrio cholerae and following its evolution by TN-seq in the presence of subinhibitory concentrations of antibiotics, we discovered that RNA modification genes can have opposite fates, being selected or counter-selected. We, thus have undertaken the phenotypic characterization of 23 transfer RNA (tRNA) and ribosomal RNA (rRNA) modifications deletion mutants, for which growth is globally not affected in the absence of stress. We uncover a specific involvement of different RNA modification genes in the response to aminoglycosides (tobramycin and gentamicin), fluoroquinolones (ciprofloxacin), β-lactams (carbenicillin), chloramphenicol, and trimethoprim. Our results identify t/rRNA modification genes, not previously associated to any antibiotic resistance phenotype, as important factors affecting the bacterial response to low doses of antibiotics from different families. This suggests differential translation and codon decoding as critical factors involved in the bacterial response to stress.
Collapse
Affiliation(s)
| | | | - Evelyne Krin
- Département Génomes et Génétique, Institut Pasteur, UMR3525, CNRS, Unité Plasticité du Génome Bactérien, 25 rue du Dr Roux 75015 Paris, France
| | - André Carvalho
- Département Génomes et Génétique, Institut Pasteur, UMR3525, CNRS, Unité Plasticité du Génome Bactérien, 25 rue du Dr Roux 75015 Paris, France
- Sorbonne Université, Collège Doctoral, F-75005 Paris, France
| | - Didier Mazel
- Corresponding author: Institut Pasteur, 25 rue du Dr Roux 75015 Paris. E-mail:
| | | |
Collapse
|
3
|
Babosan A, Gaschet M, Muggeo A, Jové T, Skurnik D, Ploy MC, de Champs C, Reffuveille F, Guillard T. A qnrD-Plasmid Promotes Biofilm Formation and Class 1 Integron Gene Cassette Rearrangements in Escherichia coli. Antibiotics (Basel) 2022; 11:antibiotics11060715. [PMID: 35740122 PMCID: PMC9220102 DOI: 10.3390/antibiotics11060715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 05/20/2022] [Accepted: 05/24/2022] [Indexed: 11/17/2022] Open
Abstract
Bacteria within biofilms may be exposed to sub-minimum inhibitory concentrations (sub-MICs) of antibiotics. Cell-to-cell contact within biofilms facilitates horizontal gene transfers and favors induction of the SOS response. Altogether, it participates in the emergence of antibiotic resistance. Aminoglycosides at sub-MICs can induce the SOS response through NO accumulation in E. coli carrying the small plasmid with the quinolone resistance qnrD gene (pDIJ09-518a). In this study, we show that in E. coli pDIJ09-518a, the SOS response triggered by sub-MICs of aminoglycosides has important consequences, promoting genetic rearrangement in class 1 integrons and biofilm formation. We found that the integrase expression was increased in E. coli carrying pDIJ09-518a in the presence of tobramycin, which was not observed for the WT isogenic strain that did not carry the qnrD-plasmid. Moreover, we showed that biofilm production was significantly increased in E. coli WT/pDIJ09-518a compared to the WT strain. However, such a higher production was decreased when the Hmp-NO detoxification pathway was fully functional by overexpressing Hmp. Our results showing that a qnrD-plasmid can promote biofilm formation in E. coli and potentiate the acquisition and spread of resistance determinants for other antibiotics complicate the attempts to counteract antibiotic resistance and prevention of biofilm development even further. We anticipate that our findings emphasize the complex challenges that will impact the decisions about antibiotic stewardship, and other decisions related to retaining antibiotics as effective drugs and the development of new drugs.
Collapse
Affiliation(s)
- Anamaria Babosan
- Inserm UMR-S 1250 P3Cell, SFR CAP-Santé, Université de Reims-Champagne-Ardenne, 51100 Reims, France; (A.B.); (A.M.); (C.d.C.)
| | - Margaux Gaschet
- Université de Limoges, Inserm, CHU Limoges, UMR-S 1092, 87032 Limoges, France; (M.G.); (T.J.); (M.-C.P.)
| | - Anaëlle Muggeo
- Inserm UMR-S 1250 P3Cell, SFR CAP-Santé, Université de Reims-Champagne-Ardenne, 51100 Reims, France; (A.B.); (A.M.); (C.d.C.)
- Laboratoire de Bactériologie-Virologie-Hygiène Hospitalière-Parasitologie-Mycologie, CHU Reims, Hôpital Robert Debré, Avenue du Général Koenig, CEDEX, 51092 Reims, France
| | - Thomas Jové
- Université de Limoges, Inserm, CHU Limoges, UMR-S 1092, 87032 Limoges, France; (M.G.); (T.J.); (M.-C.P.)
| | - David Skurnik
- Institut Necker-Enfants Malades, Inserm U1151-Equipe 11, Université Paris Descartes, 75015 Paris, France;
- Laboratoire de Bactériologie, AP-HP, Hôpital Necker-Enfants Malades, 75015 Paris, France
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Marie-Cécile Ploy
- Université de Limoges, Inserm, CHU Limoges, UMR-S 1092, 87032 Limoges, France; (M.G.); (T.J.); (M.-C.P.)
| | - Christophe de Champs
- Inserm UMR-S 1250 P3Cell, SFR CAP-Santé, Université de Reims-Champagne-Ardenne, 51100 Reims, France; (A.B.); (A.M.); (C.d.C.)
- Laboratoire de Bactériologie-Virologie-Hygiène Hospitalière-Parasitologie-Mycologie, CHU Reims, Hôpital Robert Debré, Avenue du Général Koenig, CEDEX, 51092 Reims, France
| | - Fany Reffuveille
- EA 4691 BiOS, SFR CAP-Santé, Université de Reims Champagne-Ardenne, 51100 Reims, France;
| | - Thomas Guillard
- Inserm UMR-S 1250 P3Cell, SFR CAP-Santé, Université de Reims-Champagne-Ardenne, 51100 Reims, France; (A.B.); (A.M.); (C.d.C.)
- Laboratoire de Bactériologie-Virologie-Hygiène Hospitalière-Parasitologie-Mycologie, CHU Reims, Hôpital Robert Debré, Avenue du Général Koenig, CEDEX, 51092 Reims, France
- Correspondence: ; Tel.: +33-3-26-78-32-10; Fax: +33-3-26-78-41
| |
Collapse
|
4
|
Babosan A, Skurnik D, Muggeo A, Pier G, Baharoglu Z, Jové T, Ploy MC, Griveau S, Bedioui F, Vergnolle S, Moussalih S, de Champs C, Mazel D, Guillard T. A qnr-plasmid allows aminoglycosides to induce SOS in Escherichia coli. eLife 2022; 11:69511. [PMID: 35037621 PMCID: PMC8789287 DOI: 10.7554/elife.69511] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 01/12/2022] [Indexed: 11/16/2022] Open
Abstract
The plasmid-mediated quinolone resistance (PMQR) genes have been shown to promote high-level bacterial resistance to fluoroquinolone antibiotics, potentially leading to clinical treatment failures. In Escherichia coli, sub-minimum inhibitory concentrations (sub-MICs) of the widely used fluoroquinolones are known to induce the SOS response. Interestingly, the expression of several PMQR qnr genes is controlled by the SOS master regulator, LexA. During the characterization of a small qnrD-plasmid carried in E. coli, we observed that the aminoglycosides become able to induce the SOS response in this species, thus leading to the elevated transcription of qnrD. Our findings show that the induction of the SOS response is due to nitric oxide (NO) accumulation in the presence of sub-MIC of aminoglycosides. We demonstrated that the NO accumulation is driven by two plasmid genes, ORF3 and ORF4, whose products act at two levels. ORF3 encodes a putative flavin adenine dinucleotide (FAD)-binding oxidoreductase which helps NO synthesis, while ORF4 codes for a putative fumarate and nitrate reductase (FNR)-type transcription factor, related to an O2-responsive regulator of hmp expression, able to repress the Hmp-mediated NO detoxification pathway of E. coli. Thus, this discovery, that other major classes of antibiotics may induce the SOS response could have worthwhile implications for antibiotic stewardship efforts in preventing the emergence of resistance.
Collapse
Affiliation(s)
- Anamaria Babosan
- Inserm UMR-S 1250 P3Cell, SFR CAP-Santé, Université de Reims-Champagne-Ardenne, Reims, France
| | - David Skurnik
- Institut Necker-Enfants Malades, Inserm U1151-Equipe 11, Université Paris Descartes, Paris, France
| | - Anaëlle Muggeo
- Inserm UMR-S 1250 P3Cell, SFR CAP-Santé, Université de Reims-Champagne-Ardenne, Reims, France
| | - Gerald Pier
- Department of Medicine, Brigham and Women's Hospital, Boston, United States
| | - Zeynep Baharoglu
- Unité Plasticité du Génome Bactérien, CNRS UMR3525, Institut Pasteur, Paris, France
| | - Thomas Jové
- CHU Limoges, RESINFIT, UMR 1092, Université de Limoges, Inserm, Limoges, France
| | - Marie-Cécile Ploy
- CHU Limoges, RESINFIT, UMR 1092, Université de Limoges, Inserm, Limoges, France
| | - Sophie Griveau
- Institute of Chemistry for Life and Health Sciences, PSL Research University, CNRS, Paris, France
| | - Fethi Bedioui
- Institute of Chemistry for Life and Health Sciences, PSL Research University, CNRS, Paris, France
| | | | - Sophie Moussalih
- Inserm UMR-S 1250 P3Cell, SFR CAP-Santé, Université de Reims-Champagne-Ardenne, Reims, France
| | - Christophe de Champs
- Inserm UMR-S 1250 P3Cell, SFR CAP-Santé, Université de Reims-Champagne-Ardenne, Reims, France
| | - Didier Mazel
- Unité Plasticité du Génome Bactérien, CNRS UMR3525, Institut Pasteur, Paris, France
| | - Thomas Guillard
- Inserm UMR-S 1250 P3Cell, SFR CAP-Santé, Université de Reims-Champagne-Ardenne, Reims, France
| |
Collapse
|
5
|
Baharoglu Z, Babosan A, Mazel D. Identification of genes involved in low aminoglycoside-induced SOS response in Vibrio cholerae: a role for transcription stalling and Mfd helicase. Nucleic Acids Res 2013; 42:2366-79. [PMID: 24319148 PMCID: PMC3936754 DOI: 10.1093/nar/gkt1259] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Sub-inhibitory concentrations (sub-MIC) of antibiotics play a very important role in selection and development of resistances. Unlike Escherichia coli, Vibrio cholerae induces its SOS response in presence of sub-MIC aminoglycosides. A role for oxidized guanine residues was observed, but the mechanisms of this induction remained unclear. To select for V. cholerae mutants that do not induce low aminoglycoside-mediated SOS induction, we developed a genetic screen that renders induction of SOS lethal. We identified genes involved in this pathway using two strategies, inactivation by transposition and gene overexpression. Interestingly, we obtained mutants inactivated for the expression of proteins known to destabilize the RNA polymerase complex. Reconstruction of the corresponding mutants confirmed their specific involvement in induction of SOS by low aminoglycoside concentrations. We propose that DNA lesions formed on aminoglycoside treatment are repaired through the formation of single-stranded DNA intermediates, inducing SOS. Inactivation of functions that dislodge RNA polymerase leads to prolonged stalling on these lesions, which hampers SOS induction and repair and reduces viability under antibiotic stress. The importance of these mechanisms is illustrated by a reduction of aminoglycoside sub-MIC. Our results point to a central role for transcription blocking at DNA lesions in SOS induction, so far underestimated.
Collapse
Affiliation(s)
- Zeynep Baharoglu
- Département Génomes et Génétique, Unité Plasticité du Génome Bactérien, Institut Pasteur, 75015 Paris, France and Centre National de la Recherche Scientifique, CNRS, UMR3525 Paris, France
| | | | | |
Collapse
|