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Saha I, Ghosh B, Dasgupta J. Structural insights in to the atypical type-I ABC Glucose-6-phosphate importer VCA0625-27 of Vibrio cholerae. Biochem Biophys Res Commun 2024; 716:150030. [PMID: 38704889 DOI: 10.1016/j.bbrc.2024.150030] [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: 04/18/2024] [Accepted: 04/28/2024] [Indexed: 05/07/2024]
Abstract
Sugar phosphates are potential sources of carbon and phosphate for bacteria. Despite that the process of internalization of Glucose-6-Phosphate (G6P) through plasma membrane remained elusive in several bacteria. VCA0625-27, made of periplasmic ligand binding protein (PLBP) VCA0625, an atypical monomeric permease VCA0626, and a cytosolic ATPase VCA0627, recently emerged as hexose-6-phosphate uptake system of Vibrio cholerae. Here we report high resolution crystal structure of VCA0625 in G6P bound state that largely resembles AfuA of Actinobacillus pleuropneumoniae. MD simulations on VCA0625 in apo and G6P bound states unraveled an 'open to close' and swinging bi-lobal motions, which are diminished upon G6P binding. Mutagenesis followed by biochemical assays on VCA0625 underscored that R34 works as gateway to bind G6P. Although VCA0627 binds ATP, it is ATPase deficient in the absence of VCA0625 and VCA0626, which is a signature phenomenon of type-I ABC importer. Further, modeling, docking and systematic sequence analysis allowed us to envisage the existence of similar atypical type-I G6P importer with fused monomeric permease in 27 other gram-negative bacteria.
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Affiliation(s)
- Indrila Saha
- Department of Biotechnology, St. Xavier's College (Autonomous), 30, Mother Teresa Sarani, Kolkata, 700016, India
| | - Biplab Ghosh
- Macromolecular Crystallography Section, Beamline Development & Application Section, Bhabha Atomic Research Center, Trombay, Mumbai, 400085, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, India.
| | - Jhimli Dasgupta
- Department of Biotechnology, St. Xavier's College (Autonomous), 30, Mother Teresa Sarani, Kolkata, 700016, India.
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2
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Yang X, Hu T, Liang J, Xiong Z, Lin Z, Zhao Y, Zhou X, Gao Y, Sun S, Yang X, Guddat LW, Yang H, Rao Z, Zhang B. An oligopeptide permease, OppABCD, requires an iron-sulfur cluster domain for functionality. Nat Struct Mol Biol 2024; 31:1072-1082. [PMID: 38548954 DOI: 10.1038/s41594-024-01256-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 02/23/2024] [Indexed: 07/20/2024]
Abstract
Oligopeptide permease, OppABCD, belongs to the type I ABC transporter family. Its role is to import oligopeptides into bacteria for nutrient uptake and to modulate the host immune response. OppABCD consists of a cluster C substrate-binding protein (SBP), OppA, membrane-spanning OppB and OppC subunits, and an ATPase, OppD, that contains two nucleotide-binding domains (NBDs). Here, using cryo-electron microscopy, we determined the high-resolution structures of Mycobacterium tuberculosis OppABCD in the resting state, oligopeptide-bound pre-translocation state, AMPPNP-bound pre-catalytic intermediate state and ATP-bound catalytic intermediate state. The structures show an assembly of a cluster C SBP with its ABC translocator and a functionally required [4Fe-4S] cluster-binding domain in OppD. Moreover, the ATP-bound OppABCD structure has an outward-occluded conformation, although no substrate was observed in the transmembrane cavity. Here, we reveal an oligopeptide recognition and translocation mechanism of OppABCD, which provides a perspective on how this and other type I ABC importers facilitate bulk substrate transfer across the lipid bilayer.
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Affiliation(s)
- Xiaolin Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, China.
| | - Tianyu Hu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jingxi Liang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Zhiqi Xiong
- Laboratory of Structural Biology, Tsinghua University, Beijing, China
| | - Zhenli Lin
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yao Zhao
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, China
| | - Xiaoting Zhou
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Yan Gao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Shan Sun
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xiuna Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Clinical Research and Trial Center, Shanghai, China
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane Queensland, Australia
| | - Haitao Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- Shanghai Clinical Research and Trial Center, Shanghai, China.
| | - Zihe Rao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China.
- Laboratory of Structural Biology, Tsinghua University, Beijing, China.
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
| | - Bing Zhang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- Shanghai Clinical Research and Trial Center, Shanghai, China.
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3
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Hu T, Yang X, Zhu Y, Liu F, Yang X, Xiong Z, Liang J, Lin Z, Ran Y, Guddat LW, Rao Z, Zhang B. Molecular basis for substrate transport of Mycobacterium tuberculosis ABC importer DppABCD. SCIENCE ADVANCES 2024; 10:eadk8521. [PMID: 38507491 PMCID: PMC10954201 DOI: 10.1126/sciadv.adk8521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 02/15/2024] [Indexed: 03/22/2024]
Abstract
The type I adenosine 5'-triphosphate (ATP)-binding cassette (ABC) transporter DppABCD is believed to be responsible for the import of exogenous heme as an iron source into the cytoplasm of the human pathogen Mycobacterium tuberculosis (Mtb). Additionally, this system is also known to be involved in the acquisition of tri- or tetra-peptides. Here, we report the cryo-electron microscopy structures of the dual-function Mtb DppABCD transporter in three forms, namely, the apo, substrate-bound, and ATP-bound states. The apo structure reveals an unexpected and previously uncharacterized assembly mode for ABC importers, where the lipoprotein DppA, a cluster C substrate-binding protein (SBP), stands upright on the translocator DppBCD primarily through its hinge region and N-lobe. These structural data, along with biochemical studies, reveal the assembly of DppABCD complex and the detailed mechanism of DppABCD-mediated transport. Together, these findings provide a molecular roadmap for understanding the transport mechanism of a cluster C SBP and its translocator.
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Affiliation(s)
- Tianyu Hu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xiaolin Yang
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen 518112, China
| | - Yuanchen Zhu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Fengjiang Liu
- Innovative Center for Pathogen Research, Guangzhou Laboratory, Guangzhou 510005, China
| | - Xiuna Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Shanghai Clinical Research and Trial Center, Shanghai 201210, China
| | - Zhiqi Xiong
- Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China
| | - Jingxi Liang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300353, China
| | - Zhenli Lin
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yuting Ran
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Luke W. Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Zihe Rao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen 518112, China
- Innovative Center for Pathogen Research, Guangzhou Laboratory, Guangzhou 510005, China
- Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300353, China
| | - Bing Zhang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Shanghai Clinical Research and Trial Center, Shanghai 201210, China
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4
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Fang T, Szklarczyk D, Hachilif R, von Mering C. Enhancing coevolutionary signals in protein-protein interaction prediction through clade-wise alignment integration. Sci Rep 2024; 14:6009. [PMID: 38472223 PMCID: PMC10933411 DOI: 10.1038/s41598-024-55655-9] [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: 12/06/2023] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
Protein-protein interactions (PPIs) play essential roles in most biological processes. The binding interfaces between interacting proteins impose evolutionary constraints that have successfully been employed to predict PPIs from multiple sequence alignments (MSAs). To construct MSAs, critical choices have to be made: how to ensure the reliable identification of orthologs, and how to optimally balance the need for large alignments versus sufficient alignment quality. Here, we propose a divide-and-conquer strategy for MSA generation: instead of building a single, large alignment for each protein, multiple distinct alignments are constructed under distinct clades in the tree of life. Coevolutionary signals are searched separately within these clades, and are only subsequently integrated using machine learning techniques. We find that this strategy markedly improves overall prediction performance, concomitant with better alignment quality. Using the popular DCA algorithm to systematically search pairs of such alignments, a genome-wide all-against-all interaction scan in a bacterial genome is demonstrated. Given the recent successes of AlphaFold in predicting direct PPIs at atomic detail, a discover-and-refine approach is proposed: our method could provide a fast and accurate strategy for pre-screening the entire genome, submitting to AlphaFold only promising interaction candidates-thus reducing false positives as well as computation time.
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Affiliation(s)
- Tao Fang
- Department of Molecular Life Sciences, University of Zurich, 8057, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Damian Szklarczyk
- Department of Molecular Life Sciences, University of Zurich, 8057, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Radja Hachilif
- Department of Molecular Life Sciences, University of Zurich, 8057, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Christian von Mering
- Department of Molecular Life Sciences, University of Zurich, 8057, Zurich, Switzerland.
- SIB Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.
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5
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Takemiya K, Wang S, Liu Y, Murthy N, Goodman MM, Taylor WR. Isothermal titration calorimetry analysis of the binding between the maltodextrin binding protein malE of Staphylococcus aureus with maltodextrins of various lengths. Biochem Biophys Res Commun 2024; 695:149467. [PMID: 38211531 PMCID: PMC10842747 DOI: 10.1016/j.bbrc.2023.149467] [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: 09/05/2023] [Revised: 12/12/2023] [Accepted: 12/30/2023] [Indexed: 01/13/2024]
Abstract
Staphylococcus aureus (S. aureus), a Gram-positive bacterium, causes a wide range of infections, and diagnosis at an early stage is challenging. Targeting the maltodextrin transporter has emerged as a promising strategy for imaging bacteria and has been able to image a wide range of bacteria including S. aureus. However, little is known about the maltodextrin transporter in S. aureus, and this prevents new S. aureus specific ligands for the maltodextrin transporter from being developed. In Gram-positive bacteria, including S. aureus, the first step of maltodextrin transport is the binding of the maltodextrin-binding protein malE to maltodextrins. Thus, understanding the binding affinity and characteristics of malE from S. aureus is important to developing efficient maltodextrin-based imaging probes. We evaluated the affinity of malE of S. aureus to maltodextrins of various lengths. MalE of S. aureus (SAmalE) was expressed in E. coli BL21(DE3) and purified by Ni-NTA resin. The affinities of SAmalE to maltodextrins were evaluated with isothermal titration calorimetry. SAmalE has low affinity to maltose but binds to maltotriose and longer maltodextrins up to maltoheptaose with affinities up to Ka = 9.02 ± 0.49 × 105 M-1. SAmalE binding to maltotriose-maltoheptaose was exothermic and fit a single-binding site model. The van't Hoff enthalpy in the binding reaction of SAmalE with maltotriose was 9.9 ± 1.3 kcal/mol, and the highest affinity of SAmalE was observed with maltotetraose with Ka = 9.02 ± 0.49 × 105 M-1. In the plot of ΔH-T*ΔS, the of Enthalpy-Entropy Compensation effect was observed in binding reaction of SAmalE to maltodextrins. Acarbose and maltotetraiol bind with SAmalE indicating that SAmalE is tolerant of modifications on both the reducing and non-reducing ends of maltodextrins. Our results show that unlike ECmalE and similar to the maltodextrin binding protein of Streptococci, SAmalE primarily binds to maltodextrins via hydrogen bonds. This is distinct from the maltodextrin binding protein of Streptococci, SAmalE that binds to maltotetraiol with high affinity. Understanding the binding characteristics and tolerance to maltodextrins modifications by maltodextrin binding proteins will hopefully provide the basis for developing bacterial species-specific maltodextrin-based imaging probes.
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Affiliation(s)
- Kiyoko Takemiya
- Division of Cardiology, Department of Medicine, Emory University School of Medicine, 1750 Haygood Dr. NE, Atlanta, GA, 30322, USA.
| | - Shelly Wang
- Division of Cardiology, Department of Medicine, Emory University School of Medicine, 1750 Haygood Dr. NE, Atlanta, GA, 30322, USA
| | - Yu Liu
- Division of Cardiology, Department of Medicine, Emory University School of Medicine, 1750 Haygood Dr. NE, Atlanta, GA, 30322, USA
| | - Niren Murthy
- Department of Bioengineering, Stanley Hall 306 University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Mark M Goodman
- Department of Radiology and Imaging Sciences, School of Medicine, Emory University, 1364 Clifton Road NE, Atlanta, GA, 30322, USA; Center for Systems Imaging, Emory University, 1364 Clifton Rd NE, Atlanta, 30322, Georgia
| | - W Robert Taylor
- Division of Cardiology, Department of Medicine, Emory University School of Medicine, 1750 Haygood Dr. NE, Atlanta, GA, 30322, USA; Joseph Maxwell Cleland Atlanta VA Medical Center, 1670 Clairmont Road, Decatur, GA, 30033, USA; Wallace H. Coulter Department of Biomedical Engineering School of Medicine, Emory University, 1750 Haygood Dr. NE, Atlanta, GA, 30322, USA
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6
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Liang J, Yang X, Hu T, Gao Y, Yang Q, Yang H, Peng W, Zhou X, Guddat LW, Zhang B, Rao Z, Liu F. Structural insights into trehalose capture and translocation by mycobacterial LpqY-SugABC. Structure 2023; 31:1158-1165.e3. [PMID: 37619560 DOI: 10.1016/j.str.2023.07.014] [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: 03/23/2023] [Revised: 06/25/2023] [Accepted: 07/28/2023] [Indexed: 08/26/2023]
Abstract
The human pathogen, Mycobacterium tuberculosis (Mtb) relies heavily on trehalose for both survival and pathogenicity. The type I ATP-binding cassette (ABC) transporter LpqY-SugABC is the only trehalose import pathway in Mtb. Conformational dynamics of ABC transporters is an important feature to explain how they operate, but experimental structures are determined in a static environment. Therefore, a detailed transport mechanism cannot be elucidated because there is a lack of intermediate structures. Here, we used single-particle cryo-electron microscopy (cryo-EM) to determine the structure of the Mycobacterium smegmatis (M. smegmatis) trehalose-specific importer LpqY-SugABC complex in five different conformations. These structures have been classified and reconstructed from a single cryo-EM dataset. This study allows a comprehensive understanding of the trehalose recycling mechanism in Mycobacteria and also demonstrates the potential of single-particle cryo-EM to explore the dynamic structures of other ABC transporters and molecular machines.
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Affiliation(s)
- Jingxi Liang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China; Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China; Innovative Center for Pathogen Research, Guangzhou Laboratory, Guangzhou, China
| | - Xiuna Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Tianyu Hu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yan Gao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Qi Yang
- Innovative Center for Pathogen Research, Guangzhou Laboratory, Guangzhou, China
| | - Haitao Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Wei Peng
- Innovative Center for Pathogen Research, Guangzhou Laboratory, Guangzhou, China
| | - Xiaoting Zhou
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, the University of Queensland, Brisbane, QLD, Australia
| | - Bing Zhang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
| | - Zihe Rao
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China; Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China; Innovative Center for Pathogen Research, Guangzhou Laboratory, Guangzhou, China; National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, CAS, Beijing, China; Laboratory of Structural Biology, Tsinghua University, Beijing, China.
| | - Fengjiang Liu
- Innovative Center for Pathogen Research, Guangzhou Laboratory, Guangzhou, China.
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7
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Thangaratnarajah C, Nijland M, Borges-Araújo L, Jeucken A, Rheinberger J, Marrink SJ, Souza PCT, Paulino C, Slotboom DJ. Expulsion mechanism of the substrate-translocating subunit in ECF transporters. Nat Commun 2023; 14:4484. [PMID: 37491368 PMCID: PMC10368641 DOI: 10.1038/s41467-023-40266-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 07/20/2023] [Indexed: 07/27/2023] Open
Abstract
Energy-coupling factor (ECF)-type transporters mediate the uptake of micronutrients in many bacteria. They consist of a substrate-translocating subunit (S-component) and an ATP-hydrolysing motor (ECF module) Previous data indicate that the S-component topples within the membrane to alternately expose the binding site to either side of the membrane. In many ECF transporters, the substrate-free S-component can be expelled from the ECF module. Here we study this enigmatic expulsion step by cryogenic electron microscopy and reveal that ATP induces a concave-to-convex shape change of two long helices in the motor, thereby destroying the S-component's docking site and allowing for its dissociation. We show that adaptation of the membrane morphology to the conformational state of the motor may favour expulsion of the substrate-free S-component when ATP is bound and docking of the substrate-loaded S-component after hydrolysis. Our work provides a picture of bilayer-assisted chemo-mechanical coupling in the transport cycle of ECF transporters.
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Affiliation(s)
- Chancievan Thangaratnarajah
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Electron Microscopy Group, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Mark Nijland
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Luís Borges-Araújo
- Molecular Microbiology and Structural Biochemistry, CNRS and University of Lyon, 69367, Lyon, France
| | - Aike Jeucken
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Jan Rheinberger
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Electron Microscopy Group, University of Groningen, 9747 AG, Groningen, The Netherlands
- Biochemistry Center, University of Heidelberg, Im Neuenheimer Feld 328, 69120, Heidelberg, Germany
| | - Siewert J Marrink
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Molecular Dynamics Group, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry, CNRS and University of Lyon, 69367, Lyon, France
| | - Cristina Paulino
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands.
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Electron Microscopy Group, University of Groningen, 9747 AG, Groningen, The Netherlands.
- Biochemistry Center, University of Heidelberg, Im Neuenheimer Feld 328, 69120, Heidelberg, Germany.
| | - Dirk J Slotboom
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands.
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8
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Chen Y, Wang L, Hou WT, Zha Z, Xu K, Zhou CZ, Li Q, Chen Y. Structural insights into human ABCC4-mediated transport of platelet agonist and antagonist. NATURE CARDIOVASCULAR RESEARCH 2023; 2:693-701. [PMID: 39195918 DOI: 10.1038/s44161-023-00289-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 05/19/2023] [Indexed: 08/29/2024]
Abstract
Human platelets contribute to hemostasis and thrombosis, the imbalance of which can cause cardiovascular diseases. The activation and accumulation of platelets can be induced by agonists or inhibited by antagonists. Thus, the human ABC transporter ABCC4, which pumps out platelet agonists and antagonists, might become a promising target for preventing cardiovascular diseases. Here we define five structures of human ABCC4: the apo and three complexed forms in the inward-facing conformation, in addition to an outward-facing occluded conformation upon ATP binding. Combined with biochemical assays, we structurally prove that U46619, a synthetic analog of the unstable agonist TXA2, and the antagonist aspirin are substrates of ABCC4. In addition, we found that the platelet antagonist dipyridamole is a strong competitive inhibitor against ABCC4. These complex structures also enable us to identify a transmembrane pocket in ABCC4 that provides a defined space for the rational design of specific platelet antagonists.
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Affiliation(s)
- Yu Chen
- Department of Endocrinology, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- School of Life Sciences, University of Science and Technology of China, Hefei, China
- Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China
| | - Liang Wang
- School of Life Sciences, University of Science and Technology of China, Hefei, China
- Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China
| | - Wen-Tao Hou
- School of Life Sciences, University of Science and Technology of China, Hefei, China
- Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China
| | - Zhihui Zha
- School of Life Sciences, University of Science and Technology of China, Hefei, China
- Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China
| | - Kang Xu
- School of Life Sciences, University of Science and Technology of China, Hefei, China
- Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China
| | - Cong-Zhao Zhou
- School of Life Sciences, University of Science and Technology of China, Hefei, China.
- Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China.
| | - Qiong Li
- Department of Endocrinology, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
- School of Life Sciences, University of Science and Technology of China, Hefei, China.
- Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China.
| | - Yuxing Chen
- Department of Endocrinology, Institute of Endocrine and Metabolic Diseases, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
- School of Life Sciences, University of Science and Technology of China, Hefei, China.
- Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China.
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9
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Ousalem F, Singh S, Bailey NA, Wong KH, Zhu L, Neky MJ, Sibindi C, Fei J, Gonzalez RL, Boël G, Hunt JF. Comparative genetic, biochemical, and biophysical analyses of the four E. coli ABCF paralogs support distinct functions related to mRNA translation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.11.543863. [PMID: 37398404 PMCID: PMC10312648 DOI: 10.1101/2023.06.11.543863] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Multiple paralogous ABCF ATPases are encoded in most genomes, but the physiological functions remain unknown for most of them. We herein compare the four Escherichia coli K12 ABCFs - EttA, Uup, YbiT, and YheS - using assays previously employed to demonstrate EttA gates the first step of polypeptide elongation on the ribosome dependent on ATP/ADP ratio. A Δ uup knockout, like Δ ettA , exhibits strongly reduced fitness when growth is restarted from long-term stationary phase, but neither Δ ybiT nor Δ yheS exhibits this phenotype. All four proteins nonetheless functionally interact with ribosomes based on in vitro translation and single-molecule fluorescence resonance energy transfer experiments employing variants harboring glutamate-to-glutamine active-site mutations (EQ 2 ) that trap them in the ATP-bound conformation. These variants all strongly stabilize the same global conformational state of a ribosomal elongation complex harboring deacylated tRNA Val in the P site. However, EQ 2 -Uup uniquely exchanges on/off the ribosome on a second timescale, while EQ 2 -YheS-bound ribosomes uniquely sample alternative global conformations. At sub-micromolar concentrations, EQ 2 -EttA and EQ 2 -YbiT fully inhibit in vitro translation of an mRNA encoding luciferase, while EQ 2 -Uup and EQ 2 -YheS only partially inhibit it at ~10-fold higher concentrations. Moreover, tripeptide synthesis reactions are not inhibited by EQ 2 -Uup or EQ 2 -YheS, while EQ 2 -YbiT inhibits synthesis of both peptide bonds and EQ 2 -EttA specifically traps ribosomes after synthesis of the first peptide bond. These results support the four E. coli ABCF paralogs all having different activities on translating ribosomes, and they suggest that there remains a substantial amount of functionally uncharacterized "dark matter" involved in mRNA translation.
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10
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Abstract
ABC transporters are essential for cellular physiology. Humans have 48 ABC genes organized into seven distinct families. Of these genes, 44 (in five distinct families) encode for membrane transporters, of which several are involved in drug resistance and disease pathways resulting from transporter dysfunction. Over the last decade, advances in structural biology have vastly expanded our mechanistic understanding of human ABC transporter function, revealing details of their molecular arrangement, regulation, and interactions, facilitated in large part by advances in cryo-EM that have rendered hitherto inaccessible targets amenable to high-resolution structural analysis. As a result, experimentally determined structures of multiple members of each of the five families of ABC transporters in humans are now available. Here we review this recent progress, highlighting the physiological relevance of human ABC transporters and mechanistic insights gleaned from their direct structure determination. We also discuss the impact and limitations of model systems and structure prediction methods in understanding human ABC transporters and discuss current challenges and future research directions.
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Affiliation(s)
- Amer Alam
- The Hormel Institute, University of Minnesota, Austin, Minnesota, USA
| | - Kaspar P Locher
- Institute of Molecular Biology and Biophysics, ETH Zurich, Switzerland;
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11
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Sauve S, Williamson J, Polasa A, Moradi M. Ins and Outs of Rocker Switch Mechanism in Major Facilitator Superfamily of Transporters. MEMBRANES 2023; 13:membranes13050462. [PMID: 37233523 DOI: 10.3390/membranes13050462] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/20/2023] [Accepted: 04/23/2023] [Indexed: 05/27/2023]
Abstract
The major facilitator superfamily (MFS) of transporters consists of three classes of membrane transporters: symporters, uniporters, and antiporters. Despite such diverse functions, MFS transporters are believed to undergo similar conformational changes within their distinct transport cycles, known as the rocker-switch mechanism. While the similarities between conformational changes are noteworthy, the differences are also important since they could potentially explain the distinct functions of symporters, uniporters, and antiporters of the MFS superfamily. We reviewed a variety of experimental and computational structural data on a select number of antiporters, symporters, and uniporters from the MFS family to compare the similarities and differences of the conformational dynamics of three different classes of transporters.
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Affiliation(s)
- Stephanie Sauve
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Joseph Williamson
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Adithya Polasa
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Mahmoud Moradi
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
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12
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Liu M, Chu B, Sun R, Ding J, Ye H, Yang Y, Wu Y, Shi H, Song B, He Y, Wang H, Hong J. Antisense Oligonucleotides Selectively Enter Human-Derived Antibiotic-Resistant Bacteria through Bacterial-Specific ATP-Binding Cassette Sugar Transporter. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023:e2300477. [PMID: 37002615 DOI: 10.1002/adma.202300477] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/24/2023] [Indexed: 05/28/2023]
Abstract
Current vehicles used to deliver antisense oligonucleotides (ASOs) cannot distinguish between bacterial and mammalian cells, greatly hindering the preclinical or clinical treatment of bacterial infections, especially those caused by antibiotic-resistant bacteria. Herein, bacteria-specific ATP-binding cassette (ABC) sugar transporters are leveraged to selectively internalize ASOs by hitchhiking them on α (1-4)-glucosidically linked glucose polymers. Compared with their cell-penetrating peptide counterparts, which are non-specifically engulfed by mammalian and bacterial cells, the presented therapeutics consisting of glucose polymer and antisense peptide nucleic-acid-modified nanoparticles are selectively internalized into the human-derived multidrug-resistant Escherichia coli and methicillin-resistant Staphylococcus aureus, and they display a much higher uptake rate (i.e., 51.6%). The developed strategy allows specific and efficient killing of nearly 100% of the antibiotic-resistant bacteria. Its significant curative efficacy against bacterial keratitis and endophthalmitis is also shown. This strategy will expand the focus of antisense technology to include bacterial cells other than mammalian cells.
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Affiliation(s)
- Mingzhu Liu
- Institute of Functional Nano and Soft Materials, Soochow University, Suzhou, China
- Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
| | - Binbin Chu
- Institute of Functional Nano and Soft Materials, Soochow University, Suzhou, China
- Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
| | - Rong Sun
- Institute of Functional Nano and Soft Materials, Soochow University, Suzhou, China
- Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
| | - Jiali Ding
- Institute of Functional Nano and Soft Materials, Soochow University, Suzhou, China
- Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
| | - Han Ye
- Department of Ophthalmology and Vision Science, Shanghai Eye Ear Nose and Throat Hospital, Fudan University, 83 Road Fenyang, Shanghai, 200031, China
| | - Yunmin Yang
- Institute of Functional Nano and Soft Materials, Soochow University, Suzhou, China
- Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
| | - Yuqi Wu
- Institute of Functional Nano and Soft Materials, Soochow University, Suzhou, China
- Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
| | - Haoliang Shi
- Institute of Functional Nano and Soft Materials, Soochow University, Suzhou, China
- Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
| | - Bin Song
- Institute of Functional Nano and Soft Materials, Soochow University, Suzhou, China
- Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
| | - Yao He
- Institute of Functional Nano and Soft Materials, Soochow University, Suzhou, China
- Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
| | - Houyu Wang
- Institute of Functional Nano and Soft Materials, Soochow University, Suzhou, China
- Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Soochow University, 199 Ren'ai Rd, Suzhou Industrial Park, Suzhou, 215123, China
| | - Jiaxu Hong
- Department of Ophthalmology and Vision Science, Shanghai Eye Ear Nose and Throat Hospital, Fudan University, 83 Road Fenyang, Shanghai, 200031, China
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13
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Hirota R, Katsuura ZI, Momokawa N, Murakami H, Watanabe S, Ishida T, Ikeda T, Funabashi H, Kuroda A. Gatekeeper Residue Replacement in a Phosphite Transporter Enhances Mutational Robustness of the Biocontainment Strategy. ACS Synth Biol 2022; 11:3397-3404. [PMID: 36202772 DOI: 10.1021/acssynbio.2c00296] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Biocontainment is a key methodology to reduce environmental risk through the deliberate release of genetically modified microorganisms. Previously, we developed a phosphite (HPO32-)-dependent biocontainment strategy, by expressing a phosphite-specific transporter HtxBCDE and phosphite dehydrogenase in bacteria devoid of their indigenous phosphate (HPO42-) transporters. This strategy did not allow Escherichia coli to generate escape mutants (EMs) in growth media containing phosphate as a phosphorus source using an assay with a detection limit of 1.9 × 10-13. In this study, we found that the coexistence of a high dose of phosphate (>0.5 mM) with phosphite in the growth medium allows the phosphite-dependent E. coli strain to generate EMs at a frequency of approximately 5.4 × 10-10. In all EMs, the mutation was a single amino acid substitution of phenylalanine to cysteine or serine at position 210 of HtxC, the transmembrane domain protein of the phosphorus compound transporter HtxBCDE. Replacement of the HtxC F210 residue with the other 17 amino acids revealed that HtxC F210 is crucial in determining substrate specificity of HtxBCDE. Based on the finding of the role of HtxC F210 as a "gatekeeper" residue for this transporter, we demonstrate that the replacement of HtxC F210 with amino acids resulting from codons that require two simultaneous point mutations to generate phosphate permissive HtxC mutants can reduce the rate of EM generation to an undetectable level. These findings also provide novel insights into the functional classification of HtxBCDE as a noncanonical ATP-binding cassette transporter in which the transmembrane domain protein participates in substrate recognition.
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Affiliation(s)
- Ryuichi Hirota
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Zen-Ichiro Katsuura
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Naoki Momokawa
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Hiroki Murakami
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Satoru Watanabe
- Department of Bioscience, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Takenori Ishida
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Takeshi Ikeda
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Hisakage Funabashi
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Akio Kuroda
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
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14
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Akhtar AA, Turner DP. The role of bacterial ATP-binding cassette (ABC) transporters in pathogenesis and virulence: Therapeutic and vaccine potential. Microb Pathog 2022; 171:105734. [PMID: 36007845 DOI: 10.1016/j.micpath.2022.105734] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 11/24/2022]
Abstract
The ATP-binding cassette (ABC) transporter superfamily is found in all domains of life, facilitating critical biological processes through the translocation of a wide variety of substrates from, ions to proteins, across cellular membranes in an ATP-coupled process. The role of ABC transporters in eukaryotes has been well established: the facilitation of genetic diseases and multi-drug resistance (MDR) in cancer patients. In contrast, the role of ABC transporters in prokaryotes has been ambiguous due to their diverse functions and the sheer number of organisms in which they reside. This review examines the role of bacterial ABC transporters in pathogenesis and virulence, and their potential for therapeutic and vaccine application. We demonstrate how ABC transporters play a vital role in the virulence and pathogenesis of several pathogenic bacteria through the import of essential molecules, such as metal ions, amino acids, peptides, vitamins and osmoprotectants, as well as, the export of virulent determinants involved in glycoconjugate biosynthesis and Type I secretion. Furthermore, ABC exporters facilitate the persistence of pathogenic bacteria through the export of toxic xenobiotic substances, thus, contributing to the development of antimicrobial resistance. We also show that ABC transporters display considerable potential for therapeutic application through immunisation and resistance reversal. In conclusion, bacterial ABC transporters play an immense role in virulence and pathogenesis and display desirable traits for clinical use, therefore, potentially aiding in the battle against MDR.
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Affiliation(s)
- Armaan A Akhtar
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom.
| | - David Pj Turner
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom
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15
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Peter MF, Ruland JA, Depping P, Schneberger N, Severi E, Moecking J, Gatterdam K, Tindall S, Durand A, Heinz V, Siebrasse JP, Koenig PA, Geyer M, Ziegler C, Kubitscheck U, Thomas GH, Hagelueken G. Structural and mechanistic analysis of a tripartite ATP-independent periplasmic TRAP transporter. Nat Commun 2022; 13:4471. [PMID: 35927235 PMCID: PMC9352664 DOI: 10.1038/s41467-022-31907-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 07/08/2022] [Indexed: 11/27/2022] Open
Abstract
Tripartite ATP-independent periplasmic (TRAP) transporters are found widely in bacteria and archaea and consist of three structural domains, a soluble substrate-binding protein (P-domain), and two transmembrane domains (Q- and M-domains). HiSiaPQM and its homologs are TRAP transporters for sialic acid and are essential for host colonization by pathogenic bacteria. Here, we reconstitute HiSiaQM into lipid nanodiscs and use cryo-EM to reveal the structure of a TRAP transporter. It is composed of 16 transmembrane helices that are unexpectedly structurally related to multimeric elevator-type transporters. The idiosyncratic Q-domain of TRAP transporters enables the formation of a monomeric elevator architecture. A model of the tripartite PQM complex is experimentally validated and reveals the coupling of the substrate-binding protein to the transporter domains. We use single-molecule total internal reflection fluorescence (TIRF) microscopy in solid-supported lipid bilayers and surface plasmon resonance to study the formation of the tripartite complex and to investigate the impact of interface mutants. Furthermore, we characterize high-affinity single variable domains on heavy chain (VHH) antibodies that bind to the periplasmic side of HiSiaQM and inhibit sialic acid uptake, providing insight into how TRAP transporter function might be inhibited in vivo.
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Affiliation(s)
- Martin F Peter
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Jan A Ruland
- Institute for Physical und Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53127, Bonn, Germany
| | - Peer Depping
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
- Aston Centre for Membrane Proteins and Lipids Research, Aston St., B4 7ET, Birmingham, UK
| | - Niels Schneberger
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Emmanuele Severi
- Department of Biology (Area 10), University of York, York, YO10 5YW, UK
- Biosciences Institute, Newcastle University, Newcastle, NE2 4HH, UK
| | - Jonas Moecking
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Karl Gatterdam
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Sarah Tindall
- Department of Biology (Area 10), University of York, York, YO10 5YW, UK
| | - Alexandre Durand
- Institut de Génétique et de Biologie Molecule et Cellulaire, 1 Rue Laurent Fries, 67404, Illkirch Cedex, France
| | - Veronika Heinz
- Institute of Biophysics and Biophysical Chemistry, University of Regensburg, Universitätsstr. 31, 93053, Regensburg, Germany
| | - Jan Peter Siebrasse
- Institute for Physical und Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53127, Bonn, Germany
| | - Paul-Albert Koenig
- Core Facility Nanobodies, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Matthias Geyer
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Christine Ziegler
- Institute of Biophysics and Biophysical Chemistry, University of Regensburg, Universitätsstr. 31, 93053, Regensburg, Germany
| | - Ulrich Kubitscheck
- Institute for Physical und Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53127, Bonn, Germany
| | - Gavin H Thomas
- Department of Biology (Area 10), University of York, York, YO10 5YW, UK
| | - Gregor Hagelueken
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany.
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16
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Müller C, Zhang L, Zipfel S, Topitsch A, Lutz M, Eckert J, Prasser B, Chami M, Lü W, Du J, Einsle O. Molecular interplay of an assembly machinery for nitrous oxide reductase. Nature 2022; 608:626-631. [PMID: 35896743 DOI: 10.1038/s41586-022-05015-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/23/2022] [Indexed: 11/09/2022]
Abstract
Emissions of the critical ozone-depleting and greenhouse gas nitrous oxide (N2O) from soils and industrial processes have increased considerably over the last decades1-3. As the final step of bacterial denitrification, N2O is reduced to chemically inert N2 (refs. 1,4) in a reaction that is catalysed by the copper-dependent nitrous oxide reductase (N2OR) (ref. 5). The assembly of its unique [4Cu:2S] active site cluster CuZ requires both the ATP-binding-cassette (ABC) complex NosDFY and the membrane-anchored copper chaperone NosL (refs. 4,6). Here we report cryo-electron microscopy structures of Pseudomonas stutzeri NosDFY and its complexes with NosL and N2OR, respectively. We find that the periplasmic NosD protein contains a binding site for a Cu+ ion and interacts specifically with NosL in its nucleotide-free state, whereas its binding to N2OR requires a conformational change that is triggered by ATP binding. Mutually exclusive structures of NosDFY in complex with NosL and with N2OR reveal a sequential metal-trafficking and assembly pathway for a highly complex copper site. Within this pathway, NosDFY acts as a mechanical energy transducer rather than as a transporter. It links ATP hydrolysis in the cytoplasm to a conformational transition of the NosD subunit in the periplasm, which is required for NosDFY to switch its interaction partner so that copper ions are handed over from the chaperone NosL to the enzyme N2OR.
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Affiliation(s)
- Christoph Müller
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Lin Zhang
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Sara Zipfel
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Annika Topitsch
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Marleen Lutz
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Johannes Eckert
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Benedikt Prasser
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Mohamed Chami
- BioEM Lab, Biozentrum, Universität Basel, Basel, Switzerland
| | - Wei Lü
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Juan Du
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.
| | - Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.
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17
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Zhao F, Lin X, Cai K, Jiang Y, Ni T, Chen Y, Feng J, Dang S, Zhou CZ, Zeng Q. Biochemical and structural characterization of the cyanophage-encoded phosphate binding protein: implications for enhanced phosphate uptake of infected cyanobacteria. Environ Microbiol 2022; 24:3037-3050. [PMID: 35590460 DOI: 10.1111/1462-2920.16043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 05/07/2022] [Accepted: 05/08/2022] [Indexed: 12/01/2022]
Abstract
To acquire phosphorus, cyanobacteria use the typical bacterial ABC-type phosphate transporter, which is composed of a periplasmic high-affinity phosphate-binding protein PstS and a channel formed by two transmembrane proteins PstC and PstA. A putative pstS gene was identified in the genomes of cyanophages that infect the unicellular marine cyanobacteria Prochlorococcus and Synechococcus. However, it has not been determined whether the cyanophage PstS protein is functional during infection to enhance the phosphate uptake rate of host cells. Here we showed that the cyanophage P-SSM2 PstS protein was abundant in the infected Prochlorococcus NATL2A cells and the host phosphate uptake rate was enhanced after infection. This is consistent with our biochemical and structural analyses showing that the phage PstS protein is indeed a high-affinity phosphate-binding protein. We further modeled the complex structure of phage PstS with host PstCA and revealed three putative interfaces that may facilitate the formation of a chimeric ABC transporter. Our results provide insights into the molecular mechanism by which cyanophages enhance the phosphate uptake rate of cyanobacteria. Phosphate acquisition by infected bacteria can increase the phosphorus contents of released cellular debris and virus particles, which together constitute a significant proportion of the marine dissolved organic phosphorus pool. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Fangxin Zhao
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Xingqin Lin
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Kun Cai
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, 230027, China.,School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - YongLiang Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, 230027, China.,School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Tianchi Ni
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Yue Chen
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Jianrong Feng
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Shangyu Dang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.,Center of Systems Biology and Human Health, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Cong-Zhao Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, 230027, China.,School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Qinglu Zeng
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.,HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Futian, Shenzhen, China
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18
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Internal Transcription Terminators Control Stoichiometry of ABC Transporters in Cellulolytic Clostridia. Microbiol Spectr 2022; 10:e0165621. [PMID: 35286151 PMCID: PMC9045158 DOI: 10.1128/spectrum.01656-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The extracellular substrate-binding proteins (SBPs) of ATP-binding cassette (ABC) importers tend to be expressed in excess relative to their cognate translocators, but how the stoichiometry of ABC transporters is controlled remains unclear. Here, we elucidated a mechanism contributing to differential gene expression in operons encoding ABC importers by employing cellulolytic Clostridia species, specifically Ruminiclostridium cellulolyticum. We found that there were usually stem-loop structures downstream of SBP genes, which could prematurely terminate the transcription of ABC importers and were putative internal intrinsic terminators, resulting in high transcript levels of upstream SBP genes and low transcript levels of downstream cognate translocator genes. This was determined by their termination efficiencies. Internal terminators had a lower U content in their 3′ U-rich tracts and longer GC-rich stems, which distinguishes them from canonical terminators and potentially endows them with special termination efficiencies. The pairing of U-rich tracts and the formation of unpaired regions in these internal terminators contributed to their folding energies, affecting the stability of their upstream SBP transcripts. Our findings revealed a strategy of internal transcriptional terminators controlling in vivo stoichiometry of their flanking transcripts. IMPORTANCE Operons encoding protein complexes or metabolic pathways usually require fine-tuned gene expression ratios to create and maintain the appropriate stoichiometry for biological functions. In this study, a strategy for controlling differential expression of genes in an operon was proposed by utilizing ABC importers from Ruminiclostridium cellulolyticum. We found that a stem-loop structure is introduced into the intergenic regions of operons encoding ABC importers as the putative internal terminator, which results in the premature termination of transcription. Consequently, the stoichiometric ratio of genes flanking terminators is precisely determined by their termination efficiencies and folding energies at the transcriptional level. Thus, it can be utilized as a promising synthetic biology tool to control the differential expression of genes in an operon.
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19
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Aller SG, Segrest JP. The regulatory domains of the lipid exporter ABCA1 form domain swapped latches. PLoS One 2022; 17:e0262746. [PMID: 35120130 PMCID: PMC8815970 DOI: 10.1371/journal.pone.0262746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/04/2022] [Indexed: 12/19/2022] Open
Abstract
ABCA1 and ABCA4 are enigmatic because they transport substrates in opposite directions yet share >50% amino acid identity. ABCA4 imports lipid conjugates but ABCA1 exports lipids. Both hydrolyze ATP to drive transport, and both contain cytoplasmic regulatory domains (RDs) following nucleotide-binding domains (NBDs) in the primary structure. The tertiary structures of several ABC importers, including ABCA4, show that each RD forms a domain-swapped latch that locks onto the opposing RD and holds the NBDs close together. Crucially, sequences encoding the RDs and their bridges are among the most conserved in the entire ABC-A subfamily. In the original cryo-EM structure of ABCA1, the RDs were modeled without crossover. After close inspection of that cryo-EM density map and the recent structure of ABCA4, we propose that the RDs of ABCA1 also form a domain-swapped latch. A refined ABCA1 model containing latches exhibited significantly improved overall protein geometry. Critically, the conserved crossover sequence leading to the RD-domain swap is directly supported by the original cryo-EM density map of ABCA1 and appears to have been overlooked. Our refined ABCA1 model suggests the possibility that ABCA1, despite being an exporter, has highly restrained NBDs that suggest a transport mechanism that is distinct from 'alternating access'.
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Affiliation(s)
- Stephen G. Aller
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Jere P. Segrest
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States of America
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20
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Santhakumar V, Manuel Mascarenhas N. The role of C-terminal helix in the conformational transition of an arginine binding protein. J Struct Biol X 2022; 6:100071. [PMID: 36035778 PMCID: PMC9402392 DOI: 10.1016/j.yjsbx.2022.100071] [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: 04/04/2022] [Accepted: 08/06/2022] [Indexed: 11/27/2022] Open
Abstract
Probe the role of C-ter. helix (CTH) in conformational transition of TmArgBP. Presence of CTH almost doubles the barrier to access the closed-state. In the absence of CTH, the protein can fluctuate between the two conformations. CTH not only constraints the open-state conformation but also guides in accessing it.
The thermotoga maritima arginine binding protein (TmArgBP) is a periplasmic binding protein that has a short helix at the C-terminal end (CTH), which is swapped between the two chains. We apply a coarse-grained structure-based model (SBM) and all-atom MD simulation on this protein to understand the mechanism and the role of CTH in the conformational transition. When the results of SBM simulations of TmArgBP in the presence and absence of CTH are compared, we find that CTH is strategically located at the back of the binding pocket restraining the open-state conformation thereby disengaging access to the closed-state. We also ran all-atom MD simulations of open-state TmArgBP with and without CTH and discovered that in the absence of CTH the protein could reach the closed-state within 250 ns, while in its presence, the protein remained predominantly in its open-state conformation. In the simulation started from unliganded closed-state conformation without CTH, the protein exhibited multiple transitions between the two states, suggesting CTH as an essential structural element to stabilize the open-state conformation. In another simulation that began with an unliganded closed-state conformation with CTH, the protein was able to access the open-state. In this simulation the CTH was observed to reorient itself to interact with the protein emphasizing its role in assisting the conformational change. Based on our findings, we believe that CTH not only acts as a structural element that constraints the protein in its open-state but it may also guide the protein back to its open-state conformation upon ligand unbinding.
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21
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MURATA K, KAWAI S, HASHIMOTO W. Bacteria with a mouth: Discovery and new insights into cell surface structure and macromolecule transport. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2022; 98:529-552. [PMID: 36504195 PMCID: PMC9751261 DOI: 10.2183/pjab.98.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 10/13/2022] [Indexed: 06/17/2023]
Abstract
A bacterium with a "mouth"-like pit structure isolated for the first time in the history of microbiology was a Gram-negative rod, containing glycosphingolipids in the cell envelope, and named Sphingomonas sp. strain A1. The pit was dynamic, with repetitive opening and closing during growth on alginate, and directly included alginate concentrated around the pit, particularly by flagellins, an alginate-binding protein localized on the cell surface. Alginate incorporated into the periplasm was subsequently transferred to the cytoplasm by cooperative interactions of periplasmic solute-binding proteins and an ATP-binding cassette transporter in the cytoplasmic membrane. The mechanisms of assembly, functions, and interactions between the above-mentioned molecules were clarified using structural biology. The pit was transplanted into other strains of sphingomonads, and the pitted recombinant cells were effectively applied to the production of bioethanol, bioremediation for dioxin removal, and other tasks. Studies of the function of the pit shed light on the biological significance of cell surface structures and macromolecule transport in bacteria.
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Affiliation(s)
| | - Shigeyuki KAWAI
- Research Institute for Bioresource and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
| | - Wataru HASHIMOTO
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan
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22
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Hu W, Zheng H. Cryo-EM reveals unique structural features of the FhuCDB Escherichia coli ferrichrome importer. Commun Biol 2021; 4:1383. [PMID: 34887516 PMCID: PMC8660799 DOI: 10.1038/s42003-021-02916-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 11/24/2021] [Indexed: 11/11/2022] Open
Abstract
As one of the most elegant biological processes developed in bacteria, the siderophore-mediated iron uptake demands the action of specific ATP-binding cassette (ABC) importers. Although extensive studies have been done on various ABC importers, the molecular basis of these iron-chelated-siderophore importers are still not fully understood. Here, we report the structure of a ferrichrome importer FhuCDB from Escherichia coli at 3.4 Å resolution determined by cryo electron microscopy. The structure revealed a monomeric membrane subunit of FhuB with a substrate translocation pathway in the middle. In the pathway, there were unique arrangements of residues, especially layers of methionines. Important residues found in the structure were interrogated by mutagenesis and functional studies. Surprisingly, the importer’s ATPase activity was decreased upon FhuD binding, which deviated from the current understanding about bacterial ABC importers. In summary, to the best of our knowledge, these studies not only reveal a new structural twist in the type II ABC importer subfamily, but also provide biological insights in the transport of iron-chelated siderophores. Wenxin Hu et al. use cryo-EM and biochemical assays to describe the functional activity and structure of the ferrichrome importer, FhuCDB in E. coli. Their results provide further insight on the mechanism of siderophore transport in bacteria.
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Affiliation(s)
- Wenxin Hu
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, USA
| | - Hongjin Zheng
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, USA.
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23
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Okumura K, Maruyama Y, Takase R, Mikami B, Murata K, Hashimoto W. The role of calcium binding to the EF-hand-like motif in bacterial solute-binding protein for alginate import. Biosci Biotechnol Biochem 2021; 85:2410-2419. [PMID: 34610097 DOI: 10.1093/bbb/zbab170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 09/23/2021] [Indexed: 11/14/2022]
Abstract
Gram-negative Sphingomonas sp. A1 incorporates acidic polysaccharide alginate into the cytoplasm via a cell-surface alginate-binding protein (AlgQ2)-dependent ATP-binding cassette transporter (AlgM1M2SS). We investigated the function of calcium bound to the EF-hand-like motif in AlgQ2 by introducing mutations at the calcium-binding site. The X-ray crystallography of the AlgQ2 mutant (D179A/E180A) demonstrated the absence of calcium binding and significant disorder of the EF-hand-like motif. Distinct from the wild-type AlgQ2, the mutant was quite unstable at temperature of strain A1 growth, although unsaturated alginate oligosaccharides stabilized the mutant by formation of substrate/protein complex. In the assay of ATPase and alginate transport by AlgM1M2SS reconstructed in the liposome, the wild-type and mutant AlgQ2 induced AlgM1M2SS ATPase activity in the presence of unsaturated alginate tetrasaccharide. These results indicate that the calcium bound to EF-hand-like motif stabilizes the substrate-unbound AlgQ2 but is not required for the complexation of substrate-bound AlgQ2 and AlgM1M2SS.
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Affiliation(s)
- Kenji Okumura
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan
| | - Yukie Maruyama
- Laboratory of Food Microbiology, Department of Life Science, Faculty of Science and Engineering, Setsunan University, Neyagawa, Osaka, Japan
| | - Ryuichi Takase
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan
| | - Bunzo Mikami
- Laboratory of Metabolic Sciences of Forest Plants and Microorganisms, Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto, Japan
| | - Kousaku Murata
- Laboratory of Food Microbiology, Department of Life Science, Faculty of Science and Engineering, Setsunan University, Neyagawa, Osaka, Japan
| | - Wataru Hashimoto
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto, Japan
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24
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Recruitment of the TolA protein to cell constriction sites in Escherichia coli via three separate mechanisms, and a critical role for FtsWI activity in recruitment of both TolA and TolQ. J Bacteriol 2021; 204:e0046421. [PMID: 34748387 DOI: 10.1128/jb.00464-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The Tol-Pal system of Gram-negative bacteria helps maintain integrity of the cell envelope and ensures that invagination of the envelope layers during cell fission occurs in a well-coordinated manner. In E. coli, the five Tol-Pal proteins (TolQ, R, A, B and Pal) accumulate at cell constriction sites in a manner that normally requires the activity of the cell constriction initiation protein FtsN. While septal recruitment of TolR, TolB and Pal also requires the presence of TolQ and/or TolA, each of the the latter two can recognize constriction sites independently of the other system proteins. What attracts TolQ or TolA to these sites is unclear. We show that FtsN attracts both proteins in an indirect fashion, and that PBP1A, PBP1B and CpoB are dispensable for their septal recruitment. However, the β-lactam aztreonam readily interferes with septal accumulation of both TolQ and TolA, indicating that FtsN-stimulated production of septal peptidoglycan by the FtsWI synthase is critical to their recruitment. We also discovered that each of TolA's three domains can recognize division sites in a separate fashion. Notably, the middle domain (TolAII) is responsible for directing TolA to constriction sites in the absence of other Tol-Pal proteins and CpoB, while recruitment of TolAI and TolAIII requires TolQ and a combination of TolB, Pal, and CpoB, respectively. Additionally, we describe the construction and use of functional fluorescent sandwich fusions of the ZipA division protein, which should be more broadly valuable in future studies of the E. coli cell division machinery. IMPORTANCE Cell division (cytokinesis) is a fundamental biological process that is incompletely understood for any organism. Division of bacterial cells relies on a ring-like machinery called the septal ring or divisome that assembles along the circumference of the mother cell at the site where constriction will eventually occur. In the well-studied bacterium Escherichia coli, this machinery contains over thirty distinct proteins. We studied how two such proteins, TolA and TolQ, which also play a role in maintaining integrity of the outer-membrane, are recruited to the machinery. We find that TolA can be recruited by three separate mechanisms, and that both proteins rely on the activity of a well-studied cell division enzyme for their recruitment.
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25
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Guan L, Hariharan P. X-ray crystallography reveals molecular recognition mechanism for sugar binding in a melibiose transporter MelB. Commun Biol 2021; 4:931. [PMID: 34341464 PMCID: PMC8329300 DOI: 10.1038/s42003-021-02462-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 07/07/2021] [Indexed: 12/15/2022] Open
Abstract
Major facilitator superfamily_2 transporters are widely found from bacteria to mammals. The melibiose transporter MelB, which catalyzes melibiose symport with either Na+, Li+, or H+, is a prototype of the Na+-coupled MFS transporters, but its sugar recognition mechanism has been a long-unsolved puzzle. Two high-resolution X-ray crystal structures of a Salmonella typhimurium MelB mutant with a bound ligand, either nitrophenyl-α-d-galactoside or dodecyl-β-d-melibioside, were refined to a resolution of 3.05 or 3.15 Å, respectively. In the substrate-binding site, the interaction of both galactosyl moieties on the two ligands with MelBSt are virturally same, so the sugar specificity determinant pocket can be recognized, and hence the molecular recognition mechanism for sugar binding in MelB has been deciphered. The conserved cation-binding pocket is also proposed, which directly connects to the sugar specificity pocket. These key structural findings have laid a solid foundation for our understanding of the cooperative binding and symport mechanisms in Na+-coupled MFS transporters, including eukaryotic transporters such as MFSD2A. Guan and Hariharan report two crystal structures of melibiose transporter MelB in complex with substrate analogs, nitrophenyl-galactoside, and dodecyl-melibioside. Both structures revealed similar specific site for sugar recognition and resolved the cation-binding pocket, advancing the understanding of MelB and related transporters.
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Affiliation(s)
- Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA.
| | - Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA
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26
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Neville SL, Sjöhamn J, Watts JA, MacDermott-Opeskin H, Fairweather SJ, Ganio K, Carey Hulyer A, McGrath AP, Hayes AJ, Malcolm TR, Davies MR, Nomura N, Iwata S, O'Mara ML, Maher MJ, McDevitt CA. The structural basis of bacterial manganese import. SCIENCE ADVANCES 2021; 7:7/32/eabg3980. [PMID: 34362732 PMCID: PMC8346216 DOI: 10.1126/sciadv.abg3980] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 06/10/2021] [Indexed: 05/23/2023]
Abstract
Metal ions are essential for all forms of life. In prokaryotes, ATP-binding cassette (ABC) permeases serve as the primary import pathway for many micronutrients including the first-row transition metal manganese. However, the structural features of ionic metal transporting ABC permeases have remained undefined. Here, we present the crystal structure of the manganese transporter PsaBC from Streptococcus pneumoniae in an open-inward conformation. The type II transporter has a tightly closed transmembrane channel due to "extracellular gating" residues that prevent water permeation or ion reflux. Below these residues, the channel contains a hitherto unreported metal coordination site, which is essential for manganese translocation. Mutagenesis of the extracellular gate perturbs manganese uptake, while coordination site mutagenesis abolishes import. These structural features are highly conserved in metal-specific ABC transporters and are represented throughout the kingdoms of life. Collectively, our results define the structure of PsaBC and reveal the features required for divalent cation transport.
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Affiliation(s)
- Stephanie L Neville
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jennie Sjöhamn
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Jacinta A Watts
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | | | - Stephen J Fairweather
- Research School of Chemistry, Australian National University, Canberra, ACT, Australia
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Katherine Ganio
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Alex Carey Hulyer
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Aaron P McGrath
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Andrew J Hayes
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Tess R Malcolm
- School of Chemistry and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Mark R Davies
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Norimichi Nomura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - So Iwata
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Research Acceleration Program, Membrane Protein Crystallography Project, Japan Science and Technology Agency, Kyoto, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, Japan
| | - Megan L O'Mara
- Research School of Chemistry, Australian National University, Canberra, ACT, Australia
| | - Megan J Maher
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia.
- School of Chemistry and The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Christopher A McDevitt
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia.
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27
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Yang C, Lu L, Liao L, Zhang B, Zeng M, Zou K, Liu X, Zhang M. Establishment of GC-MS method for the determination of Pseudomonas aeruginosa biofilm and its application in metabolite enrichment analysis. J Chromatogr B Analyt Technol Biomed Life Sci 2021; 1179:122839. [PMID: 34218096 DOI: 10.1016/j.jchromb.2021.122839] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/10/2021] [Accepted: 06/14/2021] [Indexed: 10/21/2022]
Abstract
PA forms a biofilm resistant to antibiotics, hindering antibiotics efficacy and preventing the eradication of PA, has attracted much attention for its biofilm. In this study, we first established and validated an efficient and sensitive gas chromatography-mass spectrometry (GC-MS) method for the quantification of metabolites in biofilm. Decanoic acid was used as the internal standard. The separation of Palmitic acid, stearic acid and Decanoic acid was conducted on an Elite-5 MS column (30 m × 0.25 mm, 0.25 μm) using gradient elution condition at a flow rate of 1 mL/min. Palmitic acid, stearic acid and Decanoic acid were determined under the positive ionization mode, respectively. The calibration curve of Palmitic acid and stearic acid were established in the range of 4 to 128 μg/mL (r2 = 0.999). The recovery of palmitic acid and stearic acid were between 98.76% and 113.91%, RSD < 5%. The well validated method was used to detect the metabolites of Pseudomonas aeruginosa biofilm. 54 metabolites were isolated and identified from biofilm samples, and 7 important signal pathways were identified by KEGG enrichment analysis. ABC transporters and bacterial chemotaxis signaling pathways have an important impact on the growth of PA biofilm among these metabolic pathways. This study provides valuable references for the further study of PA biofilm, especially the change of metabolite content and the search for biomarkers.
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Affiliation(s)
- Chen Yang
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China; Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of pharmacy, Chengdu University, Chengdu, China
| | - Lan Lu
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of pharmacy, Chengdu University, Chengdu, China
| | - Li Liao
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of pharmacy, Chengdu University, Chengdu, China
| | - Bin Zhang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of pharmacy, Chengdu University, Chengdu, China
| | - Min Zeng
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of pharmacy, Chengdu University, Chengdu, China
| | - Kun Zou
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of pharmacy, Chengdu University, Chengdu, China
| | - Xia Liu
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Mei Zhang
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China.
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28
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Itoh T, Yaguchi M, Nakaichi A, Yoda M, Hibi T, Kimoto H. Structural characterization of two solute-binding proteins for N,N'-diacetylchitobiose/ N,N',N''-triacetylchitotoriose of the gram-positive bacterium, Paenibacillus sp. str. FPU-7. J Struct Biol X 2021; 5:100049. [PMID: 34195603 PMCID: PMC8233162 DOI: 10.1016/j.yjsbx.2021.100049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 05/28/2021] [Indexed: 10/27/2022] Open
Abstract
The chitinolytic bacterium Paenibacillus sp. str. FPU-7 efficiently degrades chitin into oligosaccharides such as N-acetyl-D-glucosamine (GlcNAc) and disaccharides (GlcNAc)2 through multiple secretory chitinases. Transport of these oligosaccharides by P. str. FPU-7 has not yet been clarified. In this study, we identified nagB1, predicted to encode a sugar solute-binding protein (SBP), which is a component of the ABC transport system. However, the genes next to nagB1 were predicted to encode two-component regulatory system proteins rather than transmembrane domains (TMDs). We also identified nagB2, which is highly homologous to nagB1. Adjacent to nagB2, two genes were predicted to encode TMDs. Binding experiments of the recombinant NagB1 and NagB2 to several oligosaccharides using differential scanning fluorimetry and surface plasmon resonance confirmed that both proteins are SBPs of (GlcNAc)2 and (GlcNAc)3. We determined their crystal structures complexed with and without chitin oligosaccharides at a resolution of 1.2 to 2.0 Å. The structures shared typical SBP structural folds and were classified as subcluster D-I. Large domain motions were observed in the structures, suggesting that they were induced by ligand binding via the "Venus flytrap" mechanism. These structures also revealed chitin oligosaccharide recognition mechanisms. In conclusion, our study provides insight into the recognition and transport of chitin oligosaccharides in bacteria.
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Key Words
- ABC transporter
- ABC, ATP-binding cassette
- Chitin oligosaccharide
- DSF, differential scanning fluorimetry
- GH, glycoside hydrolase
- GlcN, D-glucosamine
- GlcNAc, N-acetyl-D-glucosamine
- OD600, optical density at 600 nm
- PDB, Protein Data Bank
- PTS, phosphoenolpyruvate phosphotransferase system
- Paenibacillus
- RU, response unit
- SBP, solute binding protein
- Se-Met, selenomethionine
- Solute binding protein
- TMD, transmembrane domain
- Two-component regulatory system
- a.a., amino acid
- r.m.s.d., root mean-square deviation
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Affiliation(s)
- Takafumi Itoh
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuokakenjyoujima, Eiheiji-cho, Yoshida-gun, Fukui 910-1195, Japan
| | - Misaki Yaguchi
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuokakenjyoujima, Eiheiji-cho, Yoshida-gun, Fukui 910-1195, Japan
| | - Akari Nakaichi
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuokakenjyoujima, Eiheiji-cho, Yoshida-gun, Fukui 910-1195, Japan
| | - Moe Yoda
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuokakenjyoujima, Eiheiji-cho, Yoshida-gun, Fukui 910-1195, Japan
| | - Takao Hibi
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuokakenjyoujima, Eiheiji-cho, Yoshida-gun, Fukui 910-1195, Japan
| | - Hisashi Kimoto
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Matsuokakenjyoujima, Eiheiji-cho, Yoshida-gun, Fukui 910-1195, Japan
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29
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Abstract
ATP-binding cassette (ABC) transporters constitute one of the largest and most ancient protein superfamilies found in all living organisms. They function as molecular machines by coupling ATP binding, hydrolysis, and phosphate release to translocation of diverse substrates across membranes. The substrates range from vitamins, steroids, lipids, and ions to peptides, proteins, polysaccharides, and xenobiotics. ABC transporters undergo substantial conformational changes during substrate translocation. A comprehensive understanding of their inner workings thus requires linking these structural rearrangements to the different functional state transitions. Recent advances in single-particle cryogenic electron microscopy have not only delivered crucial information on the architecture of several medically relevant ABC transporters and their supramolecular assemblies, including the ATP-sensitive potassium channel and the peptide-loading complex, but also made it possible to explore the entire conformational space of these nanomachines under turnover conditions and thereby gain detailed mechanistic insights into their mode of action.
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Affiliation(s)
- Christoph Thomas
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany; ,
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany; ,
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30
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Rybenkov VV, Zgurskaya HI, Ganguly C, Leus IV, Zhang Z, Moniruzzaman M. The Whole Is Bigger than the Sum of Its Parts: Drug Transport in the Context of Two Membranes with Active Efflux. Chem Rev 2021; 121:5597-5631. [PMID: 33596653 PMCID: PMC8369882 DOI: 10.1021/acs.chemrev.0c01137] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cell envelope plays a dual role in the life of bacteria by simultaneously protecting it from a hostile environment and facilitating access to beneficial molecules. At the heart of this ability lie the restrictive properties of the cellular membrane augmented by efflux transporters, which preclude intracellular penetration of most molecules except with the help of specialized uptake mediators. Recently, kinetic properties of the cell envelope came into focus driven on one hand by the urgent need in new antibiotics and, on the other hand, by experimental and theoretical advances in studies of transmembrane transport. A notable result from these studies is the development of a kinetic formalism that integrates the Michaelis-Menten behavior of individual transporters with transmembrane diffusion and offers a quantitative basis for the analysis of intracellular penetration of bioactive compounds. This review surveys key experimental and computational approaches to the investigation of transport by individual translocators and in whole cells, summarizes key findings from these studies and outlines implications for antibiotic discovery. Special emphasis is placed on Gram-negative bacteria, whose envelope contains two separate membranes. This feature sets these organisms apart from Gram-positive bacteria and eukaryotic cells by providing them with full benefits of the synergy between slow transmembrane diffusion and active efflux.
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Affiliation(s)
- Valentin V Rybenkov
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Chhandosee Ganguly
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Inga V Leus
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Zhen Zhang
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Mohammad Moniruzzaman
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
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31
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Cryo-EM structure of ABCG5/G8 in complex with modulating antibodies. Commun Biol 2021; 4:526. [PMID: 33953337 PMCID: PMC8100176 DOI: 10.1038/s42003-021-02039-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 03/25/2021] [Indexed: 12/20/2022] Open
Abstract
The heterodimer of ATP-binding cassette transporter ABCG5 and ABCG8 mediates the excretion of sterols from liver and intestine, playing a critical role in cholesterol homeostasis. Here, we present the cryo-EM structure of ABCG5/G8 in complex with the Fab fragments from two monoclonal antibodies at 3.3Å resolution. The high-resolution structure reveals a unique dimer interface between the nucleotide-binding domains (NBD) of opposing transporters, consisting of an ordered network of salt bridges between the conserved NPXDFXXD motif and serving as a pivot point that may be important for the transport cycle. While mAb 11F4 increases the ATPase activity potentially by stabilization of the NBD dimer formation, mAb 2E10 inhibits ATP hydrolysis, likely by restricting the relative movement between the RecA and helical domain of ABCG8 NBD. Our study not only provides insights into the structural elements important for the transport cycle but also reveals novel epitopes for potential therapeutic interventions.
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32
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Khunweeraphong N, Kuchler K. Multidrug Resistance in Mammals and Fungi-From MDR to PDR: A Rocky Road from Atomic Structures to Transport Mechanisms. Int J Mol Sci 2021; 22:4806. [PMID: 33946618 PMCID: PMC8124828 DOI: 10.3390/ijms22094806] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 12/19/2022] Open
Abstract
Multidrug resistance (MDR) can be a serious complication for the treatment of cancer as well as for microbial and parasitic infections. Dysregulated overexpression of several members of the ATP-binding cassette transporter families have been intimately linked to MDR phenomena. Three paradigm ABC transporter members, ABCB1 (P-gp), ABCC1 (MRP1) and ABCG2 (BCRP) appear to act as brothers in arms in promoting or causing MDR in a variety of therapeutic cancer settings. However, their molecular mechanisms of action, the basis for their broad and overlapping substrate selectivity, remains ill-posed. The rapidly increasing numbers of high-resolution atomic structures from X-ray crystallography or cryo-EM of mammalian ABC multidrug transporters initiated a new era towards a better understanding of structure-function relationships, and for the dynamics and mechanisms driving their transport cycles. In addition, the atomic structures offered new evolutionary perspectives in cases where transport systems have been structurally conserved from bacteria to humans, including the pleiotropic drug resistance (PDR) family in fungal pathogens for which high resolution structures are as yet unavailable. In this review, we will focus the discussion on comparative mechanisms of mammalian ABCG and fungal PDR transporters, owing to their close evolutionary relationships. In fact, the atomic structures of ABCG2 offer excellent models for a better understanding of fungal PDR transporters. Based on comparative structural models of ABCG transporters and fungal PDRs, we propose closely related or even conserved catalytic cycles, thus offering new therapeutic perspectives for preventing MDR in infectious disease settings.
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Affiliation(s)
| | - Karl Kuchler
- Center for Medical Biochemistry, Max Perutz Labs Vienna, Campus Vienna Biocenter, Medical University of Vienna, Dr. Bohr-Gasse 9/2, A-1030 Vienna, Austria;
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33
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Choi CC, Ford RC. ATP binding cassette importers in eukaryotic organisms. Biol Rev Camb Philos Soc 2021; 96:1318-1330. [PMID: 33655617 DOI: 10.1111/brv.12702] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 02/21/2021] [Accepted: 02/23/2021] [Indexed: 11/28/2022]
Abstract
ATP-binding cassette (ABC) transporters are ubiquitous across all realms of life. Dogma suggests that bacterial ABC transporters include both importers and exporters, whilst eukaryotic members of this family are solely exporters, implying that ABC import function was lost during evolution. This view is being challenged, for example energy-coupling factor (ECF)-type ABC importers appear to fulfil important roles in both algae and plants where they form the ABCI sub-family. Herein we discuss whether bacterial Type I and Type II ABC importers also made the transition into extant eukaryotes. Various studies suggest that Type I importers exist in algae and the liverwort family of primitive non-vascular plants, but not in higher plants. The existence of eukaryotic Type II importers is also supported: a transmembrane protein homologous to vitamin B12 import system transmembrane protein (BtuC), hemin transport system transmembrane protein (HmuU) and high-affinity zinc uptake system membrane protein (ZnuB) is present in the Cyanophora paradoxa genome. This protein has homologs within the genomes of red algae. Furthermore, its candidate nucleotide-binding domain (NBD) shows closest similarity to other bacterial Type II importer NBDs such as BtuD. Functional studies suggest that Type I importers have roles in maintaining sulphate levels in the chloroplast, whilst Type II importers probably act as importers of Mn2+ or Zn2+ , as inferred by comparisons with bacterial homologs. Possible explanations for the presence of these transporters in simple plants, but not in other eukaryotic organisms, are considered. In order to utilise the existing nomenclature for eukaryotic ABC proteins, we propose that eukaryotic Type I and II importers be classified as ABCJ and ABCK transporters, respectively.
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Affiliation(s)
- Cheri C Choi
- Faculty of Biology Medicine and Health, School of Biological Sciences, The University of Manchester, Oxford Road, Manchester, M13 9PL, U.K.,Department of Biology, University of York, York, YO10 5DD, U.K
| | - Robert C Ford
- Faculty of Biology Medicine and Health, School of Biological Sciences, The University of Manchester, Oxford Road, Manchester, M13 9PL, U.K
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34
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Liu F, Lee J, Chen J. Molecular structures of the eukaryotic retinal importer ABCA4. eLife 2021; 10:63524. [PMID: 33605212 PMCID: PMC7932691 DOI: 10.7554/elife.63524] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 02/18/2021] [Indexed: 12/20/2022] Open
Abstract
The ATP-binding cassette (ABC) transporter family contains thousands of members with diverse functions. Movement of the substrate, powered by ATP hydrolysis, can be outward (export) or inward (import). ABCA4 is a eukaryotic importer transporting retinal to the cytosol to enter the visual cycle. It also removes toxic retinoids from the disc lumen. Mutations in ABCA4 cause impaired vision or blindness. Despite decades of clinical, biochemical, and animal model studies, the molecular mechanism of ABCA4 is unknown. Here, we report the structures of human ABCA4 in two conformations. In the absence of ATP, ABCA4 adopts an outward-facing conformation, poised to recruit substrate. The presence of ATP induces large conformational changes that could lead to substrate release. These structures provide a molecular basis to understand many disease-causing mutations and a rational guide for new experiments to uncover how ABCA4 recruits, flips, and releases retinoids.
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Affiliation(s)
- Fangyu Liu
- Laboratory of Membrane Biology and Biophysics, The Rockefeller University, New York, United States.,Tri-Institutional Training Program in Chemical Biology, New York, United States
| | - James Lee
- Laboratory of Membrane Biology and Biophysics, The Rockefeller University, New York, United States
| | - Jue Chen
- Laboratory of Membrane Biology and Biophysics, The Rockefeller University, New York, United States.,Howard Hughes Medical Institute, Chevy Chase, United States
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35
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Amuc_1102 from Akkermansia muciniphila adopts an immunoglobulin-like fold related to archaeal type IV pilus. Biochem Biophys Res Commun 2021; 547:59-64. [PMID: 33592380 DOI: 10.1016/j.bbrc.2021.02.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 02/05/2021] [Indexed: 11/23/2022]
Abstract
Akkermansia muciniphila is a kind of beneficial microorganism colonized in the human gut. A. muciniphila is closely related to human intestinal health and has a good effect on diseases related to intestinal metabolism. The proteins encoded by the Amuc_1098-Amuc_1102 gene cluster, which are related to the formation and assembly of the pilus, are highly expressed in the membrane protein components of A. muciniphila. In this paper, we report the crystal structure of Amuc_1102 at a resolution of 1.75 Å, which adopts an immunoglobulin (Ig)-like fold. Amuc_1102 shares a similar fold to three archaeal proteins related to type IV pilus (T4P)-like structure, Pilin, FlaF, and FlaG, indicating a similar function. Amuc_1102 exists as a trimer both in the crystal structure and in solution, which differs from the assemblies of Pilin, FlaF, and FlaG. This study provides a structural basis for the elucidation of the T4P formation of A. muciniphila.
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36
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Peter MF, Gebhardt C, Glaenzer J, Schneberger N, de Boer M, Thomas GH, Cordes T, Hagelueken G. Triggering Closure of a Sialic Acid TRAP Transporter Substrate Binding Protein through Binding of Natural or Artificial Substrates. J Mol Biol 2021; 433:166756. [PMID: 33316271 DOI: 10.1016/j.jmb.2020.166756] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/07/2020] [Accepted: 12/07/2020] [Indexed: 12/20/2022]
Abstract
The pathogens Vibrio cholerae and Haemophilus influenzae use tripartite ATP-independent periplasmic transporters (TRAPs) to scavenge sialic acid from host tissues. They use it as a nutrient or to evade the innate immune system by sialylating surface lipopolysaccharides. An essential component of TRAP transporters is a periplasmic substrate binding protein (SBP). Without substrate, the SBP has been proposed to rest in an open-state, which is not recognised by the transporter. Substrate binding induces a conformational change of the SBP and it is thought that this closed state is recognised by the transporter, triggering substrate translocation. Here we use real time single molecule FRET experiments and crystallography to investigate the open- to closed-state transition of VcSiaP, the SBP of the sialic acid TRAP transporter from V. cholerae. We show that the conformational switching of VcSiaP is strictly substrate induced, confirming an important aspect of the proposed transport mechanism. Two new crystal structures of VcSiaP provide insights into the closing mechanism. While the first structure contains the natural ligand, sialic acid, the second structure contains an artificial peptide in the sialic acid binding site. Together, the two structures suggest that the ligand itself stabilises the closed state and that SBP closure is triggered by physically bridging the gap between the two lobes of the SBP. Finally, we demonstrate that the affinity for the artificial peptide substrate can be substantially increased by varying its amino acid sequence and by this, serve as a starting point for the development of peptide-based inhibitors of TRAP transporters.
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Affiliation(s)
- Martin F Peter
- Institute of Structural Biology, University of Bonn, 53127 Bonn, Germany
| | - Christian Gebhardt
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Janin Glaenzer
- Institute of Structural Biology, University of Bonn, 53127 Bonn, Germany
| | - Niels Schneberger
- Institute of Structural Biology, University of Bonn, 53127 Bonn, Germany
| | - Marijn de Boer
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Gavin H Thomas
- Department of Biology (Area 10), University of York, York YO10 5YW, UK
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany; Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Gregor Hagelueken
- Institute of Structural Biology, University of Bonn, 53127 Bonn, Germany.
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37
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Li F, Egea PF, Vecchio AJ, Asial I, Gupta M, Paulino J, Bajaj R, Dickinson MS, Ferguson-Miller S, Monk BC, Stroud RM. Highlighting membrane protein structure and function: A celebration of the Protein Data Bank. J Biol Chem 2021; 296:100557. [PMID: 33744283 PMCID: PMC8102919 DOI: 10.1016/j.jbc.2021.100557] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 02/10/2021] [Accepted: 03/16/2021] [Indexed: 12/13/2022] Open
Abstract
Biological membranes define the boundaries of cells and compartmentalize the chemical and physical processes required for life. Many biological processes are carried out by proteins embedded in or associated with such membranes. Determination of membrane protein (MP) structures at atomic or near-atomic resolution plays a vital role in elucidating their structural and functional impact in biology. This endeavor has determined 1198 unique MP structures as of early 2021. The value of these structures is expanded greatly by deposition of their three-dimensional (3D) coordinates into the Protein Data Bank (PDB) after the first atomic MP structure was elucidated in 1985. Since then, free access to MP structures facilitates broader and deeper understanding of MPs, which provides crucial new insights into their biological functions. Here we highlight the structural and functional biology of representative MPs and landmarks in the evolution of new technologies, with insights into key developments influenced by the PDB in magnifying their impact.
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Affiliation(s)
- Fei Li
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA; Department of Neurology, University of California San Francisco, San Francisco, California, USA
| | - Pascal F Egea
- Department of Biological Chemistry, School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Alex J Vecchio
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | | | - Meghna Gupta
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Joana Paulino
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Ruchika Bajaj
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA
| | - Miles Sasha Dickinson
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Shelagh Ferguson-Miller
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Brian C Monk
- Sir John Walsh Research Institute and Department of Oral Sciences, University of Otago, North Dunedin, Dunedin, New Zealand
| | - Robert M Stroud
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA.
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38
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Setyawati I, Stanek WK, Majsnerowska M, Swier LJYM, Pardon E, Steyaert J, Guskov A, Slotboom DJ. In vitro reconstitution of dynamically interacting integral membrane subunits of energy-coupling factor transporters. eLife 2020; 9:64389. [PMID: 33350937 PMCID: PMC7755397 DOI: 10.7554/elife.64389] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/02/2020] [Indexed: 01/03/2023] Open
Abstract
Energy-coupling factor (ECF) transporters mediate import of micronutrients in prokaryotes. They consist of an integral membrane S-component (that binds substrate) and ECF module (that powers transport by ATP hydrolysis). It has been proposed that different S-components compete for docking onto the same ECF module, but a minimal liposome-reconstituted system, required to substantiate this idea, is lacking. Here, we co-reconstituted ECF transporters for folate (ECF-FolT2) and pantothenate (ECF-PanT) into proteoliposomes, and assayed for crosstalk during active transport. The kinetics of transport showed that exchange of S-components is part of the transport mechanism. Competition experiments suggest much slower substrate association with FolT2 than with PanT. Comparison of a crystal structure of ECF-PanT with previously determined structures of ECF-FolT2 revealed larger conformational changes upon binding of folate than pantothenate, which could explain the kinetic differences. Our work shows that a minimal in vitro system with two reconstituted transporters recapitulates intricate kinetics behaviour observed in vivo.
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Affiliation(s)
- Inda Setyawati
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands.,Biochemistry Department, Bogor Agricultural University, Bogor, Indonesia
| | - Weronika K Stanek
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Maria Majsnerowska
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Lotteke J Y M Swier
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel, VUB, Brussels, Belgium.,VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel, VUB, Brussels, Belgium.,VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Albert Guskov
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands.,Moscow Institute of Physics and Technology, Dolgoprudny, Russian Federation
| | - Dirk J Slotboom
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
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39
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Fostier CR, Monlezun L, Ousalem F, Singh S, Hunt JF, Boël G. ABC-F translation factors: from antibiotic resistance to immune response. FEBS Lett 2020; 595:675-706. [PMID: 33135152 DOI: 10.1002/1873-3468.13984] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 12/24/2022]
Abstract
Energy-dependent translational throttle A (EttA) from Escherichia coli is a paradigmatic ABC-F protein that controls the first step in polypeptide elongation on the ribosome according to the cellular energy status. Biochemical and structural studies have established that ABC-F proteins generally function as translation factors that modulate the conformation of the peptidyl transferase center upon binding to the ribosomal tRNA exit site. These factors, present in both prokaryotes and eukaryotes but not in archaea, use related molecular mechanisms to modulate protein synthesis for heterogenous purposes, ranging from antibiotic resistance and rescue of stalled ribosomes to modulation of the mammalian immune response. Here, we review the canonical studies characterizing the phylogeny, regulation, ribosome interactions, and mechanisms of action of the bacterial ABC-F proteins, and discuss the implications of these studies for the molecular function of eukaryotic ABC-F proteins, including the three human family members.
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Affiliation(s)
- Corentin R Fostier
- UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
| | - Laura Monlezun
- UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
| | - Farès Ousalem
- UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
| | - Shikha Singh
- Department of Biological Sciences, 702A Sherman Fairchild Center, Columbia University, New York, NY, USA
| | - John F Hunt
- Department of Biological Sciences, 702A Sherman Fairchild Center, Columbia University, New York, NY, USA
| | - Grégory Boël
- UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
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40
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Nethathe B, Abera A, Naidoo V. Expression and phylogeny of multidrug resistance protein 2 and 4 in African white backed vulture (Gyps africanus). PeerJ 2020; 8:e10422. [PMID: 33344079 PMCID: PMC7718797 DOI: 10.7717/peerj.10422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 11/02/2020] [Indexed: 11/20/2022] Open
Abstract
Diclofenac toxicity in old world vultures is well described in the literature by both the severity of the toxicity induced and the speed of death. While the mechanism of toxicity remains unknown at present, the necropsy signs of gout suggests primary renal involvement at the level of the uric acid excretory pathways. From information in the chicken and man, uric acid excretion is known to be a complex process that involves a combination of glomerular filtration and active tubular excretion. For the proximal convoluted tubules excretion occurs as a two-step process with the basolateral cell membrane using the organic anion transporters and the apical membrane using the multidrug resistant protein to transport uric acid from the blood into the tubular fluid. With uric acid excretion seemingly inhibited by diclofenac, it becomes important to characterize these transporter mechanism at the species level. With no information being available on the molecular characterization/expression of MRPs of Gyps africanus, for this study we used next generation sequencing, and Sanger sequencing on the renal tissue of African white backed vulture (AWB), as the first step to establish if the MRPs gene are expressed in AWB. In silico analysis was conducted using different software to ascertain the function of the latter genes. The sequencing results revealed that the MRP2 and MRP4 are expressed in AWB vultures. Phylogeny of avian MRPs genes confirms that vultures and eagles are closely related, which could be attributed to having the same ancestral genes and foraging behavior. In silico analysis confirmed the transcribed proteins would transports anionic compounds and glucose.
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Affiliation(s)
- Bono Nethathe
- Department of Paraclinical Science, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, Pretoria, South Africa.,Department of Food Science and Technology, University of Venda, Thohoyandou, Limpopo, South Africa
| | - Aron Abera
- Inqaba Biotechnology, Sunnyside, Pretoria, South Africa
| | - Vinny Naidoo
- Department of Paraclinical Science, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, Pretoria, South Africa
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41
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Liu X, Biboy J, Consoli E, Vollmer W, den Blaauwen T. MreC and MreD balance the interaction between the elongasome proteins PBP2 and RodA. PLoS Genet 2020; 16:e1009276. [PMID: 33370261 PMCID: PMC7793260 DOI: 10.1371/journal.pgen.1009276] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 01/08/2021] [Accepted: 11/12/2020] [Indexed: 12/23/2022] Open
Abstract
Rod-shape of most bacteria is maintained by the elongasome, which mediates the synthesis and insertion of peptidoglycan into the cylindrical part of the cell wall. The elongasome contains several essential proteins, such as RodA, PBP2, and the MreBCD proteins, but how its activities are regulated remains poorly understood. Using E. coli as a model system, we investigated the interactions between core elongasome proteins in vivo. Our results show that PBP2 and RodA form a complex mediated by their transmembrane and periplasmic parts and independent of their catalytic activity. MreC and MreD also interact directly with PBP2. MreC elicits a change in the interaction between PBP2 and RodA, which is suppressed by MreD. The cytoplasmic domain of PBP2 is required for this suppression. We hypothesize that the in vivo measured PBP2-RodA interaction change induced by MreC corresponds to the conformational change in PBP2 as observed in the MreC-PBP2 crystal structure, which was suggested to be the "on state" of PBP2. Our results indicate that the balance between MreC and MreD determines the activity of PBP2, which could open new strategies for antibiotic drug development.
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Affiliation(s)
- Xiaolong Liu
- Bacterial Cell Biology & Physiology, Swammerdam Institute for Life Science, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - Jacob Biboy
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Elisa Consoli
- Bacterial Cell Biology & Physiology, Swammerdam Institute for Life Science, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Tanneke den Blaauwen
- Bacterial Cell Biology & Physiology, Swammerdam Institute for Life Science, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
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42
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Thomas C, Aller SG, Beis K, Carpenter EP, Chang G, Chen L, Dassa E, Dean M, Duong Van Hoa F, Ekiert D, Ford R, Gaudet R, Gong X, Holland IB, Huang Y, Kahne DK, Kato H, Koronakis V, Koth CM, Lee Y, Lewinson O, Lill R, Martinoia E, Murakami S, Pinkett HW, Poolman B, Rosenbaum D, Sarkadi B, Schmitt L, Schneider E, Shi Y, Shyng SL, Slotboom DJ, Tajkhorshid E, Tieleman DP, Ueda K, Váradi A, Wen PC, Yan N, Zhang P, Zheng H, Zimmer J, Tampé R. Structural and functional diversity calls for a new classification of ABC transporters. FEBS Lett 2020; 594:3767-3775. [PMID: 32978974 PMCID: PMC8386196 DOI: 10.1002/1873-3468.13935] [Citation(s) in RCA: 154] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 08/19/2020] [Accepted: 09/08/2020] [Indexed: 12/16/2022]
Abstract
Members of the ATP-binding cassette (ABC) transporter superfamily translocate a broad spectrum of chemically diverse substrates. While their eponymous ATP-binding cassette in the nucleotide-binding domains (NBDs) is highly conserved, their transmembrane domains (TMDs) forming the translocation pathway exhibit distinct folds and topologies, suggesting that during evolution the ancient motor domains were combined with different transmembrane mechanical systems to orchestrate a variety of cellular processes. In recent years, it has become increasingly evident that the distinct TMD folds are best suited to categorize the multitude of ABC transporters. We therefore propose a new ABC transporter classification that is based on structural homology in the TMDs.
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Affiliation(s)
- Christoph Thomas
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Germany
| | - Stephen G Aller
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, AL, USA
| | - Konstantinos Beis
- Department of Life Sciences, Imperial College London, London South Kensington, UK
- Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, UK
| | | | - Geoffrey Chang
- Skaggs School of Pharmacy and Pharmaceutical Sciences and Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Lei Chen
- State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Elie Dassa
- Institut Pasteur, Paris Cedex 15, France
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Gaithersburg, MD, USA
| | - Franck Duong Van Hoa
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Damian Ekiert
- Department of Cell Biology and Department of Microbiology, New York University School of Medicine, NY, USA
| | - Robert Ford
- Faculty of Biology, Medicine and Health, The University of Manchester, UK
| | - Rachelle Gaudet
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Xin Gong
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - I Barry Holland
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Sud, Orsay, France
| | - Yihua Huang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Daniel K Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Hiroaki Kato
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Japan
| | | | | | - Youngsook Lee
- Division of Integrative Bioscience and Biotechnology, POSTECH, Pohang, Korea
| | - Oded Lewinson
- Department of Biochemistry, The Bruce and Ruth Rappaport Faculty of Medicine, The Technion-Israel Institute of Technology, Haifa, Israel
| | - Roland Lill
- Institut für Zytobiologie, Philipps-Universität Marburg, Germany
| | - Enrico Martinoia
- Department of Plant and Microbial Biology, University Zurich, Switzerland
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, China
| | - Satoshi Murakami
- Department of Life Science, Tokyo Institute of Technology, Yokohama, Japan
| | - Heather W Pinkett
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Bert Poolman
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
| | - Daniel Rosenbaum
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Balazs Sarkadi
- Institute of Enzymology, Research Center for Natural Sciences (RCNS), Budapest, Hungary
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Erwin Schneider
- Department of Biology/Microbial Physiology, Humboldt-University of Berlin, Germany
| | - Yigong Shi
- Institute of Biology, Westlake Institute for Advanced Study, School of Life Sciences, Westlake University, Hangzhou, China
| | - Show-Ling Shyng
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR, USA
| | - Dirk J Slotboom
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
| | - Emad Tajkhorshid
- Department of Biochemistry, Center for Biophysics and Quantitative Biology, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, IL, USA
| | - D Peter Tieleman
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, AB, Canada
| | - Kazumitsu Ueda
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), KUIAS, Kyoto University, Japan
| | - András Váradi
- Institute of Enzymology, Research Center for Natural Sciences (RCNS), Budapest, Hungary
| | - Po-Chao Wen
- Department of Biochemistry, Center for Biophysics and Quantitative Biology, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, IL, USA
| | - Nieng Yan
- Department of Molecular Biology, Princeton University, NJ, USA
| | - Peng Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Hongjin Zheng
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Jochen Zimmer
- Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Germany
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43
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Khunweeraphong N, Kuchler K. The first intracellular loop is essential for the catalytic cycle of the human ABCG2 multidrug resistance transporter. FEBS Lett 2020; 594:4059-4075. [PMID: 33169382 PMCID: PMC7756363 DOI: 10.1002/1873-3468.13994] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 09/03/2020] [Indexed: 12/16/2022]
Abstract
The human multidrug transporter ABCG2 is required for physiological detoxification and mediates anticancer drug resistance. Here, we identify pivotal residues in the first intracellular loop (ICL1), constituting an intrinsic part of the transmission interface. The architecture includes a triple helical bundle formed by the hot spot helix of the nucleotide‐binding domain, the elbow helix, and ICL1. We show here that the highly conserved ICL1 residues G462, Y463, and Y464 are essential for the proper cross talk of the closed nucleotide‐binding domain dimer with the transmembrane domains. Hence, ICL1 acts as a molecular spring, triggering the conformational switch of ABCG2 before substrate extrusion. These data suggest that the ABCG2 transmission interface may offer therapeutic options for the treatment of drug‐resistant malignancies.
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Affiliation(s)
- Narakorn Khunweeraphong
- Max Perutz Labs Vienna, Center for Medical Biochemistry, Campus Vienna Biocenter, Medical University of Vienna, Austria.,St. Anna Children's Cancer Research Institute-CCRI, Vienna, Austria
| | - Karl Kuchler
- Max Perutz Labs Vienna, Center for Medical Biochemistry, Campus Vienna Biocenter, Medical University of Vienna, Austria
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44
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Srikant S. Evolutionary history of ATP-binding cassette proteins. FEBS Lett 2020; 594:3882-3897. [PMID: 33145769 DOI: 10.1002/1873-3468.13985] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 10/01/2020] [Accepted: 10/15/2020] [Indexed: 12/11/2022]
Abstract
ATP-binding cassette (ABC) proteins are found in every sequenced genome and evolved deep in the phylogenetic tree of life. ABC proteins form one of the largest homologous protein families, with most being involved in substrate transport across biological membranes, and a few cytoplasmic members regulating in essential processes like translation. The predominant ABC protein classification scheme is derived from human members, but the increasing number of fully sequenced genomes permits to reevaluate this paradigm in the light of the evolutionary history the ABC-protein superfamily. As we study the diversity of substrates, mechanisms, and physiological roles of ABC proteins, knowledge of the evolutionary relationships highlights similarities and differences that can be attributed to specific branches in protein divergence. While alignments and trees built on natural sequence variation account for the evolutionary divergence of ABC proteins, high-throughput experiments and next-generation sequencing creating experimental sequence variation are instrumental in identifying functional constraints. The combination of natural and experimentally produced sequence variation allows a broader and more rational study of the function and physiological roles of ABC proteins.
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Affiliation(s)
- Sriram Srikant
- Department of Biology, Massachusetts Institute of Technology
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45
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Lewinson O, Orelle C, Seeger MA. Structures of ABC transporters: handle with care. FEBS Lett 2020; 594:3799-3814. [PMID: 33098660 PMCID: PMC7756565 DOI: 10.1002/1873-3468.13966] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/22/2020] [Accepted: 10/15/2020] [Indexed: 12/11/2022]
Abstract
In the past two decades, the ATP‐binding cassette (ABC) transporters' field has undergone a structural revolution. The importance of structural biology to the development of the field of ABC transporters cannot be overstated, as the ensemble of structures not only revealed the architecture of ABC transporters but also shaped our mechanistic view of these remarkable molecular machines. Nevertheless, we advocate that the mechanistic interpretation of the structures is not trivial and should be carried out with prudence. Herein, we bring several examples of structures of ABC transporters that merit re‐interpretation via careful comparison to experimental data. We propose that it is of the upmost importance to place new structures within the context of the available experimental data.
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Affiliation(s)
- Oded Lewinson
- Department of Molecular Microbiology and the Rappaport Institute for Medical Sciences, Faculty of Medicine, The Technion-Israel Institute of Technology, Haifa, Israel
| | - Cédric Orelle
- CNRS, Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), University of Lyon, Lyon, France
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
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46
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Multitask ATPases (NBDs) of bacterial ABC importers type I and their interspecies exchangeability. Sci Rep 2020; 10:19564. [PMID: 33177617 PMCID: PMC7658222 DOI: 10.1038/s41598-020-76444-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 10/22/2020] [Indexed: 12/30/2022] Open
Abstract
ATP-binding cassette (ABC) type I importers are widespread in bacteria and play a crucial role in its survival and pathogenesis. They share the same modular architecture comprising two intracellular nucleotide-binding domains (NBDs), two transmembrane domains (TMDs) and a substrate-binding protein. The NBDs bind and hydrolyze ATP, thereby generating conformational changes that are coupled to the TMDs and lead to substrate translocation. A group of multitask NBDs that are able to serve as the cellular motor for multiple sugar importers was recently discovered. To understand why some ABC importers share energy-coupling components, we used the MsmX ATPase from Bacillus subtilis as a model for biological and structural studies. Here we report the first examples of functional hybrid interspecies ABC type I importers in which the NBDs could be exchanged. Furthermore, the first crystal structure of an assigned multitask NBD provides a framework to understand the molecular basis of the broader specificity of interaction with the TMDs.
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47
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Sikkema HR, van den Noort M, Rheinberger J, de Boer M, Krepel ST, Schuurman-Wolters GK, Paulino C, Poolman B. Gating by ionic strength and safety check by cyclic-di-AMP in the ABC transporter OpuA. SCIENCE ADVANCES 2020; 6:6/47/eabd7697. [PMID: 33208376 PMCID: PMC7673798 DOI: 10.1126/sciadv.abd7697] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 10/01/2020] [Indexed: 05/02/2023]
Abstract
(Micro)organisms are exposed to fluctuating environmental conditions, and adaptation to stress is essential for survival. Increased osmolality (hypertonicity) causes outflow of water and loss of turgor and is dangerous if the cell is not capable of rapidly restoring its volume. The osmoregulatory adenosine triphosphate-binding cassette transporter OpuA restores the cell volume by accumulating large amounts of compatible solute. OpuA is gated by ionic strength and inhibited by the second messenger cyclic-di-AMP, a molecule recently shown to affect many cellular processes. Despite the master regulatory role of cyclic-di-AMP, structural and functional insights into how the second messenger regulates (transport) proteins on the molecular level are lacking. Here, we present high-resolution cryo-electron microscopy structures of OpuA and in vitro activity assays that show how the osmoregulator OpuA is activated by high ionic strength and how cyclic-di-AMP acts as a backstop to prevent unbridled uptake of compatible solutes.
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Affiliation(s)
- Hendrik R Sikkema
- Department of Biochemistry, Membrane Enzymology Group, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
| | - Marco van den Noort
- Department of Biochemistry, Membrane Enzymology Group, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
| | - Jan Rheinberger
- Department of Biochemistry, Structural Biology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
| | - Marijn de Boer
- Department of Biochemistry, Membrane Enzymology Group, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
| | - Sabrina T Krepel
- Department of Biochemistry, Membrane Enzymology Group, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
| | - Gea K Schuurman-Wolters
- Department of Biochemistry, Membrane Enzymology Group, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
| | - Cristina Paulino
- Department of Biochemistry, Structural Biology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands.
| | - Bert Poolman
- Department of Biochemistry, Membrane Enzymology Group, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands.
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48
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Khunweeraphong N, Mitchell-White J, Szöllősi D, Hussein T, Kuchler K, Kerr ID, Stockner T, Lee JY. Picky ABCG5/G8 and promiscuous ABCG2 - a tale of fatty diets and drug toxicity. FEBS Lett 2020; 594:4035-4058. [PMID: 32978801 PMCID: PMC7756502 DOI: 10.1002/1873-3468.13938] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 09/03/2020] [Indexed: 12/20/2022]
Abstract
Structural data on ABCG5/G8 and ABCG2 reveal a unique molecular architecture for subfamily G ATP‐binding cassette (ABCG) transporters and disclose putative substrate‐binding sites. ABCG5/G8 and ABCG2 appear to use several unique structural motifs to execute transport, including the triple helical bundles, the membrane‐embedded polar relay, the re‐entry helices, and a hydrophobic valve. Interestingly, ABCG2 shows extreme substrate promiscuity, whereas ABCG5/G8 transports only sterol molecules. ABCG2 structures suggest a large internal cavity, serving as a binding region for substrates and inhibitors, while mutational and pharmacological analyses support the notion of multiple binding sites. By contrast, ABCG5/G8 shows a collapsed cavity of insufficient size to hold substrates. Indeed, mutational analyses indicate a sterol‐binding site at the hydrophobic interface between the transporter and the lipid bilayer. In this review, we highlight key differences and similarities between ABCG2 and ABCG5/G8 structures. We further discuss the relevance of distinct and shared structural features in the context of their physiological functions. Finally, we elaborate on how ABCG2 and ABCG5/G8 could pave the way for studies on other ABCG transporters.
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Affiliation(s)
- Narakorn Khunweeraphong
- Max Perutz Labs Vienna, Campus Vienna Biocenter, Center for Medical Biochemistry, Medical University of Vienna, Vienna, Austria.,CCRI-St. Anna Children's Cancer Research Institute, Vienna, Austria
| | - James Mitchell-White
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, UK
| | - Dániel Szöllősi
- Center for Physiology and Pharmacology, Institute of Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Toka Hussein
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Karl Kuchler
- Max Perutz Labs Vienna, Campus Vienna Biocenter, Center for Medical Biochemistry, Medical University of Vienna, Vienna, Austria
| | - Ian D Kerr
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, UK
| | - Thomas Stockner
- Center for Physiology and Pharmacology, Institute of Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Jyh-Yeuan Lee
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
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49
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Goda K, Dönmez-Cakil Y, Tarapcsák S, Szalóki G, Szöllősi D, Parveen Z, Türk D, Szakács G, Chiba P, Stockner T. Human ABCB1 with an ABCB11-like degenerate nucleotide binding site maintains transport activity by avoiding nucleotide occlusion. PLoS Genet 2020; 16:e1009016. [PMID: 33031417 PMCID: PMC7544095 DOI: 10.1371/journal.pgen.1009016] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 07/29/2020] [Indexed: 11/28/2022] Open
Abstract
Several ABC exporters carry a degenerate nucleotide binding site (NBS) that is unable to hydrolyze ATP at a rate sufficient for sustaining transport activity. A hallmark of a degenerate NBS is the lack of the catalytic glutamate in the Walker B motif in the nucleotide binding domain (NBD). The multidrug resistance transporter ABCB1 (P-glycoprotein) has two canonical NBSs, and mutation of the catalytic glutamate E556 in NBS1 renders ABCB1 transport-incompetent. In contrast, the closely related bile salt export pump ABCB11 (BSEP), which shares 49% sequence identity with ABCB1, naturally contains a methionine in place of the catalytic glutamate. The NBD-NBD interfaces of ABCB1 and ABCB11 differ only in four residues, all within NBS1. Mutation of the catalytic glutamate in ABCB1 results in the occlusion of ATP in NBS1, leading to the arrest of the transport cycle. Here we show that despite the catalytic glutamate mutation (E556M), ABCB1 regains its ATP-dependent transport activity, when three additional diverging residues are also replaced. Molecular dynamics simulations revealed that the rescue of ATPase activity is due to the modified geometry of NBS1, resulting in a weaker interaction with ATP, which allows the quadruple mutant to evade the conformationally locked pre-hydrolytic state to proceed to ATP-driven transport. In summary, we show that ABCB1 can be transformed into an active transporter with only one functional catalytic site by preventing the formation of the ATP-locked pre-hydrolytic state in the non-canonical site. ABC transporters are one of the largest membrane protein superfamilies, present in all organisms from archaea to humans. They transport a wide range of molecules including amino acids, sugars, vitamins, nucleotides, peptides, lipids, metabolites, antibiotics, and xenobiotics. ABC transporters energize substrate transport by hydrolyzing ATP in two symmetrically arranged nucleotide binding sites (NBSs). The human multidrug resistance transporter ABCB1 has two active NBSs, and it is generally believed that integrity and cooperation of both sites are needed for transport. Several human ABC transporters, such as the bile salt transporter ABCB11, have one degenerate NBS, which has significantly reduced ATPase activity. Interestingly, unilateral mutations affecting one of the two NBSs completely abolish the function of symmetrical ABC transporters. Here we engineered an ABCB1 variant with a degenerate, ABCB11-like NBS1, which can nevertheless transport substrates. Our results indicate that ABCB1 can mediate active transport with a single active site, questioning the validity of models assuming strictly alternating catalysis.
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Affiliation(s)
- Katalin Goda
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem tér, Debrecen, Hungary
| | - Yaprak Dönmez-Cakil
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Waehringerstrasse, Vienna, Austria
- Department of Histology and Embryology, Faculty of Medicine, Maltepe University, Maltepe, Istanbul, Turkey
| | - Szabolcs Tarapcsák
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem tér, Debrecen, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, Egyetem tér, Debrecen, Hungary
| | - Gábor Szalóki
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem tér, Debrecen, Hungary
| | - Dániel Szöllősi
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Waehringerstrasse, Vienna, Austria
| | - Zahida Parveen
- Institute of Medical Chemistry, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Waehringerstrasse, Vienna, Austria
- Department of Biochemistry, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Dóra Türk
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok körútja, Budapest, Hungary
| | - Gergely Szakács
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar Tudósok körútja, Budapest, Hungary
- Institute of Cancer Research, Medical University of Vienna, Borschkegasse, Vienna, Austria
| | - Peter Chiba
- Institute of Medical Chemistry, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Waehringerstrasse, Vienna, Austria
- * E-mail: (PC); (TS)
| | - Thomas Stockner
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Waehringerstrasse, Vienna, Austria
- * E-mail: (PC); (TS)
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50
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Liu F, Liang J, Zhang B, Gao Y, Yang X, Hu T, Yang H, Xu W, Guddat LW, Rao Z. Structural basis of trehalose recycling by the ABC transporter LpqY-SugABC. SCIENCE ADVANCES 2020; 6:6/44/eabb9833. [PMID: 33127676 PMCID: PMC7608808 DOI: 10.1126/sciadv.abb9833] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 09/10/2020] [Indexed: 05/04/2023]
Abstract
In bacteria, adenosine 5'-triphosphate (ATP)-binding cassette (ABC) importers are essential for the uptake of nutrients including the nonreducing disaccharide trehalose, a metabolite that is crucial for the survival and virulence of several human pathogens including Mycobacterium tuberculosis SugABC is an ABC transporter that translocates trehalose from the periplasmic lipoprotein LpqY into the cytoplasm of mycobacteria. Here, we report four high-resolution cryo-electron microscopy structures of the mycobacterial LpqY-SugABC complex to reveal how it binds and passes trehalose through the membrane to the cytoplasm. A unique feature observed in this system is the initial mode of capture of the trehalose at the LpqY interface. Uptake is achieved by a pivotal rotation of LpqY relative to SugABC, moving from an open and accessible conformation to a clamped conformation upon trehalose binding. These findings enrich our understanding as to how ABC transporters facilitate substrate transport across the membrane in Gram-positive bacteria.
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Affiliation(s)
- Fengjiang Liu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100101, China
| | - Jingxi Liang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300353, China
| | - Bing Zhang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
| | - Yan Gao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China
| | - Xiuna Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Tianyu Hu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Haitao Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Wenqing Xu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Zihe Rao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300353, China
- Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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