1
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Lauber F, Deme JC, Liu X, Kjær A, Miller HL, Alcock F, Lea SM, Berks BC. Structural insights into the mechanism of protein transport by the Type 9 Secretion System translocon. Nat Microbiol 2024; 9:1089-1102. [PMID: 38538833 PMCID: PMC10994853 DOI: 10.1038/s41564-024-01644-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/19/2024] [Indexed: 04/06/2024]
Abstract
Secretion systems are protein export machines that enable bacteria to exploit their environment through the release of protein effectors. The Type 9 Secretion System (T9SS) is responsible for protein export across the outer membrane (OM) of bacteria of the phylum Bacteroidota. Here we trap the T9SS of Flavobacterium johnsoniae in the process of substrate transport by disrupting the T9SS motor complex. Cryo-EM analysis of purified substrate-bound T9SS translocons reveals an extended translocon structure in which the previously described translocon core is augmented by a periplasmic structure incorporating the proteins SprE, PorD and a homologue of the canonical periplasmic chaperone Skp. Substrate proteins bind to the extracellular loops of a carrier protein within the translocon pore. As transport intermediates accumulate on the translocon when energetic input is removed, we deduce that release of the substrate-carrier protein complex from the translocon is the energy-requiring step in T9SS transport.
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Affiliation(s)
- Frédéric Lauber
- Department of Biochemistry, University of Oxford, Oxford, UK
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Justin C Deme
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- The Central Oxford Structural Molecular Imaging Centre (COSMIC), University of Oxford, Oxford, UK
| | - Xiaolong Liu
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Andreas Kjær
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Helen L Miller
- Biological Physics Research Group, Department of Physics, University of Oxford, Oxford, UK
| | - Felicity Alcock
- Department of Biochemistry, University of Oxford, Oxford, UK
- Newcastle University Biosciences Institute, Newcastle University, Newcastle, UK
| | - Susan M Lea
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
- The Central Oxford Structural Molecular Imaging Centre (COSMIC), University of Oxford, Oxford, UK.
| | - Ben C Berks
- Department of Biochemistry, University of Oxford, Oxford, UK.
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2
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Johnson S, Deme JC, Furlong EJ, Caesar JJE, Chevance FFV, Hughes KT, Lea SM. Structural basis of directional switching by the bacterial flagellum. Nat Microbiol 2024:10.1038/s41564-024-01630-z. [PMID: 38459206 DOI: 10.1038/s41564-024-01630-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 02/01/2024] [Indexed: 03/10/2024]
Abstract
The bacterial flagellum is a macromolecular protein complex that harvests energy from uni-directional ion flow across the inner membrane to power bacterial swimming via rotation of the flagellar filament. Rotation is bi-directional, with binding of a cytoplasmic chemotactic response regulator controlling reversal, though the structural and mechanistic bases for rotational switching are not well understood. Here we present cryoelectron microscopy structures of intact Salmonella flagellar basal bodies (3.2-5.5 Å), including the cytoplasmic C-ring complexes required for power transmission, in both counter-clockwise and clockwise rotational conformations. These reveal 180° movements of both the N- and C-terminal domains of the FliG protein, which, when combined with a high-resolution cryoelectron microscopy structure of the MotA5B2 stator, show that the stator shifts from the outside to the inside of the C-ring. This enables rotational switching and reveals how uni-directional ion flow across the inner membrane is used to accomplish bi-directional rotation of the flagellum.
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Affiliation(s)
- Steven Johnson
- Center for Structural Biology, CCR, NCI, Frederick, MD, USA.
| | - Justin C Deme
- Center for Structural Biology, CCR, NCI, Frederick, MD, USA
| | - Emily J Furlong
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Division of Biomedical Science and Biochemistry, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Joseph J E Caesar
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Central Oxford Structural Molecular Imaging Centre, University of Oxford, Oxford, UK
| | | | - Kelly T Hughes
- Department of Biology, University of Utah, Salt Lake City, UT, USA
| | - Susan M Lea
- Center for Structural Biology, CCR, NCI, Frederick, MD, USA.
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3
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Garrett SR, Mietrach N, Deme J, Bitzer A, Yang Y, Ulhuq FR, Kretschmer D, Heilbronner S, Smith TK, Lea SM, Palmer T. A type VII-secreted lipase toxin with reverse domain arrangement. Nat Commun 2023; 14:8438. [PMID: 38114483 PMCID: PMC10730906 DOI: 10.1038/s41467-023-44221-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 12/05/2023] [Indexed: 12/21/2023] Open
Abstract
The type VII protein secretion system (T7SS) is found in many Gram-positive bacteria and in pathogenic mycobacteria. All T7SS substrate proteins described to date share a common helical domain architecture at the N-terminus that typically interacts with other helical partner proteins, forming a composite signal sequence for targeting to the T7SS. The C-terminal domains are functionally diverse and in Gram-positive bacteria such as Staphylococcus aureus often specify toxic anti-bacterial activity. Here we describe the first example of a class of T7 substrate, TslA, that has a reverse domain organisation. TslA is widely found across Bacillota including Staphylococcus, Enterococcus and Listeria. We show that the S. aureus TslA N-terminal domain is a phospholipase A with anti-staphylococcal activity that is neutralised by the immunity lipoprotein TilA. Two small helical partner proteins, TlaA1 and TlaA2 are essential for T7-dependent secretion of TslA and at least one of these interacts with the TslA C-terminal domain to form a helical stack. Cryo-EM analysis of purified TslA complexes indicate that they share structural similarity with canonical T7 substrates. Our findings suggest that the T7SS has the capacity to recognise a secretion signal present at either end of a substrate.
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Affiliation(s)
- Stephen R Garrett
- Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Nicole Mietrach
- Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Justin Deme
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD, 21702, USA
| | - Alina Bitzer
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076, Tübingen, Germany
| | - Yaping Yang
- Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Fatima R Ulhuq
- Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Dorothee Kretschmer
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076, Tübingen, Germany
| | - Simon Heilbronner
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, 72076, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Terry K Smith
- School of Biology, Biomedical Sciences Research Complex, University of St. Andrews, North Haugh, St. Andrews, United Kingdom
| | - Susan M Lea
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD, 21702, USA
| | - Tracy Palmer
- Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
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4
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Alteen MG, Deme JC, Alvarez CP, Loppnau P, Hutchinson A, Seitova A, Chandrasekaran R, Silva Ramos E, Secker C, Alqazzaz M, Wanker EE, Lea SM, Arrowsmith CH, Harding RJ. Delineation of functional subdomains of Huntingtin protein and their interaction with HAP40. Structure 2023; 31:1121-1131.e6. [PMID: 37390814 PMCID: PMC10527579 DOI: 10.1016/j.str.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 04/14/2023] [Accepted: 06/05/2023] [Indexed: 07/02/2023]
Abstract
The huntingtin (HTT) protein plays critical roles in numerous cellular pathways by functioning as a scaffold for its many interaction partners and HTT knock out is embryonic lethal. Interrogation of HTT function is complicated by the large size of this protein so we studied a suite of structure-rationalized subdomains to investigate the structure-function relationships within the HTT-HAP40 complex. Protein samples derived from the subdomain constructs were validated using biophysical methods and cryo-electron microscopy, revealing they are natively folded and can complex with validated binding partner, HAP40. Derivatized versions of these constructs enable protein-protein interaction assays in vitro, with biotin tags, and in cells, with luciferase two-hybrid assay-based tags, which we use in proof-of-principle analyses to further interrogate the HTT-HAP40 interaction. These open-source biochemical tools enable studies of fundamental HTT biochemistry and biology, will aid the discovery of macromolecular or small-molecule binding partners and help map interaction sites across this large protein.
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Affiliation(s)
- Matthew G Alteen
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada; POINT Biopharma, 22 St Clair Avenue E Suite 1201, Toronto, ON M4T 2S3, Canada
| | - Justin C Deme
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Claudia P Alvarez
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada; SCIEX, 71 Four Valley Dr, Vaughan, ON L4K 4V8, Canada
| | - Peter Loppnau
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Ashley Hutchinson
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Alma Seitova
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Renu Chandrasekaran
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Eduardo Silva Ramos
- Neuroproteomics, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Christopher Secker
- Neuroproteomics, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Mona Alqazzaz
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Erich E Wanker
- Neuroproteomics, Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Susan M Lea
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada.
| | - Rachel J Harding
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada.
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5
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Levdansky Y, Raisch T, Deme JC, Pekovic F, Elmlund H, Lea SM, Valkov E. Structure and assembly of the NOT10:11 module of the CCR4-NOT complex. Commun Biol 2023; 6:739. [PMID: 37460791 PMCID: PMC10352241 DOI: 10.1038/s42003-023-05122-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 07/07/2023] [Indexed: 07/20/2023] Open
Abstract
NOT1, NOT10, and NOT11 form a conserved module in the CCR4-NOT complex, critical for post-transcriptional regulation in eukaryotes, but how this module contributes to the functions of the CCR4-NOT remains poorly understood. Here, we present cryo-EM structures of human and chicken NOT1:NOT10:NOT11 ternary complexes to sub-3 Å resolution, revealing an evolutionarily conserved, flexible structure. Through biochemical dissection studies, which include the Drosophila orthologs, we show that the module assembly is hierarchical, with NOT11 binding to NOT10, which then organizes it for binding to NOT1. A short proline-rich motif in NOT11 stabilizes the entire module assembly.
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Affiliation(s)
- Yevgen Levdansky
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Tobias Raisch
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
| | - Justin C Deme
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Filip Pekovic
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Hans Elmlund
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Susan M Lea
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Eugene Valkov
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
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6
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Nim YS, Fong IYH, Deme J, Tsang KL, Caesar J, Johnson S, Pang LTH, Yuen NMH, Ng TLC, Choi T, Wong YYH, Lea SM, Wong KB. Delivering a toxic metal to the active site of urease. Sci Adv 2023; 9:eadf7790. [PMID: 37083535 PMCID: PMC10121161 DOI: 10.1126/sciadv.adf7790] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 03/17/2023] [Indexed: 05/03/2023]
Abstract
Urease is a nickel (Ni) enzyme that is essential for the colonization of Helicobacter pylori in the human stomach. To solve the problem of delivering the toxic Ni ion to the active site without diffusing into the cytoplasm, cells have evolved metal carrier proteins, or metallochaperones, to deliver the toxic ions to specific protein complexes. Ni delivery requires urease to form an activation complex with the urease accessory proteins UreFD and UreG. Here, we determined the cryo-electron microscopy structures of H. pylori UreFD/urease and Klebsiella pneumoniae UreD/urease complexes at 2.3- and 2.7-angstrom resolutions, respectively. Combining structural, mutagenesis, and biochemical studies, we show that the formation of the activation complex opens a 100-angstrom-long tunnel, where the Ni ion is delivered through UreFD to the active site of urease.
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Affiliation(s)
- Yap Shing Nim
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Ivan Yu Hang Fong
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Justin Deme
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
- Center for Structural Biology, CCR, NCI, Boyles Street, Frederick, MD 21702, USA
| | - Ka Lung Tsang
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Joseph Caesar
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
- Center for Structural Biology, CCR, NCI, Boyles Street, Frederick, MD 21702, USA
| | - Steven Johnson
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
- Center for Structural Biology, CCR, NCI, Boyles Street, Frederick, MD 21702, USA
| | - Longson Tsz Hin Pang
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Nicholas Man Hon Yuen
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Tin Long Chris Ng
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Tung Choi
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Yakie Yat Hei Wong
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Susan M. Lea
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
- Center for Structural Biology, CCR, NCI, Boyles Street, Frederick, MD 21702, USA
| | - Kam-Bo Wong
- School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
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7
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Lea SM, Williams PA. Cryo-EM diversifies. Curr Opin Struct Biol 2022; 77:102469. [PMID: 36183448 DOI: 10.1016/j.sbi.2022.102469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Susan M Lea
- Center for Structural Biology, CCR, NCI, USA.
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8
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Braunger K, Ahn J, Jore MM, Johnson S, Tang TTL, Pedersen DV, Andersen GR, Lea SM. Structure and function of a family of tick-derived complement inhibitors targeting properdin. Nat Commun 2022; 13:317. [PMID: 35031611 PMCID: PMC8760278 DOI: 10.1038/s41467-021-27920-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 12/17/2021] [Indexed: 12/12/2022] Open
Abstract
Activation of the serum-resident complement system begins a cascade that leads to activation of membrane-resident complement receptors on immune cells, thus coordinating serum and cellular immune responses. Whilst many molecules act to control inappropriate activation, Properdin is the only known positive regulator of the human complement system. By stabilising the alternative pathway C3 convertase it promotes complement self-amplification and persistent activation boosting the magnitude of the serum complement response by all triggers. In this work, we identify a family of tick-derived alternative pathway complement inhibitors, hereafter termed CirpA. Functional and structural characterisation reveals that members of the CirpA family directly bind to properdin, inhibiting its ability to promote complement activation, and leading to potent inhibition of the complement response in a species specific manner. We provide a full functional and structural characterisation of a properdin inhibitor, opening avenues for future therapeutic approaches.
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Affiliation(s)
- Katharina Braunger
- Sir William Dunn School of Pathology, University of Oxford, OX1 3RE, Oxford, UK
| | - Jiyoon Ahn
- Sir William Dunn School of Pathology, University of Oxford, OX1 3RE, Oxford, UK
| | - Matthijs M Jore
- Sir William Dunn School of Pathology, University of Oxford, OX1 3RE, Oxford, UK
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Steven Johnson
- Sir William Dunn School of Pathology, University of Oxford, OX1 3RE, Oxford, UK.
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, 21702, Frederick, MD, USA.
| | - Terence T L Tang
- Sir William Dunn School of Pathology, University of Oxford, OX1 3RE, Oxford, UK
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Dennis V Pedersen
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000, Aarhus, Denmark
| | - Gregers R Andersen
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000, Aarhus, Denmark
| | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, OX1 3RE, Oxford, UK.
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, 21702, Frederick, MD, USA.
- Central Oxford Structural Molecular Imaging Centre, University of Oxford, OX1 3RE, Oxford, UK.
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9
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Harding RJ, Deme JC, Hevler JF, Tamara S, Lemak A, Cantle JP, Szewczyk MM, Begeja N, Goss S, Zuo X, Loppnau P, Seitova A, Hutchinson A, Fan L, Truant R, Schapira M, Carroll JB, Heck AJR, Lea SM, Arrowsmith CH. Huntingtin structure is orchestrated by HAP40 and shows a polyglutamine expansion-specific interaction with exon 1. Commun Biol 2021; 4:1374. [PMID: 34880419 PMCID: PMC8654980 DOI: 10.1038/s42003-021-02895-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 11/09/2021] [Indexed: 12/14/2022] Open
Abstract
Huntington's disease results from expansion of a glutamine-coding CAG tract in the huntingtin (HTT) gene, producing an aberrantly functioning form of HTT. Both wildtype and disease-state HTT form a hetero-dimer with HAP40 of unknown functional relevance. We demonstrate in vivo and in cell models that HTT and HAP40 cellular abundance are coupled. Integrating data from a 2.6 Å cryo-electron microscopy structure, cross-linking mass spectrometry, small-angle X-ray scattering, and modeling, we provide a near-atomic-level view of HTT, its molecular interaction surfaces and compacted domain architecture, orchestrated by HAP40. Native mass spectrometry reveals a remarkably stable hetero-dimer, potentially explaining the cellular inter-dependence of HTT and HAP40. The exon 1 region of HTT is dynamic but shows greater conformational variety in the polyglutamine expanded mutant than wildtype exon 1. Our data provide a foundation for future functional and drug discovery studies targeting Huntington's disease and illuminate the structural consequences of HTT polyglutamine expansion.
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Affiliation(s)
- Rachel J Harding
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada.
| | - Justin C Deme
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
- Central Oxford Structural Molecular Imaging Centre, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Johannes F Hevler
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Sem Tamara
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Alexander Lemak
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Jeffrey P Cantle
- Behavioral Neuroscience Program, Department of Psychology, Western Washington University, Bellingham, WA, 98225, USA
| | - Magdalena M Szewczyk
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Nola Begeja
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Siobhan Goss
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Xiaobing Zuo
- X-ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Peter Loppnau
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Alma Seitova
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Ashley Hutchinson
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Lixin Fan
- Basic Science Program, Frederick National Laboratory for Cancer Research, SAXS Core of NCI, National Institutes of Health, Frederick, MD, 21701, USA
| | - Ray Truant
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Jeffrey B Carroll
- Behavioral Neuroscience Program, Department of Psychology, Western Washington University, Bellingham, WA, 98225, USA
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
- Central Oxford Structural Molecular Imaging Centre, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada.
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada.
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10
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Parker JL, Deme JC, Kolokouris D, Kuteyi G, Biggin PC, Lea SM, Newstead S. Molecular basis for redox control by the human cystine/glutamate antiporter system xc . Nat Commun 2021; 12:7147. [PMID: 34880232 PMCID: PMC8654953 DOI: 10.1038/s41467-021-27414-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 11/17/2021] [Indexed: 12/13/2022] Open
Abstract
Cysteine plays an essential role in cellular redox homoeostasis as a key constituent of the tripeptide glutathione (GSH). A rate limiting step in cellular GSH synthesis is the availability of cysteine. However, circulating cysteine exists in the blood as the oxidised di-peptide cystine, requiring specialised transport systems for its import into the cell. System xc- is a dedicated cystine transporter, importing cystine in exchange for intracellular glutamate. To counteract elevated levels of reactive oxygen species in cancerous cells system xc- is frequently upregulated, making it an attractive target for anticancer therapies. However, the molecular basis for ligand recognition remains elusive, hampering efforts to specifically target this transport system. Here we present the cryo-EM structure of system xc- in both the apo and glutamate bound states. Structural comparisons reveal an allosteric mechanism for ligand discrimination, supported by molecular dynamics and cell-based assays, establishing a mechanism for cystine transport in human cells.
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Affiliation(s)
- Joanne L Parker
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
| | - Justin C Deme
- Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
- Central Oxford Structural Molecular Imaging Centre, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | | | - Gabriel Kuteyi
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Philip C Biggin
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Susan M Lea
- Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK.
- Central Oxford Structural Molecular Imaging Centre, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK.
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.
| | - Simon Newstead
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
- The Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, OX1 3QU, UK.
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11
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Klug YA, Deme JC, Corey RA, Renne MF, Stansfeld PJ, Lea SM, Carvalho P. Mechanism of lipid droplet formation by the yeast Sei1/Ldb16 Seipin complex. Nat Commun 2021; 12:5892. [PMID: 34625558 PMCID: PMC8501077 DOI: 10.1038/s41467-021-26162-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 09/21/2021] [Indexed: 11/09/2022] Open
Abstract
Lipid droplets (LDs) are universal lipid storage organelles with a core of neutral lipids, such as triacylglycerols, surrounded by a phospholipid monolayer. This unique architecture is generated during LD biogenesis at endoplasmic reticulum (ER) sites marked by Seipin, a conserved membrane protein mutated in lipodystrophy. Here structural, biochemical and molecular dynamics simulation approaches reveal the mechanism of LD formation by the yeast Seipin Sei1 and its membrane partner Ldb16. We show that Sei1 luminal domain assembles a homooligomeric ring, which, in contrast to other Seipins, is unable to concentrate triacylglycerol. Instead, Sei1 positions Ldb16, which concentrates triacylglycerol within the Sei1 ring through critical hydroxyl residues. Triacylglycerol recruitment to the complex is further promoted by Sei1 transmembrane segments, which also control Ldb16 stability. Thus, we propose that LD assembly by the Sei1/Ldb16 complex, and likely other Seipins, requires sequential triacylglycerol-concentrating steps via distinct elements in the ER membrane and lumen.
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Affiliation(s)
- Yoel A Klug
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Justin C Deme
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Robin A Corey
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Mike F Renne
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, Oxford, UK
- School of Life Sciences & Department of Chemistry, University of Warwick, Coventry, UK
| | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
| | - Pedro Carvalho
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
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12
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Adams O, Deme JC, Parker JL, Fowler PW, Lea SM, Newstead S. Cryo-EM structure and resistance landscape of M. tuberculosis MmpL3: An emergent therapeutic target. Structure 2021; 29:1182-1191.e4. [PMID: 34242558 PMCID: PMC8752444 DOI: 10.1016/j.str.2021.06.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/24/2021] [Accepted: 06/14/2021] [Indexed: 11/09/2022]
Abstract
Tuberculosis (TB) is the leading cause of death from a single infectious agent and in 2019 an estimated 10 million people worldwide contracted the disease. Although treatments for TB exist, continual emergence of drug-resistant variants necessitates urgent development of novel antituberculars. An important new target is the lipid transporter MmpL3, which is required for construction of the unique cell envelope that shields Mycobacterium tuberculosis (Mtb) from the immune system. However, a structural understanding of the mutations in Mtb MmpL3 that confer resistance to the many preclinical leads is lacking, hampering efforts to circumvent resistance mechanisms. Here, we present the cryoelectron microscopy structure of Mtb MmpL3 and use it to comprehensively analyze the mutational landscape of drug resistance. Our data provide a rational explanation for resistance variants local to the central drug binding site, and also highlight a potential alternative route to resistance operating within the periplasmic domain.
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Affiliation(s)
- Oliver Adams
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Justin C Deme
- The Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK; Central Oxford Structural Molecular Imaging Centre (COSMIC), University of Oxford, Oxford OX1 3RE, UK; Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Joanne L Parker
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Philip W Fowler
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK; National Institute of Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe, Oxford OX3 9DU, UK
| | - Susan M Lea
- The Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK; Central Oxford Structural Molecular Imaging Centre (COSMIC), University of Oxford, Oxford OX1 3RE, UK; Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA.
| | - Simon Newstead
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; The Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK.
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13
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Martins T, Meng Y, Korona B, Suckling R, Johnson S, Handford PA, Lea SM, Bray SJ. The conserved C2 phospholipid-binding domain in Delta contributes to robust Notch signalling. EMBO Rep 2021; 22:e52729. [PMID: 34347930 PMCID: PMC8490980 DOI: 10.15252/embr.202152729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 07/10/2021] [Accepted: 07/15/2021] [Indexed: 11/09/2022] Open
Abstract
Accurate Notch signalling is critical for development and homeostasis. Fine‐tuning of Notch–ligand interactions has substantial impact on signalling outputs. Recent structural studies have identified a conserved N‐terminal C2 domain in human Notch ligands which confers phospholipid binding in vitro. Here, we show that Drosophila ligands Delta and Serrate adopt the same C2 domain structure with analogous variations in the loop regions, including the so‐called β1‐2 loop that is involved in phospholipid binding. Mutations in the β1‐2 loop of the Delta C2 domain retain Notch binding but have impaired ability to interact with phospholipids in vitro. To investigate its role in vivo, we deleted five residues within the β1‐2 loop of endogenous Delta. Strikingly, this change compromises ligand function. The modified Delta enhances phenotypes produced by Delta loss‐of‐function alleles and suppresses that of Notch alleles. As the modified protein is present on the cell surface in normal amounts, these results argue that C2 domain phospholipid binding is necessary for robust signalling in vivo fine‐tuning the balance of trans and cis ligand–receptor interactions.
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Affiliation(s)
- Torcato Martins
- Department of Physiology Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Yao Meng
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Richard Suckling
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Steven Johnson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | | | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Sarah J Bray
- Department of Physiology Development and Neuroscience, University of Cambridge, Cambridge, UK
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14
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Parker JL, Deme JC, Wu Z, Kuteyi G, Huo J, Owens RJ, Biggin PC, Lea SM, Newstead S. Cryo-EM structure of PepT2 reveals structural basis for proton-coupled peptide and prodrug transport in mammals. Sci Adv 2021; 7:eabh3355. [PMID: 34433568 PMCID: PMC8386928 DOI: 10.1126/sciadv.abh3355] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 07/02/2021] [Indexed: 05/26/2023]
Abstract
The SLC15 family of proton-coupled solute carriers PepT1 and PepT2 play a central role in human physiology as the principal route for acquiring and retaining dietary nitrogen. A remarkable feature of the SLC15 family is their extreme substrate promiscuity, which has enabled the targeting of these transporters for the improvement of oral bioavailability for several prodrug molecules. Although recent structural and biochemical studies on bacterial homologs have identified conserved sites of proton and peptide binding, the mechanism of peptide capture and ligand promiscuity remains unclear for mammalian family members. Here, we present the cryo-electron microscopy structure of the outward open conformation of the rat peptide transporter PepT2 in complex with an inhibitory nanobody. Our structure, combined with molecular dynamics simulations and biochemical and cell-based assays, establishes a framework for understanding peptide and prodrug recognition within this pharmaceutically important transporter family.
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Affiliation(s)
- Joanne L Parker
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
| | - Justin C Deme
- Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
- Central Oxford Structural Molecular Imaging Centre, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Zhiyi Wu
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Gabriel Kuteyi
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Jiandong Huo
- Structural Biology, The Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, UK
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Protein Production UK, The Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, UK
| | - Raymond J Owens
- Structural Biology, The Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, UK
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Protein Production UK, The Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, UK
| | - Philip C Biggin
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
| | - Susan M Lea
- Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK.
- Central Oxford Structural Molecular Imaging Centre, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Simon Newstead
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
- The Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
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15
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Parker JL, Deme JC, Kuteyi G, Wu Z, Huo J, Goldman ID, Owens RJ, Biggin PC, Lea SM, Newstead S. Structural basis of antifolate recognition and transport by PCFT. Nature 2021; 595:130-134. [PMID: 34040256 PMCID: PMC9990147 DOI: 10.1038/s41586-021-03579-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 04/23/2021] [Indexed: 12/20/2022]
Abstract
Folates (also known as vitamin B9) have a critical role in cellular metabolism as the starting point in the synthesis of nucleic acids, amino acids and the universal methylating agent S-adenylsmethionine1,2. Folate deficiency is associated with a number of developmental, immune and neurological disorders3-5. Mammals cannot synthesize folates de novo; several systems have therefore evolved to take up folates from the diet and distribute them within the body3,6. The proton-coupled folate transporter (PCFT) (also known as SLC46A1) mediates folate uptake across the intestinal brush border membrane and the choroid plexus4,7, and is an important route for the delivery of antifolate drugs in cancer chemotherapy8-10. How PCFT recognizes folates or antifolate agents is currently unclear. Here we present cryo-electron microscopy structures of PCFT in a substrate-free state and in complex with a new-generation antifolate drug (pemetrexed). Our results provide a structural basis for understanding antifolate recognition and provide insights into the pH-regulated mechanism of folate transport mediated by PCFT.
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Affiliation(s)
- Joanne L Parker
- Department of Biochemistry, University of Oxford, Oxford, UK.
| | - Justin C Deme
- Dunn School of Pathology, University of Oxford, Oxford, UK
- Central Oxford Structural Molecular Imaging Centre, University of Oxford, Oxford, UK
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Gabriel Kuteyi
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Zhiyi Wu
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Jiandong Huo
- Structural Biology, The Rosalind Franklin Institute, Didcot, UK
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Protein Production UK, The Research Complex at Harwell, Didcot, UK
| | - I David Goldman
- Departments of Molecular Pharmacology and Medicine, Albert Einstein College of Medicine, New York, NY, USA
| | - Raymond J Owens
- Structural Biology, The Rosalind Franklin Institute, Didcot, UK
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Protein Production UK, The Research Complex at Harwell, Didcot, UK
| | - Philip C Biggin
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Susan M Lea
- Dunn School of Pathology, University of Oxford, Oxford, UK.
- Central Oxford Structural Molecular Imaging Centre, University of Oxford, Oxford, UK.
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
| | - Simon Newstead
- Department of Biochemistry, University of Oxford, Oxford, UK.
- The Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK.
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16
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Kuhlen L, Johnson S, Cao J, Deme JC, Lea SM. Nonameric structures of the cytoplasmic domain of FlhA and SctV in the context of the full-length protein. PLoS One 2021; 16:e0252800. [PMID: 34143799 PMCID: PMC8213127 DOI: 10.1371/journal.pone.0252800] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 05/21/2021] [Indexed: 12/18/2022] Open
Abstract
Type three secretion is the mechanism of protein secretion found in bacterial flagella and injectisomes. At its centre is the export apparatus (EA), a complex of five membrane proteins through which secretion substrates pass the inner membrane. While the complex formed by four of the EA proteins has been well characterised structurally, little is known about the structure of the membrane domain of the largest subunit, FlhA in flagella, SctV in injectisomes. Furthermore, the biologically relevant nonameric assembly of FlhA/SctV has been infrequently observed and differences in conformation of the cytoplasmic portion of FlhA/SctV between open and closed states have been suggested to reflect secretion system specific differences. FlhA has been shown to bind to chaperone-substrate complexes in an open state, but in previous assembled ring structures, SctV is in a closed state. Here, we identify FlhA and SctV homologues that can be recombinantly produced in the oligomeric state and study them using cryo-electron microscopy. The structures of the cytoplasmic domains from both FlhA and SctV are in the open state and we observe a conserved interaction between a short stretch of residues at the N-terminus of the cytoplasmic domain, known as FlhAL/SctVL, with a groove on the adjacent protomer’s cytoplasmic domain, which stabilises the nonameric ring assembly.
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Affiliation(s)
- Lucas Kuhlen
- Sir William Dunn School of Pathology, Oxford, United Kingdom
| | - Steven Johnson
- Sir William Dunn School of Pathology, Oxford, United Kingdom
- Center for Structural Biology, Center for Cancer Research, National Insititutes of Health, Frederick, MD, United States of America
| | - Jerry Cao
- Sir William Dunn School of Pathology, Oxford, United Kingdom
| | - Justin C. Deme
- Sir William Dunn School of Pathology, Oxford, United Kingdom
- Center for Structural Biology, Center for Cancer Research, National Insititutes of Health, Frederick, MD, United States of America
- Central Oxford Structural Molecular Imaging Centre, Oxford, United Kingdom
| | - Susan M. Lea
- Sir William Dunn School of Pathology, Oxford, United Kingdom
- Center for Structural Biology, Center for Cancer Research, National Insititutes of Health, Frederick, MD, United States of America
- Central Oxford Structural Molecular Imaging Centre, Oxford, United Kingdom
- * E-mail:
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17
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Johnson S, Furlong EJ, Deme JC, Nord AL, Caesar JJE, Chevance FFV, Berry RM, Hughes KT, Lea SM. Molecular structure of the intact bacterial flagellar basal body. Nat Microbiol 2021; 6:712-721. [PMID: 33931760 PMCID: PMC7610862 DOI: 10.1038/s41564-021-00895-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/23/2021] [Indexed: 02/03/2023]
Abstract
The bacterial flagellum is a macromolecular protein complex that enables motility in many species. Bacterial flagella self-assemble a strong, multicomponent drive shaft that couples rotation in the inner membrane to the micrometre-long flagellar filament that powers bacterial swimming in viscous fluids1-3. Here, we present structures of the intact Salmonella flagellar basal body4, encompassing the inner membrane rotor, drive shaft and outer-membrane bushing, solved using cryo-electron microscopy to resolutions of 2.2-3.7 Å. The structures reveal molecular details of how 173 protein molecules of 13 different types assemble into a complex spanning two membranes and a cell wall. The helical drive shaft at one end is intricately interwoven with the rotor component with both the export gate complex and the proximal rod forming interactions with the MS-ring. At the other end, the drive shaft distal rod passes through the LP-ring bushing complex, which functions as a molecular bearing anchored in the outer membrane through interactions with the lipopolysaccharide. The in situ structure of a protein complex capping the drive shaft provides molecular insights into the assembly process of this molecular machine.
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Affiliation(s)
- Steven Johnson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
- Center for Structural Biology, CCR, NCI, Frederick, MD, USA.
| | - Emily J Furlong
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Justin C Deme
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Center for Structural Biology, CCR, NCI, Frederick, MD, USA
- Central Oxford Structural Molecular Imaging Centre, University of Oxford, Oxford, UK
| | - Ashley L Nord
- Department of Physics, University of Oxford, Oxford, UK
- Centre de Biologie Structurale, INSERM, CNRS, Université de Montpellier, Montpellier, France
| | - Joseph J E Caesar
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Central Oxford Structural Molecular Imaging Centre, University of Oxford, Oxford, UK
| | | | | | - Kelly T Hughes
- Department of Biology, University of Utah, Salt Lake City, UT, USA
| | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
- Center for Structural Biology, CCR, NCI, Frederick, MD, USA.
- Central Oxford Structural Molecular Imaging Centre, University of Oxford, Oxford, UK.
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18
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Silale A, Lea SM, Berks BC. The DNA transporter ComEC has metal-dependent nuclease activity that is important for natural transformation. Mol Microbiol 2021; 116:416-426. [PMID: 33772889 PMCID: PMC8579336 DOI: 10.1111/mmi.14720] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 12/25/2022]
Abstract
In the process of natural transformation bacteria import extracellular DNA molecules for integration into their genome. One strand of the incoming DNA molecule is degraded, whereas the remaining strand is transported across the cytoplasmic membrane. The DNA transport channel is provided by the protein ComEC. Many ComEC proteins have an extracellular C-terminal domain (CTD) with homology to the metallo-β-lactamase fold. Here we show that this CTD binds Mn2+ ions and exhibits Mn2+ -dependent phosphodiesterase and nuclease activities. Inactivation of the enzymatic activity of the CTD severely inhibits natural transformation in Bacillus subtilis. These data suggest that the ComEC CTD is a nuclease responsible for degrading the nontransforming DNA strand during natural transformation and that this process is important for efficient DNA import.
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Affiliation(s)
- Augustinas Silale
- Department of Biochemistry, University of Oxford, Oxford, UK.,Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Ben C Berks
- Department of Biochemistry, University of Oxford, Oxford, UK
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19
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Dhillon A, Deme JC, Furlong E, Roem D, Jongerius I, Johnson S, Lea SM. Molecular Basis for Bordetella pertussis Interference with Complement, Coagulation, Fibrinolytic, and Contact Activation Systems: the Cryo-EM Structure of the Vag8-C1 Inhibitor Complex. mBio 2021; 12:e02823-20. [PMID: 33758081 PMCID: PMC8092270 DOI: 10.1128/mbio.02823-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 02/18/2021] [Indexed: 12/27/2022] Open
Abstract
Complement, contact activation, coagulation, and fibrinolysis are serum protein cascades that need strict regulation to maintain human health. Serum glycoprotein, a C1 inhibitor (C1-INH), is a key regulator (inhibitor) of serine proteases of all the above-mentioned pathways. Recently, an autotransporter protein, virulence-associated gene 8 (Vag8), produced by the whooping cough pathogen, Bordetella pertussis, was shown to bind to C1-INH and interfere with its function. Here, we present the structure of the Vag8-C1-INH complex determined using cryo-electron microscopy at a 3.6-Å resolution. The structure shows a unique mechanism of C1-INH inhibition not employed by other pathogens, where Vag8 sequesters the reactive center loop of C1-INH, preventing its interaction with the target proteases.IMPORTANCE The structure of a 10-kDa protein complex is one of the smallest to be determined using cryo-electron microscopy at high resolution. The structure reveals that C1-INH is sequestered in an inactivated state by burial of the reactive center loop in Vag8. By so doing, the bacterium is able to simultaneously perturb the many pathways regulated by C1-INH. Virulence mechanisms such as the one described here assume more importance given the emerging evidence about dysregulation of contact activation, coagulation, and fibrinolysis leading to COVID-19 pneumonia.
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Affiliation(s)
- Arun Dhillon
- Sir William Dunn School of Pathology, Oxford, United Kingdom
| | - Justin C Deme
- Sir William Dunn School of Pathology, Oxford, United Kingdom
- Central Oxford Structural Molecular Imaging Centre, Oxford, United Kingdom
| | - Emily Furlong
- Sir William Dunn School of Pathology, Oxford, United Kingdom
| | - Dorina Roem
- Sanquin Research, Department of Immunopathology, and Landsteiner Laboratory, Amsterdam University Medical Centre, Amsterdam Infection and Immunity Institute, Amsterdam, the Netherlands
| | - Ilse Jongerius
- Sanquin Research, Department of Immunopathology, and Landsteiner Laboratory, Amsterdam University Medical Centre, Amsterdam Infection and Immunity Institute, Amsterdam, the Netherlands
- Department of Pediatric Immunology, Rheumatology, and Infectious Diseases, Emma Children's Hospital, Amsterdam University Medical Centre, Amsterdam, the Netherlands
| | - Steven Johnson
- Sir William Dunn School of Pathology, Oxford, United Kingdom
| | - Susan M Lea
- Sir William Dunn School of Pathology, Oxford, United Kingdom
- Central Oxford Structural Molecular Imaging Centre, Oxford, United Kingdom
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20
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Hennell James R, Deme JC, Kjӕr A, Alcock F, Silale A, Lauber F, Johnson S, Berks BC, Lea SM. Structure and mechanism of the proton-driven motor that powers type 9 secretion and gliding motility. Nat Microbiol 2021; 6:221-233. [PMID: 33432152 PMCID: PMC7116788 DOI: 10.1038/s41564-020-00823-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/28/2020] [Indexed: 12/11/2022]
Abstract
Three classes of ion-driven protein motors have been identified to date: ATP synthase, the bacterial flagellar motor and a proton-driven motor that powers gliding motility and the type 9 protein secretion system in Bacteroidetes bacteria. Here, we present cryo-electron microscopy structures of the gliding motility/type 9 protein secretion system motors GldLM from Flavobacterium johnsoniae and PorLM from Porphyromonas gingivalis. The motor is an asymmetric inner membrane protein complex in which the single transmembrane helices of two periplasm-spanning GldM/PorM proteins are positioned inside a ring of five GldL/PorL proteins. Mutagenesis and single-molecule tracking identify protonatable amino acid residues in the transmembrane domain of the complex that are important for motor function. Our data provide evidence for a mechanism in which proton flow results in rotation of the periplasm-spanning GldM/PorM dimer inside the intra-membrane GldL/PorL ring to drive processes at the bacterial outer membrane.
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Affiliation(s)
- Rory Hennell James
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Justin C Deme
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
- The Central Oxford Structural Molecular Imaging Centre (COSMIC), University of Oxford, Oxford, UK
| | - Andreas Kjӕr
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Felicity Alcock
- Department of Biochemistry, University of Oxford, Oxford, UK
- CBCB, Newcastle University, Newcastle upon Tyne, UK
| | - Augustinas Silale
- Department of Biochemistry, University of Oxford, Oxford, UK
- CBCB, Newcastle University, Newcastle upon Tyne, UK
| | - Frédéric Lauber
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Steven Johnson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Ben C Berks
- Department of Biochemistry, University of Oxford, Oxford, UK.
| | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
- The Central Oxford Structural Molecular Imaging Centre (COSMIC), University of Oxford, Oxford, UK.
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21
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Caesar J, Reboul CF, Machello C, Kiesewetter S, Tang ML, Deme JC, Johnson S, Elmlund D, Lea SM, Elmlund H. WITHDRAWN: SIMPLE 3.0. Stream single-particle cryo-EM analysis in real time. J Struct Biol 2020; 212:107635. [PMID: 33022362 DOI: 10.1016/j.jsb.2020.107635] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/26/2020] [Accepted: 09/28/2020] [Indexed: 11/29/2022]
Affiliation(s)
- Joseph Caesar
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK; Central Oxford Structural Microscopy and Imaging Centre, University of Oxford, Oxford UK
| | - Cyril F Reboul
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, Victoria, Australia
| | - Chiara Machello
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, Victoria, Australia
| | - Simon Kiesewetter
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, Victoria, Australia
| | - Molly L Tang
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK; Central Oxford Structural Microscopy and Imaging Centre, University of Oxford, Oxford UK
| | - Justin C Deme
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK; Central Oxford Structural Microscopy and Imaging Centre, University of Oxford, Oxford UK
| | - Steven Johnson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Dominika Elmlund
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, Victoria, Australia
| | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK; Central Oxford Structural Microscopy and Imaging Centre, University of Oxford, Oxford UK.
| | - Hans Elmlund
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, Victoria, Australia.
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22
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Deme JC, Johnson S, Vickery O, Aron A, Monkhouse H, Griffiths T, James RH, Berks BC, Coulton JW, Stansfeld PJ, Lea SM. Structures of the stator complex that drives rotation of the bacterial flagellum. Nat Microbiol 2020; 5:1553-1564. [PMID: 32929189 PMCID: PMC7610383 DOI: 10.1038/s41564-020-0788-8] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 08/11/2020] [Indexed: 01/17/2023]
Abstract
The bacterial flagellum is the prototypical protein nanomachine and comprises a rotating helical propeller attached to a membrane-embedded motor complex. The motor consists of a central rotor surrounded by stator units that couple ion flow across the cytoplasmic membrane to generate torque. Here, we present the structures of the stator complexes from Clostridium sporogenes, Bacillus subtilis and Vibrio mimicus, allowing interpretation of the extensive body of data on stator mechanism. The structures reveal an unexpected asymmetric A5B2 subunit assembly where the five A subunits enclose the two B subunits. Comparison to structures of other ion-driven motors indicates that this A5B2 architecture is fundamental to bacterial systems that couple energy from ion flow to generate mechanical work at a distance and suggests that such events involve rotation in the motor structures.
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Affiliation(s)
- Justin C Deme
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Central Oxford Structural Molecular Imaging Centre, University of Oxford, Oxford, UK
| | - Steven Johnson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Owen Vickery
- Department of Biochemistry, University of Oxford, Oxford, UK
- School of Life Sciences & Department of Chemistry, University of Warwick, Coventry, UK
| | - Amy Aron
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Holly Monkhouse
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Thomas Griffiths
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | | | - Ben C Berks
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - James W Coulton
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
- Département de Biochemie et Médecine Moleculaire, Université de Montréal, Montréal, Quebec, Canada
| | - Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, Oxford, UK
- School of Life Sciences & Department of Chemistry, University of Warwick, Coventry, UK
| | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
- Central Oxford Structural Molecular Imaging Centre, University of Oxford, Oxford, UK.
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23
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Caesar J, Reboul CF, Machello C, Kiesewetter S, Tang ML, Deme JC, Johnson S, Elmlund D, Lea SM, Elmlund H. SIMPLE 3.0. Stream single-particle cryo-EM analysis in real time. J Struct Biol X 2020; 4:100040. [PMID: 33294840 PMCID: PMC7695977 DOI: 10.1016/j.yjsbx.2020.100040] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We here introduce the third major release of the SIMPLE (Single-particle IMage Processing Linux Engine) open-source software package for analysis of cryogenic transmission electron microscopy (cryo-EM) movies of single-particles (Single-Particle Analysis, SPA). Development of SIMPLE 3.0 has been focused on real-time data processing using minimal CPU computing resources to allow easy and cost-efficient scaling of processing as data rates escalate. Our stream SPA tool implements the steps of anisotropic motion correction and CTF estimation, rapid template-based particle identification and 2D clustering with automatic class rejection. SIMPLE 3.0 additionally features an easy-to-use web-based graphical user interface (GUI) that can be run on any device (workstation, laptop, tablet or phone) and supports a remote multi-user environment over the network. The new project-based execution model automatically records the executed workflow and represents it as a flow diagram in the GUI. This facilitates meta-data handling and greatly simplifies usage. Using SIMPLE 3.0, it is possible to automatically obtain a clean SP data set amenable to high-resolution 3D reconstruction directly upon completion of the data acquisition, without the need for extensive image processing post collection. Only minimal standard CPU computing resources are required to keep up with a rate of ∼300 Gatan K3 direct electron detector movies per hour. SIMPLE 3.0 is available for download from simplecryoem.com.
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Affiliation(s)
- Joseph Caesar
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.,Central Oxford Structural Microscopy and Imaging Centre, University of Oxford, Oxford UK
| | - Cyril F Reboul
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, Victoria, Australia
| | - Chiara Machello
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, Victoria, Australia
| | - Simon Kiesewetter
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, Victoria, Australia
| | - Molly L Tang
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.,Central Oxford Structural Microscopy and Imaging Centre, University of Oxford, Oxford UK
| | - Justin C Deme
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.,Central Oxford Structural Microscopy and Imaging Centre, University of Oxford, Oxford UK
| | - Steven Johnson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Dominika Elmlund
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, Victoria, Australia
| | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.,Central Oxford Structural Microscopy and Imaging Centre, University of Oxford, Oxford UK
| | - Hans Elmlund
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, Victoria, Australia
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24
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Johnson S, Fong YH, Deme JC, Furlong EJ, Kuhlen L, Lea SM. Symmetry mismatch in the MS-ring of the bacterial flagellar rotor explains the structural coordination of secretion and rotation. Nat Microbiol 2020; 5:966-975. [PMID: 32284565 PMCID: PMC7320910 DOI: 10.1038/s41564-020-0703-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 03/05/2020] [Indexed: 11/14/2022]
Abstract
The bacterial flagellum is a complex self-assembling nanomachine that confers motility to the cell. Despite great variation across species, all flagella are ultimately constructed from a helical propeller that is attached to a motor embedded in the inner membrane. The motor consists of a series of stator units surrounding a central rotor made up of two ring complexes, the MS-ring and the C-ring. Despite many studies, high-resolution structural information is still lacking for the MS-ring of the rotor, and proposed mismatches in stoichiometry between the two rings have long provided a source of confusion for the field. Here, we present structures of the Salmonella MS-ring, revealing a high level of variation in inter- and intrachain symmetry that provides a structural explanation for the ability of the MS-ring to function as a complex and elegant interface between the two main functions of the flagellum-protein secretion and rotation.
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Affiliation(s)
- Steven Johnson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Yu Hang Fong
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Justin C Deme
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Central Oxford Structural Molecular Imaging Centre, University of Oxford, Oxford, UK
| | - Emily J Furlong
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Lucas Kuhlen
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
- Central Oxford Structural Molecular Imaging Centre, University of Oxford, Oxford, UK.
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25
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Reichhardt MP, Loimaranta V, Lea SM, Johnson S. Structures of SALSA/DMBT1 SRCR domains reveal the conserved ligand-binding mechanism of the ancient SRCR fold. Life Sci Alliance 2020; 3:3/4/e201900502. [PMID: 32098784 PMCID: PMC7043408 DOI: 10.26508/lsa.201900502] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 02/14/2020] [Accepted: 02/14/2020] [Indexed: 02/06/2023] Open
Abstract
The structures of SALSA SRCR domains 1 and 8 reveal a cation-dependent mechanism for ligand recognition, contributing to important roles in the immune system and cellular signalling. The cation-binding sites are conserved across all SRCR domains, suggesting conserved functional mechanisms. The scavenger receptor cysteine-rich (SRCR) family of proteins comprises more than 20 membrane-associated and secreted molecules. Characterised by the presence of one or more copies of the ∼110 amino-acid SRCR domain, this class of proteins have widespread functions as antimicrobial molecules, scavenger receptors, and signalling receptors. Despite the high level of structural conservation of SRCR domains, no unifying mechanism for ligand interaction has been described. The SRCR protein SALSA, also known as DMBT1/gp340, is a key player in mucosal immunology. Based on detailed structural data of SALSA SRCR domains 1 and 8, we here reveal a novel universal ligand-binding mechanism for SALSA ligands. The binding interface incorporates a dual cation-binding site, which is highly conserved across the SRCR superfamily. Along with the well-described cation dependency on most SRCR domain–ligand interactions, our data suggest that the binding mechanism described for the SALSA SRCR domains is applicable to all SRCR domains. We thus propose to have identified in SALSA a conserved functional mechanism for the SRCR class of proteins.
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Affiliation(s)
| | | | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.,Central Oxford Structural Molecular Imaging Centre, University of Oxford, Oxford, UK
| | - Steven Johnson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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26
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Deme JC, Kuhlen L, Abrusci P, Johnson S, Lauber F, Berks BC, Lea SM. Core components of bacterial protein secretion systems revealed at high resolution by cryo-electron microscopy. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s0108767318097891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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27
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Kuhlen L, Abrusci P, Johnson S, Gault J, Deme J, Caesar J, Dietsche T, Mebrhatu MT, Ganief T, Macek B, Wagner S, Robinson CV, Lea SM. Author Correction: Structure of the core of the type III secretion system export apparatus. Nat Struct Mol Biol 2018; 25:743. [PMID: 30018321 DOI: 10.1038/s41594-018-0095-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the version of this article initially published, the PDB code associated with the study was given as 6F2E but should have been 6F2D in Table 1 and the data availability statement. The error has been corrected in the HTML and PDF versions of the article.
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Affiliation(s)
- Lucas Kuhlen
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.,Department of Chemistry, University of Oxford, Oxford, UK
| | - Patrizia Abrusci
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.,Structural Genomics Consortium, University of Oxford, Oxford, UK
| | - Steven Johnson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Joseph Gault
- Department of Chemistry, University of Oxford, Oxford, UK
| | - Justin Deme
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.,Central Oxford Structural Microscopy and Imaging Centre, University of Oxford, Oxford, UK
| | - Joseph Caesar
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.,Central Oxford Structural Microscopy and Imaging Centre, University of Oxford, Oxford, UK
| | - Tobias Dietsche
- Section of Cellular and Molecular Microbiology, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, Tübingen, Germany
| | - Mehari Tesfazgi Mebrhatu
- Section of Cellular and Molecular Microbiology, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, Tübingen, Germany
| | - Tariq Ganief
- Proteome Center Tübingen, University of Tübingen, Tübingen, Germany
| | - Boris Macek
- Proteome Center Tübingen, University of Tübingen, Tübingen, Germany
| | - Samuel Wagner
- Section of Cellular and Molecular Microbiology, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, Tübingen, Germany.,German Center for Infection Research, Partner-site Tübingen, Tübingen, Germany
| | | | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK. .,Central Oxford Structural Microscopy and Imaging Centre, University of Oxford, Oxford, UK.
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28
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Kuhlen L, Abrusci P, Johnson S, Gault J, Deme J, Caesar J, Dietsche T, Mebrhatu MT, Ganief T, Macek B, Wagner S, Robinson CV, Lea SM. Structure of the core of the type III secretion system export apparatus. Nat Struct Mol Biol 2018; 25:583-590. [PMID: 29967543 PMCID: PMC6233869 DOI: 10.1038/s41594-018-0086-9] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 06/01/2018] [Indexed: 12/04/2022]
Abstract
Export of proteins through type three secretion systems is critical for motility and virulence of many major bacterial pathogens. Three putative integral membrane proteins (FliP, FliQ, FliR) are suggested to form the core of an export gate in the inner membrane, but their structure, assembly and location within the final nanomachine remain unclear. We here present the structure of the Salmonella Typhimurium complex at 4.2 Å by cryo-electron microscopy. None of the subunits adopt canonical integral membrane protein topologies and common helix-turn-helix structural elements allow them to form a helical assembly with 5:4:1 stoichiometry. Fitting of the structure into reconstructions of intact secretion systems, combined with cross-linking, localize the export gate as a core component of the periplasmic portion of the machinery. This study thereby identifies the export gate as a key element of the secretion channel and implies that it primes the helical architecture of the components assembling downstream.
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Affiliation(s)
- Lucas Kuhlen
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.,Department of Chemistry, University of Oxford, Oxford, UK
| | - Patrizia Abrusci
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.,Structural Genomics Consortium, University of Oxford, Oxford, UK
| | - Steven Johnson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Joseph Gault
- Department of Chemistry, University of Oxford, Oxford, UK
| | - Justin Deme
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.,Central Oxford Structural Microscopy and Imaging Centre, University of Oxford, Oxford, UK
| | - Joseph Caesar
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.,Central Oxford Structural Microscopy and Imaging Centre, University of Oxford, Oxford, UK
| | - Tobias Dietsche
- Section of Cellular and Molecular Microbiology, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, Tübingen, Germany
| | - Mehari Tesfazgi Mebrhatu
- Section of Cellular and Molecular Microbiology, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, Tübingen, Germany
| | - Tariq Ganief
- Proteome Center Tübingen, University of Tübingen, Tübingen, Germany
| | - Boris Macek
- Proteome Center Tübingen, University of Tübingen, Tübingen, Germany
| | - Samuel Wagner
- Section of Cellular and Molecular Microbiology, Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, Tübingen, Germany.,German Center for Infection Research, Partner-site Tübingen, Tübingen, Germany
| | | | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK. .,Central Oxford Structural Microscopy and Imaging Centre, University of Oxford, Oxford, UK.
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29
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Abstract
Pioneering cell aggregation experiments from the Artavanis-Tsakonas group in the late 1980's localized the core ligand recognition sequence in the Drosophila Notch receptor to epidermal growth factor-like (EGF) domains 11 and 12. Since then, advances in protein expression, structure determination methods and functional assays have enabled us to define the molecular basis of the core receptor/ligand interaction and given new insights into the architecture of the Notch complex at the cell surface. We now know that Notch EGF11 and 12 interact with the Delta/Serrate/LAG-2 (DSL) and C2 domains of ligand and that membrane-binding, together with additional protein-protein interactions outside the core recognition domains, are likely to fine-tune generation of the Notch signal. Furthermore, structure determination of O-glycosylated variants of Notch alone or in complex with receptor fragments, has shown that these sugars contribute directly to the binding interface, as well as to stabilizing intra-molecular domain structure, providing some mechanistic insights into the observed modulatory effects of O-glycosylation on Notch activity.Future challenges lie in determining the complete extracellular architecture of ligand and receptor in order to understand (i) how Notch/ligand complexes may form at the cell surface in response to physiological cues, (ii) the role of lipid binding in stabilizing the Notch/ligand complex, (iii) the impact of O-glycosylation on binding and signalling and (iv) to dissect the different pathologies that arise as a consequence of mutations that affect proteins involved in the Notch pathway.
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Affiliation(s)
- Penny A Handford
- Department of Biochemistry, University of Oxford, Oxford, OX1 3RE, UK.
| | - Boguslawa Korona
- Department of Biochemistry, University of Oxford, Oxford, OX1 3RE, UK
| | - Richard Suckling
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | | | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
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30
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Roversi P, Johnson S, Preston SG, Nunn MA, Paesen GC, Austyn JM, Nuttall PA, Lea SM. Structural basis of cholesterol binding by a novel clade of dendritic cell modulators from ticks. Sci Rep 2017; 7:16057. [PMID: 29167574 PMCID: PMC5700055 DOI: 10.1038/s41598-017-16413-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 11/13/2017] [Indexed: 12/13/2022] Open
Abstract
Two crystal structures of Japanin, an 18 kDa immune-modulatory lipocalin from the Brown Ear Tick (Rhipicephalus appendiculatus), have been determined at 2.2 and 2.4 Å resolution. In both crystal forms the protein is in complex with cholesterol, which sits in a closed pocket at the centre of the lipocalin barrel. Both crystal forms are dimers, which are also observed in solution. Molecular modelling suggests that previously-described members of a tick protein family bearing high sequence homology to Japanin are also likely to bind cholesterol or cholesterol derivatives.
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Affiliation(s)
- Pietro Roversi
- Biochemistry Department, University of Oxford, Oxford, OX1 3QU, England, United Kingdom. .,Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, LE1 7RH, England, United Kingdom.
| | - Steven Johnson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, England, United Kingdom
| | - Stephen G Preston
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, England, United Kingdom
| | - Miles A Nunn
- Akari Therapeutics, Plc, 75/76 Wimpole Street, London, W1G 9RT, England, United Kingdom
| | - Guido C Paesen
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom
| | - Jonathan M Austyn
- Nuffield Department of Surgical Sciences, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, England, United Kingdom
| | - Patricia A Nuttall
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, England, United Kingdom
| | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, England, United Kingdom.
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31
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Suckling RJ, Korona B, Whiteman P, Chillakuri C, Holt L, Handford PA, Lea SM. Structural and functional dissection of the interplay between lipid and Notch binding by human Notch ligands. EMBO J 2017; 36:2204-2215. [PMID: 28572448 PMCID: PMC5538765 DOI: 10.15252/embj.201796632] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 04/06/2017] [Accepted: 04/07/2017] [Indexed: 12/30/2022] Open
Abstract
Recent data have expanded our understanding of Notch signalling by identifying a C2 domain at the N-terminus of Notch ligands, which has both lipid- and receptor-binding properties. We present novel structures of human ligands Jagged2 and Delta-like4 and human Notch2, together with functional assays, which suggest that ligand-mediated coupling of membrane recognition and Notch binding is likely to be critical in establishing the optimal context for Notch signalling. Comparisons between the Jagged and Delta family show a huge diversity in the structures of the loops at the apex of the C2 domain implicated in membrane recognition and Jagged1 missense mutations, which affect these loops and are associated with extrahepatic biliary atresia, lead to a loss of membrane recognition, but do not alter Notch binding. Taken together, these data suggest that C2 domain binding to membranes is an important element in tuning ligand-dependent Notch signalling in different physiological contexts.
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Affiliation(s)
| | | | - Pat Whiteman
- Department of BiochemistryUniversity of OxfordOxfordUK
| | | | - Laurie Holt
- Department of BiochemistryUniversity of OxfordOxfordUK
| | | | - Susan M Lea
- Sir William Dunn School of PathologyUniversity of OxfordOxfordUK
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32
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Feng Z, Caballe A, Wainman A, Johnson S, Haensele AFM, Cottee MA, Conduit PT, Lea SM, Raff JW. Structural Basis for Mitotic Centrosome Assembly in Flies. Cell 2017; 169:1078-1089.e13. [PMID: 28575671 PMCID: PMC5457487 DOI: 10.1016/j.cell.2017.05.030] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 03/23/2017] [Accepted: 05/15/2017] [Indexed: 11/16/2022]
Abstract
In flies, Centrosomin (Cnn) forms a phosphorylation-dependent scaffold that recruits proteins to the mitotic centrosome, but how Cnn assembles into a scaffold is unclear. We show that scaffold assembly requires conserved leucine zipper (LZ) and Cnn-motif 2 (CM2) domains that co-assemble into a 2:2 complex in vitro. We solve the crystal structure of the LZ:CM2 complex, revealing that both proteins form helical dimers that assemble into an unusual tetramer. A slightly longer version of the LZ can form micron-scale structures with CM2, whose assembly is stimulated by Plk1 phosphorylation in vitro. Mutating individual residues that perturb LZ:CM2 tetramer assembly perturbs the formation of these micron-scale assemblies in vitro and Cnn-scaffold assembly in vivo. Thus, Cnn molecules have an intrinsic ability to form large, LZ:CM2-interaction-dependent assemblies that are critical for mitotic centrosome assembly. These studies provide the first atomic insight into a molecular interaction required for mitotic centrosome assembly. The conserved PReM and CM2 domains of Cnn co-assemble into micron-scale structures The crystal structure of the PReM-LZ:CM2 complex is solved to 1.82 Å Mutations that block PReM-LZ:CM2 assembly in vitro block centrosome assembly in vivo Phosphorylation of PReM by Polo/Plk1 promotes scaffold assembly in vitro and in vivo
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Affiliation(s)
- Zhe Feng
- The Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Anna Caballe
- The Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Alan Wainman
- The Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Steven Johnson
- The Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Andreas F M Haensele
- The Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Matthew A Cottee
- The Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Paul T Conduit
- The Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Susan M Lea
- The Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
| | - Jordan W Raff
- The Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
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Chattaway J, Ramirez-Valdez RA, Chappell PE, Caesar JJE, Lea SM, Kaufman J. Different modes of variation for each BG lineage suggest different functions. Open Biol 2017; 6:rsob.160188. [PMID: 27628321 PMCID: PMC5043582 DOI: 10.1098/rsob.160188] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Accepted: 08/17/2016] [Indexed: 01/14/2023] Open
Abstract
Mammalian butyrophilins have various important functions, one for lipid binding but others as ligands for co-inhibition of αβ T cells or for stimulation of γδ T cells in the immune system. The chicken BG homologues are dimers, with extracellular immunoglobulin variable (V) domains joined by cysteines in the loop equivalent to complementarity-determining region 1 (CDR1). BG genes are found in three genomic locations: BG0 on chromosome 2, BG1 in the classical MHC (the BF-BL region) and many BG genes in the BG region just outside the MHC. Here, we show that BG0 is virtually monomorphic, suggesting housekeeping function(s) consonant with the ubiquitous tissue distribution. BG1 has allelic polymorphism but minimal sequence diversity, with the few polymorphic residues at the interface of the two V domains, suggesting that BG1 is recognized by receptors in a conserved fashion. Any phenotypic variation should be due to the intracellular region, with differential exon usage between alleles. BG genes in the BG region can generate diversity by exchange of sequence cassettes located in loops equivalent to CDR1 and CDR2, consonant with recognition of many ligands or antigens for immune defence. Unlike the mammalian butyrophilins, there are at least three modes by which BG genes evolve.
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Affiliation(s)
- John Chattaway
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | | | - Paul E Chappell
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Joseph J E Caesar
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Jim Kaufman
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
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Csincsi ÁI, Szabó Z, Bánlaki Z, Uzonyi B, Cserhalmi M, Kárpáti É, Tortajada A, Caesar JJE, Prohászka Z, Jokiranta TS, Lea SM, Rodríguez de Córdoba S, Józsi M. FHR-1 Binds to C-Reactive Protein and Enhances Rather than Inhibits Complement Activation. J Immunol 2017; 199:292-303. [PMID: 28533443 DOI: 10.4049/jimmunol.1600483] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 04/21/2017] [Indexed: 01/28/2023]
Abstract
Factor H-related protein (FHR) 1 is one of the five human FHRs that share sequence and structural homology with the alternative pathway complement inhibitor FH. Genetic studies on disease associations and functional analyses indicate that FHR-1 enhances complement activation by competitive inhibition of FH binding to some surfaces and immune proteins. We have recently shown that FHR-1 binds to pentraxin 3. In this study, our aim was to investigate whether FHR-1 binds to another pentraxin, C-reactive protein (CRP), analyze the functional relevance of this interaction, and study the role of FHR-1 in complement activation and regulation. FHR-1 did not bind to native, pentameric CRP, but it bound strongly to monomeric CRP via its C-terminal domains. FHR-1 at high concentration competed with FH for CRP binding, indicating possible complement deregulation also on this ligand. FHR-1 did not inhibit regulation of solid-phase C3 convertase by FH and did not inhibit terminal complement complex formation induced by zymosan. On the contrary, by binding C3b, FHR-1 allowed C3 convertase formation and thereby enhanced complement activation. FHR-1/CRP interactions increased complement activation via the classical and alternative pathways on surfaces such as the extracellular matrix and necrotic cells. Altogether, these results identify CRP as a ligand for FHR-1 and suggest that FHR-1 enhances, rather than inhibits, complement activation, which may explain the protective effect of FHR-1 deficiency in age-related macular degeneration.
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Affiliation(s)
- Ádám I Csincsi
- Hungarian Academy of Sciences-Eötvös Loránd University MTA-ELTE Lendület Complement Research Group, Department of Immunology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary
| | - Zsóka Szabó
- Hungarian Academy of Sciences-Eötvös Loránd University MTA-ELTE Lendület Complement Research Group, Department of Immunology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary
| | - Zsófia Bánlaki
- Hungarian Academy of Sciences-Eötvös Loránd University MTA-ELTE Lendület Complement Research Group, Department of Immunology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary
| | - Barbara Uzonyi
- Hungarian Academy of Sciences-Eötvös Loránd University MTA-ELTE Immunology Research Group, Department of Immunology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary
| | - Marcell Cserhalmi
- Hungarian Academy of Sciences-Eötvös Loránd University MTA-ELTE Lendület Complement Research Group, Department of Immunology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary
| | - Éva Kárpáti
- Hungarian Academy of Sciences-Eötvös Loránd University MTA-ELTE Lendület Complement Research Group, Department of Immunology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary
| | - Agustín Tortajada
- Departamento Medicina Celular y Molecular, Centro de Investigaciones Biológicas, 28040 Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras, 28040 Madrid, Spain
| | - Joseph J E Caesar
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Zoltán Prohászka
- Research Laboratory, 3rd Department of Internal Medicine, Semmelweis University, H-1125 Budapest, Hungary; and
| | - T Sakari Jokiranta
- Research Programs Unit, Immunobiology, Haartman Institute, University of Helsinki, FI-00014 Helsinki, Finland
| | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Santiago Rodríguez de Córdoba
- Departamento Medicina Celular y Molecular, Centro de Investigaciones Biológicas, 28040 Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras, 28040 Madrid, Spain
| | - Mihály Józsi
- Hungarian Academy of Sciences-Eötvös Loránd University MTA-ELTE Lendület Complement Research Group, Department of Immunology, ELTE Eötvös Loránd University, 1117 Budapest, Hungary;
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35
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Cottee MA, Johnson S, Raff JW, Lea SM. A key centriole assembly interaction interface between human PLK4 and STIL appears to not be conserved in flies. Biol Open 2017; 6:381-389. [PMID: 28202467 PMCID: PMC5374404 DOI: 10.1242/bio.024661] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
A small number of proteins form a conserved pathway of centriole duplication. In
humans and flies, the binding of PLK4/Sak to STIL/Ana2 initiates
daughter centriole assembly. In humans, this interaction is mediated by an
interaction between the Polo-Box-3 (PB3) domain of PLK4 and the coiled-coil
domain of STIL (HsCCD). We showed previously that the
Drosophila Ana2 coiled-coil domain (DmCCD) is essential for
centriole assembly, but it forms a tight parallel tetramer in
vitro that likely precludes an interaction with PB3. Here, we show
that the isolated HsCCD and HsPB3 domains form a mixture of homo-multimers
in vitro, but these readily dissociate when mixed to form
the previously described 1:1 HsCCD:HsPB3 complex. In contrast, although
Drosophila PB3 (DmPB3) adopts a canonical polo-box fold, it
does not detectably interact with DmCCD in vitro. Thus,
surprisingly, a key centriole assembly interaction interface appears to differ
between humans and flies. Summary: PLK4 and STIL/Ana2 proteins interact to promote centriole
duplication. We show that these proteins may homo-multimerise in multiple ways,
and that their interaction is likely complex and may differ between species.
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Affiliation(s)
- Matthew A Cottee
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Steven Johnson
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Jordan W Raff
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
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36
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Ahn J, Jore MM, Johnson S, Lea SM. Structural and functional insights into properdin of the complement alternative pathway. Immunobiology 2016. [DOI: 10.1016/j.imbio.2016.06.224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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37
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Berry JL, Xu Y, Ward PN, Lea SM, Matthews SJ, Pelicic V. A Comparative Structure/Function Analysis of Two Type IV Pilin DNA Receptors Defines a Novel Mode of DNA Binding. Structure 2016; 24:926-34. [PMID: 27161979 PMCID: PMC4906244 DOI: 10.1016/j.str.2016.04.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 03/19/2016] [Accepted: 04/04/2016] [Indexed: 11/29/2022]
Abstract
DNA transformation is a widespread process allowing bacteria to capture free DNA by using filamentous nano-machines composed of type IV pilins. These proteins can act as DNA receptors as demonstrated by the finding that Neisseria meningitidis ComP minor pilin has intrinsic DNA-binding ability. ComP binds DNA better when it contains the DNA-uptake sequence (DUS) motif abundant in this species genome, playing a role in its trademark ability to selectively take up its own DNA. Here, we report high-resolution structures for meningococcal ComP and Neisseria subflava ComPsub, which recognize different DUS motifs. We show that they are structurally identical type IV pilins that pack readily into filament models and display a unique DD region delimited by two disulfide bonds. Functional analysis of ComPsub defines a new mode of DNA binding involving the DD region, adapted for exported DNA receptors.
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Affiliation(s)
- Jamie-Lee Berry
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Yingqi Xu
- Centre for Structural Biology, Imperial College London, London SW7 2AZ, UK
| | - Philip N Ward
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Stephen J Matthews
- Centre for Structural Biology, Imperial College London, London SW7 2AZ, UK.
| | - Vladimir Pelicic
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK.
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38
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Jore MM, Johnson S, Sheppard D, Barber NM, Li YI, Nunn MA, Elmlund H, Lea SM. Structural basis for therapeutic inhibition of complement C5. Nat Struct Mol Biol 2016; 23:378-86. [PMID: 27018802 PMCID: PMC5771465 DOI: 10.1038/nsmb.3196] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 03/02/2016] [Indexed: 01/03/2023]
Abstract
Activation of complement C5 generates the potent anaphylatoxin C5a and leads to pathogen lysis, inflammation and cell damage. The therapeutic potential of C5 inhibition has been demonstrated by eculizumab, one of the world's most expensive drugs. However, the mechanism of C5 activation by C5 convertases remains elusive, thus limiting development of therapeutics. Here we identify and characterize a new protein family of tick-derived C5 inhibitors. Structures of C5 in complex with the new inhibitors, the phase I and phase II inhibitor OmCI, or an eculizumab Fab reveal three distinct binding sites on C5 that all prevent activation of C5. The positions of the inhibitor-binding sites and the ability of all three C5-inhibitor complexes to competitively inhibit the C5 convertase conflict with earlier steric-inhibition models, thus suggesting that a priming event is needed for activation.
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Affiliation(s)
- Matthijs M Jore
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Steven Johnson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Devon Sheppard
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Natalie M Barber
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Yang I Li
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Miles A Nunn
- Centre for Ecology and Hydrology, Wallingford, UK
| | - Hans Elmlund
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, Victoria, Australia
| | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, Victoria, Australia
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39
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Weisshuhn PC, Sheppard D, Taylor P, Whiteman P, Lea SM, Handford PA, Redfield C. Non-Linear and Flexible Regions of the Human Notch1 Extracellular Domain Revealed by High-Resolution Structural Studies. Structure 2016; 24:555-566. [PMID: 26996961 PMCID: PMC4826273 DOI: 10.1016/j.str.2016.02.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 02/09/2016] [Accepted: 02/17/2016] [Indexed: 12/30/2022]
Abstract
The Notch receptor is a key component of a core metazoan signaling pathway activated by Delta/Serrate/Lag-2 ligands expressed on an adjacent cell. This results in a short-range signal with profound effects on cell-fate determination, cell proliferation, and cell death. Key to understanding receptor function is structural knowledge of the large extracellular portion of Notch which contains multiple repeats of epidermal growth factor (EGF)-like domains. Here we investigate the EGF4-13 region of human Notch1 (hN1) using a multidisciplinary approach. Ca(2+)-binding measurements, X-ray crystallography, {(1)H}-(15)N heteronuclear nuclear Overhauser effects, and residual dipolar couplings support a non-linear organization for the EGF4-13 region with a rigid, bent conformation for EGF4-7 and a single flexible linkage between EGF9 and EGF10. These data allow us to construct an informed model for EGF10-13 which, in conjunction with comparative binding studies, demonstrates that EGF10 has an important role in determining Notch receptor sensitivity to Dll-4.
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Affiliation(s)
- Philip C Weisshuhn
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Devon Sheppard
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Paul Taylor
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Pat Whiteman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Penny A Handford
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
| | - Christina Redfield
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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40
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McDowell MA, Marcoux J, McVicker G, Johnson S, Fong YH, Stevens R, Bowman LAH, Degiacomi MT, Yan J, Wise A, Friede ME, Benesch JLP, Deane JE, Tang CM, Robinson CV, Lea SM. Characterisation of Shigella Spa33 and Thermotoga FliM/N reveals a new model for C-ring assembly in T3SS. Mol Microbiol 2015; 99:749-66. [PMID: 26538516 PMCID: PMC4832279 DOI: 10.1111/mmi.13267] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2015] [Indexed: 11/06/2022]
Abstract
Flagellar type III secretion systems (T3SS) contain an essential cytoplasmic‐ring (C‐ring) largely composed of two proteins FliM and FliN, whereas an analogous substructure for the closely related non‐flagellar (NF) T3SS has not been observed in situ. We show that the spa33 gene encoding the putative NF‐T3SS C‐ring component in Shigella flexneri is alternatively translated to produce both full‐length (Spa33‐FL) and a short variant (Spa33‐C), with both required for secretion. They associate in a 1:2 complex (Spa33‐FL/C2) that further oligomerises into elongated arrays in vitro. The structure of Spa33‐C2 and identification of an unexpected intramolecular pseudodimer in Spa33‐FL reveal a molecular model for their higher order assembly within NF‐T3SS. Spa33‐FL and Spa33‐C are identified as functional counterparts of a FliM–FliN fusion and free FliN respectively. Furthermore, we show that Thermotoga maritima
FliM and FliN form a 1:3 complex structurally equivalent to Spa33‐FL/C2, allowing us to propose a unified model for C‐ring assembly by NF‐T3SS and flagellar‐T3SS.
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Affiliation(s)
| | - Julien Marcoux
- Department of Chemistry, University of Oxford, Oxford, UK
| | - Gareth McVicker
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Steven Johnson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Yu Hang Fong
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Rebecca Stevens
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Lesley A H Bowman
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | | | - Jun Yan
- Department of Chemistry, University of Oxford, Oxford, UK
| | - Adam Wise
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Miriam E Friede
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | | | - Janet E Deane
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Christoph M Tang
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | | | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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41
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Chappell PE, Garner LI, Yan J, Metcalfe C, Hatherley D, Johnson S, Robinson CV, Lea SM, Brown MH. Structures of CD6 and Its Ligand CD166 Give Insight into Their Interaction. Structure 2015; 23:1426-1436. [PMID: 26146185 PMCID: PMC4533223 DOI: 10.1016/j.str.2015.05.019] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 05/18/2015] [Accepted: 05/21/2015] [Indexed: 11/28/2022]
Abstract
CD6 is a transmembrane protein with an extracellular region containing three scavenger receptor cysteine rich (SRCR) domains. The membrane proximal domain of CD6 binds the N-terminal immunoglobulin superfamily (IgSF) domain of another cell surface receptor, CD166, which also engages in homophilic interactions. CD6 expression is mainly restricted to T cells, and the interaction between CD6 and CD166 regulates T-cell activation. We have solved the X-ray crystal structures of the three SRCR domains of CD6 and two N-terminal domains of CD166. This first structure of consecutive SRCR domains reveals a nonlinear organization. We characterized the binding sites on CD6 and CD166 and showed that a SNP in CD6 causes glycosylation that hinders the CD6/CD166 interaction. Native mass spectrometry analysis showed that there is competition between the heterophilic and homophilic interactions. These data give insight into how interactions of consecutive SRCR domains are perturbed by SNPs and potential therapeutic reagents. First structure of consecutive scavenger receptor cysteine rich domains in CD6 Structure of the two N-terminal domains of CD166 which is the ligand for CD6 Mapping binding sites on CD6 and CD166 Insight into how CD6 and its interactions are perturbed by polymorphisms and mAbs
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Affiliation(s)
- Paul E Chappell
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Lee I Garner
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Jun Yan
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Clive Metcalfe
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Deborah Hatherley
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Steven Johnson
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Carol V Robinson
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Marion H Brown
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
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42
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Cottee MA, Muschalik N, Johnson S, Leveson J, Raff JW, Lea SM. The homo-oligomerisation of both Sas-6 and Ana2 is required for efficient centriole assembly in flies. eLife 2015; 4:e07236. [PMID: 26002084 PMCID: PMC4471874 DOI: 10.7554/elife.07236] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 05/22/2015] [Indexed: 12/29/2022] Open
Abstract
Sas-6 and Ana2/STIL proteins are required for centriole duplication and the homo-oligomerisation properties of Sas-6 help establish the ninefold symmetry of the central cartwheel that initiates centriole assembly. Ana2/STIL proteins are poorly conserved, but they all contain a predicted Central Coiled-Coil Domain (CCCD). Here we show that the Drosophila Ana2 CCCD forms a tetramer, and we solve its structure to 0.8 Å, revealing that it adopts an unusual parallel-coil topology. We also solve the structure of the Drosophila Sas-6 N-terminal domain to 2.9 Å revealing that it forms higher-order oligomers through canonical interactions. Point mutations that perturb Sas-6 or Ana2 homo-oligomerisation in vitro strongly perturb centriole assembly in vivo. Thus, efficient centriole duplication in flies requires the homo-oligomerisation of both Sas-6 and Ana2, and the Ana2 CCCD tetramer structure provides important information on how these proteins might cooperate to form a cartwheel structure. DOI:http://dx.doi.org/10.7554/eLife.07236.001 Most animal cells contain structures known as centrioles. Typically, a cell that is not dividing contains a pair of centrioles. But when a cell prepares to divide, the centrioles are duplicated. The two pairs of centrioles then organize the scaffolding that shares the genetic material equally between the newly formed cells at cell division. Centriole assembly is tightly regulated and abnormalities in this process can lead to developmental defects and cancer. Centrioles likely contain several hundred proteins, but only a few of these are strictly needed for centriole assembly. New centrioles usually assemble from a cartwheel-like arrangement of proteins, which includes a protein called SAS-6. Previous work has suggested that in the fruit fly Drosophila melanogaster, Sas-6 can only form this cartwheel when another protein called Ana2 is also present, but the details of this process are unclear. Now, Cottee, Muschalik et al. have investigated potential features in the Ana2 protein that might be important for centriole assembly. These experiments revealed that a region in the Ana2 protein, called the ‘central coiled-coil domain’, is required to target Ana2 to centrioles. Furthermore, purified coiled-coil domains were found to bind together in groups of four (called tetramers). Cottee, Muschalik et al. then used a technique called X-ray crystallography to work out the three-dimensional structure of one of these tetramers and part of the Sas-6 protein with a high level of detail. These structures confirmed that Sas-6 proteins also associate with each other. When fruit flies were engineered to produce either Ana2 or Sas-6 proteins that cannot self-associate, the flies' cells were unable to efficiently make centrioles. Furthermore, an independent study by Rogala et al. found similar results for a protein that is related to Ana2: a protein called SAS-5 from the microscopic worm Caenorhabditis elegans. Further work is needed to understand how Sas-6 and Ana2 work with each other to form the cartwheel-like arrangement at the core of centrioles. DOI:http://dx.doi.org/10.7554/eLife.07236.002
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Affiliation(s)
- Matthew A Cottee
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Nadine Muschalik
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Steven Johnson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Joanna Leveson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Jordan W Raff
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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43
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Chappell P, Meziane EK, Harrison M, Magiera Ł, Hermann C, Mears L, Wrobel AG, Durant C, Nielsen LL, Buus S, Ternette N, Mwangi W, Butter C, Nair V, Ahyee T, Duggleby R, Madrigal A, Roversi P, Lea SM, Kaufman J. Expression levels of MHC class I molecules are inversely correlated with promiscuity of peptide binding. eLife 2015; 4:e05345. [PMID: 25860507 PMCID: PMC4420994 DOI: 10.7554/elife.05345] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Accepted: 04/10/2015] [Indexed: 11/13/2022] Open
Abstract
Highly polymorphic major histocompatibility complex (MHC) molecules are at the heart of adaptive immune responses, playing crucial roles in many kinds of disease and in vaccination. We report that breadth of peptide presentation and level of cell surface expression of class I molecules are inversely correlated in both chickens and humans. This relationship correlates with protective responses against infectious pathogens including Marek's disease virus leading to lethal tumours in chickens and human immunodeficiency virus infection progressing to AIDS in humans. We propose that differences in peptide binding repertoire define two groups of MHC class I molecules strategically evolved as generalists and specialists for different modes of pathogen resistance. We suggest that differences in cell surface expression level ensure the development of optimal peripheral T cell responses. The inverse relationship of peptide repertoire and expression is evidently a fundamental property of MHC molecules, with ramifications extending beyond immunology and medicine to evolutionary biology and conservation.
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Affiliation(s)
- Paul Chappell
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - El Kahina Meziane
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Michael Harrison
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Łukasz Magiera
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Clemens Hermann
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Laura Mears
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Antony G Wrobel
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Charlotte Durant
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Lise Lotte Nielsen
- Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Søren Buus
- Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nicola Ternette
- Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | | | | | | | - Trudy Ahyee
- Anthony Nolan Research Institute, The Royal Free Hospital, London, United Kingdom
| | - Richard Duggleby
- Anthony Nolan Research Institute, The Royal Free Hospital, London, United Kingdom
| | - Alejandro Madrigal
- Anthony Nolan Research Institute, The Royal Free Hospital, London, United Kingdom
| | - Pietro Roversi
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Jim Kaufman
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
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44
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Csincsi ÁI, Kopp A, Zöldi M, Bánlaki Z, Uzonyi B, Hebecker M, Caesar JJE, Pickering MC, Daigo K, Hamakubo T, Lea SM, Goicoechea de Jorge E, Józsi M. Factor H-related protein 5 interacts with pentraxin 3 and the extracellular matrix and modulates complement activation. J Immunol 2015; 194:4963-73. [PMID: 25855355 PMCID: PMC4416742 DOI: 10.4049/jimmunol.1403121] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 03/11/2015] [Indexed: 01/28/2023]
Abstract
The physiological roles of the factor H (FH)-related proteins are controversial and poorly understood. Based on genetic studies, FH-related protein 5 (CFHR5) is implicated in glomerular diseases, such as atypical hemolytic uremic syndrome, dense deposit disease, and CFHR5 nephropathy. CFHR5 was also identified in glomerular immune deposits at the protein level. For CFHR5, weak complement regulatory activity and competition for C3b binding with the plasma complement inhibitor FH have been reported, but its function remains elusive. In this study, we identify pentraxin 3 (PTX3) as a novel ligand of CFHR5. Binding of native CFHR5 to PTX3 was detected in human plasma and the interaction was characterized using recombinant proteins. The binding of PTX3 to CFHR5 is of ∼2-fold higher affinity compared with that of FH. CFHR5 dose-dependently inhibited FH binding to PTX3 and also to the monomeric, denatured form of the short pentraxin C-reactive protein. Binding of PTX3 to CFHR5 resulted in increased C1q binding. Additionally, CFHR5 bound to extracellular matrix in vitro in a dose-dependent manner and competed with FH for binding. Altogether, CFHR5 reduced FH binding and its cofactor activity on pentraxins and the extracellular matrix, while at the same time allowed for enhanced C1q binding. Furthermore, CFHR5 allowed formation of the alternative pathway C3 convertase and supported complement activation. Thus, CFHR5 may locally enhance complement activation via interference with the complement-inhibiting function of FH, by enhancement of C1q binding, and by activating complement, thereby contributing to glomerular disease.
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Affiliation(s)
- Ádám I Csincsi
- Hungarian Academy of Sciences-Eötvös Loránd University "Lendület" Complement Research Group, Department of Immunology, Eötvös Loránd University, 1117 Budapest, Hungary
| | - Anne Kopp
- Junior Research Group for Cellular Immunobiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, 07745 Jena, Germany
| | - Miklós Zöldi
- Hungarian Academy of Sciences-Eötvös Loránd University "Lendület" Complement Research Group, Department of Immunology, Eötvös Loránd University, 1117 Budapest, Hungary
| | - Zsófia Bánlaki
- Hungarian Academy of Sciences-Eötvös Loránd University "Lendület" Complement Research Group, Department of Immunology, Eötvös Loránd University, 1117 Budapest, Hungary
| | - Barbara Uzonyi
- Hungarian Academy of Sciences-Eötvös Loránd University Immunology Research Group, Department of Immunology, Eötvös Loránd University, 1117 Budapest, Hungary
| | - Mario Hebecker
- Junior Research Group for Cellular Immunobiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, 07745 Jena, Germany
| | - Joseph J E Caesar
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RF, United Kingdom
| | - Matthew C Pickering
- Centre for Complement and Inflammation Research, Department of Medicine, Imperial College, London W12 0NN, United Kingdom; and
| | - Kenji Daigo
- Research Center for Advanced Science and Technology, University of Tokyo, Tokyo 153-8904, Japan
| | - Takao Hamakubo
- Research Center for Advanced Science and Technology, University of Tokyo, Tokyo 153-8904, Japan
| | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RF, United Kingdom
| | - Elena Goicoechea de Jorge
- Centre for Complement and Inflammation Research, Department of Medicine, Imperial College, London W12 0NN, United Kingdom; and
| | - Mihály Józsi
- Hungarian Academy of Sciences-Eötvös Loránd University "Lendület" Complement Research Group, Department of Immunology, Eötvös Loránd University, 1117 Budapest, Hungary; Junior Research Group for Cellular Immunobiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, 07745 Jena, Germany;
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45
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Grabarczyk DB, Chappell PE, Eisel B, Johnson S, Lea SM, Berks BC. Mechanism of thiosulfate oxidation in the SoxA family of cysteine-ligated cytochromes. J Biol Chem 2015; 290:9209-21. [PMID: 25673696 PMCID: PMC4423706 DOI: 10.1074/jbc.m114.618025] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Indexed: 11/23/2022] Open
Abstract
Thiosulfate dehydrogenase (TsdA) catalyzes the oxidation of two thiosulfate molecules to form tetrathionate and is predicted to use an unusual cysteine-ligated heme as the catalytic cofactor. We have determined the structure of Allochromatium vinosum TsdA to a resolution of 1.3 Å. This structure confirms the active site heme ligation, identifies a thiosulfate binding site within the active site cavity, and reveals an electron transfer route from the catalytic heme, through a second heme group to the external electron acceptor. We provide multiple lines of evidence that the catalytic reaction proceeds through the intermediate formation of a S-thiosulfonate derivative of the heme cysteine ligand: the cysteine is reactive and is accessible to electrophilic attack; cysteine S-thiosulfonate is formed by the addition of thiosulfate or following the reverse reaction with tetrathionate; the S-thiosulfonate modification is removed through catalysis; and alkylating the cysteine blocks activity. Active site amino acid residues required for catalysis were identified by mutagenesis and are inferred to also play a role in stabilizing the S-thiosulfonate intermediate. The enzyme SoxAX, which catalyzes the first step in the bacterial Sox thiosulfate oxidation pathway, is homologous to TsdA and can be inferred to use a related catalytic mechanism.
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Affiliation(s)
- Daniel B Grabarczyk
- From the Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom and
| | - Paul E Chappell
- the Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom
| | - Bianca Eisel
- From the Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom and
| | - Steven Johnson
- the Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom
| | - Susan M Lea
- the Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom
| | - Ben C Berks
- From the Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom and
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46
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Caesar JJE, Lavender H, Ward PN, Exley RM, Eaton J, Chittock E, Malik TH, Goiecoechea De Jorge E, Pickering MC, Tang CM, Lea SM. Competition between antagonistic complement factors for a single protein on N. meningitidis rules disease susceptibility. eLife 2014; 3. [PMID: 25534642 PMCID: PMC4273445 DOI: 10.7554/elife.04008] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 11/25/2014] [Indexed: 11/13/2022] Open
Abstract
Genome-wide association studies have found variation within the complement factor H gene family links to host susceptibility to meningococcal disease caused by infection with Neisseria meningitidis (Davila et al., 2010). Mechanistic insights have been challenging since variation within this locus is complex and biological roles of the factor H-related proteins, unlike factor H, are incompletely understood. N. meningitidis subverts immune responses by hijacking a host-immune regulator, complement factor H (CFH), to the bacterial surface (Schneider et al., 2006; Madico et al., 2007; Schneider et al., 2009). We demonstrate that complement factor-H related 3 (CFHR3) promotes immune activation by acting as an antagonist of CFH. Conserved sequences between CFH and CFHR3 mean that the bacterium cannot sufficiently distinguish between these two serum proteins to allow it to hijack the regulator alone. The level of protection from complement attack achieved by circulating N. meningitidis therefore depends on the relative levels of CFH and CFHR3 in serum. These data may explain the association between genetic variation in both CFH and CFHR3 and susceptibility to meningococcal disease.
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Affiliation(s)
- Joseph J E Caesar
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Hayley Lavender
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Philip N Ward
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Rachel M Exley
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Jack Eaton
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Emily Chittock
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Talat H Malik
- Centre for Complement and Inflammation Research, Department of Medicine, Imperial College, London, United Kingdom
| | - Elena Goiecoechea De Jorge
- Centre for Complement and Inflammation Research, Department of Medicine, Imperial College, London, United Kingdom
| | - Matthew C Pickering
- Centre for Complement and Inflammation Research, Department of Medicine, Imperial College, London, United Kingdom
| | - Christoph M Tang
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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47
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Yong SC, Roversi P, Lillington J, Rodriguez F, Krehenbrink M, Zeldin OB, Garman EF, Lea SM, Berks BC. A complex iron-calcium cofactor catalyzing phosphotransfer chemistry. Science 2014; 345:1170-1173. [PMID: 25190793 DOI: 10.1126/science.1254237] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Alkaline phosphatases play a crucial role in phosphate acquisition by microorganisms. To expand our understanding of catalysis by this class of enzymes, we have determined the structure of the widely occurring microbial alkaline phosphatase PhoX. The enzyme contains a complex active-site cofactor comprising two antiferromagnetically coupled ferric iron ions (Fe(3+)), three calcium ions (Ca(2+)), and an oxo group bridging three of the metal ions. Notably, the main part of the cofactor resembles synthetic oxide-centered triangular metal complexes. Structures of PhoX-ligand complexes reveal how the active-site metal ions bind substrate and implicate the cofactor oxo group in the catalytic mechanism. The presence of iron in PhoX raises the possibility that iron bioavailability limits microbial phosphate acquisition.
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Affiliation(s)
- Shee Chien Yong
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Pietro Roversi
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom
| | - James Lillington
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom
| | - Fernanda Rodriguez
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Martin Krehenbrink
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Oliver B Zeldin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Elspeth F Garman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom
| | - Ben C Berks
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
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48
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Rodriguez F, Lillington J, Johnson S, Timmel CR, Lea SM, Berks BC. Crystal structure of the Bacillus subtilis phosphodiesterase PhoD reveals an iron and calcium-containing active site. J Biol Chem 2014; 289:30889-99. [PMID: 25217636 PMCID: PMC4223295 DOI: 10.1074/jbc.m114.604892] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The PhoD family of extra-cytoplasmic phosphodiesterases are among the most commonly occurring bacterial phosphatases. The exemplars for this family are the PhoD protein of Bacillus subtilis and the phospholipase D of Streptomyces chromofuscus. We present the crystal structure of B. subtilis PhoD. PhoD is most closely related to purple acid phosphatases (PAPs) with both types of enzyme containing a tyrosinate-ligated Fe3+ ion. However, the PhoD active site diverges from that found in PAPs and uses two Ca2+ ions instead of the single extra Fe2+, Mn2+, or Zn2+ ion present in PAPs. The PhoD crystals contain a phosphate molecule that coordinates all three active site metal ions and that is proposed to represent a product complex. A C-terminal helix lies over the active site and controls access to the catalytic center. The structure of PhoD defines a new phosphatase active site architecture based on Fe3+ and Ca2+ ions.
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Affiliation(s)
- Fernanda Rodriguez
- From the Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU
| | - James Lillington
- the Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, and the Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Steven Johnson
- the Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, and
| | - Christiane R Timmel
- the Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Susan M Lea
- the Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, and
| | - Ben C Berks
- From the Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU,
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49
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Watson R, Wearmouth E, McLoughlin AC, Jackson A, Ward S, Bertram P, Bennaceur K, Barker CE, Pappworth IY, Kavanagh D, Lea SM, Atkinson JP, Goodship THJ, Marchbank KJ. Autoantibodies to CD59, CD55, CD46 or CD35 are not associated with atypical haemolytic uraemic syndrome (aHUS). Mol Immunol 2014; 63:287-96. [PMID: 25150608 DOI: 10.1016/j.molimm.2014.07.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Accepted: 07/16/2014] [Indexed: 01/31/2023]
Abstract
Autoantibody formation against Factor H (FH) is found in 7-10% of patients who are diagnosed with atypical haemolytic uraemic syndrome (aHUS). These autoantibodies predominately target the C-terminal cell binding recognition domain of FH and are associated with absence of FHR1. Additional autoantibodies have also been identified in association with aHUS, for example autoantibodies to Factor I. Based on this, and that there are genetic mutations in other complement regulators and activators associated with aHUS, we hypothesised that other complement regulator proteins, particularly surface bound regulators in the kidney, might be the target for autoantibody formation in aHUS. Therefore, we assayed serum derived from 89 patients in the Newcastle aHUS cohort for the presence of autoantibodies to CD46 (membrane cofactor protein, MCP), CD55 (decay accelerating factor, DAF), CD35 (complement receptor type 1, CR1; TP10) and CD59. We also assayed 100 healthy blood donors to establish the normal levels of reactivity towards these proteins in the general population. Recombinant proteins CD46 and CD55 (purified from Escherichia coli) as well as soluble CR1 (CD35) and oligomeric C4BP-CD59 (purified from eukaryotic cell media) were used in ELISA to detect high responders. False positive results were established though Western blot and flow cytometric analysis. After excluding false positive responders to bacterial proteins in the CD46 and CD55 preparations, and responses to blood group antigens in CD35, we found no significant level of patient serum IgG reactivity with CD46, CD55, CD35 or CD59 above that detected in the normal population. These results suggest that membrane anchored complement regulators are not a target for autoantibody generation in aHUS.
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Affiliation(s)
- Rachael Watson
- Institutes of Cellular and Genetic Medicine, Newcastle University, Newcastle-upon-Tyne, UK
| | - Emma Wearmouth
- Institutes of Cellular and Genetic Medicine, Newcastle University, Newcastle-upon-Tyne, UK
| | - Amy-Claire McLoughlin
- Institutes of Cellular and Genetic Medicine, Newcastle University, Newcastle-upon-Tyne, UK
| | - Arthur Jackson
- Institutes of Cellular and Genetic Medicine, Newcastle University, Newcastle-upon-Tyne, UK
| | - Sophie Ward
- Institutes of Cellular and Genetic Medicine, Newcastle University, Newcastle-upon-Tyne, UK
| | - Paula Bertram
- Division of Rheumatology, Washington University School of Medicine, St. Louis, MO, USA
| | - Karim Bennaceur
- Institutes of Cellular and Genetic Medicine, Newcastle University, Newcastle-upon-Tyne, UK
| | - Catriona E Barker
- Institutes of Cellular and Genetic Medicine, Newcastle University, Newcastle-upon-Tyne, UK
| | - Isabel Y Pappworth
- Institutes of Cellular and Genetic Medicine, Newcastle University, Newcastle-upon-Tyne, UK
| | - David Kavanagh
- Institutes of Cellular and Genetic Medicine, Newcastle University, Newcastle-upon-Tyne, UK
| | - Susan M Lea
- Sir William Dunn School of Pathology, University of Oxford, UK
| | - John P Atkinson
- Division of Rheumatology, Washington University School of Medicine, St. Louis, MO, USA
| | - Timothy H J Goodship
- Institutes of Cellular and Genetic Medicine, Newcastle University, Newcastle-upon-Tyne, UK
| | - Kevin J Marchbank
- Institutes of Cellular and Genetic Medicine, Newcastle University, Newcastle-upon-Tyne, UK.
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50
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Abstract
The Tat protein transport system is found in the cytoplasmic membrane of prokaryotes and the thylakoid membrane of plant chloroplasts. Unusually, the Tat system translocates proteins only after they have folded. Proteins are targeted to the Tat system by specific N-terminal signal peptides. High resolution structures have recently been determined for the TatA and TatC proteins that form the Tat translocation site. These structures provide a molecular framework for understanding the mechanism of Tat transport. The interactions between TatC and the signal peptide of the substrate protein can be provisionally modelled. However, the way that TatA and TatC combine in the active translocation site remains to be definitively established.
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Affiliation(s)
- Ben C Berks
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.
| | - Susan M Lea
- Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, United Kingdom.
| | - Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
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