1
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Zhang T, Lyu J, Yang B, Yun SD, Scott E, Zhao M, Laganowsky A. Native mass spectrometry and structural studies reveal modulation of MsbA-nucleotide interactions by lipids. Nat Commun 2024; 15:5946. [PMID: 39009687 PMCID: PMC11251056 DOI: 10.1038/s41467-024-50350-9] [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: 09/08/2023] [Accepted: 07/07/2024] [Indexed: 07/17/2024] Open
Abstract
The ATP-binding cassette (ABC) transporter, MsbA, plays a pivotal role in lipopolysaccharide (LPS) biogenesis by facilitating the transport of the LPS precursor lipooligosaccharide (LOS) from the cytoplasmic to the periplasmic leaflet of the inner membrane. Despite multiple studies shedding light on MsbA, the role of lipids in modulating MsbA-nucleotide interactions remains poorly understood. Here we use native mass spectrometry (MS) to investigate and resolve nucleotide and lipid binding to MsbA, demonstrating that the transporter has a higher affinity for adenosine 5'-diphosphate (ADP). Moreover, native MS shows the LPS-precursor 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo)2-lipid A (KDL) can tune the selectivity of MsbA for adenosine 5'-triphosphate (ATP) over ADP. Guided by these studies, four open, inward-facing structures of MsbA are determined that vary in their openness. We also report a 2.7 Å-resolution structure of MsbA in an open, outward-facing conformation that is not only bound to KDL at the exterior site, but with the nucleotide binding domains (NBDs) adopting a distinct nucleotide-free structure. The results obtained from this study offer valuable insight and snapshots of MsbA during the transport cycle.
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Affiliation(s)
- Tianqi Zhang
- Department of Chemistry, Texas A&M University, College Station, TX, USA
| | - Jixing Lyu
- Department of Chemistry, Texas A&M University, College Station, TX, USA
| | - Bowei Yang
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Sangho D Yun
- Department of Chemistry, Texas A&M University, College Station, TX, USA
| | - Elena Scott
- Department of Chemistry, Texas A&M University, College Station, TX, USA
| | - Minglei Zhao
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, TX, USA.
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2
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Nasrollahian S, Graham JP, Halaji M. A review of the mechanisms that confer antibiotic resistance in pathotypes of E. coli. Front Cell Infect Microbiol 2024; 14:1387497. [PMID: 38638826 PMCID: PMC11024256 DOI: 10.3389/fcimb.2024.1387497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 03/15/2024] [Indexed: 04/20/2024] Open
Abstract
The dissemination of antibiotic resistance in Escherichia coli poses a significant threat to public health worldwide. This review provides a comprehensive update on the diverse mechanisms employed by E. coli in developing resistance to antibiotics. We primarily focus on pathotypes of E. coli (e.g., uropathogenic E. coli) and investigate the genetic determinants and molecular pathways that confer resistance, shedding light on both well-characterized and recently discovered mechanisms. The most prevalent mechanism continues to be the acquisition of resistance genes through horizontal gene transfer, facilitated by mobile genetic elements such as plasmids and transposons. We discuss the role of extended-spectrum β-lactamases (ESBLs) and carbapenemases in conferring resistance to β-lactam antibiotics, which remain vital in clinical practice. The review covers the key resistant mechanisms, including: 1) Efflux pumps and porin mutations that mediate resistance to a broad spectrum of antibiotics, including fluoroquinolones and aminoglycosides; 2) adaptive strategies employed by E. coli, including biofilm formation, persister cell formation, and the activation of stress response systems, to withstand antibiotic pressure; and 3) the role of regulatory systems in coordinating resistance mechanisms, providing insights into potential targets for therapeutic interventions. Understanding the intricate network of antibiotic resistance mechanisms in E. coli is crucial for the development of effective strategies to combat this growing public health crisis. By clarifying these mechanisms, we aim to pave the way for the design of innovative therapeutic approaches and the implementation of prudent antibiotic stewardship practices to preserve the efficacy of current antibiotics and ensure a sustainable future for healthcare.
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Affiliation(s)
- Sina Nasrollahian
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Jay P. Graham
- Environmental Health Sciences Division, School of Public Health, University of California, Berkeley, CA, United States
| | - Mehrdad Halaji
- Infectious Diseases and Tropical Medicine Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
- Department of Medical Microbiology and Biotechnology, School of Medicine, Babol University of Medical Sciences, Babol, Iran
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3
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Lyu J, Zhang T, Marty MT, Clemmer D, Russell DH, Laganowsky A. Double and triple thermodynamic mutant cycles reveal the basis for specific MsbA-lipid interactions. eLife 2024; 12:RP91094. [PMID: 38252560 PMCID: PMC10945598 DOI: 10.7554/elife.91094] [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] [Indexed: 01/24/2024] Open
Abstract
Structural and functional studies of the ATP-binding cassette transporter MsbA have revealed two distinct lipopolysaccharide (LPS) binding sites: one located in the central cavity and the other at a membrane-facing, exterior site. Although these binding sites are known to be important for MsbA function, the thermodynamic basis for these specific MsbA-LPS interactions is not well understood. Here, we use native mass spectrometry to determine the thermodynamics of MsbA interacting with the LPS-precursor 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo)2-lipid A (KDL). The binding of KDL is solely driven by entropy, despite the transporter adopting an inward-facing conformation or trapped in an outward-facing conformation with adenosine 5'-diphosphate and vanadate. An extension of the mutant cycle approach is employed to probe basic residues that interact with KDL. We find the molecular recognition of KDL is driven by a positive coupling entropy (as large as -100 kJ/mol at 298 K) that outweighs unfavorable coupling enthalpy. These findings indicate that alterations in solvent reorganization and conformational entropy can contribute significantly to the free energy of protein-lipid association. The results presented herein showcase the advantage of native MS to obtain thermodynamic insight into protein-lipid interactions that would otherwise be intractable using traditional approaches, and this enabling technology will be instrumental in the life sciences and drug discovery.
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Affiliation(s)
- Jixing Lyu
- Department of Chemistry, Texas A&M UniversityCollege StationUnited States
| | - Tianqi Zhang
- Department of Chemistry, Texas A&M UniversityCollege StationUnited States
| | - Michael T Marty
- Department of Chemistry and Biochemistry and Bio5 Institute, The University of ArizonaTucsonUnited States
| | - David Clemmer
- Department of Chemistry, Indiana UniversityBloomingtonUnited States
| | - David H Russell
- Department of Chemistry, Texas A&M UniversityCollege StationUnited States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M UniversityCollege StationUnited States
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4
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Novischi SYP, Karoly-Lakatos A, Chok K, Bonifer C, Becker-Baldus J, Glaubitz C. Probing the allosteric NBD-TMD crosstalk in the ABC transporter MsbA by solid-state NMR. Commun Biol 2024; 7:43. [PMID: 38182790 PMCID: PMC10770068 DOI: 10.1038/s42003-023-05617-0] [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: 06/11/2023] [Accepted: 11/21/2023] [Indexed: 01/07/2024] Open
Abstract
The ABC transporter MsbA plays a critical role in Gram-negative bacteria in the regulation of the outer membrane by translocating core-LPS across the inner membrane. Additionally, a broad substrate specificity for lipophilic drugs has been shown. The allosteric interplay between substrate binding in the transmembrane domains and ATP binding and turnover in the nucleotide-binding domains must be mediated via the NBD/TMD interface. Previous studies suggested the involvement of two intracellular loops called coupling helix 1 and 2 (CH1, CH2). Here, we demonstrate by solid-state NMR spectroscopy that substantial chemical shift changes within both CH1 and CH2 occur upon substrate binding, in the ATP hydrolysis transition state, and upon inhibitor binding. CH2 is domain-swapped within the MsbA structure, and it is noteworthy that substrate binding induces a larger response in CH2 compared to CH1. Our data demonstrate that CH1 and CH2 undergo structural changes as part of the TMD-NBD cross-talk.
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Affiliation(s)
- S Y Phoebe Novischi
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max von Laue Str. 9, 60438, Frankfurt, Germany
| | - Andrea Karoly-Lakatos
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max von Laue Str. 9, 60438, Frankfurt, Germany
| | - Kerby Chok
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max von Laue Str. 9, 60438, Frankfurt, Germany
| | - Christian Bonifer
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max von Laue Str. 9, 60438, Frankfurt, Germany
| | - Johanna Becker-Baldus
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max von Laue Str. 9, 60438, Frankfurt, Germany
| | - Clemens Glaubitz
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max von Laue Str. 9, 60438, Frankfurt, Germany.
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5
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Qian L, Mohanty P, Jayaraman A, Mittal J, Zhu X. Specific residues and conformational plasticity define the substrate specificity of short-chain dehydrogenases/reductases. J Biol Chem 2024; 300:105596. [PMID: 38145745 PMCID: PMC10827548 DOI: 10.1016/j.jbc.2023.105596] [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: 11/08/2023] [Revised: 12/13/2023] [Accepted: 12/18/2023] [Indexed: 12/27/2023] Open
Abstract
Short-chain dehydrogenases/reductases (SDRs) are one of the most prevalent enzyme families distributed among the sequenced microorganisms. Despite the presence of a conserved catalytic tetrad and high structural similarity, these enzymes exhibit different substrate specificities. The insufficient knowledge regarding the amino acids underlying substrate specificity hinders the understanding of the SDRs' roles in diverse and significant biological processes. Here, we performed bioinformatic analysis, molecular modeling, and mutagenesis studies to identify the key residues that regulate the substrate specificities of two homologous microbial SDRs (i.e., DesE and KduD). Further, we investigated the impact of altering the physicochemical properties of these amino acids on enzyme activity. Interestingly, molecular dynamics simulations also suggest a critical role of enzyme conformational flexibility in substrate recognition and catalysis. Overall, our findings improve the understanding of microbial SDR substrate specificity and shed light on future rational design of more efficient and effective biocatalysts.
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Affiliation(s)
- Liangyu Qian
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, USA
| | - Priyesh Mohanty
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, USA
| | - Arul Jayaraman
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, USA; Department of Biomedical Engineering, Texas A&M University, College Station, USA
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, USA; Department of Chemistry, Texas A&M University, College Station, USA; Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, USA
| | - Xuejun Zhu
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, USA; Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, USA.
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6
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Di Cesare M, Kaplan E, Rendon J, Gerbaud G, Valimehr S, Gobet A, Ngo TAT, Chaptal V, Falson P, Martinho M, Dorlet P, Hanssen E, Jault JM, Orelle C. The transport activity of the multidrug ABC transporter BmrA does not require a wide separation of the nucleotide-binding domains. J Biol Chem 2024; 300:105546. [PMID: 38072053 PMCID: PMC10821409 DOI: 10.1016/j.jbc.2023.105546] [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: 07/07/2023] [Revised: 11/13/2023] [Accepted: 11/30/2023] [Indexed: 01/13/2024] Open
Abstract
ATP-binding cassette (ABC) transporters are ubiquitous membrane proteins responsible for the translocation of a wide diversity of substrates across biological membranes. Some of them confer multidrug or antimicrobial resistance to cancer cells and pathogenic microorganisms, respectively. Despite a wealth of structural data gained in the last two decades, the molecular mechanism of these multidrug efflux pumps remains elusive, including the extent of separation between the two nucleotide-binding domains (NBDs) during the transport cycle. Based on recent outward-facing structures of BmrA, a homodimeric multidrug ABC transporter from Bacillus subtilis, we introduced a cysteine mutation near the C-terminal end of the NBDs to analyze the impact of disulfide-bond formation on BmrA function. Interestingly, the presence of the disulfide bond between the NBDs did not prevent the ATPase, nor did it affect the transport of Hoechst 33342 and doxorubicin. Yet, the 7-amino-actinomycin D was less efficiently transported, suggesting that a further opening of the transporter might improve its ability to translocate this larger compound. We solved by cryo-EM the apo structures of the cross-linked mutant and the WT protein. Both structures are highly similar, showing an intermediate opening between their NBDs while their C-terminal extremities remain in close proximity. Distance measurements obtained by electron paramagnetic resonance spectroscopy support the intermediate opening found in these 3D structures. Overall, our data suggest that the NBDs of BmrA function with a tweezers-like mechanism distinct from the related lipid A exporter MsbA.
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Affiliation(s)
- Margot Di Cesare
- Bacterial Nucleotide-Binding Proteins Team, Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Elise Kaplan
- Bacterial Nucleotide-Binding Proteins Team, Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Julia Rendon
- CNRS, Aix-Marseille Université, BIP, IMM, Marseille, France
| | | | - Sepideh Valimehr
- Ian Holmes Imaging Center and Department of Biochemistry and Pharmacology and ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Bio21 Institute, University of Melbourne, Parkville, VIC, Australia
| | - Alexia Gobet
- Drug Resistance and Membrane Proteins Team, Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Thu-Anh Thi Ngo
- Bacterial Nucleotide-Binding Proteins Team, Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Vincent Chaptal
- Drug Resistance and Membrane Proteins Team, Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | - Pierre Falson
- Drug Resistance and Membrane Proteins Team, Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France
| | | | - Pierre Dorlet
- CNRS, Aix-Marseille Université, BIP, IMM, Marseille, France
| | - Eric Hanssen
- Ian Holmes Imaging Center and Department of Biochemistry and Pharmacology and ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Bio21 Institute, University of Melbourne, Parkville, VIC, Australia
| | - Jean-Michel Jault
- Bacterial Nucleotide-Binding Proteins Team, Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France.
| | - Cédric Orelle
- Bacterial Nucleotide-Binding Proteins Team, Molecular Microbiology and Structural Biochemistry (MMSB), UMR 5086 CNRS/University of Lyon, Lyon, France.
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7
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Liuu S, Nepelska M, Pfister H, Gamelas Magalhaes J, Chevalier G, Strozzi F, Billerey C, Maresca M, Nicoletti C, Di Pasquale E, Pechard C, Bardouillet L, Girardin SE, Boneca IG, Doré J, Blottière HM, Bonny C, Chene L, Cultrone A. Identification of a muropeptide precursor transporter from gut microbiota and its role in preventing intestinal inflammation. Proc Natl Acad Sci U S A 2023; 120:e2306863120. [PMID: 38127978 PMCID: PMC10756304 DOI: 10.1073/pnas.2306863120] [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: 05/10/2023] [Accepted: 10/31/2023] [Indexed: 12/23/2023] Open
Abstract
The gut microbiota is a considerable source of biologically active compounds that can promote intestinal homeostasis and improve immune responses. Here, we used large expression libraries of cloned metagenomic DNA to identify compounds able to sustain an anti-inflammatory reaction on host cells. Starting with a screen for NF-κB activation, we have identified overlapping clones harbouring a heterodimeric ATP-binding cassette (ABC)-transporter from a Firmicutes. Extensive purification of the clone's supernatant demonstrates that the ABC-transporter allows for the efficient extracellular accumulation of three muropeptide precursor, with anti-inflammatory properties. They induce IL-10 secretion from human monocyte-derived dendritic cells and proved effective in reducing AIEC LF82 epithelial damage and IL-8 secretion in human intestinal resections. In addition, treatment with supernatants containing the muropeptide precursor reduces body weight loss and improves histological parameters in Dextran Sulfate Sodium (DSS)-treated mice. Until now, the source of peptidoglycan fragments was shown to come from the natural turnover of the peptidoglycan layer by endogenous peptidoglycan hydrolases. This is a report showing an ABC-transporter as a natural source of secreted muropeptide precursor and as an indirect player in epithelial barrier strengthening. The mechanism described here might represent an important component of the host immune homeostasis.
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Affiliation(s)
| | - Malgorzata Nepelska
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), AgroParisTech, Food Microbial Ecology lab (Micalis), Université Paris-Saclay, Jouy-en-Josas78350, France
| | | | | | | | | | | | - Marc Maresca
- CNRS, Centrale Marseille, Institut des Sciences Moléculaires (iSm2) UMR7313, Aix Marseille Université, Marseille13013, France
| | - Cendrine Nicoletti
- CNRS, Centrale Marseille, Institut des Sciences Moléculaires (iSm2) UMR7313, Aix Marseille Université, Marseille13013, France
| | - Eric Di Pasquale
- Institut de NeuroPhysioPathologie (INP), Aix Marseille Université, UMR 7051, Marseille13005, France
| | | | | | - Stephen E. Girardin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Ivo Gomperts Boneca
- Institut Pasteur, Université Paris Cité, CNRS Unité Mixe de Recherche 6047, INSERM U1306, Unité de Biologie et génétique de la paroi bactérienne, Paris75015, France
| | - Joel Doré
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), AgroParisTech, Food Microbial Ecology lab (Micalis), Université Paris-Saclay, Jouy-en-Josas78350, France
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), MetaGenoPolis, Université Paris-Saclay, Jouy-en-Josas78350, France
| | - Hervé M. Blottière
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), AgroParisTech, Food Microbial Ecology lab (Micalis), Université Paris-Saclay, Jouy-en-Josas78350, France
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), MetaGenoPolis, Université Paris-Saclay, Jouy-en-Josas78350, France
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8
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Lyu J, Zhang T, Marty MT, Clemmer D, Russell DH, Laganowsky A. Double and triple thermodynamic mutant cycles reveal the basis for specific MsbA-lipid interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.03.547565. [PMID: 37461710 PMCID: PMC10350010 DOI: 10.1101/2023.07.03.547565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Structural and functional studies of the ATP-binding cassette transporter MsbA have revealed two distinct lipopolysaccharide (LPS) binding sites: one located in the central cavity and the other at a membrane-facing, exterior site. Although these binding sites are known to be important for MsbA function, the thermodynamic basis for these specific MsbA-LPS interactions is not well understood. Here, we use native mass spectrometry to determine the thermodynamics of MsbA interacting with the LPS-precursor 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo)2-lipid A (KDL). The binding of KDL is solely driven by entropy, despite the transporter adopting an inward-facing conformation or trapped in an outward-facing conformation with adenosine 5'-diphosphate and vanadate. An extension of the mutant cycle approach is employed to probe basic residues that interact with KDL. We find the molecular recognition of KDL is driven by a positive coupling entropy (as large as -100 kJ/mol at 298K) that outweighs unfavorable coupling enthalpy. These findings indicate that alterations in solvent reorganization and conformational entropy can contribute significantly to the free energy of protein-lipid association. The results presented herein showcase the advantage of native MS to obtain thermodynamic insight into protein-lipid interactions that would otherwise be intractable using traditional approaches, and this enabling technology will be instrumental in the life sciences and drug discovery.
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Affiliation(s)
- Jixing Lyu
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - Tianqi Zhang
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - Michael T. Marty
- Department of Chemistry and Biochemistry and Bio5 Institute, The University of Arizona, Tucson, AZ 85721
| | - David Clemmer
- Department of Chemistry, Indiana University, Bloomington, IN 47405
| | - David H. Russell
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, TX 77843
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9
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Goncharuk MV, Vasileva EV, Ananiev EA, Gorokhovatsky AY, Bocharov EV, Mineev KS, Goncharuk SA. Facade-Based Bicelles as a New Tool for Production of Active Membrane Proteins in a Cell-Free System. Int J Mol Sci 2023; 24:14864. [PMID: 37834312 PMCID: PMC10573531 DOI: 10.3390/ijms241914864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 09/18/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023] Open
Abstract
Integral membrane proteins are important components of a cell. Their structural and functional studies require production of milligram amounts of proteins, which nowadays is not a routine process. Cell-free protein synthesis is a prospective approach to resolve this task. However, there are few known membrane mimetics that can be used to synthesize active membrane proteins in high amounts. Here, we present the application of commercially available "Facade" detergents for the production of active rhodopsin. We show that the yield of active protein in lipid bicelles containing Facade-EM, Facade-TEM, and Facade-EPC is several times higher than in the case of conventional bicelles with CHAPS and DHPC and is comparable to the yield in the presence of lipid-protein nanodiscs. Moreover, the effects of the lipid-to-detergent ratio, concentration of detergent in the feeding mixture, and lipid composition of the bicelles on the total, soluble, and active protein yields are discussed. We show that Facade-based bicelles represent a prospective membrane mimetic, available for the production of membrane proteins in a cell-free system.
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Affiliation(s)
- Marina V. Goncharuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; (M.V.G.); (A.Y.G.); (E.V.B.)
| | - Ekaterina V. Vasileva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; (M.V.G.); (A.Y.G.); (E.V.B.)
| | - Egor A. Ananiev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; (M.V.G.); (A.Y.G.); (E.V.B.)
| | - Andrey Y. Gorokhovatsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; (M.V.G.); (A.Y.G.); (E.V.B.)
| | - Eduard V. Bocharov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; (M.V.G.); (A.Y.G.); (E.V.B.)
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Konstantin S. Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; (M.V.G.); (A.Y.G.); (E.V.B.)
| | - Sergey A. Goncharuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; (M.V.G.); (A.Y.G.); (E.V.B.)
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
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10
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Ma X, Wang L, Yang F, Li J, Guo L, Guo Y, He S. Drug sensitivity and genome-wide analysis of two strains of Mycoplasma gallisepticum with different biofilm intensity. Front Microbiol 2023; 14:1196747. [PMID: 37621399 PMCID: PMC10445764 DOI: 10.3389/fmicb.2023.1196747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 07/24/2023] [Indexed: 08/26/2023] Open
Abstract
Mycoplasma gallisepticum (MG) is one of the major causative agents of chronic respiratory diseases in poultry. The biofilms of MG are highly correlated to its chronic infection. However data on genes involved in biofilm formation ability are still scarse. MG strains with distinct biofilm intensity were screened by crystal violet staining morphotyped and characterized for the drug sensitivity. Two MG strains NX-01 and NX-02 showed contrasted ability to biofilm formation. The biofilm formation ability of NX-01 strain was significantly higher than that of NX-02 strain (p < 0.01). The drug sensitivity test showed that the stronger the ability of MG stain to form biofilms, the weaker its sensitivity to 17 antibiotic drugs. Moreover, putative key genes related to biofilm formation were screened by genome-wide analysis. A total of 13 genes and proteins related to biofilm formation, including ManB, oppA, oppD, PDH, eno, RelA, msbA, deoA, gapA, rpoS, Adhesin P1 precursor, S-adenosine methionine synthetase, and methionyl tRNA synthetase were identified. There were five major discrepancies between the two isolated MG strains and the five NCBI-published MG strains. These findings provide potential targets for inhibiting the formation of biofilm of MG, and lay a foundation for treating chronic infection.
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Affiliation(s)
- Xiaoyan Ma
- Clinical Veterinary Laboratory, Institute of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Li Wang
- Clinical Veterinary Laboratory, Institute of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Fei Yang
- Clinical Veterinary Laboratory, Institute of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Jidong Li
- Clinical Veterinary Laboratory, Institute of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Lei Guo
- Ningxia Xiaoming Agriculture and Animal Husbandry Co., Ltd., Yinchuan, China
| | - Yanan Guo
- Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Shenghu He
- Clinical Veterinary Laboratory, Institute of Animal Science and Technology, Ningxia University, Yinchuan, China
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11
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Badiee SA, Isu UH, Khodadadi E, Moradi M. The Alternating Access Mechanism in Mammalian Multidrug Resistance Transporters and Their Bacterial Homologs. MEMBRANES 2023; 13:568. [PMID: 37367772 PMCID: PMC10305233 DOI: 10.3390/membranes13060568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 05/23/2023] [Accepted: 05/27/2023] [Indexed: 06/28/2023]
Abstract
Multidrug resistance (MDR) proteins belonging to the ATP-Binding Cassette (ABC) transporter group play a crucial role in the export of cytotoxic drugs across cell membranes. These proteins are particularly fascinating due to their ability to confer drug resistance, which subsequently leads to the failure of therapeutic interventions and hinders successful treatments. One key mechanism by which multidrug resistance (MDR) proteins carry out their transport function is through alternating access. This mechanism involves intricate conformational changes that enable the binding and transport of substrates across cellular membranes. In this extensive review, we provide an overview of ABC transporters, including their classifications and structural similarities. We focus specifically on well-known mammalian multidrug resistance proteins such as MRP1 and Pgp (MDR1), as well as bacterial counterparts such as Sav1866 and lipid flippase MsbA. By exploring the structural and functional features of these MDR proteins, we shed light on the roles of their nucleotide-binding domains (NBDs) and transmembrane domains (TMDs) in the transport process. Notably, while the structures of NBDs in prokaryotic ABC proteins, such as Sav1866, MsbA, and mammalian Pgp, are identical, MRP1 exhibits distinct characteristics in its NBDs. Our review also emphasizes the importance of two ATP molecules for the formation of an interface between the two binding sites of NBD domains across all these transporters. ATP hydrolysis occurs following substrate transport and is vital for recycling the transporters in subsequent cycles of substrate transportation. Specifically, among the studied transporters, only NBD2 in MRP1 possesses the ability to hydrolyze ATP, while both NBDs of Pgp, Sav1866, and MsbA are capable of carrying out this reaction. Furthermore, we highlight recent advancements in the study of MDR proteins and the alternating access mechanism. We discuss the experimental and computational approaches utilized to investigate the structure and dynamics of MDR proteins, providing valuable insights into their conformational changes and substrate transport. This review not only contributes to an enhanced understanding of multidrug resistance proteins but also holds immense potential for guiding future research and facilitating the development of effective strategies to overcome multidrug resistance, thus improving therapeutic interventions.
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Affiliation(s)
| | | | | | - Mahmoud Moradi
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA; (S.A.B.); (U.H.I.); (E.K.)
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12
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Mann D, Labudda K, Zimmermann S, Vocke KU, Gasper R, Kötting C, Hofmann E. ATP binding and ATP hydrolysis in full-length MsbA monitored via time-resolved Fourier transform infrared spectroscopy. Biol Chem 2023:hsz-2023-0122. [PMID: 37185095 DOI: 10.1515/hsz-2023-0122] [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: 02/05/2023] [Accepted: 04/07/2023] [Indexed: 05/17/2023]
Abstract
The essential Escherichia coli ATPase MsbA is a lipid flippase that serves as a prototype for multi drug resistant ABC transporters. Its physiological function is the transport of lipopolisaccharides to build up the outer membranes of gram negative bacteria. Although several structural and biochemical studies of MsbA have been conducted previously, a detailed picture of the dynamic processes that link ATP hydrolysis to allocrit transport remains elusive. We report here for the first time time-resolved Fourier transform infrared (FTIR) spectroscopic measurements of the ATP binding and ATP hydrolysis reaction of full-length MsbA and determined reaction rates at 288 K of k 1 = 0.49 ± 0.28 s-1 and k 2 = 0.014 ± 0.003 s-1, respectively. We further verified these rates with photocaged NPEcgAppNHp where only nucleotide binding was observable and the negative mutant MsbA-H537A that showed slow hydrolysis (k 2 < 2 × 10-4 s-1). Besides single turnover kinetics, FTIR measurements also deliver IR signatures of all educts, products and the protein. ADP remains protein-bound after ATP hydrolysis. In addition, the spectral changes observed for the two variants MsbA-S378A and MsbA-S482A correlated with the loss of hydrogen bonding to the γ-phosphate of ATP. This study paves the way for FTIR-spectroscopic investigations of allocrite transport in full-length MsbA.
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Affiliation(s)
- Daniel Mann
- Ruhr University Bochum, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
- Forschungszentrum Jülich GmbH, Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons / ER-C-3: Structural Biology, D-52425 Jülich, Germany
- Forschungszentrum Jülich GmbH, Institute for Biological Information Processing / IBI-6 Cellular Structural Biology, D-52425 Jülich, Germany
| | - Kristin Labudda
- Ruhr University Bochum, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
- Ruhr University Bochum, Protein Crystallography, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
- Ruhr University Bochum, Center for Protein Diagnostics (PRODI), Biospectroscopy, D-44780 Bochum, Germany
| | - Sophie Zimmermann
- Ruhr University Bochum, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
- Ruhr University Bochum, Protein Crystallography, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
| | - Kai Ulrich Vocke
- Ruhr University Bochum, Protein Crystallography, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
| | - Raphael Gasper
- Ruhr University Bochum, Protein Crystallography, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
- Max Planck Institute of Molecular Physiology, Crystallography and Biophysics Facility, D-44227 Dortmund, Germany
| | - Carsten Kötting
- Ruhr University Bochum, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
- Ruhr University Bochum, Center for Protein Diagnostics (PRODI), Biospectroscopy, D-44780 Bochum, Germany
| | - Eckhard Hofmann
- Ruhr University Bochum, Protein Crystallography, Department of Biophysics, Universitätsstraße 150, D-44780 Bochum, Germany
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13
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Raina S. Lipopolysaccharides: Regulated Biosynthesis and Structural Diversity. Int J Mol Sci 2023; 24:7498. [PMID: 37108660 PMCID: PMC10145120 DOI: 10.3390/ijms24087498] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
The cell envelope of Gram-negative bacteria contains two distinct membranes, an inner (IM) and an outer (OM) membrane, separated by the periplasm, a hydrophilic compartment that includes a thin layer of peptidoglycan [...].
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Affiliation(s)
- Satish Raina
- Laboratory of Bacterial Genetics, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland
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14
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Orelle C, Schmitt L, Jault JM. Waste or die: The price to pay to stay alive. Trends Microbiol 2023; 31:233-241. [PMID: 36192292 DOI: 10.1016/j.tim.2022.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/06/2022] [Accepted: 09/06/2022] [Indexed: 11/19/2022]
Abstract
Microorganisms need to constantly exchange with their habitat to capture nutrients and expel toxic compounds. The ATP-binding cassette (ABC) transporters, a family of membrane proteins especially abundant in microorganisms, are at the core of these processes. Due to their extraordinary ability to expel structurally unrelated compounds, some transporters play a protective role in different organisms. Yet, the downside of these multidrug transporters is their entanglement in the resistance to therapeutic treatments. Intriguingly, some multidrug ABC transporters show a high level of ATPase activity, even in the absence of transported substrates. Although this basal ATPase activity might seem a waste, we surmise that this inherent capacity allows multidrug transporters to promptly translocate any bound drug before it penetrates into the cell.
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Affiliation(s)
- Cédric Orelle
- University of Lyon, CNRS, UMR5086 'Molecular Microbiology and Structural Biochemistry', IBCP, 7 Passage du Vercors, F-69367, Lyon, France.
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich Heine University, Universitätsstrasse 1, 40225 Düsseldorf, Germany.
| | - Jean-Michel Jault
- University of Lyon, CNRS, UMR5086 'Molecular Microbiology and Structural Biochemistry', IBCP, 7 Passage du Vercors, F-69367, Lyon, France.
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15
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Johansen NT, Tidemand FG, Pedersen MC, Arleth L. Travel light: Essential packing for membrane proteins with an active lifestyle. Biochimie 2023; 205:3-26. [PMID: 35963461 DOI: 10.1016/j.biochi.2022.07.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/29/2022] [Accepted: 07/23/2022] [Indexed: 11/02/2022]
Abstract
We review the considerable progress during the recent decade in the endeavours of designing, optimising, and utilising carrier particle systems for structural and functional studies of membrane proteins in near-native environments. New and improved systems are constantly emerging, novel studies push the perceived limits of a given carrier system, and specific carrier systems consolidate and entrench themselves as the system of choice for particular classes of target membrane protein systems. This review covers the most frequently used carrier systems for such studies and emphasises similarities and differences between these systems as well as current trends and future directions for the field. Particular interest is devoted to the biophysical properties and membrane mimicking ability of each system and the manner in which this may impact an embedded membrane protein and an eventual structural or functional study.
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Affiliation(s)
- Nicolai Tidemand Johansen
- Section for Transport Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark.
| | - Frederik Grønbæk Tidemand
- Section for Transport Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
| | - Martin Cramer Pedersen
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, Copenhagen E, 2100, Denmark
| | - Lise Arleth
- Condensed Matter Physics, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, Copenhagen E, 2100, Denmark
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16
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Jones PM, George AM. The Switch and Reciprocating Models for the Function of ABC Multidrug Exporters: Perspectives on Recent Research. Int J Mol Sci 2023; 24:ijms24032624. [PMID: 36768947 PMCID: PMC9917156 DOI: 10.3390/ijms24032624] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/23/2023] [Accepted: 01/26/2023] [Indexed: 02/03/2023] Open
Abstract
ATP-binding cassette (ABC) transporters comprise a large superfamily of primary active transporters, which are integral membrane proteins that couple energy to the uphill vectorial transport of substrates across cellular membranes, with concomitant hydrolysis of ATP. ABC transporters are found in all living organisms, coordinating mostly import in prokaryotes and export in eukaryotes. Unlike the highly conserved nucleotide binding domains (NBDs), sequence conservation in the transmembrane domains (TMDs) is low, with their divergent nature likely reflecting a need to accommodate a wide range of substrate types in terms of mass and polarity. An explosion in high resolution structural analysis over the past decade and a half has produced a wealth of structural information for ABCs. Based on the structures, a general mechanism for ABC transporters has been proposed, known as the Switch or Alternating Access Model, which holds that the NBDs are widely separated, with the TMDs and NBDs together forming an intracellular-facing inverted "V" shape. Binding of two ATPs and the substrate to the inward-facing conformation induces a transition to an outward conformation. Despite this apparent progress, certainty around the transport mechanism for any given ABC remains elusive. How substrate binding and transport is coupled to ATP binding and hydrolysis is not known, and there is a large body of biochemical and biophysical data that is at odds with the widely separated NBDs being a functional physiological state. An alternative Constant Contact model has been proposed in which the two NBSs operate 180 degrees out of phase with respect to ATP hydrolysis, with the NBDs remaining in close proximity throughout the transport cycle and operating in an asymmetric allosteric manner. The two models are discussed in the light of recent nuclear magnetic resonance and hydrogen-deuterium exchange mass spectrometry analyses of three ABC exporters.
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17
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Avendaño R, Muñoz-Montero S, Rojas-Gätjens D, Fuentes-Schweizer P, Vieto S, Montenegro R, Salvador M, Frew R, Kim J, Chavarría M, Jiménez JI. Production of selenium nanoparticles occurs through an interconnected pathway of sulphur metabolism and oxidative stress response in Pseudomonas putida KT2440. Microb Biotechnol 2023; 16:931-946. [PMID: 36682039 PMCID: PMC10128140 DOI: 10.1111/1751-7915.14215] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 01/23/2023] Open
Abstract
The soil bacterium Pseudomonas putida KT2440 has been shown to produce selenium nanoparticles aerobically from selenite; however, the molecular actors involved in this process are unknown. Here, through a combination of genetic and analytical techniques, we report the first insights into selenite metabolism in this bacterium. Our results suggest that the reduction of selenite occurs through an interconnected metabolic network involving central metabolic reactions, sulphur metabolism, and the response to oxidative stress. Genes such as sucA, D2HGDH and PP_3148 revealed that the 2-ketoglutarate and glutamate metabolism is important to convert selenite into selenium. On the other hand, mutations affecting the activity of the sulphite reductase decreased the bacteria's ability to transform selenite. Other genes related to sulphur metabolism (ssuEF, sfnCE, sqrR, sqr and pdo2) and stress response (gqr, lsfA, ahpCF and sadI) were also identified as involved in selenite transformation. Interestingly, suppression of genes sqrR, sqr and pdo2 resulted in the production of selenium nanoparticles at a higher rate than the wild-type strain, which is of biotechnological interest. The data provided in this study brings us closer to understanding the metabolism of selenium in bacteria and offers new targets for the development of biotechnological tools for the production of selenium nanoparticles.
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Affiliation(s)
- Roberto Avendaño
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, Costa Rica
| | | | - Diego Rojas-Gätjens
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, Costa Rica
| | - Paola Fuentes-Schweizer
- Escuela de Química, Universidad de Costa Rica, San José, Costa Rica.,Centro de Electroquímica y Energía Química (CELEQ), Universidad de Costa Rica, San José, Costa Rica
| | - Sofía Vieto
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, Costa Rica
| | - Rafael Montenegro
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, Costa Rica
| | - Manuel Salvador
- Biotechnology Applications, IDENER Research & Development, Seville, Spain
| | - Rufus Frew
- Department of Chemistry, University of Leicester, Leicester, UK
| | - Juhyun Kim
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, KNU Institute for Microorganisms, Kyungpook National University, Daegu, Korea
| | - Max Chavarría
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, Costa Rica.,Escuela de Química, Universidad de Costa Rica, San José, Costa Rica.,Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica
| | - Jose I Jiménez
- Department of Life Sciences, Imperial College London, London, UK
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18
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Lyu J, Liu C, Zhang T, Schrecke S, Elam NP, Packianathan C, Hochberg GKA, Russell D, Zhao M, Laganowsky A. Structural basis for lipid and copper regulation of the ABC transporter MsbA. Nat Commun 2022; 13:7291. [PMID: 36435815 PMCID: PMC9701195 DOI: 10.1038/s41467-022-34905-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/10/2022] [Indexed: 11/28/2022] Open
Abstract
A critical step in lipopolysaccharide (LPS) biogenesis involves flipping lipooligosaccharide, an LPS precursor, from the cytoplasmic to the periplasmic leaflet of the inner membrane, an operation carried out by the ATP-binding cassette transporter MsbA. Although LPS binding to the inner cavity of MsbA is well established, the selectivity of MsbA-lipid interactions at other site(s) remains poorly understood. Here we use native mass spectrometry (MS) to characterize MsbA-lipid interactions and guide structural studies. We show the transporter co-purifies with copper(II) and metal binding modulates protein-lipid interactions. A 2.15 Å resolution structure of an N-terminal region of MsbA in complex with copper(II) is presented, revealing a structure reminiscent of the GHK peptide, a high-affinity copper(II) chelator. Our results demonstrate conformation-dependent lipid binding affinities, particularly for the LPS-precursor, 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo)2-lipid A (KDL). We report a 3.6 Å-resolution structure of MsbA trapped in an open, outward-facing conformation with adenosine 5'-diphosphate and vanadate, revealing a distinct KDL binding site, wherein the lipid forms extensive interactions with the transporter. Additional studies provide evidence that the exterior KDL binding site is conserved and a positive allosteric modulator of ATPase activity, serving as a feedforward activation mechanism to couple transporter activity with LPS biosynthesis.
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Affiliation(s)
- Jixing Lyu
- Department of Chemistry, Texas A&M University, College Station, 77843, TX, USA
| | - Chang Liu
- Department of Biochemistry and Molecular biology, University of Chicago, Chicago, 60637, IL, USA
| | - Tianqi Zhang
- Department of Chemistry, Texas A&M University, College Station, 77843, TX, USA
| | - Samantha Schrecke
- Department of Chemistry, Texas A&M University, College Station, 77843, TX, USA
| | - Nicklaus P Elam
- Department of Chemistry, Texas A&M University, College Station, 77843, TX, USA
| | - Charles Packianathan
- Department of Chemistry, Texas A&M University, College Station, 77843, TX, USA
- Walter Reed Army Institute of Research, Pilot Bioproduction Facility, Silver Spring, 20910, MD, USA
| | - Georg K A Hochberg
- Max Planck Institute for Terrestrial Microbiology and Department of Chemistry, University of Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Department of Chemistry, University of Marburg, Marburg, Germany
| | - David Russell
- Department of Chemistry, Texas A&M University, College Station, 77843, TX, USA
| | - Minglei Zhao
- Department of Biochemistry and Molecular biology, University of Chicago, Chicago, 60637, IL, USA
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, 77843, TX, USA.
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19
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Galazzo L, Meier G, Januliene D, Parey K, De Vecchis D, Striednig B, Hilbi H, Schäfer LV, Kuprov I, Moeller A, Bordignon E, Seeger MA. The ABC transporter MsbA adopts the wide inward-open conformation in E. coli cells. SCIENCE ADVANCES 2022; 8:eabn6845. [PMID: 36223470 PMCID: PMC9555771 DOI: 10.1126/sciadv.abn6845] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 08/24/2022] [Indexed: 05/28/2023]
Abstract
Membrane proteins are currently investigated after detergent extraction from native cellular membranes and reconstitution into artificial liposomes or nanodiscs, thereby removing them from their physiological environment. However, to truly understand the biophysical properties of membrane proteins in a physiological environment, they must be investigated within living cells. Here, we used a spin-labeled nanobody to interrogate the conformational cycle of the ABC transporter MsbA by double electron-electron resonance. Unexpectedly, the wide inward-open conformation of MsbA, commonly considered a nonphysiological state, was found to be prominently populated in Escherichia coli cells. Molecular dynamics simulations revealed that extensive lateral portal opening is essential to provide access of its large natural substrate core lipid A to the binding cavity. Our work paves the way to investigate the conformational landscape of membrane proteins in cells.
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Affiliation(s)
- Laura Galazzo
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany
- Department of Physical Chemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Gianmarco Meier
- Institute of Medical Microbiology, University of Zurich, 8006 Zurich, Switzerland
| | - Dovile Januliene
- Department of Structural Biology, Osnabrück University, 49076 Osnabrück, Germany
| | - Kristian Parey
- Department of Structural Biology, Osnabrück University, 49076 Osnabrück, Germany
| | - Dario De Vecchis
- Center for Theoretical Chemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Bianca Striednig
- Institute of Medical Microbiology, University of Zurich, 8006 Zurich, Switzerland
| | - Hubert Hilbi
- Institute of Medical Microbiology, University of Zurich, 8006 Zurich, Switzerland
| | - Lars V. Schäfer
- Center for Theoretical Chemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Ilya Kuprov
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, UK
| | - Arne Moeller
- Department of Structural Biology, Osnabrück University, 49076 Osnabrück, Germany
| | - Enrica Bordignon
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany
- Department of Physical Chemistry, University of Geneva, 1211 Geneva, Switzerland
| | - Markus A. Seeger
- Institute of Medical Microbiology, University of Zurich, 8006 Zurich, Switzerland
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20
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Giacometti SI, MacRae MR, Dancel-Manning K, Bhabha G, Ekiert DC. Lipid Transport Across Bacterial Membranes. Annu Rev Cell Dev Biol 2022; 38:125-153. [PMID: 35850151 DOI: 10.1146/annurev-cellbio-120420-022914] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The movement of lipids within and between membranes in bacteria is essential for building and maintaining the bacterial cell envelope. Moving lipids to their final destination is often energetically unfavorable and does not readily occur spontaneously. Bacteria have evolved several protein-mediated transport systems that bind specific lipid substrates and catalyze the transport of lipids across membranes and from one membrane to another. Specific protein flippases act in translocating lipids across the plasma membrane, overcoming the obstacle of moving relatively large and chemically diverse lipids between leaflets of the bilayer. Active transporters found in double-membraned bacteria have evolved sophisticated mechanisms to traffic lipids between the two membranes, including assembling to form large, multiprotein complexes that resemble bridges, shuttles, and tunnels, shielding lipids from the hydrophilic environment of the periplasm during transport. In this review, we explore our current understanding of the mechanisms thought to drive bacterial lipid transport.
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Affiliation(s)
- Sabrina I Giacometti
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA; , , ,
| | - Mark R MacRae
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA; , , ,
| | - Kristen Dancel-Manning
- Office of Science and Research, New York University School of Medicine, New York, NY, USA;
| | - Gira Bhabha
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA; , , ,
| | - Damian C Ekiert
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA; , , ,
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
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21
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A New Factor LapD Is Required for the Regulation of LpxC Amounts and Lipopolysaccharide Trafficking. Int J Mol Sci 2022; 23:ijms23179706. [PMID: 36077106 PMCID: PMC9456370 DOI: 10.3390/ijms23179706] [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] [Received: 07/29/2022] [Revised: 08/20/2022] [Accepted: 08/23/2022] [Indexed: 11/17/2022] Open
Abstract
Lipopolysaccharide (LPS) constitutes the major component of the outer membrane and is essential for bacteria, such as Escherichia coli. Recent work has revealed the essential roles of LapB and LapC proteins in regulating LPS amounts; although, if any additional partners are involved is unknown. Examination of proteins co-purifying with LapB identified LapD as a new partner. The purification of LapD reveals that it forms a complex with several proteins involved in LPS and phospholipid biosynthesis, including FtsH-LapA/B and Fab enzymes. Loss of LapD causes a reduction in LpxC amounts and vancomycin sensitivity, which can be restored by mutations that stabilize LpxC (mutations in lapB, ftsH and lpxC genes), revealing that LapD acts upstream of LapB-FtsH in regulating LpxC amounts. Interestingly, LapD absence results in the substantial retention of LPS in the inner membranes and synthetic lethality when either the lauroyl or the myristoyl acyl transferase is absent, which can be overcome by single-amino acid suppressor mutations in LPS flippase MsbA, suggesting LPS translocation defects in ΔlapD bacteria. Several genes whose products are involved in cell envelope homeostasis, including clsA, waaC, tig and micA, become essential in LapD’s absence. Furthermore, the overproduction of acyl carrier protein AcpP or transcriptional factors DksA, SrrA can overcome certain defects of the LapD-lacking strain.
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22
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Segrest JP, Tang C, Song HD, Jones MK, Davidson WS, Aller SG, Heinecke JW. ABCA1 is an extracellular phospholipid translocase. Nat Commun 2022; 13:4812. [PMID: 35974019 PMCID: PMC9381790 DOI: 10.1038/s41467-022-32437-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 07/29/2022] [Indexed: 11/18/2022] Open
Abstract
Production of high density lipoprotein (HDL) requires ATP-binding cassette transporter A1 (ABCA1) to drive phospholipid (PL) from the plasma membrane into extracellular apolipoprotein A-I. Here, we use simulations to show that domains of ABCA1 within the plasma membrane remove PL from the membrane’s outer leaflet. In our simulations, after the lipid diffuses into the interior of ABCA1’s outward-open cavity, PL extracted by the gateway passes through a ring-shaped domain, the annulus orifice, which forms the base of an elongated hydrophobic tunnel in the transporter’s extracellular domain. Engineered mutations in the gateway and annulus strongly inhibit lipid export by ABCA1 without affecting cell-surface expression levels. Our finding that ABCA1 extracts lipid from the outer face of the plasma membrane and forces it through its gateway and annulus into an elongated hydrophobic tunnel contrasts with the alternating access model, which proposes that ABCA1 flops PL substrate from the inner leaflet to the outer leaflet of the membrane. Consistent with our model, ABCA1 lacks the charged amino acid residues in the transmembrane domain found in the floppase members of the ABC transporter family. ATP-binding cassette transporter A1 (ABCA1) drives phospholipid (PL) from the plasma membrane into extracellular apolipoprotein A-I, for the production of high density lipoprotein (HDL). Here, the authors use simulations to assess the mechanism of ABCA1 function and show that ABCA1 extracts lipid from the outer face of the plasma membrane.
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Affiliation(s)
- Jere P Segrest
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Chongren Tang
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Hyun D Song
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Martin K Jones
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - W Sean Davidson
- Department of Pathology and Laboratory Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Stephen G Aller
- Department of Pharmacology & Toxicology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jay W Heinecke
- Department of Medicine, University of Washington, Seattle, WA, USA
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23
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Zhao F, Zhu Z, Xie L, Luo F, Wang H, Qiu Y, Luo W, Zhou F, Xue D, Zhang Z, Hua T, Wu D, Liu Z, Le Z, Tao H. Two‐Dimensional Detergent Expansion Strategy for Membrane Protein Studies. Chemistry 2022; 28:e202201388. [DOI: 10.1002/chem.202201388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Fei Zhao
- iHuman Institute ShanghaiTech University Shanghai 201210 China
| | - Zhihao Zhu
- College of Chemistry Nanchang University Nanchang, Jiangxi Province 330031 China
| | - Linshan Xie
- iHuman Institute ShanghaiTech University Shanghai 201210 China
- School of Life Science and Technology ShanghaiTech University Shanghai 201210 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Feng Luo
- iHuman Institute ShanghaiTech University Shanghai 201210 China
| | - Huixia Wang
- iHuman Institute ShanghaiTech University Shanghai 201210 China
| | - Yanli Qiu
- iHuman Institute ShanghaiTech University Shanghai 201210 China
- School of Life Science and Technology ShanghaiTech University Shanghai 201210 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Weiling Luo
- iHuman Institute ShanghaiTech University Shanghai 201210 China
- School of Life Science and Technology ShanghaiTech University Shanghai 201210 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Fang Zhou
- iHuman Institute ShanghaiTech University Shanghai 201210 China
| | - Dongxiang Xue
- iHuman Institute ShanghaiTech University Shanghai 201210 China
| | - Zhihui Zhang
- iHuman Institute ShanghaiTech University Shanghai 201210 China
| | - Tian Hua
- iHuman Institute ShanghaiTech University Shanghai 201210 China
- School of Life Science and Technology ShanghaiTech University Shanghai 201210 China
| | - Dong Wu
- iHuman Institute ShanghaiTech University Shanghai 201210 China
| | - Zhi‐Jie Liu
- iHuman Institute ShanghaiTech University Shanghai 201210 China
- School of Life Science and Technology ShanghaiTech University Shanghai 201210 China
| | - Zhiping Le
- College of Chemistry Nanchang University Nanchang, Jiangxi Province 330031 China
| | - Houchao Tao
- iHuman Institute ShanghaiTech University Shanghai 201210 China
- Shanghai Frontiers Science Center of TCM Chemical Biology Innovation Research Institute of Traditional Chinese Medicine Shanghai University of Traditional Chinese Medicine Shanghai 201203 China
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24
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Hulen C, Racine PJ, Feuilloley M, Elomri A, Lomri NE. Effects of Verapamil and Two Bisbenzylisoquinolines, Curine and Guattegaumerine Extracted from Isolona hexaloba, on the Inhibition of ABC Transporters from Pseudomonas aeruginosa. Antibiotics (Basel) 2022; 11:700. [PMID: 35625344 PMCID: PMC9137725 DOI: 10.3390/antibiotics11050700] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 05/13/2022] [Accepted: 05/17/2022] [Indexed: 02/05/2023] Open
Abstract
The biological effects of alkaloids, curine, guattegaumerine, and verapamil, on Pseudomonas aeruginosa were investigated. These molecules did not inhibit P. aeruginosa growth but increased the sensitivity of this bacterium to carbenicillin, novobiocin, and erythromycin. The results of another study indicate that curine and guattegaumerine were competitors of verapamil and acted as inhibitors of eukaryotic ABCB1 efflux pump. A BLAST-P carried out between a bacterial MDR transporter LmrA from Lactococcus lactis, a human MDR1/P-glycoprotein (ABCB1), and ABC proteins of P.aeruginosa highlighted five potential candidates that have this bacterium. A study on the sensitivity to carbenicillin in the presence of verapamil allowed us to identify the product of gene PA1113 as the ABC transporter involved in the influx of carbenicillin. Similarly, novobiocin transport performed in the presence of verapamil and a docking analysis highlighted protein MsbA (Lipid A flippase, gene PA4997) as a potential candidate in novobiocin efflux. MsbA has previously been identified as a multidrug transporter in E. coli, and as P. aeruginosa MsbA presented 76% identity with E. coli MsbA, it is possible that novobiocin efflux involves this ABC transporter, accounting for about 30% of the bacterium resistance to this antibiotic.
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Affiliation(s)
- Christian Hulen
- Bacterial Communication and Antimicrobial Strategies Research Unit, University of Rouen Normandy, 55 Rue Saint Germain, 2700 Evreux, France; (C.H.); (P.-J.R.); (M.F.)
| | - Pierre-Jean Racine
- Bacterial Communication and Antimicrobial Strategies Research Unit, University of Rouen Normandy, 55 Rue Saint Germain, 2700 Evreux, France; (C.H.); (P.-J.R.); (M.F.)
| | - Marc Feuilloley
- Bacterial Communication and Antimicrobial Strategies Research Unit, University of Rouen Normandy, 55 Rue Saint Germain, 2700 Evreux, France; (C.H.); (P.-J.R.); (M.F.)
| | - Abdelhakim Elomri
- UNIROUEN, INSA Rouen, CNRS, COBRA (UMR 6014), Normandie University, 76000 Rouen, France;
| | - Nour-Eddine Lomri
- Bacterial Communication and Antimicrobial Strategies Research Unit, University of Rouen Normandy, 55 Rue Saint Germain, 2700 Evreux, France; (C.H.); (P.-J.R.); (M.F.)
- Department of Biology, UFR Sciences and Techniques, University of Cergy-Pontoise, 2 Ave A. Chauvin, 95302 Cergy-Pontoise, France
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25
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Yang M, Luo W, Zhang W, Wang H, Xue D, Wu Y, Zhao S, Zhao F, Zheng X, Tao H. Ugi Reaction Mediated Detergent Assembly for Membrane Protein Studies. Chem Asian J 2022; 17:e202200372. [PMID: 35575910 DOI: 10.1002/asia.202200372] [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: 04/11/2022] [Revised: 05/16/2022] [Indexed: 11/11/2022]
Abstract
Despite the continuous efforts, the current repertoire of detergents is still far from sufficient for the biophysics studies of membrane proteins (MPs). Toward the rapid expansion of detergent diversity, we herein report a new strategy based on Ugi reaction mediated modular assembly. Structural varieties, including hydrophobic tails and hydrophilic heads, could be conveniently introduced from the multiple reaction components. New detergents then were comprehensively evaluated in the physical properties and preliminarily screened by the thermal stabilization for a transporter MsbA and a spectrum of G protein-coupled receptors (GPCRs). For the glucagon-like peptide-1 receptor (GLP-1R), a class B GPCR, detergent M-23-M finally stood out in a second evaluation for the maintenance of homogeneity and was further illustrated its application in the improvement of NMR study. Besides the promising utility in the MP study, the current results exhibit intriguing structural-physical relationship that would allow the guidance in the tuning of detergent properties in the future.
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Affiliation(s)
- Meifang Yang
- University of South China, Department of Pharmacy, CHINA
| | - Weiling Luo
- ShanghaiTech University, iHuman Institute, CHINA
| | - Wei Zhang
- ShanghaiTech University, iHuman Institute, CHINA
| | - Huixia Wang
- ShanghaiTech University, iHuman Institute, CHINA
| | | | - Yiran Wu
- ShanghaiTech University, iHuman Institute, CHINA
| | - Suwen Zhao
- ShanghaiTech University, iHuman Institute, CHINA
| | - Fei Zhao
- ShanghaiTech University, iHuman Institute, 230 Haike Road, 201210, Shanghai, CHINA
| | - Xing Zheng
- University of South China, Department of Pharmacy, CHINA
| | - Houchao Tao
- Shanghai University of Traditional Chinese Medicine, Shanghai Frontiers Science Center of TCM Chemical Biology, Room 2421, Building 2, 1200 Cailun Road, 230032, Shanghai, CHINA
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26
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Kehlenbeck DM, Traore DAK, Josts I, Sander S, Moulin M, Haertlein M, Prevost S, Forsyth VT, Tidow H. Cryo-EM structure of MsbA in saposin-lipid nanoparticles (Salipro) provides insights into nucleotide coordination. FEBS J 2022; 289:2959-2970. [PMID: 34921499 DOI: 10.1111/febs.16327] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/05/2021] [Accepted: 12/16/2021] [Indexed: 01/28/2023]
Abstract
The ATP-binding cassette transporter MsbA is a lipid flippase, translocating lipid A, glycolipids, and lipopolysaccharides from the inner to the outer leaflet of the inner membrane of Gram-negative bacteria. It has been used as a model system for time-resolved structural studies as several MsbA structures in different states and reconstitution systems (detergent/nanodiscs/peptidiscs) are available. However, due to the limited resolution of the available structures, detailed structural information on the bound nucleotides has remained elusive. Here, we have reconstituted MsbA in saposin A-lipoprotein nanoparticles (Salipro) and determined the structure of ADP-vanadate-bound MsbA by single-particle cryo-electron microscopy to 3.5 Å resolution. This procedure has resulted in significantly improved resolution and enabled us to model all side chains and visualise detailed ADP-vanadate interactions in the nucleotide-binding domains. The approach may be applicable to other dynamic membrane proteins.
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Affiliation(s)
- Dominique-Maurice Kehlenbeck
- The Hamburg Advanced Research Center for Bioorganic Chemistry (HARBOR), Germany.,Department of Chemistry, Institute for Biochemistry and Molecular Biology, University of Hamburg, Germany.,Life Sciences Group, Institut Laue-Langevin, Grenoble, France.,Partnership for Structural Biology (PSB), Grenoble, France
| | - Daouda A K Traore
- Life Sciences Group, Institut Laue-Langevin, Grenoble, France.,Partnership for Structural Biology (PSB), Grenoble, France.,Faculty of Natural Sciences, Keele University, UK.,Faculté des Sciences et Techniques, Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Bamako, Mali
| | - Inokentijs Josts
- The Hamburg Advanced Research Center for Bioorganic Chemistry (HARBOR), Germany.,Department of Chemistry, Institute for Biochemistry and Molecular Biology, University of Hamburg, Germany
| | - Simon Sander
- The Hamburg Advanced Research Center for Bioorganic Chemistry (HARBOR), Germany.,Department of Chemistry, Institute for Biochemistry and Molecular Biology, University of Hamburg, Germany
| | - Martine Moulin
- Life Sciences Group, Institut Laue-Langevin, Grenoble, France.,Partnership for Structural Biology (PSB), Grenoble, France
| | - Michael Haertlein
- Life Sciences Group, Institut Laue-Langevin, Grenoble, France.,Partnership for Structural Biology (PSB), Grenoble, France
| | - Sylvain Prevost
- Large Scale Structures Group, Institut Laue-Langevin, Grenoble, France
| | - V Trevor Forsyth
- Life Sciences Group, Institut Laue-Langevin, Grenoble, France.,Partnership for Structural Biology (PSB), Grenoble, France.,Faculty of Natural Sciences, Keele University, UK
| | - Henning Tidow
- The Hamburg Advanced Research Center for Bioorganic Chemistry (HARBOR), Germany
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27
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Structural insights into the catalytic cycle of a bacterial multidrug ABC efflux pump. J Mol Biol 2022; 434:167541. [DOI: 10.1016/j.jmb.2022.167541] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/02/2022] [Accepted: 03/09/2022] [Indexed: 12/19/2022]
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28
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Thélot FA, Liao M. Cryo-EM Analysis of the Lipopolysaccharide Flippase MsbA. Methods Mol Biol 2022; 2548:233-247. [PMID: 36151501 DOI: 10.1007/978-1-0716-2581-1_14] [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] [Indexed: 06/16/2023]
Abstract
MsbA is a member of the ATP-binding cassette (ABC) transporter family and harnesses the energy from adenosine triphosphate (ATP) binding and hydrolysis to flip lipopolysaccharide (LPS) across the cytoplasmic membrane in Gram-negative bacteria. MsbA is an essential component of the bacterial envelope biogenesis pathway and an attractive target for developing novel antibiotics against multidrug-resistant strains. Structural characterization of MsbA in different conformations provides crucial insights in understanding druggable pockets and mechanisms of inhibition of this transporter. Recent advances in membrane-mimetic environments and cryo-EM data acquisition and processing have enabled high-resolution imaging of MsbA in complex with its native LPS substrate. Despite these technical advances, MsbA remains a challenging target for cryo-EM analysis due to its small size and extraordinary conformational flexibility. Herein, we provide a protocol for the purification and incorporation of MsbA in lipid nanodiscs, cryo-EM sample preparation, and cryo-EM image processing. The method outlined here is generalizable to the study of other bacterial ABC transporters, including the LPS extractor LptB2FGC.
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Affiliation(s)
- François A Thélot
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Biological and Biomedical Sciences Program, Harvard University, Cambridge, MA, USA
| | - Maofu Liao
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
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29
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Checkpoints That Regulate Balanced Biosynthesis of Lipopolysaccharide and Its Essentiality in Escherichia coli. Int J Mol Sci 2021; 23:ijms23010189. [PMID: 35008618 PMCID: PMC8745692 DOI: 10.3390/ijms23010189] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/17/2021] [Accepted: 12/22/2021] [Indexed: 12/17/2022] Open
Abstract
The outer membrane (OM) of Gram-negative bacteria, such as Escherichia coli, is essential for their viability. Lipopolysaccharide (LPS) constitutes the major component of OM, providing the permeability barrier, and a tight balance exists between LPS and phospholipids amounts as both of these essential components use a common metabolic precursor. Hence, checkpoints are in place, right from the regulation of the first committed step in LPS biosynthesis mediated by LpxC through its turnover by FtsH and HslUV proteases in coordination with LPS assembly factors LapB and LapC. After the synthesis of LPS on the inner leaflet of the inner membrane (IM), LPS is flipped by the IM-located essential ATP-dependent transporter to the periplasmic face of IM, where it is picked up by the LPS transport complex spanning all three components of the cell envelope for its delivery to OM. MsbA exerts its intrinsic hydrocarbon ruler function as another checkpoint to transport hexa-acylated LPS as compared to underacylated LPS. Additional checkpoints in LPS assembly are: LapB-assisted coupling of LPS synthesis and translocation; cardiolipin presence when LPS is underacylated; the recruitment of RfaH transcriptional factor ensuring the transcription of LPS core biosynthetic genes; and the regulated incorporation of non-stoichiometric modifications, controlled by the stress-responsive RpoE sigma factor, small RNAs and two-component systems.
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30
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Abstract
Rapid flip-flop of phospholipids across the two leaflets of biological membranes is crucial for many aspects of cellular life. The transport proteins that facilitate this process are classified as pump-like flippases and floppases and channel-like scramblases. Unexpectedly, Class A G protein-coupled receptors (GPCRs), a large class of signaling proteins exemplified by the visual receptor rhodopsin and its apoprotein opsin, are constitutively active as scramblases in vitro. In liposomes, opsin scrambles lipids at a unitary rate of >100,000 per second. Atomistic molecular dynamics simulations of opsin in a lipid membrane reveal conformational transitions that expose a polar groove between transmembrane helices 6 and 7. This groove enables transbilayer lipid movement, conceptualized as the swiping of a credit card (lipid) through a card reader (GPCR). Conformational changes that facilitate scrambling are distinct from those associated with GPCR signaling. In this review, we discuss the physiological significance of GPCR scramblase activity and the modes of its regulation in cells. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, USA; .,Institute of Computational Biomedicine, Weill Cornell Medical College, New York, New York, USA
| | - Anant K Menon
- Department of Biochemistry, Weill Cornell Medical College, New York, New York, USA;
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31
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MsbA: an ABC transporter paradigm. Biochem Soc Trans 2021; 49:2917-2927. [PMID: 34821931 DOI: 10.1042/bst20211030] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/27/2021] [Accepted: 11/03/2021] [Indexed: 12/27/2022]
Abstract
ATP-binding cassette (ABC) transporters play an important role in various cellular processes. They display a similar architecture and share a mechanism which couples ATP hydrolysis to substrate transport. However, in the light of current data and recent experimental progress, this protein superfamily appears as multifaceted as their broad substrate range. Among the prokaryotic ABC transporters, MsbA can serve as a paradigm for research in this field. It is located in the inner membrane of Gram-negative bacteria and functions as a floppase for the lipopolysaccharide (LPS) precursor core-LPS, which is involved in the biogenesis of the bacterial outer membrane. While MsbA shows high similarity to eukaryotic ABC transporters, its expression in Gram-negative bacteria makes it conveniently accessible for many experimental approaches from spectroscopy to 3D structure determination. As an essential protein for bacterial membrane integrity, MsbA has also become an attractive target for the development of novel antibiotics. Furthermore, it serves as a model for multidrug efflux pumps. Here we provide an overview of recent findings and their relevance to the field, highlight the potential of methods such as solid-state NMR and EPR spectroscopy and provide a perspective for future work.
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32
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Guo D, Singh H, Shimoyama A, Guffick C, Tang Y, Rowe SM, Noel T, Spring DR, Fukase K, van Veen HW. Energetics of lipid transport by the ABC transporter MsbA is lipid dependent. Commun Biol 2021; 4:1379. [PMID: 34887543 PMCID: PMC8660845 DOI: 10.1038/s42003-021-02902-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 11/18/2021] [Indexed: 12/13/2022] Open
Abstract
The ABC multidrug exporter MsbA mediates the translocation of lipopolysaccharides and phospholipids across the plasma membrane in Gram-negative bacteria. Although MsbA is structurally well characterised, the energetic requirements of lipid transport remain unknown. Here, we report that, similar to the transport of small-molecule antibiotics and cytotoxic agents, the flopping of physiologically relevant long-acyl-chain 1,2-dioleoyl (C18)-phosphatidylethanolamine in proteoliposomes requires the simultaneous input of ATP binding and hydrolysis and the chemical proton gradient as sources of metabolic energy. In contrast, the flopping of the large hexa-acylated (C12-C14) Lipid-A anchor of lipopolysaccharides is only ATP dependent. This study demonstrates that the energetics of lipid transport by MsbA is lipid dependent. As our mutational analyses indicate lipid and drug transport via the central binding chamber in MsbA, the lipid availability in the membrane can affect the drug transport activity and vice versa.
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Affiliation(s)
- Dawei Guo
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
| | - Himansha Singh
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
| | - Atsushi Shimoyama
- Department of Chemistry, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Charlotte Guffick
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
| | - Yakun Tang
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
| | - Sam M Rowe
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Timothy Noel
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
| | - David R Spring
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Koichi Fukase
- Department of Chemistry, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Hendrik W van Veen
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK.
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33
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Thélot FA, Zhang W, Song K, Xu C, Huang J, Liao M. Distinct allosteric mechanisms of first-generation MsbA inhibitors. Science 2021; 374:580-585. [PMID: 34554829 DOI: 10.1126/science.abi9009] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- François A Thélot
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Biological and Biomedical Sciences Program, Harvard University, Cambridge, MA, USA
| | - Wenyi Zhang
- Key Laboratory of Structural Biology of Zhejiang Province, Westlake University, Hangzhou, China.,Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - KangKang Song
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.,Cryo-EM Core Facility, University of Massachusetts Medical School, Worcester, MA, USA
| | - Chen Xu
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.,Cryo-EM Core Facility, University of Massachusetts Medical School, Worcester, MA, USA
| | - Jing Huang
- Key Laboratory of Structural Biology of Zhejiang Province, Westlake University, Hangzhou, China.,Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Maofu Liao
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
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34
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Liu L, Zhu Z, Zhou F, Xue D, Hu T, Luo W, Qiu Y, Wu D, Zhao F, Le Z, Tao H. Catalytically Cleavable Detergent for Membrane Protein Studies. ACS OMEGA 2021; 6:21087-21093. [PMID: 34423216 PMCID: PMC8375090 DOI: 10.1021/acsomega.1c02894] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 07/26/2021] [Indexed: 05/04/2023]
Abstract
Throughout the in vitro studies of membrane proteins (MPs), proper detergents are essential for the preparation of stable aqueous samples. To date, universally applicable detergents have not yet been reported to accommodate the distinct requirements for the highly diversified MPs and at the different stages of MP manipulation. Detergent exchange often has to be performed. We report herein the catalytically cleavable detergents (CatCDs) that can be efficiently removed to facilitate a complete exchange. To this end, functional groups, like propargyl and allyl, are introduced as branched chains or built in the hydrophobic chain close to the hydrophilic head. The representative CatCDs can be used as usual detergents in the extraction and purification of MPs and later be removed upon the addition of catalytic palladium. Mediated by CatCD-1, reconstitution of a transporter protein MsbA into a series of detergents was achieved. The extension of these designs could facilitate the future optimization of other biophysics studies.
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Affiliation(s)
- Lu Liu
- Department
of Chemistry, Nanchang University, 999 Xuefu Avenue, Nanchang 330031, China
| | - Zhihao Zhu
- Department
of Chemistry, Nanchang University, 999 Xuefu Avenue, Nanchang 330031, China
| | - Fang Zhou
- iHuman
Institute, ShanghaiTech University, Y Building, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Dongxiang Xue
- iHuman
Institute, ShanghaiTech University, Y Building, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Tao Hu
- iHuman
Institute, ShanghaiTech University, Y Building, 393 Middle Huaxia Road, Shanghai 201210, China
- School
of Life Science and Technology, ShanghaiTech
University, L Building,
393 Middle Huaxia Road, Shanghai 201210, China
| | - Weiling Luo
- iHuman
Institute, ShanghaiTech University, Y Building, 393 Middle Huaxia Road, Shanghai 201210, China
- School
of Life Science and Technology, ShanghaiTech
University, L Building,
393 Middle Huaxia Road, Shanghai 201210, China
| | - Yanli Qiu
- iHuman
Institute, ShanghaiTech University, Y Building, 393 Middle Huaxia Road, Shanghai 201210, China
- School
of Life Science and Technology, ShanghaiTech
University, L Building,
393 Middle Huaxia Road, Shanghai 201210, China
| | - Dong Wu
- iHuman
Institute, ShanghaiTech University, Y Building, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Fei Zhao
- iHuman
Institute, ShanghaiTech University, Y Building, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Zhiping Le
- Department
of Chemistry, Nanchang University, 999 Xuefu Avenue, Nanchang 330031, China
| | - Houchao Tao
- iHuman
Institute, ShanghaiTech University, Y Building, 393 Middle Huaxia Road, Shanghai 201210, China
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35
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Molecular Basis of Essentiality of Early Critical Steps in the Lipopolysaccharide Biogenesis in Escherichia coli K-12: Requirement of MsbA, Cardiolipin, LpxL, LpxM and GcvB. Int J Mol Sci 2021; 22:ijms22105099. [PMID: 34065855 PMCID: PMC8151780 DOI: 10.3390/ijms22105099] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 05/09/2021] [Accepted: 05/10/2021] [Indexed: 12/11/2022] Open
Abstract
To identify the physiological factors that limit the growth of Escherichia coli K-12 strains synthesizing minimal lipopolysaccharide (LPS), we describe the first construction of strains devoid of the entire waa locus and concomitantly lacking all three acyltransferases (LpxL/LpxM/LpxP), synthesizing minimal lipid IVA derivatives with a restricted ability to grow at around 21 °C. Suppressors restoring growth up to 37 °C of Δ(gmhD-waaA) identified two independent single-amino-acid substitutions—P50S and R310S—in the LPS flippase MsbA. Interestingly, the cardiolipin synthase-encoding gene clsA was found to be essential for the growth of ΔlpxLMP, ΔlpxL, ΔwaaA, and Δ(gmhD-waaA) bacteria, with a conditional lethal phenotype of Δ(clsA lpxM), which could be overcome by suppressor mutations in MsbA. Suppressor mutations basS A20D or basR G53V, causing a constitutive incorporation of phosphoethanolamine (P-EtN) in the lipid A, could abolish the Ca++ sensitivity of Δ(waaC eptB), thereby compensating for P-EtN absence on the second Kdo. A single-amino-acid OppA S273G substitution is shown to overcome the synthetic lethality of Δ(waaC surA) bacteria, consistent with the chaperone-like function of the OppA oligopeptide-binding protein. Furthermore, overexpression of GcvB sRNA was found to repress the accumulation of LpxC and suppress the lethality of LapAB absence. Thus, this study identifies new and limiting factors in regulating LPS biosynthesis.
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36
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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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Liston SD, Willis LM. Racing to build a wall: glycoconjugate assembly in Gram-positive and Gram-negative bacteria. Curr Opin Struct Biol 2021; 68:55-65. [PMID: 33429200 DOI: 10.1016/j.sbi.2020.11.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/20/2020] [Accepted: 11/22/2020] [Indexed: 12/17/2022]
Abstract
The last two years have seen major advances in understanding the structural basis of bacterial cell envelope glycoconjugate biosynthesis, including capsules, lipopolysaccharide, teichoic acid, cellulose, and peptidoglycan. The recent crystal and cryo-electron microscopy structures of proteins involved in the initial glycosyltransferase steps in the cytoplasm, the transport of large and small lipid-linked glycoconjugates across the inner membrane, the polymerization of glycans in the periplasm, and the export of molecules from the cell have shed light on the mechanisms by which cell envelope glycoconjugates are made. We discuss these recent advances and highlight remaining unanswered questions.
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Affiliation(s)
- Sean D Liston
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5G1M1, Canada
| | - Lisa M Willis
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G2T2, Canada; Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, T6G2T2, Canada; Women and Children's Health Research Institute, Edmonton, AB, T6G2T2, Canada.
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Jones PM, George AM. Is the emperor wearing shorts? The published structures of ABC transporters. FEBS Lett 2020; 594:3790-3798. [PMID: 32981041 DOI: 10.1002/1873-3468.13941] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/24/2020] [Accepted: 09/13/2020] [Indexed: 12/20/2022]
Abstract
ABC transporters use the energy of ATP binding and hydrolysis to transport substrates across cellular membranes. They comprise two highly conserved nucleotide binding domains and two transmembrane domains that form the transmembrane channel and contain the substrate binding sites. Structural analyses have found a variety of seemingly unrelated folds for the ABC transporter transmembrane domains, and from these, a set of diverse mechanistic models has been inferred. Nevertheless, in spite of the explosion in structure determination of ABC transporters in the last decade, advancement in certainty and clarity as to fundamental aspects of their molecular mechanisms remains elusive. With this in mind, here we put and examine the question: Could current ABC structures differ from the physiologic membrane-embedded forms?
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Affiliation(s)
- Peter M Jones
- School of Life Sciences, University of Technology Sydney, Broadway, NSW, Australia
| | - Anthony M George
- School of Life Sciences, University of Technology Sydney, Broadway, NSW, Australia
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