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Montserrat-Gomez M, Gogl G, Carrasco K, Betzi S, Durbesson F, Cousido-Siah A, Kostmann C, Essig DJ, Strømgaard K, Østergaard S, Morelli X, Trave G, Vincentelli R, Bailly E, Borg JP. PDZome-wide and structural characterization of the PDZ-binding motif of VANGL2. Biochim Biophys Acta Proteins Proteom 2024; 1872:140989. [PMID: 38142947 DOI: 10.1016/j.bbapap.2023.140989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 12/26/2023]
Abstract
VANGL2 is a core component of the non-canonical Wnt/Planar Cell Polarity signaling pathway that uses its highly conserved carboxy-terminal type 1 PDZ-binding motif (PBM) to bind a variety of PDZ proteins. In this study, we characterize and quantitatively assess the largest VANGL2 PDZome-binding profile documented so far, using orthogonal methods. The results of our holdup approach support VANGL2 interactions with a large panel of both long-recognized and unprecedented PDZ domains. Truncation and point mutation analyses of the VANGL2 PBM establish that, beyond the strict requirement of the P-0 / V521 and P-2 / T519 amino acids, upstream residues, including E518, Q516 and R514 at, respectively, P-3, P-5 and P-7 further contribute to the robustness of VANGL2 interactions with two distinct PDZ domains, SNX27 and SCRIBBLE-PDZ3. In agreement with these data, incremental amino-terminal deletions of the VANGL2 PBM causes its overall affinity to progressively decline. Moreover, the holdup data establish that the PDZome binding repertoire of VANGL2 starts to diverge significantly with the truncation of E518. A structural analysis of the SYNJ2BP-PDZ/VANGL2 interaction with truncated PBMs identifies a major conformational change in the binding direction of the PBM peptide after the P-2 position. Finally, we report that the PDZome binding profile of VANGL2 is dramatically rearranged upon phosphorylation of S517, T519 and S520. Our crystallographic approach illustrates how SYNJ2BP accommodates a S520-phosphorylated PBM peptide through the ideal positioning of two basic residues, K48 and R86. Altogether our data provides a comprehensive view of the VANGL2 PDZ network and how this network specifically responds to the post-translation modification of distinct PBM residues. These findings should prove useful in guiding future functional and molecular studies of the key PCP component VANGL2.
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Affiliation(s)
- Marta Montserrat-Gomez
- Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe labellisée Ligue 'Cell polarity, cell signaling and cancer', Marseille, France
| | - Gergo Gogl
- Universite de Strasbourg, INSERM, CNRS, IGBMC, Department of Integrated Structural Biology, Illkirch, France
| | - Kendall Carrasco
- Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe Integrative Structural & Chemical Biology, Marseille, France
| | - Stephane Betzi
- Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe Integrative Structural & Chemical Biology, Marseille, France
| | - Fabien Durbesson
- Aix Marseille Université, CNRS, Architecture et fonction des macromolécules biologiques (AFMB), Marseille, France
| | - Alexandra Cousido-Siah
- Universite de Strasbourg, INSERM, CNRS, IGBMC, Department of Integrated Structural Biology, Illkirch, France
| | - Camille Kostmann
- Universite de Strasbourg, INSERM, CNRS, IGBMC, Department of Integrated Structural Biology, Illkirch, France
| | - Dominic J Essig
- Center for Biopharmaceuticals, Jagtvej 162, 2100 Copenhagen, Denmark; Global Research Technologies, Novo Nordisk Research Park, 2760 Maaloev, Denmark
| | | | - Søren Østergaard
- Global Research Technologies, Novo Nordisk Research Park, 2760 Maaloev, Denmark
| | - Xavier Morelli
- Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe Integrative Structural & Chemical Biology, Marseille, France
| | - Gilles Trave
- Universite de Strasbourg, INSERM, CNRS, IGBMC, Department of Integrated Structural Biology, Illkirch, France
| | - Renaud Vincentelli
- Aix Marseille Université, CNRS, Architecture et fonction des macromolécules biologiques (AFMB), Marseille, France.
| | - Eric Bailly
- Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe labellisée Ligue 'Cell polarity, cell signaling and cancer', Marseille, France.
| | - Jean-Paul Borg
- Aix Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe labellisée Ligue 'Cell polarity, cell signaling and cancer', Marseille, France; Institut Universitaire de France (IUF), France.
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2
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Menzies SK, Arinto-Garcia R, Amorim FG, Cardoso IA, Abada C, Crasset T, Durbesson F, Edge RJ, El-Kazzi P, Hall S, Redureau D, Stenner R, Boldrini-França J, Sun H, Roldão A, Alves PM, Harrison RA, Vincentelli R, Berger I, Quinton L, Casewell NR, Schaffitzel C. ADDovenom: Thermostable Protein-Based ADDomer Nanoparticles as New Therapeutics for Snakebite Envenoming. Toxins (Basel) 2023; 15:673. [PMID: 38133177 PMCID: PMC10747859 DOI: 10.3390/toxins15120673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/13/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023] Open
Abstract
Snakebite envenoming can be a life-threatening medical emergency that requires prompt medical intervention to neutralise the effects of venom toxins. Each year up to 138,000 people die from snakebites and threefold more victims suffer life-altering disabilities. The current treatment of snakebite relies solely on antivenom-polyclonal antibodies isolated from the plasma of hyperimmunised animals-which is associated with numerous deficiencies. The ADDovenom project seeks to deliver a novel snakebite therapy, through the use of an innovative protein-based scaffold as a next-generation antivenom. The ADDomer is a megadalton-sized, thermostable synthetic nanoparticle derived from the adenovirus penton base protein; it has 60 high-avidity binding sites to neutralise venom toxins. Here, we outline our experimental strategies to achieve this goal using state-of-the-art protein engineering, expression technology and mass spectrometry, as well as in vitro and in vivo venom neutralisation assays. We anticipate that the approaches described here will produce antivenom with unparalleled efficacy, safety and affordability.
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Affiliation(s)
- Stefanie K. Menzies
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
- Centre for Drugs & Diagnostics, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Raquel Arinto-Garcia
- iBET, Instituto de Biologia Experimental e Technológica, Apartado 12, 2781-901 Oeiras, Portugal
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Fernanda Gobbi Amorim
- Mass Spectrometry Laboratory, MolSys Research Unit, Allée du six Aout 11, Quartier Agora, Liège Université, 4000 Liège, Belgium
| | - Iara Aimê Cardoso
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Camille Abada
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Thomas Crasset
- Mass Spectrometry Laboratory, MolSys Research Unit, Allée du six Aout 11, Quartier Agora, Liège Université, 4000 Liège, Belgium
| | - Fabien Durbesson
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 13009 Marseille, France
| | - Rebecca J. Edge
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Priscila El-Kazzi
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 13009 Marseille, France
| | - Sophie Hall
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK
- Max Planck Bristol Centre for Minimal Biology, Cantock’s Close, Bristol BS8 1TS, UK
| | - Damien Redureau
- Mass Spectrometry Laboratory, MolSys Research Unit, Allée du six Aout 11, Quartier Agora, Liège Université, 4000 Liège, Belgium
| | - Richard Stenner
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK
- Max Planck Bristol Centre for Minimal Biology, Cantock’s Close, Bristol BS8 1TS, UK
| | - Johara Boldrini-França
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK
- Max Planck Bristol Centre for Minimal Biology, Cantock’s Close, Bristol BS8 1TS, UK
| | - Huan Sun
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK
- Max Planck Bristol Centre for Minimal Biology, Cantock’s Close, Bristol BS8 1TS, UK
| | - António Roldão
- iBET, Instituto de Biologia Experimental e Technológica, Apartado 12, 2781-901 Oeiras, Portugal
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Paula M. Alves
- iBET, Instituto de Biologia Experimental e Technológica, Apartado 12, 2781-901 Oeiras, Portugal
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Robert A. Harrison
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
- Centre for Drugs & Diagnostics, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Renaud Vincentelli
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 13009 Marseille, France
| | - Imre Berger
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK
- Max Planck Bristol Centre for Minimal Biology, Cantock’s Close, Bristol BS8 1TS, UK
| | - Loïc Quinton
- Mass Spectrometry Laboratory, MolSys Research Unit, Allée du six Aout 11, Quartier Agora, Liège Université, 4000 Liège, Belgium
| | - Nicholas R. Casewell
- Centre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
- Centre for Drugs & Diagnostics, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Christiane Schaffitzel
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, UK
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3
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Buzas D, Bunzel AH, Staufer O, Milodowski EJ, Edmunds GL, Bufton JC, Vidana Mateo BV, Yadav SKN, Gupta K, Fletcher C, Williamson MK, Harrison A, Borucu U, Capin J, Francis O, Balchin G, Hall S, Vega MV, Durbesson F, Lingappa S, Vincentelli R, Roe J, Wooldridge L, Burt R, Anderson RJL, Mulholland AJ, Bristol UNCOVER Group, Hare J, Bailey M, Davidson AD, Finn A, Morgan D, Mann J, Spatz J, Garzoni F, Schaffitzel C, Berger I. In vitro generated antibodies guide thermostable ADDomer nanoparticle design for nasal vaccination and passive immunization against SARS-CoV-2. Antib Ther 2023; 6:277-297. [PMID: 38075238 PMCID: PMC10702856 DOI: 10.1093/abt/tbad024] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 10/12/2023] [Accepted: 10/14/2023] [Indexed: 01/10/2024] Open
Abstract
Background Due to COVID-19, pandemic preparedness emerges as a key imperative, necessitating new approaches to accelerate development of reagents against infectious pathogens. Methods Here, we developed an integrated approach combining synthetic, computational and structural methods with in vitro antibody selection and in vivo immunization to design, produce and validate nature-inspired nanoparticle-based reagents against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Results Our approach resulted in two innovations: (i) a thermostable nasal vaccine called ADDoCoV, displaying multiple copies of a SARS-CoV-2 receptor binding motif derived epitope and (ii) a multivalent nanoparticle superbinder, called Gigabody, against SARS-CoV-2 including immune-evasive variants of concern (VOCs). In vitro generated neutralizing nanobodies and electron cryo-microscopy established authenticity and accessibility of epitopes displayed by ADDoCoV. Gigabody comprising multimerized nanobodies prevented SARS-CoV-2 virion attachment with picomolar EC50. Vaccinating mice resulted in antibodies cross-reacting with VOCs including Delta and Omicron. Conclusion Our study elucidates Adenovirus-derived dodecamer (ADDomer)-based nanoparticles for use in active and passive immunization and provides a blueprint for crafting reagents to combat respiratory viral infections.
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Affiliation(s)
- Dora Buzas
- Max Planck Bristol Centre for Minimal Biology, University of Bristol, Bristol BS8 1TS, UK
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Adrian H Bunzel
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Oskar Staufer
- Max Planck Bristol Centre for Minimal Biology, University of Bristol, Bristol BS8 1TS, UK
- Leibniz Institute for New Materials, Helmholtz Institute for Pharmaceutical Research and Center for Biophysics, Saarland University, Saarbrücken 66123, Germany
| | | | - Grace L Edmunds
- Bristol Veterinary School, University of Bristol, Bristol BS40 5DU UK
| | - Joshua C Bufton
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | | | | | - Kapil Gupta
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
- Imophoron Ltd, Science Creates Old Market, Midland Rd, Bristol BS2 0JZ UK
| | | | - Maia K Williamson
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | | | - Ufuk Borucu
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Julien Capin
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Ore Francis
- Bristol Veterinary School, University of Bristol, Bristol BS40 5DU UK
| | - Georgia Balchin
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Sophie Hall
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Mirella V Vega
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Fabien Durbesson
- Architecture et Fonction des Macromolécules Biologiques, UMR 7257, CNRS, Aix-Marseille Université, Marseille, France
| | | | - Renaud Vincentelli
- Architecture et Fonction des Macromolécules Biologiques, UMR 7257, CNRS, Aix-Marseille Université, Marseille, France
| | - Joe Roe
- Bristol Veterinary School, University of Bristol, Bristol BS40 5DU UK
| | - Linda Wooldridge
- Bristol Veterinary School, University of Bristol, Bristol BS40 5DU UK
| | - Rachel Burt
- Bristol Veterinary School, University of Bristol, Bristol BS40 5DU UK
| | | | | | | | - Jonathan Hare
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Mick Bailey
- Bristol Veterinary School, University of Bristol, Bristol BS40 5DU UK
| | - Andrew D Davidson
- Imophoron Ltd, Science Creates Old Market, Midland Rd, Bristol BS2 0JZ UK
| | - Adam Finn
- Bristol University COVID-19 Emergency Research Group, Bristol BS8 1TH, UK
- Children's Vaccine Centre, Bristol Medical School, Bristol BS2 8EF UK
| | - David Morgan
- Imophoron Ltd, Science Creates Old Market, Midland Rd, Bristol BS2 0JZ UK
| | - Jamie Mann
- Bristol Veterinary School, University of Bristol, Bristol BS40 5DU UK
| | - Joachim Spatz
- Max Planck Bristol Centre for Minimal Biology, University of Bristol, Bristol BS8 1TS, UK
- Max Planck Institute for Medical Research, Heidelberg 69120, Germany
| | - Frederic Garzoni
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Christiane Schaffitzel
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
- Bristol University COVID-19 Emergency Research Group, Bristol BS8 1TH, UK
| | - Imre Berger
- Max Planck Bristol Centre for Minimal Biology, University of Bristol, Bristol BS8 1TS, UK
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
- School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
- Bristol University COVID-19 Emergency Research Group, Bristol BS8 1TH, UK
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4
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Jaeger M, Anastasio A, Chamy L, Brustlein S, Vincentelli R, Durbesson F, Gigan J, Thépaut M, Char R, Boussand M, Lechelon M, Argüello RJ, Marguet D, He HT, Lasserre R. Light-inducible T cell engagers trigger, tune, and shape the activation of primary T cells. Proc Natl Acad Sci U S A 2023; 120:e2302500120. [PMID: 37722050 PMCID: PMC10523538 DOI: 10.1073/pnas.2302500120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 08/17/2023] [Indexed: 09/20/2023] Open
Abstract
To mount appropriate responses, T cells integrate complex sequences of receptor stimuli perceived during transient interactions with antigen-presenting cells. Although it has been hypothesized that the dynamics of these interactions influence the outcome of T cell activation, methodological limitations have hindered its formal demonstration. Here, we have engineered the Light-inducible T cell engager (LiTE) system, a recombinant optogenetics-based molecular tool targeting the T cell receptor (TCR). The LiTE system constitutes a reversible molecular switch displaying exquisite reactivity. As proof of concept, we dissect how specific temporal patterns of TCR stimulation shape T cell activation. We established that CD4+ T cells respond to intermittent TCR stimulation more efficiently than their CD8+ T cells counterparts and provide evidence that distinct sequences of TCR stimulation encode different cytokine programs. Finally, we show that the LiTE system could be exploited to create light-activated bispecific T cell engagers and manipulate tumor cell killing. Overall, the LiTE system provides opportunities to understand how T cells integrate TCR stimulations and to trigger T cell cytotoxicity with high spatiotemporal control.
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Affiliation(s)
- Morgane Jaeger
- Aix Marseille Université, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Centre d’Immunologie de Marseille Luminy, Turing Center for Living Systems, 13 288Marseille, France
| | - Amandine Anastasio
- Aix Marseille Université, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Centre d’Immunologie de Marseille Luminy, Turing Center for Living Systems, 13 288Marseille, France
| | - Léa Chamy
- Aix Marseille Université, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Centre d’Immunologie de Marseille Luminy, Turing Center for Living Systems, 13 288Marseille, France
| | - Sophie Brustlein
- Aix Marseille Université, Institut National de la Santé et de la Recherche Médicale, Institut de neurobiologie de la Méditerranée, Turing Center for Living Systems, 13 273Marseille, France
| | - Renaud Vincentelli
- Aix Marseille Université, Centre National de la Recherche Scientifique, Architecture et Fonction des Macromolécules Biologiques, 13 288Marseille, France
| | - Fabien Durbesson
- Aix Marseille Université, Centre National de la Recherche Scientifique, Architecture et Fonction des Macromolécules Biologiques, 13 288Marseille, France
| | - Julien Gigan
- Aix Marseille Université, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Centre d’Immunologie de Marseille Luminy, Turing Center for Living Systems, 13 288Marseille, France
| | - Morgane Thépaut
- Aix Marseille Université, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Centre d’Immunologie de Marseille Luminy, Turing Center for Living Systems, 13 288Marseille, France
| | - Rémy Char
- Aix Marseille Université, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Centre d’Immunologie de Marseille Luminy, Turing Center for Living Systems, 13 288Marseille, France
| | - Maud Boussand
- Aix Marseille Université, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Centre d’Immunologie de Marseille Luminy, Turing Center for Living Systems, 13 288Marseille, France
| | - Mathias Lechelon
- Aix Marseille Université, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Centre d’Immunologie de Marseille Luminy, Turing Center for Living Systems, 13 288Marseille, France
| | - Rafael J. Argüello
- Aix Marseille Université, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Centre d’Immunologie de Marseille Luminy, Turing Center for Living Systems, 13 288Marseille, France
| | - Didier Marguet
- Aix Marseille Université, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Centre d’Immunologie de Marseille Luminy, Turing Center for Living Systems, 13 288Marseille, France
| | - Hai-Tao He
- Aix Marseille Université, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Centre d’Immunologie de Marseille Luminy, Turing Center for Living Systems, 13 288Marseille, France
| | - Rémi Lasserre
- Aix Marseille Université, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Centre d’Immunologie de Marseille Luminy, Turing Center for Living Systems, 13 288Marseille, France
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5
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Hage H, Couillaud J, Salamov A, Loussouarn-Yvon M, Durbesson F, Ormeño E, Grisel S, Duquesne K, Vincentelli R, Grigoriev I, Iacazio G, Rosso MN. An HMM approach expands the landscape of sesquiterpene cyclases across the kingdom Fungi. Microb Genom 2023; 9. [PMID: 37073784 DOI: 10.1099/mgen.0.000990] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023] Open
Abstract
Sesquiterpene cyclases (STC) catalyse the cyclization of the C15 molecule farnesyl diphosphate into a vast variety of mono- or polycyclic hydrocarbons and, for a few enzymes, oxygenated structures, with diverse stereogenic centres. The huge diversity in sesquiterpene skeleton structures in nature is primarily the result of the type of cyclization driven by the STC. Despite the phenomenal impact of fungal sesquiterpenes on the ecology of fungi and their potentials for applications, the fungal sesquiterpenome is largely untapped. The identification of fungal STC is generally based on protein sequence similarity with characterized enzymes. This approach has improved our knowledge on STC in a few fungal species, but it has limited success for the discovery of distant sequences. Besides, the tools based on secondary metabolite biosynthesis gene clusters have shown poor performance for terpene cyclases. Here, we used four sets of sequences of fungal STC that catalyse four types of cyclization, and specific amino acid motives to identify phylogenetically related sequences in the genomes of basidiomycetes fungi from the order Polyporales. We validated that four STC genes newly identified from the genome sequence of Leiotrametes menziesii, each classified in a different phylogenetic clade, catalysed a predicted cyclization of farnesyl diphosphate. We built HMM models and searched STC genes in 656 fungal genomes genomes. We identified 5605 STC genes, which were classified in one of the four clades and had a predicted cyclization mechanism. We noticed that the HMM models were more accurate for the prediction of the type of cyclization catalysed by basidiomycete STC than for ascomycete STC.
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Affiliation(s)
- Hayat Hage
- INRAE, Aix Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, France
- Present address: Bioaster, Lyon, France
| | - Julie Couillaud
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France
- Present address: Department of Biology and Biological Engineering, Systems and Synthetic Biology Division, Chalmers university of Technology, Gothenburg, Sweden
| | - Asaf Salamov
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Margot Loussouarn-Yvon
- INRAE, Aix Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, France
| | | | - Elena Ormeño
- CNRS, Aix Marseille Univ, IRD, Avignon Univ, IMBE, Marseille, France
| | - Sacha Grisel
- INRAE, Aix Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, France
| | - Katia Duquesne
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France
| | | | - Igor Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Gilles Iacazio
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Marie-Noëlle Rosso
- INRAE, Aix Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, Marseille, France
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6
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Gogl G, Zambo B, Kostmann C, Cousido-Siah A, Morlet B, Durbesson F, Negroni L, Eberling P, Jané P, Nominé Y, Zeke A, Østergaard S, Monsellier É, Vincentelli R, Travé G. Author Correction: Quantitative fragmentomics allow affinity mapping of interactomes. Nat Commun 2022; 13:7555. [PMID: 36477203 PMCID: PMC9729566 DOI: 10.1038/s41467-022-35177-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Gergo Gogl
- grid.420255.40000 0004 0638 2716Équipe Labellisée Ligue 2015, Département de Biologie Structurale Intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, 1 rue Laurent Fries, BP 10142, F-67404 Illkirch, France
| | - Boglarka Zambo
- grid.420255.40000 0004 0638 2716Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Universite de Strasbourg, 1 rue Laurent Fries, BP 10142, F-67404 Illkirch, France
| | - Camille Kostmann
- grid.420255.40000 0004 0638 2716Équipe Labellisée Ligue 2015, Département de Biologie Structurale Intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, 1 rue Laurent Fries, BP 10142, F-67404 Illkirch, France
| | - Alexandra Cousido-Siah
- grid.420255.40000 0004 0638 2716Équipe Labellisée Ligue 2015, Département de Biologie Structurale Intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, 1 rue Laurent Fries, BP 10142, F-67404 Illkirch, France
| | - Bastien Morlet
- grid.420255.40000 0004 0638 2716Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Universite de Strasbourg, 1 rue Laurent Fries, BP 10142, F-67404 Illkirch, France
| | - Fabien Durbesson
- grid.463764.40000 0004 1798 275XArchitecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 CNRS-Aix-Marseille Université, Marseille, France
| | - Luc Negroni
- grid.420255.40000 0004 0638 2716Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Universite de Strasbourg, 1 rue Laurent Fries, BP 10142, F-67404 Illkirch, France
| | - Pascal Eberling
- grid.420255.40000 0004 0638 2716Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Universite de Strasbourg, 1 rue Laurent Fries, BP 10142, F-67404 Illkirch, France
| | - Pau Jané
- grid.420255.40000 0004 0638 2716Équipe Labellisée Ligue 2015, Département de Biologie Structurale Intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, 1 rue Laurent Fries, BP 10142, F-67404 Illkirch, France
| | - Yves Nominé
- grid.420255.40000 0004 0638 2716Équipe Labellisée Ligue 2015, Département de Biologie Structurale Intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, 1 rue Laurent Fries, BP 10142, F-67404 Illkirch, France
| | - Andras Zeke
- grid.425578.90000 0004 0512 3755Bioinformatics Research Group, Research Centre for Natural Sciences, Magyar tudosok korutja 2, 1117 Budapest, Hungary
| | - Søren Østergaard
- grid.425956.90000 0004 0391 2646Novo Nordisk A/S, Global Research Technologies, Novo Nordisk Research Park, 2760 Maaloev, Denmark
| | - Élodie Monsellier
- grid.420255.40000 0004 0638 2716Équipe Labellisée Ligue 2015, Département de Biologie Structurale Intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, 1 rue Laurent Fries, BP 10142, F-67404 Illkirch, France
| | - Renaud Vincentelli
- grid.463764.40000 0004 1798 275XArchitecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 CNRS-Aix-Marseille Université, Marseille, France
| | - Gilles Travé
- grid.420255.40000 0004 0638 2716Équipe Labellisée Ligue 2015, Département de Biologie Structurale Intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, 1 rue Laurent Fries, BP 10142, F-67404 Illkirch, France
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7
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Gogl G, Zambo B, Kostmann C, Cousido-Siah A, Morlet B, Durbesson F, Negroni L, Eberling P, Jané P, Nominé Y, Zeke A, Østergaard S, Monsellier É, Vincentelli R, Travé G. Quantitative fragmentomics allow affinity mapping of interactomes. Nat Commun 2022; 13:5472. [PMID: 36115835 PMCID: PMC9482650 DOI: 10.1038/s41467-022-33018-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 08/24/2022] [Indexed: 12/18/2022] Open
Abstract
Human protein networks have been widely explored but most binding affinities remain unknown, hindering quantitative interactome-function studies. Yet interactomes rely on minimal interacting fragments displaying quantifiable affinities. Here, we measure the affinities of 65,000 interactions involving PDZ domains and their target PDZ-binding motifs (PBM) within a human interactome region particularly relevant for viral infection and cancer. We calculate interactomic distances, identify hot spots for viral interference, generate binding profiles and specificity logos, and explain selected cases by crystallographic studies. Mass spectrometry experiments on cell extracts and literature surveys show that quantitative fragmentomics effectively complements protein interactomics by providing affinities and completeness of coverage, putting a full human interactome affinity survey within reach. Finally, we show that interactome hijacking by the viral PBM of human papillomavirus E6 oncoprotein substantially impacts the host cell proteome beyond immediate E6 binders, illustrating the complex system-wide relationship between interactome and function. Protein networks have been widely explored but most binding affinities remain unknown, limiting the quantitative interpretation of interactomes. Here the authors measure affinities of 65,000 interactions involving human PDZ domains and target sequence motifs relevant for viral infection and cancer.
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8
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Lopez E, Barthélémy M, Baronti C, Masse S, Falchi A, Durbesson F, Vincentelli R, de Lamballerie X, Charrel R, Coutard B. Endonuclease-based genotyping of the RBM as a method to track the emergence or evolution of SARS-CoV-2 variants. iScience 2021; 24:103329. [PMID: 34697603 PMCID: PMC8529542 DOI: 10.1016/j.isci.2021.103329] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 08/23/2021] [Accepted: 10/19/2021] [Indexed: 12/02/2022] Open
Abstract
Since the beginning of the COVID-19 pandemics, variants have emerged. Some of them display increased transmissibility and/or resistance to immune response. Most of the mutations involved in the functional adaptation are found in the receptor-binding motif (RBM), close to the interface with the receptor ACE2. We thus developed a fast molecular assay to detect mutations in the RBM coding sequence. After amplification, the amplicon is heat-denatured and hybridized with an amplicon of reference. The presence of a mutation can be detected using a mismatch-specific endonuclease and the cleavage pattern is analyzed by capillary electrophoresis. The method was validated on RNA of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants produced in vitro before being implemented for clinical samples. The assay showed 97.8% sensitivity and 97.8% specificity. The procedure can be set up for high-throughput identification of the presence of mutations and serve as a first-line screening to select the samples for full genome sequencing.
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Affiliation(s)
- Eva Lopez
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Margot Barthélémy
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Cécile Baronti
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Shirley Masse
- UR7310, Laboratoire de Virologie, Université de Corse-Inserm, 20250 Corte, France
| | - Alessandra Falchi
- UR7310, Laboratoire de Virologie, Université de Corse-Inserm, 20250 Corte, France
| | - Fabien Durbesson
- Unité Mixte de Recherche (UMR) 7257, Centre National de la Recherche Scientifique (CNRS) Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille, France
| | - Renaud Vincentelli
- Unité Mixte de Recherche (UMR) 7257, Centre National de la Recherche Scientifique (CNRS) Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille, France
| | - Xavier de Lamballerie
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Rémi Charrel
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
- Comité de Lutte contre les Infections Nosocomiales, Hôpitaux Universitaires de Marseille, AP-HM, Marseille, France
| | - Bruno Coutard
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
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9
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Nason R, Büll C, Konstantinidi A, Sun L, Ye Z, Halim A, Du W, Sørensen DM, Durbesson F, Furukawa S, Mandel U, Joshi HJ, Dworkin LA, Hansen L, David L, Iverson TM, Bensing BA, Sullam PM, Varki A, Vries ED, de Haan CAM, Vincentelli R, Henrissat B, Vakhrushev SY, Clausen H, Narimatsu Y. Display of the human mucinome with defined O-glycans by gene engineered cells. Nat Commun 2021; 12:4070. [PMID: 34210959 PMCID: PMC8249670 DOI: 10.1038/s41467-021-24366-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [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] [Received: 10/22/2020] [Accepted: 06/08/2021] [Indexed: 02/08/2023] Open
Abstract
Mucins are a large family of heavily O-glycosylated proteins that cover all mucosal surfaces and constitute the major macromolecules in most body fluids. Mucins are primarily defined by their variable tandem repeat (TR) domains that are densely decorated with different O-glycan structures in distinct patterns, and these arguably convey much of the informational content of mucins. Here, we develop a cell-based platform for the display and production of human TR O-glycodomains (~200 amino acids) with tunable structures and patterns of O-glycans using membrane-bound and secreted reporters expressed in glycoengineered HEK293 cells. Availability of defined mucin TR O-glycodomains advances experimental studies into the versatile role of mucins at the interface with pathogenic microorganisms and the microbiome, and sparks new strategies for molecular dissection of specific roles of adhesins, glycoside hydrolases, glycopeptidases, viruses and other interactions with mucin TRs as highlighted by examples.
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Affiliation(s)
- Rebecca Nason
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christian Büll
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Andriana Konstantinidi
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lingbo Sun
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Zilu Ye
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Adnan Halim
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Wenjuan Du
- Section Virology, Division of Infectious Diseases and Immunology, Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, CL, Utrecht, the Netherlands
| | - Daniel M Sørensen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Fabien Durbesson
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France
| | - Sanae Furukawa
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ulla Mandel
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hiren J Joshi
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Leo Alexander Dworkin
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lars Hansen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Leonor David
- Institute of Molecular Pathology and Immunology of the University of Porto/I3S, Porto, Portugal.,Medical Faculty of the University of Porto, Porto, Portugal
| | - Tina M Iverson
- Departments of Pharmacology and Biochemistry, Vanderbilt University, Nashville, TN, USA
| | - Barbara A Bensing
- Department of Medicine, The San Francisco Veterans Affairs Medical Center, and the University of California, San Francisco, CA, USA
| | - Paul M Sullam
- Department of Medicine, The San Francisco Veterans Affairs Medical Center, and the University of California, San Francisco, CA, USA
| | - Ajit Varki
- The Glycobiology Research and Training Center, and the Department of Cellular and Molecular Medicine, University of California, San Diego, CA, USA
| | - Erik de Vries
- Section Virology, Division of Infectious Diseases and Immunology, Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, CL, Utrecht, the Netherlands
| | - Cornelis A M de Haan
- Section Virology, Division of Infectious Diseases and Immunology, Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, CL, Utrecht, the Netherlands
| | - Renaud Vincentelli
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France
| | - Bernard Henrissat
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.,Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Yoshiki Narimatsu
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark. .,GlycoDisplay ApS, Copenhagen, Denmark.
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10
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Caillet-Saguy C, Durbesson F, Rezelj VV, Gogl G, Tran QD, Twizere JC, Vignuzzi M, Vincentelli R, Wolff N. Host PDZ-containing proteins targeted by SARS-CoV-2. FEBS J 2021; 288:5148-5162. [PMID: 33864728 PMCID: PMC8250131 DOI: 10.1111/febs.15881] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [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: 02/02/2021] [Revised: 03/31/2021] [Accepted: 04/13/2021] [Indexed: 12/16/2022]
Abstract
Small linear motifs targeting protein interacting domains called PSD‐95/Dlg/ZO‐1 (PDZ) have been identified at the C terminus of the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) proteins E, 3a, and N. Using a high‐throughput approach of affinity‐profiling against the full human PDZome, we identified sixteen human PDZ binders of SARS‐CoV‐2 proteins E, 3A, and N showing significant interactions with dissociation constants values ranging from 3 to 82 μm. Six of them (TJP1, PTPN13, HTRA1, PARD3, MLLT4, LNX2) are also recognized by SARS‐CoV while three (NHERF1, MAST2, RADIL) are specific to SARS‐CoV‐2 E protein. Most of these SARS‐CoV‐2 protein partners are involved in cellular junctions/polarity and could be also linked to evasion mechanisms of the immune responses during viral infection. Among the binders of the SARS‐CoV‐2 proteins E, 3a, or N, seven significantly affect viral replication under knock down gene expression in infected cells. This PDZ profiling identifying human proteins potentially targeted by SARS‐CoV‐2 can help to understand the multifactorial severity of COVID19 and to conceive effective anti‐coronaviral agents for therapeutic purposes.
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Affiliation(s)
| | | | - Veronica V Rezelj
- Institut Pasteur, Unité Populations Virales et Pathogénèse, UMR CNRS 3569, Paris, France
| | - Gergö Gogl
- IGBMC, INSERM U1258/UMR CNRS 7104, Illkirch, France
| | - Quang Dinh Tran
- Institut Pasteur, Unité Populations Virales et Pathogénèse, UMR CNRS 3569, Paris, France.,École doctorale BioSPC, Université Paris Diderot, Sorbonne Paris Cité, France
| | - Jean-Claude Twizere
- GIGA Institute, Molecular Biology of Diseases, Viral Interactomes laboratory, University of Liege, Belgium
| | - Marco Vignuzzi
- Institut Pasteur, Unité Populations Virales et Pathogénèse, UMR CNRS 3569, Paris, France
| | | | - Nicolas Wolff
- Institut Pasteur, Unité Récepteurs-Canaux, UMR CNRS 3571, Paris, France
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11
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Gógl G, Biri-Kovács B, Durbesson F, Jane P, Nomine Y, Kostmann C, Bilics V, Simon M, Reményi A, Vincentelli R, Trave G, Nyitray L. Rewiring of RSK-PDZ Interactome by Linear Motif Phosphorylation. J Mol Biol 2019; 431:1234-1249. [PMID: 30726710 PMCID: PMC6424611 DOI: 10.1016/j.jmb.2019.01.038] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [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: 12/10/2018] [Revised: 01/16/2019] [Accepted: 01/28/2019] [Indexed: 10/27/2022]
Abstract
Phosphorylation of short linear peptide motifs is a widespread process for the dynamic regulation of protein-protein interactions. However, the global impact of phosphorylation events on the protein-protein interactome is rarely addressed. The disordered C-terminal tail of ribosomal S6 kinase 1 (RSK1) binds to PDZ domain-containing scaffold proteins, and it harbors a phosphorylatable PDZ-binding motif (PBM) responsive to epidermal growth factor stimulation. Here, we examined binding of two versions of the RSK1 PBM, either phosphorylated or unphosphorylated at position -3, to almost all (95%) of the 266 PDZ domains of the human proteome. PBM phosphorylation dramatically altered the PDZ domain-binding landscape of RSK1, by strengthening or weakening numerous interactions to various degrees. The RSK-PDZome interactome analyzed in this study reveals how linear motif-based phospho-switches convey stimulus-dependent changes in the context of related network components.
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Affiliation(s)
- Gergő Gógl
- Department of Biochemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Beáta Biri-Kovács
- Department of Biochemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Fabien Durbesson
- Unite Mixte de Recherche (UMR) 7257, Centre National de la Recherche Scientifique (CNRS) Aix-Marseille Universite, Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille, France
| | - Pau Jane
- Equipe Labellisee Ligue 2015, Department of Integrated Structural Biology, Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Universite de Strasbourg, 1 rue Laurent Fries, BP 10142, F-67404 Illkirch, France
| | - Yves Nomine
- Equipe Labellisee Ligue 2015, Department of Integrated Structural Biology, Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Universite de Strasbourg, 1 rue Laurent Fries, BP 10142, F-67404 Illkirch, France
| | - Camille Kostmann
- Equipe Labellisee Ligue 2015, Department of Integrated Structural Biology, Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Universite de Strasbourg, 1 rue Laurent Fries, BP 10142, F-67404 Illkirch, France
| | - Viktória Bilics
- Department of Biochemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Márton Simon
- Department of Biochemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Attila Reményi
- Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Renaud Vincentelli
- Unite Mixte de Recherche (UMR) 7257, Centre National de la Recherche Scientifique (CNRS) Aix-Marseille Universite, Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille, France
| | - Gilles Trave
- Equipe Labellisee Ligue 2015, Department of Integrated Structural Biology, Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Universite de Strasbourg, 1 rue Laurent Fries, BP 10142, F-67404 Illkirch, France.
| | - László Nyitray
- Department of Biochemistry, ELTE Eötvös Loránd University, Budapest, Hungary.
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12
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Duhoo Y, Girault V, Turchetto J, Ramond L, Durbesson F, Fourquet P, Nominé Y, Cardoso V, Sequeira AF, Brás JLA, Fontes CMGA, Travé G, Wolff N, Vincentelli R. High-Throughput Production of a New Library of Human Single and Tandem PDZ Domains Allows Quantitative PDZ-Peptide Interaction Screening Through High-Throughput Holdup Assay. Methods Mol Biol 2019; 2025:439-476. [PMID: 31267466 DOI: 10.1007/978-1-4939-9624-7_21] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
PDZ domains recognize PDZ Binding Motifs (PBMs) at the extreme C-terminus of their partner proteins. The human proteome contains 266 identified PDZ domains, the PDZome, spread over 152 proteins. We previously developed the "holdup" chromatographic assay for high-throughput determination of PDZ-PBM affinities. In that work, we had used an expression library of 241 PDZ constructs (the "PDZome V.1"). Here, we cloned, produced, and characterized a new bacterial expression library ("PDZome V.2"), which comprises all the 266 known human PDZ domains as well as 37 PDZ tandem constructs. To ensure the best expression level, folding, and solubility, all construct boundaries were redesigned using available structural data and all DNA sequences were optimized for Escherichia coli expression. Consequently, all the PDZ constructs are produced in a soluble form. Precise quantification and quality control were carried out. The binding profiles previously published using "PDZome V.1" were reproduced and completed using the novel "PDZome V.2" library. We provide here the detailed description of the high-throughput protocols followed through the PDZ gene synthesis and cloning, PDZ production, holdup assay and data treatment.
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Affiliation(s)
- Yoan Duhoo
- Architecture et Fonction des Macromolécules Biologiques (AFMB), Unité Mixte de Recherche (UMR) 7257, Centre National de la Recherche Scientifique (CNRS) Aix-Marseille Université, Marseille cedex 9, France
| | - Virginie Girault
- Unité Récepteurs-Canaux, Département of Neuroscience, CNRS UMR 3571, Institut Pasteur, Paris Cedex 15, France
| | - Jeremy Turchetto
- Architecture et Fonction des Macromolécules Biologiques (AFMB), Unité Mixte de Recherche (UMR) 7257, Centre National de la Recherche Scientifique (CNRS) Aix-Marseille Université, Marseille cedex 9, France
| | - Laurie Ramond
- Architecture et Fonction des Macromolécules Biologiques (AFMB), Unité Mixte de Recherche (UMR) 7257, Centre National de la Recherche Scientifique (CNRS) Aix-Marseille Université, Marseille cedex 9, France
| | - Fabien Durbesson
- Architecture et Fonction des Macromolécules Biologiques (AFMB), Unité Mixte de Recherche (UMR) 7257, Centre National de la Recherche Scientifique (CNRS) Aix-Marseille Université, Marseille cedex 9, France
| | - Patrick Fourquet
- Université Aix-Marseille, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, Marseille, France
| | - Yves Nominé
- Équipe Labellisée Ligue 2015, Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, Illkirch, France
| | | | | | | | | | - Gilles Travé
- Équipe Labellisée Ligue 2015, Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, Illkirch, France
| | - Nicolas Wolff
- Unité Récepteurs-Canaux, Département of Neuroscience, CNRS UMR 3571, Institut Pasteur, Paris Cedex 15, France
| | - Renaud Vincentelli
- Architecture et Fonction des Macromolécules Biologiques (AFMB), Unité Mixte de Recherche (UMR) 7257, Centre National de la Recherche Scientifique (CNRS) Aix-Marseille Université, Marseille cedex 9, France.
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