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Kloula Ben Ghorbal S, Dhaya I, Ouzari IH, Chatti A. Cyclopropanation and membrane unsaturation improve antibiotic resistance of swarmer Pseudomonas and its sod mutants exposed to radiations, in vitro and in silico approch. World J Microbiol Biotechnol 2024; 40:243. [PMID: 38869625 DOI: 10.1007/s11274-024-04033-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 05/22/2024] [Indexed: 06/14/2024]
Abstract
It was known that UVc irradiation increases the reactive oxygen species' (ROS) levels in bacteria hence the intervention of antioxidant enzymes and causes also changes in fatty acids (FAs) composition enabling bacteria to face antibiotics. Here, we intended to elucidate an interrelationship between SOD and susceptibility to antibiotics by studying FA membrane composition of UVc-treated P. aeruginosa PAO1 and its isogenic mutants (sodM, sodB and sod MB) membrane, after treatment with antibiotics. Swarmer mutants defective in genes encoding superoxide dismutase were pre-exposed to UVc radiations and then tested by disk diffusion method for their contribution to antibiotic tolerance in comparison with the P. aeruginosa wild type (WT). Moreover, fatty acid composition of untreated and UVc-treated WT and sod mutants was examined by Gaz chromatography and correlated to antibiotic resistance. Firstly, it has been demonstrated that after UVc exposure, swarmer WT strain, sodM and sodB mutants remain resistant to polymixin B, a membrane target antibiotic, through membrane unsaturation supported by the intervention of Mn-SOD after short UVc exposure and cyclopropanation of unsaturated FAs supported by the action of Fe-SOD after longer UVc exposure. However, resistance for ciprofloxacin is correlated with increase in saturated FAs. This correlation has been confirmed by a molecular docking approach showing that biotin carboxylase, involved in the initial stage of FA biosynthesis, exhibits a high affinity for ciprofloxacin. This investigation has explored the correlation of antibiotic resistance with FA content of swarmer P.aeruginosa pre-exposed to UVc radiations, confirmed to be antibiotic target dependant.
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Affiliation(s)
- Salma Kloula Ben Ghorbal
- Laboratoire de Traitement des Eaux Usées, Centre de Recherches et Technologies des Eaux Usées, Technopole Borj Cedria, BP 273, 8020, Soliman, Tunisia.
| | - Ibtihel Dhaya
- LR18ES03- Laboratory of Neurophysiology Cellular Physiopathology and Biomolecules Valorization, University of Tunis El Manar, Tunis, Tunisia
| | - Imene-Hadda Ouzari
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Physiques et Naturelles de Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Abdelwaheb Chatti
- Laboratoire de Traitement des Eaux Usées, Centre de Recherches et Technologies des Eaux Usées, Technopole Borj Cedria, BP 273, 8020, Soliman, Tunisia
- Unite de Biochimie des Lipides et Interactions des Macromolécules en Biologie (03/UR/0902), Laboratoire de Biochimie et Biologie Moléculaire, Faculté des Sciences de Bizerte, Zarzouna, 7021, Bizerte, Tunisia
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2
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Roy RK, Patra N. Probing the pH Sensitivity of OprM: Insights into Metastable States and Semi-Open Conformation. J Phys Chem B 2024; 128:622-634. [PMID: 38047375 DOI: 10.1021/acs.jpcb.3c05384] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Efflux pumps are specialized transport proteins that play a key role in the bacterial defense against a wide spectrum of antibiotics. Hence, understanding the biophysical mechanism associated with this complex system of drug expulsion becomes crucial. This work deals with some vital aspects of the outer membrane factor (OMF) of MexAB-OprM. After being passed through MexB and MexA, efflux substrates have to go through OprM for their final judgment. Thus, it is very important to understand the periplasmic pore opening mechanism and the associated biophysical changes during this process. Our study captures a detailed analysis of the pore opening mechanism involving OprM. With powerful molecular dynamics (MD) techniques such as well-tempered metadynamics, the presence of metastable states in between open and closed states was confirmed. Also, upon mutating R376, the energy barrier for the conversion of the close to open conformation decreases, indicating an important role played by the residue. Further, constant pH MD was performed to capture the effect of pH in both conformations. OprM exhibits distinct conformational states at pH values greater than 5.5 and lower than 5.5, suggesting its pH-responsive characteristics. Overall, our study elucidates a crucial undertaking toward discovering potential inhibitors for MexAB-OprM efflux pumps.
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Affiliation(s)
- Rakesh Kumar Roy
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (ISM) Dhanbad, Dhanbad 826004, India
| | - Niladri Patra
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (ISM) Dhanbad, Dhanbad 826004, India
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3
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Adrien V, Reffay M, Taulier N, Verchère A, Monlezun L, Picard M, Ducruix A, Broutin I, Pincet F, Urbach W. Kinetic study of membrane protein interactions: from three to two dimensions. Sci Rep 2024; 14:882. [PMID: 38195620 PMCID: PMC10776792 DOI: 10.1038/s41598-023-50827-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 12/26/2023] [Indexed: 01/11/2024] Open
Abstract
Molecular interactions are contingent upon the system's dimensionality. Notably, comprehending the impact of dimensionality on protein-protein interactions holds paramount importance in foreseeing protein behaviour across diverse scenarios, encompassing both solution and membrane environments. Here, we unravel interactions among membrane proteins across various dimensionalities by quantifying their binding rates through fluorescence recovery experiments. Our findings are presented through the examination of two protein systems: streptavidin-biotin and a protein complex constituting a bacterial efflux pump. We present here an original approach for gauging a two-dimensional binding constant between membrane proteins embedded in two opposite membranes. The quotient of protein binding rates in solution and on the membrane represents a metric denoting the exploration distance of the interacting sites-a novel interpretation.
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Affiliation(s)
- Vladimir Adrien
- Laboratoire de Physique de l'École normale superieure, École Normale Supérieure, Université Paris Sciences et Lettres, CNRS, Sorbonne Université, Université Paris Cité, F-75005, Paris, France.
- Department of Infectious Diseases, Avicenne Hospital, AP-HP, Université Sorbonne Paris Nord, Bobigny, France.
- Université Paris Cité, Inserm UMR-S 1266, Institute of Psychiatry and Neuroscience of Paris (IPNP), Paris, France.
| | - Myriam Reffay
- Laboratoire Matière et Systèmes Complexes, UMR 7057, CNRS and Université de Paris Cité, 75205, Paris Cedex 13, France
| | - Nicolas Taulier
- Sorbonne Université, CNRS, INSERM, Laboratoire d'Imagerie Biomédicale-LIB, 75006, Paris, France
| | - Alice Verchère
- Laboratoire CiTCoM, Faculté de Santé, Université Paris Cité, CNRS, 75006, Paris, France
| | - Laura Monlezun
- Université Paris Cité, CNRS, Expression Génétique Microbienne, Institut de Biologie Physico-Chimique, Paris, France
| | - Martin Picard
- Université Paris Cité, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires CNRS UMR7099, 75005, Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 75005, Paris, France
| | - Arnaud Ducruix
- Laboratoire CiTCoM, Faculté de Santé, Université Paris Cité, CNRS, 75006, Paris, France
| | - Isabelle Broutin
- Laboratoire CiTCoM, Faculté de Santé, Université Paris Cité, CNRS, 75006, Paris, France
| | - Frédéric Pincet
- Laboratoire de Physique de l'École normale superieure, École Normale Supérieure, Université Paris Sciences et Lettres, CNRS, Sorbonne Université, Université Paris Cité, F-75005, Paris, France.
| | - Wladimir Urbach
- Laboratoire de Physique de l'École normale superieure, École Normale Supérieure, Université Paris Sciences et Lettres, CNRS, Sorbonne Université, Université Paris Cité, F-75005, Paris, France.
- Sorbonne Université, CNRS, INSERM, Laboratoire d'Imagerie Biomédicale-LIB, 75006, Paris, France.
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4
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Dwivedi GR, Rai R, Pratap R, Singh K, Pati S, Sahu SN, Kant R, Darokar MP, Yadav DK. Drug resistance reversal potential of multifunctional thieno[3,2-c]pyran via potentiation of antibiotics in MDR P. aeruginosa. Biomed Pharmacother 2021; 142:112084. [PMID: 34449308 DOI: 10.1016/j.biopha.2021.112084] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 08/17/2021] [Indexed: 10/20/2022] Open
Abstract
We explored the antibacterial potential (alone and combination) against multidrug resistant (MDR) Pseudomonas aeruginosa isolates KG-P2 using synthesized thieno[3,2-c]pyran-2-ones in combination with different antibiotics. Out of 14 compounds, two compounds (3g and 3l) abridged the MIC of tetracycline (TET) by 16 folds. Compounds was killing the KG-P2 cells, in time dependent manner, lengthened post-antibiotic effect (PAE) of TET and found decreased the mutant prevention concentration (MPC) of TET. In ethidium bromide efflux experiment, two compounds repressed the drug transporter (efflux pumps) which is further supported by molecular docking of these compounds with efflux complex MexAB-OprM. In another study, these compounds inhibited the synthesis of biofilm.
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Affiliation(s)
- Gaurav Raj Dwivedi
- Microbiology Department, ICMR-Regional Medical Research Centre, BRD Medical College Campus, Gorakhpur 273013, India.
| | - Reeta Rai
- Department of Biochemistry, AIIMS Ansari Nagar, New Delhi 110029, India
| | - Ramendra Pratap
- Department of Chemistry, North campus University of Delhi, Delhi 110007, India.
| | - Khusbu Singh
- Microbiology Department, ICMR-Regional Medical Research Centre, Bhubaneshwar 751023, Odisha, India
| | - Sanghamitra Pati
- Microbiology Department, ICMR-Regional Medical Research Centre, Bhubaneshwar 751023, Odisha, India
| | - Satya Narayan Sahu
- Government College Balrampur, Balrampur-Ramanujganj, Chhattisgarh 497119, India
| | - Rajni Kant
- Microbiology Department, ICMR-Regional Medical Research Centre, BRD Medical College Campus, Gorakhpur 273013, India
| | - Mahendra P Darokar
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, ̥Near Kukrail Picnic Spot, P.O. CIMAP, Lucknow 226015, India
| | - Dharmendra K Yadav
- Gachon Institute of Pharmaceutical Science and Department of Pharmacy, College of Pharmacy, Gachon University, 191 Hambakmoeiro, Yeonsu-gu, Incheon 21924, Republic of Korea.
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5
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MexAB-OprM Efflux Pump Interaction with the Peptidoglycan of Escherichia coli and Pseudomonas aeruginosa. Int J Mol Sci 2021; 22:ijms22105328. [PMID: 34070225 PMCID: PMC8158685 DOI: 10.3390/ijms22105328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 11/17/2022] Open
Abstract
One of the major families of membrane proteins found in prokaryote genome corresponds to the transporters. Among them, the resistance-nodulation-cell division (RND) transporters are highly studied, as being responsible for one of the most problematic mechanisms used by bacteria to resist to antibiotics, i.e., the active efflux of drugs. In Gram-negative bacteria, these proteins are inserted in the inner membrane and form a tripartite assembly with an outer membrane factor and a periplasmic linker in order to cross the two membranes to expulse molecules outside of the cell. A lot of information has been collected to understand the functional mechanism of these pumps, especially with AcrAB-TolC from Escherichia coli, but one missing piece from all the suggested models is the role of peptidoglycan in the assembly. Here, by pull-down experiments with purified peptidoglycans, we precise the MexAB-OprM interaction with the peptidoglycan from Escherichia coli and Pseudomonas aeruginosa, highlighting a role of the peptidoglycan in stabilizing the MexA-OprM complex and also differences between the two Gram-negative bacteria peptidoglycans.
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6
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Alav I, Kobylka J, Kuth MS, Pos KM, Picard M, Blair JMA, Bavro VN. Structure, Assembly, and Function of Tripartite Efflux and Type 1 Secretion Systems in Gram-Negative Bacteria. Chem Rev 2021; 121:5479-5596. [PMID: 33909410 PMCID: PMC8277102 DOI: 10.1021/acs.chemrev.1c00055] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Indexed: 12/11/2022]
Abstract
Tripartite efflux pumps and the related type 1 secretion systems (T1SSs) in Gram-negative organisms are diverse in function, energization, and structural organization. They form continuous conduits spanning both the inner and the outer membrane and are composed of three principal components-the energized inner membrane transporters (belonging to ABC, RND, and MFS families), the outer membrane factor channel-like proteins, and linking the two, the periplasmic adaptor proteins (PAPs), also known as the membrane fusion proteins (MFPs). In this review we summarize the recent advances in understanding of structural biology, function, and regulation of these systems, highlighting the previously undescribed role of PAPs in providing a common architectural scaffold across diverse families of transporters. Despite being built from a limited number of basic structural domains, these complexes present a staggering variety of architectures. While key insights have been derived from the RND transporter systems, a closer inspection of the operation and structural organization of different tripartite systems reveals unexpected analogies between them, including those formed around MFS- and ATP-driven transporters, suggesting that they operate around basic common principles. Based on that we are proposing a new integrated model of PAP-mediated communication within the conformational cycling of tripartite systems, which could be expanded to other types of assemblies.
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Affiliation(s)
- Ilyas Alav
- Institute
of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Jessica Kobylka
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Miriam S. Kuth
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Klaas M. Pos
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Martin Picard
- Laboratoire
de Biologie Physico-Chimique des Protéines Membranaires, CNRS
UMR 7099, Université de Paris, 75005 Paris, France
- Fondation
Edmond de Rothschild pour le développement de la recherche
Scientifique, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Jessica M. A. Blair
- Institute
of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Vassiliy N. Bavro
- School
of Life Sciences, University of Essex, Colchester, CO4 3SQ United Kingdom
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7
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Marshall RL, Bavro VN. Mutations in the TolC Periplasmic Domain Affect Substrate Specificity of the AcrAB-TolC Pump. Front Mol Biosci 2020; 7:166. [PMID: 32850959 PMCID: PMC7396618 DOI: 10.3389/fmolb.2020.00166] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 07/01/2020] [Indexed: 01/08/2023] Open
Abstract
TolC and the other members of the outer membrane factor (OMF) family are outer membrane proteins forming trimeric channels that serve as a conduit for most actively effluxed substrates in Gram-negative bacteria by providing a key component in a multitude of tripartite efflux-pumps. Current models of tripartite pump assembly ascribe substrate selection to the inner-membrane transporter and periplasmic-adapter protein (PAP) assembly, suggesting that TolC is a passive, non-selective channel. While the membrane-embedded portion of the protein adopts a porin-like fold, the periplasmic domain of TolC presents a unique "alpha-barrel" architecture. This alpha-barrel consists of pseudo-continuous α-helices forming curved coiled-coils, whose tips form α-helical hairpins, relaxation of which results in a transition of TolC from a closed to an open-aperture state allowing effective efflux of substrates through its channel. Here, we analyzed the effects of site-directed mutations targeting the alpha-barrel of TolC, of the principal tripartite efflux-pump Escherichia coli AcrAB-TolC, on the activity and specificity of efflux. Live-cell functional assays with these TolC mutants revealed that positions both at the periplasmic tip of, and partway up the TolC coiled-coil alpha-barrel domain are involved in determining the functionality of the complex. We report that mutations affecting the electrostatic properties of the channel, particularly the D371V mutation, significantly impact growth even in the absence of antibiotics, causing hyper-susceptibility to all tested efflux-substrates. These results suggest that inhibition of TolC functionality is less well-tolerated than deletion of tolC, and such inhibition may have an antibacterial effect. Significantly and unexpectedly, we identified antibiotic-specific phenotypes associated with novel TolC mutations, suggesting that substrate specificity may not be determined solely by the transporter protein or the PAP, but may reside at least partially with the TolC-channel. Furthermore, some of the effects of mutations are difficult to reconcile with the currently prevalent tip-to-tip model of PAP-TolC interaction due to their location higher-up on the TolC alpha-barrel relative to the proposed PAP-docking sites. Taken together our results suggest a possible new role for TolC in vetting of efflux substrates, alongside its established role in tripartite complex assembly.
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Affiliation(s)
- Robert L. Marshall
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Vassiliy N. Bavro
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
- School of Life Sciences, University of Essex, Colchester, United Kingdom
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Sabeti Azad M, Okuda M, Cyrenne M, Bourge M, Heck MP, Yoshizawa S, Fourmy D. Fluorescent Aminoglycoside Antibiotics and Methods for Accurately Monitoring Uptake by Bacteria. ACS Infect Dis 2020; 6:1008-1017. [PMID: 32195576 DOI: 10.1021/acsinfecdis.9b00421] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Characterizing how multidrug-resistant bacteria circumvent the action of clinically used or novel antibiotics requires a detailed understanding of how the antibiotics interact with and cross bacterial membranes to accumulate in the cells and exert their action. When monitoring the interactions of drugs with bacteria, it remains challenging to differentiate functionally relevant internalized drug levels from nonspecific binding. Fluorescence is a method of choice for observing dynamics of biomolecules. In order to facilitate studies involving aminoglycoside antibiotics, we have generated fluorescently labeled aminoglycoside derivatives with uptake and bactericidal activities similar, albeit with a moderate loss, to those of the parent drug. The method combines fluorescence microscopy with fluorescence-activated cell sorting (FACS) using neomycin coupled to nonpermeable cyanine dyes. Fluorescence imaging allowed membrane-bound antibiotic to be distinguished from molecules in the cytoplasm. Patterns of uptake were assigned to different populations in the FACS analysis. Our study illustrates how fluorescent derivatives of an aminoglycoside enable a robust characterization of the three components of uptake: membrane binding, EDPI, and EDPII. Because EDPI levels are weak compared to the two other types of accumulation and critical for the action of these drugs, the three components of uptake must be taken into account separately when drawing conclusions about aminoglycoside function.
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Affiliation(s)
- Mahnaz Sabeti Azad
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Maho Okuda
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Mélina Cyrenne
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Mickael Bourge
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Marie-Pierre Heck
- Université Paris-Saclay, CEA, Service de Chimie Bio-organique et de Marquage, 91191 Gif-sur-Yvette, France
| | - Satoko Yoshizawa
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Dominique Fourmy
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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9
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Gaviard C, Jouenne T, Hardouin J. Proteomics ofPseudomonas aeruginosa: the increasing role of post-translational modifications. Expert Rev Proteomics 2018; 15:757-772. [DOI: 10.1080/14789450.2018.1516550] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Charlotte Gaviard
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, PBS, 76000, Rouen, France
- PISSARO proteomic facility, IRIB, 76821 Mont-Saint-Aignan, France
| | - Thierry Jouenne
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, PBS, 76000, Rouen, France
- PISSARO proteomic facility, IRIB, 76821 Mont-Saint-Aignan, France
| | - Julie Hardouin
- Normandie Univ, UNIROUEN, INSA Rouen, CNRS, PBS, 76000, Rouen, France
- PISSARO proteomic facility, IRIB, 76821 Mont-Saint-Aignan, France
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10
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Housseini B Issa K, Phan G, Broutin I. Functional Mechanism of the Efflux Pumps Transcription Regulators From Pseudomonas aeruginosa Based on 3D Structures. Front Mol Biosci 2018; 5:57. [PMID: 29971236 PMCID: PMC6018408 DOI: 10.3389/fmolb.2018.00057] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/31/2018] [Indexed: 01/19/2023] Open
Abstract
Bacterial antibiotic resistance is a worldwide health problem that deserves important research attention in order to develop new therapeutic strategies. Recently, the World Health Organization (WHO) classified Pseudomonas aeruginosa as one of the priority bacteria for which new antibiotics are urgently needed. In this opportunistic pathogen, antibiotics efflux is one of the most prevalent mechanisms where the drug is efficiently expulsed through the cell-wall. This resistance mechanism is highly correlated to the expression level of efflux pumps of the resistance-nodulation-cell division (RND) family, which is finely tuned by gene regulators. Thus, it is worthwhile considering the efflux pump regulators of P. aeruginosa as promising therapeutical targets alternative. Several families of regulators have been identified, including activators and repressors that control the genetic expression of the pumps in response to an extracellular signal, such as the presence of the antibiotic or other environmental modifications. In this review, based on different crystallographic structures solved from archetypal bacteria, we will first focus on the molecular mechanism of the regulator families involved in the RND efflux pump expression in P. aeruginosa, which are TetR, LysR, MarR, AraC, and the two-components system (TCS). Finally, the regulators of known structure from P. aeruginosa will be presented.
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Affiliation(s)
- Karim Housseini B Issa
- Laboratoire de Cristallographie et RMN Biologiques (UMR 8015), Centre National de la Recherche Scientifique, Faculté de Pharmacie, Université Paris Descartes, Université Sorbonne Paris Cité, Paris, France
| | - Gilles Phan
- Laboratoire de Cristallographie et RMN Biologiques (UMR 8015), Centre National de la Recherche Scientifique, Faculté de Pharmacie, Université Paris Descartes, Université Sorbonne Paris Cité, Paris, France
| | - Isabelle Broutin
- Laboratoire de Cristallographie et RMN Biologiques (UMR 8015), Centre National de la Recherche Scientifique, Faculté de Pharmacie, Université Paris Descartes, Université Sorbonne Paris Cité, Paris, France
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11
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Dwivedi GR, Tyagi R, Sanchita, Tripathi S, Pati S, Srivastava SK, Darokar MP, Sharma A. Antibiotics potentiating potential of catharanthine against superbug Pseudomonas aeruginosa. J Biomol Struct Dyn 2018; 36:4270-4284. [DOI: 10.1080/07391102.2017.1413424] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Gaurav Raj Dwivedi
- Microbiology Department, ICMR-Regional Medical Research Centre Bhubaneswar, Bhubaneswar 751023, Odisha, India
| | - Rekha Tyagi
- Medicinal Chemistry Department, Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), P.O.- CIMAP, Lucknow 226015, India
| | - Sanchita
- Biotechnology Division, Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), P.O.- CIMAP, Lucknow 226015, India
| | - Shubhandra Tripathi
- Biotechnology Division, Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), P.O.- CIMAP, Lucknow 226015, India
| | - Sanghamitra Pati
- Microbiology Department, ICMR-Regional Medical Research Centre Bhubaneswar, Bhubaneswar 751023, Odisha, India
| | - Santosh K. Srivastava
- Medicinal Chemistry Department, Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), P.O.- CIMAP, Lucknow 226015, India
| | - Mahendra P. Darokar
- Biotechnology Division, Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), P.O.- CIMAP, Lucknow 226015, India
| | - Ashok Sharma
- Biotechnology Division, Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), P.O.- CIMAP, Lucknow 226015, India
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12
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López CA, Travers T, Pos KM, Zgurskaya HI, Gnanakaran S. Dynamics of Intact MexAB-OprM Efflux Pump: Focusing on the MexA-OprM Interface. Sci Rep 2017; 7:16521. [PMID: 29184094 PMCID: PMC5705723 DOI: 10.1038/s41598-017-16497-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 10/30/2017] [Indexed: 11/30/2022] Open
Abstract
Antibiotic efflux is one of the most critical mechanisms leading to bacterial multidrug resistance. Antibiotics are effluxed out of the bacterial cell by a tripartite efflux pump, a complex machinery comprised of outer membrane, periplasmic adaptor, and inner membrane protein components. Understanding the mechanism of efflux pump assembly and its dynamics could facilitate discovery of novel approaches to counteract antibiotic resistance in bacteria. We built here an intact atomistic model of the Pseudomonas aeruginosa MexAB-OprM pump in a Gram-negative membrane model that contained both inner and outer membranes separated by a periplasmic space. All-atom molecular dynamics (MD) simulations confirm that the fully assembled pump is stable in the microsecond timescale. Using a combination of all-atom and coarse-grained MD simulations and sequence covariation analysis, we characterized the interface between MexA and OprM in the context of the entire efflux pump. These analyses suggest a plausible mechanism by which OprM is activated via opening of its periplasmic aperture through a concerted interaction with MexA.
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Affiliation(s)
- Cesar A López
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, United States
| | - Timothy Travers
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, United States.,Center for Nonlinear Sciences, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, United States
| | - Klaas M Pos
- Institute of Biochemistry, Goethe University, Frankfurt am Main, Germany.,Cluster of Excellence Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma, 73019, United States
| | - S Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, United States.
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Yonehara R, Yamashita E, Nakagawa A. Crystal structures of OprN and OprJ, outer membrane factors of multidrug tripartite efflux pumps of P
seudomonas aeruginosa. Proteins 2016; 84:759-69. [DOI: 10.1002/prot.25022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 02/10/2016] [Accepted: 02/11/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Ryo Yonehara
- Institute for Protein Research, Osaka University; Suita Japan
| | - Eiki Yamashita
- Institute for Protein Research, Osaka University; Suita Japan
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14
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Focus on the Outer Membrane Factor OprM, the Forgotten Player from Efflux Pumps Assemblies. Antibiotics (Basel) 2015; 4:544-66. [PMID: 27025640 PMCID: PMC4790312 DOI: 10.3390/antibiotics4040544] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 10/26/2015] [Accepted: 11/02/2015] [Indexed: 12/14/2022] Open
Abstract
Antibiotics have been used extensively during several decades and we are now facing the emergence of multidrug resistant strains. It has become a major public concern, urging the need to discover new strategies to combat them. Among the different ways used by bacteria to resist antibiotics, the active efflux is one of the main mechanisms. In Gram-negative bacteria the efflux pumps are comprised of three components forming a long edifice crossing the complete cell wall from the inside to the outside of the cell. Blocking these pumps would permit the restoration of the effectiveness of the current antibiotherapy which is why it is important to increase our knowledge on the different proteins involved in these complexes. A tremendous number of experiments have been performed on the inner membrane protein AcrB from Escherichia coli and, to a lesser extent, the protein partners forming the AcrAB-TolC pump, but less information is available concerning the efflux pumps from other virulent Gram-negative bacteria. The present review will focus on the OprM outer membrane protein from the MexAB-OprM pump of Pseudomonas aeruginosa, highlighting similarities and differences compare to the archetypal AcrAB-TolC in terms of structure, function, and assembly properties.
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