1
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Ferrante L, Rajpoot K, Jeeves M, Ludwig C. Automated analysis for multiplet identification from ultra-high resolution 2D- 1H, 13C-HSQC NMR spectra. Wellcome Open Res 2023; 7:262. [PMID: 37008249 PMCID: PMC10050905 DOI: 10.12688/wellcomeopenres.18248.2] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/27/2023] [Indexed: 05/26/2023] Open
Abstract
Background: Metabolism is essential for cell survival and proliferation. A deep understanding of the metabolic network and its regulatory processes is often vital to understand and overcome disease. Stable isotope tracing of metabolism using nuclear magnetic resonance (NMR) and mass spectrometry (MS) is a powerful tool to derive mechanistic information of metabolic network activity. However, to retrieve meaningful information, automated tools are urgently needed to analyse these complex spectra and eliminate the bias introduced by manual analysis. Here, we present a data-driven algorithm to automatically annotate and analyse NMR signal multiplets in 2D- 1H, 13C-HSQC NMR spectra arising from 13C - 13C scalar couplings. The algorithm minimises the need for user input to guide the analysis of 2D- 1H, 13C-HSQC NMR spectra by performing automated peak picking and multiplet analysis. This enables non-NMR specialists to use this technology. The algorithm has been integrated into the existing MetaboLab software package. Methods: To evaluate the algorithm performance two criteria are tested: is the peak correctly annotated and secondly how confident is the algorithm with its analysis. For the latter a coefficient of determination is introduced. Three datasets were used for testing. The first was to test reproducibility with three biological replicates, the second tested the robustness of the algorithm for different amounts of scaling of the apparent J-coupling constants and the third focused on different sampling amounts. Results: The algorithm annotated overall >90% of NMR signals correctly with average coefficient of determination ρ of 94.06 ± 5.08%, 95.47 ± 7.20% and 80.47 ± 20.98% respectively. Conclusions: Our results indicate that the proposed algorithm accurately identifies and analyses NMR signal multiplets in ultra-high resolution 2D- 1H, 13C-HSQC NMR spectra. It is robust to signal splitting enhancement and up to 25% of non-uniform sampling.
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Affiliation(s)
- Laura Ferrante
- School of Computer Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Kashif Rajpoot
- University of Birmingham Dubai, Dubai International Academic City, United Arab Emirates
| | - Mark Jeeves
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Christian Ludwig
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, B15 2TT, UK
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2
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Willcox CR, Salim M, Begley CR, Karunakaran MM, Easton EJ, von Klopotek C, Berwick KA, Herrmann T, Mohammed F, Jeeves M, Willcox BE. Phosphoantigen sensing combines TCR-dependent recognition of the BTN3A IgV domain and germline interaction with BTN2A1. Cell Rep 2023; 42:112321. [PMID: 36995939 DOI: 10.1016/j.celrep.2023.112321] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [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: 10/20/2022] [Revised: 02/21/2023] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
Vγ9Vδ2 T cells play critical roles in microbial immunity by detecting target cells exposed to pathogen-derived phosphoantigens (P-Ags). Target cell expression of BTN3A1, the "P-Ag sensor," and BTN2A1, a direct ligand for T cell receptor (TCR) Vγ9, is essential for this process; however, the molecular mechanisms involved are unclear. Here, we characterize BTN2A1 interactions with Vγ9Vδ2 TCR and BTN3A1. Nuclear magnetic resonance (NMR), modeling, and mutagenesis establish a BTN2A1-immunoglobulin V (IgV)/BTN3A1-IgV structural model compatible with their cell-surface association in cis. However, TCR and BTN3A1-IgV binding to BTN2A1-IgV is mutually exclusive, owing to binding site proximity and overlap. Moreover, mutagenesis indicates that the BTN2A1-IgV/BTN3A1-IgV interaction is non-essential for recognition but instead identifies a molecular surface on BTN3A1-IgV essential to P-Ag sensing. These results establish a critical role for BTN3A-IgV in P-Ag sensing, in mediating direct or indirect interactions with the γδ-TCR. They support a composite-ligand model whereby intracellular P-Ag detection coordinates weak extracellular germline TCR/BTN2A1 and clonotypically influenced TCR/BTN3A-mediated interactions to initiate Vγ9Vδ2 TCR triggering.
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Affiliation(s)
- Carrie R Willcox
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK; Cancer Immunology and Immunotherapy Centre, University of Birmingham, Birmingham, UK.
| | - Mahboob Salim
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK; Cancer Immunology and Immunotherapy Centre, University of Birmingham, Birmingham, UK
| | - Charlotte R Begley
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK; Cancer Immunology and Immunotherapy Centre, University of Birmingham, Birmingham, UK
| | | | - Emily J Easton
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK; Cancer Immunology and Immunotherapy Centre, University of Birmingham, Birmingham, UK
| | | | - Katie A Berwick
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK; Cancer Immunology and Immunotherapy Centre, University of Birmingham, Birmingham, UK
| | - Thomas Herrmann
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Fiyaz Mohammed
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK; Cancer Immunology and Immunotherapy Centre, University of Birmingham, Birmingham, UK
| | - Mark Jeeves
- Henry Wellcome Building for NMR, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK.
| | - Benjamin E Willcox
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK; Cancer Immunology and Immunotherapy Centre, University of Birmingham, Birmingham, UK.
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3
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Ferrante L, Rajpoot K, Jeeves M, Ludwig C. Automated analysis for multiplet identification from ultra-high resolution 2D-1H,13C-HSQC NMR spectra. Wellcome Open Res 2022; 7:262. [PMID: 37008249 PMCID: PMC10050905 DOI: 10.12688/wellcomeopenres.18248.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2022] [Indexed: 11/20/2022] Open
Abstract
Background: Metabolism is essential for cell survival and proliferation. A deep understanding of the metabolic network and its regulatory processes is often vital to understand and overcome disease. Stable isotope tracing of metabolism using nuclear magnetic resonance (NMR) and mass spectrometry (MS) is a powerful tool to derive mechanistic information of metabolic network activity. However, to retrieve meaningful information, automated tools are urgently needed to analyse these complex spectra and eliminate the bias introduced by manual analysis. Here, we present a data-driven algorithm to automatically annotate and analyse NMR signal multiplets in 2D-1H,13C-HSQC NMR spectra arising from 13C -13C scalar couplings. The algorithm minimises the need for user input to guide the analysis of 2D-1H,13C-HSQC NMR spectra by performing automated peak picking and multiplet analysis. This enables non-NMR specialists to use this technology. The algorithm has been integrated into the existing MetaboLab software package. Methods: To evaluate the algorithm performance two criteria are tested: is the peak correctly annotated and secondly how confident is the algorithm with its analysis. For the latter a coefficient of determination is introduced. Three datasets were used for testing. The first was to test reproducibility with three biological replicates, the second tested the robustness of the algorithm for different amounts of scaling of the apparent J-coupling constants and the third focused on different sampling amounts. Results: The algorithm annotated overall >90% of NMR signals correctly with average coefficient of determination ρ of 94.06 ± 5.08%, 95.47 ± 7.20% and 80.47 ± 20.98% respectively. Conclusions: Our results indicate that the proposed algorithm accurately identifies and analyses NMR signal multiplets in ultra-high resolution 2D-1H,13C-HSQC NMR spectra. It is robust to signal splitting enhancement and up to 25% of non-uniform sampling.
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Affiliation(s)
- Laura Ferrante
- School of Computer Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Kashif Rajpoot
- University of Birmingham Dubai, Dubai International Academic City, United Arab Emirates
| | - Mark Jeeves
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Christian Ludwig
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, B15 2TT, UK
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4
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Vilaplana-Lopera N, Cuminetti V, Almaghrabi R, Papatzikas G, Rout AK, Jeeves M, González E, Alyahyawi Y, Cunningham A, Erdem A, Schnütgen F, Raghavan M, Potluri S, Cazier JB, Schuringa JJ, Reed MAC, Arranz L, Günther UL, Garcia P. Crosstalk between AML and stromal cells triggers acetate secretion through the metabolic rewiring of stromal cells. eLife 2022; 11:e75908. [PMID: 36052997 PMCID: PMC9477493 DOI: 10.7554/elife.75908] [Citation(s) in RCA: 4] [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: 11/26/2021] [Accepted: 09/01/2022] [Indexed: 11/18/2022] Open
Abstract
Acute myeloid leukaemia (AML) cells interact and modulate components of their surrounding microenvironment into their own benefit. Stromal cells have been shown to support AML survival and progression through various mechanisms. Nonetheless, whether AML cells could establish beneficial metabolic interactions with stromal cells is underexplored. By using a combination of human AML cell lines and AML patient samples together with mouse stromal cells and a MLL-AF9 mouse model, here we identify a novel metabolic crosstalk between AML and stromal cells where AML cells prompt stromal cells to secrete acetate for their own consumption to feed the tricarboxylic acid cycle (TCA) and lipid biosynthesis. By performing transcriptome analysis and tracer-based metabolic NMR analysis, we observe that stromal cells present a higher rate of glycolysis when co-cultured with AML cells. We also find that acetate in stromal cells is derived from pyruvate via chemical conversion under the influence of reactive oxygen species (ROS) following ROS transfer from AML to stromal cells via gap junctions. Overall, we present a unique metabolic communication between AML and stromal cells and propose two different molecular targets, ACSS2 and gap junctions, that could potentially be exploited for adjuvant therapy.
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Affiliation(s)
- Nuria Vilaplana-Lopera
- Institute of Cancer and Genomic Sciences, University of BirminghamBirminghamUnited Kingdom
| | - Vincent Cuminetti
- Stem Cells, Ageing and Cancer Research Group, Department of Medical Biology, Faculty of Health Sciences, UiT – The Arctic University of NorwayTromsoNorway
| | - Ruba Almaghrabi
- Institute of Cancer and Genomic Sciences, University of BirminghamBirminghamUnited Kingdom
- Department of Laboratory Medicine (hematology), Faculty of Applied Medical Sciences. Albaha University, Kingdom of Saudi ArabiaAl BahahSaudi Arabia
| | - Grigorios Papatzikas
- Institute of Cancer and Genomic Sciences, University of BirminghamBirminghamUnited Kingdom
- Centre for Computational Biology, University of BirminghamBirminghamUnited Kingdom
| | - Ashok Kumar Rout
- Institute of Chemistry and Metabolomics, University of LübeckLübeckGermany
| | - Mark Jeeves
- Institute of Cancer and Genomic Sciences, University of BirminghamBirminghamUnited Kingdom
| | - Elena González
- Institute of Cancer and Genomic Sciences, University of BirminghamBirminghamUnited Kingdom
| | - Yara Alyahyawi
- Institute of Cancer and Genomic Sciences, University of BirminghamBirminghamUnited Kingdom
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Jazan UniversityJazanSaudi Arabia
| | - Alan Cunningham
- Department of Experimental Hematology, University Medical Center Groningen, University of GroningenGroningenNetherlands
| | - Ayşegül Erdem
- Department of Experimental Hematology, University Medical Center Groningen, University of GroningenGroningenNetherlands
| | - Frank Schnütgen
- Department of Medicine, Hematology/Oncology, University Hospital Frankfurt, Goethe University FrankfurtFrankfurtGermany
- Frankfurt Cancer Institute, Goethe University FrankfurtFrankfurtGermany
- German Cancer Consortium (DKTK), partner site Frankfurt/Mainz, and German Cancer Research Center (DKFZ)HeidelbergGermany
| | - Manoj Raghavan
- Institute of Cancer and Genomic Sciences, University of BirminghamBirminghamUnited Kingdom
- Centre for Clinical Haematology, University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital, Queen Elizabeth Medical CentreBirminghamUnited Kingdom
| | - Sandeep Potluri
- Institute of Cancer and Genomic Sciences, University of BirminghamBirminghamUnited Kingdom
- Centre for Clinical Haematology, University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital, Queen Elizabeth Medical CentreBirminghamUnited Kingdom
| | - Jean-Baptiste Cazier
- Institute of Cancer and Genomic Sciences, University of BirminghamBirminghamUnited Kingdom
- Centre for Computational Biology, University of BirminghamBirminghamUnited Kingdom
| | - Jan Jacob Schuringa
- Department of Experimental Hematology, University Medical Center Groningen, University of GroningenGroningenNetherlands
| | - Michelle AC Reed
- Institute of Cancer and Genomic Sciences, University of BirminghamBirminghamUnited Kingdom
| | - Lorena Arranz
- Stem Cells, Ageing and Cancer Research Group, Department of Medical Biology, Faculty of Health Sciences, UiT – The Arctic University of NorwayTromsoNorway
| | - Ulrich L Günther
- Institute of Cancer and Genomic Sciences, University of BirminghamBirminghamUnited Kingdom
- Institute of Chemistry and Metabolomics, University of LübeckLübeckGermany
| | - Paloma Garcia
- Institute of Cancer and Genomic Sciences, University of BirminghamBirminghamUnited Kingdom
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5
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Hall SCL, Clifton LA, Sridhar P, Hardy DJ, Wotherspoon P, Wright J, Whitehouse J, Gamage N, Laxton CS, Hatton C, Hughes GW, Jeeves M, Knowles TJ. Surface-tethered planar membranes containing the β-barrel assembly machinery: a platform for investigating bacterial outer membrane protein folding. Biophys J 2021; 120:5295-5308. [PMID: 34757080 PMCID: PMC8715194 DOI: 10.1016/j.bpj.2021.10.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 02/25/2021] [Revised: 09/06/2021] [Accepted: 10/26/2021] [Indexed: 11/16/2022] Open
Abstract
The outer membrane of Gram-negative bacteria presents a robust physicochemical barrier protecting the cell from both the natural environment and acting as the first line of defense against antimicrobial materials. The proteins situated within the outer membrane are responsible for a range of biological functions including controlling influx and efflux. These outer membrane proteins (OMPs) are ultimately inserted and folded within the membrane by the β-barrel assembly machine (Bam) complex. The precise mechanism by which the Bam complex folds and inserts OMPs remains unclear. Here, we have developed a platform for investigating Bam-mediated OMP insertion. By derivatizing a gold surface with a copper-chelating self-assembled monolayer, we were able to assemble a planar system containing the complete Bam complex reconstituted within a phospholipid bilayer. Structural characterization of this interfacial protein-tethered bilayer by polarized neutron reflectometry revealed distinct regions consistent with known high-resolution models of the Bam complex. Additionally, by monitoring changes of mass associated with OMP insertion by quartz crystal microbalance with dissipation monitoring, we were able to demonstrate the functionality of this system by inserting two diverse OMPs within the membrane, pertactin, and OmpT. This platform has promising application in investigating the mechanism of Bam-mediated OMP insertion, in addition to OMP function and activity within a phospholipid bilayer environment.
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Affiliation(s)
- Stephen C L Hall
- ISIS Pulsed Neutron and Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Oxfordshire, United Kingdom
| | - Luke A Clifton
- ISIS Pulsed Neutron and Muon Source, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Oxfordshire, United Kingdom
| | - Pooja Sridhar
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - David J Hardy
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Peter Wotherspoon
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Jack Wright
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - James Whitehouse
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Nadisha Gamage
- Membrane Protein Laboratory, Diamond Light Source, Harwell Science & Innovation Campus, Oxfordshire, United Kingdom
| | - Claire S Laxton
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Caitlin Hatton
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Gareth W Hughes
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Mark Jeeves
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Timothy J Knowles
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom.
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6
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Rehman MF, Jeeves M, Hyde EI. Backbone assignments, and effect of Asn deamidation, of the N-terminal region of the partitioning protein IncC1 from the plasmid RK2. Biomol NMR Assign 2021; 15:305-310. [PMID: 33856628 PMCID: PMC8481139 DOI: 10.1007/s12104-021-10021-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] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/05/2021] [Indexed: 06/12/2023]
Abstract
IncC from the low-copy number plasmid RK2, is a member of the ParA family of proteins required for partitioning DNA in many bacteria and plasmids. It is an ATPase that binds DNA and its ParB protein partner, KorB. Together, the proteins move replicated DNA to appropriate cellular positions, so that each daughter cell inherits a copy on cell division. IncC from RK2 is expressed in two forms. IncC2 is homologous to bacterial ParA proteins, while IncC1 has an N-terminal extension of 105 amino acids and is similar in length to ParA homologues in other plasmids. We have been examining the role of this extension, here called IncC NTD. We present its backbone NMR chemical shift assignments and show that it is entirely intrinsically disordered. The assignments were achieved using C-detected, CON-based spectra, complemented by HNN spectra to obtain connectivities from three adjacent amino acids. We also observed evidence of deamidation of the protein at a GNGG sequence, to give isoAsp, giving 2 sets of peaks for residues up to 5 amino acids on either side of the modification. We have assigned resonances from around the position of modification for this form of the protein.
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Affiliation(s)
- M Fayyaz Rehman
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Institute of Chemistry, University of Sargodha, Sargodha, Punjab, Pakistan
| | - M Jeeves
- Henry Wellcome NMR Centre, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - E I Hyde
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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7
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Jeeves M, Roberts J, Ludwig C. Optimised collection of non-uniformly sampled 2D-HSQC NMR spectra for use in metabolic flux analysis. Magn Reson Chem 2021; 59:287-299. [PMID: 32830359 DOI: 10.1002/mrc.5089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 04/03/2020] [Revised: 08/06/2020] [Accepted: 08/18/2020] [Indexed: 06/11/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is integral to metabolic studies; yet, it can suffer from the long acquisition times required to collect data of sufficient signal strength and resolution. The use of non-uniform sampling (NUS) allows faster collection of NMR spectra without loss of spectral integrity. When planning experimental methodologies to perform metabolic flux analysis (MFA) of cell metabolism, a variety of options are available for the acquisition of NUS NMR data. Before beginning data collection, decisions have to be made regarding selection of pulse sequence, number of transients and NUS specific parameters such as the sampling level and sampling schedule. Poor choices will impact data quality, which may have a negative effect on the subsequent analysis and biological interpretation. Herein, we describe factors that should be considered when setting up non-uniformly sampled 2D-1 H,13 C HSQC NMR experiments for MFA and provide a standard protocol for users to follow.
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Affiliation(s)
- Mark Jeeves
- Henry Wellcome Building for Biomolecular NMR Spectroscopy, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Jennie Roberts
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Christian Ludwig
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
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8
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Bryant JA, Morris FC, Knowles TJ, Maderbocus R, Heinz E, Boelter G, Alodaini D, Colyer A, Wotherspoon PJ, Staunton KA, Jeeves M, Browning DF, Sevastsyanovich YR, Wells TJ, Rossiter AE, Bavro VN, Sridhar P, Ward DG, Chong ZS, Goodall EC, Icke C, Teo AC, Chng SS, Roper DI, Lithgow T, Cunningham AF, Banzhaf M, Overduin M, Henderson IR. Structure of dual BON-domain protein DolP identifies phospholipid binding as a new mechanism for protein localisation. eLife 2020; 9:62614. [PMID: 33315009 PMCID: PMC7806268 DOI: 10.7554/elife.62614] [Citation(s) in RCA: 16] [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: 08/31/2020] [Accepted: 12/11/2020] [Indexed: 12/16/2022] Open
Abstract
The Gram-negative outer-membrane envelops the bacterium and functions as a permeability barrier against antibiotics, detergents, and environmental stresses. Some virulence factors serve to maintain the integrity of the outer membrane, including DolP (formerly YraP) a protein of unresolved structure and function. Here, we reveal DolP is a lipoprotein functionally conserved amongst Gram-negative bacteria and that loss of DolP increases membrane fluidity. We present the NMR solution structure for Escherichia coli DolP, which is composed of two BON domains that form an interconnected opposing pair. The C-terminal BON domain binds anionic phospholipids through an extensive membrane:protein interface. This interaction is essential for DolP function and is required for sub-cellular localisation of the protein to the cell division site, providing evidence of subcellular localisation of these phospholipids within the outer membrane. The structure of DolP provides a new target for developing therapies that disrupt the integrity of the bacterial cell envelope.
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Affiliation(s)
- Jack Alfred Bryant
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom
| | - Faye C Morris
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom
| | - Timothy J Knowles
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom.,School of Biosciences, University of Birmingham, Edgbaston, United Kingdom
| | - Riyaz Maderbocus
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom.,Institute for Cancer and Genomic Sciences, University of Birmingham, Edgbaston, United Kingdom
| | - Eva Heinz
- Infection & Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
| | - Gabriela Boelter
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom
| | - Dema Alodaini
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom
| | - Adam Colyer
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom
| | - Peter J Wotherspoon
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom
| | - Kara A Staunton
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom
| | - Mark Jeeves
- Institute for Cancer and Genomic Sciences, University of Birmingham, Edgbaston, United Kingdom
| | - Douglas F Browning
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom
| | | | - Timothy J Wells
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom
| | - Amanda E Rossiter
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom
| | - Vassiliy N Bavro
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom
| | - Pooja Sridhar
- School of Biosciences, University of Birmingham, Edgbaston, United Kingdom
| | - Douglas G Ward
- School of Biosciences, University of Birmingham, Edgbaston, United Kingdom
| | - Zhi-Soon Chong
- Department of Chemistry, National University of Singapore, Singapore, Singapore
| | - Emily Ca Goodall
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom.,Institute for Molecular Bioscience, University of Queensland, St. Lucia, Australia
| | - Christopher Icke
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom.,Institute for Molecular Bioscience, University of Queensland, St. Lucia, Australia
| | - Alvin Ck Teo
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Shu-Sin Chng
- Department of Chemistry, National University of Singapore, Singapore, Singapore.,School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - David I Roper
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Trevor Lithgow
- Infection & Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
| | - Adam F Cunningham
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom.,Institute of Inflammation and Immunotherapy, University of Birmingham, Edgbaston, United Kingdom
| | - Manuel Banzhaf
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom
| | - Michael Overduin
- School of Biosciences, University of Birmingham, Edgbaston, United Kingdom.,Department of Biochemistry, University of Alberta, Edmonton, Canada
| | - Ian R Henderson
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom.,Department of Chemistry, National University of Singapore, Singapore, Singapore
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9
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Tong MHG, Jeeves M, Rajesh S, Ludwig C, Lenoir M, Kumar J, McClelland DM, Berditchevski F, Hubbard JA, Kenyon C, Butterworth S, Knapp S, Overduin M. Backbone resonance assignments of the catalytic and regulatory domains of Ca 2+/calmodulin-dependent protein kinase 1D. Biomol NMR Assign 2020; 14:221-225. [PMID: 32535836 PMCID: PMC7462902 DOI: 10.1007/s12104-020-09950-x] [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] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/21/2020] [Indexed: 06/11/2023]
Abstract
The CaMK subfamily of Ser/Thr kinases are regulated by calmodulin interactions with their C-terminal regions. They are exemplified by Ca2+/calmodulin dependent protein kinase 1δ which is known as CaMK1D, CaMKIδ or CKLiK. CaMK1D mediates intracellular signalling downstream of Ca2+ influx and thereby exhibits amplifications of Ca2+signals and polymorphisms that have been implicated in breast cancer and diabetes. Here we report the backbone 1H, 13C, 15N assignments of the 38 kDa human CaMK1D protein in its free state, including both the canonical bi-lobed kinase fold as well as the autoinhibitory and calmodulin binding domains.
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Affiliation(s)
- Michael H G Tong
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Mark Jeeves
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Sundaresan Rajesh
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Christian Ludwig
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Marc Lenoir
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Jitendra Kumar
- Department of Biochemistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada
| | - Darren M McClelland
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Fedor Berditchevski
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Julia A Hubbard
- Computational, Analytical and Structural Sciences, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Colin Kenyon
- Faculty of Medicine and Health Sciences, Stellenbosch University, Francie Van Zijl Dr, Parow, Cape Town, 7505, South Africa
| | - Sam Butterworth
- Division of Pharmacy and Optometry, School of Health Sciences, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, M13 9PL, UK
| | - Stefan Knapp
- Structural Genomics Consortium and Buchmann Institute for Molecular Life Sciences, Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Straße 9, 60438, Frankfurt am Main, Germany
| | - Michael Overduin
- Department of Biochemistry, University of Alberta, Edmonton, AB, T6G 2H7, Canada.
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10
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Cranford-Smith T, Jamshad M, Jeeves M, Chandler RA, Yule J, Robinson A, Alam F, Dunne KA, Aponte Angarita EH, Alanazi M, Carter C, Henderson IR, Lovett JE, Winn P, Knowles T, Huber D. Iron is a ligand of SecA-like metal-binding domains in vivo. J Biol Chem 2020; 295:7516-7528. [PMID: 32241912 PMCID: PMC7247292 DOI: 10.1074/jbc.ra120.012611] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 01/10/2020] [Revised: 03/26/2020] [Indexed: 12/12/2022] Open
Abstract
The ATPase SecA is an essential component of the bacterial Sec machinery, which transports proteins across the cytoplasmic membrane. Most SecA proteins contain a long C-terminal tail (CTT). In Escherichia coli, the CTT contains a structurally flexible linker domain and a small metal-binding domain (MBD). The MBD coordinates zinc via a conserved cysteine-containing motif and binds to SecB and ribosomes. In this study, we screened a high-density transposon library for mutants that affect the susceptibility of E. coli to sodium azide, which inhibits SecA-mediated translocation. Results from sequencing this library suggested that mutations removing the CTT make E. coli less susceptible to sodium azide at subinhibitory concentrations. Copurification experiments suggested that the MBD binds to iron and that azide disrupts iron binding. Azide also disrupted binding of SecA to membranes. Two other E. coli proteins that contain SecA-like MBDs, YecA and YchJ, also copurified with iron, and NMR spectroscopy experiments indicated that YecA binds iron via its MBD. Competition experiments and equilibrium binding measurements indicated that the SecA MBD binds preferentially to iron and that a conserved serine is required for this specificity. Finally, structural modeling suggested a plausible model for the octahedral coordination of iron. Taken together, our results suggest that SecA-like MBDs likely bind to iron in vivo.
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Affiliation(s)
- Tamar Cranford-Smith
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Mohammed Jamshad
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Mark Jeeves
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Rachael A Chandler
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Jack Yule
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Ashley Robinson
- Institute for Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Farhana Alam
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Karl A Dunne
- Institute for Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Edwin H Aponte Angarita
- Centre for Computational Biology, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Mashael Alanazi
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom; Department of Biology, College of Science, Jouf University, Saudi Arabia
| | - Cailean Carter
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Ian R Henderson
- Institute for Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Janet E Lovett
- SUPA, School of Physics and Astronomy and BSRC, University of St. Andrews, St. Andrews KY16 9SS, United Kingdom
| | - Peter Winn
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom; Centre for Computational Biology, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Timothy Knowles
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Damon Huber
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom.
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11
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Milton-Harris L, Jeeves M, Walker SA, Ward SE, Mancini EJ. Small molecule inhibits T-cell acute lymphoblastic leukaemia oncogenic interaction through conformational modulation of LMO2. Oncotarget 2020; 11:1737-1748. [PMID: 32477463 PMCID: PMC7233811 DOI: 10.18632/oncotarget.27580] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 12/24/2019] [Accepted: 04/03/2020] [Indexed: 01/05/2023] Open
Abstract
Ectopic expression in T-cell precursors of LIM only protein 2 (LMO2), a key factor in hematopoietic development, has been linked to the onset of T-cell acute lymphoblastic leukaemia (T-ALL). In the T-ALL context, LMO2 drives oncogenic progression through binding to erythroid-specific transcription factor SCL/TAL1 and sequestration of E-protein transcription factors, normally required for T-cell differentiation. A key requirement for the formation of this oncogenic protein-protein interaction (PPI) is the conformational flexibility of LMO2. Here we identify a small molecule inhibitor of the SCL-LMO2 PPI, which hinders the interaction in vitro through direct binding to LMO2. Biophysical analysis demonstrates that this inhibitor acts through a mechanism of conformational modulation of LMO2. Importantly, this work has led to the identification of a small molecule inhibitor of the SCL-LMO2 PPI, which can provide a starting point for the development of new agents for the treatment of T-ALL. These results suggest that similar approaches, based on the modulation of protein conformation by small molecules, might be used for therapeutic targeting of other oncogenic PPIs.
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Affiliation(s)
- Leanne Milton-Harris
- School of Life Sciences, Biochemistry Department, University of Sussex, Falmer, Brighton, BN1 9QG, United Kingdom
| | - Mark Jeeves
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Sarah A Walker
- Sussex Drug Discovery Centre, University of Sussex, Brighton, BN1 9QJ, United Kingdom
| | - Simon E Ward
- Medicines Discovery Institute, Cardiff University, Park Place, Cardiff, CF10 3AT, United Kingdom
| | - Erika J Mancini
- School of Life Sciences, Biochemistry Department, University of Sussex, Falmer, Brighton, BN1 9QG, United Kingdom
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12
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Karunakaran MM, Willcox CR, Salim M, Paletta D, Fichtner AS, Noll A, Starick L, Nöhren A, Begley CR, Berwick KA, Chaleil RAG, Pitard V, Déchanet-Merville J, Bates PA, Kimmel B, Knowles TJ, Kunzmann V, Walter L, Jeeves M, Mohammed F, Willcox BE, Herrmann T. Butyrophilin-2A1 Directly Binds Germline-Encoded Regions of the Vγ9Vδ2 TCR and Is Essential for Phosphoantigen Sensing. Immunity 2020; 52:487-498.e6. [PMID: 32155411 PMCID: PMC7083227 DOI: 10.1016/j.immuni.2020.02.014] [Citation(s) in RCA: 135] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/18/2020] [Accepted: 02/24/2020] [Indexed: 01/24/2023]
Abstract
Vγ9Vδ2 T cells respond in a TCR-dependent fashion to both microbial and host-derived pyrophosphate compounds (phosphoantigens, or P-Ag). Butyrophilin-3A1 (BTN3A1), a protein structurally related to the B7 family of costimulatory molecules, is necessary but insufficient for this process. We performed radiation hybrid screens to uncover direct TCR ligands and cofactors that potentiate BTN3A1's P-Ag sensing function. These experiments identified butyrophilin-2A1 (BTN2A1) as essential to Vγ9Vδ2 T cell recognition. BTN2A1 synergised with BTN3A1 in sensitizing P-Ag-exposed cells for Vγ9Vδ2 TCR-mediated responses. Surface plasmon resonance experiments established Vγ9Vδ2 TCRs used germline-encoded Vγ9 regions to directly bind the BTN2A1 CFG-IgV domain surface. Notably, somatically recombined CDR3 loops implicated in P-Ag recognition were uninvolved. Immunoprecipitations demonstrated close cell-surface BTN2A1-BTN3A1 association independent of P-Ag stimulation. Thus, BTN2A1 is a BTN3A1-linked co-factor critical to Vγ9Vδ2 TCR recognition. Furthermore, these results suggest a composite-ligand model of P-Ag sensing wherein the Vγ9Vδ2 TCR directly interacts with both BTN2A1 and an additional ligand recognized in a CDR3-dependent manner.
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MESH Headings
- Animals
- Antigens/immunology
- Antigens/metabolism
- Antigens, CD/chemistry
- Antigens, CD/immunology
- Antigens, CD/metabolism
- Butyrophilins/chemistry
- Butyrophilins/immunology
- Butyrophilins/metabolism
- CHO Cells
- Cricetinae
- Cricetulus
- Germ Cells/immunology
- Germ Cells/metabolism
- HEK293 Cells
- Humans
- Phosphorylation
- Protein Binding
- Protein Multimerization
- Receptors, Antigen, T-Cell, gamma-delta/chemistry
- Receptors, Antigen, T-Cell, gamma-delta/immunology
- Receptors, Antigen, T-Cell, gamma-delta/metabolism
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
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Affiliation(s)
| | - Carrie R Willcox
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK; Cancer Immunology and Immunotherapy Centre, University of Birmingham, Birmingham, UK
| | - Mahboob Salim
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK; Cancer Immunology and Immunotherapy Centre, University of Birmingham, Birmingham, UK
| | - Daniel Paletta
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Alina S Fichtner
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Angela Noll
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Lisa Starick
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Anna Nöhren
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Charlotte R Begley
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK; Cancer Immunology and Immunotherapy Centre, University of Birmingham, Birmingham, UK
| | - Katie A Berwick
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK; Cancer Immunology and Immunotherapy Centre, University of Birmingham, Birmingham, UK
| | | | - Vincent Pitard
- ImmunoConcEpT Laboratory, Equipe labellisée, LIGUE 2017, UMR 5164, Bordeaux University, CNRS, 33076 Bordeaux, France; Flow Cytometry Facility, TransBioMed Core, Bordeaux University, CNRS UMS 3427, INSERM US05, 33076 Bordeaux, France
| | - Julie Déchanet-Merville
- ImmunoConcEpT Laboratory, Equipe labellisée, LIGUE 2017, UMR 5164, Bordeaux University, CNRS, 33076 Bordeaux, France; Flow Cytometry Facility, TransBioMed Core, Bordeaux University, CNRS UMS 3427, INSERM US05, 33076 Bordeaux, France
| | - Paul A Bates
- Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK
| | - Brigitte Kimmel
- Medical Clinic and Policlinic II, University of Würzburg, Würzburg, Germany
| | | | - Volker Kunzmann
- Medical Clinic and Policlinic II, University of Würzburg, Würzburg, Germany
| | - Lutz Walter
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Mark Jeeves
- Henry Wellcome Building for NMR, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Fiyaz Mohammed
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK; Cancer Immunology and Immunotherapy Centre, University of Birmingham, Birmingham, UK
| | - Benjamin E Willcox
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK; Cancer Immunology and Immunotherapy Centre, University of Birmingham, Birmingham, UK.
| | - Thomas Herrmann
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany.
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13
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Odintsova E, Mohammed F, Trieber C, Rodriguez-Zamora P, Al-Jassar C, Huang TH, Fogl C, Knowles T, Sridhar P, Kumar J, Jeeves M, Chidgey M, Overduin M. Binding of the periplakin linker requires vimentin acidic residues D176 and E187. Commun Biol 2020; 3:83. [PMID: 32081916 PMCID: PMC7035337 DOI: 10.1038/s42003-020-0810-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 07/03/2019] [Accepted: 02/06/2020] [Indexed: 01/18/2023] Open
Abstract
Plakin proteins form connections that link the cell membrane to the intermediate filament cytoskeleton. Their interactions are mediated by a highly conserved linker domain through an unresolved mechanism. Here analysis of the human periplakin linker domain structure reveals a bi-lobed module transected by an electropositive groove. Key basic residues within the periplakin groove are vital for co-localization with vimentin in human cells and compromise direct binding which also requires acidic residues D176 and E187 in vimentin. We propose a model whereby basic periplakin linker domain residues recognize acidic vimentin side chains and form a complementary binding groove. The model is shared amongst diverse linker domains and can be used to investigate the effects of pathogenic mutations in the desmoplakin linker associated with arrhythmogenic right ventricular cardiomyopathy. Linker modules either act solely or collaborate with adjacent plakin repeat domains to create strong and adaptable tethering within epithelia and cardiac muscle.
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Affiliation(s)
- Elena Odintsova
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Fiyaz Mohammed
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK
| | - Catharine Trieber
- Department of Biochemistry, Faculty of Medicine & Dentistry, 474 Medical Sciences Building, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
| | - Penelope Rodriguez-Zamora
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- Instituto de Fisica, Universidad Nacional Autonoma de Mexico, Mexico City, 04510, Mexico
| | - Caezar Al-Jassar
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Tzu-Han Huang
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Claudia Fogl
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- The Binding Site, Birmingham, B15 1QT, UK
| | - Timothy Knowles
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Pooja Sridhar
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Jitendra Kumar
- Department of Biochemistry, Faculty of Medicine & Dentistry, 474 Medical Sciences Building, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
| | - Mark Jeeves
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Martyn Chidgey
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
- Institute of Clinical Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Michael Overduin
- Department of Biochemistry, Faculty of Medicine & Dentistry, 474 Medical Sciences Building, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
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14
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Hughes GW, Hall SCL, Laxton CS, Sridhar P, Mahadi AH, Hatton C, Piggot TJ, Wotherspoon PJ, Leney AC, Ward DG, Jamshad M, Spana V, Cadby IT, Harding C, Isom GL, Bryant JA, Parr RJ, Yakub Y, Jeeves M, Huber D, Henderson IR, Clifton LA, Lovering AL, Knowles TJ. Evidence for phospholipid export from the bacterial inner membrane by the Mla ABC transport system. Nat Microbiol 2019; 4:1692-1705. [DOI: 10.1038/s41564-019-0481-y] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 05/03/2019] [Indexed: 12/24/2022]
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15
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AlAmri MA, Kadri H, Alderwick LJ, Jeeves M, Mehellou Y. The Photosensitising Clinical Agent Verteporfin Is an Inhibitor of SPAK and OSR1 Kinases. Chembiochem 2018; 19:2072-2080. [PMID: 29999233 DOI: 10.1002/cbic.201800272] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [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: 05/21/2018] [Indexed: 12/27/2022]
Abstract
STE20/SPS1-related proline/alanine-rich kinase (SPAK) and oxidative-stress-responsive kinase 1 (OSR1) are two serine/threonine protein kinases that play key roles in regulating ion homeostasis. Various SPAK and OSR1 mouse models exhibited reduced blood pressure. Herein, the discovery of verteporfin, a photosensitising agent used in photodynamic therapy, as a potent inhibitor of SPAK and OSR1 kinases is reported. It is shown that verteporfin binds the kinase domains of SPAK and OSR1 and inhibits their catalytic activity in an adenosine triphosphate (ATP)-independent manner. In cells, verteporfin was able to suppress the phosphorylation of the ion co-transporter NKCC1; a downstream physiological substrate of SPAK and OSR1 kinases. Kinase panel screening indicated that verteporfin inhibited a further eight protein kinases more potently than that of SPAK and OSR1. Although verteporfin has largely been studied as a modifier of the Hippo signalling pathway, this work indicates that the WNK-SPAK/OSR1 signalling cascade is also a target of this clinical agent. This finding could explain the fluctuation in blood pressure noted in patients and animals treated with this drug.
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Affiliation(s)
- Mubarak A AlAmri
- School of Pharmacy, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Hachemi Kadri
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, King Edward VII Avenue, Cardiff, CF10 3NB, UK
| | - Luke J Alderwick
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Mark Jeeves
- School of Cancer Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Youcef Mehellou
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, King Edward VII Avenue, Cardiff, CF10 3NB, UK
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16
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Hollinshead KER, Munford H, Eales KL, Bardella C, Li C, Escribano-Gonzalez C, Thakker A, Nonnenmacher Y, Kluckova K, Jeeves M, Murren R, Cuozzo F, Ye D, Laurenti G, Zhu W, Hiller K, Hodson DJ, Hua W, Tomlinson IP, Ludwig C, Mao Y, Tennant DA. Oncogenic IDH1 Mutations Promote Enhanced Proline Synthesis through PYCR1 to Support the Maintenance of Mitochondrial Redox Homeostasis. Cell Rep 2018; 22:3107-3114. [PMID: 29562167 PMCID: PMC5883319 DOI: 10.1016/j.celrep.2018.02.084] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 12/21/2017] [Accepted: 02/22/2018] [Indexed: 01/04/2023] Open
Abstract
Since the discovery of mutations in isocitrate dehydrogenase 1 (IDH1) in gliomas and other tumors, significant efforts have been made to gain a deeper understanding of the consequences of this oncogenic mutation. One aspect of the neomorphic function of the IDH1 R132H enzyme that has received less attention is the perturbation of cellular redox homeostasis. Here, we describe a biosynthetic pathway exhibited by cells expressing mutant IDH1. By virtue of a change in cellular redox homeostasis, IDH1-mutated cells synthesize excess glutamine-derived proline through enhanced activity of pyrroline 5-carboxylate reductase 1 (PYCR1), coupled to NADH oxidation. Enhanced proline biosynthesis partially uncouples the electron transport chain from tricarboxylic acid (TCA) cycle activity through the maintenance of a lower NADH/NAD+ ratio and subsequent reduction in oxygen consumption. Thus, we have uncovered a mechanism by which tumor cell survival may be promoted in conditions associated with perturbed redox homeostasis, as occurs in IDH1-mutated glioma.
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Affiliation(s)
- Kate E R Hollinshead
- Institute of Metabolism and Systems Research, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Haydn Munford
- Institute of Metabolism and Systems Research, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Katherine L Eales
- Institute of Metabolism and Systems Research, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Chiara Bardella
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; Molecular & Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Chunjie Li
- Department of Neurosurgery, Huashan Hospital, Fudan University, #12 Middle Wulumuqi Road, Shanghai 200040, China; Institute of Biomedical Sciences, Fudan University, #131 Dong'an Road, Shanghai 200040, China
| | | | - Alpesh Thakker
- Institute of Metabolism and Systems Research, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Yannic Nonnenmacher
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Katarina Kluckova
- Institute of Metabolism and Systems Research, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Mark Jeeves
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Robert Murren
- Institute of Metabolism and Systems Research, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Federica Cuozzo
- Institute of Metabolism and Systems Research, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Dan Ye
- Institute of Biomedical Sciences, Fudan University, #131 Dong'an Road, Shanghai 200040, China
| | - Giulio Laurenti
- Institute of Metabolism and Systems Research, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Wei Zhu
- Department of Neurosurgery, Huashan Hospital, Fudan University, #12 Middle Wulumuqi Road, Shanghai 200040, China
| | - Karsten Hiller
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - David J Hodson
- Institute of Metabolism and Systems Research, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
| | - Wei Hua
- Department of Neurosurgery, Huashan Hospital, Fudan University, #12 Middle Wulumuqi Road, Shanghai 200040, China
| | - Ian P Tomlinson
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Christian Ludwig
- Institute of Metabolism and Systems Research, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Ying Mao
- Department of Neurosurgery, Huashan Hospital, Fudan University, #12 Middle Wulumuqi Road, Shanghai 200040, China; Institute of Biomedical Sciences, Fudan University, #131 Dong'an Road, Shanghai 200040, China; State Key Laboratory of Medical Neurobiology, School of Basic Medical Sciences and Institutes of Brain Science, Fudan University, Shanghai 200040, China; The Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, 200040, China
| | - Daniel A Tennant
- Institute of Metabolism and Systems Research, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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17
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Abstract
Tracing the fate of stable isotopically-enriched nutrients is a sophisticated method of describing and quantifying the activity of metabolic pathways. Nuclear Magnetic Resonance (NMR) offers high resolution data, yet is under-utilised due to length of time required to collect the data, quantification requiring multiple samples and complicated analysis. Here we present two techniques, quantitative spectral filters and enhancement of the splitting due to J-coupling in 1H,13C-HSQC NMR spectra, which allow the rapid collection of NMR data in a quantitative manner on a single sample. The reduced duration of HSQC spectra data acquisition opens up the possibility of real-time tracing of metabolism including the study of metabolic pathways in vivo. We show how these novel techniques can be used to trace the fate of labelled nutrients in a whole organ model of kidney preservation prior to transplantation using a porcine kidney as a model organ, and also show how the use of multiple nutrients, differentially labelled with 13C and 15N, can be used to provide additional information with which to profile metabolic pathways.
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18
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Abstract
Tracing the fate of stable isotopically-enriched nutrients is a sophisticated method of describing and quantifying the activity of metabolic pathways. Nuclear Magnetic Resonance (NMR) spectroscopy offers high resolution data in terms of resolving metabolic pathway utilisation. Despite this, NMR spectroscopy is under-utilised due to length of time required to collect the data, quantification requiring multiple samples and complicated analysis. Here we present two techniques, quantitative spectral filters and enhancement of the splitting of
13C signals due to homonuclear
13C,
13C or heteronuclear
13C,
15N J-coupling in
1H,
13C-HSQC NMR spectra. Together, these allow the rapid collection of NMR spectroscopy data in a quantitative manner on a single sample. The reduced duration of HSQC spectra data acquisition opens up the possibility of real-time tracing of metabolism including the study of metabolic pathways
in vivo. We show how these techniques can be used to trace the fate of labelled nutrients in a whole organ model of kidney preservation prior to transplantation using a porcine kidney as a model organ. In addition, we show how the use of multiple nutrients, differentially labelled with
13C and
15N, can be used to provide additional information with which to profile metabolic pathways.
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Affiliation(s)
- Thomas Brendan Smith
- Institute of Metabolism and Systems Research, University of Birmingham, West Midlands, UK
| | - Kamlesh Patel
- Institute of Metabolism and Systems Research, University of Birmingham, West Midlands, UK
| | - Haydn Munford
- Institute of Metabolism and Systems Research, University of Birmingham, West Midlands, UK
| | - Andrew Peet
- Institute of Cancer and Genomic Sciences, University of Birmingham, West Midlands, UK.,Birmingham Children's Hospital NHS Foundation Trust, West Midlands, UK
| | - Daniel A Tennant
- Institute of Metabolism and Systems Research, University of Birmingham, West Midlands, UK
| | - Mark Jeeves
- Institute of Cancer and Genomic Sciences, University of Birmingham, West Midlands, UK
| | - Christian Ludwig
- Institute of Metabolism and Systems Research, University of Birmingham, West Midlands, UK
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19
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Emam AA, Arbon D, Jeeves M, Kysela B. Ku70 N-terminal lysines acetylation/deacetylation is required for radiation-induced DNA-double strand breaks repair. Neoplasma 2018; 65:708-719. [DOI: 10.4149/neo_2018_171020n673] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 02/01/2018] [Indexed: 11/08/2022]
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20
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Salim M, Knowles TJ, Baker AT, Davey MS, Jeeves M, Sridhar P, Wilkie J, Willcox CR, Kadri H, Taher TE, Vantourout P, Hayday A, Mehellou Y, Mohammed F, Willcox BE. BTN3A1 Discriminates γδ T Cell Phosphoantigens from Nonantigenic Small Molecules via a Conformational Sensor in Its B30.2 Domain. ACS Chem Biol 2017; 12:2631-2643. [PMID: 28862425 DOI: 10.1021/acschembio.7b00694] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [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
Human Vγ9/Vδ2 T-cells detect tumor cells and microbial infections by recognizing small phosphorylated prenyl metabolites termed phosphoantigens (P-Ag). The type-1 transmembrane protein Butyrophilin 3A1 (BTN3A1) is critical to the P-Ag-mediated activation of Vγ9/Vδ2 T-cells; however, the molecular mechanisms involved in BTN3A1-mediated metabolite sensing are unclear, including how P-Ag's are discriminated from nonantigenic small molecules. Here, we utilized NMR and X-ray crystallography to probe P-Ag sensing by BTN3A1. Whereas the BTN3A1 immunoglobulin variable domain failed to bind P-Ag, the intracellular B30.2 domain bound a range of negatively charged small molecules, including P-Ag, in a positively charged surface pocket. However, NMR chemical shift perturbations indicated BTN3A1 discriminated P-Ag from nonantigenic small molecules by their ability to induce a specific conformational change in the B30.2 domain that propagated from the P-Ag binding site to distal parts of the domain. These results suggest BTN3A1 selectively detects P-Ag intracellularly via a conformational antigenic sensor in its B30.2 domain and have implications for rational design of antigens for Vγ9/Vδ2-based T-cell immunotherapies.
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Affiliation(s)
- Mahboob Salim
- Institute
of Immunology and Immunotherapy, University of Birmingham, Edgbaston, Birmingham, United Kingdom, B15 2TT
| | - Timothy J Knowles
- School
of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom, B15 2TT
| | - Alfie T. Baker
- Institute
of Immunology and Immunotherapy, University of Birmingham, Edgbaston, Birmingham, United Kingdom, B15 2TT
| | - Martin S. Davey
- Institute
of Immunology and Immunotherapy, University of Birmingham, Edgbaston, Birmingham, United Kingdom, B15 2TT
| | - Mark Jeeves
- Institute
of Cancer and Genomics, Henry Wellcome Building for Biomolecular NMR, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Pooja Sridhar
- School
of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom, B15 2TT
| | - John Wilkie
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, United Kingdom, B15 2TT
| | - Carrie R. Willcox
- Institute
of Immunology and Immunotherapy, University of Birmingham, Edgbaston, Birmingham, United Kingdom, B15 2TT
| | - Hachemi Kadri
- Cardiff
School of Pharmacy and Pharmaceutical Sciences, King Edward VII Avenue, Cardiff University, Cardiff CF10 3NB, United Kingdom
| | - Taher E. Taher
- Institute
of Immunology and Immunotherapy, University of Birmingham, Edgbaston, Birmingham, United Kingdom, B15 2TT
| | - Pierre Vantourout
- Peter
Gorer Department of Immunobiology, King’s College London, London SE1 9RT, United Kingdom
- The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Adrian Hayday
- Peter
Gorer Department of Immunobiology, King’s College London, London SE1 9RT, United Kingdom
- The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Youcef Mehellou
- Cardiff
School of Pharmacy and Pharmaceutical Sciences, King Edward VII Avenue, Cardiff University, Cardiff CF10 3NB, United Kingdom
| | - Fiyaz Mohammed
- Institute
of Immunology and Immunotherapy, University of Birmingham, Edgbaston, Birmingham, United Kingdom, B15 2TT
| | - Benjamin E. Willcox
- Institute
of Immunology and Immunotherapy, University of Birmingham, Edgbaston, Birmingham, United Kingdom, B15 2TT
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21
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Jeeves M, Fogl C, Al-Jassar C, Chidgey M, Overduin M. Sequence-specific 1H, 13C and 15N backbone resonance assignments of the plakin repeat domain of human envoplakin. Biomol NMR Assign 2016; 10:167-170. [PMID: 26590577 PMCID: PMC4788679 DOI: 10.1007/s12104-015-9659-2] [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] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 10/31/2015] [Indexed: 06/05/2023]
Abstract
The plakin repeat domain is a distinctive hallmark of the plakin superfamily of proteins, which are found within all epithelial tissues. Plakin repeat domains mediate the interactions of these proteins with the cell cytoskeleton and are critical for the maintenance of tissue integrity. Despite their biological importance, no solution state resonance assignments are available for any homologue. Here we report the essentially complete (1)H, (13)C and (15)N backbone chemical shift assignments of the singular 22 kDa plakin repeat domain of human envoplakin, providing the means to investigate its interactions with ligands including intermediate filaments.
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Affiliation(s)
- Mark Jeeves
- Henry Wellcome Building for Biomolecular NMR Spectroscopy, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Claudia Fogl
- Henry Wellcome Building for Biomolecular NMR Spectroscopy, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Caezar Al-Jassar
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
- School of Cancer Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Martyn Chidgey
- School of Cancer Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Michael Overduin
- Henry Wellcome Building for Biomolecular NMR Spectroscopy, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, 474 Medical Sciences Building, Edmonton, AB, T6G 2H7, Canada.
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22
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Browning DF, Bavro VN, Mason JL, Sevastsyanovich YR, Rossiter AE, Jeeves M, Wells TJ, Knowles TJ, Cunningham AF, Donald JW, Palmer T, Overduin M, Henderson IR. Cross-species chimeras reveal BamA POTRA and β-barrel domains must be fine-tuned for efficient OMP insertion. Mol Microbiol 2015; 97:646-59. [PMID: 25943387 PMCID: PMC4950039 DOI: 10.1111/mmi.13052] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [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] [Indexed: 01/07/2023]
Abstract
BAM is a conserved molecular machine, the central component of which is BamA. Orthologues of BamA are found in all Gram-negative bacteria, chloroplasts and mitochondria where it is required for the folding and insertion of β-barrel containing integral outer membrane proteins (OMPs) into the outer membrane. BamA binds unfolded β-barrel precursors via the five polypeptide transport-associated (POTRA) domains at its N-terminus. The C-terminus of BamA folds into a β-barrel domain, which tethers BamA to the outer membrane and is involved in OMP insertion. BamA orthologues are found in all Gram-negative bacteria and appear to function in a species-specific manner. Here we investigate the nature of this species-specificity by examining whether chimeric Escherichia coli BamA fusion proteins, carrying either the β-barrel or POTRA domains from various BamA orthologues, can functionally replace E. coli BamA. We demonstrate that the β-barrel domains of many BamA orthologues are functionally interchangeable. We show that defects in the orthologous POTRA domains can be rescued by compensatory mutations within the β-barrel. These data reveal that the POTRA and barrel domains must be precisely aligned to ensure efficient OMP insertion.
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Affiliation(s)
- Douglas F Browning
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Vassiliy N Bavro
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Jessica L Mason
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | | | - Amanda E Rossiter
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Mark Jeeves
- School of Cancer Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Timothy J Wells
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Timothy J Knowles
- School of Cancer Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Adam F Cunningham
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - James W Donald
- College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Tracy Palmer
- College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Michael Overduin
- School of Cancer Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Ian R Henderson
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
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23
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Abstract
The understanding of the biogenesis of the outer membrane of Gram‐negative bacteria is of critical importance due to the emergence of bacteria that are becoming resistant to available antibiotics. A problem that is most serious for Gram‐negative bacteria, with essentially few antibiotics under development or likely to be available for clinical use in the near future. The understanding of the Gram‐negative bacterial outer membrane is therefore critical to developing new antimicrobial agents, as this membrane makes direct contact with the external milieu, and the proteins present within this membrane are the instruments of microbial warfare, playing key roles in microbial pathogenesis, virulence and multidrug resistance. To date, a single outer membrane complex has been identified as essential for the folding and insertion of proteins into the outer membrane, this is the β‐barrel assembly machine (BAM) complex, which in some cases is supplemented by the Translocation and Assembly Module (TAM). In this issue of Molecular Microbiology, Dunstan et al. have identified a novel pathway for the insertion of a subset of integral membrane proteins into the Gram‐negative outer membrane that is independent of the BAM complex and TAM.
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Affiliation(s)
- Mark Jeeves
- School of Cancer Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Timothy J Knowles
- School of Cancer Sciences, University of Birmingham, Birmingham, B15 2TT, UK
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24
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Jeeves M, Sridhar P, Knowles TJ. Expression, Purification, and Screening of BamE, a Component of the BAM Complex, for Structural Characterization. Methods Mol Biol 2015; 1329:245-58. [PMID: 26427690 DOI: 10.1007/978-1-4939-2871-2_19] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
In Gram-negative bacteria, integral outer membrane β-barrel proteins (OMP) are assembled by the β-barrel assembly machine complex, or BAM complex. This complex includes the essential components BamA, an OMP composed of a carboxyl terminal β-barrel domain and five polypeptide transport-associated domains (POTRA), and the lipoprotein BamD. In Escherichia coli, the complex contains an additional three lipoproteins, BamB, C and E required for efficient delivery of OMPs to the outer membrane. Here we provide methods for production, isotope labeling, purification, and functional screening of BamE for research purposes. Purification strategies of both the soluble and wild-type membrane-tethered forms of BamE are described using techniques including osmotic shock, Ni-NTA purification, and size-exclusion chromatography. Functional screening using a simple plate assay is also described which allows screening for defects in outer membrane permeability.
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Affiliation(s)
- Mark Jeeves
- School of Cancer Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Pooja Sridhar
- School of Cancer Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Timothy J Knowles
- School of Cancer Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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25
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Browning DF, Matthews SA, Rossiter AE, Sevastsyanovich YR, Jeeves M, Mason JL, Wells TJ, Wardius CA, Knowles TJ, Cunningham AF, Bavro VN, Overduin M, Henderson IR. Mutational and topological analysis of the Escherichia coli BamA protein. PLoS One 2013; 8:e84512. [PMID: 24376817 PMCID: PMC3871556 DOI: 10.1371/journal.pone.0084512] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [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: 08/20/2013] [Accepted: 11/15/2013] [Indexed: 11/18/2022] Open
Abstract
The multi-protein β-barrel assembly machine (BAM) of Escherichia coli is responsible for the folding and insertion of β-barrel containing integral outer membrane proteins (OMPs) into the bacterial outer membrane. An essential component of this complex is the BamA protein, which binds unfolded β-barrel precursors via the five polypeptide transport-associated (POTRA) domains in its N-terminus. The C-terminus of BamA contains a β-barrel domain, which tethers BamA to the outer membrane and is also thought to be involved in OMP insertion. Here we mutagenize BamA using linker scanning mutagenesis and demonstrate that all five POTRA domains are essential for BamA protein function in our experimental system. Furthermore, we generate a homology based model of the BamA β-barrel and test our model using insertion mutagenesis, deletion analysis and immunofluorescence to identify β-strands, periplasmic turns and extracellular loops. We show that the surface-exposed loops of the BamA β-barrel are essential.
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Affiliation(s)
- Douglas F. Browning
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
- * E-mail: (DFB); (IRH)
| | - Sophie A. Matthews
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Amanda E. Rossiter
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Yanina R. Sevastsyanovich
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Mark Jeeves
- School of Cancer Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Jessica L. Mason
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Timothy J. Wells
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Catherine A. Wardius
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Timothy J. Knowles
- School of Cancer Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Adam F. Cunningham
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Vassiliy N. Bavro
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Michael Overduin
- School of Cancer Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Ian R. Henderson
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
- * E-mail: (DFB); (IRH)
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26
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Jeeves M, McClelland DM, Barr AJ, Overduin M. Sequence-specific 1H, 13C and 15N backbone resonance assignments of the 34 kDa catalytic domain of human PTPN7. Biomol NMR Assign 2008; 2:101-103. [PMID: 19636879 DOI: 10.1007/s12104-008-9095-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2008] [Accepted: 05/06/2008] [Indexed: 05/28/2023]
Abstract
PTPN7 is a protein tyrosine phosphatase responsible for inactivation of MAPK in leukocytes. Here we report the backbone resonance assignments of the 34 kDa phosphatase domain of human PTPN7, which is amplified in myeloid malignancies and deleted in lymphoproliferative disorders.
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Affiliation(s)
- Mark Jeeves
- Cancer Research UK Institute for Cancer Studies, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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27
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Knowles TJ, Jeeves M, Bobat S, Dancea F, McClelland D, Palmer T, Overduin M, Henderson IR. Fold and function of polypeptide transport-associated domains responsible for delivering unfolded proteins to membranes. Mol Microbiol 2008; 68:1216-27. [DOI: 10.1111/j.1365-2958.2008.06225.x] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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28
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Knowles TJ, Bobat S, Jeeves M, Henderson IR, Overduin M. Secondary structure and 1H, 13C and 15N resonance assignments of the Escherichia coli YaeT POTRA domain. Biomol NMR Assign 2007; 1:113-115. [PMID: 19636842 DOI: 10.1007/s12104-007-9032-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2007] [Revised: 06/25/2007] [Accepted: 06/26/2007] [Indexed: 05/28/2023]
Abstract
We report the first 1H, 13C and 15N chemical shift assignments and secondary structure of the Escherichia coli YaeT POTRA domain; a domain found in the Omp85 family of proteins which is critical for insertion and folding of outer membrane proteins in Gram-negative bacteria.
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Affiliation(s)
- Timothy J Knowles
- Cancer Research UK Institute for Cancer Studies, University of Birmingham, Edgbaston, Birmingham B152TT, UK
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29
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Nunn CM, Jeeves M, Cliff MJ, Urquhart GT, George RR, Chao LH, Tscuchia Y, Djordjevic S. Crystal structure of tobacco etch virus protease shows the protein C terminus bound within the active site. J Mol Biol 2005; 350:145-55. [PMID: 15919091 DOI: 10.1016/j.jmb.2005.04.013] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2005] [Revised: 04/06/2005] [Accepted: 04/07/2005] [Indexed: 11/29/2022]
Abstract
Tobacco etch virus (TEV) protease is a cysteine protease exhibiting stringent sequence specificity. The enzyme is widely used in biotechnology for the removal of the affinity tags from recombinant fusion proteins. Crystal structures of two TEV protease mutants as complexes with a substrate and a product peptide provided the first insight into the mechanism of substrate specificity of this enzyme. We now report a 2.7A crystal structure of a full-length inactive C151A mutant protein crystallised in the absence of peptide. The structure reveals the C terminus of the protease bound to the active site. In addition, we determined dissociation constants of TEV protease substrate and product peptides using isothermal titration calorimetry for various forms of this enzyme. Data suggest that TEV protease could be inhibited by the peptide product of autolysis. Separate modes of recognition for native substrates and the site of TEV protease self-cleavage are proposed.
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Affiliation(s)
- Christine M Nunn
- Department of Biochemistry and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK
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30
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Jaseja M, Jeeves M, Hyde EI. Trp repressor-operator binding: NMR and electrophoretic mobility shift studies of the effect of DNA sequence and corepressor binding on two Trp repressor-operator complexes. Biochemistry 2002; 41:14866-78. [PMID: 12475235 DOI: 10.1021/bi020072y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In Trp repressor-DNA complexes, most interactions either occur with phosphate groups or are water-mediated hydrogen bonds to bases. To examine the factors involved in DNA selectivity, we have studied Trp repressor binding to two operator sequences, trpR(S)() and trpO(M)(), with L-tryptophan or 5-methyltryptophan as corepressor. These operators contain all the consensus bases but differ at base pairs contacted by their phosphate groups. In electrophoretic mobility shift assays (EMSAs) the trpR(S)() sequence gives solely 1:1 protein-DNA complexes with either corepressor. The trpO(M )()sequence binds more weakly than trpR(S)(). It gives dissociating 2:1 complexes in EMSAs with L-tryptophan, but both 1:1 and 2:1 complexes are observed with 5-methyltryptophan or if glycerol is present in the gel. The backbone resonances of the TrpR-L-tryptophan-DNA complexes were assigned using triple-resonance experiments and selectively (15)N labeled protein. On changing the DNA sequence, the largest differences in the NMR spectra are at residues 78-81, at the turn of the helix-turn-helix motif and the tip of the recognition helix. I79 and A80 interact with the conserved bases of the operators, while G78 and T81 interact with phosphate groups at bases that differ between the two sequences. Changing the corepressor from L-tryptophan to 5-methyltryptophan causes effects at residues 52, 60, 61, and 85, which do not interact with the DNA. The spectra suggest that there is mutual induced fit between protein and DNA so that sequence changes at bases contacted only by the phosphate groups affect the environment of the protein at residues that bind to conserved bases elsewhere in the DNA.
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Affiliation(s)
- Mahesh Jaseja
- School of Biosciences, University of Birmingham, Edgbaston, UK
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31
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Abstract
The persistence and stability of selective deficits in interhemispheric processing resulting from known callosal pathology have been monitored over periods ranging from ten to thirty five years. The present study included five patients: two with complete agenesis of the corpus callosum, one with partial dysgenesis, and two with a partial section of the corpus callosum. A crossed-uncrossed difference task and four bilateral visual matching tasks were administered to these patients and to groups of normal individuals matched on age and intelligence. As expected, all of the patients showed deficits in speed or accuracy relative to the performance of their control groups. The profile of performance for each patient across the five tasks demonstrated a systematic (but not perfectly consistent) relationship with the location and extent of callosal pathology.
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32
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Jeeves M, Smith KJ, Quirk PG, Cotton NP, Jackson JB. Solution structure of the NADP(H)-binding component (dIII) of proton-translocating transhydrogenase from Rhodospirillum rubrum. Biochim Biophys Acta 2000; 1459:248-57. [PMID: 11004437 DOI: 10.1016/s0005-2728(00)00159-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Transhydrogenase is a proton pump found in the membranes of bacteria and animal mitochondria. The solution structure of the expressed, 21.5 kDa, NADP(H)-binding component (dIII) of transhydrogenase from Rhodospirillum rubrum has been solved by NMR methods. This is the first description of the structure of dIII from a bacterial source. The protein adopts a Rossmann fold: an open, twisted, parallel beta-sheet, flanked by helices. However, the binding of NADP(+) to dIII is profoundly different to that seen in other Rossmann structures, in that its orientation is reversed: the adenosine moiety interacts with the first betaalphabetaalphabeta motif, and the nicotinamide with the second. Features in the structure that might be responsible for changes in nucleotide-binding affinity during catalysis, and for interaction with other components of the enzyme, are identified. The results are compared with the recently determined, high-resolution crystal structures of human and bovine dIII which also show the reversed nucleotide orientation.
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Affiliation(s)
- M Jeeves
- School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
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33
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Jeeves M, Evans PD, Parslow RA, Jaseja M, Hyde EI. Studies of the Escherichia coli Trp repressor binding to its five operators and to variant operator sequences. Eur J Biochem 1999; 265:919-28. [PMID: 10518785 DOI: 10.1046/j.1432-1327.1999.00792.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The Escherichia coli Trp repressor binds to promoters of very different sequence and intrinsic activity. Its mode of binding to trp operator DNA has been studied extensively yet remains highly controversial. In order to examine the selectivity of the protein for DNA, we have used electromobility shift assays (EMSAs) to study its binding to synthetic DNA containing the core sequences of each of its five operators and of operator variants. Our results for DNA containing sequences of two of the operators, trpEDCBA and aroH are similar to those of previous studies. Up to three bands of lower mobility than the free DNA are obtained which are assigned to complexes of stoichiometry 1 : 1, 2 : 1 and 3 : 1 Trp repressor dimer to DNA. The mtr and aroL operators have not been studied previously in vitro. For DNA containing these sequences, we observe predominantly one retarded band in EMSA with mobility corresponding to 2 : 1 complexes. We have also obtained retardation of DNA containing the trpR operator sequence, which has only been previously obtained with super-repressor Trp mutants. This gives bands with mobilities corresponding to 1 : 1 and 2 : 1 complexes. In contrast, DNA containing containing a symmetrized trpR operator sequence, trpRs, gives a single retarded band with mobility corresponding solely to a 1 : 1 protein dimer-DNA complex. Using trpR operator variants, we show that a change in a single base pair in the core 20 base pairs can alter the number of retarded DNA bands in EMSA and the length of the DNase I footprint observed. This shows that the binding of the second dimer is sequence selective. We propose that the broad selectivity of Trp repressor coupled to tandem 2 : 1 binding, which we have observed with all five operator sequences, enables the Trp repressor to bind to a limited number of sites with diverse sequences. This allows it to co-ordinately control promoters of different intrinsic strength. This mechanism may be of importance in a number of promoters that bind multiple effector molecules.
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Affiliation(s)
- M Jeeves
- School of Biochemistry, University of Birmingham, UK
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34
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Abstract
PURPOSE To evaluate long-term follow-up in eyes of children who had sulcus fixation of an intraocular lens (IOL) without capsular support. SETTING St. Eriks Eye Hospital/Karolinska Institute, Stockholm, Sweden. METHODS This retrospective study included 21 eyes of 13 children. Seven eyes had Marfan's syndrome, 7 essential lens dislocation, 2 perforation with lens injury, and 5 spherophakia. The IOL implantation was primary in 16 eyes and secondary in 5 eyes. Lensectomy was performed with a limbal approach. An IOL with holes in the haptics was sutured in the sulcus, with the knots buried in the scleral bed. RESULTS Mean patient age was 5.8 years +/- 2.6 (SD). Follow-up ranged from 9 to 33 months. No complications occurred during surgery. In all cases after IOL implantation, best corrected visual acuity was equal to or better than preoperatively. After surgery, no opacification of the visual axis, secondary glaucoma, or retinal complication was recorded. Posterior synechia formation occurred in 4 eyes, and 4 had cells on the IOL surface in 2 eyes, the IOL optic subluxated into the anterior chamber with the haptics in place. Both cases were successfully treated with pilocarpine 4%. CONCLUSION Our results suggest that sulcus fixation of an IOL without capsular support is an option to correct aphakia in children.
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Affiliation(s)
- C Zetterström
- Department of Ophthalmology, St. Eriks Eye Hospital/Karolinska Institute, Stockholm, Sweden
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35
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Quirk PG, Jeeves M, Cotton NP, Smith JK, Jackson BJ. Structural changes in the recombinant, NADP(H)-binding component of proton translocating transhydrogenase revealed by NMR spectroscopy. FEBS Lett 1999; 446:127-32. [PMID: 10100628 DOI: 10.1016/s0014-5793(99)00198-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [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] [Indexed: 11/16/2022]
Abstract
We have analysed 1H, 15N-HSQC spectra of the recombinant, NADP(H)-binding component of transhydrogenase in the context of the emerging three dimensional structure of the protein. Chemical shift perturbations of amino acid residues following replacement of NADP+ with NADPH were observed in both the adenosine and nicotinamide parts of the dinucleotide binding site and in a region which straddles the protein. These observations reflect the structural changes resulting from hydride transfer. The interactions between the recombinant, NADP(H)-binding component and its partner, NAD(H)-binding protein, are complicated. Helix B of the recombinant, NADP(H)-binding component may play an important role in the binding process.
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Affiliation(s)
- P G Quirk
- School of Biochemistry, University of Birmingham, Edgbaston, UK
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36
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Jeeves M, Smith KJ, Quirk PG, Cotton NP, Baz Jackson J. Letter to the Editor: Sequence-specific resonance assignments for the NADP(H)-binding component (domain III) of proton- translocating transhydrogenase from Rhodospisrillum rubrum. J Biomol NMR 1999; 13:305-306. [PMID: 20700820 DOI: 10.1023/a:1008300609352] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Affiliation(s)
- M Jeeves
- School of Biochemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, U.K
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37
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Abstract
To understand the specificity of the Escherichia coli Trp repressor for its operators, we have begun to study complexes of the protein with alternative DNA sequences, using 1H-NMR spectroscopy. We report here the 1H-NMR chemical shifts of a 20-bp oligodeoxynucleotide containing the sequence of a symmetrised form of the trpR operator in the presence and absence of the holorepressor. Deuterated protein was used to assign the spectrum of the oligodeoxynucleotide in a 37-kDa complex with the Trp holorepressor. Many of the resonances of the DNA shift on binding to the protein, which suggests changes in conformation throughout the sequence. The largest changes in shifts for the aromatic protons in the major groove are for A15 and G16, which are thought to hydrogen bond to the protein, possibly via water molecules. We have also examined the effect of DNA binding on the corepressor, tryptophan, in this complex. The indole proton resonance of the tryptophan undergoes a downfield shift of 1.2 ppm upon binding of DNA. This large shift is consistent with hydrogen bonding of the tryptophan to the phosphate backbone of the trpR operator DNA, as in the crystal structure of the holoprotein with the trp operator.
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Affiliation(s)
- P D Evans
- School of Biochemistry, University of Birmingham, Edgbaston, UK
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38
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Geffen G, Walsh A, Simpson D, Jeeves M. Comparison of the effects of transcortical and transcallosal removal of intraventricular tumours. Brain 1980; 103:773-88. [PMID: 7437889 DOI: 10.1093/brain/103.4.773] [Citation(s) in RCA: 84] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Intelligence and memory functions were tested in 2 patients in whom the corpus callosum had been partially sectioned to remove intraventricular cysts or tumours and in 2 patients in whom similarly-located cysts or tumours had been removed transcortically. A patient with congenital absence of the corpus callosum was also tested. Callosal lesions per se did not appear to be responsible for memory deficits.
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