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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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Korona B, Korona D, Zhao W, Wotherspoon AC, Du MQ. CCR6 activation links innate immune responses to mucosa-associated lymphoid tissue lymphoma development. Haematologica 2022; 107:1384-1396. [PMID: 35142152 PMCID: PMC9152962 DOI: 10.3324/haematol.2021.280067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 01/31/2022] [Indexed: 11/24/2022] Open
Abstract
The genesis of extranodal marginal zone lymphoma of mucosa-associated lymphoid tissue (MALT) is driven by oncogenic co-operation among immunological stimulations and acquired genetic changes. We previously identified recurrent CCR6 mutations in MALT lymphoma, with majority predicted to result in truncated proteins lacking the phosphorylation motif important for receptor desensitization. Functional consequences of these mutational changes, the molecular mechanisms of CCR6 activation and how this receptor signaling contributes to MALT lymphoma development remain to be investigated. In the present study, we demonstrated that these mutations impaired CCR6 receptor internalization and were activating changes, being more potent in apoptosis resistance, malignant transformation, migration and intracellular signaling, particularly in the presence of the ligands CCL20, HBD2 (human b defensin 2) and HD5 (human a defensin 5). CCR6 was highly expressed in malignant B cells irrespective of the lymphoma sites. HBD2 and CCL20 were constitutively expressed by the duct epithelial cells of salivary glands, and also those involved in lymphoepithelial lesions (LEL) in salivary gland MALT lymphoma. While in the gastric setting, HBD2, and HD5, to a less extent CCL20, were highly expressed in epithelial cells of pyloric and intestinal metaplasia respectively including those involved in LEL, which are adaptive responses to chronic Helicobacter pylori infection. These findings suggest that CCR6 signaling is most likely active in MALT lymphoma, independent of its mutation status. The observations explain why the emergence of malignant B cells and their clonal expansion in MALT lymphoma are typically around LEL, linking the innate immune responses to lymphoma genesis.
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Affiliation(s)
- Boguslawa Korona
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge
| | - Dagmara Korona
- Department of Genetics, University of Cambridge, Cambridge
| | - Wanfeng Zhao
- The Human Research Tissue Bank, Cambridge University Hospitals NHS Foundation Trust, Cambridge
| | | | - Ming-Qing Du
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK; Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge.
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3
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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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4
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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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5
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Korona D, Nightingale D, Fabre B, Nelson M, Fischer B, Johnson G, Lees J, Hubbard S, Lilley K, Russell S. Characterisation of protein isoforms encoded by the Drosophila Glycogen Synthase Kinase 3 gene shaggy. PLoS One 2020; 15:e0236679. [PMID: 32760087 PMCID: PMC7410302 DOI: 10.1371/journal.pone.0236679] [Citation(s) in RCA: 4] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 07/09/2020] [Indexed: 12/15/2022] Open
Abstract
The Drosophila shaggy gene (sgg, GSK-3) encodes multiple protein isoforms with serine/threonine kinase activity and is a key player in diverse developmental signalling pathways. Currently it is unclear whether different Sgg proteoforms are similarly involved in signalling or if different proteoforms have distinct functions. We used CRISPR/Cas9 genome engineering to tag eight different Sgg proteoform classes and determined their localization during embryonic development. We performed proteomic analysis of the two major proteoform classes and generated mutant lines for both of these for transcriptomic and phenotypic analysis. We uncovered distinct tissue-specific localization patterns for all of the tagged proteoforms we examined, most of which have not previously been characterised directly at the protein level, including one proteoform initiating with a non-standard codon. Collectively, this suggests complex developmentally regulated splicing of the sgg primary transcript. Further, affinity purification followed by mass spectrometric analyses indicate a different repertoire of interacting proteins for the two major proteoforms we examined, one with ubiquitous expression (Sgg-PB) and one with nervous system specific expression (Sgg-PA). Specific mutation of these proteoforms shows that Sgg-PB performs the well characterised maternal and zygotic segmentations functions of the sgg locus, while Sgg-PA mutants show adult lifespan and locomotor defects consistent with its nervous system localisation. Our findings provide new insights into the role of GSK-3 proteoforms and intriguing links with the GSK-3α and GSK-3β proteins encoded by independent vertebrate genes. Our analysis suggests that different proteoforms generated by alternative splicing are likely to perform distinct functions.
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Affiliation(s)
- Dagmara Korona
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Daniel Nightingale
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, United Kingdom
| | - Bertrand Fabre
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, United Kingdom
| | - Michael Nelson
- Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre Manchester, University of Manchester, Manchester, United Kingdom
| | - Bettina Fischer
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Glynnis Johnson
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Jonathan Lees
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Simon Hubbard
- Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre Manchester, University of Manchester, Manchester, United Kingdom
| | - Kathryn Lilley
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, United Kingdom
| | - Steven Russell
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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6
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Fabre B, Korona D, Lees JG, Lazar I, Livneh I, Brunet M, Orengo CA, Russell S, Lilley KS. Comparison of Drosophila melanogaster Embryo and Adult Proteome by SWATH-MS Reveals Differential Regulation of Protein Synthesis, Degradation Machinery, and Metabolism Modules. J Proteome Res 2019; 18:2525-2534. [DOI: 10.1021/acs.jproteome.9b00076] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Bertrand Fabre
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge CB2 1QR, U.K
- Department of Biochemistry, University of Cambridge, University of Cambridge, Cambridge CB2 1GA, U.K
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, U.K
- Technion Integrated Cancer Center (TICC), The Rappaport Faculty of Medicine and Research Institute, Haifa, Israel
| | - Dagmara Korona
- Department of Genetics, University of Cambridge, University of Cambridge, Cambridge CB2 3EH, U.K
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, U.K
| | - Jonathan G. Lees
- Institute of Structural and Molecular Biology, University College London, London WC1E 7HX, United Kingdom
| | - Ikrame Lazar
- Technion Integrated Cancer Center (TICC), The Rappaport Faculty of Medicine and Research Institute, Haifa, Israel
| | - Ido Livneh
- Technion Integrated Cancer Center (TICC), The Rappaport Faculty of Medicine and Research Institute, Haifa, Israel
| | - Manon Brunet
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge CB2 1QR, U.K
- Department of Biochemistry, University of Cambridge, University of Cambridge, Cambridge CB2 1GA, U.K
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, U.K
| | - Christine A. Orengo
- Institute of Structural and Molecular Biology, University College London, London WC1E 7HX, United Kingdom
| | - Steven Russell
- Department of Genetics, University of Cambridge, University of Cambridge, Cambridge CB2 3EH, U.K
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, U.K
| | - Kathryn S. Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge CB2 1QR, U.K
- Department of Biochemistry, University of Cambridge, University of Cambridge, Cambridge CB2 1GA, U.K
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, U.K
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7
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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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Korona D, Koestler SA, Russell S. Engineering the Drosophila Genome for Developmental Biology. J Dev Biol 2017; 5:jdb5040016. [PMID: 29615571 PMCID: PMC5831791 DOI: 10.3390/jdb5040016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/07/2017] [Accepted: 12/08/2017] [Indexed: 02/07/2023] Open
Abstract
The recent development of transposon and CRISPR-Cas9-based tools for manipulating the fly genome in vivo promises tremendous progress in our ability to study developmental processes. Tools for introducing tags into genes at their endogenous genomic loci facilitate imaging or biochemistry approaches at the cellular or subcellular levels. Similarly, the ability to make specific alterations to the genome sequence allows much more precise genetic control to address questions of gene function.
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Affiliation(s)
- Dagmara Korona
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK.
| | - Stefan A Koestler
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK.
| | - Steven Russell
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK.
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9
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Fabre B, Korona D, Nightingale DJH, Russell S, Lilley KS. SWATH-MS dataset of heat-shock treated Drosophila melanogaster embryos. Data Brief 2016; 9:991-995. [PMID: 27900350 PMCID: PMC5123040 DOI: 10.1016/j.dib.2016.11.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 08/22/2016] [Revised: 10/15/2016] [Accepted: 11/10/2016] [Indexed: 11/16/2022] Open
Abstract
Data independent acquisition (DIA) has emerged as a promising mass spectrometry based approach, combining the advantages of shotgun and targeted proteomics. Here we applied a DIA approach (termed SWATH) to monitor the dynamics of the Drosophila melanogaster embryonic proteome upon heat-shock treatment. Embryos were incubated for 0.5, 1 or 3 h at 37 °C to induce heat-shock or maintained at 25 °C. The present dataset contains SWATH files acquired on a Sciex Triple-TOF 6600. A spectral library built in-house was used to analyse these data and led to the quantification of more than 2500 proteins at every timepoint. The files presented here are permanent digital maps and can be reanalysed to search for new questions. The data have been deposited with the ProteomeXchange Consortium with the dataset identifier PRIDE: PXD004753.
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Affiliation(s)
- Bertrand Fabre
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, U.K; Department of Biochemistry, University of Cambridge, Cambridge, U.K; Cambridge Systems Biology Centre, University of Cambridge, Cambridge, U.K
| | - Dagmara Korona
- Department of Genetics, University of Cambridge, Cambridge, U.K; Cambridge Systems Biology Centre, University of Cambridge, Cambridge, U.K
| | - Daniel J H Nightingale
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, U.K; Department of Biochemistry, University of Cambridge, Cambridge, U.K; Cambridge Systems Biology Centre, University of Cambridge, Cambridge, U.K
| | - Steven Russell
- Department of Genetics, University of Cambridge, Cambridge, U.K; Cambridge Systems Biology Centre, University of Cambridge, Cambridge, U.K
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, U.K; Department of Biochemistry, University of Cambridge, Cambridge, U.K; Cambridge Systems Biology Centre, University of Cambridge, Cambridge, U.K
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10
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Fabre B, Korona D, Nightingale DJH, Russell S, Lilley KS. SWATH-MS data of Drosophila melanogaster proteome dynamics during embryogenesis. Data Brief 2016; 9:771-775. [PMID: 27844044 PMCID: PMC5097952 DOI: 10.1016/j.dib.2016.10.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 09/25/2016] [Accepted: 10/18/2016] [Indexed: 11/11/2022] Open
Abstract
Embryogenesis is one of the most important processes in the life of an animal. During this dynamic process, progressive cell division and cellular differentiation are accompanied by significant changes in protein expression at the level of the proteome. However, very few studies to date have described the dynamics of the proteome during the early development of an embryo in any organism. In this dataset, we monitor changes in protein expression across a timecourse of more than 20 h of Drosophila melanogaster embryonic development. Mass-spectrometry data were produced using a SWATH acquisition mode on a Sciex Triple-TOF 6600. A spectral library built in-house was used to analyse these data and more than 1950 proteins were quantified at each embryonic timepoint. The files presented here are a permanent digital map and can be reanalysed to test against new hypotheses. The data have been deposited with the ProteomeXchange Consortium with the dataset identifier PRIDE: PXD0031078.
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Affiliation(s)
- Bertrand Fabre
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, U.K; Department of Biochemistry, University of Cambridge, Cambridge, U.K; Cambridge Systems Biology Centre, University of Cambridge, Cambridge, U.K
| | - Dagmara Korona
- Department of Genetics, University of Cambridge, Cambridge, U.K; Cambridge Systems Biology Centre, University of Cambridge, Cambridge, U.K
| | - Daniel J H Nightingale
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, U.K; Department of Biochemistry, University of Cambridge, Cambridge, U.K; Cambridge Systems Biology Centre, University of Cambridge, Cambridge, U.K
| | - Steven Russell
- Department of Genetics, University of Cambridge, Cambridge, U.K; Cambridge Systems Biology Centre, University of Cambridge, Cambridge, U.K
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, U.K; Department of Biochemistry, University of Cambridge, Cambridge, U.K; Cambridge Systems Biology Centre, University of Cambridge, Cambridge, U.K
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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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Korona D, Korona B, Wojcik E. Intein‐mediated protein splicing of human Eg5 kinesin. FASEB J 2009. [DOI: 10.1096/fasebj.23.1_supplement.502.19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Jedrzejczak-Krzepkowska M, Korona B, Korona D, Tkaczuk KL, Bielecki S. Beta-fructofuranosidase from Bifidobacterium longum KN29,1. J Biotechnol 2007. [DOI: 10.1016/j.jbiotec.2007.07.423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Abstract
AIMS To examine the reliability of membrane cultures as a model solid-state fermentation (SSF) system. METHODS AND RESULTS In overcultures of Aspergillus oryzae on sterilized wheat flour discs overlaid with a polycarbonate membrane, we demonstrated that the presence of membrane filters reduced the maximum respiration rate (up to 50%), and biomass and alpha-amylase production. We also show that the advantage of membrane cultures, i.e. total recovery of biomass, is not very evident for the system used, while the changes in metabolism and kinetics are serious drawbacks. CONCLUSIONS The use of membrane cultures is artificial and without substantial benefits and therefore has to be carefully considered. SIGNIFICANCE AND IMPACT OF THE STUDY In future studies on kinetics and stoichiometry of SSF, one should not completely rely on experiments using membrane cultures as a model SSF system.
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Affiliation(s)
- Y S P Rahardjo
- Wageningen Centre for Food Sciences, Wageningen, the Netherlands.
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