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Lewis BR, Uddin MR, Kuo KM, Shah LMN, Harris NJ, Booth PJ, Hammerschmid D, Gumbart JC, Zgurskaya HI, Reading E. Mg 2+-dependent mechanism of environmental versatility in a multidrug efflux pump. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.10.597921. [PMID: 38915626 PMCID: PMC11195059 DOI: 10.1101/2024.06.10.597921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Tripartite resistance nodulation and cell division multidrug efflux pumps span the periplasm and are a major driver of multidrug resistance among Gram-negative bacteria. The periplasm provides a distinct environment between the inner and outer membranes of Gram-negative bacteria. Cations, such as Mg2+, become concentrated within the periplasm and, in contrast to the cytoplasm, its pH is sensitive to conditions outside the cell. Here, we reveal an interplay between Mg2+ and pH in modulating the dynamics of the periplasmic adaptor protein, AcrA, and its function within the prototypical AcrAB-TolC multidrug efflux pump from Escherichia coli. In the absence of Mg2+, AcrA becomes increasingly plastic within acidic conditions, but when Mg2+ is bound this is ameliorated, resulting in domain specific organisation in neutral to weakly acidic regimes. We establish a unique histidine residue directs these structural dynamics and is essential for sustaining pump efflux activity across acidic, neutral, and alkaline conditions. Overall, we propose Mg2+ conserves the structural mobility of AcrA to ensure optimal AcrAB-TolC function within rapid changing environments commonly faced by the periplasm during bacterial infection and colonization. This work highlights that Mg2+ is an important mechanistic component in this pump class and possibly across other periplasmic lipoproteins.
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Affiliation(s)
- Benjamin Russell Lewis
- Department of Chemistry, Britannia House, 7 Trinity Street, King’s College London, London, SE1 1DB, UK
| | - Muhammad R. Uddin
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, USA
| | - Katie M. Kuo
- School of Physics, Georgia Institute of Technology, 837 State Street NW, Atlanta, Georgia 30332, USA
| | - Laila M. N. Shah
- Department of Chemistry, Britannia House, 7 Trinity Street, King’s College London, London, SE1 1DB, UK
| | - Nicola J. Harris
- Department of Chemistry, Britannia House, 7 Trinity Street, King’s College London, London, SE1 1DB, UK
| | - Paula J. Booth
- Department of Chemistry, Britannia House, 7 Trinity Street, King’s College London, London, SE1 1DB, UK
| | - Dietmar Hammerschmid
- Department of Chemistry, Britannia House, 7 Trinity Street, King’s College London, London, SE1 1DB, UK
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - James C. Gumbart
- School of Physics, Georgia Institute of Technology, 837 State Street NW, Atlanta, Georgia 30332, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, Georgia 30332, USA
| | - Helen I. Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, USA
| | - Eamonn Reading
- Department of Chemistry, Britannia House, 7 Trinity Street, King’s College London, London, SE1 1DB, UK
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
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2
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Kuklewicz J, Zimmer J. Molecular insights into capsular polysaccharide secretion. Nature 2024; 628:901-909. [PMID: 38570679 PMCID: PMC11041684 DOI: 10.1038/s41586-024-07248-9] [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: 08/11/2023] [Accepted: 02/27/2024] [Indexed: 04/05/2024]
Abstract
Capsular polysaccharides (CPSs) fortify the cell boundaries of many commensal and pathogenic bacteria1. Through the ABC-transporter-dependent biosynthesis pathway, CPSs are synthesized intracellularly on a lipid anchor and secreted across the cell envelope by the KpsMT ABC transporter associated with the KpsE and KpsD subunits1,2. Here we use structural and functional studies to uncover crucial steps of CPS secretion in Gram-negative bacteria. We show that KpsMT has broad substrate specificity and is sufficient for the translocation of CPSs across the inner bacterial membrane, and we determine the cell surface organization and localization of CPSs using super-resolution fluorescence microscopy. Cryo-electron microscopy analyses of the KpsMT-KpsE complex in six different states reveal a KpsE-encaged ABC transporter, rigid-body conformational rearrangements of KpsMT during ATP hydrolysis and recognition of a glycolipid inside a membrane-exposed electropositive canyon. In vivo CPS secretion assays underscore the functional importance of canyon-lining basic residues. Combined, our analyses suggest a molecular model of CPS secretion by ABC transporters.
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Affiliation(s)
- Jeremi Kuklewicz
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Jochen Zimmer
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, USA.
- Howard Hughes Medical Institute, University of Virginia, Charlottesville, VA, USA.
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3
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Wilhelm J, Pos KM. Molecular insights into the determinants of substrate specificity and efflux inhibition of the RND efflux pumps AcrB and AdeB. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001438. [PMID: 38358391 PMCID: PMC10924465 DOI: 10.1099/mic.0.001438] [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: 11/01/2022] [Accepted: 01/30/2024] [Indexed: 02/16/2024]
Abstract
Gram-negative bacterial members of the Resistance Nodulation and cell Division (RND) superfamily form tripartite efflux pump systems that span the cell envelope. One of the intriguing features of the multiple drug efflux members of this superfamily is their ability to recognize different classes of antibiotics, dyes, solvents, bile salts, and detergents. This review provides an overview of the molecular mechanisms of multiple drug efflux catalysed by the tripartite RND efflux system AcrAB-TolC from Eschericha coli. The determinants for sequential or simultaneous multiple substrate binding and efflux pump inhibitor binding are discussed. A comparison is made with the determinants for substrate binding of AdeB from Acinetobacter baumannii, which acts within the AdeABC multidrug efflux system. There is an apparent general similarity between the structures of AcrB and AdeB and their substrate specificity. However, the presence of distinct conformational states and different drug efflux capacities as revealed by single-particle cryo-EM and mutational analysis suggest that the drug binding and transport features exhibited by AcrB may not be directly extrapolated to the homolog AdeB efflux pump.
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Affiliation(s)
- Julia Wilhelm
- Institute of Biochemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Klaas Martinus Pos
- Institute of Biochemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
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4
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Pun M, Khazanov N, Galsurker O, Kerem Z, Senderowitz H, Yedidia I. Inhibition of AcrAB-TolC enhances antimicrobial activity of phytochemicals in Pectobacterium brasiliense. FRONTIERS IN PLANT SCIENCE 2023; 14:1161702. [PMID: 37229130 PMCID: PMC10203483 DOI: 10.3389/fpls.2023.1161702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/19/2023] [Indexed: 05/27/2023]
Abstract
Introduction The eons-long co-evolvement of plants and bacteria led to a plethora of interactions between the two kingdoms, in which bacterial pathogenicity is counteracted by plant-derived antimicrobial defense molecules. In return, efflux pumps (EP) form part of the resistance mechanism employed by bacteria to permit their survival in this hostile chemical environment. In this work we study the effect of combinations of efflux pump inhibitors (EPIs) and plant-derived phytochemicals on bacterial activity using Pectobacteriun brasiliense 1692 (Pb1692) as a model system. Methods We measured the minimal inhibitory concentration (MIC) of two phytochemicals, phloretin (Pht) and naringenin (Nar), and of one common antibiotic ciprofloxacin (Cip), either alone or in combinations with two known inhibitors of the AcrB EP of Escherichia coli, a close homolog of the AcrAB-TolC EP of Pb1692. In addition, we also measured the expression of genes encoding for the EP, under similar conditions. Results Using the FICI equation, we observed synergism between the EPIs and the phytochemicals, but not between the EPIs and the antibiotic, suggesting that EP inhibition potentiated the antimicrobial activity of the plant derived compounds, but not of Cip. Docking simulations were successfully used to rationalize these experimental results. Discussion Our findings suggest that AcrAB-TolC plays an important role in survival and fitness of Pb1692 in the plant environment and that its inhibition is a viable strategy for controlling bacterial pathogenicity.
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Affiliation(s)
- Manoj Pun
- The Institute of Plant Sciences, Volcani Center, Agricultural Research Organization (ARO), Rishon Lezion, Israel
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Netaly Khazanov
- Department of Chemistry, Bar-Ilan University, Ramat Gan, Israel
| | - Ortal Galsurker
- The Institute of Plant Sciences, Volcani Center, Agricultural Research Organization (ARO), Rishon Lezion, Israel
| | - Zohar Kerem
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | | | - Iris Yedidia
- The Institute of Plant Sciences, Volcani Center, Agricultural Research Organization (ARO), Rishon Lezion, Israel
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5
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Darby EM, Trampari E, Siasat P, Gaya MS, Alav I, Webber MA, Blair JMA. Molecular mechanisms of antibiotic resistance revisited. Nat Rev Microbiol 2023; 21:280-295. [PMID: 36411397 DOI: 10.1038/s41579-022-00820-y] [Citation(s) in RCA: 195] [Impact Index Per Article: 195.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2022] [Indexed: 11/22/2022]
Abstract
Antibiotic resistance is a global health emergency, with resistance detected to all antibiotics currently in clinical use and only a few novel drugs in the pipeline. Understanding the molecular mechanisms that bacteria use to resist the action of antimicrobials is critical to recognize global patterns of resistance and to improve the use of current drugs, as well as for the design of new drugs less susceptible to resistance development and novel strategies to combat resistance. In this Review, we explore recent advances in understanding how resistance genes contribute to the biology of the host, new structural details of relevant molecular events underpinning resistance, the identification of new resistance gene families and the interactions between different resistance mechanisms. Finally, we discuss how we can use this information to develop the next generation of antimicrobial therapies.
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Affiliation(s)
- Elizabeth M Darby
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | | | - Pauline Siasat
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | | | - Ilyas Alav
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Mark A Webber
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK.
- Medical School, University of East Anglia, Norwich Research Park, Norwich, UK.
| | - Jessica M A Blair
- College of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK.
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6
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Wan X, Li Q, Olsen RH, Meng H, Zhang Z, Wang J, Zheng H, Li L, Shi L. Engineering a CRISPR interference system targeting AcrAB-TolC efflux pump to prevent multidrug resistance development in Escherichia coli. J Antimicrob Chemother 2022; 77:2158-2166. [PMID: 35642356 DOI: 10.1093/jac/dkac166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 05/06/2022] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVES We engineered a CRISPR interference (CRISPRi) system targeting the AcrAB-TolC efflux pump to prevent MDR development in Escherichia coli. METHODS Nine specific single-guide RNAs (sgRNAs) were designed to target the components of the AcrAB-TolC efflux pump, namely AcrA, AcrB and TolC. A total of thirteen CRISPRi recombinant plasmids were constructed with single or clustered sgRNAs. The transcriptional levels of the target genes, MICs of multiple antibiotics and biofilm formation in each CRISPRi strain were tested. RESULTS The CRISPRi system expressing sgRNA clusters targeting acrB and tolC simultaneously exhibited the highest inhibitory effect on AcrAB-TolC efflux pump activity in E. coli HB101, with 78.3%, 90.0% and 65.4% inhibition rates on the transcriptional levels of acrA, acrB and tolC, respectively. The CRISPRi system resulted in ∼2-, ∼8- and 16-fold increased susceptibility to rifampicin, erythromycin and tetracycline, respectively. In addition, the constructed CRISPRi system reduced biofilm formation with inhibition rates in the range of 11.2% to 58.2%. CONCLUSIONS To the best of our knowledge, this is the first report on the construction of an inducible CRISPRi system targeting the AcrAB-TolC efflux pump to prevent MDR development in E. coli. This study provides insights for future regulation and manipulation of AcrAB-TolC activity and bacterial MDR by a CRISPRi system.
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Affiliation(s)
- Xiulin Wan
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Qingyang Li
- College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Rikke Heidemann Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Hecheng Meng
- School of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Zhigang Zhang
- State Key Laboratory of Food Safety Technology for Meat Products, Xiamen Yinxiang Group, Xiamen, China
| | - Junlin Wang
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Hanyu Zheng
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Lili Li
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China
| | - Lei Shi
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, China.,State Key Laboratory of Food Safety Technology for Meat Products, Xiamen Yinxiang Group, Xiamen, China
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7
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Cacciotto P, Basciu A, Oliva F, Malloci G, Zacharias M, Ruggerone P, Vargiu AV. Molecular rationale for the impairment of the MexAB-OprM efflux pump by a single mutation in MexA. Comput Struct Biotechnol J 2022; 20:252-260. [PMID: 35024097 PMCID: PMC8717590 DOI: 10.1016/j.csbj.2021.11.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 11/16/2022] Open
Abstract
Efflux pumps of the Resistance-Nodulation-cell Division (RND) superfamily contribute to intrinsic and acquired resistance in Gram-negative pathogens by expelling chemically unrelated antibiotics with high efficiency. They are tripartite systems constituted by an inner-membrane-anchored transporter, an outer membrane factor protein, and a membrane fusion protein. Multimerization of the membrane fusion protein is an essential prerequisite for full functionality of these efflux pumps. In this work, we employed complementary computational techniques to investigate the stability of a dimeric unit of MexA (the membrane fusion protein of the MexAB-OprM RND efflux pump of Pseudomonas aeruginosa), and to provide a molecular rationale for the effect of the G72S substitution, which affects MexAB-OprM functionality by impairing the assembly of MexA. Our findings indicate that: i) dimers of this protein are stable in multiple µs-long molecular dynamics simulations; ii) the mutation drastically alters the conformational equilibrium of MexA, favouring a collapsed conformation that is unlikely to form dimers or higher order assemblies. Unveiling the mechanistic aspects underlying large conformational distortions induced by minor sequence changes is informative to efforts at interfering with the activity of this elusive bacterial weapon. In this respect, our work further confirms how molecular simulations can give important contribution and useful insights to characterize the mechanism of highly complex biological systems.
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Affiliation(s)
- Pierpaolo Cacciotto
- Dipartimento di Fisica, Università degli Studi di Cagliari, S.P. Monserrato-Sestu km 0.700, I-09042 Monserrato (CA), Italy
| | - Andrea Basciu
- Dipartimento di Fisica, Università degli Studi di Cagliari, S.P. Monserrato-Sestu km 0.700, I-09042 Monserrato (CA), Italy
| | - Francesco Oliva
- Dipartimento di Fisica, Università degli Studi di Cagliari, S.P. Monserrato-Sestu km 0.700, I-09042 Monserrato (CA), Italy
| | - Giuliano Malloci
- Dipartimento di Fisica, Università degli Studi di Cagliari, S.P. Monserrato-Sestu km 0.700, I-09042 Monserrato (CA), Italy
| | - Martin Zacharias
- Physics Department, Technische Universität München, James-Franck-Str. 1, 85748 Garching, Germany
| | - Paolo Ruggerone
- Dipartimento di Fisica, Università degli Studi di Cagliari, S.P. Monserrato-Sestu km 0.700, I-09042 Monserrato (CA), Italy
| | - Attilio V Vargiu
- Dipartimento di Fisica, Università degli Studi di Cagliari, S.P. Monserrato-Sestu km 0.700, I-09042 Monserrato (CA), Italy
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8
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Gumbart JC, Ferreira JL, Hwang H, Hazel AJ, Cooper CJ, Parks JM, Smith JC, Zgurskaya HI, Beeby M. Lpp positions peptidoglycan at the AcrA-TolC interface in the AcrAB-TolC multidrug efflux pump. Biophys J 2021; 120:3973-3982. [PMID: 34411576 DOI: 10.1016/j.bpj.2021.08.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 07/02/2021] [Accepted: 08/11/2021] [Indexed: 01/07/2023] Open
Abstract
The multidrug efflux pumps of Gram-negative bacteria are a class of complexes that span the periplasm, coupling both the inner and outer membranes to expel toxic molecules. The best-characterized example of these tripartite pumps is the AcrAB-TolC complex of Escherichia coli. However, how the complex interacts with the peptidoglycan (PG) cell wall, which is anchored to the outer membrane (OM) by Braun's lipoprotein (Lpp), is still largely unknown. In this work, we present molecular dynamics simulations of a complete, atomistic model of the AcrAB-TolC complex with the inner membrane, OM, and PG layers all present. We find that the PG localizes to the junction of AcrA and TolC, in agreement with recent cryo-tomography data. Free-energy calculations reveal that the positioning of PG is determined by the length and conformation of multiple Lpp copies anchoring it to the OM. The distance between the PG and OM measured in cryo-electron microscopy images of wild-type E. coli also agrees with the simulation-derived spacing. Sequence analysis of AcrA suggests a conserved role for interactions with PG in the assembly and stabilization of efflux pumps, one that may extend to other trans-envelope complexes as well.
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Affiliation(s)
- James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia.
| | - Josie L Ferreira
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Hyea Hwang
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia
| | - Anthony J Hazel
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia
| | - Connor J Cooper
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Jerry M Parks
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma
| | - Morgan Beeby
- Department of Life Sciences, Imperial College London, London, United Kingdom
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9
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Zwama M, Nishino K. Ever-Adapting RND Efflux Pumps in Gram-Negative Multidrug-Resistant Pathogens: A Race against Time. Antibiotics (Basel) 2021; 10:774. [PMID: 34201908 PMCID: PMC8300642 DOI: 10.3390/antibiotics10070774] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 01/13/2023] Open
Abstract
The rise in multidrug resistance (MDR) is one of the greatest threats to human health worldwide. MDR in bacterial pathogens is a major challenge in healthcare, as bacterial infections are becoming untreatable by commercially available antibiotics. One of the main causes of MDR is the over-expression of intrinsic and acquired multidrug efflux pumps, belonging to the resistance-nodulation-division (RND) superfamily, which can efflux a wide range of structurally different antibiotics. Besides over-expression, however, recent amino acid substitutions within the pumps themselves-causing an increased drug efflux efficiency-are causing additional worry. In this review, we take a closer look at clinically, environmentally and laboratory-evolved Gram-negative bacterial strains and their decreased drug sensitivity as a result of mutations directly in the RND-type pumps themselves (from Escherichia coli, Salmonella enterica, Neisseria gonorrhoeae, Pseudomonas aeruginosa, Acinetobacter baumannii and Legionella pneumophila). We also focus on the evolution of the efflux pumps by comparing hundreds of efflux pumps to determine where conservation is concentrated and where differences in amino acids can shed light on the broad and even broadening drug recognition. Knowledge of conservation, as well as of novel gain-of-function efflux pump mutations, is essential for the development of novel antibiotics and efflux pump inhibitors.
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Affiliation(s)
- Martijn Zwama
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - Kunihiko Nishino
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Ibaraki, Osaka 567-0047, Japan
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan
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10
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Rout UK, Sanket AS, Sisodia BS, Mohapatra PK, Pati S, Kant R, Dwivedi GR. A Comparative Review on Current and Future Drug Targets Against Bacteria & Malaria. Curr Drug Targets 2021; 21:736-775. [PMID: 31995004 DOI: 10.2174/1389450121666200129103618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 12/13/2019] [Accepted: 12/20/2019] [Indexed: 11/22/2022]
Abstract
Long before the discovery of drugs like 'antibiotic and anti-parasitic drugs', the infectious diseases caused by pathogenic bacteria and parasites remain as one of the major causes of morbidity and mortality in developing and underdeveloped countries. The phenomenon by which the organism exerts resistance against two or more structurally unrelated drugs is called multidrug resistance (MDR) and its emergence has further complicated the treatment scenario of infectious diseases. Resistance towards the available set of treatment options and poor pipeline of novel drug development puts an alarming situation. A universal goal in the post-genomic era is to identify novel targets/drugs for various life-threatening diseases caused by such pathogens. This review is conceptualized in the backdrop of drug resistance in two major pathogens i.e. "Pseudomonas aeruginosa" and "Plasmodium falciparum". In this review, the available targets and key mechanisms of resistance of these pathogens have been discussed in detail. An attempt has also been made to analyze the common drug targets of bacteria and malaria parasite to overcome the current drug resistance scenario. The solution is also hypothesized in terms of a present pipeline of drugs and efforts made by scientific community.
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Affiliation(s)
- Usha K Rout
- Microbiology Department, ICMR-Regional Medical Research Centre, Bhubaneswar-751023, India
| | | | - Brijesh S Sisodia
- Regional Ayurveda Research Institute for Drug Development, Gwalior-474 009, India
| | | | - Sanghamitra Pati
- Microbiology Department, ICMR-Regional Medical Research Centre, Bhubaneswar-751023, India
| | - Rajni Kant
- ICMR-Regional Medical Research Centre, Gorakhpur, Uttar Pradesh- 273013, India
| | - Gaurav R Dwivedi
- ICMR-Regional Medical Research Centre, Gorakhpur, Uttar Pradesh- 273013, India
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11
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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: 85] [Impact Index Per Article: 28.3] [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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12
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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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13
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Rajapaksha P, Pandeya A, Wei Y. Probing the Dynamics of AcrB Through Disulfide Bond Formation. ACS OMEGA 2020; 5:21844-21852. [PMID: 32905396 PMCID: PMC7469415 DOI: 10.1021/acsomega.0c02921] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 08/05/2020] [Indexed: 06/11/2023]
Abstract
The resistant-nodulation-division (RND) superfamily member tripartite AcrA-AcrB-TolC efflux pump is a major contributor to the multidrug resistance in Escherichia coli. AcrB is the inner membrane protein of the efflux complex and is responsible for the recognition and binding of compounds before their transportation out of the cell. Understanding the dynamics of AcrB during functional rotation in the process of drug efflux is the focus of this study. For this purpose, we introduced six inter-subunit disulfide bonds into the periplasmic domain of AcrB using site-directed mutagenesis to study the importance of the relative flexibility at the inter-subunit interface. Western blot analysis revealed the formation of disulfide bond-linked AcrB oligomers, which were reduced into monomers under reducing conditions. The impact of mutation and formation of disulfide bond on efflux were evaluated via comparison of the minimum inhibitory concentration (MIC) of an acrB knockout strain expressing different mutants. The double Cys mutants tested led to equal or higher susceptibility to AcrB substrates compared to their corresponding single mutants. To determine if the reduction of activity in a double mutant is due to restriction on conformational changes by the disulfide bond formation, ethidium bromide accumulation assays were conducted utilizing dithiothreitol (DTT) as the reducing agent. In two cases, the activities of the double Cys mutants were partially restored by DTT reduction, confirming the importance of relative movement in the respective location for function. These findings provide new insights into the dynamics of the AcrAB-TolC efflux pump in E. coli.
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14
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Marshall RL, Bavro VN. Mutations in the TolC Periplasmic Domain Affect Substrate Specificity of the AcrAB-TolC Pump. Front Mol Biosci 2020; 7:166. [PMID: 32850959 PMCID: PMC7396618 DOI: 10.3389/fmolb.2020.00166] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 07/01/2020] [Indexed: 01/08/2023] Open
Abstract
TolC and the other members of the outer membrane factor (OMF) family are outer membrane proteins forming trimeric channels that serve as a conduit for most actively effluxed substrates in Gram-negative bacteria by providing a key component in a multitude of tripartite efflux-pumps. Current models of tripartite pump assembly ascribe substrate selection to the inner-membrane transporter and periplasmic-adapter protein (PAP) assembly, suggesting that TolC is a passive, non-selective channel. While the membrane-embedded portion of the protein adopts a porin-like fold, the periplasmic domain of TolC presents a unique "alpha-barrel" architecture. This alpha-barrel consists of pseudo-continuous α-helices forming curved coiled-coils, whose tips form α-helical hairpins, relaxation of which results in a transition of TolC from a closed to an open-aperture state allowing effective efflux of substrates through its channel. Here, we analyzed the effects of site-directed mutations targeting the alpha-barrel of TolC, of the principal tripartite efflux-pump Escherichia coli AcrAB-TolC, on the activity and specificity of efflux. Live-cell functional assays with these TolC mutants revealed that positions both at the periplasmic tip of, and partway up the TolC coiled-coil alpha-barrel domain are involved in determining the functionality of the complex. We report that mutations affecting the electrostatic properties of the channel, particularly the D371V mutation, significantly impact growth even in the absence of antibiotics, causing hyper-susceptibility to all tested efflux-substrates. These results suggest that inhibition of TolC functionality is less well-tolerated than deletion of tolC, and such inhibition may have an antibacterial effect. Significantly and unexpectedly, we identified antibiotic-specific phenotypes associated with novel TolC mutations, suggesting that substrate specificity may not be determined solely by the transporter protein or the PAP, but may reside at least partially with the TolC-channel. Furthermore, some of the effects of mutations are difficult to reconcile with the currently prevalent tip-to-tip model of PAP-TolC interaction due to their location higher-up on the TolC alpha-barrel relative to the proposed PAP-docking sites. Taken together our results suggest a possible new role for TolC in vetting of efflux substrates, alongside its established role in tripartite complex assembly.
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Affiliation(s)
- Robert L. Marshall
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Vassiliy N. Bavro
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
- School of Life Sciences, University of Essex, Colchester, United Kingdom
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15
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Kim S, Kim SH, Ahn J, Jo I, Lee ZW, Choi SH, Ha NC. Crystal Structure of the Regulatory Domain of MexT, a Transcriptional Activator of the MexEFOprN Efflux Pump in Pseudomonas aeruginosa. Mol Cells 2019; 42:850-857. [PMID: 31722511 PMCID: PMC6939650 DOI: 10.14348/molcells.2019.0168] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 09/06/2019] [Accepted: 10/07/2019] [Indexed: 12/02/2022] Open
Abstract
The Gram-negative opportunistic pathogen, Pseudomonas aeruginosa , has multiple multidrug efflux pumps. MexT, a LysR-type transcriptional regulator, functions as a transcriptional activator of the MexEF-OprN efflux system. MexT consists of an N-terminal DNA-binding domain and a C-terminal regulatory domain (RD). Little is known regarding MexT ligands and its mechanism of activation. We elucidated the crystal structure of the MexT RD at 2.0 Å resolution. The structure comprised two protomer chains in a dimeric arrangement. MexT possessed an arginine-rich region and a hydrophobic patch lined by a variable loop, both of which are putative ligand-binding sites. The three-dimensional structure of MexT provided clues to the interacting ligand structure. A DNase I footprinting assay of full-length MexT identified two MexT-binding sequence in the mexEF oprN promoter. Our findings enhance the understanding of the regulation of MexT-dependent activation of efflux pumps.
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Affiliation(s)
- Suhyeon Kim
- Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Center for Food and Bioconvergence, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
| | - Songhee H. Kim
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826,
Korea
| | - Jinsook Ahn
- Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Center for Food and Bioconvergence, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
| | - Inseong Jo
- Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Center for Food and Bioconvergence, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
| | - Zee-Won Lee
- Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Center for Food and Bioconvergence, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
| | - Sang Ho Choi
- Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Center for Food and Bioconvergence, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
| | - Nam-Chul Ha
- Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Center for Food and Bioconvergence, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826,
Korea
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16
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Xu S, Chen G, Liu Z, Xu D, Wu Z, Li Z, Hong M. Site-Directed Mutagenesis Reveals Crucial Residues in Escherichia coli Resistance-Nodulation-Division Efflux Pump OqxB. Microb Drug Resist 2019; 26:550-560. [PMID: 31834851 DOI: 10.1089/mdr.2019.0165] [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] [Indexed: 11/13/2022] Open
Abstract
Resistance-nodulation-division (RND) efflux pumps are important determinants of multidrug resistance in Gram-negative bacteria. As one of the typical members of the RND superfamily, Escherichia coli OqxAB multidrug efflux pump confers resistance to antimicrobial agents, such as olaquindox and fluoroquinolone. In the present study, site-directed mutagenesis and antimicrobial susceptibility measurement assay were applied to identify the crucial residues within OqxB, the transporter component of the OqxAB efflux pump system. It was found that alanine substitution of proton translocation pathway residues D410, D411, and R976 resulted in a complete loss of the transport function. Further studies revealed that the charge property of these residues is important for proper function of OqxB. Alanine replacement of residues involved in substrate-binding domains, including V141, F180, Y330, and F626, exhibited different responses toward different antimicrobial agents. Conservative replacement of Y330, F626, and F180 with amino acids having similar aromatic ring structure resulted in full or partial recovery of the efflux function. Molecular docking analysis demonstrated that olaquindox may form hydrogen bonds with F626, Y330, and V141, whereas only Y330 and F180 may interact with ciprofloxacin, implicating the different roles played by these residues when transporting different kinds of substrates. Graphical Abstract [Figure: see text].
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Affiliation(s)
- Shaopeng Xu
- College of Life Sciences, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, South China Agricultural University, Guangzhou, China
| | - Guanping Chen
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Ziyang Liu
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Di Xu
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Zicong Wu
- College of Life Sciences, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, South China Agricultural University, Guangzhou, China
| | - Zhikang Li
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Mei Hong
- College of Life Sciences, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, South China Agricultural University, Guangzhou, China
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17
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Hazel AJ, Abdali N, Leus IV, Parks JM, Smith JC, Zgurskaya HI, Gumbart JC. Conformational Dynamics of AcrA Govern Multidrug Efflux Pump Assembly. ACS Infect Dis 2019; 5:1926-1935. [PMID: 31517484 DOI: 10.1021/acsinfecdis.9b00273] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Multidrug efflux pumps of pathogenic, Gram-negative bacteria comprise an innate resistance mechanism and are key contributors to the emerging global pandemic of antibiotic resistance. Several increasingly detailed cryo-electron microscopy maps have been resolved of an entire efflux pump complex, AcrAB-TolC, resulting in atomistic structural models. Using a recent model, we have carried out nearly 40 μs of molecular dynamics simulations to study one of the key components of the protein complex AcrA, the membrane fusion protein that connects the inner-membrane-bound AcrB to the outer-membrane-bound TolC. We determined a three-dimensional potential of mean force (PMF) for AcrA, which displays two main conformational basins representing assembly competent and incompetent states. Corresponding experiments show that stabilizing mutations at an interdomain interface shift the dynamic equilibrium between these states to the incompetent one, disrupting pump assembly and function and resensitizing bacteria to existing antibiotics. The modulation of AcrA dynamics through pharmacological intervention therefore presents a promising route for the development of new antibiotics.
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Affiliation(s)
- Anthony J. Hazel
- School of Physics, Georgia Institute of Technology, 837 State Street NW, Atlanta, Georgia 30332, United States
| | - Narges Abdali
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Inga V. Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Jerry M. Parks
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
| | - Jeremy C. Smith
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, Tennessee 37996, United States
| | - Helen I. Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - James C. Gumbart
- School of Physics, Georgia Institute of Technology, 837 State Street NW, Atlanta, Georgia 30332, United States
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18
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Kobylka J, Kuth MS, Müller RT, Geertsma ER, Pos KM. AcrB: a mean, keen, drug efflux machine. Ann N Y Acad Sci 2019; 1459:38-68. [PMID: 31588569 DOI: 10.1111/nyas.14239] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/21/2019] [Accepted: 09/02/2019] [Indexed: 12/23/2022]
Abstract
Gram-negative bacteria are intrinsically resistant against cytotoxic substances by means of their outer membrane and a network of multidrug efflux systems, acting in synergy. Efflux pumps from various superfamilies with broad substrate preferences sequester and pump drugs across the inner membrane to supply the highly polyspecific and powerful tripartite resistance-nodulation-cell division (RND) efflux pumps with compounds to be extruded across the outer membrane barrier. In Escherichia coli, the tripartite efflux system AcrAB-TolC is the archetype RND multiple drug efflux pump complex. The homotrimeric inner membrane component acriflavine resistance B (AcrB) is the drug specificity and energy transduction center for the drug/proton antiport process. Drugs are bound and expelled via a cycle of mainly three consecutive states in every protomer, constituting a flexible alternating access channel system. This review recapitulates the molecular basis of drug and inhibitor binding, including mechanistic insights into drug efflux by AcrB. It also summarizes 17 years of mutational analysis of the gene acrB, reporting the effect of every substitution on the ability of E. coli to confer resistance toward antibiotics (http://goethe.link/AcrBsubstitutions). We emphasize the functional robustness of AcrB toward single-site substitutions and highlight regions that are more sensitive to perturbation.
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Affiliation(s)
- Jessica Kobylka
- Institute of Biochemistry, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Miriam S Kuth
- Institute of Biochemistry, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Reinke T Müller
- Institute of Biochemistry, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Eric R Geertsma
- Institute of Biochemistry, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Klaas M Pos
- Institute of Biochemistry, Goethe-University Frankfurt, Frankfurt am Main, Germany
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19
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Shi X, Chen M, Yu Z, Bell JM, Wang H, Forrester I, Villarreal H, Jakana J, Du D, Luisi BF, Ludtke SJ, Wang Z. In situ structure and assembly of the multidrug efflux pump AcrAB-TolC. Nat Commun 2019; 10:2635. [PMID: 31201302 PMCID: PMC6570770 DOI: 10.1038/s41467-019-10512-6] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 05/08/2019] [Indexed: 11/09/2022] Open
Abstract
Multidrug efflux pumps actively expel a wide range of toxic substrates from the cell and play a major role in intrinsic and acquired drug resistance. In Gram-negative bacteria, these pumps form tripartite assemblies that span the cell envelope. However, the in situ structure and assembly mechanism of multidrug efflux pumps remain unknown. Here we report the in situ structure of the Escherichia coli AcrAB-TolC multidrug efflux pump obtained by electron cryo-tomography and subtomogram averaging. The fully assembled efflux pump is observed in a closed state under conditions of antibiotic challenge and in an open state in the presence of AcrB inhibitor. We also observe intermediate AcrAB complexes without TolC and discover that AcrA contacts the peptidoglycan layer of the periplasm. Our data point to a sequential assembly process in living bacteria, beginning with formation of the AcrAB subcomplex and suggest domains to target with efflux pump inhibitors.
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Affiliation(s)
- Xiaodong Shi
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Jiangsu Province Key Laboratory of Anesthesiology and Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China
| | - Muyuan Chen
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zhili Yu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - James M Bell
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hans Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Isaac Forrester
- CryoEM Core at Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Joanita Jakana
- CryoEM Core at Baylor College of Medicine, Houston, TX, 77030, USA
| | - Dijun Du
- Department of Biochemistry, University of Cambridge, Cambridge, CB21GA, UK
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Ben F Luisi
- Department of Biochemistry, University of Cambridge, Cambridge, CB21GA, UK
| | - Steven J Ludtke
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zhao Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, 77030, USA.
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20
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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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21
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Weng J, Wang W. Structural Features and Energetics of the Periplasmic Entrance Opening of the Outer Membrane Channel TolC Revealed by Molecular Dynamics Simulation and Markov State Model Analysis. J Chem Inf Model 2019; 59:2359-2366. [DOI: 10.1021/acs.jcim.8b00957] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Jingwei Weng
- Department of Chemistry, Institute of Biomedical Sciences and Multiscale Research Institute of Complex Systems, Fudan University, Shanghai, China 200433
| | - Wenning Wang
- Department of Chemistry, Institute of Biomedical Sciences and Multiscale Research Institute of Complex Systems, Fudan University, Shanghai, China 200433
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22
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Jukič M, Rožman K, Sova M, Barreteau H, Gobec S. Anthranilic Acid Inhibitors of Undecaprenyl Pyrophosphate Synthase (UppS), an Essential Enzyme for Bacterial Cell Wall Biosynthesis. Front Microbiol 2019; 9:3322. [PMID: 30692977 PMCID: PMC6339874 DOI: 10.3389/fmicb.2018.03322] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 12/20/2018] [Indexed: 12/17/2022] Open
Abstract
We report the successful implementation of virtual screening in the discovery of new inhibitors of undecaprenyl pyrophosphate synthase (UppS) from Escherichia coli. UppS is an essential enzyme in the biosynthesis of bacterial cell wall. It catalyzes the condensation of farnesyl pyrophosphate (FPP) with eight consecutive isopentenyl pyrophosphate units (IPP), in which new cis-double bonds are formed, to generate undecaprenyl pyrophosphate. The latter serves as a lipid carrier for peptidoglycan synthesis, thus representing an important target in the antibacterial drug design. A pharmacophore model was designed on a known bisphosphonate BPH-629 and used to prepare an enriched compound library that was further docked into UppS conformational ensemble generated by molecular dynamics experiment. The docking resulted in three anthranilic acid derivatives with promising inhibitory activity against UppS. Compound 2 displayed high inhibitory potency (IC50 = 25 μM) and good antibacterial activity against E. coli BW25113 ΔtolC strain (MIC = 0.5 μg/mL).
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Affiliation(s)
- Marko Jukič
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Kaja Rožman
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Matej Sova
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Hélène Barreteau
- Bacterial Cell Envelopes and Antibiotics Group, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
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23
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Darzynkiewicz ZM, Green AT, Abdali N, Hazel A, Fulton RL, Kimball J, Gryczynski Z, Gumbart JC, Parks JM, Smith JC, Zgurskaya HI. Identification of Binding Sites for Efflux Pump Inhibitors of the AcrAB-TolC Component AcrA. Biophys J 2019; 116:648-658. [PMID: 30691677 DOI: 10.1016/j.bpj.2019.01.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 01/06/2019] [Accepted: 01/07/2019] [Indexed: 01/02/2023] Open
Abstract
The overexpression of multidrug efflux pumps is an important mechanism of clinical resistance in Gram-negative bacteria. Recently, four small molecules were discovered that inhibit efflux in Escherichia coli and interact with the AcrAB-TolC efflux pump component AcrA. However, the binding site(s) for these molecules was not determined. Here, we combine ensemble docking and molecular dynamics simulations with tryptophan fluorescence spectroscopy, site-directed mutagenesis, and antibiotic susceptibility assays to probe binding sites and effects of binding of these molecules. We conclude that clorobiocin and SLU-258 likely bind at a site located between the lipoyl and β-barrel domains of AcrA.
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Affiliation(s)
| | - Adam T Green
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee
| | - Narges Abdali
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma
| | - Anthony Hazel
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia
| | - Ronnie L Fulton
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma
| | - Joseph Kimball
- Department of Physics and Astronomy, Texas Christian University, Fort Worth, Texas
| | - Zygmunt Gryczynski
- Department of Physics and Astronomy, Texas Christian University, Fort Worth, Texas; Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, Texas
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia
| | - Jerry M Parks
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma.
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24
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Kocaturk NM, Gozuacik D. Crosstalk Between Mammalian Autophagy and the Ubiquitin-Proteasome System. Front Cell Dev Biol 2018; 6:128. [PMID: 30333975 PMCID: PMC6175981 DOI: 10.3389/fcell.2018.00128] [Citation(s) in RCA: 270] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 09/13/2018] [Indexed: 12/16/2022] Open
Abstract
Autophagy and the ubiquitin-proteasome system (UPS) are the two major intracellular quality control and recycling mechanisms that are responsible for cellular homeostasis in eukaryotes. Ubiquitylation is utilized as a degradation signal by both systems, yet, different mechanisms are in play. The UPS is responsible for the degradation of short-lived proteins and soluble misfolded proteins whereas autophagy eliminates long-lived proteins, insoluble protein aggregates and even whole organelles (e.g., mitochondria, peroxisomes) and intracellular parasites (e.g., bacteria). Both the UPS and selective autophagy recognize their targets through their ubiquitin tags. In addition to an indirect connection between the two systems through ubiquitylated proteins, recent data indicate the presence of connections and reciprocal regulation mechanisms between these degradation pathways. In this review, we summarize these direct and indirect interactions and crosstalks between autophagy and the UPS, and their implications for cellular stress responses and homeostasis.
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Affiliation(s)
- Nur Mehpare Kocaturk
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Devrim Gozuacik
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
- Center of Excellence for Functional Surfaces and Interfaces for Nano Diagnostics (EFSUN), Sabanci University, Istanbul, Turkey
- Nanotechnology Research and Application Center (SUNUM), Sabanci University, Istanbul, Turkey
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25
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Parmar M, Rawson S, Scarff CA, Goldman A, Dafforn TR, Muench SP, Postis VLG. Using a SMALP platform to determine a sub-nm single particle cryo-EM membrane protein structure. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2018; 1860:378-383. [PMID: 28993151 PMCID: PMC5780298 DOI: 10.1016/j.bbamem.2017.10.005] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 10/02/2017] [Accepted: 10/04/2017] [Indexed: 01/10/2023]
Abstract
The field of membrane protein structural biology has been revolutionized over the last few years with a number of high profile structures being solved using cryo-EM including Piezo, Ryanodine receptor, TRPV1 and the Glutamate receptor. Further developments in the EM field hold the promise of even greater progress in terms of greater resolution, which for membrane proteins is still typically within the 4-7Å range. One advantage of a cryo-EM approach is the ability to study membrane proteins in more "native" like environments for example proteoliposomes, amphipols and nanodiscs. Recently, styrene maleic acid co-polymers (SMA) have been used to extract membrane proteins surrounded by native lipids (SMALPs) maintaining a more natural environment. We report here the structure of the Escherichia coli multidrug efflux transporter AcrB in a SMALP scaffold to sub-nm resolution, with the resulting map being consistent with high resolution crystal structures and other EM derived maps. However, both the C-terminal helix (TM12) and TM7 are poorly defined in the map. These helices are at the exterior of the helical bundle and form the greater interaction with the native lipids and SMA polymer and may represent a more dynamic region of the protein. This work shows the promise of using an SMA approach for single particle cryo-EM studies to provide sub-nm structures.
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Affiliation(s)
- Mayuriben Parmar
- Biomedicine Research Group, Faculty of Health and Social Sciences, Leeds Beckett University, LS1 3HE, UK; School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK
| | - Shaun Rawson
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK; Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT, UK
| | - Charlotte A Scarff
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK; Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT, UK
| | - Adrian Goldman
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK; Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT, UK; Department of Biosciences, Division of Biochemistry, University of Helsinki, Helsinki, Finland
| | - Timothy R Dafforn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Stephen P Muench
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK; Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT, UK.
| | - Vincent L G Postis
- Biomedicine Research Group, Faculty of Health and Social Sciences, Leeds Beckett University, LS1 3HE, UK; School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK.
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Vargiu AV, Ramaswamy VK, Malloci G, Malvacio I, Atzori A, Ruggerone P. Computer simulations of the activity of RND efflux pumps. Res Microbiol 2018; 169:384-392. [PMID: 29407044 DOI: 10.1016/j.resmic.2017.12.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 12/01/2017] [Accepted: 12/05/2017] [Indexed: 12/25/2022]
Abstract
The putative mechanism by which bacterial RND-type multidrug efflux pumps recognize and transport their substrates is a complex and fascinating enigma of structural biology. How a single protein can recognize a huge number of unrelated compounds and transport them through one or just a few mechanisms is an amazing feature not yet completely unveiled. The appearance of cooperativity further complicates the understanding of structure-dynamics-activity relationships in these complex machineries. Experimental techniques may have limited access to the molecular determinants and to the energetics of key processes regulating the activity of these pumps. Computer simulations are a complementary approach that can help unveil these features and inspire new experiments. Here we review recent computational studies that addressed the various molecular processes regulating the activity of RND efflux pumps.
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Affiliation(s)
- Attilio Vittorio Vargiu
- Department of Physics, University of Cagliari, Cittadella Universitaria, S.P. Monserrato-Sestu km 0.700, 09042 Monserrato (CA), Italy.
| | - Venkata Krishnan Ramaswamy
- Department of Physics, University of Cagliari, Cittadella Universitaria, S.P. Monserrato-Sestu km 0.700, 09042 Monserrato (CA), Italy
| | - Giuliano Malloci
- Department of Physics, University of Cagliari, Cittadella Universitaria, S.P. Monserrato-Sestu km 0.700, 09042 Monserrato (CA), Italy
| | - Ivana Malvacio
- Department of Physics, University of Cagliari, Cittadella Universitaria, S.P. Monserrato-Sestu km 0.700, 09042 Monserrato (CA), Italy
| | - Alessio Atzori
- Department of Physics, University of Cagliari, Cittadella Universitaria, S.P. Monserrato-Sestu km 0.700, 09042 Monserrato (CA), Italy
| | - Paolo Ruggerone
- Department of Physics, University of Cagliari, Cittadella Universitaria, S.P. Monserrato-Sestu km 0.700, 09042 Monserrato (CA), Italy.
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27
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Structure of a MacAB-like efflux pump from Streptococcus pneumoniae. Nat Commun 2018; 9:196. [PMID: 29335499 PMCID: PMC5768738 DOI: 10.1038/s41467-017-02741-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 12/19/2017] [Indexed: 01/04/2023] Open
Abstract
The spr0693-spr0694-spr0695 operon of Streptococcus pneumoniae encodes a putative ATP-binding cassette (ABC)-type efflux pump involved in the resistance of antibiotics and antimicrobial peptides. Here we report the crystal structures of Spr0694–0695 at 3.3 Å and Spr0693 at 3.0 Å resolution, revealing a MacAB-like efflux pump. The dimeric Spr0694–0695 adopts a non-canonical fold of ABC transporter, the transmembrane domain of which consists of eight tightly packed transmembrane helices with an insertion of extracellular domain between the first and second helices, whereas Spr0693 forms a nanotube channel docked onto the ABC transporter. Structural analyses combined with ATPase activity and antimicrobial susceptibility assays, enable us to propose a putative substrate-entrance tunnel with a lateral access controlled by a guard helix. Altogether, our findings provide structural insights and putative transport mechanism of a MacAB-like efflux pump in Gram-positive bacteria. Bacterial ATP-binding cassette (ABC)-type efflux pumps are involved in the resistance of antibiotics and antimicrobial peptides. Here authors report the crystal structures and ATPase activity of the MacAB-like efflux pump from Streptococcus pneumonia and describe a putative substrate transport mechanism.
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28
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Vargiu AV, Ramaswamy VK, Malvacio I, Malloci G, Kleinekathöfer U, Ruggerone P. Water-mediated interactions enable smooth substrate transport in a bacterial efflux pump. Biochim Biophys Acta Gen Subj 2018; 1862:836-845. [PMID: 29339082 DOI: 10.1016/j.bbagen.2018.01.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 11/28/2017] [Accepted: 01/11/2018] [Indexed: 01/12/2023]
Abstract
BACKGROUND Efflux pumps of the Resistance-Nodulation-cell Division superfamily confer multi-drug resistance to Gram-negative bacteria. The most-studied polyspecific transporter belonging to this class is the inner-membrane trimeric antiporter AcrB of Escherichia coli. In previous studies, a functional rotation mechanism was proposed for its functioning, according to which the three monomers undergo concerted conformational changes facilitating the extrusion of substrates. However, the molecular determinants and the energetics of this mechanism still remain unknown, so its feasibility must be proven mechanistically. METHODS A computational protocol able to mimic the functional rotation mechanism in AcrB was developed. By using multi-bias molecular dynamics simulations we characterized the translocation of the substrate doxorubicin driven by conformational changes of the protein. In addition, we estimated for the first time the free energy profile associated to this process. RESULTS We provided a molecular view of the process in agreement with experimental data. Moreover, we showed that the conformational changes occurring in AcrB enable the formation of a layer of structured waters on the internal surface of the transport channel. This water layer, in turn, allows for a fairly constant hydration of the substrate, facilitating its diffusion over a smooth free energy profile. CONCLUSIONS Our findings reveal a new molecular mechanism of polyspecific transport whereby water contributes by screening potentially strong substrate-protein interactions. GENERAL SIGNIFICANCE We provided a mechanistic understanding of a fundamental process related to multi-drug transport. Our results can help rationalizing the behavior of other polyspecific transporters and designing compounds avoiding extrusion or inhibitors of efflux pumps.
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Affiliation(s)
- Attilio Vittorio Vargiu
- Department of Physics, University of Cagliari, s.p. 8, Cittadella Universitaria, 09042 Monserrato (CA), Italy.
| | - Venkata Krishnan Ramaswamy
- Department of Physics, University of Cagliari, s.p. 8, Cittadella Universitaria, 09042 Monserrato (CA), Italy
| | - Ivana Malvacio
- Department of Physics, University of Cagliari, s.p. 8, Cittadella Universitaria, 09042 Monserrato (CA), Italy
| | - Giuliano Malloci
- Department of Physics, University of Cagliari, s.p. 8, Cittadella Universitaria, 09042 Monserrato (CA), Italy
| | - Ulrich Kleinekathöfer
- Department of Physics & Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Paolo Ruggerone
- Department of Physics, University of Cagliari, s.p. 8, Cittadella Universitaria, 09042 Monserrato (CA), Italy
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29
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Zwama M, Yamasaki S, Nakashima R, Sakurai K, Nishino K, Yamaguchi A. Multiple entry pathways within the efflux transporter AcrB contribute to multidrug recognition. Nat Commun 2018; 9:124. [PMID: 29317622 PMCID: PMC5760665 DOI: 10.1038/s41467-017-02493-1] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 12/04/2017] [Indexed: 11/13/2022] Open
Abstract
AcrB is the major multidrug exporter in Escherichia coli. Although several substrate-entrances have been identified, the specificity of these various transport paths remains unclear. Here we present evidence for a substrate channel (channel 3) from the central cavity of the AcrB trimer, which is connected directly to the deep pocket without first passing the switch-loop and the proximal pocket . Planar aromatic cations, such as ethidium, prefer channel 3 to channels 1 and 2. The efflux through channel 3 increases by targeted mutations and is not in competition with the export of drugs such as minocycline and erythromycin through channels 1 and 2. A switch-loop mutant, in which the pathway from the proximal to the deep pocket is hindered, can export only channel 3-utilizing drugs. The usage of multiple entrances thus contributes to the recognition and transport of a wide range of drugs with different physicochemical properties. Multidrug transporters possess several drug binding sites. Here the authors describe a transport path specific for planar aromatic cations in the E. coli multi-drug transporter AcrB.
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Affiliation(s)
- Martijn Zwama
- Laboratory of Cell Membrane Structural Biology, Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka, 567-0047, Japan.,Department of Biomolecular Science and Regulation, Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka, 567-0047, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Seiji Yamasaki
- Department of Biomolecular Science and Regulation, Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka, 567-0047, Japan
| | - Ryosuke Nakashima
- Laboratory of Cell Membrane Structural Biology, Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka, 567-0047, Japan
| | - Keisuke Sakurai
- Laboratory of Cell Membrane Structural Biology, Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka, 567-0047, Japan
| | - Kunihiko Nishino
- Department of Biomolecular Science and Regulation, Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka, 567-0047, Japan
| | - Akihito Yamaguchi
- Laboratory of Cell Membrane Structural Biology, Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka, 567-0047, Japan.
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30
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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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31
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Type I Protein Secretion-Deceptively Simple yet with a Wide Range of Mechanistic Variability across the Family. EcoSal Plus 2017; 7. [PMID: 28084193 DOI: 10.1128/ecosalplus.esp-0019-2015] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A very large type I polypeptide begins to reel out from a ribosome; minutes later, the still unidentifiable polypeptide, largely lacking secondary structure, is now in some cases a thousand or more residues longer. Synthesis of the final hundred C-terminal residues commences. This includes the identity code, the secretion signal within the last 50 amino acids, designed to dock with a waiting ATP binding cassette (ABC) transporter. What happens next is the subject of this review, with the main, but not the only focus on hemolysin HlyA, an RTX protein toxin secreted by the type I system. Transport substrates range from small peptides to giant proteins produced by many pathogens. These molecules, without detectable cellular chaperones, overcome enormous barriers, crossing two membranes before final folding on the cell surface, involving a unique autocatalytic process.Unfolded HlyA is extruded posttranslationally, C-terminal first. The transenvelope "tunnel" is formed by HlyB (ABC transporter), HlyD (membrane fusion protein) straddling the inner membrane and periplasm and TolC (outer membrane). We present a new evaluation of the C-terminal secretion code, and the structure function of HlyD and HlyB at the heart of this nanomachine. Surprisingly, key details of the secretion mechanism are remarkably variable in the many type I secretion system subtypes. These include alternative folding processes, an apparently distinctive secretion code for each type I subfamily, and alternative forms of the ABC transporter; most remarkably, the ABC protein probably transports peptides or polypeptides by quite different mechanisms. Finally, we suggest a putative structure for the Hly-translocon, HlyB, the multijointed HlyD, and the TolC exit.
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32
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Hexameric assembly of membrane fusion protein YknX of the sporulation delaying efflux pump from Bacillus amyloliquefaciens. Biochem Biophys Res Commun 2017; 493:152-157. [DOI: 10.1016/j.bbrc.2017.09.059] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 09/12/2017] [Indexed: 12/25/2022]
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33
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Jo I, Hong S, Lee M, Song S, Kim JS, Mitra AK, Hyun J, Lee K, Ha NC. Stoichiometry and mechanistic implications of the MacAB-TolC tripartite efflux pump. Biochem Biophys Res Commun 2017; 494:668-673. [PMID: 29061301 DOI: 10.1016/j.bbrc.2017.10.102] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 10/19/2017] [Indexed: 11/16/2022]
Abstract
The MacAB-TolC tripartite efflux pump is involved in resistance to macrolide antibiotics and secretion of protein toxins in many Gram-negative bacteria. The pump spans the entire cell envelope and operates by expelling substances to extracellular space. X-ray crystal and electron microscopic structures have revealed the funnel-like MacA hexamer in the periplasmic space and the cylindrical TolC trimer. Nonetheless, the inner membrane transporter MacB still remains ambiguous in terms of its oligomeric state in the functional complex. In this study, we purified a stable binary complex using a fusion protein of MacA and MacB of Escherichia coli, and then supplemented MacA to meet the correct stoichiometry between the two proteins. The result demonstrated that MacB is a homodimer in the complex, which is consistent with results from the recent complex structure using cryo-electron microscopy single particle analysis. Structural comparison with the previously reported MacB periplasmic domain structure suggests a molecular mechanism for regulation of the activity of MacB via an interaction between the MacB periplasmic domain and MacA. Our results provide a better understanding of the tripartite pumps at the molecular level.
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Affiliation(s)
- Inseong Jo
- Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Seokho Hong
- Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Minho Lee
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Saemee Song
- Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jin-Sik Kim
- Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Alok K Mitra
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
| | - Jaekyung Hyun
- Electron Microscopy Research Center, Korea Basic Science Institute, Chungcheongbukdo 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, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea.
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34
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Müller RT, Travers T, Cha HJ, Phillips JL, Gnanakaran S, Pos KM. Switch Loop Flexibility Affects Substrate Transport of the AcrB Efflux Pump. J Mol Biol 2017; 429:3863-3874. [PMID: 28987732 DOI: 10.1016/j.jmb.2017.09.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 09/15/2017] [Accepted: 09/29/2017] [Indexed: 11/25/2022]
Abstract
The functionally important switch loop of the trimeric multidrug transporter AcrB separates the access and deep drug binding pockets in every protomer. This loop, comprising 11-amino-acid residues, has been shown to be crucial for substrate transport, as drugs have to travel past the loop to reach the deep binding pocket and from there are transported outside the cell via the connected AcrA and TolC channels. It contains four symmetrically arranged glycine residues suggesting that flexibility is a key feature for pump activity. Upon combinatorial substitution of these glycine residues to proline, functional and structural asymmetry was observed. Proline substitutions on the PC1-proximal side completely abolished transport and reduced backbone flexibility of the switch loop, which adopted a conformation restricting the pathway toward the deep binding pocket. Two phenylalanine residues located adjacent to the substitution sensitive glycine residues play a role in blocking the pathway upon rigidification of the loop, since the removal of the phenyl rings from the rigid loop restores drug transport activity.
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Affiliation(s)
- Reinke T Müller
- Institute of Biochemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Timothy Travers
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, United States; Center for Nonlinear Sciences, Los Alamos National Laboratory, Los Alamos, NM 87545, United States
| | - Hi-Jea Cha
- Engelhard Arzneimittel GmbH & Co. KG, Herzbergstrasse 3, 61138 Niederdorfelden, Germany
| | - Joshua L Phillips
- Department of Computer Science, Middle Tennessee State University, Murfreesboro, TN 37132, United States
| | - S Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, United States
| | - Klaas M Pos
- Institute of Biochemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany.
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35
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Hibberd MC, Wu M, Rodionov DA, Li X, Cheng J, Griffin NW, Barratt MJ, Giannone RJ, Hettich RL, Osterman AL, Gordon JI. The effects of micronutrient deficiencies on bacterial species from the human gut microbiota. Sci Transl Med 2017; 9:eaal4069. [PMID: 28515336 PMCID: PMC5524138 DOI: 10.1126/scitranslmed.aal4069] [Citation(s) in RCA: 147] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 03/14/2017] [Indexed: 12/13/2022]
Abstract
Vitamin and mineral (micronutrient) deficiencies afflict 2 billion people. Although the impact of these imbalances on host biology has been studied extensively, much less is known about their effects on the gut microbiota of developing or adult humans. Therefore, we established a community of cultured, sequenced human gut-derived bacterial species in gnotobiotic mice and fed the animals a defined micronutrient-sufficient diet, followed by a derivative diet devoid of vitamin A, folate, iron, or zinc, followed by return to the sufficient diet. Acute vitamin A deficiency had the largest effect on bacterial community structure and metatranscriptome, with Bacteroides vulgatus, a prominent responder, increasing its abundance in the absence of vitamin A. Applying retinol selection to a library of 30,300 B. vulgatus transposon mutants revealed that disruption of acrR abrogated retinol sensitivity. Genetic complementation studies, microbial RNA sequencing, and transcription factor-binding assays disclosed that AcrR is a repressor of an adjacent AcrAB-TolC efflux system. Retinol efflux measurements in wild-type and acrR-mutant strains plus treatment with a pharmacologic inhibitor of the efflux system revealed that AcrAB-TolC is a determinant of retinol and bile acid sensitivity in B. vulgatus Acute vitamin A deficiency was associated with altered bile acid metabolism in vivo, raising the possibility that retinol, bile acid metabolites, and AcrAB-TolC interact to influence the fitness of B. vulgatus and perhaps other microbiota members. This type of preclinical model can help to develop mechanistic insights about the effects of, and more effective treatment strategies for micronutrient deficiencies.
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Affiliation(s)
- Matthew C Hibberd
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Meng Wu
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Dmitry A Rodionov
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127994, Russia
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Xiaoqing Li
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Jiye Cheng
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nicholas W Griffin
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael J Barratt
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Richard J Giannone
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Andrei L Osterman
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Jeffrey I Gordon
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
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36
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Structure of the MacAB-TolC ABC-type tripartite multidrug efflux pump. Nat Microbiol 2017; 2:17070. [PMID: 28504659 PMCID: PMC5447821 DOI: 10.1038/nmicrobiol.2017.70] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 04/03/2017] [Indexed: 02/02/2023]
Abstract
The MacA-MacB-TolC assembly of Escherichia coli is a transmembrane machine that spans the cell envelope and actively extrudes substrates, including macrolide antibiotics and polypeptide virulence factors. These transport processes are energized by the ATPase MacB, a member of the ATP-binding cassette (ABC) superfamily. We present an electron cryo-microscopy structure of the ABC-type tripartite assembly at near-atomic resolution. A hexamer of the periplasmic protein MacA bridges between a TolC trimer in the outer membrane and a MacB dimer in the inner membrane, generating a quaternary structure with a central channel for substrate translocation. A gating ring found in MacA is proposed to act as a one-way valve in substrate transport. The MacB structure features an atypical transmembrane domain with a closely packed dimer interface and a periplasmic opening that is the likely portal for substrate entry from the periplasm, with subsequent displacement through an allosteric transport mechanism.
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37
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Wang Z, Fan G, Hryc CF, Blaza JN, Serysheva II, Schmid MF, Chiu W, Luisi BF, Du D. An allosteric transport mechanism for the AcrAB-TolC multidrug efflux pump. eLife 2017; 6. [PMID: 28355133 PMCID: PMC5404916 DOI: 10.7554/elife.24905] [Citation(s) in RCA: 153] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 03/14/2017] [Indexed: 12/12/2022] Open
Abstract
Bacterial efflux pumps confer multidrug resistance by transporting diverse antibiotics from the cell. In Gram-negative bacteria, some of these pumps form multi-protein assemblies that span the cell envelope. Here, we report the near-atomic resolution cryoEM structures of the Escherichia coli AcrAB-TolC multidrug efflux pump in resting and drug transport states, revealing a quaternary structural switch that allosterically couples and synchronizes initial ligand binding with channel opening. Within the transport-activated state, the channel remains open even though the pump cycles through three distinct conformations. Collectively, our data provide a dynamic mechanism for the assembly and operation of the AcrAB-TolC pump. DOI:http://dx.doi.org/10.7554/eLife.24905.001
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Affiliation(s)
- Zhao Wang
- National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, United States.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, United States
| | - Guizhen Fan
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, The University of Texas Health Science Center at Houston Medical School, Houston, United States
| | - Corey F Hryc
- National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, United States.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, United States.,Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, United States
| | - James N Blaza
- MRC Mitochondrial Biology Unit, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Irina I Serysheva
- Department of Biochemistry and Molecular Biology, Structural Biology Imaging Center, The University of Texas Health Science Center at Houston Medical School, Houston, United States
| | - Michael F Schmid
- National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, United States.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, United States
| | - Wah Chiu
- National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, United States.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, United States.,Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, United States
| | - Ben F Luisi
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Dijun Du
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
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38
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Mechanisms of envelope permeability and antibiotic influx and efflux in Gram-negative bacteria. Nat Microbiol 2017; 2:17001. [PMID: 28224989 DOI: 10.1038/nmicrobiol.2017.1] [Citation(s) in RCA: 187] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 12/23/2016] [Indexed: 01/26/2023]
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39
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Abstract
Membrane proteins can assemble and form complexes in the cell envelope. In Gram-negative bacteria, a number of multiprotein complexes, including secretion systems, efflux pumps, molecular motors, and pilus assembly machines, comprise proteins from the inner and outer membranes. Besides the structures of isolated soluble domains, only a few atomic structures of these assembled molecular machines have been elucidated. To better understand the function and to solve the structure of protein complexes, it is thus necessary to design dedicated production and purification processes. Here we present cloning procedures to overproduce membrane proteins into Escherichia coli cells and describe the cloning and purification strategy for the Type VI secretion TssJLM membrane complex.
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40
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Hernando-Amado S, Blanco P, Alcalde-Rico M, Corona F, Reales-Calderón JA, Sánchez MB, Martínez JL. Multidrug efflux pumps as main players in intrinsic and acquired resistance to antimicrobials. Drug Resist Updat 2016; 28:13-27. [PMID: 27620952 DOI: 10.1016/j.drup.2016.06.007] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 05/31/2016] [Accepted: 06/23/2016] [Indexed: 12/31/2022]
Abstract
Multidrug efflux pumps constitute a group of transporters that are ubiquitously found in any organism. In addition to other functions with relevance for the cell physiology, efflux pumps contribute to the resistance to compounds used for treating different diseases, including resistance to anticancer drugs, antibiotics or antifungal compounds. In the case of antimicrobials, efflux pumps are major players in both intrinsic and acquired resistance to drugs currently in use for the treatment of infectious diseases. One important aspect not fully explored of efflux pumps consists on the identification of effectors able to induce their expression. Indeed, whereas the analysis of clinical isolates have shown that mutants overexpressing these resistance elements are frequently found, less is known on the conditions that may trigger expression of efflux pumps, hence leading to transient induction of resistance in vivo, a situation that is barely detectable using classical susceptibility tests. In the current article we review the structure and mechanisms of regulation of the expression of bacterial and fungal efflux pumps, with a particular focus in those for which a role in clinically relevant resistance has been reported.
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Affiliation(s)
- Sara Hernando-Amado
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Paula Blanco
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Manuel Alcalde-Rico
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Fernando Corona
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Jose A Reales-Calderón
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - María B Sánchez
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - José L Martínez
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Darwin 3, Cantoblanco, 28049 Madrid, Spain.
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41
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Reddy BL, Saier MH. Properties and Phylogeny of 76 Families of Bacterial and Eukaryotic Organellar Outer Membrane Pore-Forming Proteins. PLoS One 2016; 11:e0152733. [PMID: 27064789 PMCID: PMC4827864 DOI: 10.1371/journal.pone.0152733] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 03/18/2016] [Indexed: 12/11/2022] Open
Abstract
We here report statistical analyses of 76 families of integral outer membrane pore-forming proteins (OMPPs) found in bacteria and eukaryotic organelles. 47 of these families fall into one superfamily (SFI) which segregate into fifteen phylogenetic clusters. Families with members of the same protein size, topology and substrate specificities often cluster together. Virtually all OMPP families include only proteins that form transmembrane pores. Nine such families, all of which cluster together in the SFI phylogenetic tree, contain both α- and β-structures, are multi domain, multi subunit systems, and transport macromolecules. Most other SFI OMPPs transport small molecules. SFII and SFV homologues derive from Actinobacteria while SFIII and SFIV proteins derive from chloroplasts. Three families of actinobacterial OMPPs and two families of eukaryotic OMPPs apparently consist primarily of α-helices (α-TMSs). Of the 71 families of (putative) β-barrel OMPPs, only twenty could not be assigned to a superfamily, and these derived primarily from Actinobacteria (1), chloroplasts (1), spirochaetes (8), and proteobacteria (10). Proteins were identified in which two or three full length OMPPs are fused together. Family characteristic are described and evidence agrees with a previous proposal suggesting that many arose by adjacent β-hairpin structural unit duplications.
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Affiliation(s)
- Bhaskara L. Reddy
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California, United States of America
| | - Milton H. Saier
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California, United States of America
- * E-mail:
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42
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Zuo Z, Weng J, Wang W. Insights into the Inhibitory Mechanism of D13-9001 to the Multidrug Transporter AcrB through Molecular Dynamics Simulations. J Phys Chem B 2016; 120:2145-54. [PMID: 26900716 DOI: 10.1021/acs.jpcb.5b11942] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The resistance-nodulation-cell division transporter AcrB is responsible for energy transduction and substrate recognition in the tripartite AcrAB-TolC efflux system in Escherichia coli. Despite a broad substrate specificity, only a few compounds have been cocrystallized with AcrB inside the distal binding pocket (DBP), including doxorubicin (DOX) and D13-9001. D13-9001 is a promising efflux pump inhibitor that potentiates the efficacy of a wide variety of antibiotics. To understand its inhibition effect under the framework of functional rotating mechanism, we performed targeted and steered molecular dynamics simulations to compare the binding and extrusion processes of this inhibitor and the substrate DOX in AcrB. The results demonstrate that, with respect to DOX, the interaction of D13-9001 with the hydrophobic trap results in delayed disassociation from the DBP. Notably, the detachment of D13-9001 is tightly correlated with the side-chain reorientation of Phe628 and large-scale displacement of Tyr327. Furthermore, the inhibitor induces much more significant conformational changes at the exit gate than DOX does, thereby causing higher energy cost for extrusion and contributing to the inhibitory effect in addition to the tight binding at DBP.
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Affiliation(s)
- Zhicheng Zuo
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, and Institutes of Biomedical Sciences, Fudan University , Shanghai 200433, People's Republic of China
| | - Jingwei Weng
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, and Institutes of Biomedical Sciences, Fudan University , Shanghai 200433, People's Republic of China
| | - Wenning Wang
- Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Department of Chemistry, and Institutes of Biomedical Sciences, Fudan University , Shanghai 200433, People's Republic of China
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43
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Kim JS, Song S, Lee M, Lee S, Lee K, Ha NC. Crystal Structure of a Soluble Fragment of the Membrane Fusion Protein HlyD in a Type I Secretion System of Gram-Negative Bacteria. Structure 2016; 24:477-85. [DOI: 10.1016/j.str.2015.12.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 12/15/2015] [Accepted: 12/16/2015] [Indexed: 10/22/2022]
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44
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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: 129] [Impact Index Per Article: 16.1] [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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45
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An overview of bacterial efflux pumps and computational approaches to study efflux pump inhibitors. Future Med Chem 2016; 8:195-210. [DOI: 10.4155/fmc.15.173] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Micro-organisms express a wide range of transmembrane pumps known as multidrug efflux pumps that improve the micro-organism's ability to survive in severe environments and contribute to resistance against antibiotic and antimicrobial agents. There is significant interest in developing efflux inhibitors as an adjunct to treatment with current and next generation of antibiotics. 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. We summarize some structural and functional data that could provide insights into the inhibition of transport mechanisms of these intricate molecular nanomachines with a focus on the advances in computational approaches.
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46
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Jeong H, Kim JS, Song S, Shigematsu H, Yokoyama T, Hyun J, Ha NC. Pseudoatomic Structure of the Tripartite Multidrug Efflux Pump AcrAB-TolC Reveals the Intermeshing Cogwheel-like Interaction between AcrA and TolC. Structure 2016; 24:272-6. [PMID: 26777412 DOI: 10.1016/j.str.2015.12.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 11/05/2015] [Accepted: 12/08/2015] [Indexed: 10/22/2022]
Abstract
The resistance-nodulation-division type tripartite pump AcrAB-TolC and its homologs are responsible for multidrug resistance in Gram-negative bacteria by expelling a wide variety of toxic substrates. The three essential components, AcrA, AcrB, and TolC, must function in concert with each respective binding partner within the complex. In this study, we report an 8.2-Å resolution cryo-electron microscopy (cryo-EM) 3D reconstruction of the complex that consists of an AcrAB fusion protein and a chimeric TolC protein. The pseudoatomic structure derived from the cryo-EM reconstruction clearly demonstrates a model only compatible with the adaptor bridging mechanism, wherein the funnel-like AcrA hexamer forms an intermeshing cogwheel-like interaction with the α-barrel tip region of TolC. These observations provide a structural milestone for understanding multidrug resistance in pathogenic Gram-negative bacteria, and may also lead to the design of new antibacterial drugs.
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Affiliation(s)
- Hyeongseop Jeong
- Nano-Bio Electron Microscopy Research Team, Korea Basic Science Institute, Daejeon 305-806, Republic of Korea
| | - Jin-Sik Kim
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Center for Food Safety and Toxicology, Research Institute for Agricultural and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea
| | - Saemee Song
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Center for Food Safety and Toxicology, Research Institute for Agricultural and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea
| | - Hideki Shigematsu
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Takeshi Yokoyama
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Jaekyung Hyun
- Nano-Bio Electron Microscopy Research Team, Korea Basic Science Institute, Daejeon 305-806, Republic of Korea.
| | - Nam-Chul Ha
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, Center for Food Safety and Toxicology, Research Institute for Agricultural and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea.
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47
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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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48
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AcrB-AcrA Fusion Proteins That Act as Multidrug Efflux Transporters. J Bacteriol 2015; 198:332-42. [PMID: 26527645 DOI: 10.1128/jb.00587-15] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 10/24/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The AcrAB-TolC system in Escherichia coli is an intrinsic RND-type multidrug efflux transporter that functions as a tripartite complex of the inner membrane transporter AcrB, the outer membrane channel TolC, and the adaptor protein AcrA. Although the crystal structures of each component of this system have been elucidated, the crystal structure of the whole complex has not been solved. The available crystal structures have shown that AcrB and TolC function as trimers, but the number of AcrA molecules in the complex is now under debate. Disulfide chemical cross-linking experiments have indicated that the stoichiometry of AcrB-AcrA-TolC is 1:1:1; on the other hand, recent cryo-electron microscopy images of AcrAB-TolC suggested a 1:2:1 stoichiometry. In this study, we constructed 1:1-fixed AcrB-AcrA fusion proteins using various linkers. Surprisingly, all the 1:1-fixed linker proteins showed drug export activity under both acrAB-deficient conditions and acrAB acrEF double-pump-knockout conditions regardless of the lengths of the linkers. Finally, we optimized a shorter linker lacking the conformational freedom imparted by the AcrB C terminus. These results suggest that a complex with equal amounts of AcrA and AcrB is sufficient for drug export function. IMPORTANCE The structure and stoichiometry of the RND-type multidrug exporter AcrB-AcrA-TolC complex are still under debate. Recently, electron microscopic images of the AcrB-AcrA-TolC complex have been reported, suggesting a 1:2:1 stoichiometry. However, we report here that the AcrB-AcrA 1:1 fusion protein is active for drug export under acrAB-deficient conditions and also under acrAB acrEF double-deficient conditions, which eliminate the aid of free AcrA and its close homolog AcrE, indicating that the AcrB-AcrA 1:1 stoichiometry is enough for drug export function. In addition, the AcrB-AcrA fusion protein can function without the aid of free AcrA. We believe that these results are very important for considering the structure and mechanism of AcrAB-TolC-mediated multidrug export.
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49
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Du D, van Veen HW, Murakami S, Pos KM, Luisi BF. Structure, mechanism and cooperation of bacterial multidrug transporters. Curr Opin Struct Biol 2015; 33:76-91. [PMID: 26282926 DOI: 10.1016/j.sbi.2015.07.015] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 06/29/2015] [Accepted: 07/24/2015] [Indexed: 12/13/2022]
Abstract
Cells from all domains of life encode energy-dependent trans-membrane transporters that can expel harmful substances including clinically applied therapeutic agents. As a collective body, these transporters perform as a super-system that confers tolerance to an enormous range of harmful compounds and consequently aid survival in hazardous environments. In the Gram-negative bacteria, some of these transporters serve as energy-transducing components of tripartite assemblies that actively efflux drugs and other harmful compounds, as well as deliver virulence agents across the entire cell envelope. We draw together recent structural and functional data to present the current models for the transport mechanisms for the main classes of multi-drug transporters and their higher-order assemblies.
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Affiliation(s)
- Dijun Du
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Hendrik W van Veen
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Satoshi Murakami
- Division of Structure and Function of Biomolecules, Department of Life Science, Tokyo Institute of Technology, Yokohama 226-8503, Japan
| | - Klaas M Pos
- Institute of Biochemistry, Goethe Universität Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Ben F Luisi
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK.
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50
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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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