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Dirnberger B, Korona D, Popovic R, Deery MJ, Barber H, Russell S, Lilley KS. Enrichment of Membrane Proteins for Downstream Analysis Using Styrene Maleic Acid Lipid Particles (SMALPs) Extraction. Bio Protoc 2023; 13:e4728. [PMID: 37575399 PMCID: PMC10415199 DOI: 10.21769/bioprotoc.4728] [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] [Received: 12/15/2022] [Revised: 02/17/2023] [Accepted: 05/08/2023] [Indexed: 08/15/2023] Open
Abstract
Integral membrane proteins are an important class of cellular proteins. These take part in key cellular processes such as signaling transducing receptors to transporters, many operating within the plasma membrane. More than half of the FDA-approved protein-targeting drugs operate via interaction with proteins that contain at least one membrane-spanning region, yet the characterization and study of their native interactions with therapeutic agents remains a significant challenge. This challenge is due in part to such proteins often being present in small quantities within a cell. Effective solubilization of membrane proteins is also problematic, with the detergents typically employed in solubilizing membranes leading to a loss of functional activity and key interacting partners. In recent years, alternative methods to extract membrane proteins within their native lipid environment have been investigated, with the aim of producing functional nanodiscs, maintaining protein-protein and protein-lipid interactions. A promising approach involves extracting membrane proteins in the form of styrene maleic acid lipid particles (SMALPs) that allow the retention of their native conformation. This extraction method offers many advantages for further protein analysis and allows the study of the protein interactions with other molecules, such as drugs. Here, we describe a protocol for efficient SMALP extraction of functionally active membrane protein complexes within nanodiscs. We showcase the method on the isolation of a low copy number plasma membrane receptor complex, the nicotinic acetylcholine receptor (nAChR), from adult Drosophila melanogaster heads. We demonstrate that these nanodiscs can be used to study native receptor-ligand interactions. This protocol can be applied across many biological scenarios to extract the native conformations of low copy number integral membrane proteins.
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Affiliation(s)
- Benedict Dirnberger
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, United Kingdom
| | - Dagmara Korona
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, United Kingdom
| | - Rebeka Popovic
- MRC Toxicology Unit, Gleeson Building, University of Cambridge, Cambridge, United Kingdom
| | - Michael J. Deery
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Helen Barber
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Steven Russell
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, United Kingdom
| | - Kathryn S. Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
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2
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Piovesana M, Wood AKM, Smith DP, Deery MJ, Bayliss R, Carrera E, Wellner N, Kosik O, Napier JA, Kurup S, Matthes MC. A point mutation in the kinase domain of CRK10 leads to xylem vessel collapse and activation of defence responses in Arabidopsis. J Exp Bot 2023; 74:3104-3121. [PMID: 36869735 DOI: 10.1093/jxb/erad080] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 02/27/2023] [Indexed: 05/21/2023]
Abstract
Cysteine-rich receptor-like kinases (CRKs) are a large family of plasma membrane-bound receptors ubiquitous in higher plants. However, despite their prominence, their biological roles have remained largely elusive so far. In this study we report the characterization of an Arabidopsis mutant named crk10-A397T in which alanine 397 has been replaced by a threonine in the αC helix of the kinase domain of CRK10, known to be a crucial regulatory module in mammalian kinases. The crk10-A397T mutant is a dwarf that displays collapsed xylem vessels in the root and hypocotyl, whereas the vasculature of the inflorescence develops normally. In situ phosphorylation assays with His-tagged wild type and crk10-A397T versions of the CRK10 kinase domain revealed that both alleles are active kinases capable of autophosphorylation, with the newly introduced threonine acting as an additional phosphorylation site in crk10-A397T. Transcriptomic analysis of wild type and crk10-A397T mutant hypocotyls revealed that biotic and abiotic stress-responsive genes are constitutively up-regulated in the mutant, and a root-infection assay with the vascular pathogen Fusarium oxysporum demonstrated that the mutant has enhanced resistance to this pathogen compared with wild type plants. Taken together our results suggest that crk10-A397T is a gain-of-function allele of CRK10, the first such mutant to have been identified for a CRK in Arabidopsis.
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Affiliation(s)
- Maiara Piovesana
- Department of Plant Sciences, Rothamsted Research, Harpenden AL5 2JQ, UK
- College of Life and Environmental Sciences, Streatham Campus, Exeter EX4 4PY, UK
| | - Ana K M Wood
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden AL5 2JQ, UK
| | - Daniel P Smith
- Department of Computational and Analytical Sciences, Rothamsted Research, Harpenden AL5 2JQ, UK
| | - Michael J Deery
- Cambridge Centre for Proteomics, University of Cambridge, Cambridge CB2 1QR, UK
| | - Richard Bayliss
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Esther Carrera
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politècnica de València, Valencia 46022, Spain
| | | | - Ondrej Kosik
- Department of Plant Sciences, Rothamsted Research, Harpenden AL5 2JQ, UK
| | - Johnathan A Napier
- Department of Plant Sciences, Rothamsted Research, Harpenden AL5 2JQ, UK
| | - Smita Kurup
- Department of Plant Sciences, Rothamsted Research, Harpenden AL5 2JQ, UK
| | - Michaela C Matthes
- Department of Plant Sciences, Rothamsted Research, Harpenden AL5 2JQ, UK
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Hsieh LTH, Hall BS, Newcombe J, Mendum TA, Umrania Y, Deery MJ, Shi WQ, Salguero FJ, Simmonds RE. Mycolactone causes catastrophic Sec61-dependent loss of the endothelial glycocalyx and basement membrane: a new indirect mechanism driving tissue necrosis in Mycobacterium ulcerans infection. bioRxiv 2023:2023.02.21.529382. [PMID: 36865118 PMCID: PMC9980099 DOI: 10.1101/2023.02.21.529382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
The drivers of tissue necrosis in Mycobacterium ulcerans infection (Buruli ulcer disease) have historically been ascribed solely to the directly cytotoxic action of the diffusible exotoxin, mycolactone. However, its role in the clinically-evident vascular component of disease aetiology remains poorly explained. We have now dissected mycolactone's effects on primary vascular endothelial cells in vitro and in vivo. We show that mycolactone-induced changes in endothelial morphology, adhesion, migration, and permeability are dependent on its action at the Sec61 translocon. Unbiased quantitative proteomics identified a profound effect on proteoglycans, driven by rapid loss of type II transmembrane proteins of the Golgi, including enzymes required for glycosaminoglycan (GAG) synthesis, combined with a reduction in the core proteins themselves. Loss of the glycocalyx is likely to be of particular mechanistic importance, since knockdown of galactosyltransferase II (beta-1,3-galactotransferase 6; B3Galt6), the GAG linker-building enzyme, phenocopied the permeability and phenotypic changes induced by mycolactone. Additionally, mycolactone depleted many secreted basement membrane components and microvascular basement membranes were disrupted in vivo. Remarkably, exogenous addition of laminin-511 reduced endothelial cell rounding, restored cell attachment and reversed the defective migration caused by mycolactone. Hence supplementing mycolactone-depleted extracellular matrix may be a future therapeutic avenue, to improve wound healing rates.
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Affiliation(s)
| | - Belinda S Hall
- Dept of Microbial Sciences, School of Bioscience and Medicine, University of Surrey
| | - Jane Newcombe
- Dept of Microbial Sciences, School of Bioscience and Medicine, University of Surrey
| | - Tom A Mendum
- Dept of Microbial Sciences, School of Bioscience and Medicine, University of Surrey
| | - Yagnesh Umrania
- Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK
| | - Michael J Deery
- Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK
| | - Wei Q Shi
- Department of Chemistry, Ball State University, Muncie, IN 47306, USA
| | | | - Rachel E Simmonds
- Dept of Microbial Sciences, School of Bioscience and Medicine, University of Surrey
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4
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Guffick C, Hsieh PY, Ali A, Shi W, Howard J, Chinthapalli DK, Kong AC, Salaa I, Crouch LI, Ansbro MR, Isaacson SC, Singh H, Barrera NP, Nair AV, Robinson CV, Deery MJ, van Veen HW. Drug-dependent inhibition of nucleotide hydrolysis in the heterodimeric ABC multidrug transporter PatAB from Streptococcus pneumoniae. FEBS J 2022; 289:3770-3788. [PMID: 35066976 PMCID: PMC9541285 DOI: 10.1111/febs.16366] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 12/07/2021] [Accepted: 01/20/2022] [Indexed: 02/02/2023]
Abstract
The bacterial heterodimeric ATP‐binding cassette (ABC) multidrug exporter PatAB has a critical role in conferring antibiotic resistance in multidrug‐resistant infections by Streptococcus pneumoniae. As with other heterodimeric ABC exporters, PatAB contains two transmembrane domains that form a drug translocation pathway for efflux and two nucleotide‐binding domains that bind ATP, one of which is hydrolysed during transport. The structural and functional elements in heterodimeric ABC multidrug exporters that determine interactions with drugs and couple drug binding to nucleotide hydrolysis are not fully understood. Here, we used mass spectrometry techniques to determine the subunit stoichiometry in PatAB in our lactococcal expression system and investigate locations of drug binding using the fluorescent drug‐mimetic azido‐ethidium. Surprisingly, our analyses of azido‐ethidium‐labelled PatAB peptides point to ethidium binding in the PatA nucleotide‐binding domain, with the azido moiety crosslinked to residue Q521 in the H‐like loop of the degenerate nucleotide‐binding site. Investigation into this compound and residue’s role in nucleotide hydrolysis pointed to a reduction in the activity for a Q521A mutant and ethidium‐dependent inhibition in both mutant and wild type. Most transported drugs did not stimulate or inhibit nucleotide hydrolysis of PatAB in detergent solution or lipidic nanodiscs. However, further examples for ethidium‐like inhibition were found with propidium, novobiocin and coumermycin A1, which all inhibit nucleotide hydrolysis by a non‐competitive mechanism. These data cast light on potential mechanisms by which drugs can regulate nucleotide hydrolysis by PatAB, which might involve a novel drug binding site near the nucleotide‐binding domains.
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Affiliation(s)
| | - Pei-Yu Hsieh
- Department of Pharmacology, University of Cambridge, UK
| | - Anam Ali
- Department of Pharmacology, University of Cambridge, UK
| | - Wilma Shi
- Department of Pharmacology, University of Cambridge, UK
| | - Julie Howard
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, UK
| | | | - Alex C Kong
- Department of Pharmacology, University of Cambridge, UK
| | - Ihsene Salaa
- Department of Pharmacology, University of Cambridge, UK
| | - Lucy I Crouch
- Department of Pharmacology, University of Cambridge, UK
| | | | | | | | - Nelson P Barrera
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Asha V Nair
- Department of Pharmacology, University of Cambridge, UK
| | | | - Michael J Deery
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, UK
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5
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Istrate A, Geeson MB, Navo CD, Sousa BB, Marques MC, Taylor RJ, Journeaux T, Oehler SR, Mortensen MR, Deery MJ, Bond AD, Corzana F, Jiménez-Osés G, Bernardes GJL. Platform for Orthogonal N-Cysteine-Specific Protein Modification Enabled by Cyclopropenone Reagents. J Am Chem Soc 2022; 144:10396-10406. [PMID: 35658467 PMCID: PMC9490850 DOI: 10.1021/jacs.2c02185] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Protein conjugates are valuable tools for studying biological processes or producing therapeutics, such as antibody-drug conjugates. Despite the development of several protein conjugation strategies in recent years, the ability to modify one specific amino acid residue on a protein in the presence of other reactive side chains remains a challenge. We show that monosubstituted cyclopropenone (CPO) reagents react selectively with the 1,2-aminothiol groups of N-terminal cysteine residues to give a stable 1,4-thiazepan-5-one linkage under mild, biocompatible conditions. The CPO-based reagents, all accessible from a common activated ester CPO-pentafluorophenol (CPO-PFP), allow selective modification of N-terminal cysteine-containing peptides and proteins even in the presence of internal, solvent-exposed cysteine residues. This approach enabled the preparation of a dual protein conjugate of 2×cys-GFP, containing both internal and N-terminal cysteine residues, by first modifying the N-terminal residue with a CPO-based reagent followed by modification of the internal cysteine with a traditional cysteine-modifying reagent. CPO-based reagents enabled a copper-free click reaction between two proteins, producing a dimer of a de novo protein mimic of IL2 that binds to the β-IL2 receptor with low nanomolar affinity. Importantly, the reagents are compatible with the common reducing agent dithiothreitol (DTT), a useful property for working with proteins prone to dimerization. Finally, quantum mechanical calculations uncover the origin of selectivity for CPO-based reagents for N-terminal cysteine residues. The ability to distinguish and specifically target N-terminal cysteine residues on proteins facilitates the construction of elaborate multilabeled bioconjugates with minimal protein engineering.
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Affiliation(s)
- Alena Istrate
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom
| | - Michael B Geeson
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom
| | - Claudio D Navo
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Spain
| | - Barbara B Sousa
- Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Marta C Marques
- Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Ross J Taylor
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom
| | - Toby Journeaux
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom
| | - Sebastian R Oehler
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Michael R Mortensen
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Michael J Deery
- Cambridge Centre for Proteomics, Gleeson Building, University of Cambridge, Tennis Court Road, CB2 1QR Cambridge, United Kingdom
| | - Andrew D Bond
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom
| | - Francisco Corzana
- Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, 26006 Logroño, Spain
| | - Gonzalo Jiménez-Osés
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160 Derio, Spain.,Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Gonçalo J L Bernardes
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom.,Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
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6
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Fabre B, Choteau SA, Duboé C, Pichereaux C, Montigny A, Korona D, Deery MJ, Camus M, Brun C, Burlet-Schiltz O, Russell S, Combier JP, Lilley KS, Plaza S. In Depth Exploration of the Alternative Proteome of Drosophila melanogaster. Front Cell Dev Biol 2022; 10:901351. [PMID: 35721519 PMCID: PMC9204603 DOI: 10.3389/fcell.2022.901351] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 04/25/2022] [Indexed: 12/13/2022] Open
Abstract
Recent studies have shown that hundreds of small proteins were occulted when protein-coding genes were annotated. These proteins, called alternative proteins, have failed to be annotated notably due to the short length of their open reading frame (less than 100 codons) or the enforced rule establishing that messenger RNAs (mRNAs) are monocistronic. Several alternative proteins were shown to be biologically active molecules and seem to be involved in a wide range of biological functions. However, genome-wide exploration of the alternative proteome is still limited to a few species. In the present article, we describe a deep peptidomics workflow which enabled the identification of 401 alternative proteins in Drosophila melanogaster. Subcellular localization, protein domains, and short linear motifs were predicted for 235 of the alternative proteins identified and point toward specific functions of these small proteins. Several alternative proteins had approximated abundances higher than their canonical counterparts, suggesting that these alternative proteins are actually the main products of their corresponding genes. Finally, we observed 14 alternative proteins with developmentally regulated expression patterns and 10 induced upon the heat-shock treatment of embryos, demonstrating stage or stress-specific production of alternative proteins.
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Affiliation(s)
- Bertrand Fabre
- Laboratoire de Recherche en Sciences Végétales, UMR5546, Université de Toulouse, UPS, INP, CNRS, Auzeville-Tolosane, France,Cambridge Centre for Proteomics, Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom,*Correspondence: Bertrand Fabre, ; Serge Plaza,
| | - Sebastien A. Choteau
- Aix-Marseille Université, INSERM, TAGC, Turing Centre for Living Systems, Marseille, France
| | - Carine Duboé
- Laboratoire de Recherche en Sciences Végétales, UMR5546, Université de Toulouse, UPS, INP, CNRS, Auzeville-Tolosane, France
| | - Carole Pichereaux
- Fédération de Recherche (FR3450), Agrobiosciences, Interactions et Biodiversité (AIB), CNRS, Toulouse, France,Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France,Infrastructure Nationale de Protéomique, ProFI, FR 2048, Toulouse, France
| | - Audrey Montigny
- Laboratoire de Recherche en Sciences Végétales, UMR5546, Université de Toulouse, UPS, INP, CNRS, Auzeville-Tolosane, France
| | - Dagmara Korona
- Cambridge Systems Biology Centre and Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Michael J. Deery
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Mylène Camus
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France,Infrastructure Nationale de Protéomique, ProFI, FR 2048, Toulouse, France
| | - Christine Brun
- Aix-Marseille Université, INSERM, TAGC, Turing Centre for Living Systems, Marseille, France,CNRS, Marseille, France
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France,Infrastructure Nationale de Protéomique, ProFI, FR 2048, Toulouse, France
| | - Steven Russell
- Cambridge Systems Biology Centre and Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Jean-Philippe Combier
- Laboratoire de Recherche en Sciences Végétales, UMR5546, Université de Toulouse, UPS, INP, CNRS, Auzeville-Tolosane, France
| | - Kathryn S. Lilley
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Serge Plaza
- Laboratoire de Recherche en Sciences Végétales, UMR5546, Université de Toulouse, UPS, INP, CNRS, Auzeville-Tolosane, France,*Correspondence: Bertrand Fabre, ; Serge Plaza,
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7
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Korona D, Dirnberger B, Giachello CNG, Queiroz RML, Popovic R, Müller KH, Minde DP, Deery MJ, Johnson G, Firth LC, Earley FG, Russell S, Lilley KS. Drosophila nicotinic acetylcholine receptor subunits and their native interactions with insecticidal peptide toxins. eLife 2022; 11:74322. [PMID: 35575460 PMCID: PMC9110030 DOI: 10.7554/elife.74322] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 04/19/2022] [Indexed: 12/14/2022] Open
Abstract
Drosophila nicotinic acetylcholine receptors (nAChRs) are ligand-gated ion channels that represent a target for insecticides. Peptide neurotoxins are known to block nAChRs by binding to their target subunits, however, a better understanding of this mechanism is needed for effective insecticide design. To facilitate the analysis of nAChRs we used a CRISPR/Cas9 strategy to generate null alleles for all ten nAChR subunit genes in a common genetic background. We studied interactions of nAChR subunits with peptide neurotoxins by larval injections and styrene maleic acid lipid particles (SMALPs) pull-down assays. For the null alleles, we determined the effects of α-Bungarotoxin (α-Btx) and ω-Hexatoxin-Hv1a (Hv1a) administration, identifying potential receptor subunits implicated in the binding of these toxins. We employed pull-down assays to confirm α-Btx interactions with the Drosophila α5 (Dα5), Dα6, Dα7 subunits. Finally, we report the localisation of fluorescent tagged endogenous Dα6 during Drosophila CNS development. Taken together, this study elucidates native Drosophila nAChR subunit interactions with insecticidal peptide toxins and provides a resource for the in vivo analysis of insect nAChRs.
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Affiliation(s)
- Dagmara Korona
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, United Kingdom
| | - Benedict Dirnberger
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, United Kingdom.,Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.,Syngenta, Jealott's Hill International Research Centre, Bracknell, United Kingdom
| | - Carlo N G Giachello
- Syngenta, Jealott's Hill International Research Centre, Bracknell, United Kingdom
| | - Rayner M L Queiroz
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Rebeka Popovic
- MRC Toxicology Unit, Gleeson Building, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom
| | - Karin H Müller
- Cambridge Advanced Imaging Centre, Department of Physiology, Development and Neuroscience/Anatomy Building, University of Cambridge, Cambridge, United Kingdom
| | - David-Paul Minde
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Michael J Deery
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Glynnis Johnson
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, United Kingdom
| | - Lucy C Firth
- Syngenta, Jealott's Hill International Research Centre, Bracknell, United Kingdom
| | - Fergus G Earley
- Syngenta, Jealott's Hill International Research Centre, Bracknell, United Kingdom
| | - Steven Russell
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, United Kingdom
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom
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8
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Mulvey CM, Breckels LM, Crook OM, Sanders DJ, Ribeiro ALR, Geladaki A, Christoforou A, Britovšek NK, Hurrell T, Deery MJ, Gatto L, Smith AM, Lilley KS. Spatiotemporal proteomic profiling of the pro-inflammatory response to lipopolysaccharide in the THP-1 human leukaemia cell line. Nat Commun 2021; 12:5773. [PMID: 34599159 PMCID: PMC8486773 DOI: 10.1038/s41467-021-26000-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [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: 03/02/2021] [Accepted: 09/07/2021] [Indexed: 02/07/2023] Open
Abstract
Protein localisation and translocation between intracellular compartments underlie almost all physiological processes. The hyperLOPIT proteomics platform combines mass spectrometry with state-of-the-art machine learning to map the subcellular location of thousands of proteins simultaneously. We combine global proteome analysis with hyperLOPIT in a fully Bayesian framework to elucidate spatiotemporal proteomic changes during a lipopolysaccharide (LPS)-induced inflammatory response. We report a highly dynamic proteome in terms of both protein abundance and subcellular localisation, with alterations in the interferon response, endo-lysosomal system, plasma membrane reorganisation and cell migration. Proteins not previously associated with an LPS response were found to relocalise upon stimulation, the functional consequences of which are still unclear. By quantifying proteome-wide uncertainty through Bayesian modelling, a necessary role for protein relocalisation and the importance of taking a holistic overview of the LPS-driven immune response has been revealed. The data are showcased as an interactive application freely available for the scientific community.
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Affiliation(s)
- Claire M Mulvey
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Lisa M Breckels
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Oliver M Crook
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK
- MRC Biostatistics Unit, Cambridge Institute for Public Health, Forvie Site, Robinson Way, Cambridge, CB2 0SR, UK
| | - David J Sanders
- Department of Microbial Diseases, Eastman Dental Institute, University College London, Royal Free Campus, Rowland Hill Street, London, NW3 2PF, UK
| | - Andre L R Ribeiro
- Department of Microbial Diseases, Eastman Dental Institute, University College London, Royal Free Campus, Rowland Hill Street, London, NW3 2PF, UK
| | - Aikaterini Geladaki
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK
| | | | - Nina Kočevar Britovšek
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK
- Lek d.d., Kolodvorska 27, Mengeš, 1234, Slovenia
| | - Tracey Hurrell
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Michael J Deery
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Laurent Gatto
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK
- de Duve Institute, UCLouvain, Avenue Hippocrate 75, Brussels, 1200, Belgium
| | - Andrew M Smith
- Department of Microbial Diseases, Eastman Dental Institute, University College London, Royal Free Campus, Rowland Hill Street, London, NW3 2PF, UK.
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK.
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9
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Carretero-Rodriguez L, Guðjónsdóttir R, Poparic I, Reilly ML, Chol M, Bianco IH, Chiapello M, Feret R, Deery MJ, Guthrie S. The Rac-GAP alpha2-Chimaerin Signals via CRMP2 and Stathmins in the Development of the Ocular Motor System. J Neurosci 2021; 41:6652-6672. [PMID: 34168008 PMCID: PMC8336708 DOI: 10.1523/jneurosci.0983-19.2021] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 04/02/2021] [Accepted: 04/05/2021] [Indexed: 11/21/2022] Open
Abstract
A precise sequence of axon guidance events is required for the development of the ocular motor system. Three cranial nerves grow toward, and connect with, six extraocular muscles in a stereotyped pattern, to control eye movements. The signaling protein alpha2-chimaerin (α2-CHN) plays a pivotal role in the formation of the ocular motor system; mutations in CHN1, encoding α2-CHN, cause the human eye movement disorder Duane Retraction Syndrome (DRS). Our research has demonstrated that the manipulation of α2-chn signaling in the zebrafish embryo leads to ocular motor axon wiring defects, although the signaling cascades regulated by α2-chn remain poorly understood. Here, we demonstrate that several cytoskeletal regulatory proteins-collapsin response mediator protein 2 (CRMP2; encoded by the gene dpysl2), stathmin1, and stathmin 2-bind to α2-CHN. dpysl2, stathmin1, and especially stathmin2 are expressed by ocular motor neurons. We find that the manipulation of dpysl2 and of stathmins in zebrafish larvae leads to defects in both the axon wiring of the ocular motor system and the optokinetic reflex, impairing horizontal eye movements. Knockdowns of these molecules in zebrafish larvae of either sex caused axon guidance phenotypes that included defasciculation and ectopic branching; in some cases, these phenotypes were reminiscent of DRS. chn1 knock-down phenotypes were rescued by the overexpression of CRMP2 and STMN1, suggesting that these proteins act in the same signaling pathway. These findings suggest that CRMP2 and stathmins signal downstream of α2-CHN to orchestrate ocular motor axon guidance and to control eye movements.SIGNIFICANCE STATEMENT The precise control of eye movements is crucial for the life of vertebrate animals, including humans. In humans, this control depends on the arrangement of nerve wiring of the ocular motor system, composed of three nerves and six muscles, a system that is conserved across vertebrate phyla. Mutations in the protein alpha2-chimaerin have previously been shown to cause eye movement disorders (squint) and axon wiring defects in humans. Our recent work has unraveled how alpha2-chimaerin coordinates axon guidance of the ocular motor system in animal models. In this article, we demonstrate key roles for the proteins CRMP2 and stathmin 1/2 in the signaling pathway orchestrated by alpha2-chimaerin, potentially giving insight into the etiology of eye movement disorders in humans.
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Affiliation(s)
| | | | - Ivana Poparic
- Department of Developmental Neurobiology, King's College London, London SE1 1UL, United Kingdom
| | | | - Mary Chol
- Department of Developmental Neurobiology, King's College London, London SE1 1UL, United Kingdom
| | - Isaac H Bianco
- Department of Neuroscience, Physiology and Pharmacology, University College London, London WC1E 6BT, United Kingdom
| | - Marco Chiapello
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Cambridge CB2 1QR, United Kingdom
| | - Renata Feret
- Institute for Sustainable Plant Protection, National Research Council, 10135 Torino, Italy
| | - Michael J Deery
- Institute for Sustainable Plant Protection, National Research Council, 10135 Torino, Italy
| | - Sarah Guthrie
- School of Life Sciences, University of Sussex, Brighton BN7 9QG, United Kingdom
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10
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Kamel W, Noerenberg M, Cerikan B, Chen H, Järvelin AI, Kammoun M, Lee JY, Shuai N, Garcia-Moreno M, Andrejeva A, Deery MJ, Johnson N, Neufeldt CJ, Cortese M, Knight ML, Lilley KS, Martinez J, Davis I, Bartenschlager R, Mohammed S, Castello A. Global analysis of protein-RNA interactions in SARS-CoV-2-infected cells reveals key regulators of infection. Mol Cell 2021; 81:2851-2867.e7. [PMID: 34118193 PMCID: PMC8142890 DOI: 10.1016/j.molcel.2021.05.023] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [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: 01/05/2021] [Revised: 03/30/2021] [Accepted: 05/18/2021] [Indexed: 12/15/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19). SARS-CoV-2 relies on cellular RNA-binding proteins (RBPs) to replicate and spread, although which RBPs control its life cycle remains largely unknown. Here, we employ a multi-omic approach to identify systematically and comprehensively the cellular and viral RBPs that are involved in SARS-CoV-2 infection. We reveal that SARS-CoV-2 infection profoundly remodels the cellular RNA-bound proteome, which includes wide-ranging effects on RNA metabolic pathways, non-canonical RBPs, and antiviral factors. Moreover, we apply a new method to identify the proteins that directly interact with viral RNA, uncovering dozens of cellular RBPs and six viral proteins. Among them are several components of the tRNA ligase complex, which we show regulate SARS-CoV-2 infection. Furthermore, we discover that available drugs targeting host RBPs that interact with SARS-CoV-2 RNA inhibit infection. Collectively, our results uncover a new universe of host-virus interactions with potential for new antiviral therapies against COVID-19.
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Affiliation(s)
- Wael Kamel
- MRC-University of Glasgow Centre for Virus Research, G61 1QH Glasgow, Scotland, UK; Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, UK
| | - Marko Noerenberg
- MRC-University of Glasgow Centre for Virus Research, G61 1QH Glasgow, Scotland, UK; Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, UK
| | - Berati Cerikan
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120 Heidelberg, Germany; German Center for Infection Research, Heidelberg Partner Site, 69120 Heidelberg, Germany
| | - Honglin Chen
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, UK
| | - Aino I Järvelin
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, UK
| | - Mohamed Kammoun
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Jeffrey Y Lee
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, UK
| | - Ni Shuai
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Manuel Garcia-Moreno
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, UK
| | - Anna Andrejeva
- Department of Biochemistry, University of Cambridge, CB2 1GA Cambridge, UK
| | - Michael J Deery
- Department of Biochemistry, University of Cambridge, CB2 1GA Cambridge, UK
| | - Natasha Johnson
- MRC-University of Glasgow Centre for Virus Research, G61 1QH Glasgow, Scotland, UK
| | - Christopher J Neufeldt
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120 Heidelberg, Germany; German Center for Infection Research, Heidelberg Partner Site, 69120 Heidelberg, Germany
| | - Mirko Cortese
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120 Heidelberg, Germany; German Center for Infection Research, Heidelberg Partner Site, 69120 Heidelberg, Germany
| | - Michael L Knight
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE Oxford, UK
| | - Kathryn S Lilley
- Department of Biochemistry, University of Cambridge, CB2 1GA Cambridge, UK
| | - Javier Martinez
- Center of Medical Biochemistry, Max Perutz Labs, Medical University of Vienna, Vienna, Austria
| | - Ilan Davis
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, UK
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120 Heidelberg, Germany; German Center for Infection Research, Heidelberg Partner Site, 69120 Heidelberg, Germany; Division Virus-Associated Carcinogenesis, Germany Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
| | - Shabaz Mohammed
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, UK; Department of Chemistry, University of Oxford, Mansfield Road, OX1 3TA Oxford, UK; The Rosalind Franklin Institute, OX11 0FA Oxfordshire, UK.
| | - Alfredo Castello
- MRC-University of Glasgow Centre for Virus Research, G61 1QH Glasgow, Scotland, UK; Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, UK.
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11
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Kamel W, Noerenberg M, Cerikan B, Chen H, Järvelin AI, Kammoun M, Lee JY, Shuai N, Garcia-Moreno M, Andrejeva A, Deery MJ, Johnson N, Neufeldt CJ, Cortese M, Knight ML, Lilley KS, Martinez J, Davis I, Bartenschlager R, Mohammed S, Castello A. Global analysis of protein-RNA interactions in SARS-CoV-2-infected cells reveals key regulators of infection. Mol Cell 2021; 81:2851-2867.e7. [PMID: 34118193 DOI: 10.1101/2020.11.25.398008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/30/2021] [Accepted: 05/18/2021] [Indexed: 05/22/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19). SARS-CoV-2 relies on cellular RNA-binding proteins (RBPs) to replicate and spread, although which RBPs control its life cycle remains largely unknown. Here, we employ a multi-omic approach to identify systematically and comprehensively the cellular and viral RBPs that are involved in SARS-CoV-2 infection. We reveal that SARS-CoV-2 infection profoundly remodels the cellular RNA-bound proteome, which includes wide-ranging effects on RNA metabolic pathways, non-canonical RBPs, and antiviral factors. Moreover, we apply a new method to identify the proteins that directly interact with viral RNA, uncovering dozens of cellular RBPs and six viral proteins. Among them are several components of the tRNA ligase complex, which we show regulate SARS-CoV-2 infection. Furthermore, we discover that available drugs targeting host RBPs that interact with SARS-CoV-2 RNA inhibit infection. Collectively, our results uncover a new universe of host-virus interactions with potential for new antiviral therapies against COVID-19.
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Affiliation(s)
- Wael Kamel
- MRC-University of Glasgow Centre for Virus Research, G61 1QH Glasgow, Scotland, UK; Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, UK
| | - Marko Noerenberg
- MRC-University of Glasgow Centre for Virus Research, G61 1QH Glasgow, Scotland, UK; Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, UK
| | - Berati Cerikan
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120 Heidelberg, Germany; German Center for Infection Research, Heidelberg Partner Site, 69120 Heidelberg, Germany
| | - Honglin Chen
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, UK
| | - Aino I Järvelin
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, UK
| | - Mohamed Kammoun
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Jeffrey Y Lee
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, UK
| | - Ni Shuai
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Manuel Garcia-Moreno
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, UK
| | - Anna Andrejeva
- Department of Biochemistry, University of Cambridge, CB2 1GA Cambridge, UK
| | - Michael J Deery
- Department of Biochemistry, University of Cambridge, CB2 1GA Cambridge, UK
| | - Natasha Johnson
- MRC-University of Glasgow Centre for Virus Research, G61 1QH Glasgow, Scotland, UK
| | - Christopher J Neufeldt
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120 Heidelberg, Germany; German Center for Infection Research, Heidelberg Partner Site, 69120 Heidelberg, Germany
| | - Mirko Cortese
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120 Heidelberg, Germany; German Center for Infection Research, Heidelberg Partner Site, 69120 Heidelberg, Germany
| | - Michael L Knight
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE Oxford, UK
| | - Kathryn S Lilley
- Department of Biochemistry, University of Cambridge, CB2 1GA Cambridge, UK
| | - Javier Martinez
- Center of Medical Biochemistry, Max Perutz Labs, Medical University of Vienna, Vienna, Austria
| | - Ilan Davis
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, UK
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120 Heidelberg, Germany; German Center for Infection Research, Heidelberg Partner Site, 69120 Heidelberg, Germany; Division Virus-Associated Carcinogenesis, Germany Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
| | - Shabaz Mohammed
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, UK; Department of Chemistry, University of Oxford, Mansfield Road, OX1 3TA Oxford, UK; The Rosalind Franklin Institute, OX11 0FA Oxfordshire, UK.
| | - Alfredo Castello
- MRC-University of Glasgow Centre for Virus Research, G61 1QH Glasgow, Scotland, UK; Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, UK.
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12
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Deighan WI, Winton VJ, Melani RD, Anderson LC, McGee JP, Schachner LF, Barnidge D, Murray D, Alexander HD, Gibson DS, Deery MJ, McNicholl FP, McLaughlin J, Kelleher NL, Thomas PM. Development of novel methods for non-canonical myeloma protein analysis with an innovative adaptation of immunofixation electrophoresis, native top-down mass spectrometry, and middle-down de novo sequencing. Clin Chem Lab Med 2020; 59:653-661. [PMID: 33079696 DOI: 10.1515/cclm-2020-1072] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 10/07/2020] [Indexed: 12/18/2022]
Abstract
Objectives Multiple myeloma (MM) is a malignant plasma cell neoplasm, requiring the integration of clinical examination, laboratory and radiological investigations for diagnosis. Detection and isotypic identification of the monoclonal protein(s) and measurement of other relevant biomarkers in serum and urine are pivotal analyses. However, occasionally this approach fails to characterize complex protein signatures. Here we describe the development and application of next generation mass spectrometry (MS) techniques, and a novel adaptation of immunofixation, to interrogate non-canonical monoclonal immunoproteins. Methods Immunoprecipitation immunofixation (IP-IFE) was performed on a Sebia Hydrasys Scan2. Middle-down de novo sequencing and native MS were performed with multiple instruments (21T FT-ICR, Q Exactive HF, Orbitrap Fusion Lumos, and Orbitrap Eclipse). Post-acquisition data analysis was performed using Xcalibur Qual Browser, ProSight Lite, and TDValidator. Results We adapted a novel variation of immunofixation electrophoresis (IFE) with an antibody-specific immunosubtraction step, providing insight into the clonal signature of gamma-zone monoclonal immunoglobulin (M-protein) species. We developed and applied advanced mass spectrometric techniques such as middle-down de novo sequencing to attain in-depth characterization of the primary sequence of an M-protein. Quaternary structures of M-proteins were elucidated by native MS, revealing a previously unprecedented non-covalently associated hetero-tetrameric immunoglobulin. Conclusions Next generation proteomic solutions offer great potential for characterizing complex protein structures and may eventually replace current electrophoretic approaches for the identification and quantification of M-proteins. They can also contribute to greater understanding of MM pathogenesis, enabling classification of patients into new subtypes, improved risk stratification and the potential to inform decisions on future personalized treatment modalities.
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Affiliation(s)
- W Ian Deighan
- Department of Clinical Chemistry, Altnagelvin Area Hospital, Londonderry, UK
| | - Valerie J Winton
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
| | - Rafael D Melani
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
| | - Lissa C Anderson
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Tallahassee, FL, USA
| | - John P McGee
- Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | - Luis F Schachner
- Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - David Barnidge
- Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - David Murray
- Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - H Denis Alexander
- Northern Ireland Centre for Stratified Medicine, Biomedical Sciences Research Institute, Ulster University, Londonderry, UK
| | - David S Gibson
- Northern Ireland Centre for Stratified Medicine, Biomedical Sciences Research Institute, Ulster University, Londonderry, UK
| | - Michael J Deery
- Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK
| | | | - Joseph McLaughlin
- Northern Ireland Centre for Stratified Medicine, Biomedical Sciences Research Institute, Ulster University, Londonderry, UK
| | - Neil L Kelleher
- Proteomics Center of Excellence & Departments of Chemistry and Molecular Biology,Northwestern University, Evanston, IL, USA
| | - Paul M Thomas
- Proteomics Center of Excellence & Departments of Chemistry and Molecular Biology,Northwestern University, Evanston, IL, USA
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13
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Vantourout JC, Adusumalli SR, Knouse KW, Flood DT, Ramirez A, Padial NM, Istrate A, Maziarz K, deGruyter JN, Merchant RR, Qiao JX, Schmidt MA, Deery MJ, Eastgate MD, Dawson PE, Bernardes GJL, Baran PS. Serine-Selective Bioconjugation. J Am Chem Soc 2020; 142:17236-17242. [PMID: 32965106 DOI: 10.1021/jacs.0c05595] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
This Communication reports the first general method for rapid, chemoselective, and modular functionalization of serine residues in native polypeptides, which uses a reagent platform based on the P(V) oxidation state. This redox-economical approach can be used to append nearly any kind of cargo onto serine, generating a stable, benign, and hydrophilic phosphorothioate linkage. The method tolerates all other known nucleophilic functional groups of naturally occurring proteinogenic amino acids. A variety of applications can be envisaged by this expansion of the toolbox of site-selective bioconjugation methods.
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Affiliation(s)
- Julien C Vantourout
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Srinivasa Rao Adusumalli
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Kyle W Knouse
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Dillon T Flood
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Antonio Ramirez
- Chemical Process Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Natalia M Padial
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Alena Istrate
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Katarzyna Maziarz
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Justine N deGruyter
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Rohan R Merchant
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jennifer X Qiao
- Chemical Process Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Michael A Schmidt
- Chemical Process Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Michael J Deery
- Cambridge Centre for Proteomics, Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, United Kingdom
| | - Martin D Eastgate
- Chemical Process Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Philip E Dawson
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Gonçalo J L Bernardes
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom.,Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Phil S Baran
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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14
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McAulay K, Hoyt EA, Thomas M, Schimpl M, Bodnarchuk MS, Lewis HJ, Barratt D, Bhavsar D, Robinson DM, Deery MJ, Ogg DJ, Bernardes GJL, Ward RA, Waring MJ, Kettle JG. Alkynyl Benzoxazines and Dihydroquinazolines as Cysteine Targeting Covalent Warheads and Their Application in Identification of Selective Irreversible Kinase Inhibitors. J Am Chem Soc 2020; 142:10358-10372. [PMID: 32412754 DOI: 10.1021/jacs.9b13391] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
With a resurgence in interest in covalent drugs, there is a need to identify new moieties capable of cysteine bond formation that are differentiated from commonly employed systems such as acrylamide. Herein, we report on the discovery of new alkynyl benzoxazine and dihydroquinazoline moieties capable of covalent reaction with cysteine. Their utility as alternative electrophilic warheads for chemical biological probes and drug molecules is demonstrated through site-selective protein modification and incorporation into kinase drug scaffolds. A potent covalent inhibitor of JAK3 kinase was identified with superior selectivity across the kinome and improvements in in vitro pharmacokinetic profile relative to the related acrylamide-based inhibitor. In addition, the use of a novel heterocycle as a cysteine reactive warhead is employed to target Cys788 in c-KIT, where acrylamide has previously failed to form covalent interactions. These new reactive and selective heterocyclic warheads supplement the current repertoire for cysteine covalent modification while avoiding some of the limitations generally associated with established moieties.
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Affiliation(s)
| | - Emily A Hoyt
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | | | - Marianne Schimpl
- Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | | | - Derek Barratt
- Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Deepa Bhavsar
- Oncology R&D, AstraZeneca, Waltham, Massachusetts 02451, United States
| | | | - Michael J Deery
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, U.K
| | - Derek J Ogg
- Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Gonçalo J L Bernardes
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.,Instituto de Medicina Molecular, Faculdade de Medicina de Universidad de Lisboa, Avenida Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | | | - Michael J Waring
- Northern Institute for Cancer Research, Chemistry, School of Natural and Environmental Sciences, Newcastle University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K
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15
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Baers LL, Breckels LM, Mills LA, Gatto L, Deery MJ, Stevens TJ, Howe CJ, Lilley KS, Lea-Smith DJ. Proteome Mapping of a Cyanobacterium Reveals Distinct Compartment Organization and Cell-Dispersed Metabolism. Plant Physiol 2019; 181:1721-1738. [PMID: 31578229 PMCID: PMC6878006 DOI: 10.1104/pp.19.00897] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 09/11/2019] [Indexed: 05/23/2023]
Abstract
Cyanobacteria are complex prokaryotes, incorporating a Gram-negative cell wall and internal thylakoid membranes (TMs). However, localization of proteins within cyanobacterial cells is poorly understood. Using subcellular fractionation and quantitative proteomics, we produced an extensive subcellular proteome map of an entire cyanobacterial cell, identifying ∼67% of proteins in Synechocystis sp. PCC 6803, ∼1000 more than previous studies. Assigned to six specific subcellular regions were 1,712 proteins. Proteins involved in energy conversion localized to TMs. The majority of transporters, with the exception of a TM-localized copper importer, resided in the plasma membrane (PM). Most metabolic enzymes were soluble, although numerous pathways terminated in the TM (notably those involved in peptidoglycan monomer, NADP+, heme, lipid, and carotenoid biosynthesis) or PM (specifically, those catalyzing lipopolysaccharide, molybdopterin, FAD, and phylloquinol biosynthesis). We also identified the proteins involved in the TM and PM electron transport chains. The majority of ribosomal proteins and enzymes synthesizing the storage compound polyhydroxybuyrate formed distinct clusters within the data, suggesting similar subcellular distributions to one another, as expected for proteins operating within multicomponent structures. Moreover, heterogeneity within membrane regions was observed, indicating further cellular complexity. Cyanobacterial TM protein localization was conserved in Arabidopsis (Arabidopsis thaliana) chloroplasts, suggesting similar proteome organization in more developed photosynthetic organisms. Successful application of this technique in Synechocystis suggests it could be applied to mapping the proteomes of other cyanobacteria and single-celled organisms. The organization of the cyanobacterial cell revealed here substantially aids our understanding of these environmentally and biotechnologically important organisms.
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Affiliation(s)
- Laura L Baers
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Lisa M Breckels
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
- Computational Proteomics Unit, Cambridge Centre for Proteomics, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Lauren A Mills
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Laurent Gatto
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
- Computational Proteomics Unit, Cambridge Centre for Proteomics, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Michael J Deery
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Tim J Stevens
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH United Kingdom
| | - Christopher J Howe
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - Kathryn S Lilley
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - David J Lea-Smith
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
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16
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Till CJ, Vicente J, Zhang H, Oszvald M, Deery MJ, Pastor V, Lilley KS, Ray RV, Theodoulou FL, Holdsworth MJ. The Arabidopsis thaliana N-recognin E3 ligase PROTEOLYSIS1 influences the immune response. Plant Direct 2019; 3:e00194. [PMID: 31891113 PMCID: PMC6933115 DOI: 10.1002/pld3.194] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 11/22/2019] [Accepted: 12/02/2019] [Indexed: 05/11/2023]
Abstract
N-degron pathways of ubiquitin-mediated proteolysis (formerly known as the N-end rule pathway) control the stability of substrate proteins dependent on the amino-terminal (Nt) residue. Unlike yeast or mammalian N-recognin E3 ligases, which each recognize several different classes of Nt residues, in Arabidopsis thaliana, N-recognin functions of different N-degron pathways are carried out independently by PROTEOLYSIS (PRT)1, PRT6, and other unknown proteins. PRT1 recognizes type 2 aromatic Nt-destabilizing residues and PRT6 recognizes type 1 basic residues. These two N-recognin functions diverged as separate proteins early in the evolution of plants, before the conquest of the land. We demonstrate that loss of PRT1 function promotes the plant immune system, as mutant prt1-1 plants showed greater apoplastic resistance than WT to infection by the bacterial hemi-biotroph Pseudomonas syringae pv tomato (Pst) DC3000. Quantitative proteomics revealed increased accumulation of proteins associated with specific components of plant defense in the prt1-1 mutant, concomitant with increased accumulation of salicylic acid. The effects of the prt1 mutation were additional to known effects of prt6 in influencing the immune system, in particular, an observed over-accumulation of pipecolic acid (Pip) in the double-mutant prt1-1 prt6-1. These results demonstrate a potential role for PRT1 in controlling aspects of the plant immune system and suggest that PRT1 limits the onset of the defense response via degradation of substrates with type 2 Nt-destabilizing residues.
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Affiliation(s)
- Christopher J. Till
- School of BiosciencesUniversity of NottinghamLoughboroughUK
- Plant Sciences DepartmentRothamsted ResearchHarpendenUK
| | - Jorge Vicente
- School of BiosciencesUniversity of NottinghamLoughboroughUK
| | - Hongtao Zhang
- Plant Sciences DepartmentRothamsted ResearchHarpendenUK
- Cambridge Centre for ProteomicsDepartment of BiochemistryUniversity of CambridgeCambridgeUK
| | - Maria Oszvald
- Plant Sciences DepartmentRothamsted ResearchHarpendenUK
| | - Michael J. Deery
- Cambridge Centre for ProteomicsDepartment of BiochemistryUniversity of CambridgeCambridgeUK
| | - Victoria Pastor
- Área de Fisiología VegetalDepartamento de Ciencias Agrarias y del Medio NaturalUniversitat Jaume ICastellónSpain
| | - Kathryn S. Lilley
- Cambridge Centre for ProteomicsDepartment of BiochemistryUniversity of CambridgeCambridgeUK
| | - Rumiana V. Ray
- School of BiosciencesUniversity of NottinghamLoughboroughUK
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17
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Chung BYW, Valli A, Deery MJ, Navarro FJ, Brown K, Hnatova S, Howard J, Molnar A, Baulcombe DC. Distinct roles of Argonaute in the green alga Chlamydomonas reveal evolutionary conserved mode of miRNA-mediated gene expression. Sci Rep 2019; 9:11091. [PMID: 31366981 PMCID: PMC6668577 DOI: 10.1038/s41598-019-47415-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 07/11/2019] [Indexed: 12/20/2022] Open
Abstract
The unicellular green alga Chlamydomonas reinhardtii is evolutionarily divergent from higher plants, but has a fully functional silencing machinery including microRNA (miRNA)-mediated translation repression and mRNA turnover. However, distinct from the metazoan machinery, repression of gene expression is primarily associated with target sites within coding sequences instead of 3′UTRs. This feature indicates that the miRNA-Argonaute (AGO) machinery is ancient and the primary function is for post transcriptional gene repression and intermediate between the mechanisms in the rest of the plant and animal kingdoms. Here, we characterize AGO2 and 3 in Chlamydomonas, and show that cytoplasmically enriched Cr-AGO3 is responsible for endogenous miRNA-mediated gene repression. Under steady state, mid-log phase conditions, Cr-AGO3 binds predominantly miR-C89, which we previously identified as the predominant miRNA with effects on both translation repression and mRNA turnover. In contrast, the paralogue Cr-AGO2 is nuclear enriched and exclusively binds to 21-nt siRNAs. Further analysis of the highly similar Cr-AGO2 and Cr-AGO 3 sequences (90% amino acid identity) revealed a glycine-arginine rich N-terminal extension of ~100 amino acids that, given previous work on unicellular protists, may associate AGO with the translation machinery. Phylogenetic analysis revealed that this glycine-arginine rich N-terminal extension is present outside the animal kingdom and is highly conserved, consistent with our previous proposal that miRNA-mediated CDS-targeting operates in this green alga.
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Affiliation(s)
- Betty Y-W Chung
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom. .,Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, United Kingdom.
| | - Adrian Valli
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom.,Department of Plant Molecular Genetics, Spanish National Centre for Biotechnology, Madrid, 28049, Spain
| | - Michael J Deery
- Cambridge System Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, United Kingdom
| | - Francisco J Navarro
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Katherine Brown
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, United Kingdom
| | - Silvia Hnatova
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom
| | - Julie Howard
- Cambridge System Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, United Kingdom
| | - Attila Molnar
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom
| | - David C Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, United Kingdom.
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18
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Alcock LJ, Oliveira BL, Deery MJ, Pukala TL, Perkins MV, Bernardes GJL, Chalker JM. Norbornene Probes for the Detection of Cysteine Sulfenic Acid in Cells. ACS Chem Biol 2019; 14:594-598. [PMID: 30893551 DOI: 10.1021/acschembio.8b01104] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Norbornene derivatives were validated as probes for cysteine sulfenic acid on proteins and in live cells. Trapping sulfenic acids with norbornene probes is highly selective and revealed a different reactivity profile than the traditional dimedone reagent. The norbornene probe also revealed a superior chemoselectivity when compared to a commonly used dimedone probe. Together, these results advance the study of cysteine oxidation in biological systems.
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Affiliation(s)
- Lisa J. Alcock
- Flinders University, College of Science and Engineering, Sturt Road, Bedford Park, South Australia 5042, Australia
- Flinders University, Institute for NanoScale Science and Technology, Sturt Road, Bedford Park, South Australia 5042, Australia
| | - Bruno L. Oliveira
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Michael J. Deery
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, United Kingdom
| | - Tara L. Pukala
- The University of Adelaide, School of Physical Sciences, Adelaide, South Australia 5005, Australia
| | - Michael V. Perkins
- Flinders University, College of Science and Engineering, Sturt Road, Bedford Park, South Australia 5042, Australia
| | - Gonçalo J. L. Bernardes
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
| | - Justin M. Chalker
- Flinders University, College of Science and Engineering, Sturt Road, Bedford Park, South Australia 5042, Australia
- Flinders University, Institute for NanoScale Science and Technology, Sturt Road, Bedford Park, South Australia 5042, Australia
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19
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Weckmann K, Deery MJ, Howard JA, Feret R, Asara JM, Dethloff F, Filiou MD, Labermaier C, Maccarrone G, Lilley KS, Mueller M, Turck CW. Ketamine's Effects on the Glutamatergic and GABAergic Systems: A Proteomics and Metabolomics Study in Mice. Mol Neuropsychiatry 2018; 5:42-51. [PMID: 31019917 DOI: 10.1159/000493425] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 08/31/2018] [Indexed: 12/15/2022]
Abstract
Ketamine, a noncompetitive, voltage-dependent N-Methyl-D-aspartate receptor (NMDAR) antagonist, has been shown to have a rapid antidepressant effect and is used for patients experiencing treatment-resistant depression. We carried out a time-dependent targeted mass spectrometry-based metabolomics profiling analysis combined with a quantitative based on in vivo 15N metabolic labeling proteome comparison of ketamine- and vehicle-treated mice. The metabolomics and proteomics datasets were used to further elucidate ketamine's mode of action on the gamma-aminobutyric acid (GABA)ergic and glutamatergic systems. In addition, myelin basic protein levels were analyzed by Western Blot. We found altered GABA, glutamate and glutamine metabolite levels and ratios as well as increased levels of putrescine and serine - 2 positive modulators of the NMDAR. In addition, GABA receptor (GABAR) protein levels were reduced, whereas the alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) subunit Gria2 protein levels were increased upon ketamine treatment. The significantly altered metabolite and protein levels further significantly correlated with the antidepressant-like behavior, which was assessed using the forced swim test. In conclusion and in line with previous research, our data indicate that ketamine impacts the AMPAR subunit Gria2 and results in decreased GABAergic inhibitory neurotransmission leading to increased excitatory neuronal activity.
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Affiliation(s)
- Katja Weckmann
- Max Planck Institute of Psychiatry, Department of Translational Research in Psychiatry, Munich, Germany.,Institute for Pathobiochemistry, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Michael J Deery
- Cambridge Centre for Proteomics, Cambridge System Biology Centre, University of Cambridge, Cambridge, United Kingdom
| | - Julie A Howard
- Cambridge Centre for Proteomics, Cambridge System Biology Centre, University of Cambridge, Cambridge, United Kingdom
| | - Renata Feret
- Cambridge Centre for Proteomics, Cambridge System Biology Centre, University of Cambridge, Cambridge, United Kingdom
| | - John M Asara
- Division of Signal Transduction, Beth Israel Deaconess Medical Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Frederik Dethloff
- Max Planck Institute of Psychiatry, Department of Translational Research in Psychiatry, Munich, Germany
| | - Michaela D Filiou
- Department of Biological Applications and Technology, School of Health Sciences, University of Ioannina, Ioannina, Greece
| | - Christiana Labermaier
- Max Planck Institute of Psychiatry, Department of Translational Research in Psychiatry, Munich, Germany
| | - Giuseppina Maccarrone
- Max Planck Institute of Psychiatry, Department of Translational Research in Psychiatry, Munich, Germany
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Cambridge System Biology Centre, University of Cambridge, Cambridge, United Kingdom
| | - Marianne Mueller
- Experimental Psychiatry, Department of Psychiatry and Psychotherapy and Focus Program Translational Neuroscience, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Christoph W Turck
- Max Planck Institute of Psychiatry, Department of Translational Research in Psychiatry, Munich, Germany
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20
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Agboh K, Lau CHF, Khoo YSK, Singh H, Raturi S, Nair AV, Howard J, Chiapello M, Feret R, Deery MJ, Murakami S, van Veen HW. Powering the ABC multidrug exporter LmrA: How nucleotides embrace the ion-motive force. Sci Adv 2018; 4:eaas9365. [PMID: 30255140 PMCID: PMC6155054 DOI: 10.1126/sciadv.aas9365] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 08/02/2018] [Indexed: 05/09/2023]
Abstract
LmrA is a bacterial ATP-binding cassette (ABC) multidrug exporter that uses metabolic energy to transport ions, cytotoxic drugs, and lipids. Voltage clamping in a Port-a-Patch was used to monitor electrical currents associated with the transport of monovalent cationic HEPES+ by single-LmrA transporters and ensembles of transporters. In these experiments, one proton and one chloride ion are effluxed together with each HEPES+ ion out of the inner compartment, whereas two sodium ions are transported into this compartment. Consequently, the sodium-motive force (interior negative and low) can drive this electrogenic ion exchange mechanism in cells under physiological conditions. The same mechanism is also relevant for the efflux of monovalent cationic ethidium, a typical multidrug transporter substrate. Studies in the presence of Mg-ATP (adenosine 5'-triphosphate) show that ion-coupled HEPES+ transport is associated with ATP-bound LmrA, whereas ion-coupled ethidium transport requires ATP binding and hydrolysis. HEPES+ is highly soluble in a water-based environment, whereas ethidium has a strong preference for residence in the water-repelling plasma membrane. We conclude that the mechanism of the ABC transporter LmrA is fundamentally related to that of an ion antiporter that uses extra steps (ATP binding and hydrolysis) to retrieve and transport membrane-soluble substrates from the phospholipid bilayer.
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Affiliation(s)
- Kelvin Agboh
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Calvin H. F. Lau
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Yvonne S. K. Khoo
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Himansha Singh
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Sagar Raturi
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Asha V. Nair
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Julie Howard
- Cambridge Centre for Proteomics, University of Cambridge, Cambridge CB2 1GA, UK
| | - Marco Chiapello
- Cambridge Centre for Proteomics, University of Cambridge, Cambridge CB2 1GA, UK
| | - Renata Feret
- Cambridge Centre for Proteomics, University of Cambridge, Cambridge CB2 1GA, UK
| | - Michael J. Deery
- Cambridge Centre for Proteomics, University of Cambridge, Cambridge CB2 1GA, UK
| | - Satoshi Murakami
- Department of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Hendrik W. van Veen
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
- Corresponding author.
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21
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Fabre B, Korona D, Mata CI, Parsons HT, Deery MJ, Hertog MLATM, Nicolaï BM, Russell S, Lilley KS. Spectral Libraries for SWATH-MS Assays for Drosophila melanogaster and Solanum lycopersicum. Proteomics 2018; 17. [PMID: 28922568 DOI: 10.1002/pmic.201700216] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 08/02/2017] [Indexed: 12/21/2022]
Abstract
Quantitative proteomics methods have emerged as powerful tools for measuring protein expression changes at the proteome level. Using MS-based approaches, it is now possible to routinely quantify thousands of proteins. However, prefractionation of the samples at the protein or peptide level is usually necessary to go deep into the proteome, increasing both MS analysis time and technical variability. Recently, a new MS acquisition method named SWATH is introduced with the potential to provide good coverage of the proteome as well as a good measurement precision without prior sample fractionation. In contrast to shotgun-based MS however, a library containing experimental acquired spectra is necessary for the bioinformatics analysis of SWATH data. In this study, spectral libraries for two widely used models are built to study crop ripening or animal embryogenesis, Solanum lycopersicum (tomato) and Drosophila melanogaster, respectively. The spectral libraries comprise fragments for 5197 and 6040 proteins for S. lycopersicum and D. melanogaster, respectively, and allow reproducible quantification for thousands of peptides per MS analysis. The spectral libraries and all MS data are available in the MassIVE repository with the dataset identifiers MSV000081074 and MSV000081075 and the PRIDE repository with the dataset identifiers PXD006493 and PXD006495.
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Affiliation(s)
- Bertrand Fabre
- Cambridge Centre for Proteomics Department of Biochemistry, University of Cambridge, Cambridge, UK.,Department of Biochemistry, University of Cambridge, Cambridge, UK.,Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.,Bertrand Fabre, Technion Integrated Cancer Center (TICC), The Rappaport Faculty of Medicine and Research Institute, Haifa, Israel
| | - Dagmara Korona
- Department of Genetics University of Cambridge, Cambridge, UK.,Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | | | - Harriet T Parsons
- Cambridge Centre for Proteomics Department of Biochemistry, University of Cambridge, Cambridge, UK.,Department of Biochemistry, University of Cambridge, Cambridge, UK.,Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.,Department of Plant and Environmental Sciences, Copenhagen University, Copenhagen, Denmark
| | - Michael J Deery
- Cambridge Centre for Proteomics Department of Biochemistry, University of Cambridge, Cambridge, UK.,Department of Biochemistry, University of Cambridge, Cambridge, UK.,Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | | | | | - Steven Russell
- Department of Genetics University of Cambridge, Cambridge, UK.,Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics Department of Biochemistry, University of Cambridge, Cambridge, UK.,Department of Biochemistry, University of Cambridge, Cambridge, UK.,Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
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22
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Zhang H, Gannon L, Hassall KL, Deery MJ, Gibbs DJ, Holdsworth MJ, van der Hoorn RAL, Lilley KS, Theodoulou FL. N-terminomics reveals control of Arabidopsis seed storage proteins and proteases by the Arg/N-end rule pathway. New Phytol 2018; 218:1106-1126. [PMID: 29168982 PMCID: PMC5947142 DOI: 10.1111/nph.14909] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 10/23/2017] [Indexed: 05/04/2023]
Abstract
The N-end rule pathway of targeted protein degradation is an important regulator of diverse processes in plants but detailed knowledge regarding its influence on the proteome is lacking. To investigate the impact of the Arg/N-end rule pathway on the proteome of etiolated seedlings, we used terminal amine isotopic labelling of substrates with tandem mass tags (TMT-TAILS) for relative quantification of N-terminal peptides in prt6, an Arabidopsis thaliana N-end rule mutant lacking the E3 ligase PROTEOLYSIS6 (PRT6). TMT-TAILS identified over 4000 unique N-terminal peptides representing c. 2000 protein groups. Forty-five protein groups exhibited significantly increased N-terminal peptide abundance in prt6 seedlings, including cruciferins, major seed storage proteins, which were regulated by Group VII Ethylene Response Factor (ERFVII) transcription factors, known substrates of PRT6. Mobilisation of endosperm α-cruciferin was delayed in prt6 seedlings. N-termini of several proteases were downregulated in prt6, including RD21A. RD21A transcript, protein and activity levels were downregulated in a largely ERFVII-dependent manner. By contrast, cathepsin B3 protein and activity were upregulated by ERFVIIs independent of transcript. We propose that the PRT6 branch of the pathway regulates protease activities in a complex manner and optimises storage reserve mobilisation in the transition from seed to seedling via control of ERFVII action.
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Affiliation(s)
- Hongtao Zhang
- Plant Sciences DepartmentRothamsted ResearchHarpendenAL5 2JQUK
- Cambridge Centre for ProteomicsDepartment of Biochemistry and Cambridge Systems Biology CentreUniversity of CambridgeCambridge, CB2 1QRUK
| | - Lucy Gannon
- Plant Sciences DepartmentRothamsted ResearchHarpendenAL5 2JQUK
| | - Kirsty L. Hassall
- Computational and Analytical Sciences DepartmentRothamsted ResearchHarpendenAL5 2JQUK
| | - Michael J. Deery
- Cambridge Centre for ProteomicsDepartment of Biochemistry and Cambridge Systems Biology CentreUniversity of CambridgeCambridge, CB2 1QRUK
| | - Daniel J. Gibbs
- School of BiosciencesUniversity of BirminghamEdgbastonB15 2TTUK
| | | | | | - Kathryn S. Lilley
- Cambridge Centre for ProteomicsDepartment of Biochemistry and Cambridge Systems Biology CentreUniversity of CambridgeCambridge, CB2 1QRUK
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23
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Lloyd-Lewis B, Krueger CC, Sargeant TJ, D'Angelo ME, Deery MJ, Feret R, Howard JA, Lilley KS, Watson CJ. Stat3-mediated alterations in lysosomal membrane protein composition. J Biol Chem 2018; 293:4244-4261. [PMID: 29343516 PMCID: PMC5868265 DOI: 10.1074/jbc.ra118.001777] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [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: 01/07/2018] [Indexed: 12/19/2022] Open
Abstract
Lysosome function is essential in cellular homeostasis. In addition to its recycling role, the lysosome has recently been recognized as a cellular signaling hub. We have shown in mammary epithelial cells, both in vivo and in vitro, that signal transducer and activator of transcription 3 (Stat3) modulates lysosome biogenesis and can promote the release of lysosomal proteases that culminates in cell death. To further investigate the impact of Stat3 on lysosomal function, we conducted a proteomic screen of changes in lysosomal membrane protein components induced by Stat3 using an iron nanoparticle enrichment strategy. Our results show that Stat3 activation not only elevates the levels of known membrane proteins but results in the appearance of unexpected factors, including cell surface proteins such as annexins and flotillins. These data suggest that Stat3 may coordinately regulate endocytosis, intracellular trafficking, and lysosome biogenesis to drive lysosome-mediated cell death in mammary epithelial cells. The methodologies described in this study also provide significant improvements to current techniques used for the purification and analysis of the lysosomal proteome.
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Affiliation(s)
- Bethan Lloyd-Lewis
- From the Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom,
| | - Caroline C Krueger
- From the Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Timothy J Sargeant
- the Lysosomal Diseases Research Unit, South Australian Health and Medical Research Institute, Adelaide, South Australia 5000, Australia, and
| | - Michael E D'Angelo
- From the Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Michael J Deery
- the Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, United Kingdom
| | - Renata Feret
- the Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, United Kingdom
| | - Julie A Howard
- the Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, United Kingdom
| | - Kathryn S Lilley
- the Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, United Kingdom
| | - Christine J Watson
- From the Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom,
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24
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Matos MJ, Oliveira BL, Martínez-Sáez N, Guerreiro A, Cal PMSD, Bertoldo J, Maneiro M, Perkins E, Howard J, Deery MJ, Chalker JM, Corzana F, Jiménez-Osés G, Bernardes GJL. Chemo- and Regioselective Lysine Modification on Native Proteins. J Am Chem Soc 2018; 140:4004-4017. [PMID: 29473744 PMCID: PMC5880509 DOI: 10.1021/jacs.7b12874] [Citation(s) in RCA: 202] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
Site-selective chemical
conjugation of synthetic molecules to proteins
expands their functional and therapeutic capacity. Current protein
modification methods, based on synthetic and biochemical technologies,
can achieve site selectivity, but these techniques often require extensive
sequence engineering or are restricted to the N-
or C-terminus. Here we show the computer-assisted
design of sulfonyl acrylate reagents for the modification of a single lysine residue on native protein sequences. This
feature of the designed sulfonyl acrylates, together with the innate
and subtle reactivity differences conferred by the unique local microenvironment
surrounding each lysine, contribute to the observed regioselectivity
of the reaction. Moreover, this site selectivity was predicted computationally,
where the lysine with the lowest pKa was
the kinetically favored residue at slightly basic pH. Chemoselectivity
was also observed as the reagent reacted preferentially at lysine,
even in those cases when other nucleophilic residues such as cysteine
were present. The reaction is fast and proceeds using a single molar
equivalent of the sulfonyl acrylate reagent under biocompatible conditions
(37 °C, pH 8.0). This technology was demonstrated by the quantitative
and irreversible modification of five different proteins including
the clinically used therapeutic antibody Trastuzumab without prior
sequence engineering. Importantly, their native secondary structure
and functionality is retained after the modification. This regioselective
lysine modification method allows for further bioconjugation through
aza-Michael addition to the acrylate electrophile that is generated
by spontaneous elimination of methanesulfinic acid upon lysine labeling.
We showed that a protein–antibody conjugate bearing a site-specifically
installed fluorophore at lysine could be used for selective imaging
of apoptotic cells and detection of Her2+ cells, respectively. This
simple, robust method does not require genetic engineering and may
be generally used for accessing diverse, well-defined protein conjugates
for basic biology and therapeutic studies.
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Affiliation(s)
- Maria J Matos
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , U.K
| | - Bruno L Oliveira
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , U.K
| | - Nuria Martínez-Sáez
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , U.K
| | - Ana Guerreiro
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa , Avenida Professor Egas Moniz , Lisboa , Portugal
| | - Pedro M S D Cal
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa , Avenida Professor Egas Moniz , Lisboa , Portugal
| | - Jean Bertoldo
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , U.K
| | - María Maneiro
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica , Universidade de Santiago de Compostela , calle Jenaro de la Fuente s/n , Santiago de Compostela , Spain
| | - Elizabeth Perkins
- Albumedix Ltd, Castle Court, 59 Castle Boulevard , Nottingham , United Kingdom
| | - Julie Howard
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, Department of Biochemistry , University of Cambridge , Tennis Court Road , Cambridge , U.K
| | - Michael J Deery
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, Department of Biochemistry , University of Cambridge , Tennis Court Road , Cambridge , U.K
| | - Justin M Chalker
- Centre for NanoScale Science and Technology, College of Science and Engineering , Flinders University Bedford Park , South Australia , Australia
| | - Francisco Corzana
- Departamento de Química , Universidad de La Rioja , Centro de Investigación en Síntesis Química , Logroño , Spain
| | - Gonzalo Jiménez-Osés
- Departamento de Química , Universidad de La Rioja , Centro de Investigación en Síntesis Química , Logroño , Spain
| | - Gonçalo J L Bernardes
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , U.K.,Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa , Avenida Professor Egas Moniz , Lisboa , Portugal
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25
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Hooper CM, Stevens TJ, Saukkonen A, Castleden IR, Singh P, Mann GW, Fabre B, Ito J, Deery MJ, Lilley KS, Petzold CJ, Millar AH, Heazlewood JL, Parsons HT. Multiple marker abundance profiling: combining selected reaction monitoring and data-dependent acquisition for rapid estimation of organelle abundance in subcellular samples. Plant J 2017; 92:1202-1217. [PMID: 29024340 PMCID: PMC5863471 DOI: 10.1111/tpj.13743] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [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: 08/28/2017] [Revised: 09/25/2017] [Accepted: 09/28/2017] [Indexed: 05/20/2023]
Abstract
Measuring changes in protein or organelle abundance in the cell is an essential, but challenging aspect of cell biology. Frequently-used methods for determining organelle abundance typically rely on detection of a very few marker proteins, so are unsatisfactory. In silico estimates of protein abundances from publicly available protein spectra can provide useful standard abundance values but contain only data from tissue proteomes, and are not coupled to organelle localization data. A new protein abundance score, the normalized protein abundance scale (NPAS), expands on the number of scored proteins and the scoring accuracy of lower-abundance proteins in Arabidopsis. NPAS was combined with subcellular protein localization data, facilitating quantitative estimations of organelle abundance during routine experimental procedures. A suite of targeted proteomics markers for subcellular compartment markers was developed, enabling independent verification of in silico estimates for relative organelle abundance. Estimation of relative organelle abundance was found to be reproducible and consistent over a range of tissues and growth conditions. In silico abundance estimations and localization data have been combined into an online tool, multiple marker abundance profiling, available in the SUBA4 toolbox (http://suba.live).
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Affiliation(s)
- Cornelia M. Hooper
- ARC Centre of Excellence in Plant Energy BiologyThe University of Western AustraliaPerthWA6009Australia
| | | | - Anna Saukkonen
- Department of BiochemistryUniversity of CambridgeCambridgeCB2 1QRUK
| | - Ian R. Castleden
- ARC Centre of Excellence in Plant Energy BiologyThe University of Western AustraliaPerthWA6009Australia
| | - Pragya Singh
- Joint BioEnergy InstituteLawrence Berkeley National LaboratoryBerkeleyCA94702USA
| | - Gregory W. Mann
- Joint BioEnergy InstituteLawrence Berkeley National LaboratoryBerkeleyCA94702USA
| | - Bertrand Fabre
- Department of BiochemistryUniversity of CambridgeCambridgeCB2 1QRUK
| | - Jun Ito
- Joint BioEnergy InstituteLawrence Berkeley National LaboratoryBerkeleyCA94702USA
| | - Michael J Deery
- Department of BiochemistryUniversity of CambridgeCambridgeCB2 1QRUK
| | | | | | - A. Harvey Millar
- ARC Centre of Excellence in Plant Energy BiologyThe University of Western AustraliaPerthWA6009Australia
| | - Joshua L. Heazlewood
- Joint BioEnergy InstituteLawrence Berkeley National LaboratoryBerkeleyCA94702USA
- School of BioSciencesThe University of MelbourneMelbourneVIC3010Australia
| | - Harriet T. Parsons
- Department of BiochemistryUniversity of CambridgeCambridgeCB2 1QRUK
- Copenhagen University, Plant and Environmental SciencesFrederiksberg1871Denmark
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26
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Weckmann K, Deery MJ, Howard JA, Feret R, Asara JM, Dethloff F, Filiou MD, Iannace J, Labermaier C, Maccarrone G, Webhofer C, Teplytska L, Lilley K, Müller MB, Turck CW. Ketamine's antidepressant effect is mediated by energy metabolism and antioxidant defense system. Sci Rep 2017; 7:15788. [PMID: 29150633 PMCID: PMC5694011 DOI: 10.1038/s41598-017-16183-x] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 11/08/2017] [Indexed: 01/23/2023] Open
Abstract
Fewer than 50% of all patients with major depressive disorder (MDD) treated with currently available antidepressants (ADs) show full remission. Moreover, about one third of the patients suffering from MDD does not respond to conventional ADs and develop treatment-resistant depression (TRD). Ketamine, a non-competitive, voltage-dependent N-Methyl-D-aspartate receptor (NMDAR) antagonist, has been shown to have a rapid antidepressant effect, especially in patients suffering from TRD. Hippocampi of ketamine-treated mice were analysed by metabolome and proteome profiling to delineate ketamine treatment-affected molecular pathways and biosignatures. Our data implicate mitochondrial energy metabolism and the antioxidant defense system as downstream effectors of the ketamine response. Specifically, ketamine tended to downregulate the adenosine triphosphate (ATP)/adenosine diphosphate (ADP) metabolite ratio which strongly correlated with forced swim test (FST) floating time. Furthermore, we found increased levels of enzymes that are part of the ‘oxidative phosphorylation’ (OXPHOS) pathway. Our study also suggests that ketamine causes less protein damage by rapidly decreasing reactive oxygen species (ROS) production and lend further support to the hypothesis that mitochondria have a critical role for mediating antidepressant action including the rapid ketamine response.
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Affiliation(s)
- Katja Weckmann
- Max Planck Institute of Psychiatry, Department of Translational Research in Psychiatry, Munich, Germany.,Institute of Pathobiochemistry, Johannes Gutenberg University, Medical School, Mainz, Germany
| | - Michael J Deery
- Cambridge Centre for Proteomics, Cambridge System Biology Centre, University of Cambridge, Cambridge, UK
| | - Julie A Howard
- Cambridge Centre for Proteomics, Cambridge System Biology Centre, University of Cambridge, Cambridge, UK
| | - Renata Feret
- Cambridge Centre for Proteomics, Cambridge System Biology Centre, University of Cambridge, Cambridge, UK
| | - John M Asara
- Division of Signal Transduction, Beth Israel Deaconess Medical Center and Department of Medicine, Harvard Medical School, Boston, USA
| | - Frederik Dethloff
- Max Planck Institute of Psychiatry, Department of Translational Research in Psychiatry, Munich, Germany
| | - Michaela D Filiou
- Max Planck Institute of Psychiatry, Department of Stress Neurobiology and Neurogenetics, Munich, Germany
| | - Jamie Iannace
- Max Planck Institute of Psychiatry, Department of Translational Research in Psychiatry, Munich, Germany
| | - Christiana Labermaier
- Max Planck Institute of Psychiatry, Department of Translational Research in Psychiatry, Munich, Germany
| | - Giuseppina Maccarrone
- Max Planck Institute of Psychiatry, Department of Translational Research in Psychiatry, Munich, Germany
| | - Christian Webhofer
- Max Planck Institute of Psychiatry, Department of Translational Research in Psychiatry, Munich, Germany
| | - Larysa Teplytska
- Max Planck Institute of Psychiatry, Department of Translational Research in Psychiatry, Munich, Germany
| | - Kathryn Lilley
- Cambridge Centre for Proteomics, Cambridge System Biology Centre, University of Cambridge, Cambridge, UK
| | - Marianne B Müller
- Experimental Psychiatry, Department of Psychiatry and Psychotherapy & Focus Program Translational Neuroscience, Johannes Gutenberg University Medical Center, Mainz, Germany.
| | - Christoph W Turck
- Max Planck Institute of Psychiatry, Department of Translational Research in Psychiatry, Munich, Germany.
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27
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Hennell James R, Caceres EF, Escasinas A, Alhasan H, Howard JA, Deery MJ, Ettema TJG, Robinson NP. Functional reconstruction of a eukaryotic-like E1/E2/(RING) E3 ubiquitylation cascade from an uncultured archaeon. Nat Commun 2017; 8:1120. [PMID: 29066714 PMCID: PMC5654768 DOI: 10.1038/s41467-017-01162-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 08/22/2017] [Indexed: 11/25/2022] Open
Abstract
The covalent modification of protein substrates by ubiquitin regulates a diverse range of critical biological functions. Although it has been established that ubiquitin-like modifiers evolved from prokaryotic sulphur transfer proteins it is less clear how complex eukaryotic ubiquitylation system arose and diversified from these prokaryotic antecedents. The discovery of ubiquitin, E1-like, E2-like and small-RING finger (srfp) protein components in the Aigarchaeota and the Asgard archaea superphyla has provided a substantive step toward addressing this evolutionary question. Encoded in operons, these components are likely representative of the progenitor apparatus that founded the modern eukaryotic ubiquitin modification systems. Here we report that these proteins from the archaeon Candidatus ‘Caldiarchaeum subterraneum’ operate together as a bona fide ubiquitin modification system, mediating a sequential ubiquitylation cascade reminiscent of the eukaryotic process. Our observations support the hypothesis that complex eukaryotic ubiquitylation signalling pathways have developed from compact systems originally inherited from an archaeal ancestor. In eukaryotic cells, the ubiquitylation system regulates several cellular processes central to protein homoeostasis. Here the authors demonstrate the existence of an eukaryotic-like ubiquitylation cascade requiring E1, E2 and E3-like enzymes in the archaeon C. subterraneum, shedding light on the evolution of the ubiquitin-proteasome system.
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Affiliation(s)
- Rory Hennell James
- Department of Biochemistry, The University of Cambridge, Cambridge, CB2 1GA, UK
| | - Eva F Caceres
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, 751 24, Sweden
| | - Alex Escasinas
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, LA1 4YG, UK
| | - Haya Alhasan
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, LA1 4YG, UK
| | - Julie A Howard
- Department of Biochemistry and Cambridge Systems Biology Centre, Cambridge Centre for Proteomics, The University of Cambridge, Cambridge, CB2 1GA, UK
| | - Michael J Deery
- Department of Biochemistry and Cambridge Systems Biology Centre, Cambridge Centre for Proteomics, The University of Cambridge, Cambridge, CB2 1GA, UK
| | - Thijs J G Ettema
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, 751 24, Sweden
| | - Nicholas P Robinson
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, LA1 4YG, UK.
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28
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Martínez-Sáez N, Sun S, Oldrini D, Sormanni P, Boutureira O, Carboni F, Compañón I, Deery MJ, Vendruscolo M, Corzana F, Adamo R, Bernardes GJL. Oxetane Grafts Installed Site-Selectively on Native Disulfides to Enhance Protein Stability and Activity In Vivo. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201708847] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Nuria Martínez-Sáez
- Department of Chemistry; University of Cambridge; Lensfield Road CB2 1EW Cambridge UK
| | - Shuang Sun
- Department of Chemistry; University of Cambridge; Lensfield Road CB2 1EW Cambridge UK
| | | | - Pietro Sormanni
- Department of Chemistry; University of Cambridge; Lensfield Road CB2 1EW Cambridge UK
| | - Omar Boutureira
- Department of Chemistry; University of Cambridge; Lensfield Road CB2 1EW Cambridge UK
| | | | - Ismael Compañón
- Departamento de Química, Centro de Investigación en Síntesis Química; Universidad de La Rioja; 26006 Logroño Spain
| | - Michael J. Deery
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre; Department of Biochemistry; University of Cambridge; Tennis Court Road Cambridge CB2 1QR UK
| | - Michele Vendruscolo
- Department of Chemistry; University of Cambridge; Lensfield Road CB2 1EW Cambridge UK
| | - Francisco Corzana
- Departamento de Química, Centro de Investigación en Síntesis Química; Universidad de La Rioja; 26006 Logroño Spain
| | | | - Gonçalo J. L. Bernardes
- Department of Chemistry; University of Cambridge; Lensfield Road CB2 1EW Cambridge UK
- Instituto de Medicina Molecular, Faculdade de Medicina; Universidade de Lisboa; Avenida Professor Egas Moniz 1649-028 Lisboa Portugal
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29
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Martínez-Sáez N, Sun S, Oldrini D, Sormanni P, Boutureira O, Carboni F, Compañón I, Deery MJ, Vendruscolo M, Corzana F, Adamo R, Bernardes GJL. Oxetane Grafts Installed Site-Selectively on Native Disulfides to Enhance Protein Stability and Activity In Vivo. Angew Chem Int Ed Engl 2017; 56:14963-14967. [PMID: 28968001 PMCID: PMC5698723 DOI: 10.1002/anie.201708847] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [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: 08/28/2017] [Revised: 09/26/2017] [Indexed: 12/11/2022]
Abstract
A four‐membered oxygen ring (oxetane) can be readily grafted into native peptides and proteins through site‐selective bis‐alkylation of cysteine residues present as disulfides under mild and biocompatible conditions. The selective installation of the oxetane graft enhances stability and activity, as demonstrated for a range of biologically relevant cyclic peptides, including somatostatin, proteins, and antibodies, such as a Fab arm of the antibody Herceptin and a designed antibody DesAb‐Aβ against the human Amyloid‐β peptide. Oxetane grafting of the genetically detoxified diphtheria toxin CRM197 improves significantly the immunogenicity of this protein in mice, which illustrates the general utility of this strategy to modulate the stability and biological activity of therapeutic proteins containing disulfides in their structures.
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Affiliation(s)
- Nuria Martínez-Sáez
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK
| | - Shuang Sun
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK
| | | | - Pietro Sormanni
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK
| | - Omar Boutureira
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK
| | | | - Ismael Compañón
- Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja, 26006, Logroño, Spain
| | - Michael J Deery
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Michele Vendruscolo
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK
| | - Francisco Corzana
- Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja, 26006, Logroño, Spain
| | | | - Gonçalo J L Bernardes
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK.,Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
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30
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Mata CI, Fabre B, Hertog MLATM, Parsons HT, Deery MJ, Lilley KS, Nicolaï BM. In-depth characterization of the tomato fruit pericarp proteome. Proteomics 2017; 17. [PMID: 27957804 DOI: 10.1002/pmic.201600406] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [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: 10/11/2016] [Revised: 11/24/2016] [Accepted: 12/07/2016] [Indexed: 12/19/2022]
Abstract
Since the genome of Solanum lycopersicum L. was published in 2012, some studies have explored its proteome although with a limited depth. In this work, we present an extended characterization of the proteome of the tomato pericarp at its ripe red stage. Fractionation of tryptic peptides generated from pericarp proteins by off-line high-pH reverse-phase phase chromatography in combination with LC-MS/MS analysis on a Fisher Scientific Q Exactive and a Sciex Triple-TOF 6600 resulted in the identification of 8588 proteins with a 1% FDR both at the peptide and protein levels. Proteins were mapped through GO and KEGG databases and a large number of the identified proteins were associated with cytoplasmic organelles and metabolic pathways categories. These results constitute one of the most extensive proteome datasets of tomato so far and provide an experimental confirmation of the existence of a high number of theoretically predicted proteins. All MS data are available in the ProteomeXchange repository with the dataset identifiers PXD004947 and PXD004932.
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Affiliation(s)
| | - Bertrand Fabre
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | | | - Harriet T Parsons
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Michael J Deery
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
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31
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Thornton P, Sevalle J, Deery MJ, Fraser G, Zhou Y, Ståhl S, Franssen EH, Dodd RB, Qamar S, Gomez Perez‐Nievas B, Nicol LSC, Eketjäll S, Revell J, Jones C, Billinton A, St George‐Hyslop PH, Chessell I, Crowther DC. TREM2 shedding by cleavage at the H157-S158 bond is accelerated for the Alzheimer's disease-associated H157Y variant. EMBO Mol Med 2017; 9:1366-1378. [PMID: 28855301 PMCID: PMC5623839 DOI: 10.15252/emmm.201707673] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
We have characterised the proteolytic cleavage events responsible for the shedding of triggering receptor expressed on myeloid cells 2 (TREM2) from primary cultures of human macrophages, murine microglia and TREM2-expressing human embryonic kidney (HEK293) cells. In all cell types, a soluble 17 kDa N-terminal cleavage fragment was shed into the conditioned media in a constitutive process that is inhibited by G1254023X and metalloprotease inhibitors and siRNA targeting ADAM10. Inhibitors of serine proteases and matrix metalloproteinases 2/9, and ADAM17 siRNA did not block TREM2 shedding. Peptidomimetic protease inhibitors highlighted a possible cleavage site, and mass spectrometry confirmed that shedding occurred predominantly at the H157-S158 peptide bond for both wild-type and H157Y human TREM2 and for the wild-type murine orthologue. Crucially, we also show that the Alzheimer's disease-associated H157Y TREM2 variant was shed more rapidly than wild type from HEK293 cells, possibly by a novel, batimastat- and ADAM10-siRNA-independent, sheddase activity. These insights offer new therapeutic targets for modulating the innate immune response in Alzheimer's and other neurological diseases.
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Affiliation(s)
- Peter Thornton
- Neuroscience, Innovative Medicines and Early DevelopmentAstraZenecaGranta ParkCambridgeUK
| | - Jean Sevalle
- Tanz Centre for Research in Neurodegenerative DiseasesUniversity of TorontoTorontoONCanada
| | - Michael J Deery
- Cambridge Centre for ProteomicsUniversity of CambridgeCambridgeUK
| | - Graham Fraser
- Neuroscience, Innovative Medicines and Early DevelopmentAstraZenecaGranta ParkCambridgeUK
| | - Ye Zhou
- Tanz Centre for Research in Neurodegenerative DiseasesUniversity of TorontoTorontoONCanada
| | - Sara Ståhl
- AstraZeneca Translational Sciences CentreKarolinska InstitutetStockholmSweden
| | - Elske H Franssen
- Neuroscience, Innovative Medicines and Early DevelopmentAstraZenecaGranta ParkCambridgeUK
| | - Roger B Dodd
- Department of Clinical NeurosciencesCambridge Institute for Medical ResearchUniversity of CambridgeCambridgeUK,MedImmune LimitedGranta ParkCambridgeUK
| | - Seema Qamar
- Department of Clinical NeurosciencesCambridge Institute for Medical ResearchUniversity of CambridgeCambridgeUK
| | | | | | - Susanna Eketjäll
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early DevelopmentAstraZeneca, ICMCHuddingeSweden
| | | | | | - Andrew Billinton
- Neuroscience, Innovative Medicines and Early DevelopmentAstraZenecaGranta ParkCambridgeUK
| | - Peter H St George‐Hyslop
- Tanz Centre for Research in Neurodegenerative DiseasesUniversity of TorontoTorontoONCanada,Department of Clinical NeurosciencesCambridge Institute for Medical ResearchUniversity of CambridgeCambridgeUK
| | - Iain Chessell
- Neuroscience, Innovative Medicines and Early DevelopmentAstraZenecaGranta ParkCambridgeUK
| | - Damian C Crowther
- Neuroscience, Innovative Medicines and Early DevelopmentAstraZenecaGranta ParkCambridgeUK
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32
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Chung BYW, Deery MJ, Groen AJ, Howard J, Baulcombe DC. Endogenous miRNA in the green alga Chlamydomonas regulates gene expression through CDS-targeting. Nat Plants 2017; 3:787-794. [PMID: 28970560 PMCID: PMC5662147 DOI: 10.1038/s41477-017-0024-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [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: 04/14/2017] [Accepted: 08/31/2017] [Indexed: 05/29/2023]
Abstract
MicroRNAs (miRNAs) are 21-24-nucleotide RNAs present in many eukaryotes that regulate gene expression as part of the RNA-induced silencing complex. The sequence identity of the miRNA provides the specificity to guide the silencing effector Argonaute (AGO) protein to target mRNAs via a base-pairing process 1 . The AGO complex promotes translation repression and/or accelerated decay of this target mRNA 2 . There is overwhelming evidence both in vivo and in vitro that translation repression plays a major role 3-7 . However, there has been controversy about which of these three mechanisms is more significant in vivo, especially when effects of miRNA on endogenous genes cannot be faithfully represented by reporter systems in which, at least in metazoans, the observed repression vastly exceeds that typically observed for endogenous mRNAs 8,9 . Here, we provide a comprehensive global analysis of the evolutionarily distant unicellular green alga Chlamydomonas reinhardtii to quantify the effects of miRNA on protein synthesis and RNA abundance. We show that, similar to metazoan steady-state systems, endogenous miRNAs in Chlamydomonas can regulate gene expression both by destabilization of the mRNA and by translational repression. However, unlike metazoan miRNA where target site utilization localizes mainly to 3' UTRs, in Chlamydomonas utilized target sites lie predominantly within coding regions. These results demonstrate the evolutionarily conserved mode of action for miRNAs, but details of the mechanism diverge between the plant and metazoan kingdoms.
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Affiliation(s)
- Betty Y-W Chung
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK.
| | - Michael J Deery
- Cambridge System Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Arnoud J Groen
- Cambridge System Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Julie Howard
- Cambridge System Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - David C Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK.
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33
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Prevosto C, Usmani MF, McDonald S, Gumienny AM, Key T, Goodman RS, Gaston JSH, Deery MJ, Busch R. Allele-Independent Turnover of Human Leukocyte Antigen (HLA) Class Ia Molecules. PLoS One 2016; 11:e0161011. [PMID: 27529174 PMCID: PMC4987023 DOI: 10.1371/journal.pone.0161011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [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: 02/29/2016] [Accepted: 07/28/2016] [Indexed: 11/29/2022] Open
Abstract
Major histocompatibility complex class I (MHCI) glycoproteins present cytosolic peptides to CD8+ T cells and regulate NK cell activity. Their heavy chains (HC) are expressed from up to three MHC gene loci (human leukocyte antigen [HLA]-A, -B, and -C in humans), whose extensive polymorphism maps predominantly to the antigen-binding groove, diversifying the bound peptide repertoire. Codominant expression of MHCI alleles is thus functionally critical, but how it is regulated is not fully understood. Here, we have examined the effect of polymorphism on the turnover rates of MHCI molecules in cell lines with functional MHCI peptide loading pathways and in monocyte-derived dendritic cells (MoDCs). Proteins were labeled biosynthetically with heavy water (2H2O), folded MHCI molecules immunoprecipitated, and tryptic digests analysed by mass spectrometry. MHCI-derived peptides were assigned to specific alleles and isotypes, and turnover rates quantified by 2H incorporation, after correcting for cell growth. MHCI turnover half-lives ranged from undetectable to a few hours, depending on cell type, activation state, donor, and MHCI isotype. However, in all settings, the turnover half-lives of alleles of the same isotype were similar. Thus, MHCI protein turnover rates appear to be allele-independent in normal human cells. We propose that this is an important feature enabling the normal function and codominant expression of MHCI alleles.
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Affiliation(s)
- Claudia Prevosto
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - M. Farooq Usmani
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Sarah McDonald
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Tim Key
- Tissue Typing Laboratory, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Reyna S. Goodman
- Tissue Typing Laboratory, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - J. S. Hill Gaston
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Michael J. Deery
- Cambridge Centre for Proteomics, University of Cambridge, Cambridge, United Kingdom
| | - Robert Busch
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Department of Life Sciences, University of Roehampton, London, United Kingdom
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34
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Fabre B, Korona D, Groen A, Vowinckel J, Gatto L, Deery MJ, Ralser M, Russell S, Lilley KS. Analysis of Drosophila melanogaster proteome dynamics during embryonic development by a combination of label-free proteomics approaches. Proteomics 2016; 16:2068-80. [PMID: 27029218 PMCID: PMC5737838 DOI: 10.1002/pmic.201500482] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [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: 11/20/2015] [Revised: 02/23/2016] [Accepted: 03/24/2016] [Indexed: 12/22/2022]
Abstract
During embryogenesis, organisms undergo considerable cellular remodelling requiring the combined action of thousands of proteins. In case of the well-studied model Drosophila melanogaster, transcriptomic studies, most notably from the modENCODE project, have described in detail changes in gene expression at the mRNA level across development. Although such data are clearly very useful to understand how the genome is regulated during embryogenesis, it is important to understand how changes in gene expression are reflected at the level of the proteome. In this study, we describe a combination of two quantitative label-free approaches, SWATH and data-dependent acquisition, to monitor changes in protein expression across a timecourse of D. melanogaster embryonic development. We demonstrate that both approaches provide robust and reproducible methods for the analysis of proteome changes. In a preliminary analysis of Drosophila embryogenesis, we identified several pathways, including the heat-shock response, nuclear protein import and energy production that are regulated during embryo development. In some cases changes in protein expression mirrored transcript levels across development, whereas other proteins showed signatures of post-transcriptional regulation. Taken together, our pilot study provides a solid platform for a more detailed exploration of the embryonic proteome.
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Affiliation(s)
- Bertrand Fabre
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, University of Cambridge, Cambridge, UK
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Dagmara Korona
- Department of Genetics, University of Cambridge, University of Cambridge, Cambridge, UK
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Arnoud Groen
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, University of Cambridge, Cambridge, UK
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Jakob Vowinckel
- Department of Biochemistry, University of Cambridge, University of Cambridge, Cambridge, UK
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Laurent Gatto
- Department of Biochemistry, University of Cambridge, University of Cambridge, Cambridge, UK
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
- Computational Proteomics Unit, Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Michael J Deery
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, University of Cambridge, Cambridge, UK
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Markus Ralser
- Department of Biochemistry, University of Cambridge, University of Cambridge, Cambridge, UK
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London, UK
| | - Steven Russell
- Department of Genetics, University of Cambridge, University of Cambridge, Cambridge, UK
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
- Department of Biochemistry, University of Cambridge, University of Cambridge, Cambridge, UK
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
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Zhang W, Aubert A, Gomez de Segura JM, Karuppasamy M, Basu S, Murthy AS, Diamante A, Drury TA, Balmer J, Cramard J, Watson AA, Lando D, Lee SF, Palayret M, Kloet SL, Smits AH, Deery MJ, Vermeulen M, Hendrich B, Klenerman D, Schaffitzel C, Berger I, Laue ED. The Nucleosome Remodeling and Deacetylase Complex NuRD Is Built from Preformed Catalytically Active Sub-modules. J Mol Biol 2016; 428:2931-42. [PMID: 27117189 PMCID: PMC4942838 DOI: 10.1016/j.jmb.2016.04.025] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 04/18/2016] [Indexed: 11/26/2022]
Abstract
The nucleosome remodeling deacetylase (NuRD) complex is a highly conserved regulator of chromatin structure and transcription. Structural studies have shed light on this and other chromatin modifying machines, but much less is known about how they assemble and whether stable and functional sub-modules exist that retain enzymatic activity. Purification of the endogenous Drosophila NuRD complex shows that it consists of a stable core of subunits, while others, in particular the chromatin remodeler CHD4, associate transiently. To dissect the assembly and activity of NuRD, we systematically produced all possible combinations of different components using the MultiBac system, and determined their activity and biophysical properties. We carried out single-molecule imaging of CHD4 in live mouse embryonic stem cells, in the presence and absence of one of core components (MBD3), to show how the core deacetylase and chromatin-remodeling sub-modules associate in vivo. Our experiments suggest a pathway for the assembly of NuRD via preformed and active sub-modules. These retain enzymatic activity and are present in both the nucleus and the cytosol, an outcome with important implications for understanding NuRD function. We have studied Drosophila nucleosome remodeling deacetylase (NuRD) assembly. NuRD consists of a core deacetylase complex, where MTA-like acts as the scaffold. This transiently associates with a chromatin remodeling sub-module including CHD4. Single-molecule imaging shows that the two sub-modules associate through MBD-like. NuRD comprises catalytically active sub-modules in both the cytosol and the nucleus.
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Affiliation(s)
- W Zhang
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - A Aubert
- EMBL Grenoble, 71 avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - J M Gomez de Segura
- EMBL Grenoble, 71 avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - M Karuppasamy
- EMBL Grenoble, 71 avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - S Basu
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - A S Murthy
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - A Diamante
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - T A Drury
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - J Balmer
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - J Cramard
- Wellcome Trust, Medical Research Council Stem Cell Institute, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR, United Kingdom
| | - A A Watson
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - D Lando
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - S F Lee
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - M Palayret
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - S L Kloet
- Department of Molecular Biology, Radboud Institute of Molecular Life Sciences, M850/3.79 Geert Grooteplein Zuid 30, 6525 GA Nijmegen, the Netherlands
| | - A H Smits
- Department of Molecular Biology, Radboud Institute of Molecular Life Sciences, M850/3.79 Geert Grooteplein Zuid 30, 6525 GA Nijmegen, the Netherlands
| | - M J Deery
- Cambridge Centre for Proteomics, Cambridge System Biology Centre, Wellcome Trust Stem Cell building, University of Cambridge, Department of Biochemistry, Tennis Court Road, Cambridge CB2 1QR, United Kingdom
| | - M Vermeulen
- Department of Molecular Biology, Radboud Institute of Molecular Life Sciences, M850/3.79 Geert Grooteplein Zuid 30, 6525 GA Nijmegen, the Netherlands
| | - B Hendrich
- Wellcome Trust, Medical Research Council Stem Cell Institute, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR, United Kingdom
| | - D Klenerman
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - C Schaffitzel
- EMBL Grenoble, 71 avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France; The School of Biochemistry, University of Bristol, University Walk, Clifton BS8 1TD, United Kingdom
| | - I Berger
- EMBL Grenoble, 71 avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France; The School of Biochemistry, University of Bristol, University Walk, Clifton BS8 1TD, United Kingdom
| | - E D Laue
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
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36
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Muñoz-Bernal E, Deery MJ, Rodríguez ME, Cantoral JM, Howard J, Feret R, Natera R, Lilley KS, Fernández-Acero FJ. Analysis of temperature-mediated changes in the wine yeast Saccharomyces bayanus var uvarum
. An oenological study of how the protein content influences wine quality. Proteomics 2016; 16:576-92. [DOI: 10.1002/pmic.201500137] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 11/10/2015] [Accepted: 11/11/2015] [Indexed: 02/02/2023]
Affiliation(s)
- Eugenia Muñoz-Bernal
- Andalusian Center for Grape and Grapevine Research; CeIA3; Marine and Environmental Sciences Faculty; University of Cadiz; Cádiz Spain
| | - Michael J. Deery
- Cambridge Centre for Proteomics; University of Cambridge; Cambridge UK
- Cambridge System Biology Centre; University of Cambridge; Cambridge UK
- Department of Biochemistry; University of Cambridge; Cambridge UK
| | - María Esther Rodríguez
- Andalusian Center for Grape and Grapevine Research; CeIA3; Marine and Environmental Sciences Faculty; University of Cadiz; Cádiz Spain
| | - Jesús M. Cantoral
- Andalusian Center for Grape and Grapevine Research; CeIA3; Marine and Environmental Sciences Faculty; University of Cadiz; Cádiz Spain
| | - Julie Howard
- Cambridge Centre for Proteomics; University of Cambridge; Cambridge UK
- Cambridge System Biology Centre; University of Cambridge; Cambridge UK
- Department of Biochemistry; University of Cambridge; Cambridge UK
| | - Renata Feret
- Cambridge Centre for Proteomics; University of Cambridge; Cambridge UK
- Cambridge System Biology Centre; University of Cambridge; Cambridge UK
- Department of Biochemistry; University of Cambridge; Cambridge UK
| | - Ramón Natera
- Department of Analytical Chemistry; Faculty of Sciences-CAIV; University of Cádiz, Agrifood Campus of International Excellence; Cádiz Spain
| | - Kathryn S. Lilley
- Cambridge Centre for Proteomics; University of Cambridge; Cambridge UK
- Cambridge System Biology Centre; University of Cambridge; Cambridge UK
- Department of Biochemistry; University of Cambridge; Cambridge UK
| | - Francisco Javier Fernández-Acero
- Andalusian Center for Grape and Grapevine Research; CeIA3; Marine and Environmental Sciences Faculty; University of Cadiz; Cádiz Spain
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37
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Quintela T, Marcelino H, Deery MJ, Feret R, Howard J, Lilley KS, Albuquerque T, Gonçalves I, Duarte AC, Santos CRA. Sex-Related Differences in Rat Choroid Plexus and Cerebrospinal Fluid: A cDNA Microarray and Proteomic Analysis. J Neuroendocrinol 2016; 28. [PMID: 26606900 DOI: 10.1111/jne.12340] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 11/13/2015] [Accepted: 11/19/2015] [Indexed: 01/09/2023]
Abstract
The choroid plexus (CP) epithelium is a unique structure in the brain that forms an interface between the peripheral blood and the cerebrospinal fluid (CSF), which is mostly produced by the CP itself. Because the CP transcriptome is regulated by the sex hormone background, the present study compared gene/protein expression profiles in the CP and CSF from male and female rats aiming to better understand sex-related differences in CP functions and brain physiology. We used data previously obtained by cDNA microarrays to compare the CP transcriptome between male and female rats, and complemented these data with the proteomic analysis of the CSF of castrated and sham-operated males and females. Microarray analysis showed that 17 128 and 17 002 genes are expressed in the male and female CP, which allowed the functional annotation of 141 and 134 pathways, respectively. Among the most expressed genes, canonical pathways associated with mitochondrial dysfunctions and oxidative phosphorylation were the most prominent, whereas the most relevant molecular and cellular functions annotated were protein synthesis, cellular growth and proliferation, cell death and survival, molecular transport, and protein trafficking. No significant differences were found between males and females regarding these pathways. Seminal functions of the CP differentially regulated between sexes were circadian rhythm signalling, as well as several canonical pathways related to stem cell differentiation, metabolism and the barrier function of the CP. The proteomic analysis identified five down-regulated proteins in the CSF samples from male rats compared to females and seven proteins exhibiting marked variation in the CSF of gonadectomised males compared to sham animals, whereas no differences were found between sham and ovariectomised females. These data clearly show sex-related differences in CP gene expression and CSF protein composition that may impact upon neurological diseases.
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Affiliation(s)
- T Quintela
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
| | - H Marcelino
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
| | - M J Deery
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - R Feret
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - J Howard
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - K S Lilley
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - T Albuquerque
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
| | - I Gonçalves
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
| | - A C Duarte
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
| | - C R A Santos
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
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Mulvey CM, Schröter C, Gatto L, Dikicioglu D, Fidaner IB, Christoforou A, Deery MJ, Cho LTY, Niakan KK, Martinez-Arias A, Lilley KS. Dynamic Proteomic Profiling of Extra-Embryonic Endoderm Differentiation in Mouse Embryonic Stem Cells. Stem Cells 2015; 33:2712-25. [DOI: 10.1002/stem.2067] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 04/20/2015] [Indexed: 01/07/2023]
Affiliation(s)
- Claire M. Mulvey
- Cambridge Centre for Proteomics; Department of Biochemistry; University of Cambridge; Cambridge United Kingdom
- Cambridge Systems Biology Centre; Wellcome Trust Stem Cell building; University of Cambridge; Cambridge United Kingdom
- Department of Genetics; University of Cambridge; Cambridge United Kingdom
| | - Christian Schröter
- Department of Genetics; University of Cambridge; Cambridge United Kingdom
| | - Laurent Gatto
- Cambridge Centre for Proteomics; Department of Biochemistry; University of Cambridge; Cambridge United Kingdom
- Cambridge Systems Biology Centre; Wellcome Trust Stem Cell building; University of Cambridge; Cambridge United Kingdom
- Computational Proteomics Unit; Department of Biochemistry; University of Cambridge; Cambridge United Kingdom
| | - Duygu Dikicioglu
- Cambridge Systems Biology Centre; Wellcome Trust Stem Cell building; University of Cambridge; Cambridge United Kingdom
- Department of Biochemistry; University of Cambridge; Cambridge United Kingdom
| | - Isik Baris Fidaner
- Department of Computer Engineering; Bogazici University; Istanbul Turkey
| | - Andy Christoforou
- Cambridge Centre for Proteomics; Department of Biochemistry; University of Cambridge; Cambridge United Kingdom
- Cambridge Systems Biology Centre; Wellcome Trust Stem Cell building; University of Cambridge; Cambridge United Kingdom
- Department of Biochemistry; University of Cambridge; Cambridge United Kingdom
| | - Michael J. Deery
- Cambridge Centre for Proteomics; Department of Biochemistry; University of Cambridge; Cambridge United Kingdom
- Cambridge Systems Biology Centre; Wellcome Trust Stem Cell building; University of Cambridge; Cambridge United Kingdom
| | - Lily T. Y. Cho
- Neusentis; Pfizer Worldwide Research and Development; Granta Park Science Park, Great Abington; Cambridge United Kingdom
| | - Kathy K. Niakan
- The Francis Crick Institute, Mill Hill Laboratory; London United Kingdom
| | | | - Kathryn S. Lilley
- Cambridge Centre for Proteomics; Department of Biochemistry; University of Cambridge; Cambridge United Kingdom
- Cambridge Systems Biology Centre; Wellcome Trust Stem Cell building; University of Cambridge; Cambridge United Kingdom
- Department of Biochemistry; University of Cambridge; Cambridge United Kingdom
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39
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Hesketh A, Deery MJ, Hong HJ. High-Resolution Mass Spectrometry Based Proteomic Analysis of the Response to Vancomycin-Induced Cell Wall Stress in Streptomyces coelicolor A3(2). J Proteome Res 2015; 14:2915-28. [PMID: 25965010 DOI: 10.1021/acs.jproteome.5b00242] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [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: 01/09/2023]
Abstract
Understanding how bacteria survive periods of cell wall stress is of fundamental interest and can help generate ideas for improved antibacterial treatments. In this study we use tandem mass tagging to characterize the proteomic response of vancomycin resistant Streptomyces coelicolor to the exposure to sublethal levels of the antibiotic. A common set of 804 proteins were identified in triplicate experiments. Contrasting changes in the abundance of proteins closely associated with the cytoplasmic membrane with those taking place in the cytosol identified aspects of protein spatial localization that are associated with the response to vancomycin. Enzymes for peptidoglycan precursor, mycothiol, ectoine and menaquinone biosynthesis together with a multisubunit nitrate reductase were recruited to the membrane following vancomycin treatment. Many proteins with regulatory functions (including sensor protein kinases) also exhibited significant changes in abundance exclusively in the membrane-associated protein fraction. Several enzymes predicted to be involved in extracellular peptidoglycan crossbridge formation became significantly depleted from the membrane. A comparison with data previously acquired on the changes in gene transcription following vancomycin treatment identified a common high-confidence set of changes in gene expression. Generalized changes in protein abundance indicate roles for proteolysis, the pentose phosphate pathway and a reorganization of amino acid biosynthesis in the stress response.
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Affiliation(s)
- Andy Hesketh
- †Department of Biochemistry, University of Cambridge, Cambridge, U.K.,‡Cambridge Systems Biology Centre, University of Cambridge, Cambridge, U.K
| | - Michael J Deery
- †Department of Biochemistry, University of Cambridge, Cambridge, U.K.,‡Cambridge Systems Biology Centre, University of Cambridge, Cambridge, U.K
| | - Hee-Jeon Hong
- †Department of Biochemistry, University of Cambridge, Cambridge, U.K
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40
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Zhang H, Deery MJ, Gannon L, Powers SJ, Lilley KS, Theodoulou FL. Quantitative proteomics analysis of the Arg/N-end rule pathway of targeted degradation in Arabidopsis roots. Proteomics 2015; 15:2447-57. [PMID: 25728785 PMCID: PMC4692092 DOI: 10.1002/pmic.201400530] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 01/29/2015] [Accepted: 02/24/2015] [Indexed: 12/03/2022]
Abstract
According to the Arg/N-end rule pathway, proteins with basic N-termini are targeted for degradation by the Arabidopsis thaliana E3 ligase, PROTEOLYSIS6 (PRT6). Proteins can also become PRT6 substrates following post-translational arginylation by arginyltransferases ATE1 and 2. Here, we undertook a quantitative proteomics study of Arg/N-end rule mutants, ate1/2 and prt6, to investigate the impact of this pathway on the root proteome. Tandem mass tag labelling identified a small number of proteins with increased abundance in the mutants, some of which represent downstream targets of transcription factors known to be N-end rule substrates. Isolation of N-terminal peptides using terminal amine isotope labelling of samples (TAILS) combined with triple dimethyl labelling identified 1465 unique N-termini. Stabilising residues were over-represented among the free neo-N-termini, but destabilising residues were not markedly enriched in N-end rule mutants. The majority of free neo-N-termini were revealed following cleavage of organellar targeting signals, thus compartmentation may account in part for the presence of destabilising residues in the wild-type N-terminome. Our data suggest that PRT6 does not have a marked impact on the global proteome of Arabidopsis roots and is likely involved in the controlled degradation of relatively few regulatory proteins. All MS data have been deposited in the ProteomeXchange with identifier PXD001719 (http://proteomecentral.proteomexchange.org/dataset/PXD001719).
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Affiliation(s)
- Hongtao Zhang
- Biological Chemistry and Crop Protection Department, Rothamsted Research, Harpenden, UK.,Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Michael J Deery
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Lucy Gannon
- Biological Chemistry and Crop Protection Department, Rothamsted Research, Harpenden, UK
| | - Stephen J Powers
- Computational and Systems Biology Department, Rothamsted Research, Harpenden, UK
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
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41
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Park JH, Szemes M, Vieira GC, Melegh Z, Malik S, Heesom KJ, Von Wallwitz-Freitas L, Greenhough A, Brown KW, Zheng YG, Catchpoole D, Deery MJ, Malik K. Protein arginine methyltransferase 5 is a key regulator of the MYCN oncoprotein in neuroblastoma cells. Mol Oncol 2014; 9:617-27. [PMID: 25475372 PMCID: PMC4359099 DOI: 10.1016/j.molonc.2014.10.015] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [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: 09/19/2014] [Accepted: 10/30/2014] [Indexed: 12/21/2022] Open
Abstract
Approximately half of poor prognosis neuroblastomas (NBs) are characterized by pathognomonic MYCN gene amplification and MYCN over-expression. Here we present data showing that short-interfering RNA mediated depletion of the protein arginine methyltransferase 5 (PRMT5) in cell-lines representative of NBs with MYCN gene amplification leads to greatly impaired growth and apoptosis. Growth suppression is not apparent in the MYCN-negative SH-SY5Y NB cell-line, or in two immortalized human fibroblast cell-lines. Immunoblotting of NB cell-lines shows that high PRMT5 expression is strongly associated with MYCN-amplification (P < 0.004, Mann-Whitney U-test) and immunohistochemical analysis of primary NBs reveals that whilst PRMT5 protein is ubiquitously expressed in the cytoplasm of most cells, MYCN-amplified tumours exhibit pronounced nuclear PRMT5 staining. PRMT5 knockdown in MYCN-overexpressing cells, including the SHEP-21N cell-line with inducible MYCN expression leads to a dramatic decrease in MYCN protein and MYCN-associated cell-death in SHEP-21N cells. Quantitative gene expression analysis and cycloheximide chase experiments suggest that PRMT5 regulates MYCN at a post-transcriptional level. Reciprocal co-immunoprecipitation experiments demonstrated that endogenous PRMT5 and MYCN interact in both SK-N-BE(2)C and NGP cell lines. By using liquid chromatography - tandem mass spectrometry (LC-MS/MS) analysis of immunoprecipitated MYCN protein, we identified several potential sites of arginine dimethylation on the MYCN protein. Together our studies implicate PRMT5 in a novel mode of MYCN post-translational regulation and suggest PRMT5 plays a major role in NB tumorigenesis. Small-molecule inhibitors of PRMT5 may therefore represent a novel therapeutic strategy for neuroblastoma and other cancers driven by the MYCN oncogene.
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Affiliation(s)
- Ji Hyun Park
- Cancer Epigenetics Laboratory University of Bristol, Bristol BS8 1TD, UK
| | - Marianna Szemes
- Cancer Epigenetics Laboratory University of Bristol, Bristol BS8 1TD, UK
| | | | - Zsombor Melegh
- Department of Cellular Pathology, Southmead Hospital, Bristol, UK
| | - Sally Malik
- Cancer Epigenetics Laboratory University of Bristol, Bristol BS8 1TD, UK
| | - Kate J Heesom
- Department of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | | | - Alexander Greenhough
- Colorectal Cancer Laboratory, School of Cellular & Molecular Medicine University of Bristol, Bristol BS8 1TD, UK
| | - Keith W Brown
- Cancer Epigenetics Laboratory University of Bristol, Bristol BS8 1TD, UK
| | - Y George Zheng
- Department of Chemistry, Georgia State University, Atlanta, GA 30302-4098, USA
| | - Daniel Catchpoole
- The Kids Research Institute, The Children's Hospital at Westmead, Westmead, New South Wales 2145, Australia
| | - Michael J Deery
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Karim Malik
- Cancer Epigenetics Laboratory University of Bristol, Bristol BS8 1TD, UK.
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42
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Teperek M, Miyamoto K, Simeone A, Feret R, Deery MJ, Gurdon JB, Jullien J. Sperm and spermatids contain different proteins and bind distinct egg factors. Int J Mol Sci 2014; 15:16719-40. [PMID: 25244019 PMCID: PMC4200797 DOI: 10.3390/ijms150916719] [Citation(s) in RCA: 2] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 07/21/2014] [Accepted: 09/09/2014] [Indexed: 01/14/2023] Open
Abstract
Spermatozoa are more efficient at supporting normal embryonic development than spermatids, their immature, immediate precursors. This suggests that the sperm acquires the ability to support embryonic development during spermiogenesis (spermatid to sperm maturation). Here, using Xenopus laevis as a model organism, we performed 2-D Fluorescence Difference Gel Electrophoresis (2D-DIGE) and mass spectrometry analysis of differentially expressed proteins between sperm and spermatids in order to identify factors that could be responsible for the efficiency of the sperm to support embryonic development. Furthermore, benefiting from the availability of egg extracts in Xenopus, we also tested whether the chromatin of sperm could attract different egg factors compared to the chromatin of spermatids. Our analysis identified: (1) several proteins which were present exclusively in sperm; but not in spermatid nuclei and (2) numerous egg proteins binding to the sperm (but not to the spermatid chromatin) after incubation in egg extracts. Amongst these factors we identified many chromatin-associated proteins and transcriptional repressors. Presence of transcriptional repressors binding specifically to sperm chromatin could suggest its preparation for the early embryonic cell cycles, during which no transcription is observed and suggests that sperm chromatin has a unique protein composition, which facilitates the recruitment of egg chromatin remodelling factors. It is therefore likely that the acquisition of these sperm-specific factors during spermiogenesis makes the sperm chromatin suitable to interact with the maternal factors and, as a consequence, to support efficient embryonic development.
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Affiliation(s)
- Marta Teperek
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.
| | - Kei Miyamoto
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.
| | - Angela Simeone
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.
| | - Renata Feret
- Cambridge Centre for Proteomics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK.
| | - Michael J Deery
- Cambridge Centre for Proteomics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK.
| | - John B Gurdon
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.
| | - Jerome Jullien
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.
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43
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Vowinckel J, Capuano F, Campbell K, Deery MJ, Lilley KS, Ralser M. The beauty of being (label)-free: sample preparation methods for SWATH-MS and next-generation targeted proteomics. F1000Res 2013. [PMID: 24741437 DOI: 10.12688/f1000research.2-272.v1] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The combination of qualitative analysis with label-free quantification has greatly facilitated the throughput and flexibility of novel proteomic techniques. However, such methods rely heavily on robust and reproducible sample preparation procedures. Here, we benchmark a selection of in gel, on filter, and in solution digestion workflows for their application in label-free proteomics. Each procedure was associated with differing advantages and disadvantages. The in gel methods interrogated were cost effective, but were limited in throughput and digest efficiency. Filter-aided sample preparations facilitated reasonable processing times and yielded a balanced representation of membrane proteins, but led to a high signal variation in quantification experiments. Two in solution digest protocols, however, gave optimal performance for label-free proteomics. A protocol based on the detergent RapiGest led to the highest number of detected proteins at second-best signal stability, while a protocol based on acetonitrile-digestion, RapidACN, scored best in throughput and signal stability but came second in protein identification. In addition, we compared label-free data dependent (DDA) and data independent (SWATH) acquisition on a TripleTOF 5600 instrument. While largely similar in protein detection, SWATH outperformed DDA in quantification, reducing signal variation and markedly increasing the number of precisely quantified peptides.
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Affiliation(s)
- Jakob Vowinckel
- Cambridge Systems Biology Centre and Dept. of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Floriana Capuano
- Cambridge Systems Biology Centre and Dept. of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Kate Campbell
- Cambridge Systems Biology Centre and Dept. of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Michael J Deery
- Cambridge Systems Biology Centre and Dept. of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Kathryn S Lilley
- Cambridge Systems Biology Centre and Dept. of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Markus Ralser
- Cambridge Systems Biology Centre and Dept. of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK ; Division of Physiology and Metabolism, MRC National Institute for Medical Research, London, NW7 1AA, UK
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44
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Vowinckel J, Capuano F, Campbell K, Deery MJ, Lilley KS, Ralser M. The beauty of being (label)-free: sample preparation methods for SWATH-MS and next-generation targeted proteomics. F1000Res 2013; 2:272. [PMID: 24741437 PMCID: PMC3983906 DOI: 10.12688/f1000research.2-272.v2] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/25/2014] [Indexed: 12/13/2022] Open
Abstract
The combination of qualitative analysis with label-free quantification has greatly facilitated the throughput and flexibility of novel proteomic techniques. However, such methods rely heavily on robust and reproducible sample preparation procedures. Here, we benchmark a selection of in gel, on filter, and in solution digestion workflows for their application in label-free proteomics. Each procedure was associated with differing advantages and disadvantages. The in gel methods interrogated were cost effective, but were limited in throughput and digest efficiency. Filter-aided sample preparations facilitated reasonable processing times and yielded a balanced representation of membrane proteins, but led to a high signal variation in quantification experiments. Two in solution digest protocols, however, gave optimal performance for label-free proteomics. A protocol based on the detergent RapiGest led to the highest number of detected proteins at second-best signal stability, while a protocol based on acetonitrile-digestion, RapidACN, scored best in throughput and signal stability but came second in protein identification. In addition, we compared label-free data dependent (DDA) and data independent (SWATH) acquisition on a TripleTOF 5600 instrument. While largely similar in protein detection, SWATH outperformed DDA in quantification, reducing signal variation and markedly increasing the number of precisely quantified peptides.
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Affiliation(s)
- Jakob Vowinckel
- Cambridge Systems Biology Centre and Dept. of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Floriana Capuano
- Cambridge Systems Biology Centre and Dept. of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Kate Campbell
- Cambridge Systems Biology Centre and Dept. of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Michael J Deery
- Cambridge Systems Biology Centre and Dept. of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Kathryn S Lilley
- Cambridge Systems Biology Centre and Dept. of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Markus Ralser
- Cambridge Systems Biology Centre and Dept. of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK ; Division of Physiology and Metabolism, MRC National Institute for Medical Research, London, NW7 1AA, UK
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De Riva A, Varley MC, Bluck LJ, Cooke A, Deery MJ, Busch R. Accelerated turnover of MHC class II molecules in nonobese diabetic mice is developmentally and environmentally regulated in vivo and dispensable for autoimmunity. J Immunol 2013; 190:5961-71. [PMID: 23677470 DOI: 10.4049/jimmunol.1300551] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The H2-A(g7) (A(g7)) MHC class II (MHCII) allele is required for type 1 diabetes (T1D) in NOD mice. A(g7) not only has a unique peptide-binding profile, it was reported to exhibit biochemical defects, including accelerated protein turnover. Such defects were proposed to impair Ag presentation and, thus, self-tolerance. Here, we report measurements of MHCII protein synthesis and turnover in vivo. NOD mice and BALB/c controls were labeled continuously with heavy water, and splenic B cells and dendritic cells were isolated. MHCII molecules were immunoprecipitated and digested with trypsin. Digests were analyzed by liquid chromatography/mass spectrometry to quantify the fraction of newly synthesized MHCII molecules and, thus, turnover. MHCII turnover was faster in dendritic cells than in B cells, varying slightly between mouse strains. Some A(g7) molecules exhibited accelerated turnover in B cells from young, but not older, prediabetic female NOD mice. This acceleration was not detected in a second NOD colony with a high incidence of T1D. Turnover rates of A(g7) and H2-A(d) were indistinguishable in (NOD × BALB/c) F1 mice. In conclusion, accelerated MHCII turnover may occur in NOD mice, but it reflects environmental and developmental regulation, rather than a structural deficit of the A(g7) allele. Moreover, this phenotype wanes before the onset of overt T1D and is dispensable for the development of autoimmune diabetes. Our observations highlight the importance of in vivo studies in understanding the role of protein turnover in genotype/phenotype relationships and offer a novel approach for addressing this fundamental research challenge.
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Affiliation(s)
- Alessandra De Riva
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom
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46
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Watson AA, Mahajan P, Mertens HD, Deery MJ, Zhang W, Pham P, Du X, Bartke T, Zhang W, Edlich C, Berridge G, Chen Y, Burgess-Brown NA, Kouzarides T, Wiechens N, Owen-Hughes T, Svergun DI, Gileadi O, Laue ED. The PHD and chromo domains regulate the ATPase activity of the human chromatin remodeler CHD4. J Mol Biol 2012; 422:3-17. [PMID: 22575888 PMCID: PMC3437443 DOI: 10.1016/j.jmb.2012.04.031] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [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: 01/21/2012] [Revised: 04/23/2012] [Accepted: 04/30/2012] [Indexed: 01/23/2023]
Abstract
The NuRD (nucleosome remodeling and deacetylase) complex serves as a crucial epigenetic regulator of cell differentiation, proliferation, and hematopoietic development by coupling the deacetylation and demethylation of histones, nucleosome mobilization, and the recruitment of transcription factors. The core nucleosome remodeling function of the mammalian NuRD complex is executed by the helicase-domain-containing ATPase CHD4 (Mi-2β) subunit, which also contains N-terminal plant homeodomain (PHD) and chromo domains. The mode of regulation of chromatin remodeling by CHD4 is not well understood, nor is the role of its PHD and chromo domains. Here, we use small-angle X-ray scattering, nucleosome binding ATPase and remodeling assays, limited proteolysis, cross-linking, and tandem mass spectrometry to propose a three-dimensional structural model describing the overall shape and domain interactions of CHD4 and discuss the relevance of these for regulating the remodeling of chromatin by the NuRD complex.
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Key Words
- chd, chromo domain helicase dna binding
- nurd, nucleosome remodeling and deacetylase
- phd, plant homeodomain
- saxs, small-angle x-ray scattering
- lc–ms/ms, liquid chromatography–tandem mass spectrometry
- duf, domain of unknown function
- tev, tobacco etch virus
- hrp, horseradish peroxidase
- bsa, bovine serum albumin
- bistris, 2-[bis(2-hydroxyethyl)amino]-2-(hydroxymethyl)propane-1,3-diol
- nurd complex
- chromatin remodeling
- chromo domain helicase dna-binding protein 4
- histone
- transcriptional regulation
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Affiliation(s)
| | - Pravin Mahajan
- The Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Haydyn D.T. Mertens
- European Molecular Biology Laboratory-Hamburg Outstation, c/o DESY, Notkestrasse 85, Hamburg, Germany
| | - Michael J. Deery
- Cambridge Centre for Proteomics, Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Wenchao Zhang
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28023, USA
| | - Peter Pham
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28023, USA
| | - Xiuxia Du
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28023, USA
| | - Till Bartke
- The Gurdon Institute, Department of Pathology, Cambridge, UK
| | - Wei Zhang
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Christian Edlich
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Georgina Berridge
- The Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Yun Chen
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Nicola A. Burgess-Brown
- The Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Tony Kouzarides
- The Gurdon Institute, Department of Pathology, Cambridge, UK
| | - Nicola Wiechens
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Tom Owen-Hughes
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory-Hamburg Outstation, c/o DESY, Notkestrasse 85, Hamburg, Germany
| | - Opher Gileadi
- The Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Ernest D. Laue
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
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47
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Habermann K, Mirgorodskaya E, Gobom J, Lehmann V, Müller H, Blümlein K, Deery MJ, Czogiel I, Erdmann C, Ralser M, von Kries JP, Lange BMH. Functional analysis of centrosomal kinase substrates in Drosophila melanogaster reveals a new function of the nuclear envelope component otefin in cell cycle progression. Mol Cell Biol 2012; 32:3554-69. [PMID: 22751930 PMCID: PMC3422010 DOI: 10.1128/mcb.00814-12] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 06/25/2012] [Indexed: 11/20/2022] Open
Abstract
Phosphorylation is one of the key mechanisms that regulate centrosome biogenesis, spindle assembly, and cell cycle progression. However, little is known about centrosome-specific phosphorylation sites and their functional relevance. Here, we identified phosphoproteins of intact Drosophila melanogaster centrosomes and found previously unknown phosphorylation sites in known and unexpected centrosomal components. We functionally characterized phosphoproteins and integrated them into regulatory signaling networks with the 3 important mitotic kinases, cdc2, polo, and aur, as well as the kinase CkIIβ. Using a combinatorial RNA interference (RNAi) strategy, we demonstrated novel functions for P granule, nuclear envelope (NE), and nuclear proteins in centrosome duplication, maturation, and separation. Peptide microarrays confirmed phosphorylation of identified residues by centrosome-associated kinases. For a subset of phosphoproteins, we identified previously unknown centrosome and/or spindle localization via expression of tagged fusion proteins in Drosophila SL2 cells. Among those was otefin (Ote), an NE protein that we found to localize to centrosomes. Furthermore, we provide evidence that it is phosphorylated in vitro at threonine 63 (T63) through Aurora-A kinase. We propose that phosphorylation of this site plays a dual role in controlling mitotic exit when phosphorylated while dephosphorylation promotes G(2)/M transition in Drosophila SL2 cells.
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Affiliation(s)
- Karin Habermann
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
| | - Ekaterina Mirgorodskaya
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
| | - Johan Gobom
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
| | - Verena Lehmann
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
| | - Hannah Müller
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
| | - Katharina Blümlein
- University of Cambridge, Department of Biochemistry and Cambridge Systems Biology Centre, Cambridge, United Kingdom
| | - Michael J. Deery
- University of Cambridge, Department of Biochemistry and Cambridge Systems Biology Centre, Cambridge, United Kingdom
| | - Irina Czogiel
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
| | - Christoph Erdmann
- Leibniz Institute for Molecular Pharmacology (FMP), Screening Unit, Berlin, Germany
| | - Markus Ralser
- University of Cambridge, Department of Biochemistry and Cambridge Systems Biology Centre, Cambridge, United Kingdom
| | - Jens Peter von Kries
- Leibniz Institute for Molecular Pharmacology (FMP), Screening Unit, Berlin, Germany
| | - Bodo M. H. Lange
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany
- Alacris Theranostics GmbH, Berlin, Germany
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48
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Thorne MAS, Worland MR, Feret R, Deery MJ, Lilley KS, Clark MS. Proteomics of cryoprotective dehydration in Megaphorura arctica Tullberg 1876 (Onychiuridae: Collembola). Insect Mol Biol 2011; 20:303-310. [PMID: 21199019 DOI: 10.1111/j.1365-2583.2010.01062.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The Arctic springtail, Megaphorura arctica Tullberg 1876 (Onychiuridae: Collembola), is one of the few organisms known to survive the extreme stresses of its environment by using cryoprotective dehydration. We have undertaken a proteomics study comparing M. arctica, acclimated at -2°C, the temperature known to induce the production of the anhydroprotectant trehalose in this species, and -6°C, the temperature at which trehalose expression plateaus, against control animals acclimated at +5°C. Using difference gel electrophoresis, and liquid chromatography tandem mass spectrometry, we identified three categories of differentially expressed proteins with specific functions, up-regulated in both the -2°C and -6°C animals, that were involved in metabolism, membrane transport and protein folding. Proteins involved in cytoskeleton organisation were only up-regulated in the -6°C animals.
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Affiliation(s)
- M A S Thorne
- British Antarctic Survey, Natural Environment Research Council, Cambridge, UK.
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49
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Lilley KS, Deery MJ, Gatto L. Challenges for proteomics core facilities. Proteomics 2011; 11:1017-25. [PMID: 21360676 DOI: 10.1002/pmic.201000693] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Revised: 11/24/2010] [Accepted: 11/29/2010] [Indexed: 11/11/2022]
Abstract
Many analytical techniques have been executed by core facilities established within academic, pharmaceutical and other industrial institutions. The centralization of such facilities ensures a level of expertise and hardware which often cannot be supported by individual laboratories. The establishment of a core facility thus makes the technology available for multiple researchers in the same institution. Often, the services within the core facility are also opened out to researchers from other institutions, frequently with a fee being levied for the service provided. In the 1990s, with the onset of the age of genomics, there was an abundance of DNA analysis facilities, many of which have since disappeared from institutions and are now available through commercial sources. Ten years on, as proteomics was beginning to be utilized by many researchers, this technology found itself an ideal candidate for being placed within a core facility. We discuss what in our view are the daily challenges of proteomics core facilities. We also examine the potential unmet needs of the proteomics core facility that may also be applicable to proteomics laboratories which do not function as core facilities.
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Affiliation(s)
- Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.
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50
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De Riva A, Deery MJ, McDonald S, Lund T, Busch R. Measurement of protein synthesis using heavy water labeling and peptide mass spectrometry: Discrimination between major histocompatibility complex allotypes. Anal Biochem 2010; 403:1-12. [PMID: 20406617 PMCID: PMC2896473 DOI: 10.1016/j.ab.2010.04.018] [Citation(s) in RCA: 32] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2009] [Revised: 03/23/2010] [Accepted: 04/15/2010] [Indexed: 01/08/2023]
Abstract
Methodological limitations have hampered the use of heavy water (2H2O), a convenient, universal biosynthetic label, for measuring protein synthesis. Analyses of 2H-labeled amino acids are sensitive to contamination; labeling of peptides has been measured for a few serum proteins, but this approach awaits full validation. Here we describe a method for quantifying protein synthesis by peptide mass spectrometry (MS) after 2H2O labeling, as applied to various proteins of the major histocompatibility complex (MHC). Human and murine antigen-presenting cells were cultured in medium containing 5% 2H2O; class I and class II MHC proteins were immunoprecipitated, bands were excised, and Ala-/Gly-rich, allele-specific tryptic peptides were identified by liquid chromatography–tandem mass spectrometry (LC–MS/MS). Mass isotopomer distributions were quantified precisely by LC–MS and shifted markedly on 2H2O labeling. Experimental data agreed closely with models obtained by mass isotopomer distribution analysis (MIDA) and were consistent with contributions from Ala, Gly, and other amino acids to labeling. Estimates of fractional protein synthesis from peptides of the same protein were precise and internally consistent. The method was capable of discriminating between MHC isotypes and alleles, applicable to primary cells, and readily extendable to other proteins. It simplifies measurements of protein synthesis, enabling novel applications in physiology, in genotype/phenotype interactions, and potentially in kinetic proteomics.
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Affiliation(s)
| | - Michael J. Deery
- Centre for Proteomics, University of Cambridge, Cambridge CB2 1QR, UK
| | - Sarah McDonald
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Torben Lund
- Department of Immunology and Molecular Pathology, School of Medicine, University College London, London WC1E 6BT, UK
| | - Robert Busch
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
- Corresponding author. Fax: +44 1223 330 160.
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