1
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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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2
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Newman KE, Khalid S. Conformational dynamics and putative substrate extrusion pathways of the N-glycosylated outer membrane factor CmeC from Campylobacter jejuni. PLoS Comput Biol 2023; 19:e1010841. [PMID: 36638139 PMCID: PMC9879487 DOI: 10.1371/journal.pcbi.1010841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 01/26/2023] [Accepted: 12/26/2022] [Indexed: 01/14/2023] Open
Abstract
The outer membrane factor CmeC of the efflux machinery CmeABC plays an important role in conferring antibiotic and bile resistance to Campylobacter jejuni. Curiously, the protein is N-glycosylated, with the glycans playing a key role in the effective function of this system. In this work we have employed atomistic equilibrium molecular dynamics simulations of CmeC in a representative model of the C. jejuni outer membrane to characterise the dynamics of the protein and its associated glycans. We show that the glycans are more conformationally labile than had previously been thought. The extracellular loops of CmeC visit the open and closed states freely suggesting the absence of a gating mechanism on this side, while the narrow periplasmic entrance remains tightly closed, regulated via coordination to solvated cations. We identify several cation binding sites on the interior surface of the protein. Additionally, we used steered molecular dynamics simulations to elucidate translocation pathways for a bile acid and a macrolide antibiotic. These, and additional equilibrium simulations suggest that the anionic bile acid utilises multivalent cations to climb the ladder of acidic residues that line the interior surface of the protein.
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Affiliation(s)
- Kahlan E. Newman
- School of Chemistry, University of Southampton, Southampton, United Kingdom
| | - Syma Khalid
- School of Chemistry, University of Southampton, Southampton, United Kingdom
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- * E-mail:
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3
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Hodges FJ, Torres VVL, Cunningham AF, Henderson IR, Icke C. Redefining the bacterial Type I protein secretion system. Adv Microb Physiol 2023; 82:155-204. [PMID: 36948654 DOI: 10.1016/bs.ampbs.2022.10.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Type I secretion systems (T1SS) are versatile molecular machines for protein transport across the Gram-negative cell envelope. The archetypal Type I system mediates secretion of the Escherichia coli hemolysin, HlyA. This system has remained the pre-eminent model of T1SS research since its discovery. The classic description of a T1SS is composed of three proteins: an inner membrane ABC transporter, a periplasmic adaptor protein and an outer membrane factor. According to this model, these components assemble to form a continuous channel across the cell envelope, an unfolded substrate molecule is then transported in a one-step mechanism, directly from the cytosol to the extracellular milieu. However, this model does not encapsulate the diversity of T1SS that have been characterized to date. In this review, we provide an updated definition of a T1SS, and propose the subdivision of this system into five subgroups. These subgroups are categorized as T1SSa for RTX proteins, T1SSb for non-RTX Ca2+-binding proteins, T1SSc for non-RTX proteins, T1SSd for class II microcins, and T1SSe for lipoprotein secretion. Although often overlooked in the literature, these alternative mechanisms of Type I protein secretion offer many avenues for biotechnological discovery and application.
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Affiliation(s)
- Freya J Hodges
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Von Vergel L Torres
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Adam F Cunningham
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Ian R Henderson
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia.
| | - Christopher Icke
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia.
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4
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Khan Z, Elahi A, Bukhari DA, Rehman A. Cadmium sources, toxicity, resistance and removal by microorganisms-A potential strategy for cadmium eradication. JOURNAL OF SAUDI CHEMICAL SOCIETY 2022. [DOI: 10.1016/j.jscs.2022.101569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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5
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Jeyaraj EJ, Nathan S, Lim YY, Choo WS. Antibiofilm properties of Clitoria ternatea flower anthocyanin-rich fraction towards Pseudomonas aeruginosa. Access Microbiol 2022; 4:000343. [PMID: 35812712 PMCID: PMC9260092 DOI: 10.1099/acmi.0.000343] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 02/14/2022] [Indexed: 11/18/2022] Open
Abstract
In Asia, Clitoria ternatea flowers are commonly used as a traditional medicinal herb and as a food colourant. Their bioactive compounds have anti-inflammatory, anti-microbial and anti-biofilm activities.
Pseudomonas aeruginosa
is one of the major pathogens that cause biofilm-associated infections resulting in an increase in antimicrobial resistance. Hence, the aim of this study was to investigate if the anti-biofilm properties of the anthocyanin-rich fraction of C. ternatea flowers were effective against
P. aeruginosa
. The effect of the anthocyanin-rich fraction of C. ternatea flowers on
P. aeruginosa
biofilms formed on a polystyrene surface was determined using the crystal violet assay and scanning electron microscopy (SEM). The anthocyanin-rich fraction reduced biofilm formation by four
P. aeruginosa
strains with a minimum biofilm inhibitory concentration value ranging between 0.625 and 5.0 mg ml−1. We further show that the biofilm-inhibiting activity of C. ternatea flowers is not due to the flavonols but is instead attributed to the anthocyanins, which had significant biofilm inhibitory activity (64.0±1.1 %) at 24 h in a time–response study. The anthocyanin-rich fraction also significantly reduced bacterial attachment on the polystyrene by 1.1 log c.f.u. cm−2 surface based on SEM analysis. Hence, anthocyanins from C. ternatea flowers have potential as an agent to decrease the risk of biofilm-associated infections.
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Affiliation(s)
- Ethel Jeyaseela Jeyaraj
- Tropical Medicine and Biology Platform, Monash University, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor, Malaysia
- School of Science, Monash University, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor, Malaysia
| | - Sheila Nathan
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
| | - Yau Yan Lim
- School of Science, Monash University, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor, Malaysia
| | - Wee Sim Choo
- School of Science, Monash University, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor, Malaysia
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6
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Stephen J, Lekshmi M, Ammini P, Kumar SH, Varela MF. Membrane Efflux Pumps of Pathogenic Vibrio Species: Role in Antimicrobial Resistance and Virulence. Microorganisms 2022; 10:microorganisms10020382. [PMID: 35208837 PMCID: PMC8875612 DOI: 10.3390/microorganisms10020382] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/15/2022] [Accepted: 01/23/2022] [Indexed: 02/06/2023] Open
Abstract
Infectious diseases caused by bacterial species of the Vibrio genus have had considerable significance upon human health for centuries. V. cholerae is the causative microbial agent of cholera, a severe ailment characterized by profuse watery diarrhea, a condition associated with epidemics, and seven great historical pandemics. V. parahaemolyticus causes wound infection and watery diarrhea, while V. vulnificus can cause wound infections and septicemia. Species of the Vibrio genus with resistance to multiple antimicrobials have been a significant health concern for several decades. Mechanisms of antimicrobial resistance machinery in Vibrio spp. include biofilm formation, drug inactivation, target protection, antimicrobial permeability reduction, and active antimicrobial efflux. Integral membrane-bound active antimicrobial efflux pump systems include primary and secondary transporters, members of which belong to closely related protein superfamilies. The RND (resistance-nodulation-division) pumps, the MFS (major facilitator superfamily) transporters, and the ABC superfamily of efflux pumps constitute significant drug transporters for investigation. In this review, we explore these antimicrobial transport systems in the context of Vibrio spp. pathogenesis and virulence.
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Affiliation(s)
- Jerusha Stephen
- QC Laboratory, Harvest and Post-Harvest Technology Division, Central Institute of Fisheries Education (CIFE), Seven Bungalows, Versova, Andheri (W), Mumbai 400061, India; (J.S.); (M.L.); (S.H.K.)
| | - Manjusha Lekshmi
- QC Laboratory, Harvest and Post-Harvest Technology Division, Central Institute of Fisheries Education (CIFE), Seven Bungalows, Versova, Andheri (W), Mumbai 400061, India; (J.S.); (M.L.); (S.H.K.)
| | - Parvathi Ammini
- Department of Biotechnology, Cochin University of Science and Technology, Kochi 682022, India;
| | - Sanath H. Kumar
- QC Laboratory, Harvest and Post-Harvest Technology Division, Central Institute of Fisheries Education (CIFE), Seven Bungalows, Versova, Andheri (W), Mumbai 400061, India; (J.S.); (M.L.); (S.H.K.)
| | - Manuel F. Varela
- Department of Biology, Eastern New Mexico University, Portales, NM 88130, USA
- Correspondence:
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7
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Tamrakar A, Singh R, Kumar A, Makde RD, Ashish, Kodgire P. Biophysical characterization of the homodimers of HomA and HomB, outer membrane proteins of Helicobacter pylori. Sci Rep 2021; 11:24471. [PMID: 34963695 PMCID: PMC8714817 DOI: 10.1038/s41598-021-04039-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 11/24/2021] [Indexed: 12/16/2022] Open
Abstract
Helicobacter pylori is a Gram-negative bacterium that causes chronic inflammations in the stomach area and is involved in ulcers, which can develop into gastric malignancies. H. pylori attaches and colonizes to the human epithelium using some of their outer membrane proteins (OMPs). HomB and HomA are the most studied OMPs from H. pylori as they play a crucial role in adherence, hyper biofilm formation, antibiotic resistance and are also associated with severe gastric malignancies. The role of HomA and HomB in pathogenesis concerning their structure and function has not been evaluated yet. In the present study, we explored the structural aspect of HomA and HomB proteins using various computational, biophysical and small-angle X-ray scattering (SAXS) techniques. Interestingly, the in-silico analysis revealed that HomA/B consists of 8 discontinuous N and C terminal β-strands forming a small β-barrel, along with a large surface-exposed globular domain. Further, biophysical experiments suggested that HomA and HomB are dimeric and most likely the cysteine residues present on surface-exposed loops participate in protein-protein interactions. Our study provides essential structural information of unexplored proteins of the Hom family that can help in a better understanding of H. pylori pathogenesis.
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Affiliation(s)
- Anubhav Tamrakar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, 453 552, India
| | - Rahul Singh
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Center, Trombay, Mumbai, India
| | - Amit Kumar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, 453 552, India
| | - Ravindra D Makde
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Center, Trombay, Mumbai, India
| | - Ashish
- Protein Science and Engineering Division, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Prashant Kodgire
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, 453 552, India.
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8
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McMillan HM, Kuehn MJ. The extracellular vesicle generation paradox: a bacterial point of view. EMBO J 2021; 40:e108174. [PMID: 34636061 PMCID: PMC8561641 DOI: 10.15252/embj.2021108174] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/29/2021] [Accepted: 07/28/2021] [Indexed: 12/23/2022] Open
Abstract
All bacteria produce secreted vesicles that carry out a variety of important biological functions. These extracellular vesicles can improve adaptation and survival by relieving bacterial stress and eliminating toxic compounds, as well as by facilitating membrane remodeling and ameliorating inhospitable environments. However, vesicle production comes with a price. It is energetically costly and, in the case of colonizing pathogens, it elicits host immune responses, which reduce bacterial viability. This raises an interesting paradox regarding why bacteria produce vesicles and begs the question as to whether the benefits of producing vesicles outweigh their costs. In this review, we discuss the various advantages and disadvantages associated with Gram-negative and Gram-positive bacterial vesicle production and offer perspective on the ultimate score. We also highlight questions needed to advance the field in determining the role for vesicles in bacterial survival, interkingdom communication, and virulence.
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Affiliation(s)
- Hannah M McMillan
- Department of Molecular Genetics and MicrobiologyDuke UniversityDurhamNCUSA
| | - Meta J Kuehn
- Department of BiochemistryDuke UniversityDurhamNCUSA
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9
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Ortiz-Hernández ML, Gama-Martínez Y, Fernández-López M, Castrejón-Godínez ML, Encarnación S, Tovar-Sánchez E, Salazar E, Rodríguez A, Mussali-Galante P. Transcriptomic analysis of Burkholderia cenocepacia CEIB S5-2 during methyl parathion degradation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:42414-42431. [PMID: 33813711 DOI: 10.1007/s11356-021-13647-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 03/22/2021] [Indexed: 06/12/2023]
Abstract
Methyl parathion (MP) is a highly toxic organophosphorus pesticide associated with water, soil, and air pollution events. The identification and characterization of microorganisms capable of biodegrading pollutants are an important environmental task for bioremediation of pesticide impacted sites. The strain Burkholderia cenocepacia CEIB S5-2 is a bacterium capable of efficiently hydrolyzing MP and biodegrade p-nitrophenol (PNP), the main MP hydrolysis product. Due to the high PNP toxicity over microbial living forms, the reports on bacterial PNP biodegradation are scarce. According to the genomic data, the MP- and PNP-degrading ability observed in B. cenocepacia CEIB S5-2 is related to the presence of the methyl parathion-degrading gene (mpd) and the gene cluster pnpABA'E1E2FDC, which include the genes implicated in the PNP degradation. In this work, the transcriptomic analysis of the strain in the presence of MP revealed the differential expression of 257 genes, including all genes implicated in the PNP degradation, as well as a set of genes related to the sensing of environmental changes, the response to stress, and the degradation of aromatic compounds, such as translational regulators, membrane transporters, efflux pumps, and oxidative stress response genes. These findings suggest that these genes play an important role in the defense against toxic effects derived from the MP and PNP exposure. Therefore, B. cenocepacia CEIB S5-2 has a great potential for application in pesticide bioremediation approaches due to its biodegradation capabilities and the differential expression of genes for resistance to MP and PNP.
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Affiliation(s)
- Ma Laura Ortiz-Hernández
- Misión Sustentabilidad México A.C., Priv. Laureles 6, Col. Chamilpa, C.P 62210, Cuernavaca, Morelos, México
| | - Yitzel Gama-Martínez
- Centro de Investigación en Biotecnología, Laboratorio de Investigaciones Ambientales, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, C.P. 62209, Cuernavaca, Morelos, México
| | - Maikel Fernández-López
- Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, C.P 62209, Cuernavaca, Morelos, México
| | - María Luisa Castrejón-Godínez
- Facultad de Ciencias Biológicas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, C.P 62209, Cuernavaca, Morelos, México
| | - Sergio Encarnación
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad s/n, Col. Chamilpa, C.P 62210, Cuernavaca, Morelos, México
| | - Efraín Tovar-Sánchez
- Centro de Investigación en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, C.P 62209, Cuernavaca, Morelos, México
| | - Emmanuel Salazar
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad s/n, Col. Chamilpa, C.P 62210, Cuernavaca, Morelos, México
| | - Alexis Rodríguez
- Centro de Investigación en Biotecnología, Laboratorio de Investigaciones Ambientales, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, C.P. 62209, Cuernavaca, Morelos, México.
| | - Patricia Mussali-Galante
- Centro de Investigación en Biotecnología, Laboratorio de Investigaciones Ambientales, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, C.P. 62209, Cuernavaca, Morelos, México.
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10
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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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11
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Klenotic PA, Moseng MA, Morgan CE, Yu EW. Structural and Functional Diversity of Resistance-Nodulation-Cell Division Transporters. Chem Rev 2021; 121:5378-5416. [PMID: 33211490 PMCID: PMC8119314 DOI: 10.1021/acs.chemrev.0c00621] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Multidrug resistant (MDR) bacteria are a global threat with many common infections becoming increasingly difficult to eliminate. While significant effort has gone into the development of potent biocides, the effectiveness of many first-line antibiotics has been diminished due to adaptive resistance mechanisms. Bacterial membrane proteins belonging to the resistance-nodulation-cell division (RND) superfamily play significant roles in mediating bacterial resistance to antimicrobials. They participate in multidrug efflux and cell wall biogenesis to transform bacterial pathogens into "superbugs" that are resistant even to last resort antibiotics. In this review, we summarize the RND superfamily of efflux transporters with a primary focus on the assembly and function of the inner membrane pumps. These pumps are critical for extrusion of antibiotics from the cell as well as the transport of lipid moieties to the outer membrane to establish membrane rigidity and stability. We analyze recently solved structures of bacterial inner membrane efflux pumps as to how they bind and transport their substrates. Our cumulative data indicate that these RND membrane proteins are able to utilize different oligomerization states to achieve particular activities, including forming MDR pumps and cell wall remodeling machineries, to ensure bacterial survival. This mechanistic insight, combined with simulated docking techniques, allows for the design and optimization of new efflux pump inhibitors to more effectively treat infections that today are difficult or impossible to cure.
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Affiliation(s)
- Philip A. Klenotic
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland OH 44106, USA
| | - Mitchell A. Moseng
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland OH 44106, USA
| | - Christopher E. Morgan
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland OH 44106, USA
| | - Edward W. Yu
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland OH 44106, USA
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12
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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: 96] [Impact Index Per Article: 32.0] [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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13
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Jaradat DMM, Al-Karablieh N, Zaarer BHM, Li W, Saleh KKY, Rasras AJ, Abu-Romman S, O'Brien-Simpson NM, Wade JD. Human glucose-dependent insulinotropic polypeptide (GIP) is an antimicrobial adjuvant re-sensitising multidrug-resistant Gram-negative bacteria. Biol Chem 2021; 402:513-524. [PMID: 33938181 DOI: 10.1515/hsz-2020-0351] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 12/09/2020] [Indexed: 11/15/2022]
Abstract
Increasing antibiotic resistance in Gram-negative bacteria has mandated the development of both novel antibiotics and alternative therapeutic strategies. Evidence of interplay between several gastrointestinal peptides and the gut microbiota led us to investigate potential and broad-spectrum roles for the incretin hormone, human glucose-dependent insulinotropic polypeptide (GIP) against the Enterobacteriaceae bacteria, Escherichia coli and Erwinia amylovora. GIP had a potent disruptive action on drug efflux pumps of the multidrug resistant bacteria E. coli TG1 and E. amylovora 1189 strains. The effect was comparable to bacterial mutants lacking the inner and outer membrane efflux pump factor proteins AcrB and TolC. While GIP was devoid of direct antimicrobial activity, it has a potent membrane depolarizing effect, and at low concentrations, it significantly potentiated the activity of eight antibiotics and bile salt by reducing MICs by 4-8-fold in E. coli TG1 and 4-20-fold in E. amylovora 1189. GIP can thus be regarded as an antimicrobial adjuvant with potential for augmenting the available antibiotic arsenal.
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Affiliation(s)
- Da'san M M Jaradat
- Faculty of Science, Department of Chemistry, Al-Balqa Applied University, P.O. Box 19117, Al-Salt, Jordan
| | - Nehaya Al-Karablieh
- Faculty of Agriculture, Department of Plant Protection, The University of Jordan, Amman, Jordan
- Hamdi Mango Center for Scientific Research, The University of Jordan, Amman, Jordan
| | - Basmah H M Zaarer
- Faculty of Science, Department of Chemistry, Al-Balqa Applied University, P.O. Box 19117, Al-Salt, Jordan
| | - Wenyi Li
- The Bio21 Institute of Molecular Science and Biotechnology, Melbourne Dental School, Centre for Oral Health Research, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Khalil K Y Saleh
- Faculty of Science, Department of Chemistry, Al-Balqa Applied University, P.O. Box 19117, Al-Salt, Jordan
| | - Anas J Rasras
- Faculty of Science, Department of Chemistry, Al-Balqa Applied University, P.O. Box 19117, Al-Salt, Jordan
| | - Saeid Abu-Romman
- Faculty of Agricultural Technology, Department of Biotechnology, Al-Balqa Applied University, P.O. Box 19117, Al-Salt, Jordan
| | - Neil M O'Brien-Simpson
- The Bio21 Institute of Molecular Science and Biotechnology, Melbourne Dental School, Centre for Oral Health Research, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - John D Wade
- School of Chemistry, University of Melbourne, Melbourne, Victoria 3010, Australia
- Howard Florey Research Laboratories, Florey Institute for Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria 3010, Australia
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14
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Pandeya A, Ojo I, Alegun O, Wei Y. Periplasmic Targets for the Development of Effective Antimicrobials against Gram-Negative Bacteria. ACS Infect Dis 2020; 6:2337-2354. [PMID: 32786281 PMCID: PMC8187054 DOI: 10.1021/acsinfecdis.0c00384] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Antibiotic resistance has emerged as a serious threat to global public health in recent years. Lack of novel antimicrobials, especially new classes of compounds, further aggravates the situation. For Gram-negative bacteria, their double layered cell envelope and an array of efflux pumps act as formidable barriers for antimicrobials to penetrate. While cytoplasmic targets are hard to reach, proteins in the periplasm are clearly more accessible, as the drug only needs to breach the outer membrane. In this review, we summarized recent efforts on the validation and testing of periplasmic proteins as potential antimicrobial targets and the development of related inhibitors that either inhibit the growth of a bacterial pathogen or reduce its virulence during interaction with host cells. We conclude that the periplasm contains a promising pool of novel antimicrobial targets that should be scrutinized more closely for the development of effective treatment against multidrug-resistant Gram-negative bacteria.
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Affiliation(s)
- Ankit Pandeya
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Isoiza Ojo
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Olaniyi Alegun
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Yinan Wei
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
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15
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Lamut A, Peterlin Mašič L, Kikelj D, Tomašič T. Efflux pump inhibitors of clinically relevant multidrug resistant bacteria. Med Res Rev 2019; 39:2460-2504. [PMID: 31004360 DOI: 10.1002/med.21591] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 03/31/2019] [Accepted: 04/02/2019] [Indexed: 12/29/2022]
Abstract
Bacterial infections are an increasingly serious issue worldwide. The inability of existing therapies to treat multidrug-resistant pathogens has been recognized as an important challenge of the 21st century. Efflux pumps are important in both intrinsic and acquired bacterial resistance and identification of small molecule efflux pump inhibitors (EPIs), capable of restoring the effectiveness of available antibiotics, is an active research field. In the last two decades, much effort has been made to identify novel EPIs. However, none of them has so far been approved for therapeutic use. In this article, we explore different structural families of currently known EPIs for multidrug resistance efflux systems in the most extensively studied pathogens (NorA in Staphylococcus aureus, AcrAB-TolC in Escherichia coli, and MexAB-OprM in Pseudomonas aeruginosa). Both synthetic and natural compounds are described, with structure-activity relationship studies and optimization processes presented systematically for each family individually. In vitro activities against selected test strains are presented in a unifying manner for all the EPIs described, together with the most important toxicity, pharmacokinetic and in vivo efficacy data. A critical evaluation of lead-likeness characteristics and the potential for clinical development of the most promising inhibitors of the three efflux systems is described. This overview of EPIs is a good starting point for the identification of novel effective antibacterial drugs.
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Affiliation(s)
- Andraž Lamut
- Chair of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Lucija Peterlin Mašič
- Chair of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Danijel Kikelj
- Chair of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Tihomir Tomašič
- Chair of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
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16
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Tsutsumi K, Yonehara R, Ishizaka-Ikeda E, Miyazaki N, Maeda S, Iwasaki K, Nakagawa A, Yamashita E. Structures of the wild-type MexAB-OprM tripartite pump reveal its complex formation and drug efflux mechanism. Nat Commun 2019; 10:1520. [PMID: 30944318 PMCID: PMC6447562 DOI: 10.1038/s41467-019-09463-9] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 03/11/2019] [Indexed: 11/30/2022] Open
Abstract
In Pseudomonas aeruginosa, MexAB–OprM plays a central role in multidrug resistance by ejecting various drug compounds, which is one of the causes of serious nosocomial infections. Although the structures of the components of MexAB–OprM have been solved individually by X-ray crystallography, no structural information for fully assembled pumps from P. aeruginosa were previously available. In this study, we present the structure of wild-type MexAB–OprM in the presence or absence of drugs at near-atomic resolution. The structure reveals that OprM does not interact with MexB directly, and that it opens its periplasmic gate by forming a complex. Furthermore, we confirm the residues essential for complex formation and observed a movement of the drug entrance gate. Based on these results, we propose mechanisms for complex formation and drug efflux. In Pseudomonas aeruginosa, MexAB–OprM plays a central role in multidrug resistance by ejecting various drug compounds. Here the authors present the structure of wild-type MexAB–OprM in the presence or absence of drugs and propose mechanisms for complex formation and drug efflux.
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Affiliation(s)
- Kenta Tsutsumi
- Institute for Protein Research, Osaka University, Suita, 565-0871, Osaka, Japan
| | - Ryo Yonehara
- Institute for Protein Research, Osaka University, Suita, 565-0871, Osaka, Japan
| | | | - Naoyuki Miyazaki
- Institute for Protein Research, Osaka University, Suita, 565-0871, Osaka, Japan
| | - Shintaro Maeda
- Institute for Protein Research, Osaka University, Suita, 565-0871, Osaka, Japan.,The Scripps Research Institute Department of Integrative Structural and Computational Biology, North Torrey Pines Road, La Jolla, CA, 10550, USA
| | - Kenji Iwasaki
- Institute for Protein Research, Osaka University, Suita, 565-0871, Osaka, Japan.,University of Tsukuba Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance 1-1-1 Tennodai, Tsukuba, 305-8577, Ibaraki, Japan
| | - Atsushi Nakagawa
- Institute for Protein Research, Osaka University, Suita, 565-0871, Osaka, Japan
| | - Eiki Yamashita
- Institute for Protein Research, Osaka University, Suita, 565-0871, Osaka, Japan.
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17
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Minimal nanodisc without exogenous lipids for stabilizing membrane proteins in detergent-free buffer. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:852-860. [DOI: 10.1016/j.bbamem.2019.01.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 12/17/2018] [Accepted: 01/24/2019] [Indexed: 01/29/2023]
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18
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Jo I, Kim JS, Xu Y, Hyun J, Lee K, Ha NC. Recent paradigm shift in the assembly of bacterial tripartite efflux pumps and the type I secretion system. J Microbiol 2019; 57:185-194. [PMID: 30806976 DOI: 10.1007/s12275-019-8520-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 12/26/2018] [Accepted: 01/10/2019] [Indexed: 01/15/2023]
Abstract
Tripartite efflux pumps and the type I secretion system of Gram-negative bacteria are large protein complexes that span the entire cell envelope. These complexes expel antibiotics and other toxic substances or transport protein toxins from bacterial cells. Elucidating the binary and ternary complex structures at an atomic resolution are crucial to understanding the assembly and working mechanism. Recent advances in cryoelectron microscopy along with the construction of chimeric proteins drastically shifted the assembly models. In this review, we describe the current assembly models from a historical perspective and emphasize the common assembly mechanism for the assembly of diverse tripartite pumps and type I secretion systems.
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Affiliation(s)
- Inseong Jo
- Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Center for Food and Bioconvergence, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jin-Sik Kim
- Unit on Structural and Chemical Biology of Membrane Proteins, Cell Biology and Neurobiology Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yongbin Xu
- Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, Liaoning, 116600, P. R. China
| | - Jaekyung Hyun
- Electron Microscopy Research Center, Korea Basic Science Institute, Cheongju, 28119, Republic of Korea
| | - Kangseok Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Nam-Chul Ha
- Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Center for Food and Bioconvergence, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
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19
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Klein K, Sonnabend MS, Frank L, Leibiger K, Franz-Wachtel M, Macek B, Trunk T, Leo JC, Autenrieth IB, Schütz M, Bohn E. Deprivation of the Periplasmic Chaperone SurA Reduces Virulence and Restores Antibiotic Susceptibility of Multidrug-Resistant Pseudomonas aeruginosa. Front Microbiol 2019; 10:100. [PMID: 30846971 PMCID: PMC6394205 DOI: 10.3389/fmicb.2019.00100] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 01/17/2019] [Indexed: 12/28/2022] Open
Abstract
Pseudomonas aeruginosa is one of the main causative agents of nosocomial infections and the spread of multidrug-resistant strains is rising. Therefore, novel strategies for therapy are urgently required. The outer membrane composition of Gram-negative pathogens and especially of Pa restricts the efficacy of antibiotic entry into the cell and determines virulence. For efficient outer membrane protein biogenesis, the β-barrel assembly machinery (BAM) complex in the outer membrane and periplasmic chaperones like Skp and SurA are crucial. Previous studies indicated that the importance of individual proteins involved in outer membrane protein biogenesis may vary between different Gram-negative species. In addition, since multidrug-resistant Pa strains pose a serious global threat, the interference with both virulence and antibiotic resistance by disturbing outer membrane protein biogenesis might be a new strategy to cope with this challenge. Therefore, deletion mutants of the non-essential BAM complex components bamB and bamC, of the skp homolog hlpA as well as a conditional mutant of surA were investigated. The most profound effects for both traits were associated with reduced levels of SurA, characterized by increased membrane permeability, enhanced sensitivity to antibiotic treatment and attenuation of virulence in a Galleria mellonella infection model. Strikingly, the depletion of SurA in a multidrug-resistant clinical bloodstream isolate re-sensitized the strain to antibiotic treatment. From our data we conclude that SurA of Pa serves as a promising target for developing a drug that shows antiinfective activity and re-sensitizes multidrug-resistant strains to antibiotics.
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Affiliation(s)
- Kristina Klein
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Institut für Medizinische Mikrobiologie und Hygiene, Universität Tübingen, Tübingen, Germany
| | - Michael S. Sonnabend
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Institut für Medizinische Mikrobiologie und Hygiene, Universität Tübingen, Tübingen, Germany
| | - Lisa Frank
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Institut für Medizinische Mikrobiologie und Hygiene, Universität Tübingen, Tübingen, Germany
| | - Karolin Leibiger
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Institut für Medizinische Mikrobiologie und Hygiene, Universität Tübingen, Tübingen, Germany
| | | | - Boris Macek
- Proteome Center Tübingen, Universität Tübingen, Tübingen, Germany
| | - Thomas Trunk
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Jack C. Leo
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Ingo B. Autenrieth
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Institut für Medizinische Mikrobiologie und Hygiene, Universität Tübingen, Tübingen, Germany
| | - Monika Schütz
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Institut für Medizinische Mikrobiologie und Hygiene, Universität Tübingen, Tübingen, Germany
| | - Erwin Bohn
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin Tübingen (IMIT), Institut für Medizinische Mikrobiologie und Hygiene, Universität Tübingen, Tübingen, Germany
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20
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Yong YY, Dykes G, Lee SM, Choo WS. Biofilm inhibiting activity of betacyanins from red pitahaya (Hylocereus polyrhizus) and red spinach (Amaranthus dubius) against Staphylococcus aureus and Pseudomonas aeruginosa biofilms. J Appl Microbiol 2018; 126:68-78. [PMID: 30153380 DOI: 10.1111/jam.14091] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/17/2018] [Accepted: 08/23/2018] [Indexed: 01/01/2023]
Abstract
AIMS To investigate the biofilm inhibitory activity of betacyanins from red pitahaya (Hylocereus polyrhizus) and red spinach (Amaranthus dubius) against Staphylococcus aureus and Pseudomonas aeruginosa biofilms. METHODS AND RESULTS The pulp of red pitahaya and the leaves of red spinach were extracted using methanol followed by subfractionation to obtain betacyanin fraction. The anti-biofilm activity was examined using broth microdilution assay on polystyrene surfaces and expressed as minimum biofilm inhibitory concentration (MBIC). The betacyanin fraction from red spinach showed better anti-biofilm activity (MBIC: 0·313-1·25 mg ml-1 ) against five Staph. aureus strains while the betacyanin fraction from red pitahaya showed better anti-biofilm activity (MBIC: 0·313-0·625 mg ml-1 ) against four P. aeruginosa strains. Both betacyanin fraction significantly reduced hydrophobicity of Staph. aureus and P. aeruginosa strains. Numbers of Staph. aureus and P. aeruginosa attached to polystyrene were also reduced without affecting their cell viability. CONCLUSION Betacyanins can act as anti-biofilm agents against the initial step of biofilm formation, particularly on a hydrophobic surface like polystyrene. SIGNIFICANCE AND IMPACT OF THE STUDY This study is the first to investigate the use of betacyanin as a biofilm inhibitory agent. Betacyanin could potentially be used to reduce the risk of biofilm-associated infections.
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Affiliation(s)
- Y Y Yong
- School of Science, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
| | - G Dykes
- School of Public Health, Curtin University, Bentley, WA, Australia
| | - S M Lee
- School of Science, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
| | - W S Choo
- School of Science, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
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21
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Travers T, Wang KJ, López CA, Gnanakaran S. Sequence- and structure-based computational analyses of Gram-negative tripartite efflux pumps in the context of bacterial membranes. Res Microbiol 2018; 169:414-424. [DOI: 10.1016/j.resmic.2018.01.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 12/28/2017] [Accepted: 01/21/2018] [Indexed: 01/12/2023]
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22
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Greene NP, Kaplan E, Crow A, Koronakis V. Antibiotic Resistance Mediated by the MacB ABC Transporter Family: A Structural and Functional Perspective. Front Microbiol 2018; 9:950. [PMID: 29892271 PMCID: PMC5985334 DOI: 10.3389/fmicb.2018.00950] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 04/24/2018] [Indexed: 12/18/2022] Open
Abstract
The MacB ABC transporter forms a tripartite efflux pump with the MacA adaptor protein and TolC outer membrane exit duct to expel antibiotics and export virulence factors from Gram-negative bacteria. Here, we review recent structural and functional data on MacB and its homologs. MacB has a fold that is distinct from other structurally characterized ABC transporters and uses a unique molecular mechanism termed mechanotransmission. Unlike other bacterial ABC transporters, MacB does not transport substrates across the inner membrane in which it is based, but instead couples cytoplasmic ATP hydrolysis with transmembrane conformational changes that are used to perform work in the extra-cytoplasmic space. In the MacAB-TolC tripartite pump, mechanotransmission drives efflux of antibiotics and export of a protein toxin from the periplasmic space via the TolC exit duct. Homologous tripartite systems from pathogenic bacteria similarly export protein-like signaling molecules, virulence factors and siderophores. In addition, many MacB-like ABC transporters do not form tripartite pumps, but instead operate in diverse cellular processes including antibiotic sensing, cell division and lipoprotein trafficking.
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Affiliation(s)
- Nicholas P Greene
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Elise Kaplan
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Allister Crow
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Vassilis Koronakis
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
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23
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Affiliation(s)
- Marcin Grabowicz
- Department of Microbiology and Immunology; Emory University School of Medicine; Atlanta GA 30322 USA
- Division of Infectious Disease; Department of Medicine; Emory University School of Medicine; Atlanta GA 30322 USA
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24
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Trans-envelope multidrug efflux pumps of Gram-negative bacteria and their synergism with the outer membrane barrier. Res Microbiol 2018; 169:351-356. [PMID: 29454787 DOI: 10.1016/j.resmic.2018.02.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 02/05/2018] [Accepted: 02/06/2018] [Indexed: 11/20/2022]
Abstract
Antibiotic resistance is a serious threat to public health. Significant efforts are currently directed toward containment of the spread of resistance, finding new therapeutic options concerning resistant human and animal pathogens, and addressing the gaps in the fundamental understanding of mechanisms of resistance. Experimental data and kinetic modeling revealed a major factor in resistance, the synergy between active efflux and the low permeability barrier of the outer membrane, which dramatically reduces the intracellular accumulation of many antibiotics. The structural and mechanistic particularities of trans-envelope efflux pumps amplify the effectiveness of cell envelopes as permeability barriers. An important feature of this synergism is that efflux pumps and the outer membrane barriers are mechanistically independent and select antibiotics based on different physicochemical properties. The synergism amplifies even weak polyspecificity of multidrug efflux pumps and creates a major hurdle in the discovery and development of new therapeutics against Gram-negative pathogens.
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25
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Role and mechanism of cell-surface hydrophobicity in the adaptation of Sphingobium hydrophobicum to electronic-waste contaminated sediment. Appl Microbiol Biotechnol 2018; 102:2803-2815. [DOI: 10.1007/s00253-017-8734-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 11/29/2017] [Accepted: 12/12/2017] [Indexed: 01/16/2023]
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26
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Ding F, Songkiatisak P, Cherukuri PK, Huang T, Xu XHN. Size-Dependent Inhibitory Effects of Antibiotic Drug Nanocarriers against Pseudomonas aeruginosa. ACS OMEGA 2018; 3:1231-1243. [PMID: 29399654 PMCID: PMC5793034 DOI: 10.1021/acsomega.7b01956] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 01/12/2018] [Indexed: 05/24/2023]
Abstract
Multidrug membrane transporters (efflux pumps) are responsible for multidrug resistance (MDR) and the low efficacy of therapeutic drugs. Noble metal nanoparticles (NPs) possess a high surface-area-to-volume ratio and size-dependent plasmonic optical properties, enabling them to serve both as imaging probes to study sized-dependent MDR and as potential drug carriers to circumvent MDR and enhance therapeutic efficacy. To this end, in this study, we synthesized three different sizes of silver nanoparticles (Ag NPs), 2.4 ± 0.7, 13.0 ± 3.1, and 92.6 ± 4.4 nm, functionalized their surface with a monolayer of 11-amino-1-undecanethiol (AUT), and covalently conjugated them with antibiotics (ofloxacin, Oflx) to prepare antibiotic drug nanocarriers with conjugation ratios of 8.6 × 102, 9.4 × 103, and 6.5 × 105 Oflx molecules per NP, respectively. We purified and characterized the nanocarriers and developed cell culture medium in which the cells grew normally and the nanocarriers were stable (non-aggregated), to quantitatively study the size, dose, and efflux pump (MexAB-OprM) dependent inhibitory effect of the nanocarriers against two strains of Pseudomonas aeruginosa, WT (normal expression of MexAB-OprM) and ΔABM (deletion of MexAB-OprM). We found that the inhibitory effect of these nanocarriers highly depended on the sizes of NPs, the doses of antibiotic, and the expression of MexAB-OprM. The same amount of Oflx on the largest nanocarriers (92.6 ± 4.4 nm) showed the highest inhibitory effect (the lowest minimal inhibitory concentration) against P. aeruginosa. Surprisingly, the smallest nanocarriers (2.4 ± 0.7 nm) exhibited a lower inhibitory effect than free Oflx. The results suggest that size-dependent multivalent effects, the distribution and localization of Oflx (pharmacodynamics), and the efflux of Oflx all play a role in the inhibitory effects. Control experiments using three sizes of AgMUNH2 NPs (absence of Oflx) showed that these NPs do not exhibit any significant inhibitory activity toward both strains. These new findings demonstrate the need for and possibility of designing optimal sized antibiotic nanocarriers to achieve the highest efficacy against P. aeruginosa.
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27
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Cacciotto P, Ramaswamy VK, Malloci G, Ruggerone P, Vargiu AV. Molecular Modeling of Multidrug Properties of Resistance Nodulation Division (RND) Transporters. Methods Mol Biol 2018; 1700:179-219. [PMID: 29177832 DOI: 10.1007/978-1-4939-7454-2_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Efflux pumps of the resistance nodulation division (RND) superfamily are among the major contributors to intrinsic and acquired multidrug resistance in Gram-negative bacteria. Structural information on AcrAB-TolC and MexAB-OprM, major efflux pumps of Escherichia coli and Pseudomonas aeruginosa respectively, boosted intensive research aimed at understanding the molecular mechanisms ruling the active extrusion processes. In particular, several studies were devoted to the understanding of the determinants behind the extraordinary broad specificity of the RND transporters AcrB and MexB. In this chapter, we discuss the ever-growing role computational methods have been playing in deciphering key structural and dynamical features of these transporters and of their interaction with substrates and inhibitors. We further discuss and illustrate examples from our lab of how molecular docking, homology modeling, all-atom molecular dynamics simulations and in silico free energy estimations can all together give precious insights into the processes of recognition and extrusion of substrates, as well as on the possible inhibition strategies.
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Affiliation(s)
- Pierpaolo Cacciotto
- Department of Physics, University of Cagliari, s.p. 8, 09042, Monserrato, CA, Italy
| | - Venkata K Ramaswamy
- Department of Physics, University of Cagliari, s.p. 8, 09042, Monserrato, CA, Italy
| | - Giuliano Malloci
- Department of Physics, University of Cagliari, s.p. 8, 09042, Monserrato, CA, Italy
| | - Paolo Ruggerone
- Department of Physics, University of Cagliari, s.p. 8, 09042, Monserrato, CA, Italy
| | - Attilio V Vargiu
- Department of Physics, University of Cagliari, s.p. 8, 09042, Monserrato, CA, Italy.
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28
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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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Chaturvedi D, Mahalakshmi R. Transmembrane β-barrels: Evolution, folding and energetics. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:2467-2482. [PMID: 28943271 DOI: 10.1016/j.bbamem.2017.09.020] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 09/16/2017] [Accepted: 09/19/2017] [Indexed: 12/23/2022]
Abstract
The biogenesis of transmembrane β-barrels (outer membrane proteins, or OMPs) is an elaborate multistep orchestration of the nascent polypeptide with translocases, barrel assembly machinery, and helper chaperone proteins. Several theories exist that describe the mechanism of chaperone-assisted OMP assembly in vivo and unassisted (spontaneous) folding in vitro. Structurally, OMPs of bacterial origin possess even-numbered strands, while mitochondrial β-barrels are even- and odd-stranded. Several underlying similarities between prokaryotic and eukaryotic β-barrels and their folding machinery are known; yet, the link in their evolutionary origin is unclear. While OMPs exhibit diversity in sequence and function, they share similar biophysical attributes and structure. Similarly, it is important to understand the intricate OMP assembly mechanism, particularly in eukaryotic β-barrels that have evolved to perform more complex functions. Here, we deliberate known facets of β-barrel evolution, folding, and stability, and attempt to highlight outstanding questions in β-barrel biogenesis and proteostasis.
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Affiliation(s)
- Deepti Chaturvedi
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal 462066, India.
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal 462066, India.
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30
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Xenon for tunnelling analysis of the efflux pump component OprN. PLoS One 2017; 12:e0184045. [PMID: 28886086 PMCID: PMC5590881 DOI: 10.1371/journal.pone.0184045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 08/17/2017] [Indexed: 12/02/2022] Open
Abstract
Tripartite efflux pumps are among the main actors responsible for antibiotics resistance in Gram-negative bacteria. In the last two decades, structural studies gave crucial information about the assembly interfaces and the mechanistic motions. Thus rigidifying the assembly seems to be an interesting way to hamper the drug efflux. In this context, xenon is a suitable probe for checking whether small ligands could act as conformational lockers by targeting hydrophobic cavities. Here we focus on OprN, the outer membrane channel of the MexEF efflux pump from Pseudomonas aeruginosa. After exposing OprN crystals to xenon gas pressure, 14 binding sites were observed using X-ray crystallography. These binding sites were unambiguously characterized in hydrophobic cavities of OprN. The major site is observed in the sensitive iris-like region gating the channel at the periplasmic side, built by the three key-residues Leu 405, Asp 109, and Arg 412. This arrangement defines along the tunnel axis a strong hydrophobic/polar gradient able to enhance the passive efflux mechanism of OprN. The other xenon atoms reveal strategic hydrophobic regions of the channel scaffold to target, with the aim to freeze the dynamic movements responsible of the open/close conformational equilibrium in OprN.
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31
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Cho CW, Park JS, Zhao Y, Yun YS. Quantitative analysis of adsorptive interactions of ionic and neutral pharmaceuticals and other chemicals with the surface of Escherichia coli cells in aquatic environment. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 227:8-14. [PMID: 28454022 DOI: 10.1016/j.envpol.2017.04.061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 04/17/2017] [Indexed: 06/07/2023]
Abstract
Since Escherichia coli is ubiquitous in nature and has been applied to biological, chemical, and environmental processes, molecular-level understanding of adsorptive interactions between chemicals and the bacterial surface is of great importance. To characterise the adsorption properties of the surface of E. coli cells in aquatic environment, the binding affinities (log Kd) of calibration compounds were experimentally measured, and then based on the values and numerically well-defined molecular interaction forces, i.e. linear free energy relationship (LFER) descriptors, a predictive model was developed. The examined substances are composed of cations, anions, and neutral compounds, and the used LFER descriptors are excess molar refraction (E), dipolarity/polarisability (S), H-bonding acidity (A) and basicity (B), McGowan volume (V), and coulombic interactions of cations (J+) and anions (J-). In experimental results, adsorption of anions on the bacterial surface was not observed, while cations exhibited high affinities. In case of neutral compounds, their low quantities were adsorbed, however whose affinities were mostly lower than those of cations. In a LFER study, it was shown that cationic interaction term has the best correlation in R2 of 0.691 and sequential additions of S, A, and V help to increase the prediction accuracy. The LFER model (log Kd = - 0.72-0.79 S + 0.81 A + 0.41 V + 0.85 J+) could predict the log Kd in R2 of 0.871 and SE of 0.402 log unit, and then to check robustness and predictability of the model, we internally validated it by a leave-one-out cross validation (Q2LOO) study. As a result, the Q2LOO value was estimated to be 0.826, which was larger than standard of model acceptability (>0.5).
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Affiliation(s)
- Chul-Woong Cho
- School of Chemical Engineering, Chonbuk National University, 567 Beakje-dearo, Deokjin-gu, Jeonju, Jeonbuk 561-756, Republic of Korea
| | - Jeong-Soo Park
- School of Chemical Engineering, Chonbuk National University, 567 Beakje-dearo, Deokjin-gu, Jeonju, Jeonbuk 561-756, Republic of Korea
| | - Yufeng Zhao
- School of Chemical Engineering, Chonbuk National University, 567 Beakje-dearo, Deokjin-gu, Jeonju, Jeonbuk 561-756, Republic of Korea
| | - Yeoung-Sang Yun
- School of Chemical Engineering, Chonbuk National University, 567 Beakje-dearo, Deokjin-gu, Jeonju, Jeonbuk 561-756, Republic of Korea.
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32
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Talukdar S, Bayan U, Saikia KK. In silico identification of vaccine candidates against Klebsiella oxytoca. Comput Biol Chem 2017; 69:48-54. [PMID: 28570984 DOI: 10.1016/j.compbiolchem.2017.05.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 05/06/2017] [Accepted: 05/20/2017] [Indexed: 01/10/2023]
Abstract
Klebsiella oxytoca causes several diseases in immunocompromised as well as healthy individuals. Increasing resistance to a number of antibiotics makes treatment options limited. Prevention using vaccine could be an important solution to get rid of infections caused by Klebsiella oxytoca. In recent time, genome based approaches have contributed significantly in vaccine development. Our aim was to identify the most conserved and immunogenic antigens that can be considered as potential vaccine candidates. KEGG database was used to find out pathways unique to the bacteria. Subcellular localization of the protein sequences taken from the selected 36 pathways were predicted using PSORTb v3.0.2 and CELLO v2.5. Prediction of B cell epitope and the probability of the antigenicity were evaluated by using IEDB and Vaxijen respectively. BLASTp was done to find out the similarity of the selected proteins with the human proteome. Proteins failing to comply with the set parameters were filtered at each step. Finally, we identified 6 surface exposed proteins as potential vaccine candidates against Klebsiella oxytoca.
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Affiliation(s)
- Sandipan Talukdar
- Dept of Bioengineering & Technology, GUIST, Gauhati University, India
| | - Udeshna Bayan
- Dept of Bioengineering & Technology, GUIST, Gauhati University, India
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33
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Redefining the essential trafficking pathway for outer membrane lipoproteins. Proc Natl Acad Sci U S A 2017; 114:4769-4774. [PMID: 28416660 DOI: 10.1073/pnas.1702248114] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The outer membrane (OM) of Gram-negative bacteria is a permeability barrier and an intrinsic antibiotic resistance factor. Lipoproteins are OM components that function in cell wall synthesis, diverse secretion systems, and antibiotic efflux pumps. Moreover, each of the essential OM machines that assemble the barrier requires one or more lipoproteins. This dependence is thought to explain the essentiality of the periplasmic chaperone LolA and its OM receptor LolB that traffic lipoproteins to the OM. However, we show that in strains lacking substrates that are toxic when mislocalized, both LolA and LolB can be completely bypassed by activating an envelope stress response without compromising trafficking of essential lipoproteins. We identify the Cpx stress response as a monitor of lipoprotein trafficking tasked with protecting the cell from mislocalized lipoproteins. Moreover, our findings reveal that an alternate trafficking pathway exists that can, under certain conditions, bypass the functions of LolA and LolB, implying that these proteins do not perform any truly essential mechanistic steps in lipoprotein trafficking. Instead, these proteins' key function is to prevent lethal accumulation of mislocalized lipoproteins.
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34
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Thai KM, Do TN, Nguyen TVP, Nguyen DKT, Tran TD. QSAR Studies on Bacterial Efflux Pump Inhibitors. PHARMACEUTICAL SCIENCES 2017. [DOI: 10.4018/978-1-5225-1762-7.ch035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Antimicrobial drug resistance occurs when bacteria undergo certain modifications to eliminate the effectiveness of drugs, chemicals, or other agents designed to cure infections. To date, the burden of resistance has remained one of the major clinical concerns as it renders prolonged and complicated treatments, thereby increasing the medical costs with lengthier hospital stays. Of complex causes for bacterial resistance, there has been increasing evidence that proved the significant role of efflux pumps in antibiotic resistance. Coadministration of Efflux Pump Inhibitors (EPIs) with antibiotics has been considered one of the promising ways not only to improve the efficacy but also to extend the clinical utility of existing antibiotics. This chapter begins with outlining current knowledge about bacterial efflux pumps and drug designs applied in identification of their modulating compounds. Following, the chapter addresses and provides a discussion on Quantitative Structure-Activity Relationship (QSAR) analyses in search of novel and potent efflux pump inhibitors.
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Affiliation(s)
| | - Trong-Nhat Do
- University of Medicine and Pharmacy at HCMC, Vietnam
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35
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Mahmood HY, Jamshidi S, Sutton JM, Rahman KM. Current Advances in Developing Inhibitors of Bacterial Multidrug Efflux Pumps. Curr Med Chem 2016; 23:1062-81. [PMID: 26947776 PMCID: PMC5425656 DOI: 10.2174/0929867323666160304150522] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Revised: 01/27/2016] [Accepted: 03/10/2016] [Indexed: 01/30/2023]
Abstract
Antimicrobial resistance represents a significant challenge to future healthcare provision. An acronym ESKAPEE has been derived from the names of the organisms recognised as the major threats although there are a number of other organisms, notably Neisseria gonorrhoeae, that have become equally challenging to treat in the clinic. These pathogens are characterised by the ability to rapidly develop and/or acquire resistance mechanisms in response to exposure to different antimicrobial agents. A key part of the armoury of these pathogens is a series of efflux pumps, which effectively exclude or reduce the intracellular concentration of a large number of antibiotics, making the pathogens significantly more resistant. These efflux pumps are the topic of considerable interest, both from the perspective of basic understanding of efflux pump function, and its role in drug resistance but also as targets for the development of novel adjunct therapies. The necessity to overcome antimicrobial resistance has encouraged investigations into the characterisation of resistance-modifying efflux pump inhibitors to block the mechanisms of drug extrusion, thereby restoring antibacterial susceptibility and returning existing antibiotics into the clinic. A greater understanding of drug recognition and transport by multidrug efflux pumps is needed to develop clinically useful inhibitors, given the breadth of molecules that can be effluxed by these systems. This review discusses different bacterial EPIs originating from both natural source and chemical synthesis and examines the challenges to designing successful EPIs that can be useful against multidrug resistant bacteria.
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Affiliation(s)
| | | | | | - Khondaker M Rahman
- Institute of Pharmaceutical Science, King's College London, Britannia House, London SE1 1DB, UK.
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36
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Molecular Epidemiology of Mutations in Antimicrobial Resistance Loci of Pseudomonas aeruginosa Isolates from Airways of Cystic Fibrosis Patients. Antimicrob Agents Chemother 2016; 60:6726-6734. [PMID: 27572404 DOI: 10.1128/aac.00724-16] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 08/23/2016] [Indexed: 01/30/2023] Open
Abstract
The chronic airway infections with Pseudomonas aeruginosa in people with cystic fibrosis (CF) are treated with aerosolized antibiotics, oral fluoroquinolones, and/or intravenous combination therapy with aminoglycosides and β-lactam antibiotics. An international strain collection of 361 P. aeruginosa isolates from 258 CF patients seen at 30 CF clinics was examined for mutations in 17 antimicrobial susceptibility and resistance loci that had been identified as hot spots of mutation by genome sequencing of serial isolates from a single CF clinic. Combinatorial amplicon sequencing of pooled PCR products identified 1,112 sequence variants that were not present in the genomes of representative strains of the 20 most common clones of the global P. aeruginosa population. A high frequency of singular coding variants was seen in spuE, mexA, gyrA, rpoB, fusA1, mexZ, mexY, oprD, ampD, parR, parS, and envZ (amgS), reflecting the pressure upon P. aeruginosa in lungs of CF patients to generate novel protein variants. The proportion of nonneutral amino acid exchanges was high. Of the 17 loci, mexA, mexZ, and pagL were most frequently affected by independent stop mutations. Private and de novo mutations seem to play a pivotal role in the response of P. aeruginosa populations to the antimicrobial load and the individual CF host.
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37
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Wątły J, Potocki S, Rowińska-Żyrek M. Zinc Homeostasis at the Bacteria/Host Interface-From Coordination Chemistry to Nutritional Immunity. Chemistry 2016; 22:15992-16010. [DOI: 10.1002/chem.201602376] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Indexed: 12/17/2022]
Affiliation(s)
- Joanna Wątły
- Faculty of Chemistry; University of Wroclaw; F. Joliot-Curie 14 50-383 Wroclaw Poland
| | - Sławomir Potocki
- Faculty of Chemistry; University of Wroclaw; F. Joliot-Curie 14 50-383 Wroclaw Poland
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38
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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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39
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Daury L, Orange F, Taveau JC, Verchère A, Monlezun L, Gounou C, Marreddy RKR, Picard M, Broutin I, Pos KM, Lambert O. Tripartite assembly of RND multidrug efflux pumps. Nat Commun 2016; 7:10731. [PMID: 26867482 PMCID: PMC4754349 DOI: 10.1038/ncomms10731] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 01/15/2016] [Indexed: 12/18/2022] Open
Abstract
Tripartite multidrug efflux systems of Gram-negative bacteria are composed of an inner membrane transporter, an outer membrane channel and a periplasmic adaptor protein. They are assumed to form ducts inside the periplasm facilitating drug exit across the outer membrane. Here we present the reconstitution of native Pseudomonas aeruginosa MexAB–OprM and Escherichia coli AcrAB–TolC tripartite Resistance Nodulation and cell Division (RND) efflux systems in a lipid nanodisc system. Single-particle analysis by electron microscopy reveals the inner and outer membrane protein components linked together via the periplasmic adaptor protein. This intrinsic ability of the native components to self-assemble also leads to the formation of a stable interspecies AcrA–MexB–TolC complex suggesting a common mechanism of tripartite assembly. Projection structures of all three complexes emphasize the role of the periplasmic adaptor protein as part of the exit duct with no physical interaction between the inner and outer membrane components. Tripartite efflux systems consist of inner membrane, outer membrane and periplasmic components. Here, Daury et al. reconstitute native versions of RND transporters in nanodiscs and present projection structures emphasizing the role of the periplasmic adaptor in linking the inner and outer membrane proteins.
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Affiliation(s)
- Laetitia Daury
- Université de Bordeaux, CBMN UMR 5248, Bordeaux INP, IECB, Pessac F-33600, France.,CNRS, CBMN UMR 5248, Pessac F-33600, France
| | - François Orange
- Université de Bordeaux, CBMN UMR 5248, Bordeaux INP, IECB, Pessac F-33600, France.,CNRS, CBMN UMR 5248, Pessac F-33600, France
| | - Jean-Christophe Taveau
- Université de Bordeaux, CBMN UMR 5248, Bordeaux INP, IECB, Pessac F-33600, France.,CNRS, CBMN UMR 5248, Pessac F-33600, France
| | - Alice Verchère
- Laboratoire de Cristallographie et RMN Biologiques, UMR 8015, CNRS, Université Paris Descartes, Faculté de Pharmacie, 4 Avenue de l'Observatoire, Paris 75006, France
| | - Laura Monlezun
- Laboratoire de Cristallographie et RMN Biologiques, UMR 8015, CNRS, Université Paris Descartes, Faculté de Pharmacie, 4 Avenue de l'Observatoire, Paris 75006, France
| | - Céline Gounou
- Université de Bordeaux, CBMN UMR 5248, Bordeaux INP, IECB, Pessac F-33600, France.,CNRS, CBMN UMR 5248, Pessac F-33600, France
| | - Ravi K R Marreddy
- Institute of Biochemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Martin Picard
- Laboratoire de Cristallographie et RMN Biologiques, UMR 8015, CNRS, Université Paris Descartes, Faculté de Pharmacie, 4 Avenue de l'Observatoire, Paris 75006, France
| | - Isabelle Broutin
- Laboratoire de Cristallographie et RMN Biologiques, UMR 8015, CNRS, Université Paris Descartes, Faculté de Pharmacie, 4 Avenue de l'Observatoire, Paris 75006, France
| | - Klaas M Pos
- Institute of Biochemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Olivier Lambert
- Université de Bordeaux, CBMN UMR 5248, Bordeaux INP, IECB, Pessac F-33600, France.,CNRS, CBMN UMR 5248, Pessac F-33600, France
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40
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Guan HH, Yoshimura M, Chuankhayan P, Lin CC, Chen NC, Yang MC, Ismail A, Fun HK, Chen CJ. Crystal structure of an antigenic outer-membrane protein from Salmonella Typhi suggests a potential antigenic loop and an efflux mechanism. Sci Rep 2015; 5:16441. [PMID: 26563565 PMCID: PMC4643347 DOI: 10.1038/srep16441] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 10/14/2015] [Indexed: 11/09/2022] Open
Abstract
ST50, an outer-membrane component of the multi-drug efflux system from Salmonella enterica serovar Typhi, is an obligatory diagnostic antigen for typhoid fever. ST50 is an excellent and unique diagnostic antigen with 95% specificity and 90% sensitivity and is used in the commercial diagnosis test kit (TYPHIDOT(TM)). The crystal structure of ST50 at a resolution of 2.98 Å reveals a trimer that forms an α-helical tunnel and a β-barrel transmembrane channel traversing the periplasmic space and outer membrane. Structural investigations suggest significant conformational variations in the extracellular loop regions, especially extracellular loop 2. This is the location of the most plausible antibody-binding domain that could be used to target the design of new antigenic epitopes for the development of better diagnostics or drugs for the treatment of typhoid fever. A molecule of the detergent n-octyl-β-D-glucoside is observed in the D-cage, which comprises three sets of Asp361 and Asp371 residues at the periplasmic entrance. These structural insights suggest a possible substrate transport mechanism in which the substrate first binds at the periplasmic entrance of ST50 and subsequently, via iris-like structural movements to open the periplasmic end, penetrates the periplasmic domain for efflux pumping of molecules, including poisonous metabolites or xenobiotics, for excretion outside the pathogen.
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Affiliation(s)
- Hong-Hsiang Guan
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu, 30076, Taiwan
| | - Masato Yoshimura
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu, 30076, Taiwan
| | - Phimonphan Chuankhayan
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu, 30076, Taiwan
| | - Chien-Chih Lin
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu, 30076, Taiwan
| | - Nai-Chi Chen
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu, 30076, Taiwan.,Institute of Biotechnology, and University Center for Bioscience and Biotechnology, National Cheng Kung University, Tainan City, 701, Taiwan
| | - Ming-Chi Yang
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu, 30076, Taiwan
| | - Asma Ismail
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Hoong-Kun Fun
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia.,X-ray Crystallography Unit, School of Physics, Universiti Sains Malaysia, 11800 USM, Penang, Malaysia
| | - Chun-Jung Chen
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu, 30076, Taiwan.,Institute of Biotechnology, and University Center for Bioscience and Biotechnology, National Cheng Kung University, Tainan City, 701, Taiwan.,Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia.,Department of Physics, National Tsing Hua University, Hsinchu, 30043, Taiwan
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41
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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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42
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Couto N, Schooling SR, Dutcher JR, Barber J. Proteome Profiles of Outer Membrane Vesicles and Extracellular Matrix of Pseudomonas aeruginosa Biofilms. J Proteome Res 2015; 14:4207-22. [PMID: 26303878 DOI: 10.1021/acs.jproteome.5b00312] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the present work, two different proteomic platforms, gel-based and gel-free, were used to map the matrix and outer membrane vesicle exoproteomes of Pseudomonas aeruginosa PAO1 biofilms. These two proteomic strategies allowed us a confident identification of 207 and 327 proteins from enriched outer membrane vesicles and whole matrix isolated from biofilms. Because of the physicochemical characteristics of these subproteomes, the two strategies showed complementarity, and thus, the most comprehensive analysis of P. aeruginosa exoproteome to date was achieved. Under our conditions, outer membrane vesicles contribute approximately 20% of the whole matrix proteome, demonstrating that membrane vesicles are an important component of the matrix. The proteomic profiles were analyzed in terms of their biological context, namely, a biofilm. Accordingly relevant metabolic processes involved in cellular adaptation to the biofilm lifestyle as well as those related to P. aeruginosa virulence capabilities were a key feature of the analyses. The diversity of the matrix proteome corroborates the idea of high heterogeneity within the biofilm; cells can display different levels of metabolism and can adapt to local microenvironments making this proteomic analysis challenging. In addition to analyzing our own primary data, we extend the analysis to published data by other groups in order to deepen our understanding of the complexity inherent within biofilm populations.
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Affiliation(s)
- Narciso Couto
- Michael Barber Centre for Mass Spectrometry, Manchester Institute for Biotechnology, University of Manchester , Princess Road, Manchester, M1 7DN, U.K
| | - Sarah R Schooling
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph , Guelph, ON N1G 2W1, Canada.,Department of Physics, University of Guelph , Guelph, ON N1G 2W1, Canada
| | - John R Dutcher
- Department of Physics, University of Guelph , Guelph, ON N1G 2W1, Canada
| | - Jill Barber
- Michael Barber Centre for Mass Spectrometry, Manchester Institute for Biotechnology, University of Manchester , Princess Road, Manchester, M1 7DN, U.K.,Manchester Pharmacy School, University of Manchester , Stopford Building, Oxford Road, Manchester, M13 9PT, U.K
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43
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Kim MK, Kim JH, Kim JS, Kang SO. Structure of the 34 kDa F-actin-bundling protein ABP34 from Dictyostelium discoideum. ACTA ACUST UNITED AC 2015; 71:1835-49. [PMID: 26327373 DOI: 10.1107/s139900471501264x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 06/30/2015] [Indexed: 11/11/2022]
Abstract
The crystal structure of the 34 kDa F-actin-bundling protein ABP34 from Dictyostelium discoideum was solved by Ca(2+)/S-SAD phasing and refined at 1.89 Å resolution. ABP34 is a calcium-regulated actin-binding protein that cross-links actin filaments into bundles. Its in vitro F-actin-binding and F-actin-bundling activities were confirmed by a co-sedimentation assay and transmission electron microscopy. The co-localization of ABP34 with actin in cells was also verified. ABP34 adopts a two-domain structure with an EF-hand-containing N-domain and an actin-binding C-domain, but has no reported overall structural homologues. The EF-hand is occupied by a calcium ion with a pentagonal bipyramidal coordination as in the canonical EF-hand. The C-domain structure resembles a three-helical bundle and superposes well onto the rod-shaped helical structures of some cytoskeletal proteins. Residues 216-244 in the C-domain form part of the strongest actin-binding sites (193-254) and exhibit a conserved sequence with the actin-binding region of α-actinin and ABP120. Furthermore, the second helical region of the C-domain is kinked by a proline break, offering a convex surface towards the solvent area which is implicated in actin binding. The F-actin-binding model suggests that ABP34 binds to the side of the actin filament and residues 216-244 fit into a pocket between actin subdomains -1 and -2 through hydrophobic interactions. These studies provide insights into the calcium coordination in the EF-hand and F-actin-binding site in the C-domain of ABP34, which are associated through interdomain interactions.
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Affiliation(s)
- Min-Kyu Kim
- Laboratory of Biophysics, School of Biological Sciences, and Institute of Microbiology, Seoul National University, Seoul 151-742, Republic of Korea
| | - Ji-Hye Kim
- Laboratory of Biophysics, School of Biological Sciences, and Institute of Microbiology, Seoul National University, Seoul 151-742, Republic of Korea
| | - Ji-Sun Kim
- Laboratory of Biophysics, School of Biological Sciences, and Institute of Microbiology, Seoul National University, Seoul 151-742, Republic of Korea
| | - Sa-Ouk Kang
- Laboratory of Biophysics, School of Biological Sciences, and Institute of Microbiology, Seoul National University, Seoul 151-742, Republic of Korea
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44
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Delmar JA, Su CC, Yu EW. Heavy metal transport by the CusCFBA efflux system. Protein Sci 2015; 24:1720-36. [PMID: 26258953 DOI: 10.1002/pro.2764] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 08/03/2015] [Indexed: 01/11/2023]
Abstract
It is widely accepted that the increased use of antibiotics has resulted in bacteria with developed resistance to such treatments. These organisms are capable of forming multi-protein structures that bridge both the inner and outer membrane to expel diverse toxic compounds directly from the cell. Proteins of the resistance nodulation cell division (RND) superfamily typically assemble as tripartite efflux pumps, composed of an inner membrane transporter, a periplasmic membrane fusion protein, and an outer membrane factor channel protein. These machines are the most powerful antimicrobial efflux machinery available to bacteria. In Escherichia coli, the CusCFBA complex is the only known RND transporter with a specificity for heavy metals, detoxifying both Cu(+) and Ag(+) ions. In this review, we discuss the known structural information for the CusCFBA proteins, with an emphasis on their assembly, interaction, and the relationship between structure and function.
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Affiliation(s)
- Jared A Delmar
- Department of Physics and Astronomy, Iowa State University, Ames, Iowa, 50011
| | - Chih-Chia Su
- Department of Physics and Astronomy, Iowa State University, Ames, Iowa, 50011
| | - Edward W Yu
- Department of Physics and Astronomy, Iowa State University, Ames, Iowa, 50011
- Department of Chemistry, Iowa State University, Ames, Iowa, 50011
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45
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Dreier J, Ruggerone P. Interaction of antibacterial compounds with RND efflux pumps in Pseudomonas aeruginosa. Front Microbiol 2015; 6:660. [PMID: 26217310 PMCID: PMC4495556 DOI: 10.3389/fmicb.2015.00660] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 06/16/2015] [Indexed: 01/14/2023] Open
Abstract
Pseudomonas aeruginosa infections are becoming increasingly difficult to treat due to intrinsic antibiotic resistance and the propensity of this pathogen to accumulate diverse resistance mechanisms. Hyperexpression of efflux pumps of the Resistance-Nodulation-Cell Division (RND)-type multidrug efflux pumps (e.g., MexAB-OprM), chromosomally encoded by mexAB-oprM, mexCD-oprJ, mexEF-oprN, and mexXY (-oprA) is often detected in clinical isolates and contributes to worrying multi-drug resistance phenotypes. Not all antibiotics are affected to the same extent by the aforementioned RND efflux pumps. The impact of efflux on antibiotic activity varies not only between different classes of antibiotics but also between members of the same family of antibiotics. Subtle differences in physicochemical features of compound-pump and compound-solvent interactions largely determine how compounds are affected by efflux activity. The combination of different high-resolution techniques helps to gain insight into the functioning of these molecular machineries. This review discusses substrate recognition patterns based on experimental evidence and computer simulations with a focus on MexB, the pump subunit of the main RND transporter in P. aeruginosa.
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Affiliation(s)
- Jürg Dreier
- Basilea Pharmaceutica International Ltd.,Basel, Switzerland
| | - Paolo Ruggerone
- Dipartimento di Fisica, Università di Cagliari – Cittadella UniversitariaMonserrato, Italy
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46
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Monlezun L, Phan G, Benabdelhak H, Lascombe MB, Enguéné VYN, Picard M, Broutin I. New OprM structure highlighting the nature of the N-terminal anchor. Front Microbiol 2015; 6:667. [PMID: 26191054 PMCID: PMC4486845 DOI: 10.3389/fmicb.2015.00667] [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: 02/10/2015] [Accepted: 06/19/2015] [Indexed: 01/11/2023] Open
Abstract
Among the different mechanisms used by bacteria to resist antibiotics, active efflux plays a major role. In Gram-negative bacteria, active efflux is carried out by tripartite efflux pumps that form a macromolecular assembly spanning both membranes of the cellular wall. At the outer membrane level, a well-conserved outer membrane factor (OMF) protein acts as an exit duct, but its sequence varies greatly among different species. The OMFs share a similar tri-dimensional structure that includes a beta-barrel pore domain that stabilizes the channel within the membrane. In addition, OMFs are often subjected to different N-terminal post-translational modifications (PTMs), such as an acylation with a lipid. The role of additional N-terminal anchors is all the more intriguing since it is not always required among the OMFs family. Understanding this optional PTM could open new research lines in the field of antibiotics resistance. In Escherichia coli, it has been shown that CusC is modified with a tri-acylated lipid, whereas TolC does not show any modification. In the case of OprM from Pseudomonas aeruginosa, the N-terminal modification remains a matter of debate, therefore, we used several approaches to investigate this issue. As definitive evidence, we present a new X-ray structure at 3.8 Å resolution that was solved in a new space group, making it possible to model the N-terminal residue as a palmitoylated cysteine.
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Affiliation(s)
- Laura Monlezun
- Laboratoire de Cristallographie et RMN Biologiques, CNRS UMR 8015, Faculté de Pharmacie, Université Paris Descartes Paris, France
| | - Gilles Phan
- Laboratoire de Cristallographie et RMN Biologiques, CNRS UMR 8015, Faculté de Pharmacie, Université Paris Descartes Paris, France
| | - Houssain Benabdelhak
- Laboratoire d'Imagerie Biomédicale, Sorbonne Universités, Université Pierre et Marie Curie Paris 6, CNRS UMR 7371, INSERM U1146 Paris, France
| | - Marie-Bernard Lascombe
- Laboratoire de Cristallographie et RMN Biologiques, CNRS UMR 8015, Faculté de Pharmacie, Université Paris Descartes Paris, France
| | - Véronique Y N Enguéné
- Laboratoire de Cristallographie et RMN Biologiques, CNRS UMR 8015, Faculté de Pharmacie, Université Paris Descartes Paris, France
| | - Martin Picard
- Laboratoire de Cristallographie et RMN Biologiques, CNRS UMR 8015, Faculté de Pharmacie, Université Paris Descartes Paris, France
| | - Isabelle Broutin
- Laboratoire de Cristallographie et RMN Biologiques, CNRS UMR 8015, Faculté de Pharmacie, Université Paris Descartes Paris, France
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47
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Iyer R, Erwin AL. Direct measurement of efflux in Pseudomonas aeruginosa using an environment-sensitive fluorescent dye. Res Microbiol 2015; 166:516-24. [PMID: 26117599 DOI: 10.1016/j.resmic.2015.06.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Revised: 06/17/2015] [Accepted: 06/18/2015] [Indexed: 11/16/2022]
Abstract
Resistance-Nodulation-Division (RND) family pumps AcrB and MexB are the major efflux routes in Escherichia coli and Pseudomonas aeruginosa respectively. Fluorescent environment-sensitive dyes provide a means to study efflux pump function in live bacterial cells in real-time. Recently, we demonstrated the utility of this approach using the dye Nile Red to quantify AcrB-mediated efflux and measured the ability of antibiotics and other efflux pump substrates to compete with efflux of Nile Red, independent of antibacterial activity. Here, we extend this method to P. aeruginosa and describe a novel application that permits the comparison and rank-ordering of bacterial strains by their inherent efflux potential. We show that glucose and l-malate re-energize Nile Red efflux in P. aeruginosa, and we highlight differences in the glucose dependence and kinetics of efflux between P. aeruginosa and E. coli. We quantify the differences in efflux among a set of P. aeruginosa laboratory strains, which include PAO1, the hyper-sensitive strain ATCC 35151 and its parent, ATCC 12055. Efflux of Nile Red in P. aeruginosa is mediated by MexAB-OprM and is slower than in E. coli. In conclusion, we describe an efflux measurement tool for use in antibacterial drug discovery and basic research on P. aeruginosa efflux pumps.
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Affiliation(s)
- Ramkumar Iyer
- Infectious Diseases Department, Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, MA, USA.
| | - Alice L Erwin
- Infectious Diseases Department, Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, MA, USA
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48
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Molecular architecture of the bacterial tripartite multidrug efflux pump focusing on the adaptor bridging model. J Microbiol 2015; 53:355-64. [DOI: 10.1007/s12275-015-5248-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 05/18/2015] [Accepted: 05/18/2015] [Indexed: 10/23/2022]
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49
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Symmons MF, Marshall RL, Bavro VN. Architecture and roles of periplasmic adaptor proteins in tripartite efflux assemblies. Front Microbiol 2015; 6:513. [PMID: 26074901 PMCID: PMC4446572 DOI: 10.3389/fmicb.2015.00513] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 05/08/2015] [Indexed: 12/12/2022] Open
Abstract
Recent years have seen major advances in the structural understanding of the different components of tripartite efflux assemblies, which encompass the multidrug efflux (MDR) pumps and type I secretion systems. The majority of these investigations have focused on the role played by the inner membrane transporters and the outer membrane factor (OMF), leaving the third component of the system – the Periplasmic Adaptor Proteins (PAPs) – relatively understudied. Here we review the current state of knowledge of these versatile proteins which, far from being passive linkers between the OMF and the transporter, emerge as active architects of tripartite assemblies, and play diverse roles in the transport process. Recognition between the PAPs and OMFs is essential for pump assembly and function, and targeting this interaction may provide a novel avenue for combating multidrug resistance. With the recent advances elucidating the drug efflux and energetics of the tripartite assemblies, the understanding of the interaction between the OMFs and PAPs is the last piece remaining in the complete structure of the tripartite pump assembly puzzle.
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Affiliation(s)
- Martyn F Symmons
- Department of Veterinary Medicine, University of Cambridge Cambridge, UK
| | - Robert L Marshall
- Institute of Microbiology and Infection, University of Birmingham Birmingham, UK
| | - Vassiliy N Bavro
- Institute of Microbiology and Infection, University of Birmingham Birmingham, UK
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50
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Zgurskaya HI, Weeks JW, Ntreh AT, Nickels LM, Wolloscheck D. Mechanism of coupling drug transport reactions located in two different membranes. Front Microbiol 2015; 6:100. [PMID: 25759685 PMCID: PMC4338810 DOI: 10.3389/fmicb.2015.00100] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 01/26/2015] [Indexed: 01/01/2023] Open
Abstract
Gram- negative bacteria utilize a diverse array of multidrug transporters to pump toxic compounds out of the cell. Some transporters, together with periplasmic membrane fusion proteins (MFPs) and outer membrane channels, assemble trans-envelope complexes that expel multiple antibiotics across outer membranes of Gram-negative bacteria and into the external medium. Others further potentiate this efflux by pumping drugs across the inner membrane into the periplasm. Together these transporters create a powerful network of efflux that protects bacteria against a broad range of antimicrobial agents. This review is focused on the mechanism of coupling transport reactions located in two different membranes of Gram-negative bacteria. Using a combination of biochemical, genetic and biophysical approaches we have reconstructed the sequence of events leading to the assembly of trans-envelope drug efflux complexes and characterized the roles of periplasmic and outer membrane proteins in this process. Our recent data suggest a critical step in the activation of intermembrane efflux pumps, which is controlled by MFPs. We propose that the reaction cycles of transporters are tightly coupled to the assembly of the trans-envelope complexes. Transporters and MFPs exist in the inner membrane as dormant complexes. The activation of complexes is triggered by MFP binding to the outer membrane channel, which leads to a conformational change in the membrane proximal domain of MFP needed for stimulation of transporters. The activated MFP-transporter complex engages the outer membrane channel to expel substrates across the outer membrane. The recruitment of the channel is likely triggered by binding of effectors (substrates) to MFP or MFP-transporter complexes. This model together with recent structural and functional advances in the field of drug efflux provides a fairly detailed understanding of the mechanism of drug efflux across the two membranes.
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Affiliation(s)
- Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma Norman, OK, USA
| | - Jon W Weeks
- Department of Chemistry and Biochemistry, University of Oklahoma Norman, OK, USA
| | - Abigail T Ntreh
- Department of Chemistry and Biochemistry, University of Oklahoma Norman, OK, USA
| | - Logan M Nickels
- Department of Chemistry and Biochemistry, University of Oklahoma Norman, OK, USA
| | - David Wolloscheck
- Department of Chemistry and Biochemistry, University of Oklahoma Norman, OK, USA
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