1
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Tan HN, Liu WQ, Ho J, Chen YJ, Shieh FJ, Liao HT, Wang SP, Hegemann JD, Chang CY, Chu J. Structure Prediction and Protein Engineering Yield New Insights into Microcin J25 Precursor Recognition. ACS Chem Biol 2024; 19:1982-1990. [PMID: 39163642 PMCID: PMC11420955 DOI: 10.1021/acschembio.4c00251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 07/25/2024] [Accepted: 08/12/2024] [Indexed: 08/22/2024]
Abstract
Microcin J25 (MccJ25), a lasso peptide antibiotic with a unique structure that resembles the lariat knot, has been a topic of intense interest since its discovery in 1992. The precursor (McjA) contains a leader and a core segment. McjB is a protease activated upon binding to the leader, and McjC converts the core segment into the mature MccJ25. Previous studies suggested that these biosynthetic steps likely proceed in a (nearly) concerted fashion; however, there is only limited information regarding the structural and molecular intricacies of MccJ25 biosynthesis. To close this knowledge gap, we used AlphaFold2 to predict the structure of the precursor (McjA) in complex with its biosynthetic enzymes (McjB and McjC) and queried the critical predicted features by protein engineering. Based on the predicted structure, we designed protein variants to show that McjB can still be functional and form a proficient biosynthetic complex with McjC when its recognition and protease domains were circularly permutated or split into separate proteins. Specific residues important for McjA recognition were also identified, which permitted us to pinpoint a compensatory mutation (McjBM108T) to restore McjA/McjB interaction that rescued an otherwise nearly nonproductive precursor variant (McjAT-2M). Studies of McjA, McjB, and McjC have long been mired by them being extremely difficult to handle experimentally, and our results suggest that the AF2 predicted ternary complex structure may serve as a reasonable starting point for understanding MccJ25 biosynthesis. The prediction-validation workflow presented herein combined artificial intelligence and laboratory experiments constructively to gain new insights.
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Affiliation(s)
- Hui-Ni Tan
- Department
of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Wei-Qi Liu
- Department
of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Josh Ho
- Department
of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Yi-Ju Chen
- Department
of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Fang-Jie Shieh
- Department
of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Hsiao-Tzu Liao
- Department
of Biological Science and Technology, National
Yang Ming Chiao Tung University, Hsinchu 300193, Taiwan
| | - Shu-Ping Wang
- Institute
of Biomedical Sciences, Academia Sinica, Taipei 115201, Taiwan
| | - Julian D. Hegemann
- Helmholtz
Institute for Pharmaceutical Research Saarland, Helmholtz Centre for
Infection Research, Saarland
University Campus, 66123 Saarbrücken, Germany
| | - Chin-Yuan Chang
- Department
of Biological Science and Technology, National
Yang Ming Chiao Tung University, Hsinchu 300193, Taiwan
| | - John Chu
- Department
of Chemistry, National Taiwan University, Taipei 10617, Taiwan
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2
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Reyna-Campos AO, Ruiz-Villafan B, Macías-Rubalcava ML, Langley E, Rodríguez-Sanoja R, Sánchez S. Heterologous expression of lasso peptides with apparent participation in the morphological development in Streptomyces. AMB Express 2024; 14:97. [PMID: 39225916 PMCID: PMC11371967 DOI: 10.1186/s13568-024-01761-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024] Open
Abstract
Lasso peptides, ribosomally synthesized and post-translationally modified peptides, are primarily produced by bacteria and some archaea. Streptomyces lasso peptides have been known for their antimicrobial, anticancer, and antiviral properties. However, understanding their role in the morphology and production of secondary metabolites remains limited. We identified a previously unknown lasso peptide gene cluster in the genome of Streptomyces sp. L06. This gene cluster (LASS) produces two distinct lasso peptides, morphosin-1 and - 2. Notably, morphosin-2 is a member of a new subfamily of lasso peptides, with BGCs exhibiting a similar structure. When LASS was expressed in different Streptomyces hosts, it led to exciting phenotypic changes, including the absence of spores and damage in aerial mycelium development. In one of the hosts, LASS even triggered antibiotic formation. These findings open up a world of possibilities, suggesting the potential role of morphosins in shaping Streptomyces' morphological and biochemical development.
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Affiliation(s)
- Alma Ofelia Reyna-Campos
- Departamento de Biología Molecular y Biotecnología del Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), 04510, CdMx, Mexico
- Posgrado en Ciencias Biológicas, Unidad de Posgrado, UNAM. , CdMx, 04510, Mexico
| | - Beatriz Ruiz-Villafan
- Departamento de Biología Molecular y Biotecnología del Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), 04510, CdMx, Mexico
| | | | - Elizabeth Langley
- Departmento de Investigación Básica, Instituto Nacional de Cancerología, CdMx, 14080, Mexico
| | - Romina Rodríguez-Sanoja
- Departamento de Biología Molecular y Biotecnología del Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), 04510, CdMx, Mexico
| | - Sergio Sánchez
- Departamento de Biología Molecular y Biotecnología del Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), 04510, CdMx, Mexico.
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3
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Lane BJ, Ma Y, Yan N, Wang B, Ackermann K, Karamanos TK, Bode BE, Pliotas C. Monitoring the conformational ensemble and lipid environment of a mechanosensitive channel under cyclodextrin-induced membrane tension. Structure 2024; 32:739-750.e4. [PMID: 38521071 DOI: 10.1016/j.str.2024.02.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/29/2023] [Accepted: 02/27/2024] [Indexed: 03/25/2024]
Abstract
Membrane forces shift the equilibria of mechanosensitive channels enabling them to convert mechanical cues into electrical signals. Molecular tools to stabilize and methods to capture their highly dynamic states are lacking. Cyclodextrins can mimic tension through the sequestering of lipids from membranes. Here we probe the conformational ensemble of MscS by EPR spectroscopy, the lipid environment with NMR, and function with electrophysiology under cyclodextrin-induced tension. We show the extent of MscS activation depends on the cyclodextrin-to-lipid ratio, and that lipids are depleted slower when MscS is present. This has implications in MscS' activation kinetics when distinct membrane scaffolds such as nanodiscs or liposomes are used. We find MscS transits from closed to sub-conducting state(s) before it desensitizes, due to the lack of lipid availability in its vicinity required for closure. Our approach allows for monitoring tension-sensitive states in membrane proteins and screening molecules capable of inducing molecular tension in bilayers.
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Affiliation(s)
- Benjamin J Lane
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Yue Ma
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic and Health Science Centre, The University of Manchester, Manchester M13 9PT, UK
| | - Nana Yan
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Bolin Wang
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic and Health Science Centre, The University of Manchester, Manchester M13 9PT, UK
| | - Katrin Ackermann
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic Resonance, University of St Andrews, St Andrews KY16 9ST, UK
| | - Theodoros K Karamanos
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK
| | - Bela E Bode
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex and Centre of Magnetic Resonance, University of St Andrews, St Andrews KY16 9ST, UK
| | - Christos Pliotas
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK; School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic and Health Science Centre, The University of Manchester, Manchester M13 9PT, UK; Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK.
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4
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Reuben RC, Torres C. Bacteriocins: potentials and prospects in health and agrifood systems. Arch Microbiol 2024; 206:233. [PMID: 38662051 PMCID: PMC11045635 DOI: 10.1007/s00203-024-03948-y] [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: 02/02/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/26/2024]
Abstract
Bacteriocins are highly diverse, abundant, and heterogeneous antimicrobial peptides that are ribosomally synthesized by bacteria and archaea. Since their discovery about a century ago, there has been a growing interest in bacteriocin research and applications. This is mainly due to their high antimicrobial properties, narrow or broad spectrum of activity, specificity, low cytotoxicity, and stability. Though initially used to improve food quality and safety, bacteriocins are now globally exploited for innovative applications in human, animal, and food systems as sustainable alternatives to antibiotics. Bacteriocins have the potential to beneficially modulate microbiota, providing viable microbiome-based solutions for the treatment, management, and non-invasive bio-diagnosis of infectious and non-infectious diseases. The use of bacteriocins holds great promise in the modulation of food microbiomes, antimicrobial food packaging, bio-sanitizers and antibiofilm, pre/post-harvest biocontrol, functional food, growth promotion, and sustainable aquaculture. This can undoubtedly improve food security, safety, and quality globally. This review highlights the current trends in bacteriocin research, especially the increasing research outputs and funding, which we believe may proportionate the soaring global interest in bacteriocins. The use of cutting-edge technologies, such as bioengineering, can further enhance the exploitation of bacteriocins for innovative applications in human, animal, and food systems.
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Affiliation(s)
- Rine Christopher Reuben
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006, Logroño, Spain.
| | - Carmen Torres
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006, Logroño, Spain
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5
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Baquero F, Beis K, Craik DJ, Li Y, Link AJ, Rebuffat S, Salomón R, Severinov K, Zirah S, Hegemann JD. The pearl jubilee of microcin J25: thirty years of research on an exceptional lasso peptide. Nat Prod Rep 2024; 41:469-511. [PMID: 38164764 DOI: 10.1039/d3np00046j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Covering: 1992 up to 2023Since their discovery, lasso peptides went from peculiarities to be recognized as a major family of ribosomally synthesized and post-translationally modified peptide (RiPP) natural products that were shown to be spread throughout the bacterial kingdom. Microcin J25 was first described in 1992, making it one of the earliest known lasso peptides. No other lasso peptide has since then been studied to such an extent as microcin J25, yet, previous review articles merely skimmed over all the research done on this exceptional lasso peptide. Therefore, to commemorate the 30th anniversary of its first report, we give a comprehensive overview of all literature related to microcin J25. This review article spans the early work towards the discovery of microcin J25, its biosynthetic gene cluster, and the elucidation of its three-dimensional, threaded lasso structure. Furthermore, the current knowledge about the biosynthesis of microcin J25 and lasso peptides in general is summarized and a detailed overview is given on the biological activities associated with microcin J25, including means of self-immunity, uptake into target bacteria, inhibition of the Gram-negative RNA polymerase, and the effects of microcin J25 on mitochondria. The in vitro and in vivo models used to study the potential utility of microcin J25 in a (veterinary) medicine context are discussed and the efforts that went into employing the microcin J25 scaffold in bioengineering contexts are summed up.
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Affiliation(s)
- Fernando Baquero
- Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
- Network Center for Research in Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - Konstantinos Beis
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
- Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, Oxfordshire OX11 0FA, UK
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, 4072 Brisbane, Queensland, Australia
| | - Yanyan Li
- Laboratoire Molécules de Communication et Adaptation des Microorganismes (MCAM), UMR 7245, Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Paris, France
| | - A James Link
- Departments of Chemical and Biological Engineering, Chemistry, and Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Sylvie Rebuffat
- Laboratoire Molécules de Communication et Adaptation des Microorganismes (MCAM), UMR 7245, Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Paris, France
| | - Raúl Salomón
- Instituto de Química Biológica "Dr Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, San Miguel de Tucumán, Argentina
| | - Konstantin Severinov
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Séverine Zirah
- Laboratoire Molécules de Communication et Adaptation des Microorganismes (MCAM), UMR 7245, Muséum National d'Histoire Naturelle (MNHN), Centre National de la Recherche Scientifique (CNRS), Paris, France
| | - Julian D Hegemann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany.
- Department of Pharmacy, Campus E8 1, Saarland University, 66123 Saarbrücken, Germany
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6
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Telhig S, Pham NP, Ben Said L, Rebuffat S, Ouellette M, Zirah S, Fliss I. Exploring the genetic basis of natural resistance to microcins. Microb Genom 2024; 10:001156. [PMID: 38407259 PMCID: PMC10926693 DOI: 10.1099/mgen.0.001156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 11/28/2023] [Indexed: 02/27/2024] Open
Abstract
Enterobacteriaceae produce an arsenal of antimicrobial compounds including microcins, ribosomally produced antimicrobial peptides showing diverse structures and mechanisms of action. Microcins target close relatives of the producing strain to promote its survival. Their narrow spectrum of antibacterial activity makes them a promising alternative to conventional antibiotics, as it should decrease the probability of resistance dissemination and collateral damage to the host's microbiota. To assess the therapeutic potential of microcins, there is a need to understand the mechanisms of resistance to these molecules. In this study, we performed genomic analyses of the resistance to four microcins [microcin C, a nucleotide peptide; microcin J25, a lasso peptide; microcin B17, a linear azol(in)e-containing peptide; and microcin E492, a siderophore peptide] on a collection of 54 Enterobacteriaceae from three species: Escherichia coli, Salmonella enterica and Klebsiella pneumoniae. A gene-targeted analysis revealed that about half of the microcin-resistant strains presented mutations of genes involved in the microcin mechanism of action, especially those involved in their uptake (fhuA, fepA, cirA and ompF). A genome-wide association study did not reveal any significant correlations, yet relevant genetic elements were associated with microcin resistance. These were involved in stress responses, biofilm formation, transport systems and acquisition of immunity genes. Additionally, microcin-resistant strains exhibited several mutations within genes involved in specific metabolic pathways, especially for S. enterica and K. pneumoniae.
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Affiliation(s)
- Soufiane Telhig
- Food Science Department, Food and Agriculture Faculty, Laval University, Quebec, Canada
- Laboratoire Molécules de Communication et Adaptation des Microorganismes, Muséum national d’Histoire naturelle, Centre national de la Recherche scientifique, Paris, France
| | - Nguyen Phuong Pham
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Laila Ben Said
- Food Science Department, Food and Agriculture Faculty, Laval University, Quebec, Canada
- Institute of Nutrition and Functional Foods, Laval University, Quebec, Canada
| | - Sylvie Rebuffat
- Laboratoire Molécules de Communication et Adaptation des Microorganismes, Muséum national d’Histoire naturelle, Centre national de la Recherche scientifique, Paris, France
| | - Marc Ouellette
- Centre de Recherche en Infectiologie du Centre de Recherche du CHU de Québec and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Séverine Zirah
- Laboratoire Molécules de Communication et Adaptation des Microorganismes, Muséum national d’Histoire naturelle, Centre national de la Recherche scientifique, Paris, France
| | - Ismaïl Fliss
- Food Science Department, Food and Agriculture Faculty, Laval University, Quebec, Canada
- Institute of Nutrition and Functional Foods, Laval University, Quebec, Canada
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7
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Tang Q, Sinclair M, Hasdemir HS, Stein RA, Karakas E, Tajkhorshid E, Mchaourab HS. Asymmetric conformations and lipid interactions shape the ATP-coupled cycle of a heterodimeric ABC transporter. Nat Commun 2023; 14:7184. [PMID: 37938578 PMCID: PMC10632425 DOI: 10.1038/s41467-023-42937-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/26/2023] [Indexed: 11/09/2023] Open
Abstract
Here we used cryo-electron microscopy (cryo-EM), double electron-electron resonance spectroscopy (DEER), and molecular dynamics (MD) simulations, to capture and characterize ATP- and substrate-bound inward-facing (IF) and occluded (OC) conformational states of the heterodimeric ATP binding cassette (ABC) multidrug exporter BmrCD in lipid nanodiscs. Supported by DEER analysis, the structures reveal that ATP-powered isomerization entails changes in the relative symmetry of the BmrC and BmrD subunits that propagates from the transmembrane domain to the nucleotide binding domain. The structures uncover asymmetric substrate and Mg2+ binding which we hypothesize are required for triggering ATP hydrolysis preferentially in one of the nucleotide-binding sites. MD simulations demonstrate that multiple lipid molecules differentially bind the IF versus the OC conformation thus establishing that lipid interactions modulate BmrCD energy landscape. Our findings are framed in a model that highlights the role of asymmetric conformations in the ATP-coupled transport with general implications to the mechanism of ABC transporters.
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Affiliation(s)
- Qingyu Tang
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Matt Sinclair
- Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Hale S Hasdemir
- Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Richard A Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Erkan Karakas
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37232, USA.
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8
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Yu L, Xu X, Chua WZ, Feng H, Ser Z, Shao K, Shi J, Wang Y, Li Z, Sobota RM, Sham LT, Luo M. Structural basis of peptide secretion for Quorum sensing by ComA. Nat Commun 2023; 14:7178. [PMID: 37935699 PMCID: PMC10630487 DOI: 10.1038/s41467-023-42852-9] [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: 04/12/2023] [Accepted: 10/23/2023] [Indexed: 11/09/2023] Open
Abstract
Quorum sensing (QS) is a crucial regulatory mechanism controlling bacterial signalling and holds promise for novel therapies against antimicrobial resistance. In Gram-positive bacteria, such as Streptococcus pneumoniae, ComA is a conserved efflux pump responsible for the maturation and secretion of peptide signals, including the competence-stimulating peptide (CSP), yet its structure and function remain unclear. Here, we functionally characterize ComA as an ABC transporter with high ATP affinity and determined its cryo-EM structures in the presence or absence of CSP or nucleotides. Our findings reveal a network of strong electrostatic interactions unique to ComA at the intracellular gate, a putative binding pocket for two CSP molecules, and negatively charged residues facilitating CSP translocation. Mutations of these residues affect ComA's peptidase activity in-vitro and prevent CSP export in-vivo. We demonstrate that ATP-Mg2+ triggers the outward-facing conformation of ComA for CSP release, rather than ATP alone. Our study provides molecular insights into the QS signal peptide secretion, highlighting potential targets for QS-targeting drugs.
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Affiliation(s)
- Lin Yu
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, 225001, Jiangsu, China
| | - Xin Xu
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore
| | - Wan-Zhen Chua
- Infectious Diseases Translational Research Programme and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117545, Singapore
| | - Hao Feng
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore
| | - Zheng Ser
- Functional Proteomics Laboratory, SingMass National Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, 138673, Singapore
| | - Kai Shao
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore
| | - Jian Shi
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore
- Center for Bioimaging Sciences, Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Yumei Wang
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Science, Beijing, 100190, China
| | - Zongli Li
- Harvard Cryo-EM Center for Structural Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Radoslaw M Sobota
- Functional Proteomics Laboratory, SingMass National Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, 138673, Singapore
| | - Lok-To Sham
- Infectious Diseases Translational Research Programme and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117545, Singapore.
| | - Min Luo
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore.
- Center for Bioimaging Sciences, Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore.
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9
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El Omari K, Duman R, Mykhaylyk V, Orr CM, Latimer-Smith M, Winter G, Grama V, Qu F, Bountra K, Kwong HS, Romano M, Reis RI, Vogeley L, Vecchia L, Owen CD, Wittmann S, Renner M, Senda M, Matsugaki N, Kawano Y, Bowden TA, Moraes I, Grimes JM, Mancini EJ, Walsh MA, Guzzo CR, Owens RJ, Jones EY, Brown DG, Stuart DI, Beis K, Wagner A. Experimental phasing opportunities for macromolecular crystallography at very long wavelengths. Commun Chem 2023; 6:219. [PMID: 37828292 PMCID: PMC10570326 DOI: 10.1038/s42004-023-01014-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 09/26/2023] [Indexed: 10/14/2023] Open
Abstract
Despite recent advances in cryo-electron microscopy and artificial intelligence-based model predictions, a significant fraction of structure determinations by macromolecular crystallography still requires experimental phasing, usually by means of single-wavelength anomalous diffraction (SAD) techniques. Most synchrotron beamlines provide highly brilliant beams of X-rays of between 0.7 and 2 Å wavelength. Use of longer wavelengths to access the absorption edges of biologically important lighter atoms such as calcium, potassium, chlorine, sulfur and phosphorus for native-SAD phasing is attractive but technically highly challenging. The long-wavelength beamline I23 at Diamond Light Source overcomes these limitations and extends the accessible wavelength range to λ = 5.9 Å. Here we report 22 macromolecular structures solved in this extended wavelength range, using anomalous scattering from a range of elements which demonstrate the routine feasibility of lighter atom phasing. We suggest that, in light of its advantages, long-wavelength crystallography is a compelling option for experimental phasing.
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Affiliation(s)
- Kamel El Omari
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Ramona Duman
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Vitaliy Mykhaylyk
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Christian M Orr
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | | | - Graeme Winter
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
| | - Vinay Grama
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
| | - Feng Qu
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Kiran Bountra
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Hok Sau Kwong
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Maria Romano
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
- Institute of Biostructures and Bioimaging, IBB, CNR, 80131, Naples, Italy
- Department of Pharmacy, University of Naples "Federico II", 80131, Naples, Italy
| | - Rosana I Reis
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK
| | - Lutz Vogeley
- Charles River Discovery Research Services UK, Chesterford Research Park, Saffron Walden, CB10 1XL, UK
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
| | - Luca Vecchia
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - C David Owen
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Sina Wittmann
- Department of Biochemistry, University of Oxford, Oxford, UK
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Max Renner
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Department of Chemistry, Umeå University, 901 87, Umeå, Sweden
| | - Miki Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, 305-0801, Japan
| | - Naohiro Matsugaki
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, 305-0801, Japan
- Department of Materials Structure Science, School of High Energy Accelerator Science, The Graduate University of Advanced Studies (Soken-dai), 1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan
| | - Yoshiaki Kawano
- Advanced Photon Technology Division, RIKEN SPring-8 Center, Hyogo, 679-5148, Japan
| | - Thomas A Bowden
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Isabel Moraes
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK
| | - Jonathan M Grimes
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Erika J Mancini
- School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QG, UK
| | - Martin A Walsh
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Cristiane R Guzzo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, 05508-000, Brazil
| | - Raymond J Owens
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- The Rosalind Franklin Institute, Harwell Campus, Oxford, OX11 0FA, UK
| | - E Yvonne Jones
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - David G Brown
- Charles River Discovery Research Services UK, Chesterford Research Park, Saffron Walden, CB10 1XL, UK
| | - Dave I Stuart
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Konstantinos Beis
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Armin Wagner
- Diamond Light Source, Harwell Science and Innovation Campus, -, OX110DE, UK.
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK.
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10
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Santos MFA, Pessoa JC. Interaction of Vanadium Complexes with Proteins: Revisiting the Reported Structures in the Protein Data Bank (PDB) since 2015. Molecules 2023; 28:6538. [PMID: 37764313 PMCID: PMC10536487 DOI: 10.3390/molecules28186538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
The structural determination and characterization of molecules, namely proteins and enzymes, is crucial to gaining a better understanding of their role in different chemical and biological processes. The continuous technical developments in the experimental and computational resources of X-ray diffraction (XRD) and, more recently, cryogenic Electron Microscopy (cryo-EM) led to an enormous growth in the number of structures deposited in the Protein Data Bank (PDB). Bioinorganic chemistry arose as a relevant discipline in biology and therapeutics, with a massive number of studies reporting the effects of metal complexes on biological systems, with vanadium complexes being one of the relevant systems addressed. In this review, we focus on the interactions of vanadium compounds (VCs) with proteins. Several types of binding are established between VCs and proteins/enzymes. Considering that the V-species that bind may differ from those initially added, the mentioned structural techniques are pivotal to clarifying the nature and variety of interactions of VCs with proteins and to proposing the mechanisms involved either in enzymatic inhibition or catalysis. As such, we provide an account of the available structural information of VCs bound to proteins obtained by both XRD and/or cryo-EM, mainly exploring the more recent structures, particularly those containing organic-based vanadium complexes.
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Affiliation(s)
- Marino F. A. Santos
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO—Applied Molecular Biosciences Unit, Chemistry Department, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Centro de Química Estrutural, Departamento de Engenharia Química, Institute of Molecular Sciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - João Costa Pessoa
- Centro de Química Estrutural, Departamento de Engenharia Química, Institute of Molecular Sciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
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11
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Haysom SF, Machin J, Whitehouse JM, Horne JE, Fenn K, Ma Y, El Mkami H, Böhringer N, Schäberle TF, Ranson NA, Radford SE, Pliotas C. Darobactin B Stabilises a Lateral-Closed Conformation of the BAM Complex in E. coli Cells. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 135:e202218783. [PMID: 38515502 PMCID: PMC10952338 DOI: 10.1002/ange.202218783] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Indexed: 03/23/2024]
Abstract
The β-barrel assembly machinery (BAM complex) is essential for outer membrane protein (OMP) folding in Gram-negative bacteria, and represents a promising antimicrobial target. Several conformational states of BAM have been reported, but all have been obtained under conditions which lack the unique features and complexity of the outer membrane (OM). Here, we use Pulsed Electron-Electron Double Resonance (PELDOR, or DEER) spectroscopy distance measurements to interrogate the conformational ensemble of the BAM complex in E. coli cells. We show that BAM adopts a broad ensemble of conformations in the OM, while in the presence of the antibiotic darobactin B (DAR-B), BAM's conformational equilibrium shifts to a restricted ensemble consistent with the lateral closed state. Our in-cell PELDOR findings are supported by new cryoEM structures of BAM in the presence and absence of DAR-B. This work demonstrates the utility of PELDOR to map conformational changes in BAM within its native cellular environment.
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Affiliation(s)
- Samuel F. Haysom
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Jonathan Machin
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - James M. Whitehouse
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Jim E. Horne
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Katherine Fenn
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Yue Ma
- Astbury Centre for Structural Molecular BiologySchool of Biomedical SciencesUniversity of LeedsLeedsLS2 9JTUK
- School of Biological Sciences, Faculty of Biology, Medicine and HealthManchester Academic and Health Science CentreThe University of ManchesterManchesterM13 9PTUK
- Manchester Institute of BiotechnologyThe University of ManchesterManchesterM1 7DNUK
| | - Hassane El Mkami
- School of Physics and AstronomyUniversity of St. AndrewsSt. AndrewsKY16 9SSUK
| | - Nils Böhringer
- Institute for Insect BiotechnologyNatural Product ResearchJustus-Liebig-University GiessenOhlebergsweg 1235392GiessenGermany
- German Center for Infection Research (DZIF)Partner Site Giessen-Marburg-LangenOhlebergsweg 1235392GiessenGermany
| | - Till F. Schäberle
- Institute for Insect BiotechnologyNatural Product ResearchJustus-Liebig-University GiessenOhlebergsweg 1235392GiessenGermany
- German Center for Infection Research (DZIF)Partner Site Giessen-Marburg-LangenOhlebergsweg 1235392GiessenGermany
- Natural Product DepartmentFraunhofer-Institute for Molecular Biology and Applied Ecology (IME)Ohlebergsweg 1235392GiessenGermany
| | - Neil A. Ranson
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Sheena E. Radford
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Christos Pliotas
- Astbury Centre for Structural Molecular BiologySchool of Biomedical SciencesUniversity of LeedsLeedsLS2 9JTUK
- School of Biological Sciences, Faculty of Biology, Medicine and HealthManchester Academic and Health Science CentreThe University of ManchesterManchesterM13 9PTUK
- Manchester Institute of BiotechnologyThe University of ManchesterManchesterM1 7DNUK
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12
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Haysom SF, Machin J, Whitehouse JM, Horne JE, Fenn K, Ma Y, El Mkami H, Böhringer N, Schäberle TF, Ranson NA, Radford SE, Pliotas C. Darobactin B Stabilises a Lateral-Closed Conformation of the BAM Complex in E. coli Cells. Angew Chem Int Ed Engl 2023; 62:e202218783. [PMID: 37162386 PMCID: PMC10952311 DOI: 10.1002/anie.202218783] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 04/26/2023] [Accepted: 05/09/2023] [Indexed: 05/11/2023]
Abstract
The β-barrel assembly machinery (BAM complex) is essential for outer membrane protein (OMP) folding in Gram-negative bacteria, and represents a promising antimicrobial target. Several conformational states of BAM have been reported, but all have been obtained under conditions which lack the unique features and complexity of the outer membrane (OM). Here, we use Pulsed Electron-Electron Double Resonance (PELDOR, or DEER) spectroscopy distance measurements to interrogate the conformational ensemble of the BAM complex in E. coli cells. We show that BAM adopts a broad ensemble of conformations in the OM, while in the presence of the antibiotic darobactin B (DAR-B), BAM's conformational equilibrium shifts to a restricted ensemble consistent with the lateral closed state. Our in-cell PELDOR findings are supported by new cryoEM structures of BAM in the presence and absence of DAR-B. This work demonstrates the utility of PELDOR to map conformational changes in BAM within its native cellular environment.
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Affiliation(s)
- Samuel F. Haysom
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Jonathan Machin
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - James M. Whitehouse
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Jim E. Horne
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Katherine Fenn
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Yue Ma
- Astbury Centre for Structural Molecular BiologySchool of Biomedical SciencesUniversity of LeedsLeedsLS2 9JTUK
- School of Biological Sciences, Faculty of Biology, Medicine and HealthManchester Academic and Health Science CentreThe University of ManchesterManchesterM13 9PTUK
- Manchester Institute of BiotechnologyThe University of ManchesterManchesterM1 7DNUK
| | - Hassane El Mkami
- School of Physics and AstronomyUniversity of St. AndrewsSt. AndrewsKY16 9SSUK
| | - Nils Böhringer
- Institute for Insect BiotechnologyNatural Product ResearchJustus-Liebig-University GiessenOhlebergsweg 1235392GiessenGermany
- German Center for Infection Research (DZIF)Partner Site Giessen-Marburg-LangenOhlebergsweg 1235392GiessenGermany
| | - Till F. Schäberle
- Institute for Insect BiotechnologyNatural Product ResearchJustus-Liebig-University GiessenOhlebergsweg 1235392GiessenGermany
- German Center for Infection Research (DZIF)Partner Site Giessen-Marburg-LangenOhlebergsweg 1235392GiessenGermany
- Natural Product DepartmentFraunhofer-Institute for Molecular Biology and Applied Ecology (IME)Ohlebergsweg 1235392GiessenGermany
| | - Neil A. Ranson
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Sheena E. Radford
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular BiologyUniversity of LeedsLeedsLS2 9JTUK
| | - Christos Pliotas
- Astbury Centre for Structural Molecular BiologySchool of Biomedical SciencesUniversity of LeedsLeedsLS2 9JTUK
- School of Biological Sciences, Faculty of Biology, Medicine and HealthManchester Academic and Health Science CentreThe University of ManchesterManchesterM13 9PTUK
- Manchester Institute of BiotechnologyThe University of ManchesterManchesterM1 7DNUK
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13
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Tang Q, Sinclair M, Hasdemir HS, Stein R, Karakas E, Tajkhorshid E, Mchaourab H. Asymmetric conformations and lipid interactions shape the ATP-coupled cycle of a heterodimeric ABC transporter. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.29.541986. [PMID: 37398337 PMCID: PMC10312460 DOI: 10.1101/2023.05.29.541986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
To illuminate the structural origin of catalytic asymmetry of heterodimeric ABC transporters and how it shapes the energetics of their conformational cycles, we used cryo-electron microscopy (cryo-EM), double electron-electron resonance spectroscopy (DEER), and molecular dynamics (MD) simulations, to capture and characterize conformational states of the heterodimeric ABC multidrug exporter BmrCD in lipid nanodiscs. In addition to multiple ATP- and substrate-bound inward-facing (IF) conformations, we obtained the structure of an occluded (OC) conformation wherein the unique extracellular domain (ECD) twists to partially open the extracellular gate. In conjunction with DEER analysis of the populations of these conformations, the structures reveal that ATP-powered isomerization entails changes in the relative symmetry of the BmrC and BmrD subunits that propagates from the transmembrane domain (TMD) to the nucleotide binding domain (NBD). The structures uncover asymmetric substrate and Mg 2+ binding which we hypothesize are required for triggering ATP hydrolysis preferentially in one of the nucleotide-binding sites. MD simulations demonstrated that multiple lipid molecules, identified from the cryo-EM density maps, differentially bind the IF versus the OC conformation thus modulating their relative stability. In addition to establishing how lipid interactions with BmrCD modulate the energy landscape, our findings are framed in a distinct transport model that highlights the role of asymmetric conformations in the ATP-coupled cycle with implications to the mechanism of ABC transporters in general.
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14
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Guryanova SV. Immunomodulation, Bioavailability and Safety of Bacteriocins. Life (Basel) 2023; 13:1521. [PMID: 37511896 PMCID: PMC10381439 DOI: 10.3390/life13071521] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/01/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023] Open
Abstract
The rise of antibiotic-resistant bacteria and the emergence of new pathogens have created a need for new strategies to fight against infectious diseases. One promising approach is the use of antimicrobial peptides produced by a certain species of bacteria, known as bacteriocins, which are active against other strains of the same or related species. Bacteriocins can help in the treatment and prevention of infectious diseases. Moreover, bacteriocins can be obtained in prokaryotic organisms, and contribute s to their widespread use. While the use of bacteriocins is currently limited to the food industry (for example, nisin is used as a preservative, E234), a large number of studies on their microbicidal properties suggest that their use in medicine may increase in the foreseeable future. However, for the successful use of bacteriocins in medicine, it is necessary to understand their effect on the immune system, especially in cases where immunity is weakened due to infectious processes, oncological, allergic, or autoimmune diseases. Studies on the immuno-modulatory activity of bacteriocins in animal models and human cells have revealed their ability to induce both pro-inflammatory and anti-inflammatory factors involved in the implementation of innate immunity. The influence of bacteriocins on acquired immunity is revealed by an increase in the number of T-lymphocytes with a simultaneous decrease in B-lymphocyte levels, which makes them attractive substances for reducing inflammation. The widespread use of bacteriocins in the food industry, their low toxicity, and their broad and narrow specificity are reasons for researchers to pay attention to their immunomodulatory properties and explore their medical applications. Inflammation regulation by bacteriocins can be used in the treatment of various pathologies. The aim of the review was to analyze scientific publications on the immunomodulatory activity, bioavailability, and safety of bacteriocins in order to use the data obtained to organize preclinical and clinical studies.
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Affiliation(s)
- Svetlana V Guryanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Medical Institute, Peoples' Friendship University of Russia (RUDN University) of the Ministry of Science and Higher Education of the Russian Federation, 117198 Moscow, Russia
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15
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Fernandez-Cantos MV, Garcia-Morena D, Yi Y, Liang L, Gómez-Vázquez E, Kuipers OP. Bioinformatic mining for RiPP biosynthetic gene clusters in Bacteroidales reveals possible new subfamily architectures and novel natural products. Front Microbiol 2023; 14:1219272. [PMID: 37469430 PMCID: PMC10352776 DOI: 10.3389/fmicb.2023.1219272] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 06/16/2023] [Indexed: 07/21/2023] Open
Abstract
The Bacteroidales order, widely distributed among diverse human populations, constitutes a key component of the human microbiota. Members of this Gram-negative order have been shown to modulate the host immune system, play a fundamental role in the gut's microbial food webs, or be involved in pathogenesis. Bacteria inhabiting such a complex environment as the human microbiome are expected to display social behaviors and, hence, possess factors that mediate cooperative and competitive interactions. Different types of molecules can mediate interference competition, including non-ribosomal peptides (NRPs), polyketides, and bacteriocins. The present study investigates the potential of Bacteroidales bacteria to biosynthesize class I bacteriocins, which are ribosomally synthesized and post-translationally modified peptides (RiPPs). For this purpose, 1,136 genome-sequenced strains from this order were mined using BAGEL4. A total of 1,340 areas of interest (AOIs) were detected. The most commonly identified enzymes involved in RiPP biosynthesis were radical S-adenosylmethionine (rSAM), either alone or in combination with other biosynthetic enzymes such as YcaO. A more comprehensive analysis of a subset of 9 biosynthetic gene clusters (BGCs) revealed a consistent association in Bacteroidales BGCs between peptidase-containing ATP-binding transporters (PCATs) and precursor peptides with GG-motifs. This finding suggests a possibly shared mechanism for leader peptide cleavage and transport of mature products. Notably, human metagenomic studies showed a high prevalence and abundance of the RiPP BGCs from Phocaeicola vulgatus and Porphyromonas gulae. The mature product of P. gulae BGC is hypothesized to display γ-thioether linkages and a C-terminal backbone amidine, a potential new combination of post-translational modifications (PTM). All these findings highlight the RiPP biosynthetic potential of Bacteroidales bacteria, as a rich source of novel peptide structures of possible relevance in the human microbiome context.
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Affiliation(s)
- Maria Victoria Fernandez-Cantos
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Diego Garcia-Morena
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Yunhai Yi
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | | | - Emilio Gómez-Vázquez
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Oscar P. Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
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16
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Cao S, Yang Y, He L, Hang Y, Yan X, Shi H, Wu J, Ouyang Z. Cryo-EM structures of mitochondrial ABC transporter ABCB10 in apo and biliverdin-bound form. Nat Commun 2023; 14:2030. [PMID: 37041204 PMCID: PMC10090120 DOI: 10.1038/s41467-023-37851-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 04/03/2023] [Indexed: 04/13/2023] Open
Abstract
ABCB10, a member of ABC transporter superfamily that locates in the inner membrane of mitochondria, plays crucial roles in hemoglobin synthesis, antioxidative stress and stabilization of the iron transporter mitoferrin-1. Recently, it was found that ABCB10 is a mitochondrial biliverdin exporter. However, the molecular mechanism of biliverdin export by ABCB10 remains elusive. Here we report the cryo-EM structures of ABCB10 in apo (ABCB10-apo) and biliverdin-bound form (ABCB10-BV) at 3.67 Å and 2.85 Å resolution, respectively. ABCB10-apo adopts a wide-open conformation and may thus represent the apo form structure. ABCB10-BV forms a closed conformation and biliverdin situates in a hydrophobic pocket in one protomer and bridges the interaction through hydrogen bonds with the opposing one. We also identify cholesterols sandwiched by BVs and discuss the export dynamics based on these structural and biochemical observations.
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Affiliation(s)
- Sheng Cao
- Wuxi Biortus Biosciences Co. Ltd., 6 Dongsheng Western Road, 214437, Jiangyin, Jiangsu, China
| | - Yihu Yang
- Wuxi Biortus Biosciences Co. Ltd., 6 Dongsheng Western Road, 214437, Jiangyin, Jiangsu, China
| | - Lili He
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, 430030, Wuhan, Hubei Province, China
| | - Yumo Hang
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, 430030, Wuhan, Hubei Province, China
| | - Xiaodong Yan
- Wuxi Biortus Biosciences Co. Ltd., 6 Dongsheng Western Road, 214437, Jiangyin, Jiangsu, China
| | - Hui Shi
- Wuxi Biortus Biosciences Co. Ltd., 6 Dongsheng Western Road, 214437, Jiangyin, Jiangsu, China
| | - Jiaquan Wu
- Wuxi Biortus Biosciences Co. Ltd., 6 Dongsheng Western Road, 214437, Jiangyin, Jiangsu, China
| | - Zhuqing Ouyang
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, 430030, Wuhan, Hubei Province, China.
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17
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Borovsky D, Rougé P, Shatters RG. Bactericidal Properties of Proline-Rich Aedes aegypti Trypsin Modulating Oostatic Factor ( AeaTMOF). LIFE (BASEL, SWITZERLAND) 2022; 13:life13010019. [PMID: 36675967 PMCID: PMC9862690 DOI: 10.3390/life13010019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
The antimicrobial properties of proline-rich Aedes aegypti decapeptide TMOF (AeaTMOF) and oncocin112 (1-13) were compared. Incubations with multidrug-resistant Escherichia coli cells showed that AeaTMOF (5 mM) was able to completely inhibit bacterial cell growth, whereas oncocin112 (1-13) (20 mM) partially inhibited bacterial growth as compared with bacterial cells that were not multidrug-resistant cells. AeaTMOF (5 mM) was very effective against Acinetobacter baumannii and Pseudomonas aeruginosa, completely inhibiting cell growth during 15 h incubations. AeaTMOF (5 mM) completely inhibited the Gram-positive bacteria Staphylococcus aureus and Bacillus thurengiensis sups. Israelensis cell growth, whereas oncocin112 (1-13) (10 and 20 mM) failed to affect bacterial cell growth. E. coli cells that lack the SbmA transporter were inhibited by AeaTMOF (5 mM) and not by oncocin112 (1-13) (10 to 20 mM), indicating that AeaTMOF can use other bacterial transporters than SbmA that is mainly used by proline-rich antimicrobial peptides. Incubation of E. coli cells with NaAzide showed that AeaTMOF does not use ABC-like transporters that use ATP hydrolysis to import molecules into bacterial cells. Three-dimensional modeling and docking of AeaTMOF to SbmA and MdtM transporters showed that AeaTMOF can bind these proteins, and the binding location of AeaTMOF inside these protein transporters allows AeaTMOF to be transported into the bacterial cytosol. These results show that AeaTMOF can be used as a future antibacterial agent against both multidrug-resistant Gram-positive and -negative bacteria.
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Affiliation(s)
- Dov Borovsky
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Correspondence:
| | - Pierre Rougé
- Faculte des Sciences Pharmaceutiques, 3106 Toulouse, France
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18
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Lane BJ, Wang B, Ma Y, Calabrese AN, El Mkami H, Pliotas C. HDX-guided EPR spectroscopy to interrogate membrane protein dynamics. STAR Protoc 2022; 3:101562. [PMID: 35874470 PMCID: PMC9304679 DOI: 10.1016/j.xpro.2022.101562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Solvent accessibilities of and distances between protein residues measured by pulsed-EPR approaches provide high-resolution information on dynamic protein motions. We describe protocols for the purification and site-directed spin labeling of integral membrane proteins. In our protocol, peptide-level HDX-MS is used as a precursor to guide single-residue resolution ESEEM accessibility measurements and spin labeling strategies for EPR applications. Exploiting the pentameric MscL channel as a model, we discuss the use of cwEPR, DEER/PELDOR, and ESEEM spectroscopies to interrogate membrane protein dynamics. For complete details on the use and execution of this protocol, please refer to Wang et al. (2022). Protocols for an integrated EPR-based approach to study membrane protein dynamics Instructions for the sample preparation of spin-labeled membrane proteins Used HDX-MS as a precursor to guide spin labeling strategies for EPR methods Probed solvent accessibility at the single-residue level by ESEEM
Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
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19
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Marrink SJ, Monticelli L, Melo MN, Alessandri R, Tieleman DP, Souza PCT. Two decades of Martini: Better beads, broader scope. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1620] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Siewert J. Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials University of Groningen Groningen The Netherlands
| | - Luca Monticelli
- Molecular Microbiology and Structural Biochemistry (MMSB ‐ UMR 5086) CNRS & University of Lyon Lyon France
| | - Manuel N. Melo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras Portugal
| | - Riccardo Alessandri
- Pritzker School of Molecular Engineering University of Chicago Chicago Illinois USA
| | - D. Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences University of Calgary Alberta Canada
| | - Paulo C. T. Souza
- Molecular Microbiology and Structural Biochemistry (MMSB ‐ UMR 5086) CNRS & University of Lyon Lyon France
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20
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Chaptal V, Zampieri V, Wiseman B, Orelle C, Martin J, Nguyen KA, Gobet A, Di Cesare M, Magnard S, Javed W, Eid J, Kilburg A, Peuchmaur M, Marcoux J, Monticelli L, Hogbom M, Schoehn G, Jault JM, Boumendjel A, Falson P. Substrate-bound and substrate-free outward-facing structures of a multidrug ABC exporter. SCIENCE ADVANCES 2022; 8:eabg9215. [PMID: 35080979 DOI: 10.1101/2021.03.12.435132] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Multidrug ABC transporters translocate drugs across membranes by a mechanism for which the molecular features of drug release are so far unknown. Here, we resolved three ATP-Mg2+-bound outward-facing conformations of the Bacillus subtilis (homodimeric) BmrA by x-ray crystallography and single-particle cryo-electron microscopy (EM) in detergent solution, one of them with rhodamine 6G (R6G), a substrate exported by BmrA when overexpressed in B. subtilis. Two R6G molecules bind to the drug-binding cavity at the level of the outer leaflet, between transmembrane (TM) helices 1-2 of one monomer and TM5'-6' of the other. They induce a rearrangement of TM1-2, highlighting a local flexibility that we confirmed by hydrogen/deuterium exchange and molecular dynamics simulations. In the absence of R6G, simulations show a fast postrelease occlusion of the cavity driven by hydrophobicity, while when present, R6G can move within the cavity, maintaining it open.
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Affiliation(s)
- Vincent Chaptal
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Veronica Zampieri
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Benjamin Wiseman
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden
| | - Cédric Orelle
- Bacterial Nucleotide-Binding Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Juliette Martin
- Modeling Biological Macromolecules Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Kim-Anh Nguyen
- University of Grenoble Alpes, INSERM, LRB, 38000 Grenoble, France
| | - Alexia Gobet
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Margot Di Cesare
- Bacterial Nucleotide-Binding Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Sandrine Magnard
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Waqas Javed
- Bacterial Nucleotide-Binding Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Jad Eid
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Arnaud Kilburg
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Marine Peuchmaur
- University of Grenoble Alpes, CNRS, DPM UMR 5063, 38041 Grenoble, France
| | - Julien Marcoux
- Institut de Pharmacologie et de Biologie Structurale (IPBS), UMR 5089, Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Luca Monticelli
- Modeling Biological Macromolecules Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Martin Hogbom
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden
| | - Guy Schoehn
- University of Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
| | - Jean-Michel Jault
- Bacterial Nucleotide-Binding Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | | | - Pierre Falson
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
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21
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Conformational trapping of an ABC transporter in polymer lipid nanoparticles. Biochem J 2022; 479:145-159. [PMID: 35050326 PMCID: PMC8883494 DOI: 10.1042/bcj20210312] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 12/14/2022]
Abstract
ATP-binding cassette (ABC) proteins play important roles in cells as importers and exporters but as membrane proteins they are subject to well-known challenges of isolating pure and stable samples for study. One solution to this problem is to use styrene-maleic acid lipid particles (SMALPs). Styrene-maleic acid (SMA) can be added directly to membranes, forming stable nanoparticles incorporating membrane proteins and lipids. Here we use Sav1866, a well-characterised bacterial protein, as a proxy for ABC proteins in general. We show that stable and monodispersed Sav1866 can be purified at high yield using SMA. This protein can be used for biophysical characterisations showing that its overall structure is consistent with existing evidence. However, like other ABC proteins in SMALPs it does not hydrolyse ATP. The lack of ATPase activity in ABC–SMALPs may result from conformational trapping of the proteins in SMALPs. Undertaken in a controlled manner, conformational trapping is a useful tool to stabilise protein samples into a single conformation for structural studies. Due to their inability to hydrolyse ATP, the conformation of Sav1866–SMALPs cannot be altered using ATP and vanadate after purification. To achieve controlled trapping of Sav1866–SMALPs we show that Sav1866 in crude membranes can be incubated with ATP, magnesium and sodium orthovanadate. Subsequent solubilisation and purification with SMA produces a sample of Sav1866–SMALPs with enhanced stability, and in a single conformational state. This method may be generally applicable to vanadate-sensitive ABC proteins and overcomes a limitation of the SMALP system for the study of this protein family.
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22
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Chaptal V, Zampieri V, Wiseman B, Orelle C, Martin J, Nguyen KA, Gobet A, Di Cesare M, Magnard S, Javed W, Eid J, Kilburg A, Peuchmaur M, Marcoux J, Monticelli L, Hogbom M, Schoehn G, Jault JM, Boumendjel A, Falson P. Substrate-bound and substrate-free outward-facing structures of a multidrug ABC exporter. SCIENCE ADVANCES 2022; 8:eabg9215. [PMID: 35080979 PMCID: PMC8791611 DOI: 10.1126/sciadv.abg9215] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Multidrug ABC transporters translocate drugs across membranes by a mechanism for which the molecular features of drug release are so far unknown. Here, we resolved three ATP-Mg2+-bound outward-facing conformations of the Bacillus subtilis (homodimeric) BmrA by x-ray crystallography and single-particle cryo-electron microscopy (EM) in detergent solution, one of them with rhodamine 6G (R6G), a substrate exported by BmrA when overexpressed in B. subtilis. Two R6G molecules bind to the drug-binding cavity at the level of the outer leaflet, between transmembrane (TM) helices 1-2 of one monomer and TM5'-6' of the other. They induce a rearrangement of TM1-2, highlighting a local flexibility that we confirmed by hydrogen/deuterium exchange and molecular dynamics simulations. In the absence of R6G, simulations show a fast postrelease occlusion of the cavity driven by hydrophobicity, while when present, R6G can move within the cavity, maintaining it open.
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Affiliation(s)
- Vincent Chaptal
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Veronica Zampieri
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Benjamin Wiseman
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden
| | - Cédric Orelle
- Bacterial Nucleotide-Binding Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Juliette Martin
- Modeling Biological Macromolecules Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Kim-Anh Nguyen
- University of Grenoble Alpes, INSERM, LRB, 38000 Grenoble, France
| | - Alexia Gobet
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Margot Di Cesare
- Bacterial Nucleotide-Binding Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Sandrine Magnard
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Waqas Javed
- Bacterial Nucleotide-Binding Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Jad Eid
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Arnaud Kilburg
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Marine Peuchmaur
- University of Grenoble Alpes, CNRS, DPM UMR 5063, 38041 Grenoble, France
| | - Julien Marcoux
- Institut de Pharmacologie et de Biologie Structurale (IPBS), UMR 5089, Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Luca Monticelli
- Modeling Biological Macromolecules Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | - Martin Hogbom
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden
| | - Guy Schoehn
- University of Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
| | - Jean-Michel Jault
- Bacterial Nucleotide-Binding Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
| | | | - Pierre Falson
- Drug Resistance and Membrane Proteins Group, Molecular Microbiology and Structural Biochemistry Laboratory, CNRS UMR 5086, University of Lyon, IBCP, 7, passage du Vercors, 69367 Lyon, France
- Corresponding author.
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23
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Generation of Lasso Peptide-Based ClpP Binders. Int J Mol Sci 2021; 23:ijms23010465. [PMID: 35008890 PMCID: PMC8745299 DOI: 10.3390/ijms23010465] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/28/2021] [Accepted: 12/30/2021] [Indexed: 11/17/2022] Open
Abstract
The Clp protease system fulfills a plethora of important functions in bacteria. It consists of a tetradecameric ClpP barrel holding the proteolytic centers and two hexameric Clp-ATPase rings, which recognize, unfold, and then feed substrate proteins into the ClpP barrel for proteolytic degradation. Flexible loops carrying conserved tripeptide motifs protrude from the Clp-ATPases and bind into hydrophobic pockets (H-pockets) on ClpP. Here, we set out to engineer microcin J25 (MccJ25), a ribosomally synthesized and post-translationally modified peptide (RiPP) of the lasso peptide subfamily, by introducing the conserved tripeptide motifs into the lasso peptide loop region to mimic the Clp-ATPase loops. We studied the capacity of the resulting lasso peptide variants to bind to ClpP and affect its activity. From the nine variants generated, one in particular (12IGF) was able to activate ClpP from Staphylococcus aureus and Bacillus subtilis. While 12IGF conferred stability to ClpP tetradecamers and stimulated peptide degradation, it did not trigger unregulated protein degradation, in contrast to the H-pocket-binding acyldepsipeptide antibiotics (ADEPs). Interestingly, synergistic interactions between 12IGF and ADEP were observed.
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24
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Rebuffat S. Ribosomally synthesized peptides, foreground players in microbial interactions: recent developments and unanswered questions. Nat Prod Rep 2021; 39:273-310. [PMID: 34755755 DOI: 10.1039/d1np00052g] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
It is currently well established that multicellular organisms live in tight association with complex communities of microorganisms including a large number of bacteria. These are immersed in complex interaction networks reflecting the relationships established between them and with host organisms; yet, little is known about the molecules and mechanisms involved in these mutual interactions. Ribosomally synthesized peptides, among which bacterial antimicrobial peptides called bacteriocins and microcins have been identified as contributing to host-microbe interplays, are either unmodified or post-translationally modified peptides. This review will unveil current knowledge on these ribosomal peptide-based natural products, their interplay with the host immune system, and their roles in microbial interactions and symbioses. It will include their major structural characteristics and post-translational modifications, the main rules of their maturation pathways, and the principal ecological functions they ensure (communication, signalization, competition), especially in symbiosis, taking select examples in various organisms. Finally, we address unanswered questions and provide a framework for deciphering big issues inspiring future directions in the field.
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Affiliation(s)
- Sylvie Rebuffat
- Laboratory Molecules of Communication and Adaptation of Microorganisms (MCAM, UMR 7245 CNRS-MNHN), National Museum of Natural History (MNHN), National Centre of Scientific Research (CNRS), CP 54, 57 rue Cuvier 75005, Paris, France.
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25
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Ghilarov D, Inaba-Inoue S, Stepien P, Qu F, Michalczyk E, Pakosz Z, Nomura N, Ogasawara S, Walker GC, Rebuffat S, Iwata S, Heddle JG, Beis K. Molecular mechanism of SbmA, a promiscuous transporter exploited by antimicrobial peptides. SCIENCE ADVANCES 2021; 7:eabj5363. [PMID: 34516884 PMCID: PMC8442886 DOI: 10.1126/sciadv.abj5363] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/16/2021] [Indexed: 05/12/2023]
Abstract
Antibiotic metabolites and antimicrobial peptides mediate competition between bacterial species. Many of them hijack inner and outer membrane proteins to enter cells. Sensitivity of enteric bacteria to multiple peptide antibiotics is controlled by the single inner membrane protein SbmA. To establish the molecular mechanism of peptide transport by SbmA and related BacA, we determined their cryo–electron microscopy structures at 3.2 and 6 Å local resolution, respectively. The structures show a previously unknown fold, defining a new class of secondary transporters named SbmA-like peptide transporters. The core domain includes conserved glutamates, which provide a pathway for proton translocation, powering transport. The structures show an outward-open conformation with a large cavity that can accommodate diverse substrates. We propose a molecular mechanism for antibacterial peptide uptake paving the way for creation of narrow-targeted therapeutics.
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Affiliation(s)
- Dmitry Ghilarov
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Satomi Inaba-Inoue
- Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London SW7 2AZ, UK
- Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, Oxfordshire OX11 0FA, UK
- Diffraction and Scattering Division, Japan Synchrotron Radiation Research Institute, SPring-8, 1-1-1, Kouto, Sayo, Hyogo 679-5198, Japan
| | - Piotr Stepien
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Feng Qu
- Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London SW7 2AZ, UK
- Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, Oxfordshire OX11 0FA, UK
| | | | - Zuzanna Pakosz
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
- Postgraduate School of Molecular Medicine, Warsaw, Poland
| | - Norimichi Nomura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Satoshi Ogasawara
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Graham Charles Walker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sylvie Rebuffat
- Molecules of Communication and Adaptation of Microorganisms Laboratory (MCAM, UMR 7245 CNRS-MNHN), Muséum National d’Histoire Naturelle, Sorbonne Universités, Centre National de la Recherche Scientifique, CP 54, 57 rue Cuvier, Paris 75005, France
| | - So Iwata
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
- Research Acceleration Program, Membrane Protein Crystallography Project, Japan Science and Technology Agency, Kyoto, Japan
| | | | - Konstantinos Beis
- Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London SW7 2AZ, UK
- Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, Oxfordshire OX11 0FA, UK
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26
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Majeed S, Ahmad AB, Sehar U, Georgieva ER. Lipid Membrane Mimetics in Functional and Structural Studies of Integral Membrane Proteins. MEMBRANES 2021; 11:685. [PMID: 34564502 PMCID: PMC8470526 DOI: 10.3390/membranes11090685] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/18/2021] [Accepted: 08/30/2021] [Indexed: 12/12/2022]
Abstract
Integral membrane proteins (IMPs) fulfill important physiological functions by providing cell-environment, cell-cell and virus-host communication; nutrients intake; export of toxic compounds out of cells; and more. However, some IMPs have obliterated functions due to polypeptide mutations, modifications in membrane properties and/or other environmental factors-resulting in damaged binding to ligands and the adoption of non-physiological conformations that prevent the protein from returning to its physiological state. Thus, elucidating IMPs' mechanisms of function and malfunction at the molecular level is important for enhancing our understanding of cell and organism physiology. This understanding also helps pharmaceutical developments for restoring or inhibiting protein activity. To this end, in vitro studies provide invaluable information about IMPs' structure and the relation between structural dynamics and function. Typically, these studies are conducted on transferred from native membranes to membrane-mimicking nano-platforms (membrane mimetics) purified IMPs. Here, we review the most widely used membrane mimetics in structural and functional studies of IMPs. These membrane mimetics are detergents, liposomes, bicelles, nanodiscs/Lipodisqs, amphipols, and lipidic cubic phases. We also discuss the protocols for IMPs reconstitution in membrane mimetics as well as the applicability of these membrane mimetic-IMP complexes in studies via a variety of biochemical, biophysical, and structural biology techniques.
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Affiliation(s)
- Saman Majeed
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Akram Bani Ahmad
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Ujala Sehar
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Elka R Georgieva
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Science Center, Lubbock, TX 79409, USA
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27
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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: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Indexed: 12/11/2022]
Abstract
Tripartite efflux pumps and the related type 1 secretion systems (T1SSs) in Gram-negative organisms are diverse in function, energization, and structural organization. They form continuous conduits spanning both the inner and the outer membrane and are composed of three principal components-the energized inner membrane transporters (belonging to ABC, RND, and MFS families), the outer membrane factor channel-like proteins, and linking the two, the periplasmic adaptor proteins (PAPs), also known as the membrane fusion proteins (MFPs). In this review we summarize the recent advances in understanding of structural biology, function, and regulation of these systems, highlighting the previously undescribed role of PAPs in providing a common architectural scaffold across diverse families of transporters. Despite being built from a limited number of basic structural domains, these complexes present a staggering variety of architectures. While key insights have been derived from the RND transporter systems, a closer inspection of the operation and structural organization of different tripartite systems reveals unexpected analogies between them, including those formed around MFS- and ATP-driven transporters, suggesting that they operate around basic common principles. Based on that we are proposing a new integrated model of PAP-mediated communication within the conformational cycling of tripartite systems, which could be expanded to other types of assemblies.
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Affiliation(s)
- Ilyas Alav
- Institute
of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Jessica Kobylka
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Miriam S. Kuth
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Klaas M. Pos
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Martin Picard
- Laboratoire
de Biologie Physico-Chimique des Protéines Membranaires, CNRS
UMR 7099, Université de Paris, 75005 Paris, France
- Fondation
Edmond de Rothschild pour le développement de la recherche
Scientifique, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Jessica M. A. Blair
- Institute
of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Vassiliy N. Bavro
- School
of Life Sciences, University of Essex, Colchester, CO4 3SQ United Kingdom
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28
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A comprehensive review on pharmacology of efflux pumps and their inhibitors in antibiotic resistance. Eur J Pharmacol 2021; 903:174151. [PMID: 33964293 DOI: 10.1016/j.ejphar.2021.174151] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 04/19/2021] [Accepted: 04/30/2021] [Indexed: 11/23/2022]
Abstract
The potential for the build-up of resistance to a particular antibiotic endangers its therapeutic application over time. In recent decades, antibiotic resistance has become one of the most severe threats to public health. It can be attributed to the relentless and unchecked use of antibiotics in healthcare sectors, cell culture, animal husbandry, and agriculture. Some classic examples of resistance mechanisms employed by bacteria include developing antibiotic degrading enzymes, modifying target sites previously targeted by antibiotics, and developing efflux mechanisms. Studies have shown that while some efflux pumps selectively extrude certain antibiotics, others extrude a structurally diverse class of antibiotics. Such extrusion of a structurally diverse class of antibiotics gives rise to multi-drug resistant (MDR) bacteria. These mechanisms are observed in gram-positive and gram-negative bacteria alike. Therefore, efflux pumps find their place in the list of high-priority targets for the treatment of antibiotic-resistance in bacteria mediated by efflux. Studies showed a significant escalation in bacteria's susceptibility to a particular antibiotic drug when tested with an efflux pump inhibitor (EPI) compared to when it was tested with the antibiotic drug alone. This review discusses the pharmacology, current status, and the future of EPIs in antibiotic resistance.
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29
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Structural Insights into Transporter-Mediated Drug Resistance in Infectious Diseases. J Mol Biol 2021; 433:167005. [PMID: 33891902 DOI: 10.1016/j.jmb.2021.167005] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/12/2021] [Accepted: 04/12/2021] [Indexed: 02/07/2023]
Abstract
Infectious diseases present a major threat to public health globally. Pathogens can acquire resistance to anti-infectious agents via several means including transporter-mediated efflux. Typically, multidrug transporters feature spacious, dynamic, and chemically malleable binding sites to aid in the recognition and transport of chemically diverse substrates across cell membranes. Here, we discuss recent structural investigations of multidrug transporters involved in resistance to infectious diseases that belong to the ATP-binding cassette (ABC) superfamily, the major facilitator superfamily (MFS), the drug/metabolite transporter (DMT) superfamily, the multidrug and toxic compound extrusion (MATE) family, the small multidrug resistance (SMR) family, and the resistance-nodulation-division (RND) superfamily. These structural insights provide invaluable information for understanding and combatting multidrug resistance.
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30
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Shukla S, Baumgart T. Enzymatic trans-bilayer lipid transport: Mechanisms, efficiencies, slippage, and membrane curvature. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2021; 1863:183534. [PMID: 33340491 PMCID: PMC8351443 DOI: 10.1016/j.bbamem.2020.183534] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/03/2020] [Accepted: 12/07/2020] [Indexed: 12/12/2022]
Abstract
The eukaryotic plasma membrane's lipid composition is found to be ubiquitously asymmetric comparing inner and outer leaflets. This membrane lipid asymmetry plays a crucial role in diverse cellular processes critical for cell survival. A specialized set of transmembrane proteins called translocases, or flippases, have evolved to maintain this membrane lipid asymmetry in an energy-dependent manner. One potential consequence of local variations in membrane lipid asymmetry is membrane remodeling, which is essential for cellular processes such as intracellular trafficking. Recently, there has been a surge in the identification and characterization of flippases, which has significantly advanced the understanding of their functional mechanisms. Furthermore, there are intriguing possibilities for a coupling between membrane curvature and flippase activity. In this review we highlight studies that link membrane shape and remodeling to differential stresses generated by the activity of lipid flippases with an emphasis on data obtained through model membrane systems. We review the common mechanistic models of flippase-mediated lipid flipping and discuss common techniques used to test lipid flippase activity. We then compare the existing data on lipid translocation rates by flippases and conclude with potential future directions for this field.
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Affiliation(s)
- Sankalp Shukla
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Tobias Baumgart
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, United States.
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PELDOR/DEER: An Electron Paramagnetic Resonance Method to Study Membrane Proteins in Lipid Bilayers. Methods Mol Biol 2021. [PMID: 33582999 DOI: 10.1007/978-1-0716-0724-4_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2023]
Abstract
Every membrane protein is involved in close interactions with the lipid environment of cellular membranes. The annular lipids, that are in direct contact with the polypeptide, can in principle be seen as an integral part of its structure, akin to the first hydration shell of soluble proteins. It is therefore desirable to investigate the structure of membrane proteins and especially their conformational flexibility under conditions that are as close as possible to their native state. This can be achieved by reconstituting the protein into proteoliposomes, nanodiscs, or bicelles. In recent years, PELDOR/DEER spectroscopy has proved to be a very useful method to study the structure and function of membrane proteins in such artificial membrane environments. The technique complements both X-ray crystallography and cryo-EM and can be used in combination with virtually any artificial membrane environment and under certain circumstances even in native membranes. Of the above-mentioned membrane mimics, bicelles are currently the least often used for PELDOR studies, although they offer some advantages, especially their ease of use. Here, we provide a step-by-step protocol for studying a bicelle reconstituted membrane protein with PELDOR/DEER spectroscopy.
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Soltani S, Hammami R, Cotter PD, Rebuffat S, Said LB, Gaudreau H, Bédard F, Biron E, Drider D, Fliss I. Bacteriocins as a new generation of antimicrobials: toxicity aspects and regulations. FEMS Microbiol Rev 2021; 45:fuaa039. [PMID: 32876664 PMCID: PMC7794045 DOI: 10.1093/femsre/fuaa039] [Citation(s) in RCA: 225] [Impact Index Per Article: 75.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 08/25/2020] [Indexed: 02/07/2023] Open
Abstract
In recent decades, bacteriocins have received substantial attention as antimicrobial compounds. Although bacteriocins have been predominantly exploited as food preservatives, they are now receiving increased attention as potential clinical antimicrobials and as possible immune-modulating agents. Infections caused by antibiotic-resistant bacteria have been declared as a global threat to public health. Bacteriocins represent a potential solution to this worldwide threat due to their broad- or narrow-spectrum activity against antibiotic-resistant bacteria. Notably, despite their role in food safety as natural alternatives to chemical preservatives, nisin remains the only bacteriocin legally approved by regulatory agencies as a food preservative. Moreover, insufficient data on the safety and toxicity of bacteriocins represent a barrier against the more widespread use of bacteriocins by the food and medical industry. Here, we focus on the most recent trends relating to the application of bacteriocins, their toxicity and impacts.
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Affiliation(s)
- Samira Soltani
- Food Science Department, Faculty of Agriculture and Food Sciences, Université Laval, G1V 0A6 Québec, Canada
| | - Riadh Hammami
- School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, 75 Laurier Ave. E, Ottawa, ON K1N 6N5, Canada
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, P61 C996 Ireland
- APC Microbiome Ireland, Institute and school of Microbiology, University College Cork, Western Road, Cork, T12 YN60, Ireland
| | - Sylvie Rebuffat
- Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, Laboratory Molecules of Communication and Adaptation of Microorganisms (MCAM), UMR 7245 CNRS-MNHN, CP 54, 57 rue Cuvier, 75005 Paris, France
| | - Laila Ben Said
- Food Science Department, Faculty of Agriculture and Food Sciences, Université Laval, G1V 0A6 Québec, Canada
| | - Hélène Gaudreau
- Food Science Department, Faculty of Agriculture and Food Sciences, Université Laval, G1V 0A6 Québec, Canada
| | - François Bédard
- Faculty of Pharmacy and Centre de Recherche en Endocrinologie Moléculaire et Oncologique et Génomique Humaine, Université Laval, 2705 Boulevard Laurier, Quebec G1V 4G2, Canada
| | - Eric Biron
- Faculty of Pharmacy and Centre de Recherche en Endocrinologie Moléculaire et Oncologique et Génomique Humaine, Université Laval, 2705 Boulevard Laurier, Quebec G1V 4G2, Canada
| | - Djamel Drider
- Institut Charles Viollette, Université de Lille, EA 7394, 53955 Villeneuve d'Ascq, France
| | - Ismail Fliss
- Food Science Department, Faculty of Agriculture and Food Sciences, Université Laval, G1V 0A6 Québec, Canada
- Institute of Nutrition and Functional Foods, Université Laval, 2440 Boulevard Hochelaga, Québec G1V 0A6, Canada
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Birch J, Cheruvara H, Gamage N, Harrison PJ, Lithgo R, Quigley A. Changes in Membrane Protein Structural Biology. BIOLOGY 2020; 9:E401. [PMID: 33207666 PMCID: PMC7696871 DOI: 10.3390/biology9110401] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/11/2020] [Accepted: 11/12/2020] [Indexed: 12/21/2022]
Abstract
Membrane proteins are essential components of many biochemical processes and are important pharmaceutical targets. Membrane protein structural biology provides the molecular rationale for these biochemical process as well as being a highly useful tool for drug discovery. Unfortunately, membrane protein structural biology is a difficult area of study due to low protein yields and high levels of instability especially when membrane proteins are removed from their native environments. Despite this instability, membrane protein structural biology has made great leaps over the last fifteen years. Today, the landscape is almost unrecognisable. The numbers of available atomic resolution structures have increased 10-fold though advances in crystallography and more recently by cryo-electron microscopy. These advances in structural biology were achieved through the efforts of many researchers around the world as well as initiatives such as the Membrane Protein Laboratory (MPL) at Diamond Light Source. The MPL has helped, provided access to and contributed to advances in protein production, sample preparation and data collection. Together, these advances have enabled higher resolution structures, from less material, at a greater rate, from a more diverse range of membrane protein targets. Despite this success, significant challenges remain. Here, we review the progress made and highlight current and future challenges that will be overcome.
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Affiliation(s)
- James Birch
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Harish Cheruvara
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Nadisha Gamage
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Peter J. Harrison
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Ryan Lithgo
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, Leicestershire, UK
| | - Andrew Quigley
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
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Telhig S, Ben Said L, Zirah S, Fliss I, Rebuffat S. Bacteriocins to Thwart Bacterial Resistance in Gram Negative Bacteria. Front Microbiol 2020; 11:586433. [PMID: 33240239 PMCID: PMC7680869 DOI: 10.3389/fmicb.2020.586433] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 10/16/2020] [Indexed: 12/16/2022] Open
Abstract
An overuse of antibiotics both in human and animal health and as growth promoters in farming practices has increased the prevalence of antibiotic resistance in bacteria. Antibiotic resistant and multi-resistant bacteria are now considered a major and increasing threat by national health agencies, making the need for novel strategies to fight bugs and super bugs a first priority. In particular, Gram-negative bacteria are responsible for a high proportion of nosocomial infections attributable for a large part to Enterobacteriaceae, such as pathogenic Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa. To cope with their highly competitive environments, bacteria have evolved various adaptive strategies, among which the production of narrow spectrum antimicrobial peptides called bacteriocins and specifically microcins in Gram-negative bacteria. They are produced as precursor peptides that further undergo proteolytic cleavage and in many cases more or less complex posttranslational modifications, which contribute to improve their stability and efficiency. Many have a high stability in the gastrointestinal tract where they can target a single pathogen whilst only slightly perturbing the gut microbiota. Several microcins and antibiotics can bind to similar bacterial receptors and use similar pathways to cross the double-membrane of Gram-negative bacteria and reach their intracellular targets, which they also can share. Consequently, bacteria may use common mechanisms of resistance against microcins and antibiotics. This review describes both unmodified and modified microcins [lasso peptides, siderophore peptides, nucleotide peptides, linear azole(in)e-containing peptides], highlighting their potential as weapons to thwart bacterial resistance in Gram-negative pathogens and discusses the possibility of cross-resistance and co-resistance occurrence between antibiotics and microcins in Gram-negative bacteria.
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Affiliation(s)
- Soufiane Telhig
- Institute of Nutrition and Functional Foods, Université Laval, Québec, QC, Canada
- Laboratory Molecules of Communication and Adaptation of Microorganisms, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Laila Ben Said
- Institute of Nutrition and Functional Foods, Université Laval, Québec, QC, Canada
| | - Séverine Zirah
- Laboratory Molecules of Communication and Adaptation of Microorganisms, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
| | - Ismail Fliss
- Institute of Nutrition and Functional Foods, Université Laval, Québec, QC, Canada
| | - Sylvie Rebuffat
- Laboratory Molecules of Communication and Adaptation of Microorganisms, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Paris, France
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El Omari K, Mohamad N, Bountra K, Duman R, Romano M, Schlegel K, Kwong HS, Mykhaylyk V, Olesen C, Moller JV, Bublitz M, Beis K, Wagner A. Experimental phasing with vanadium and application to nucleotide-binding membrane proteins. IUCRJ 2020; 7:1092-1101. [PMID: 33209320 PMCID: PMC7642786 DOI: 10.1107/s2052252520012312] [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: 04/24/2020] [Accepted: 09/07/2020] [Indexed: 06/11/2023]
Abstract
The structure determination of soluble and membrane proteins can be hindered by the crystallographic phase problem, especially in the absence of a suitable homologous structure. Experimental phasing is the method of choice for novel structures; however, it often requires heavy-atom derivatization, which can be difficult and time-consuming. Here, a novel and rapid method to obtain experimental phases for protein structure determination by vanadium phasing is reported. Vanadate is a transition-state mimic of phosphoryl-transfer reactions and it has the advantage of binding specifically to the active site of numerous enzymes catalyzing this reaction. The applicability of vanadium phasing has been validated by determining the structures of three different protein-vanadium complexes, two of which are integral membrane proteins: the rabbit sarcoplasmic reticulum Ca2+-ATPase, the antibacterial peptide ATP-binding cassette transporter McjD from Escherichia coli and the soluble enzyme RNAse A from Bos taurus. Vanadium phasing was successful even at low resolution and despite severe anisotropy in the data. This method is principally applicable to a large number of proteins, representing six of the seven Enzyme Commission classes. It relies exclusively on the specific chemistry of the protein and it does not require any modifications, making it a very powerful addition to the phasing toolkit. In addition to the phasing power of this technique, the protein-vanadium complexes also provide detailed insights into the reaction mechanisms of the studied proteins.
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Affiliation(s)
- Kamel El Omari
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
| | - Nada Mohamad
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Kiran Bountra
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
- Department of Life Sciences, Imperial College, London, United Kingdom
| | - Ramona Duman
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
| | - Maria Romano
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
- Department of Life Sciences, Imperial College, London, United Kingdom
- Institute of Biostructures and Bioimaging, National Research Council (IBB–CNR), Via Mezzocannone 16, 80134 Napoli, Italy
| | - Katja Schlegel
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Hok-Sau Kwong
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
- Department of Life Sciences, Imperial College, London, United Kingdom
| | - Vitaliy Mykhaylyk
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
| | - Claus Olesen
- Department of Biomedicine, Aarhus University, Ole Worms Allé 8, DK-8000 Aarhus, Denmark
| | - Jesper Vuust Moller
- Department of Biomedicine, Aarhus University, Ole Worms Allé 8, DK-8000 Aarhus, Denmark
| | - Maike Bublitz
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Konstantinos Beis
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
- Department of Life Sciences, Imperial College, London, United Kingdom
| | - Armin Wagner
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
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Smits SHJ, Schmitt L, Beis K. Self-immunity to antibacterial peptides by ABC transporters. FEBS Lett 2020; 594:3920-3942. [PMID: 33040342 DOI: 10.1002/1873-3468.13953] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/22/2020] [Accepted: 10/05/2020] [Indexed: 01/17/2023]
Abstract
Bacteria produce under certain stress conditions bacteriocins and microcins that display antibacterial activity against closely related species for survival. Bacteriocins and microcins exert their antibacterial activity by either disrupting the membrane or inhibiting essential intracellular processes of the bacterial target. To this end, they can lyse bacterial membranes and cause subsequent loss of their integrity or nutrients, or hijack membrane receptors for internalisation. Both bacteriocins and microcins are ribosomally synthesised and several are posttranslationally modified, whereas others are not. Such peptides are also toxic to the producer bacteria, which utilise immunity proteins or/and dedicated ATP-binding cassette (ABC) transporters to achieve self-immunity and peptide export. In this review, we discuss the structure and mechanism of self-protection that is conferred by these ABC transporters.
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Affiliation(s)
- Sander H J Smits
- Institute of Biochemistry, Heinrich-Heine-University, Duesseldorf, Germany.,Center for Structural Studies, Heinrich-Heine-University, Duesseldorf, Germany
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich-Heine-University, Duesseldorf, Germany
| | - Konstantinos Beis
- Department of Life Sciences, Imperial College London, UK.,Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, UK
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Cheng C, Hua ZC. Lasso Peptides: Heterologous Production and Potential Medical Application. Front Bioeng Biotechnol 2020; 8:571165. [PMID: 33117783 PMCID: PMC7549694 DOI: 10.3389/fbioe.2020.571165] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 09/04/2020] [Indexed: 12/15/2022] Open
Abstract
Lasso peptides are natural products found in bacteria. They belong to a specific family of ribosomally-synthesized and posttranslationally-modified peptides with an unusual lasso structure. Lasso peptides possess remarkable thermal and proteolytic stability and various biological activities, such as antimicrobial activity, enzyme inhibition, receptor blocking, anticancer properties and HIV antagonism. They have promising potential therapeutic effects on gastrointestinal diseases, tuberculosis, Alzheimer’s disease, cardiovascular disease, fungal infections and cancer. Lasso peptides with high stability have been shown to be good carriers for other bioactive peptides. These make them attractive candidates for pharmaceutical research. This review aimed to describe the strategies used for the heterologous production of lasso peptides. Also, it indicated their therapeutical potential and their capacity to use as an efficient scaffold for epitope grafting.
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Affiliation(s)
- Cheng Cheng
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Zi-Chun Hua
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China.,School of Biopharmacy, China Pharmaceutical University, Nanjing, China.,Changzhou High-Tech Research Institute of Nanjing University, Changzhou, China.,Jiangsu Target Pharma Laboratories Inc., Changzhou, China
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Sabino YNV, de Araújo KC, de Assis FGDV, Moreira SM, Lopes TDS, Mendes TADO, Huws SA, Mantovani HC. In silico Screening Unveil the Great Potential of Ruminal Bacteria Synthesizing Lasso Peptides. Front Microbiol 2020; 11:576738. [PMID: 33072042 PMCID: PMC7533575 DOI: 10.3389/fmicb.2020.576738] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 08/17/2020] [Indexed: 12/20/2022] Open
Abstract
Studies of rumen microbial ecology suggest that the capacity to produce antimicrobial peptides could be a useful trait in species competing for ecological niches in the ruminal ecosystem. However, little is known about the synthesis of lasso peptides by ruminal microorganisms. Here we analyzed the distribution and diversity of lasso peptide gene clusters in 425 bacterial genomes from the rumen ecosystem. Genome mining was performed using antiSMASH 5, BAGEL4, and a database of well-known precursor sequences. The genomic context of the biosynthetic clusters was investigated to identify putative lasA genes and protein sequences from enzymes of the biosynthetic machinery were evaluated to identify conserved motifs. Metatranscriptome analysis evaluated the expression of the biosynthetic genes in the rumen microbiome. Several incomplete (n = 23) and complete (n = 11) putative lasso peptide clusters were detected in the genomes of ruminal bacteria. The complete gene clusters were exclusively found within the phylum Firmicutes, mainly (48%) in strains of the genus Butyrivibrio. The analysis of the genetic organization of complete putative lasso peptide clusters revealed the presence of co-occurring genes, including kinases (85%), transcriptional regulators (49%), and glycosyltransferases (36%). Moreover, a conserved pattern of cluster organization was detected between strains of the same genus/species. The maturation enzymes LasB, LasC, and LasD showed regions highly conserved, including the presence of a transglutaminase core in LasB, an asparagine synthetase domain in LasC, and an ABC-type transporter system in LasD. Phylogenetic trees of the essential biosynthetic proteins revealed that sequences split into monophyletic groups according to their shared single common ancestor. Metatranscriptome analyses indicated the expression of the lasso peptides biosynthetic genes within the active rumen microbiota. Overall, our in silico screening allowed the discovery of novel biosynthetic gene clusters in the genomes of ruminal bacteria and revealed several strains with the genetic potential to synthesize lasso peptides, suggesting that the ruminal microbiota represents a potential source of these promising peptides.
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Affiliation(s)
| | | | | | | | | | | | - Sharon Ann Huws
- Institute for Global Food Security, School of Biological Sciences, Medical Biology Centre, Queen's University Belfast, Belfast, United Kingdom
| | - Hilário C Mantovani
- Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Brazil
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Ladjouzi R, Lucau-Danila A, Benachour A, Drider D. A Leaderless Two-Peptide Bacteriocin, Enterocin DD14, Is Involved in Its Own Self-Immunity: Evidence and Insights. Front Bioeng Biotechnol 2020; 8:644. [PMID: 32671042 PMCID: PMC7332713 DOI: 10.3389/fbioe.2020.00644] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 05/26/2020] [Indexed: 12/28/2022] Open
Abstract
Enterocin DD14 (EntDD14) is a two-peptide leaderless bacteriocin produced by Enterococcus faecalis 14, a strain previously isolated from meconium. EntDD14 has a strong antibacterial activity against Gram-positive bacteria. Leaderless bacteriocins, unlike bacteriocins with leader peptides, are immediately active after their translation, and a producing strain has then to develop specific mechanisms to protect both intra and extracellular compartments. The in silico analysis of Ent. faecalis 14 genome allowed to locate downstream of structural ddAB genes, 8 other adjacent genes, designed ddCDEFGHIJ, which collectively may form three operons. To gain insights on immunity mechanisms of Ent. faecalis 14, mutant strains knocked out in ddAB genes encoding bacteriocin precursor peptides (Δbac) and/or ABC transporter (ΔddI) of EntDD14 were constructed and characterized. Importantly, Δbac mutant strains, from which structural ddAB genes were deleted, resulted unable to produce EntDD14 and sensitive to exogenous EntDD14 showing their involvement in the Ent. faecalis 14 immunity system. Moreover, the sensitivity of Δbac mutants appeared not to be associated with the down-regulation of ddCDEFGHIJ gene expression since they were similarly expressed in both Δbac and wild-type strains during the log phase while they were found significantly down-regulated in the Δbac mutant strain after 24 h of growth. Data gathered from this study suggest also the implication of the ABC transporter (ddHIJ) in the active export of EntDD14 but ruled-out its involvement in the primary self-immunity system. Interestingly, non-bacteriocin producing Ent. faecalis JH2-2 cells transformed with ddAB, or ddAB plus genes encoding the ABC transporter (ddAB-HIJ) did not produce EntDD14 and remained sensitive to its action. Of note, trans-complementation of the Δbac mutant strain with these constructions allowed to recover the WT phenotype. To the best of our knowledge, this is the first study delineating the role of the intracellular two-peptide leaderless bacteriocins in their self-immunity.
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Affiliation(s)
- Rabia Ladjouzi
- UMR Transfrontalière BioEcoAgro N° 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, YNCREA, Univ. Artois, Univ. Littoral Côte d'Opale, ICV - Institut Charles Viollette, Lille, France
| | - Anca Lucau-Danila
- UMR Transfrontalière BioEcoAgro N° 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, YNCREA, Univ. Artois, Univ. Littoral Côte d'Opale, ICV - Institut Charles Viollette, Lille, France
| | | | - Djamel Drider
- UMR Transfrontalière BioEcoAgro N° 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, YNCREA, Univ. Artois, Univ. Littoral Côte d'Opale, ICV - Institut Charles Viollette, Lille, France
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40
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Kapsalis C, Ma Y, Bode BE, Pliotas C. In-Lipid Structure of Pressure-Sensitive Domains Hints Mechanosensitive Channel Functional Diversity. Biophys J 2020; 119:448-459. [PMID: 32621864 PMCID: PMC7376121 DOI: 10.1016/j.bpj.2020.06.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 06/03/2020] [Accepted: 06/10/2020] [Indexed: 11/30/2022] Open
Abstract
The mechanosensitive channel of large conductance (MscL) from Mycobacterium tuberculosis has been used as a structural model for rationalizing functional observations in multiple MscL orthologs. Although these orthologs adopt similar structural architectures, they reportedly present significant functional differences. Subtle structural discrepancies on mechanosensitive channel nanopockets are known to affect mechanical gating and may be linked to large variability in tension sensitivity among these membrane channels. Here, we modify the nanopocket regions of MscL from Escherichia coli and M. tuberculosis and employ PELDOR/DEER distance and 3pESEEM deuterium accessibility measurements to interrogate channel structure within lipids, in which both channels adopt a closed conformation. Significant in-lipid structural differences between the two constructs suggest a more compact E. coli MscL at the membrane inner-leaflet, as a consequence of a rotated TM2 helix. Observed differences within lipids could explain E. coli MscL’s higher tension sensitivity and should be taken into account in extrapolated models used for MscL gating rationalization.
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Affiliation(s)
- Charalampos Kapsalis
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, United Kingdom
| | - Yue Ma
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom; School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Bela E Bode
- Biomedical Sciences Research Complex, School of Chemistry, University of St Andrews, St Andrews, United Kingdom.
| | - Christos Pliotas
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, United Kingdom; Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom; School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom.
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Ben Said L, Emond-Rheault JG, Soltani S, Telhig S, Zirah S, Rebuffat S, Diarra MS, Goodridge L, Levesque RC, Fliss I. Phenomic and genomic approaches to studying the inhibition of multiresistant Salmonella enterica by microcin J25. Environ Microbiol 2020; 22:2907-2920. [PMID: 32363677 DOI: 10.1111/1462-2920.15045] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 04/15/2020] [Accepted: 04/25/2020] [Indexed: 12/22/2022]
Abstract
In livestock production, antibiotics are used to promote animal growth, control infections and thereby increase profitability. This practice has led to the emergence of multiresistant bacteria such as Salmonella, of which some serovars are disseminated in the environment. The objective of this study is to evaluate microcin J25 as an inhibitor of Salmonella enterica serovars of various origins including human, livestock and food. Among the 116 isolates tested, 37 (31.8%) were found resistant to at least one antibiotic, and 28 were multiresistant with 19 expressing the penta-resistant phenotype ACSSuT. Microcin J25 inhibited all isolates, with minimal inhibitory concentration values ranging from 0.06 μg/ml (28.4 nM) to 400 μg/ml (189 μM). Interestingly, no cross-resistance was found between microcin J25 and antibiotics. Multiple sequence alignments of genes encoding for the different proteins involved in the recognition and transport of microcin J25 showed that only ferric-hydroxamate uptake is an essential determinant for susceptibility of S. enterica to microcin J25. Examination of Salmonella strains exposed to microcin J25 by transmission electronic microscopy showed for the first-time involvement of a pore formation mechanism. Microcin J25 was a strong inhibitor of several multiresistant isolates of Salmonella and may have a great potential as an alternative to antibiotics.
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Affiliation(s)
- Laila Ben Said
- Institute of Nutrition and Functional Foods, Université Laval, Québec, Quebec, G1V 0A6, Canada
| | | | - Samira Soltani
- Institute of Nutrition and Functional Foods, Université Laval, Québec, Quebec, G1V 0A6, Canada
| | - Sofiane Telhig
- Institute of Nutrition and Functional Foods, Université Laval, Québec, Quebec, G1V 0A6, Canada.,Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, Laboratory of Communication Molecules and Adaptation of Micro-organisms, UMR 7245 CNRS-MNHN, Paris, CP 54, 57 rue Cuvier 75005, France
| | - Séverine Zirah
- Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, Laboratory of Communication Molecules and Adaptation of Micro-organisms, UMR 7245 CNRS-MNHN, Paris, CP 54, 57 rue Cuvier 75005, France
| | - Sylvie Rebuffat
- Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, Laboratory of Communication Molecules and Adaptation of Micro-organisms, UMR 7245 CNRS-MNHN, Paris, CP 54, 57 rue Cuvier 75005, France
| | - Moussa Sory Diarra
- Guelph Research and Development Center, Agriculture and Agri-Food Canada, 93 Stone Road West, Guelph, Ontario, N1G 5C9, Canada
| | - Lawrence Goodridge
- Department of Food Science and Agriculture, McGill University, Ste Anne de Bellevue, Québec, Quebec, H9X3V9, Canada
| | - Roger C Levesque
- Institute of Integrative Biology and Systems, Université Laval, QC, Québec, G1V 0A6, Canada
| | - Ismail Fliss
- Institute of Nutrition and Functional Foods, Université Laval, Québec, Quebec, G1V 0A6, Canada
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Szöllősi D, Chiba P, Szakacs G, Stockner T. Conversion of chemical to mechanical energy by the nucleotide binding domains of ABCB1. Sci Rep 2020; 10:2589. [PMID: 32054924 PMCID: PMC7018802 DOI: 10.1038/s41598-020-59403-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 01/27/2020] [Indexed: 01/13/2023] Open
Abstract
P-glycoprotein (ABCB1) is an important component of barrier tissues that extrudes a wide range of chemically unrelated compounds. ABCB1 consists of two transmembrane domains forming the substrate binding and translocation domain, and of two cytoplasmic nucleotide binding domains (NBDs) that provide the energy by binding and hydrolyzing ATP. We analyzed the mechanistic and energetic properties of the NBD dimer via molecular dynamics simulations. We find that MgATP stabilizes the NBD dimer through strong attractive forces by serving as an interaction hub. The irreversible ATP hydrolysis step converts the chemical energy stored in the phosphate bonds of ATP into potential energy. Following ATP hydrolysis, interactions between the NBDs and the ATP hydrolysis products MgADP + Pi remain strong, mainly because Mg2+ forms stabilizing interactions with ADP and Pi. Despite these stabilizing interactions MgADP + Pi are unable to hold the dimer together, which becomes separated by avid interactions of MgADP + Pi with water. ATP binding to the open NBDs and ATP hydrolysis in the closed NBD dimer represent two steps of energy input, each leading to the formation of a high energy state. Relaxation from these high energy states occurs through conformational changes that push ABCB1 through the transport cycle.
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Affiliation(s)
- Dániel Szöllősi
- Medical University of Vienna, Center for Physiology and Pharmacology, Institute of Pharmacology, Waehringerstr. 13A, 1090, Vienna, Austria
| | - Peter Chiba
- Medical University of Vienna, Institute of Medical Chemistry, Center for Pathobiochemistry and Genetics, Waehringerstr. 10, 1090, Vienna, Austria
| | - Gergely Szakacs
- Medical University of Vienna, Institute of Cancer Research, Borschkegasse 8A, 1090, Vienna, Austria
| | - Thomas Stockner
- Medical University of Vienna, Center for Physiology and Pharmacology, Institute of Pharmacology, Waehringerstr. 13A, 1090, Vienna, Austria.
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Li Y, Rebuffat S. The manifold roles of microbial ribosomal peptide-based natural products in physiology and ecology. J Biol Chem 2020; 295:34-54. [PMID: 31784450 PMCID: PMC6952617 DOI: 10.1074/jbc.rev119.006545] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The ribosomally synthesized and posttranslationally modified peptides (RiPPs), also called ribosomal peptide natural products (RPNPs), form a growing superfamily of natural products that are produced by many different organisms and particularly by bacteria. They are derived from precursor polypeptides whose modification by various dedicated enzymes helps to establish a vast array of chemical motifs. RiPPs have attracted much interest as a source of potential therapeutic agents, and in particular as alternatives to conventional antibiotics to address the bacterial resistance crisis. However, their ecological roles in nature are poorly understood and explored. The present review describes major RiPP actors in competition within microbial communities, the main ecological and physiological functions currently evidenced for RiPPs, and the microbial ecosystems that are the sites for these functions. We envision that the study of RiPPs may lead to discoveries of new biological functions and highlight that a better knowledge of how bacterial RiPPs mediate inter-/intraspecies and interkingdom interactions will hold promise for devising alternative strategies in antibiotic development.
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Affiliation(s)
- Yanyan Li
- Laboratory Molecules of Communication and Adaptation of Microorganisms (MCAM, UMR 7245 CNRS-MNHN), National Museum of Natural History (MNHN), CNRS, CP 54, 57 rue Cuvier 75005, Paris, France.
| | - Sylvie Rebuffat
- Laboratory Molecules of Communication and Adaptation of Microorganisms (MCAM, UMR 7245 CNRS-MNHN), National Museum of Natural History (MNHN), CNRS, CP 54, 57 rue Cuvier 75005, Paris, France.
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Beis K, Rebuffat S. Multifaceted ABC transporters associated to microcin and bacteriocin export. Res Microbiol 2019; 170:399-406. [DOI: 10.1016/j.resmic.2019.07.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 07/12/2019] [Accepted: 07/17/2019] [Indexed: 12/30/2022]
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Allosteric activation of an ion channel triggered by modification of mechanosensitive nano-pockets. Nat Commun 2019; 10:4619. [PMID: 31601809 PMCID: PMC6787021 DOI: 10.1038/s41467-019-12591-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 09/17/2019] [Indexed: 11/08/2022] Open
Abstract
Lipid availability within transmembrane nano-pockets of ion channels is linked with mechanosensation. However, the effect of hindering lipid-chain penetration into nano-pockets on channel structure has not been demonstrated. Here we identify nano-pockets on the large conductance mechanosensitive channel MscL, the high-pressure threshold channel. We restrict lipid-chain access to the nano-pockets by mutagenesis and sulfhydryl modification, and monitor channel conformation by PELDOR/DEER spectroscopy. For a single site located at the entrance of the nano-pockets and distal to the channel pore we generate an allosteric response in the absence of tension. Single-channel recordings reveal a significant decrease in the pressure activation threshold of the modified channel and a sub-conducting state in the absence of applied tension. Threshold is restored to wild-type levels upon reduction of the sulfhydryl modification. The modification associated with the conformational change restricts lipid access to the nano-pocket, interrupting the contact between the membrane and the channel that mediates mechanosensitivity.
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46
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Srikant S, Gaudet R. Mechanics and pharmacology of substrate selection and transport by eukaryotic ABC exporters. Nat Struct Mol Biol 2019; 26:792-801. [PMID: 31451804 DOI: 10.1038/s41594-019-0280-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 07/17/2019] [Indexed: 01/27/2023]
Abstract
Much structural information has been amassed on ATP-binding cassette (ABC) transporters, including hundreds of structures of isolated domains and an increasing array of full-length transporters. The structures capture different steps in the transport cycle and have aided in the design and interpretation of computational simulations and biophysics experiments. These data provide a maturing, although still incomplete, elucidation of the protein dynamics and mechanisms of substrate selection and transit through the transporters. We present an updated view of the classical alternating-access mechanism as it applies to eukaryotic ABC transporters, focusing on type I exporters. Our model helps frame the progress in, and remaining questions about, transporter energetics, how substrates are selected and how ATP is consumed to perform work at the molecular scale. Many human ABC transporters are associated with disease; we highlight progress in understanding their pharmacology through the lens of structural biology and describe how this knowledge suggests approaches to pharmacologically targeting these transporters.
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Affiliation(s)
- Sriram Srikant
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Rachelle Gaudet
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.
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Abstract
Infections arising from multidrug-resistant pathogenic bacteria are spreading rapidly throughout the world and threaten to become untreatable. The origins of resistance are numerous and complex, but one underlying factor is the capacity of bacteria to rapidly export drugs through the intrinsic activity of efflux pumps. In this Review, we describe recent advances that have increased our understanding of the structures and molecular mechanisms of multidrug efflux pumps in bacteria. Clinical and laboratory data indicate that efflux pumps function not only in the drug extrusion process but also in virulence and the adaptive responses that contribute to antimicrobial resistance during infection. The emerging picture of the structure, function and regulation of efflux pumps suggests opportunities for countering their activities.
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48
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Cameron A, Zaheer R, Adator EH, Barbieri R, Reuter T, McAllister TA. Bacteriocin Occurrence and Activity in Escherichia coli Isolated from Bovines and Wastewater. Toxins (Basel) 2019; 11:toxins11080475. [PMID: 31443193 PMCID: PMC6723558 DOI: 10.3390/toxins11080475] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 08/07/2019] [Accepted: 08/12/2019] [Indexed: 02/07/2023] Open
Abstract
The increasing prevalence of antimicrobial resistant (AMR) E. coli and related Enterobacteriaceae is a serious problem necessitating new mitigation strategies and antimicrobial agents. Bacteriocins, functionally diverse toxins produced by most microbes, have long been studied for their antimicrobial potential. Bacteriocins have once again received attention for their role as probiotic traits that could mitigate pathogen burden and AMR bacteria in livestock. Here, bacteriocins were identified by activity screening and whole-genome sequencing of bacteriocin-producers capable of inhibiting bovine and wastewater E. coli isolates enriched for resistance to cephalosporins. Producers were tested for activity against shiga toxin-producing E. coli (STEC), AMR E. coli, and related enteric pathogens. Multiple bacteriocins were found in 14 out of 90 E. coli isolates tested. Based on alignment within BACTIBASE, colicins M, B, R, Ia, Ib, S4, E1, E2, and microcins V, J25, and H47, encoded by identical, variant, or truncated genes were identified. Although some bacteriocin-producers exhibited activity against AMR and STEC E. coli in agar-based assays, most did not. Despite this idiosyncrasy, liquid co-cultures of all bacteriocinogenic isolates with luciferase-expressing generic (K12) or STEC E. coli (EDL933) resulted in inhibited growth or reduced viability. These abundant toxins may have real potential as next-generation control strategies in livestock production systems but separating the bacteriocin from its immunity gene may be necessary for such a strategy to be effective.
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Affiliation(s)
- Andrew Cameron
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Rahat Zaheer
- Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada
| | - Emelia H Adator
- Department of Food Science and Human Nutritional Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Ruth Barbieri
- Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada
| | - Tim Reuter
- Alberta Agriculture and Forestry, Lethbridge, AB T1J 4V6, Canada
| | - Tim A McAllister
- Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada.
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Severi E, Thomas GH. Antibiotic export: transporters involved in the final step of natural product production. Microbiology (Reading) 2019; 165:805-818. [DOI: 10.1099/mic.0.000794] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Emmanuele Severi
- Department of Biology, University of York, Wentworth Way, York, UK
| | - Gavin H. Thomas
- Department of Biology, University of York, Wentworth Way, York, UK
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50
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Michou M, Kapsalis C, Pliotas C, Skretas G. Optimization of Recombinant Membrane Protein Production in the Engineered Escherichia coli Strains SuptoxD and SuptoxR. ACS Synth Biol 2019; 8:1631-1641. [PMID: 31243979 DOI: 10.1021/acssynbio.9b00120] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Membrane proteins (MPs) execute a wide variety of critical biological functions in all living organisms and constitute approximately half of current targets for drug discovery. As in the case of soluble proteins, the bacterium Escherichia coli has served as a very popular overexpression host for biochemical/structural studies of membrane proteins as well. Bacterial recombinant membrane protein production, however, is typically hampered by poor cellular accumulation and severe toxicity for the host, which leads to low levels of final biomass and minute volumetric yields. In previous work, we generated the engineered E. coli strains SuptoxD and SuptoxR, which upon coexpression of the effector genes djlA or rraA, respectively, can suppress the cytotoxicity caused by MP overexpression and produce enhanced MP yields. Here, we systematically looked for gene overexpression and culturing conditions that maximize the accumulation of membrane-integrated and well-folded recombinant MPs in these strains. We have found that, under optimal conditions, SuptoxD and SuptoxR achieve greatly enhanced recombinant production for a variety of MP, irrespective of their archaeal, eubacterial, or eukaryotic origin. Furthermore, we demonstrate that the use of these engineered strains enables the production of well-folded recombinant MPs of high quality and at high yields, which are suitable for functional and structural studies. We anticipate that SuptoxD and SuptoxR will become broadly utilized expression hosts for recombinant MP production in bacteria.
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Affiliation(s)
- Myrsini Michou
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens 11635, Greece
- Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Larisa 41500, Greece
| | - Charalampos Kapsalis
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY169ST, United Kingdom
| | - Christos Pliotas
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY169ST, United Kingdom
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Georgios Skretas
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens 11635, Greece
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