1
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Oberoi J, Guiu XA, Outwin EA, Schellenberger P, Roumeliotis TI, Choudhary JS, Pearl LH. HSP90-CDC37-PP5 forms a structural platform for kinase dephosphorylation. Nat Commun 2022; 13:7343. [PMID: 36446791 PMCID: PMC9709061 DOI: 10.1038/s41467-022-35143-2] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 11/18/2022] [Indexed: 12/02/2022] Open
Abstract
Activation of client protein kinases by the HSP90 molecular chaperone system is affected by phosphorylation at multiple sites on HSP90, the kinase-specific co-chaperone CDC37, and the kinase client itself. Removal of regulatory phosphorylation from client kinases and their release from the HSP90-CDC37 system depends on the Ser/Thr phosphatase PP5, which associates with HSP90 via its N-terminal TPR domain. Here, we present the cryoEM structure of the oncogenic protein kinase client BRAFV600E bound to HSP90-CDC37, showing how the V600E mutation favours BRAF association with HSP90-CDC37. Structures of HSP90-CDC37-BRAFV600E complexes with PP5 in autoinhibited and activated conformations, together with proteomic analysis of its phosphatase activity on BRAFV600E and CRAF, reveal how PP5 is activated by recruitment to HSP90 complexes. PP5 comprehensively dephosphorylates client proteins, removing interaction sites for regulatory partners such as 14-3-3 proteins and thus performing a 'factory reset' of the kinase prior to release.
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Affiliation(s)
- Jasmeen Oberoi
- grid.12082.390000 0004 1936 7590Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ UK
| | - Xavi Aran Guiu
- grid.12082.390000 0004 1936 7590Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ UK
| | - Emily A. Outwin
- grid.12082.390000 0004 1936 7590Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ UK
| | - Pascale Schellenberger
- grid.12082.390000 0004 1936 7590Electron Microscopy Imaging centre, School of Life Sciences, University of Sussex, Falmer, BN1 9QG UK
| | - Theodoros I. Roumeliotis
- grid.18886.3fInstitute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London, SW3 6JB UK
| | - Jyoti S. Choudhary
- grid.18886.3fInstitute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London, SW3 6JB UK
| | - Laurence H. Pearl
- grid.12082.390000 0004 1936 7590Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ UK ,grid.18886.3fInstitute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London, SW3 6JB UK
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2
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Hallett ST, Campbell Harry I, Schellenberger P, Zhou L, Cronin N, Baxter J, Etheridge T, Murray J, Oliver A. Cryo-EM structure of the Smc5/6 holo-complex. Nucleic Acids Res 2022; 50:9505-9520. [PMID: 35993814 PMCID: PMC9458440 DOI: 10.1093/nar/gkac692] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 06/09/2022] [Revised: 07/14/2022] [Accepted: 07/30/2022] [Indexed: 01/06/2023] Open
Abstract
The Smc5/6 complex plays an essential role in the resolution of recombination intermediates formed during mitosis or meiosis, or as a result of the cellular response to replication stress. It also functions as a restriction factor preventing viral replication. Here, we report the cryogenic EM (cryo-EM) structure of the six-subunit budding yeast Smc5/6 holo-complex, reconstituted from recombinant proteins expressed in insect cells - providing both an architectural overview of the entire complex and an understanding of how the Nse1/3/4 subcomplex binds to the hetero-dimeric SMC protein core. In addition, we demonstrate that a region within the head domain of Smc5, equivalent to the 'W-loop' of Smc4 or 'F-loop' of Smc1, mediates an important interaction with Nse1. Notably, mutations that alter the surface-charge profile of the region of Nse1 which accepts the Smc5-loop, lead to a slow-growth phenotype and a global reduction in the chromatin-associated fraction of the Smc5/6 complex, as judged by single molecule localisation microscopy experiments in live yeast. Moreover, when taken together, our data indicates functional equivalence between the structurally unrelated KITE and HAWK accessory subunits associated with SMC complexes.
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Affiliation(s)
- Stephen T Hallett
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, UK
| | - Isabella Campbell Harry
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, UK
| | - Pascale Schellenberger
- Electron Microscopy Imaging Centre, School of Life Sciences, University of Sussex, Falmer, UK
| | - Lihong Zhou
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, UK
| | - Nora B Cronin
- London Consortium for CryoEM (LonCEM) Facility, The Francis Crick Institute, London, UK
| | - Jonathan Baxter
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, UK
| | - Thomas J Etheridge
- Correspondence may also be addressed to Thomas J. Etheridge. Tel: +44 1273 678123;
| | - Johanne M Murray
- Correspondence may also be addressed to Johanne M. Murray. Tel: +44 1273 877191;
| | - Antony W Oliver
- To whom correspondence should be addressed. Tel: +44 1273 678349;
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3
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Hallett ST, Schellenberger P, Zhou L, Beuron F, Morris E, Murray JM, Oliver AW. Nse5/6 is a negative regulator of the ATPase activity of the Smc5/6 complex. Nucleic Acids Res 2021; 49:4534-4549. [PMID: 33849072 PMCID: PMC8096239 DOI: 10.1093/nar/gkab234] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 12/13/2022] Open
Abstract
The multi-component Smc5/6 complex plays a critical role in the resolution of recombination intermediates formed during mitosis and meiosis, and in the cellular response to replication stress. Using recombinant proteins, we have reconstituted a series of defined Saccharomyces cerevisiae Smc5/6 complexes, visualised them by negative stain electron microscopy, and tested their ability to function as an ATPase. We find that only the six protein ‘holo-complex’ is capable of turning over ATP and that its activity is significantly increased by the addition of double-stranded DNA to reaction mixes. Furthermore, stimulation is wholly dependent on functional ATP-binding pockets in both Smc5 and Smc6. Importantly, we demonstrate that budding yeast Nse5/6 acts as a negative regulator of Smc5/6 ATPase activity, binding to the head-end of the complex to suppress turnover, irrespective of the DNA-bound status of the complex.
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Affiliation(s)
- Stephen T Hallett
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, UK
| | - Pascale Schellenberger
- Electron Microscopy Imaging Centre, School of Life Sciences, University of Sussex, Falmer, UK
| | - Lihong Zhou
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, UK
| | | | - Ed Morris
- The Institute of Cancer Research, London, UK
| | - Johanne M Murray
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, UK
| | - Antony W Oliver
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, UK
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4
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Alves DR, Nzakizwanayo J, Dedi C, Olympiou C, Hanin A, Kot W, Hansen L, Lametsch R, Gahan CGM, Schellenberger P, Ogilvie LA, Jones BV. Genomic and Ecogenomic Characterization of Proteus mirabilis Bacteriophages. Front Microbiol 2019; 10:1783. [PMID: 31447809 PMCID: PMC6691071 DOI: 10.3389/fmicb.2019.01783] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 07/18/2019] [Indexed: 01/21/2023] Open
Abstract
Proteus mirabilis often complicates the care of catheterized patients through the formation of crystalline biofilms which block urine flow. Bacteriophage therapy has been highlighted as a promising approach to control this problem, but relatively few phages infecting P. mirabilis have been characterized. Here we characterize five phages capable of infecting P. mirabilis, including those shown to reduce biofilm formation, and provide insights regarding the wider ecological and evolutionary relationships of these phages. Transmission electron microscopy (TEM) imaging of phages vB_PmiP_RS1pmA, vB_PmiP_RS1pmB, vB_PmiP_RS3pmA, and vB_PmiP_RS8pmA showed that all share morphologies characteristic of the Podoviridae family. The genome sequences of vB_PmiP_RS1pmA, vB_PmiP_RS1pmB, and vB_PmiP_RS3pmA showed these are species of the same phage differing only by point mutations, and are closely related to vB_PmiP_RS8pmA. Podophages characterized in this study were also found to share similarity in genome architecture and composition to other previously described P. mirabilis podophages (PM16 and PM75). In contrast, vB_PimP_RS51pmB showed morphology characteristic of the Myoviridae family, with no notable similarity to other phage genomes examined. Ecogenomic profiling of all phages revealed no association with human urinary tract viromes, but sequences similar to vB_PimP_RS51pmB were found within human gut, and human oral microbiomes. Investigation of wider host-phage evolutionary relationships through tetranucleotide profiling of phage genomes and bacterial chromosomes, indicated vB_PimP_RS51pmB has a relatively recent association with Morganella morganii and other non-Proteus members of the Morganellaceae family. Subsequent host range assays confirmed vB_PimP_RS51pmB can infect M. morganii.
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Affiliation(s)
- Diana R. Alves
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, United Kingdom
- Blond McIndoe Research Foundation, Queen Victoria Hospital, East Grinstead, United Kingdom
- Queen Victoria Hospital NHS Foundation Trust, East Grinstead, United Kingdom
| | - Jonathan Nzakizwanayo
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, United Kingdom
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Cinzia Dedi
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, United Kingdom
| | - Chara Olympiou
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, United Kingdom
- School of Pharmacy, Queen’s University, Belfast, United Kingdom
| | - Aurélie Hanin
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Witold Kot
- Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lars Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rene Lametsch
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Cormac G. M. Gahan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Pharmacy, University College Cork, Cork, Ireland
| | | | - Lesley A. Ogilvie
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, United Kingdom
| | - Brian V. Jones
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, United Kingdom
- Queen Victoria Hospital NHS Foundation Trust, East Grinstead, United Kingdom
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
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5
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Simon T, Pinioti S, Schellenberger P, Rajeeve V, Wendler F, Cutillas PR, King A, Stebbing J, Giamas G. Shedding of bevacizumab in tumour cells-derived extracellular vesicles as a new therapeutic escape mechanism in glioblastoma. Mol Cancer 2018; 17:132. [PMID: 30165850 PMCID: PMC6117885 DOI: 10.1186/s12943-018-0878-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [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: 07/16/2018] [Accepted: 08/15/2018] [Indexed: 12/11/2022] Open
Abstract
Glioblastoma (GBM) is the most aggressive type of primary brain tumours. Anti-angiogenic therapies (AAT), such as bevacizumab, have been developed to target the tumour blood supply. However, GBM presents mechanisms of escape from AAT activity, including a speculated direct effect of AAT on GBM cells. Furthermore, bevacizumab can alter the intercellular communication of GBM cells with their direct microenvironment. Extracellular vesicles (EVs) have been recently described as main acts in the GBM microenvironment, allowing tumour and stromal cells to exchange genetic and proteomic material. Herein, we examined and described the alterations in the EVs produced by GBM cells following bevacizumab treatment. Interestingly, bevacizumab that is able to neutralise GBM cells-derived VEGF-A, was found to be directly captured by GBM cells and eventually sorted at the surface of the respective EVs. We also identified early endosomes as potential pathways involved in the bevacizumab internalisation by GBM cells. Via MS analysis, we observed that treatment with bevacizumab induces changes in the EVs proteomic content, which are associated with tumour progression and therapeutic resistance. Accordingly, inhibition of EVs production by GBM cells improved the anti-tumour effect of bevacizumab. Together, this data suggests of a potential new mechanism of GBM escape from bevacizumab activity.
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Affiliation(s)
- Thomas Simon
- Department of Biochemistry and Biomedicine, University of Sussex, School of Life Sciences, Brighton, BN1 9QG, UK.
| | - Sotiria Pinioti
- Department of Biochemistry and Biomedicine, University of Sussex, School of Life Sciences, Brighton, BN1 9QG, UK.,Present address: Laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology (CCB), VIB, Leuven, Belgium
| | - Pascale Schellenberger
- Department of Biochemistry and Biomedicine, University of Sussex, School of Life Sciences, Brighton, BN1 9QG, UK
| | - Vinothini Rajeeve
- Cell Signalling & Proteomics Group, Centre for HaematoOncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Franz Wendler
- Department of Biochemistry and Biomedicine, University of Sussex, School of Life Sciences, Brighton, BN1 9QG, UK
| | - Pedro R Cutillas
- Cell Signalling & Proteomics Group, Centre for HaematoOncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Alice King
- Department of Biochemistry and Biomedicine, University of Sussex, School of Life Sciences, Brighton, BN1 9QG, UK
| | - Justin Stebbing
- Department of Surgery and Cancer, Hammersmith Hospital Campus, Imperial College London, Division of Cancer, Du Cane Road, London, W12 0NN, UK
| | - Georgios Giamas
- Department of Biochemistry and Biomedicine, University of Sussex, School of Life Sciences, Brighton, BN1 9QG, UK.
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6
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Al-Hilaly YK, Pollack SJ, Rickard JE, Simpson M, Raulin AC, Baddeley T, Schellenberger P, Storey JMD, Harrington CR, Wischik CM, Serpell LC. Cysteine-Independent Inhibition of Alzheimer's Disease-like Paired Helical Filament Assembly by Leuco-Methylthioninium (LMT). J Mol Biol 2018; 430:4119-4131. [PMID: 30121297 DOI: 10.1016/j.jmb.2018.08.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [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: 06/01/2018] [Revised: 07/12/2018] [Accepted: 08/09/2018] [Indexed: 12/01/2022]
Abstract
Alzheimer's disease is a tauopathy characterized by pathological fibrillization of tau protein to form the paired helical filaments (PHFs), which constitute neurofibrillary tangles. The methylthioninium (MT) moiety reverses the proteolytic stability of the PHF core and is in clinical development for treatment of Alzheimer's disease in a stable reduced form as leuco-MT. It has been hypothesized that MT acts via oxidation of cysteine residues, which is incompatible with activity in the predominantly reducing environment of living cells. We have shown recently that the PHF-core tau unit assembles spontaneously in vitro to form PHF-like filaments. Here we describe studies using circular dichroism, SDS-PAGE, transmission electron microscopy and site-directed mutagenesis to elucidate the mechanism of action of the MT moiety. We show that MT inhibitory activity is optimal in reducing conditions, that the active moiety is the reduced leuco-MT form of the molecule and that its mechanism of action is cysteine independent.
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Affiliation(s)
- Youssra K Al-Hilaly
- Dementia Research Group, School of Life Sciences, University of Sussex, Falmer, E Sussex, BN1 9QG, United Kingdom; Chemistry Department, College of Science, Mustansiriyah University, Baghdad, Iraq
| | - Saskia J Pollack
- Dementia Research Group, School of Life Sciences, University of Sussex, Falmer, E Sussex, BN1 9QG, United Kingdom
| | - Janet E Rickard
- Institute of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, AB25 2ZP, United Kingdom
| | - Michael Simpson
- TauRx Therapeutics Ltd., Aberdeen, AB25 2ZP, United Kingdom; Department of Chemistry, University of Aberdeen, Aberdeen, AB24 3UE, United Kingdom
| | - Ana-Caroline Raulin
- Dementia Research Group, School of Life Sciences, University of Sussex, Falmer, E Sussex, BN1 9QG, United Kingdom
| | - Thomas Baddeley
- TauRx Therapeutics Ltd., Aberdeen, AB25 2ZP, United Kingdom; Department of Chemistry, University of Aberdeen, Aberdeen, AB24 3UE, United Kingdom
| | - Pascale Schellenberger
- Dementia Research Group, School of Life Sciences, University of Sussex, Falmer, E Sussex, BN1 9QG, United Kingdom
| | - John M D Storey
- TauRx Therapeutics Ltd., Aberdeen, AB25 2ZP, United Kingdom; Department of Chemistry, University of Aberdeen, Aberdeen, AB24 3UE, United Kingdom
| | - Charles R Harrington
- Institute of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, AB25 2ZP, United Kingdom; Department of Chemistry, University of Aberdeen, Aberdeen, AB24 3UE, United Kingdom
| | - Claude M Wischik
- Institute of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, AB25 2ZP, United Kingdom; Department of Chemistry, University of Aberdeen, Aberdeen, AB24 3UE, United Kingdom.
| | - Louise C Serpell
- Dementia Research Group, School of Life Sciences, University of Sussex, Falmer, E Sussex, BN1 9QG, United Kingdom.
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7
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Alves DR, Booth SP, Scavone P, Schellenberger P, Salvage J, Dedi C, Thet NT, Jenkins ATA, Waters R, Ng KW, Overall ADJ, Metcalfe AD, Nzakizwanayo J, Jones BV. Development of a High-Throughput ex-Vivo Burn Wound Model Using Porcine Skin, and Its Application to Evaluate New Approaches to Control Wound Infection. Front Cell Infect Microbiol 2018; 8:196. [PMID: 29963501 PMCID: PMC6013584 DOI: 10.3389/fcimb.2018.00196] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [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: 03/28/2018] [Accepted: 05/25/2018] [Indexed: 12/05/2022] Open
Abstract
Biofilm formation in wounds is considered a major barrier to successful treatment, and has been associated with the transition of wounds to a chronic non-healing state. Here, we present a novel laboratory model of wound biofilm formation using ex-vivo porcine skin and a custom burn wound array device. The model supports high-throughput studies of biofilm formation and is compatible with a range of established methods for monitoring bacterial growth, biofilm formation, and gene expression. We demonstrate the use of this model by evaluating the potential for bacteriophage to control biofilm formation by Staphylococcus aureus, and for population density dependant expression of S. aureus virulence factors (regulated by the Accessory Gene Regulator, agr) to signal clinically relevant wound infection. Enumeration of colony forming units and metabolic activity using the XTT assay, confirmed growth of bacteria in wounds and showed a significant reduction in viable cells after phage treatment. Confocal laser scanning microscopy confirmed the growth of biofilms in wounds, and showed phage treatment could significantly reduce the formation of these communities. Evaluation of agr activity by qRT-PCR showed an increase in activity during growth in wound models for most strains. Activation of a prototype infection-responsive dressing designed to provide a visual signal of wound infection, was related to increased agr activity. In all assays, excellent reproducibility was observed between replicates using this model.
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Affiliation(s)
- Diana R Alves
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, United Kingdom.,The Blond McIndoe Research Foundation, Queen Victoria Hospital, East Grinstead, United Kingdom.,The Queen Victoria Hospital NHS Foundation Trust, East Grinstead, United Kingdom
| | - Simon P Booth
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, United Kingdom.,The Queen Victoria Hospital NHS Foundation Trust, East Grinstead, United Kingdom
| | - Paola Scavone
- Department of Microbiology, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Pascale Schellenberger
- Electron Microscopy Imaging Centre, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Jonathan Salvage
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, United Kingdom
| | - Cinzia Dedi
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, United Kingdom
| | - Naing-Tun Thet
- Department of Chemistry, University of Bath, Bath, United Kingdom
| | - A Toby A Jenkins
- Department of Chemistry, University of Bath, Bath, United Kingdom
| | - Ryan Waters
- The Pirbright Institute, Woking, United Kingdom
| | - Keng W Ng
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, United Kingdom.,School of Pharmacy, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | - Andrew D J Overall
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, United Kingdom
| | - Anthony D Metcalfe
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, United Kingdom.,The Blond McIndoe Research Foundation, Queen Victoria Hospital, East Grinstead, United Kingdom.,School of Chemical Engineering, University of Birmingham, Birmingham, United Kingdom
| | - Jonathan Nzakizwanayo
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, United Kingdom
| | - Brian V Jones
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, United Kingdom.,The Queen Victoria Hospital NHS Foundation Trust, East Grinstead, United Kingdom.,Department of Biology and Biological Sciences, University of Bath, Bath, United Kingdom
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8
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Baker LA, Sinnige T, Schellenberger P, de Keyzer J, Siebert CA, Driessen AJM, Baldus M, Grünewald K. Combined 1H-Detected Solid-State NMR Spectroscopy and Electron Cryotomography to Study Membrane Proteins across Resolutions in Native Environments. Structure 2017; 26:161-170.e3. [PMID: 29249608 PMCID: PMC5758107 DOI: 10.1016/j.str.2017.11.011] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [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: 07/03/2017] [Revised: 10/02/2017] [Accepted: 11/15/2017] [Indexed: 11/15/2022]
Abstract
Membrane proteins remain challenging targets for structural biology, despite much effort, as their native environment is heterogeneous and complex. Most methods rely on detergents to extract membrane proteins from their native environment, but this removal can significantly alter the structure and function of these proteins. Here, we overcome these challenges with a hybrid method to study membrane proteins in their native membranes, combining high-resolution solid-state nuclear magnetic resonance spectroscopy and electron cryotomography using the same sample. Our method allows the structure and function of membrane proteins to be studied in their native environments, across different spatial and temporal resolutions, and the combination is more powerful than each technique individually. We use the method to demonstrate that the bacterial membrane protein YidC adopts a different conformation in native membranes and that substrate binding to YidC in these native membranes differs from purified and reconstituted systems. CryoET and ssNMR give complementary information about proteins in native membranes One sample can be prepared for both methods without the use of detergents Hybrid method shows differences between purified and native preparations of YidC Sample preparation reduces costs and time and suggests new strategy for assignment
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Affiliation(s)
- Lindsay A Baker
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands; Oxford Particle Imaging Centre, Division of Structural Biology, University of Oxford, The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK.
| | - Tessa Sinnige
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Pascale Schellenberger
- Oxford Particle Imaging Centre, Division of Structural Biology, University of Oxford, The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Jeanine de Keyzer
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands; The Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 11, 9747 AG Groningen, the Netherlands
| | - C Alistair Siebert
- Oxford Particle Imaging Centre, Division of Structural Biology, University of Oxford, The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Arnold J M Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands; The Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 11, 9747 AG Groningen, the Netherlands
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands.
| | - Kay Grünewald
- Oxford Particle Imaging Centre, Division of Structural Biology, University of Oxford, The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK.
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9
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Schellenberger P, Sauter C, Lorber B, Bron P, Trapani S, Bergdoll M, Marmonier A, Schmitt-Keichinger C, Lemaire O, Demangeat G, Ritzenthaler C. Correction: Structural Insights into Viral Determinants of Nematode Mediated Grapevine fanleaf virus Transmission. PLoS Pathog 2017; 13:e1006268. [PMID: 28296962 PMCID: PMC5352166 DOI: 10.1371/journal.ppat.1006268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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10
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Kaufmann R, Schellenberger P, Seiradake E, Dobbie IM, Jones EY, Davis I, Hagen C, Grünewald K. Super-resolution microscopy using standard fluorescent proteins in intact cells under cryo-conditions. Nano Lett 2014; 14:4171-5. [PMID: 24884378 PMCID: PMC4092024 DOI: 10.1021/nl501870p] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Indexed: 05/08/2023]
Abstract
We introduce a super-resolution technique for fluorescence cryo-microscopy based on photoswitching of standard genetically encoded fluorescent marker proteins in intact mammalian cells at low temperature (81 K). Given the limit imposed by the lack of cryo-immersion objectives, current applications of fluorescence cryo-microscopy to biological specimens achieve resolutions between 400-500 nm only. We demonstrate that the single molecule characteristics of reversible photobleaching of mEGFP and mVenus at liquid nitrogen temperature are suitable for the basic concept of single molecule localization microscopy. This enabled us to perform super-resolution imaging of vitrified biological samples and to visualize structures in unperturbed fast frozen cells for the first time with a structural resolution of ∼125 nm (average single molecule localization accuracy ∼40 nm), corresponding to a 3-5 fold resolution improvement.
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Affiliation(s)
- Rainer Kaufmann
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics and Department of
Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Pascale Schellenberger
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics and Department of
Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Elena Seiradake
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics and Department of
Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Ian M. Dobbie
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics and Department of
Biochemistry, University of Oxford, Oxford, United Kingdom
| | - E. Yvonne Jones
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics and Department of
Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Ilan Davis
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics and Department of
Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Christoph Hagen
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics and Department of
Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Kay Grünewald
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics and Department of
Biochemistry, University of Oxford, Oxford, United Kingdom
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Schellenberger P, Kaufmann R, Siebert CA, Hagen C, Wodrich H, Grünewald K. High-precision correlative fluorescence and electron cryo microscopy using two independent alignment markers. Ultramicroscopy 2013; 143:41-51. [PMID: 24262358 PMCID: PMC4045203 DOI: 10.1016/j.ultramic.2013.10.011] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [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: 08/14/2013] [Revised: 10/08/2013] [Accepted: 10/10/2013] [Indexed: 11/29/2022]
Abstract
Correlative light and electron microscopy (CLEM) is an emerging technique which combines functional information provided by fluorescence microscopy (FM) with the high-resolution structural information of electron microscopy (EM). So far, correlative cryo microscopy of frozen-hydrated samples has not reached better than micrometre range accuracy. Here, a method is presented that enables the correlation between fluorescently tagged proteins and electron cryo tomography (cryoET) data with nanometre range precision. Specifically, thin areas of vitrified whole cells are examined by correlative fluorescence cryo microscopy (cryoFM) and cryoET. Novel aspects of the presented cryoCLEM workflow not only include the implementation of two independent electron dense fluorescent markers to improve the precision of the alignment, but also the ability of obtaining an estimate of the correlation accuracy for each individual object of interest. The correlative workflow from plunge-freezing to cryoET is detailed step-by-step for the example of locating fluorescence-labelled adenovirus particles trafficking inside a cell. Vitrified mammalian cell were imaged by fluorescence and electron cryo microscopy. TetraSpeck fluorescence markers were added to correct shifts between cryo fluorescence channels. FluoSpheres fiducials were used as reference points to assign new coordinates to cryoEM images. Adenovirus particles were localised with an average correlation precision of 63 nm.
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Affiliation(s)
- Pascale Schellenberger
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Rainer Kaufmann
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK; Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - C Alistair Siebert
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Christoph Hagen
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Harald Wodrich
- Microbiologie Fondamentale et Pathogénicité, MFP CNRS UMR 5234, University of Bordeaux SEGALEN, 146 rue Leo Seignat, 33076 Bordeaux, France
| | - Kay Grünewald
- Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.
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Lai-Kee-Him J, Schellenberger P, Dumas C, Richard E, Trapani S, Komar V, Demangeat G, Ritzenthaler C, Bron P. The backbone model of the Arabis mosaic virus reveals new insights into functional domains of Nepovirus capsid. J Struct Biol 2013; 182:1-9. [DOI: 10.1016/j.jsb.2013.01.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 01/22/2013] [Accepted: 01/22/2013] [Indexed: 01/22/2023]
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