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Langella O, Renne T, Balliau T, Davanture M, Brehmer S, Zivy M, Blein-Nicolas M, Rusconi F. Full Native timsTOF PASEF-Enabled Quantitative Proteomics with the i2MassChroQ Software Package. J Proteome Res 2024; 23:3353-3366. [PMID: 39016325 DOI: 10.1021/acs.jproteome.3c00732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
Ion mobility mass spectrometry has become popular in proteomics lately, in particular because the Bruker timsTOF instruments have found significant adoption in proteomics facilities. The Bruker's implementation of the ion mobility dimension generates massive amounts of mass spectrometric data that require carefully designed software both to extract meaningful information and to perform processing tasks at reasonable speed. In a historical move, the Bruker company decided to harness the skills of the scientific software development community by releasing to the public the timsTOF data file format specification. As a proteomics facility that has been developing Free Open Source Software (FOSS) solutions since decades, we took advantage of this opportunity to implement the very first FOSS proteomics complete solution to natively read the timsTOF data, low-level process them, and explore them in an integrated quantitative proteomics software environment. We dubbed our software i2MassChroQ because it implements a (peptide)identification-(protein)inference-mass-chromatogram-quantification processing workflow. The software benchmarking results reported in this paper show that i2MassChroQ performed better than competing software on two critical characteristics: (1) feature extraction capability and (2) protein quantitative dynamic range. Altogether, i2MassChroQ yielded better quantified protein numbers, both in a technical replicate MS runs setting and in a differential protein abundance analysis setting.
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Affiliation(s)
- Olivier Langella
- GQE-Le Moulon, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, IDEEV, 12, Route 128, Gif-sur-Yvette F-91272, France
| | - Thomas Renne
- GQE-Le Moulon, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, IDEEV, 12, Route 128, Gif-sur-Yvette F-91272, France
| | - Thierry Balliau
- GQE-Le Moulon, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, IDEEV, 12, Route 128, Gif-sur-Yvette F-91272, France
| | - Marlène Davanture
- GQE-Le Moulon, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, IDEEV, 12, Route 128, Gif-sur-Yvette F-91272, France
| | - Sven Brehmer
- Bruker Software Development, Bruker Daltonics GmbH & Co. KG, Bremen D-28359, Germany
| | - Michel Zivy
- GQE-Le Moulon, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, IDEEV, 12, Route 128, Gif-sur-Yvette F-91272, France
| | - Mélisande Blein-Nicolas
- GQE-Le Moulon, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, IDEEV, 12, Route 128, Gif-sur-Yvette F-91272, France
| | - Filippo Rusconi
- GQE-Le Moulon, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, IDEEV, 12, Route 128, Gif-sur-Yvette F-91272, France
- INSERM, UMR-S 1138, Centre de Recherche des Cordeliers, Paris F-75005, France
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2
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Perron T, Boissan M, Bièche I, Courtois L, Dingli F, Loew D, Chouchène M, Colasse S, Levy L, Prunier C. CYYR1 promotes the degradation of the E3 ubiquitin ligase WWP1 and is associated with favorable prognosis in breast cancer. J Biol Chem 2024; 300:107601. [PMID: 39059493 DOI: 10.1016/j.jbc.2024.107601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 06/26/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
Ubiquitination plays a crucial role in cellular homeostasis by regulating the degradation, localization, and activity of proteins, ensuring proper cell function and balance. Among E3 ubiquitin ligases, WW domain-containing protein 1 (WWP1) is implicated in cell proliferation, survival, and apoptosis. Notably WWP1 is frequently amplified in breast cancer and associated with poor prognosis. Here, we identify the protein cysteine and tyrosine-rich protein 1 (CYYR1) that had previously no assigned function, as a regulator of WWP1 activity and stability. We show that CYYR1 binds to the WW domains of the E3 ubiquitin ligase WWP1 through its PPxY motifs. This interaction triggers K63-linked autoubiquitination and subsequent degradation of WWP1. We furthermore demonstrate that CYYR1 localizes to late endosomal vesicles and directs polyubiquitinated WWP1 toward lysosomal degradation through binding to ANKyrin repeat domain-containing protein 13 A (ANKRD13A). Moreover, we found that CYYR1 expression attenuates breast cancer cell growth in anchorage-dependent and independent colony formation assays in a PPxY-dependent manner. Finally, we highlight that CYYR1 expression is significantly decreased in breast cancer and is associated with beneficial clinical outcome. Taken together our study suggests tumor suppressor properties for CYYR1 through regulation of WWP1 autoubiquitination and lysosomal degradation.
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Affiliation(s)
- Tiphaine Perron
- Sorbonne Université, INSERM UMR_S 938, Centre de Recherche Saint-Antoine, CRSA, Paris, France
| | - Mathieu Boissan
- Sorbonne Université, INSERM UMR_S 938, Centre de Recherche Saint-Antoine, CRSA, Paris, France; APHP, Hôpitaux Universitaires Pitié-Salpêtrière-Charles Foix, Laboratoire de Biochimie Endocrinienne et Oncologique, Oncobiologie Cellulaire et Moléculaire, Paris, France
| | - Ivan Bièche
- Department of Genetics, Institut Curie, Université Paris Cité, Paris, France
| | - Laura Courtois
- Department of Genetics, Institut Curie, Université Paris Cité, Paris, France
| | - Florent Dingli
- CurieCoreTech Mass Spectrometry Proteomics, Institut Curie, PSL Research University, Paris, France
| | - Damarys Loew
- CurieCoreTech Mass Spectrometry Proteomics, Institut Curie, PSL Research University, Paris, France
| | - Mouna Chouchène
- Sorbonne Université, INSERM UMR_S 938, Centre de Recherche Saint-Antoine, CRSA, Paris, France
| | - Sabrina Colasse
- Sorbonne Université, INSERM UMR_S 938, Centre de Recherche Saint-Antoine, CRSA, Paris, France
| | - Laurence Levy
- Sorbonne Université, INSERM UMR_S 938, Centre de Recherche Saint-Antoine, CRSA, Paris, France.
| | - Céline Prunier
- Sorbonne Université, INSERM UMR_S 938, Centre de Recherche Saint-Antoine, CRSA, Paris, France.
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Réthoré E, Pelletier S, Balliau T, Zivy M, Avelange-Macherel MH, Macherel D. Multi-scale analysis of heat stress acclimation in Arabidopsis seedlings highlights the primordial contribution of energy-transducing organelles. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:300-331. [PMID: 38613336 DOI: 10.1111/tpj.16763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 03/08/2024] [Accepted: 03/14/2024] [Indexed: 04/14/2024]
Abstract
Much progress has been made in understanding the molecular mechanisms of plant adaptation to heat stress. However, the great diversity of models and stress conditions, and the fact that analyses are often limited to a small number of approaches, complicate the picture. We took advantage of a liquid culture system in which Arabidopsis seedlings are arrested in their development, thus avoiding interference with development and drought stress responses, to investigate through an integrative approach seedlings' global response to heat stress and acclimation. Seedlings perfectly tolerate a noxious heat shock (43°C) when subjected to a heat priming treatment at a lower temperature (38°C) the day before, displaying a thermotolerance comparable to that previously observed for Arabidopsis. A major effect of the pre-treatment was to partially protect energy metabolism under heat shock and favor its subsequent rapid recovery, which was correlated with the survival of seedlings. Rapid recovery of actin cytoskeleton and mitochondrial dynamics were another landmark of heat shock tolerance. The omics confirmed the role of the ubiquitous heat shock response actors but also revealed specific or overlapping responses to priming, heat shock, and their combination. Since only a few components or functions of chloroplast and mitochondria were highlighted in these analyses, the preservation and rapid recovery of their bioenergetic roles upon acute heat stress do not require extensive remodeling of the organelles. Protection of these organelles is rather integrated into the overall heat shock response, thus allowing them to provide the energy required to elaborate other cellular responses toward acclimation.
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Affiliation(s)
- Elise Réthoré
- Univ Angers, Institut Agro Rennes-Angers, INRAE, IRHS-UMR 1345, F-49000, Angers, France
| | - Sandra Pelletier
- Univ Angers, Institut Agro Rennes-Angers, INRAE, IRHS-UMR 1345, F-49000, Angers, France
| | - Thierry Balliau
- INRAE, PAPPSO, UMR/UMR Génétique Végétale, Gif sur Yvette, France
| | - Michel Zivy
- INRAE, PAPPSO, UMR/UMR Génétique Végétale, Gif sur Yvette, France
| | | | - David Macherel
- Univ Angers, Institut Agro Rennes-Angers, INRAE, IRHS-UMR 1345, F-49000, Angers, France
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4
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Palmulli R, Couty M, Piontek MC, Ponnaiah M, Dingli F, Verweij FJ, Charrin S, Tantucci M, Sasidharan S, Rubinstein E, Kontush A, Loew D, Lhomme M, Roos WH, Raposo G, van Niel G. CD63 sorts cholesterol into endosomes for storage and distribution via exosomes. Nat Cell Biol 2024; 26:1093-1109. [PMID: 38886558 DOI: 10.1038/s41556-024-01432-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 05/01/2024] [Indexed: 06/20/2024]
Abstract
Extracellular vesicles such as exosomes are now recognized as key players in intercellular communication. Their role is influenced by the specific repertoires of proteins and lipids, which are enriched when they are generated as intraluminal vesicles (ILVs) in multivesicular endosomes. Here we report that a key component of small extracellular vesicles, the tetraspanin CD63, sorts cholesterol to ILVs, generating a pool that can be mobilized by the NPC1/2 complex, and exported via exosomes to recipient cells. In the absence of CD63, cholesterol is retrieved from the endosomes by actin-dependent vesicular transport, placing CD63 and cholesterol at the centre of a balance between inward and outward budding of endomembranes. These results establish CD63 as a lipid-sorting mechanism within endosomes, and show that ILVs and exosomes are alternative providers of cholesterol.
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Affiliation(s)
- Roberta Palmulli
- Institut Curie, PSL Research University, CNRS, UMR144, 26 rue d'Ulm, 75248, Paris Cedex 05, France
- Institute of Psychiatry and Neuroscience of Paris (IPNP), Université de Paris, Paris, France
| | - Mickaël Couty
- Institute of Psychiatry and Neuroscience of Paris (IPNP), Université de Paris, Paris, France
- CRCI2NA, Nantes Université, Inserm UMR1307, CNRS UMR6075, Université d'Angers, Nantes, France
| | - Melissa C Piontek
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, The Netherlands
| | - Maharajah Ponnaiah
- Foundation for Innovation in Cardiometabolism and Nutrition (IHU ICAN, ICAN OMICS and ICAN I/O), F-75013, Paris, France
| | - Florent Dingli
- CurieCoreTech Spectrométrie de Masse Protéomique, Institut Curie, PSL Research University, Paris, France
| | - Frederik J Verweij
- Institute of Psychiatry and Neuroscience of Paris (IPNP), Université de Paris, Paris, France
| | - Stéphanie Charrin
- Centre d'Immunologie et des Maladies Infectieuses (CIMI), Sorbonne Université, Inserm, Paris, France
| | - Matteo Tantucci
- Institute of Psychiatry and Neuroscience of Paris (IPNP), Université de Paris, Paris, France
| | - Sajitha Sasidharan
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, The Netherlands
| | - Eric Rubinstein
- Centre d'Immunologie et des Maladies Infectieuses (CIMI), Sorbonne Université, Inserm, Paris, France
| | - Anatol Kontush
- ICAN, National Institute for Health and Medical Research, Paris, France
| | - Damarys Loew
- CurieCoreTech Spectrométrie de Masse Protéomique, Institut Curie, PSL Research University, Paris, France
| | - Marie Lhomme
- Foundation for Innovation in Cardiometabolism and Nutrition (IHU ICAN, ICAN OMICS and ICAN I/O), F-75013, Paris, France
| | - Wouter H Roos
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, The Netherlands
| | - Graça Raposo
- Institut Curie, PSL Research University, CNRS, UMR144, 26 rue d'Ulm, 75248, Paris Cedex 05, France
- Institut Curie, PSL Research University, CNRS, UMR144, Cell and Tissue Imaging Facility (PICT-IBiSA), 26, rue d'Ulm, 75248, Paris Cedex 05, France
| | - Guillaume van Niel
- Institut Curie, PSL Research University, CNRS, UMR144, 26 rue d'Ulm, 75248, Paris Cedex 05, France.
- Institute of Psychiatry and Neuroscience of Paris (IPNP), Université de Paris, Paris, France.
- CRCI2NA, Nantes Université, Inserm UMR1307, CNRS UMR6075, Université d'Angers, Nantes, France.
- GHU-Paris Psychiatrie et Neurosciences, Hôpital Sainte Anne, Paris, France.
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5
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Diffendall G, Claes A, Barcons-Simon A, Nyarko P, Dingli F, Santos MM, Loew D, Claessens A, Scherf A. RNA polymerase III is involved in regulating Plasmodium falciparum virulence. eLife 2024; 13:RP95879. [PMID: 38921824 PMCID: PMC11208047 DOI: 10.7554/elife.95879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2024] Open
Abstract
While often undetected and untreated, persistent seasonal asymptomatic malaria infections remain a global public health problem. Despite the presence of parasites in the peripheral blood, no symptoms develop. Disease severity is correlated with the levels of infected red blood cells (iRBCs) adhering within blood vessels. Changes in iRBC adhesion capacity have been linked to seasonal asymptomatic malaria infections, however how this is occurring is still unknown. Here, we present evidence that RNA polymerase III (RNA Pol III) transcription in Plasmodium falciparum is downregulated in field isolates obtained from asymptomatic individuals during the dry season. Through experiments with in vitro cultured parasites, we have uncovered an RNA Pol III-dependent mechanism that controls pathogen proliferation and expression of a major virulence factor in response to external stimuli. Our findings establish a connection between P. falciparum cytoadhesion and a non-coding RNA family transcribed by Pol III. Additionally, we have identified P. falciparum Maf1 as a pivotal regulator of Pol III transcription, both for maintaining cellular homeostasis and for responding adaptively to external signals. These results introduce a novel perspective that contributes to our understanding of P. falciparum virulence. Furthermore, they establish a connection between this regulatory process and the occurrence of seasonal asymptomatic malaria infections.
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Affiliation(s)
- Gretchen Diffendall
- Institut Pasteur, Universite Paris CitéParisFrance
- Institut Pasteur, Sorbonne Université Ecole doctorale Complexité du VivantParisFrance
| | | | - Anna Barcons-Simon
- Institut Pasteur, Universite Paris CitéParisFrance
- Institut Pasteur, Sorbonne Université Ecole doctorale Complexité du VivantParisFrance
- Institut Pasteur, Biomedical Center, Division of Physiological Chemistry, Faculty of Medicine, Ludwig-Maximilians-Universität MünchenMunichGermany
| | - Prince Nyarko
- Institut Pasteur, Laboratory of Pathogen-Host Interaction (LPHI), CNRS, University of MontpellierMontpellierFrance
| | - Florent Dingli
- Institut Pasteur, Institut Curie, PSL Research University, Centre de Recherche, CurieCoreTech Mass Spectrometry ProteomicsParisFrance
| | - Miguel M Santos
- Institut Pasteur, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de LisboaLisboaPortugal
| | - Damarys Loew
- Institut Pasteur, Institut Curie, PSL Research University, Centre de Recherche, CurieCoreTech Mass Spectrometry ProteomicsParisFrance
| | - Antoine Claessens
- Institut Pasteur, Laboratory of Pathogen-Host Interaction (LPHI), CNRS, University of MontpellierMontpellierFrance
- Institut Pasteur, LPHI, MIVEGEC, CNRS, INSERM, University of MontpellierMontpellierFrance
| | - Artur Scherf
- Institut Pasteur, Universite Paris CitéParisFrance
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6
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Pichol-Thievend C, Anezo O, Pettiwala AM, Bourmeau G, Montagne R, Lyne AM, Guichet PO, Deshors P, Ballestín A, Blanchard B, Reveilles J, Ravi VM, Joseph K, Heiland DH, Julien B, Leboucher S, Besse L, Legoix P, Dingli F, Liva S, Loew D, Giani E, Ribecco V, Furumaya C, Marcos-Kovandzic L, Masliantsev K, Daubon T, Wang L, Diaz AA, Schnell O, Beck J, Servant N, Karayan-Tapon L, Cavalli FMG, Seano G. VC-resist glioblastoma cell state: vessel co-option as a key driver of chemoradiation resistance. Nat Commun 2024; 15:3602. [PMID: 38684700 PMCID: PMC11058782 DOI: 10.1038/s41467-024-47985-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 04/17/2024] [Indexed: 05/02/2024] Open
Abstract
Glioblastoma (GBM) is a highly lethal type of cancer. GBM recurrence following chemoradiation is typically attributed to the regrowth of invasive and resistant cells. Therefore, there is a pressing need to gain a deeper understanding of the mechanisms underlying GBM resistance to chemoradiation and its ability to infiltrate. Using a combination of transcriptomic, proteomic, and phosphoproteomic analyses, longitudinal imaging, organotypic cultures, functional assays, animal studies, and clinical data analyses, we demonstrate that chemoradiation and brain vasculature induce cell transition to a functional state named VC-Resist (vessel co-opting and resistant cell state). This cell state is midway along the transcriptomic axis between proneural and mesenchymal GBM cells and is closer to the AC/MES1-like state. VC-Resist GBM cells are highly vessel co-opting, allowing significant infiltration into the surrounding brain tissue and homing to the perivascular niche, which in turn induces even more VC-Resist transition. The molecular and functional characteristics of this FGFR1-YAP1-dependent GBM cell state, including resistance to DNA damage, enrichment in the G2M phase, and induction of senescence/stemness pathways, contribute to its enhanced resistance to chemoradiation. These findings demonstrate how vessel co-option, perivascular niche, and GBM cell plasticity jointly drive resistance to therapy during GBM recurrence.
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Affiliation(s)
- Cathy Pichol-Thievend
- Institut Curie, INSERM U1021, CNRS UMR3347, Tumor Microenvironment Lab, Paris-Saclay University, 91400, Orsay, France
| | - Oceane Anezo
- Institut Curie, INSERM U1021, CNRS UMR3347, Tumor Microenvironment Lab, Paris-Saclay University, 91400, Orsay, France
| | - Aafrin M Pettiwala
- Institut Curie, INSERM U1021, CNRS UMR3347, Tumor Microenvironment Lab, Paris-Saclay University, 91400, Orsay, France
- Institut Curie, PSL University, 75005, Paris, France
| | - Guillaume Bourmeau
- Institut Curie, INSERM U1021, CNRS UMR3347, Tumor Microenvironment Lab, Paris-Saclay University, 91400, Orsay, France
| | - Remi Montagne
- Institut Curie, PSL University, 75005, Paris, France
- INSERM U900, 75005, Paris, France
- MINES ParisTeach, CBIO-Centre for Computational Biology, PSL Research University, 75006, Paris, France
| | - Anne-Marie Lyne
- Institut Curie, PSL University, 75005, Paris, France
- INSERM U900, 75005, Paris, France
- MINES ParisTeach, CBIO-Centre for Computational Biology, PSL Research University, 75006, Paris, France
| | - Pierre-Olivier Guichet
- Université de Poitiers, CHU Poitiers, ProDiCeT, F-86000, Poitiers, France
- CHU Poitiers, Laboratoire de Cancérologie Biologique, F-86000, Poitiers, France
| | - Pauline Deshors
- Institut Curie, INSERM U1021, CNRS UMR3347, Tumor Microenvironment Lab, Paris-Saclay University, 91400, Orsay, France
| | - Alberto Ballestín
- Institut Curie, INSERM U1021, CNRS UMR3347, Tumor Microenvironment Lab, Paris-Saclay University, 91400, Orsay, France
| | - Benjamin Blanchard
- Institut Curie, INSERM U1021, CNRS UMR3347, Tumor Microenvironment Lab, Paris-Saclay University, 91400, Orsay, France
| | - Juliette Reveilles
- Institut Curie, INSERM U1021, CNRS UMR3347, Tumor Microenvironment Lab, Paris-Saclay University, 91400, Orsay, France
| | - Vidhya M Ravi
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany
| | - Kevin Joseph
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany
| | - Dieter H Heiland
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany
| | - Boris Julien
- Institut Curie, INSERM U1021, CNRS UMR3347, Tumor Microenvironment Lab, Paris-Saclay University, 91400, Orsay, France
| | | | - Laetitia Besse
- Institut Curie, PSL University, Université Paris-Saclay, CNRS UMS2016, INSERM US43, Multimodal Imaging Center, 91400, Orsay, France
| | - Patricia Legoix
- Institut Curie, PSL University, ICGex Next-Generation Sequencing Platform, 75005, Paris, France
| | - Florent Dingli
- Institut Curie, PSL University, CurieCoreTech Spectrométrie de Masse Protéomique, 75005, Paris, France
| | - Stephane Liva
- Institut Curie, PSL University, 75005, Paris, France
- INSERM U900, 75005, Paris, France
- MINES ParisTeach, CBIO-Centre for Computational Biology, PSL Research University, 75006, Paris, France
| | - Damarys Loew
- Institut Curie, PSL University, CurieCoreTech Spectrométrie de Masse Protéomique, 75005, Paris, France
| | - Elisa Giani
- Department of Biomedical Sciences, Humanitas University, 20072, Pieve Emanuele, Italy
| | - Valentino Ribecco
- Institut Curie, INSERM U1021, CNRS UMR3347, Tumor Microenvironment Lab, Paris-Saclay University, 91400, Orsay, France
| | - Charita Furumaya
- Institut Curie, INSERM U1021, CNRS UMR3347, Tumor Microenvironment Lab, Paris-Saclay University, 91400, Orsay, France
| | - Laura Marcos-Kovandzic
- Institut Curie, INSERM U1021, CNRS UMR3347, Tumor Microenvironment Lab, Paris-Saclay University, 91400, Orsay, France
| | - Konstantin Masliantsev
- Université de Poitiers, CHU Poitiers, ProDiCeT, F-86000, Poitiers, France
- CHU Poitiers, Laboratoire de Cancérologie Biologique, F-86000, Poitiers, France
| | - Thomas Daubon
- Université Bordeaux, CNRS, IBGC, UMR5095, Bordeaux, France
| | - Lin Wang
- Department of Computational and Quantitative Medicine, Hematologic Malignancies Research Institute and Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Aaron A Diaz
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Oliver Schnell
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany
| | - Jürgen Beck
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany
| | - Nicolas Servant
- Institut Curie, PSL University, 75005, Paris, France
- INSERM U900, 75005, Paris, France
- MINES ParisTeach, CBIO-Centre for Computational Biology, PSL Research University, 75006, Paris, France
| | - Lucie Karayan-Tapon
- Université de Poitiers, CHU Poitiers, ProDiCeT, F-86000, Poitiers, France
- CHU Poitiers, Laboratoire de Cancérologie Biologique, F-86000, Poitiers, France
| | - Florence M G Cavalli
- Institut Curie, PSL University, 75005, Paris, France
- INSERM U900, 75005, Paris, France
- MINES ParisTeach, CBIO-Centre for Computational Biology, PSL Research University, 75006, Paris, France
| | - Giorgio Seano
- Institut Curie, INSERM U1021, CNRS UMR3347, Tumor Microenvironment Lab, Paris-Saclay University, 91400, Orsay, France.
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7
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Ravichandran Y, Hänisch J, Murray K, Roca V, Dingli F, Loew D, Sabatet V, Boëda B, Stradal TE, Etienne-Manneville S. The distinct localization of CDC42 isoforms is responsible for their specific functions during migration. J Cell Biol 2024; 223:e202004092. [PMID: 38386112 PMCID: PMC10883850 DOI: 10.1083/jcb.202004092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 07/26/2023] [Accepted: 01/04/2024] [Indexed: 02/23/2024] Open
Abstract
The small G-protein CDC42 is an evolutionary conserved polarity protein and a key regulator of polarized cell functions, including directed cell migration. In vertebrates, alternative splicing gives rise to two CDC42 proteins: the ubiquitously expressed isoform (CDC42u) and the brain isoform (CDC42b), which only differ in their carboxy-terminal sequence, including the CAAX motif essential for their association with membranes. We show that these divergent sequences do not directly affect the range of CDC42's potential binding partners but indirectly influence CDC42-driven signaling by controlling the subcellular localization of the two isoforms. In astrocytes and neural precursors, which naturally express both variants, CDC42u associates with the leading-edge plasma membrane of migrating cells, where it recruits the Par6-PKCζ complex to fulfill its polarity function. In contrast, CDC42b mainly localizes to intracellular membrane compartments, where it regulates N-WASP-mediated endocytosis. Both CDC42 isoforms contribute their specific functions to promote the chemotaxis of neural precursors, demonstrating that their expression pattern is decisive for tissue-specific cell behavior.
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Affiliation(s)
- Yamini Ravichandran
- UMR3691 CNRS, Equipe Labellisée Ligue 2023, Université de Paris, Cell Polarity, Migration and Cancer Unit, Institut Pasteur, Paris, France
- Collège Doctoral, Sorbonne Université, Paris, France
| | - Jan Hänisch
- UMR3691 CNRS, Equipe Labellisée Ligue 2023, Université de Paris, Cell Polarity, Migration and Cancer Unit, Institut Pasteur, Paris, France
| | - Kerren Murray
- UMR3691 CNRS, Equipe Labellisée Ligue 2023, Université de Paris, Cell Polarity, Migration and Cancer Unit, Institut Pasteur, Paris, France
| | - Vanessa Roca
- UMR3691 CNRS, Equipe Labellisée Ligue 2023, Université de Paris, Cell Polarity, Migration and Cancer Unit, Institut Pasteur, Paris, France
| | - Florent Dingli
- PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Institut Curie, Paris, France
| | - Damarys Loew
- PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Institut Curie, Paris, France
| | - Valentin Sabatet
- PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Institut Curie, Paris, France
| | - Batiste Boëda
- UMR3691 CNRS, Equipe Labellisée Ligue 2023, Université de Paris, Cell Polarity, Migration and Cancer Unit, Institut Pasteur, Paris, France
| | - Theresia E. Stradal
- Helmholtz Centre for Infection Research, Inhoffenstrasse 7, Braunschweig, Germany
| | - Sandrine Etienne-Manneville
- UMR3691 CNRS, Equipe Labellisée Ligue 2023, Université de Paris, Cell Polarity, Migration and Cancer Unit, Institut Pasteur, Paris, France
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8
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Voedts H, Anoyatis-Pelé C, Langella O, Rusconi F, Hugonnet JE, Arthur M. (p)ppGpp modifies RNAP function to confer β-lactam resistance in a peptidoglycan-independent manner. Nat Microbiol 2024; 9:647-656. [PMID: 38443580 DOI: 10.1038/s41564-024-01609-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 01/16/2024] [Indexed: 03/07/2024]
Abstract
(p)ppGpp is a nucleotide alarmone that controls bacterial response to nutrient deprivation. Since elevated (p)ppGpp levels confer mecillinam resistance and are essential for broad-spectrum β-lactam resistance as mediated by the β-lactam-insensitive transpeptidase YcbB (LdtD), we hypothesized that (p)ppGpp might affect cell wall peptidoglycan metabolism. Here we report that (p)ppGpp-dependent β-lactam resistance does not rely on any modification of peptidoglycan metabolism, as established by analysis of Escherichia coli peptidoglycan structure using high-resolution mass spectrometry. Amino acid substitutions in the β or β' RNA polymerase (RNAP) subunits, alone or in combination with the CRISPR interference-mediated downregulation of three of seven ribosomal RNA operons, were sufficient for resistance, although β-lactams have no known impact on the RNAP or ribosomes. This implies that modifications of RNAP and ribosome functions are critical to prevent downstream effects of the inactivation of peptidoglycan transpeptidases by β-lactams.
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Affiliation(s)
- Henri Voedts
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université Paris Cité, Paris, France
| | - Constantin Anoyatis-Pelé
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université Paris Cité, Paris, France
| | - Olivier Langella
- GQE-Le Moulon/PAPPSO, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, IDEEV, Gif-sur-Yvette, France
| | - Filippo Rusconi
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université Paris Cité, Paris, France
- GQE-Le Moulon/PAPPSO, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, IDEEV, Gif-sur-Yvette, France
| | - Jean-Emmanuel Hugonnet
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université Paris Cité, Paris, France.
| | - Michel Arthur
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, Université Paris Cité, Paris, France.
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9
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Romo BA, Karakyriakou B, Cressey L, Brauer BL, Yang H, Warren A, Johnson AL, Kettenbach AN, Miller TW. TRIM33 Is a Co-Regulator of Estrogen Receptor Alpha. Cancers (Basel) 2024; 16:845. [PMID: 38473207 PMCID: PMC10930732 DOI: 10.3390/cancers16050845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/15/2024] [Accepted: 02/17/2024] [Indexed: 03/14/2024] Open
Abstract
Estrogen receptor alpha (ER)-positive breast cancer is responsible for over 60% of breast cancer cases in the U.S. Among patients diagnosed with early-stage ER+ disease, 1/3 will experience recurrence despite treatment with adjuvant endocrine therapy. ER is a nuclear hormone receptor responsible for estrogen-driven tumor growth. ER transcriptional activity is modulated by interactions with coregulators. Dysregulation of the levels of these coregulators is involved in the development of endocrine resistance. To identify ER interactors that modulate transcriptional activity in breast cancer, we utilized biotin ligase proximity profiling of ER interactomes. Mass spectrometry analysis revealed tripartite motif containing 33 (TRIM33) as an estrogen-dependent interactor of ER. shRNA knockdown showed that TRIM33 promoted ER transcriptional activity and estrogen-induced cell growth. Despite its known role as an E3 ubiquitin ligase, TRIM33 increased the stability of endogenous ER in breast cancer cells. TRIM33 offers a novel target for inhibiting estrogen-induced cancer cell growth, particularly in cases of endocrine resistance driven by ER (ESR1) gene amplification or overexpression.
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Affiliation(s)
- Bianca A. Romo
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03755, USA
| | - Barbara Karakyriakou
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03755, USA
| | - Lauren Cressey
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03755, USA
| | - Brooke L. Brauer
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03755, USA
| | - Huijuan Yang
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03755, USA
| | - Alexa Warren
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03755, USA
| | - Anneka L. Johnson
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03755, USA
| | - Arminja N. Kettenbach
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03755, USA
| | - Todd W. Miller
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03755, USA
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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10
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Kruse T, Garvanska DH, Varga J, Garland W, McEwan B, Hein JB, Weisser MB, Puy IB, Chan CB, Parrila PS, Mendez BL, Arulanandam J, Schueler-Furman O, Jensen TH, Kettenbach A, Nilsson J. Substrate recognition principles for the PP2A-B55 protein phosphatase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.10.579793. [PMID: 38370611 PMCID: PMC10871369 DOI: 10.1101/2024.02.10.579793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
The PP2A-B55 phosphatase regulates a plethora of signaling pathways throughout eukaryotes. How PP2A-B55 selects its substrates presents a severe knowledge gap. By integrating AlphaFold modelling with comprehensive high resolution mutational scanning, we show that α-helices in substrates bind B55 through an evolutionary conserved mechanism. Despite a large diversity in sequence and composition, these α-helices share key amino acid determinants that engage discrete hydrophobic and electrostatic patches. Using deep learning protein design, we generate a specific and potent competitive peptide inhibitor of PP2A-B55 substrate interactions. With this inhibitor, we uncover that PP2A-B55 regulates the nuclear exosome targeting complex by binding to an α-helical recruitment module in RBM7. Collectively, our findings provide a framework for the understanding and interrogation of PP2A-B55 in health and disease.
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Affiliation(s)
- Thomas Kruse
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Dimitriya H Garvanska
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Julia Varga
- Department of Microbiology and Molecular Genetics, Institute for Biomedical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 9112001, Israel
| | - William Garland
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Brennan McEwan
- Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
| | - Jamin B Hein
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200 Copenhagen, Denmark
- Current address: Amgen Research Copenhagen, Rønnegade 8, 5, 2100 Copenhagen, Denmark
| | - Melanie Bianca Weisser
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Iker Benavides Puy
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Camilla Bachman Chan
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Paula Sotelo Parrila
- Gene Center Munich, Ludwig-Maximilians- Universität München, Munich, 81377, Germany
| | - Blanca Lopez Mendez
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Jeyaprakash Arulanandam
- Gene Center Munich, Ludwig-Maximilians- Universität München, Munich, 81377, Germany
- Wellcome Centre for Cell Biology, University of Edinburg, Edinburgh, EH9 3BF, UK
| | - Ora Schueler-Furman
- Department of Microbiology and Molecular Genetics, Institute for Biomedical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 9112001, Israel
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Arminja Kettenbach
- Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
| | - Jakob Nilsson
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200 Copenhagen, Denmark
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11
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Tarkowski ŁP, Clochard T, Blein-Nicolas M, Zivy M, Baillau T, Abadie C, Morère-Le Paven MC, Limami AM, Tcherkez G, Montrichard F. The nitrate transporter-sensor MtNPF6.8 regulates the branched chain amino acid/pantothenate metabolic pathway in barrel medic (Medicago truncatula Gaertn.) root tip. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108213. [PMID: 38043253 DOI: 10.1016/j.plaphy.2023.108213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 11/02/2023] [Accepted: 11/19/2023] [Indexed: 12/05/2023]
Abstract
Nitrogen is the most limiting nutrient for plants, and it is preferentially absorbed in the form of nitrate by roots, which adapt to nitrate fluctuations by remodelling their architecture. Although core mechanisms of the response to nitrate availability are relatively well-known, signalling events controlling root growth and architecture have not all been identified, in particular in Legumes. However, the developmental effect of nitrate in Legumes is critical since external nitrate not only regulates root architecture but also N2-fixing nodule development. We have previously shown that in barrel medic (Medicago truncatula), the nitrate transporter MtNPF6.8 is required for nitrate sensitivity in root tip. However, uncertainty remains as to whether nitrogen metabolism itself is involved in the MtNPF6.8-mediated response. Here, we examine the metabolic effects of MtNPF6.8-dependent nitrate signalling using metabolomics and proteomics in WT and mtnpf6.8 root tips in presence or absence of nitrate. We found a reorchestration of metabolism due to the mutation, in favour of the branched chain amino acids/pantothenate metabolic pathway, and lipid catabolism via glyoxylate. That is, the mtnpf6.8 mutation was likely associated with a specific rerouting of acetyl-CoA production (glyoxylic cycle) and utilisation (pantothenate and branched chain amino acid synthesis). In agreement with our previous findings, class III peroxidases were confirmed as the main protein class responsive to nitrate, although in an MtNPF6.8-independent fashion. Our data rather suggest the involvement of other pathways within mtnpf6.8 root tips, such as Ca2+ signalling or cell wall methylation.
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Affiliation(s)
| | | | - Mélisande Blein-Nicolas
- GQE - Le Moulon, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Gif-sur-Yvette, France
| | - Michel Zivy
- GQE - Le Moulon, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Gif-sur-Yvette, France
| | - Thierry Baillau
- GQE - Le Moulon, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Gif-sur-Yvette, France
| | - Cyril Abadie
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | | | - Anis M Limami
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France
| | - Guillaume Tcherkez
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, France; Research School of Biology, ANU Joint College of Sciences, Australian National University, Canberra, Australia
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12
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Ngom SI, Maski S, Rached B, Chouati T, Oliveira Correia L, Juste C, Meylheuc T, Henrissat B, El Fahime E, Amar M, Béra-Maillet C. Exploring the hemicellulolytic properties and safety of Bacillus paralicheniformis as stepping stone in the use of new fibrolytic beneficial microbes. Sci Rep 2023; 13:22785. [PMID: 38129471 PMCID: PMC10740013 DOI: 10.1038/s41598-023-49724-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023] Open
Abstract
Bacillus strains from the Moroccan Coordinated Collections of Microorganisms (CCMM) were characterised and tested for fibrolytic function and safety properties that would be beneficial for maintaining intestinal homeostasis, and recommend beneficial microbes in the field of health promotion research. Forty strains were investigated for their fibrolytic activities towards complex purified polysaccharides and natural fibres representative of dietary fibres (DFs) entering the colon for digestion. We demonstrated hemicellulolytic activities for nine strains of Bacillus aerius, re-identified as Bacillus paralicheniformis and Bacillus licheniformis, using xylan, xyloglucan or lichenan as purified polysaccharides, and orange, apple and carrot natural fibres, with strain- and substrate-dependent production of glycoside hydrolases (GHs). Our combined methods, based on enzymatic assays, secretome, and genome analyses, highlighted the hemicellulolytic activities of B. paralicheniformis and the secretion of specific glycoside hydrolases, in particular xylanases, compared to B. licheniformis. Genomic features of these strains revealed a complete set of GH genes dedicated to the degradation of various polysaccharides from DFs, including cellulose, hemicellulose and pectin, which may confer on the strains the ability to digest a variety of DFs. Preliminary experiments on the safety and immunomodulatory properties of B. paralicheniformis fibrolytic strains were evaluated in light of applications as beneficial microbes' candidates for health improvement. B. paralicheniformis CCMM B969 was therefore proposed as a new fibrolytic beneficial microbe candidate.
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Affiliation(s)
- Serigne Inssa Ngom
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Soufiane Maski
- Laboratoire de Microbiologie et Biologie Moléculaire, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Département de Biologie, Faculté des Sciences, Université Mohammed V, Rabat, Morocco
| | - Bahia Rached
- Collections Coordonnées Marocaines de Microorganismes, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Plateforme Génomique Fonctionnelle, Unité d'Appui Technique à la Recherche Scientifique, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Laboratoire de Chimie-Physique et Biotechnologies des Biomolécules et Matériaux/Equipe Microbiologie Biomolécules et Biotechnologies, Faculté des Sciences et Techniques, Mohammedia, Morocco
| | - Taha Chouati
- Collections Coordonnées Marocaines de Microorganismes, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Plateforme Génomique Fonctionnelle, Unité d'Appui Technique à la Recherche Scientifique, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Biologie médicale, Pathologie humaine et Expérimentale et Environnement, Faculté de Médecine et de pharmacie de Rabat, Rabat, Morocco
| | - Lydie Oliveira Correia
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, PAPPSO, 78350, Jouy-en-Josas, France
| | - Catherine Juste
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Thierry Meylheuc
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, MIMA2, 78350, Jouy en Josas, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, Aix-Marseille Université, 13288, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Elmostafa El Fahime
- Plateforme Génomique Fonctionnelle, Unité d'Appui Technique à la Recherche Scientifique, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Biologie médicale, Pathologie humaine et Expérimentale et Environnement, Faculté de Médecine et de pharmacie de Rabat, Rabat, Morocco
| | - Mohamed Amar
- Laboratoire de Microbiologie et Biologie Moléculaire, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Collections Coordonnées Marocaines de Microorganismes, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
| | - Christel Béra-Maillet
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France.
- Laboratoire de Microbiologie et Biologie Moléculaire, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco.
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13
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Cocozza F, Martin‐Jaular L, Lippens L, Di Cicco A, Arribas YA, Ansart N, Dingli F, Richard M, Merle L, Jouve San Roman M, Poullet P, Loew D, Lévy D, Hendrix A, Kassiotis G, Joliot A, Tkach M, Théry C. Extracellular vesicles and co-isolated endogenous retroviruses from murine cancer cells differentially affect dendritic cells. EMBO J 2023; 42:e113590. [PMID: 38073509 PMCID: PMC10711651 DOI: 10.15252/embj.2023113590] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 10/31/2023] [Accepted: 11/02/2023] [Indexed: 12/18/2023] Open
Abstract
Cells secrete extracellular vesicles (EVs) and non-vesicular extracellular (nano)particles (NVEPs or ENPs) that may play a role in intercellular communication. Tumor-derived EVs have been proposed to induce immune priming of antigen presenting cells or to be immuno-suppressive agents. We suspect that such disparate functions are due to variable compositions in EV subtypes and ENPs. We aimed to characterize the array of secreted EVs and ENPs of murine tumor cell lines. Unexpectedly, we identified virus-like particles (VLPs) from endogenous murine leukemia virus in preparations of EVs produced by many tumor cells. We established a protocol to separate small EVs from VLPs and ENPs. We compared their protein composition and analyzed their functional interaction with target dendritic cells. ENPs were poorly captured and did not affect dendritic cells. Small EVs specifically induced dendritic cell death. A mixed large/dense EV/VLP preparation was most efficient to induce dendritic cell maturation and antigen presentation. Our results call for systematic re-evaluation of the respective proportions and functions of non-viral EVs and VLPs produced by murine tumors and their contribution to tumor progression.
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Affiliation(s)
- Federico Cocozza
- INSERM U932, Institut Curie Centre de Recherche, PSL Research UniversityParisFrance
- Université de ParisParisFrance
| | - Lorena Martin‐Jaular
- INSERM U932, Institut Curie Centre de Recherche, PSL Research UniversityParisFrance
- Institut Curie Centre de RechercheCurieCoreTech Extracellular VesiclesParisFrance
| | - Lien Lippens
- Laboratory of Experimental Cancer Research, Department of Human Structure and RepairGhent University, and Cancer Research Institute GhentGhentBelgium
| | - Aurelie Di Cicco
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, Laboratoire Physico‐chimie CurieParisFrance
- Institut Curie, PSL Research University, CNRS UMR144, Cell and Tissue Imaging Facility (PICT‐IBiSA)ParisFrance
| | - Yago A Arribas
- INSERM U932, Institut Curie Centre de Recherche, PSL Research UniversityParisFrance
| | - Nicolas Ansart
- INSERM U932, Institut Curie Centre de Recherche, PSL Research UniversityParisFrance
| | - Florent Dingli
- Institut Curie, PSL Research University, Centre de Recherche, CurieCoreTech Spectrométrie de Masse ProtéomiqueParisFrance
| | - Michael Richard
- Institut Curie, PSL Research University, Centre de Recherche, CurieCoreTech Spectrométrie de Masse ProtéomiqueParisFrance
| | - Louise Merle
- INSERM U932, Institut Curie Centre de Recherche, PSL Research UniversityParisFrance
| | | | - Patrick Poullet
- Institut Curie, Bioinformatics core facility (CUBIC), INSERM U900, PSL Research University, Mines Paris TechParisFrance
| | - Damarys Loew
- Institut Curie, PSL Research University, Centre de Recherche, CurieCoreTech Spectrométrie de Masse ProtéomiqueParisFrance
| | - Daniel Lévy
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, Laboratoire Physico‐chimie CurieParisFrance
- Institut Curie, PSL Research University, CNRS UMR144, Cell and Tissue Imaging Facility (PICT‐IBiSA)ParisFrance
| | - An Hendrix
- Laboratory of Experimental Cancer Research, Department of Human Structure and RepairGhent University, and Cancer Research Institute GhentGhentBelgium
| | - George Kassiotis
- Retroviral Immunology, The Francis Crick Institute and Department of Medicine, Faculty of MedicineImperial CollegeLondonUK
| | - Alain Joliot
- INSERM U932, Institut Curie Centre de Recherche, PSL Research UniversityParisFrance
| | - Mercedes Tkach
- INSERM U932, Institut Curie Centre de Recherche, PSL Research UniversityParisFrance
| | - Clotilde Théry
- INSERM U932, Institut Curie Centre de Recherche, PSL Research UniversityParisFrance
- Institut Curie Centre de RechercheCurieCoreTech Extracellular VesiclesParisFrance
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14
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Hein JB, Nguyen HT, Garvanska DH, Nasa I, Kruse T, Feng Y, Lopez Mendez B, Davey N, Kettenbach AN, Fordyce PM, Nilsson J. Phosphatase specificity principles uncovered by MRBLE:Dephos and global substrate identification. Mol Syst Biol 2023; 19:e11782. [PMID: 37916966 PMCID: PMC10698503 DOI: 10.15252/msb.202311782] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 10/14/2023] [Accepted: 10/16/2023] [Indexed: 11/03/2023] Open
Abstract
Phosphoprotein phosphatases (PPPs) regulate major signaling pathways, but the determinants of phosphatase specificity are poorly understood. This is because methods to investigate this at scale are lacking. Here, we develop a novel in vitro assay, MRBLE:Dephos, that allows multiplexing of dephosphorylation reactions to determine phosphatase preferences. Using MRBLE:Dephos, we establish amino acid preferences of the residues surrounding the dephosphorylation site for PP1 and PP2A-B55, which reveals common and unique preferences. To compare the MRBLE:Dephos results to cellular substrates, we focused on mitotic exit that requires extensive dephosphorylation by PP1 and PP2A-B55. We use specific inhibition of PP1 and PP2A-B55 in mitotic exit lysates coupled with phosphoproteomics to identify more than 2,000 regulated sites. Importantly, the sites dephosphorylated during mitotic exit reveal key signatures that are consistent with MRBLE:Dephos. Furthermore, integration of our phosphoproteomic data with mitotic interactomes of PP1 and PP2A-B55 provides insight into how binding of phosphatases to substrates shapes dephosphorylation. Collectively, we develop novel approaches to investigate protein phosphatases that provide insight into mitotic exit regulation.
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Affiliation(s)
- Jamin B Hein
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
- Department of BioengineeringStanford UniversityStanfordCAUSA
| | - Hieu T Nguyen
- Biochemistry and Cell BiologyGeisel School of Medicine at Dartmouth CollegeHanoverNHUSA
| | - Dimitriya H Garvanska
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Isha Nasa
- Department of BioengineeringStanford UniversityStanfordCAUSA
| | - Thomas Kruse
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Yinnian Feng
- Department of GeneticsStanford UniversityStanfordCAUSA
| | - Blanca Lopez Mendez
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Norman Davey
- Division of Cancer BiologyThe Institute of Cancer ResearchLondonUK
| | - Arminja N Kettenbach
- Biochemistry and Cell BiologyGeisel School of Medicine at Dartmouth CollegeHanoverNHUSA
| | - Polly M Fordyce
- Department of BioengineeringStanford UniversityStanfordCAUSA
- Department of GeneticsStanford UniversityStanfordCAUSA
- Sarafan ChEM‐HStanford UniversityStanfordCAUSA
- Chan Zuckerberg BiohubSan FranciscoCAUSA
| | - Jakob Nilsson
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
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15
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Berg P, Popescu G. Baldur: Bayesian Hierarchical Modeling for Label-Free Proteomics with Gamma Regressing Mean-Variance Trends. Mol Cell Proteomics 2023; 22:100658. [PMID: 37806340 PMCID: PMC10687340 DOI: 10.1016/j.mcpro.2023.100658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 09/20/2023] [Accepted: 10/04/2023] [Indexed: 10/10/2023] Open
Abstract
Label-free proteomics is a fast-growing methodology to infer abundances in mass spectrometry proteomics. Extensive research has focused on spectral quantification and peptide identification. However, research toward modeling and understanding quantitative proteomics data is scarce. Here we propose a Bayesian hierarchical decision model (Baldur) to test for differences in means between conditions for proteins, peptides, and post-translational modifications. We developed a Bayesian regression model to characterize local mean-variance trends in data, to estimate measurement uncertainty and hyperparameters for the decision model. A key contribution is the development of a new gamma regression model that describes the mean-variance dependency as a mixture of a common and a latent trend-allowing for localized trend estimates. We then evaluate the performance of Baldur, limma-trend, and t test on six benchmark datasets: five total proteomics and one post-translational modification dataset. We find that Baldur drastically improves the decision in noisier post-translational modification data over limma-trend and t test. In addition, we see significant improvements using Baldur over the other methods in the total proteomics datasets. Finally, we analyzed Baldur's performance when increasing the number of replicates and found that the method always increases precision with sample size, while showing robust control of the false positive rate. We conclude that our model vastly improves over popular data analysis methods (limma-trend and t test) in several spike-in datasets by achieving a high true positive detection rate, while greatly reducing the false-positive rate.
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Affiliation(s)
- Philip Berg
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, Mississippi, USA; Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, Mississippi, USA.
| | - George Popescu
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, Mississippi, USA; Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, Mississippi, USA.
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Kovacs MT, Vallette M, Wiertsema P, Dingli F, Loew D, Nader GPDF, Piel M, Ceccaldi R. DNA damage induces nuclear envelope rupture through ATR-mediated phosphorylation of lamin A/C. Mol Cell 2023; 83:3659-3668.e10. [PMID: 37832547 PMCID: PMC10597398 DOI: 10.1016/j.molcel.2023.09.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 08/01/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023]
Abstract
The integrity of the nuclear envelope (NE) is essential for maintaining the structural stability of the nucleus. Rupture of the NE has been frequently observed in cancer cells, especially in the context of mechanical challenges, such as physical confinement and migration. However, spontaneous NE rupture events, without any obvious physical challenges to the cell, have also been described. The molecular mechanism(s) of these spontaneous NE rupture events remain to be explored. Here, we show that DNA damage and subsequent ATR activation leads to NE rupture. Upon DNA damage, lamin A/C is phosphorylated in an ATR-dependent manner, leading to changes in lamina assembly and, ultimately, NE rupture. In addition, we show that cancer cells with intrinsic DNA repair defects undergo frequent events of DNA-damage-induced NE rupture, which renders them extremely sensitive to further NE perturbations. Exploiting this NE vulnerability could provide a new angle to complement traditional, DNA-damage-based chemotherapy.
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Affiliation(s)
| | - Marie Vallette
- Inserm U830, PSL Research University, Institut Curie, 75005 Paris, France
| | - Pauline Wiertsema
- Inserm U830, PSL Research University, Institut Curie, 75005 Paris, France
| | - Florent Dingli
- Institut Curie, PSL Research University, Centre de Recherche, CurieCoreTech Spectrométrie de Masse Protéomique, 26 rue d'Ulm, Paris 75248 Cedex 05, France
| | - Damarys Loew
- Institut Curie, PSL Research University, Centre de Recherche, CurieCoreTech Spectrométrie de Masse Protéomique, 26 rue d'Ulm, Paris 75248 Cedex 05, France
| | | | - Matthieu Piel
- Institut Curie and Institut Pierre Gilles de Gennes, PSL Research University, CNRS, UMR 144, Paris, France
| | - Raphael Ceccaldi
- Inserm U830, PSL Research University, Institut Curie, 75005 Paris, France.
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17
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Lavoisier A, Morzel M, Chevalier S, Henry G, Jardin J, Harel-Oger M, Garric G, Dupont D. In vitro digestion of two protein-rich dairy products in the ageing gastrointestinal tract. Food Funct 2023; 14:9377-9390. [PMID: 37789767 DOI: 10.1039/d3fo02693k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
It is still unclear if changes in protein digestibility and absorption kinetics in old age may affect the anabolic effect of high-protein foods. The objective of this study was to investigate the digestion of two high-protein (10% w/w) dairy products in vitro: a fermented dairy product formulated with a ratio of whey proteins to caseins of 80 to 20% (WBD) and a Skyr containing mainly caseins. The new static in vitro digestion model adapted to the general older adult population (≥65 years) proposed by the INFOGEST international consortium was implemented to investigate the digestion of these products and compared with the standard version of the protocol. Kinetics of proteolysis was compared between both models for each product, in the gastric and intestinal phases of digestion. Protein hydrolysis was studied by the OPA method, SDS-PAGE, and LC-MS/MS, and amino acids were quantified by HPLC. Protein hydrolysis by pepsin was slower with the older adult model than with the young adult model, and consequently, in spite of a longer gastric phase duration, the degree of proteolysis (DH) at the end of the gastric phase was lower. Two different scenarios were observed depending on the type of dairy product studied: -10 and -40% DH for Skyr and WBD, respectively. In the intestinal phase, lower concentrations of free leucine were observed in older adult conditions (approx. -10%), but no significant differences in proteolysis were observed overall between the models. Therefore, the digestion conditions used influenced significantly the rate and extent of proteolysis in the gastric phase but not in the intestinal phase.
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18
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Le Guillou S, Ciobotaru C, Laubier J, Castille J, Aujean E, Hue-Beauvais C, Cherbuy C, Liuu S, Henry C, David A, Jaffrezic F, Laloë D, Charlier M, Alexandre-Gouabau MC, Le Provost F. Specific Milk Composition of miR-30b Transgenic Mice Associated with Early Duodenum Maturation in Offspring with Lasting Consequences for Growth. J Nutr 2023; 153:2808-2826. [PMID: 37543213 DOI: 10.1016/j.tjnut.2023.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 07/18/2023] [Accepted: 08/01/2023] [Indexed: 08/07/2023] Open
Abstract
BACKGROUND Milk composition is complex and includes numerous components essential for offspring growth and development. In addition to the high abundance of miR-30b microRNA, milk produced by the transgenic mouse model of miR-30b-mammary deregulation displays a significantly altered fatty acid profile. Moreover, wild-type adopted pups fed miR-30b milk present an early growth defect. OBJECTIVE This study aimed to investigate the consequences of miR-30b milk feeding on the duodenal development of wild-type neonates, a prime target of suckled milk, along with comprehensive milk phenotyping. METHODS The duodenums of wild-type pups fed miR-30b milk were extensively characterized at postnatal day (PND)-5, PND-6, and PND-15 using histological, transcriptomic, proteomic, and duodenal permeability analyses and compared with those of pups fed wild-type milk. Milk of miR-30b foster dams collected at mid-lactation was extensively analyzed using proteomic, metabolomic, and lipidomic approaches and hormonal immunoassays. RESULTS At PND-5, wild-type pups fed miR-30b milk showed maturation of their duodenum with 1.5-fold (P < 0.05) and 1.3-fold (P < 0.10) increased expression of Claudin-3 and Claudin-4, respectively, and changes in 8 duodenal proteins (P < 0.10), with an earlier reduction in paracellular and transcellular permeability (183 ng/mL fluorescein sulfonic acid [FSA] and 12 ng/mL horseradish peroxidase [HRP], respectively, compared with 5700 ng/mL FSA and 90 ng/mL HRP in wild-type; P < 0.001). Compared with wild-type milk, miR-30b milk displayed an increase in total lipid (219 g/L compared with 151 g/L; P < 0.05), ceramide (17.6 μM compared with 6.9 μM; P < 0.05), and sphingomyelin concentrations (163.7 μM compared with 76.3 μM; P < 0.05); overexpression of 9 proteins involved in the gut barrier (P < 0.1); and higher insulin and leptin concentrations (1.88 ng/mL and 2.04 ng/mL, respectively, compared with 0.79 ng/mL and 1.06 ng/mL; P < 0.01). CONCLUSIONS miR-30b milk displays significant changes in bioactive components associated with neonatal duodenal integrity and maturation, which could be involved in the earlier intestinal closure phenotype of the wild-type pups associated with a lower growth rate.
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Affiliation(s)
| | - Céline Ciobotaru
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Johann Laubier
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Johan Castille
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Etienne Aujean
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Cathy Hue-Beauvais
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Claire Cherbuy
- Université Paris-Saclay, INRAE, MICALIS Institute, Jouy-en-Josas, France
| | - Sophie Liuu
- Université Paris-Saclay, INRAE, AgroParisTech, MICALIS Institute, PAPPSO, Jouy-en-Josas, France
| | - Céline Henry
- Université Paris-Saclay, INRAE, AgroParisTech, MICALIS Institute, PAPPSO, Jouy-en-Josas, France
| | - Agnès David
- Nantes Université, CRNH-OUEST, INRAE, UMR 1280, PhAN, Nantes, France
| | - Florence Jaffrezic
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Denis Laloë
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Madia Charlier
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
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Priya A, Antoine-Bally S, Macé AS, Monteiro P, Sabatet V, Remy D, Dingli F, Loew D, Demetriades C, Gautreau AM, Chavrier P. Codependencies of mTORC1 signaling and endolysosomal actin structures. SCIENCE ADVANCES 2023; 9:eadd9084. [PMID: 37703363 PMCID: PMC10881074 DOI: 10.1126/sciadv.add9084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 08/11/2023] [Indexed: 09/15/2023]
Abstract
The mechanistic target of rapamycin complex 1 (mTORC1) is part of the amino acid sensing machinery that becomes activated on the endolysosomal surface in response to nutrient cues. Branched actin generated by WASH and Arp2/3 complexes defines endolysosomal microdomains. Here, we find mTORC1 components in close proximity to endolysosomal actin microdomains. We investigated for interactors of the mTORC1 lysosomal tether, RAGC, by proteomics and identified multiple actin filament capping proteins and their modulators. Perturbation of RAGC function affected the size of endolysosomal actin, consistent with a regulation of actin filament capping by RAGC. Reciprocally, the pharmacological inhibition of actin polymerization or alteration of endolysosomal actin obtained upon silencing of WASH or Arp2/3 complexes impaired mTORC1 activity. Mechanistically, we show that actin is required for proper association of RAGC and mTOR with endolysosomes. This study reveals an unprecedented interplay between actin and mTORC1 signaling on the endolysosomal system.
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Affiliation(s)
- Amulya Priya
- Institut Curie, CNRS UMR144, PSL Research University, Research Center, Actin and Membrane Dynamics Laboratory, 26 rue d’Ulm, Paris 75248 Cedex 05, France
| | - Sandra Antoine-Bally
- Institut Curie, CNRS UMR144, PSL Research University, Research Center, Actin and Membrane Dynamics Laboratory, 26 rue d’Ulm, Paris 75248 Cedex 05, France
| | - Anne-Sophie Macé
- Institut Curie, PSL Research University, Cell and Tissue Imaging Facility (PICT-IBiSA), 26 rue d’Ulm, Paris 75248 Cedex 05, France
| | - Pedro Monteiro
- Institut Curie, CNRS UMR144, PSL Research University, Research Center, Actin and Membrane Dynamics Laboratory, 26 rue d’Ulm, Paris 75248 Cedex 05, France
| | - Valentin Sabatet
- Institut Curie, PSL Research University, CurieCoreTech Mass Spectrometry Proteomics, 26 rue d’Ulm, Paris 75248 Cedex 05, France
| | - David Remy
- Institut Curie, CNRS UMR144, PSL Research University, Research Center, Actin and Membrane Dynamics Laboratory, 26 rue d’Ulm, Paris 75248 Cedex 05, France
| | - Florent Dingli
- Institut Curie, PSL Research University, CurieCoreTech Mass Spectrometry Proteomics, 26 rue d’Ulm, Paris 75248 Cedex 05, France
| | - Damarys Loew
- Institut Curie, PSL Research University, CurieCoreTech Mass Spectrometry Proteomics, 26 rue d’Ulm, Paris 75248 Cedex 05, France
| | - Constantinos Demetriades
- Max Planck Institute for Biology of Ageing (MPI-AGE), Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Alexis M. Gautreau
- Laboratoire de Biologie Structurale de la Cellule, CNRS, École Polytechnique, Institut Polytechnique de Paris, Palaiseau, France
| | - Philippe Chavrier
- Institut Curie, CNRS UMR144, PSL Research University, Research Center, Actin and Membrane Dynamics Laboratory, 26 rue d’Ulm, Paris 75248 Cedex 05, France
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20
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Pasquereau-Kotula E, Nigro G, Dingli F, Loew D, Poullet P, Xu Y, Kopetz S, Davis J, Peduto L, Robbe-Masselot C, Sansonetti P, Trieu-Cuot P, Dramsi S. Global proteomic identifies multiple cancer-related signaling pathways altered by a gut pathobiont associated with colorectal cancer. Sci Rep 2023; 13:14960. [PMID: 37696912 PMCID: PMC10495336 DOI: 10.1038/s41598-023-41951-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 09/04/2023] [Indexed: 09/13/2023] Open
Abstract
In this work, we investigated the oncogenic role of Streptococcus gallolyticus subsp. gallolyticus (SGG), a gut bacterium associated with colorectal cancer (CRC). We showed that SGG UCN34 accelerates colon tumor development in a chemically induced CRC murine model. Full proteome and phosphoproteome analysis of murine colons chronically colonized by SGG UCN34 revealed that 164 proteins and 725 phosphorylation sites were differentially regulated. Ingenuity Pathway Analysis (IPA) indicates a pro-tumoral shift specifically induced by SGG UCN34, as ~ 90% of proteins and phosphoproteins identified were associated with digestive cancer. Comprehensive analysis of the altered phosphoproteins using ROMA software revealed up-regulation of several cancer hallmark pathways such as MAPK, mTOR and integrin/ILK/actin, affecting epithelial and stromal colonic cells. Importantly, an independent analysis of protein arrays of human colon tumors colonized with SGG showed up-regulation of PI3K/Akt/mTOR and MAPK pathways, providing clinical relevance to our findings. To test SGG's capacity to induce pre-cancerous transformation of the murine colonic epithelium, we grew ex vivo organoids which revealed unusual structures with compact morphology. Taken together, our results demonstrate the oncogenic role of SGG UCN34 in a murine model of CRC associated with activation of multiple cancer-related signaling pathways.
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Affiliation(s)
- Ewa Pasquereau-Kotula
- Biology of Gram-Positive Pathogens Unit, Institut Pasteur, Université Paris Cité, CNRS UMR6047, 75015, Paris, France.
| | - Giulia Nigro
- Stroma, Inflammation and Tissue Repair Unit, Institut Pasteur, Université Paris Cité, INSERM U1224, 75015, Paris, France
- Microenvironment and Immunity Unit, Institut Pasteur, Université Paris Cité, INSERM U1224, 75015, Paris, France
| | - Florent Dingli
- Institut Curie, PSL Research University, CurieCoreTech Spectrométrie de Masse Protéomique, 75005, Paris, France
| | - Damarys Loew
- Institut Curie, PSL Research University, CurieCoreTech Spectrométrie de Masse Protéomique, 75005, Paris, France
| | - Patrick Poullet
- Institut Curie, Bioinformatics Core Facility (CUBIC), INSERM U900, PSL Research University, Mines Paris Tech, 75005, Paris, France
| | - Yi Xu
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, USA
- Department of Microbial Pathogenesis and Immunology, School of Medicine, Bryan, TX, USA
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, TX, USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jennifer Davis
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- University of Kansas, Kansas City, KS, USA
| | - Lucie Peduto
- Stroma, Inflammation and Tissue Repair Unit, Institut Pasteur, Université Paris Cité, INSERM U1224, 75015, Paris, France
| | - Catherine Robbe-Masselot
- Université de Lille, CNRS, UMR8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, 59000, Lille, France
| | - Philippe Sansonetti
- Institut Pasteur, Unité de Pathogénie Microbienne Moléculaire, INSERM U1202, and College de France, 75005, Paris, France
| | - Patrick Trieu-Cuot
- Biology of Gram-Positive Pathogens Unit, Institut Pasteur, Université Paris Cité, CNRS UMR6047, 75015, Paris, France
| | - Shaynoor Dramsi
- Biology of Gram-Positive Pathogens Unit, Institut Pasteur, Université Paris Cité, CNRS UMR6047, 75015, Paris, France.
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21
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Mariano NC, Rusin SF, Nasa I, Kettenbach AN. Inducible Protein Degradation as a Strategy to Identify Phosphoprotein Phosphatase 6 Substrates in RAS-Mutant Colorectal Cancer Cells. Mol Cell Proteomics 2023; 22:100614. [PMID: 37392812 PMCID: PMC10400926 DOI: 10.1016/j.mcpro.2023.100614] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 06/13/2023] [Accepted: 06/28/2023] [Indexed: 07/03/2023] Open
Abstract
Protein phosphorylation is an essential regulatory mechanism that controls most cellular processes, including cell cycle progression, cell division, and response to extracellular stimuli, among many others, and is deregulated in many diseases. Protein phosphorylation is coordinated by the opposing activities of protein kinases and protein phosphatases. In eukaryotic cells, most serine/threonine phosphorylation sites are dephosphorylated by members of the Phosphoprotein Phosphatase (PPP) family. However, we only know for a few phosphorylation sites which specific PPP dephosphorylates them. Although natural compounds such as calyculin A and okadaic acid inhibit PPPs at low nanomolar concentrations, no selective chemical PPP inhibitors exist. Here, we demonstrate the utility of endogenous tagging of genomic loci with an auxin-inducible degron (AID) as a strategy to investigate specific PPP signaling. Using Protein Phosphatase 6 (PP6) as an example, we demonstrate how rapidly inducible protein degradation can be employed to identify dephosphorylation sites and elucidate PP6 biology. Using genome editing, we introduce AID-tags into each allele of the PP6 catalytic subunit (PP6c) in DLD-1 cells expressing the auxin receptor Tir1. Upon rapid auxin-induced degradation of PP6c, we perform quantitative mass spectrometry-based proteomics and phosphoproteomics to identify PP6 substrates in mitosis. PP6 is an essential enzyme with conserved roles in mitosis and growth signaling. Consistently, we identify candidate PP6c-dependent dephosphorylation sites on proteins implicated in coordinating the mitotic cell cycle, cytoskeleton, gene expression, and mitogen-activated protein kinase (MAPK) and Hippo signaling. Finally, we demonstrate that PP6c opposes the activation of large tumor suppressor 1 (LATS1) by dephosphorylating Threonine 35 (T35) on Mps One Binder (MOB1), thereby blocking the interaction of MOB1 and LATS1. Our analyses highlight the utility of combining genome engineering, inducible degradation, and multiplexed phosphoproteomics to investigate signaling by individual PPPs on a global level, which is currently limited by the lack of tools for specific interrogation.
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Affiliation(s)
- Natasha C Mariano
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Scott F Rusin
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Isha Nasa
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA; Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
| | - Arminja N Kettenbach
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA; Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA.
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22
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Ferrant J, Pontis A, Zimmermann F, Dingli F, Poullet P, Loew D, Tarte K, Dumontet E. Phenotypic and proteomic analysis of plasma extracellular vesicles highlights them as potential biomarkers of primary Sjögren syndrome. Front Immunol 2023; 14:1207545. [PMID: 37529039 PMCID: PMC10388367 DOI: 10.3389/fimmu.2023.1207545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 06/14/2023] [Indexed: 08/03/2023] Open
Abstract
Sjögren syndrome (SjS) is an autoimmune disease characterized by the destruction of the exocrine gland epithelia, causing a dryness of mucosa called sicca symptoms, and whose main life-threatening complication is lymphoma. There is a need for new biomarkers in this disease, notably diagnostic biomarkers for patients with genuine sicca symptoms that do not meet current criteria, and prognostic biomarkers for patients at risk of lymphoma. Plasma extracellular vesicles (EVs) are promising biomarker candidates in several diseases, but their potential has not yet been explored in SjS. In this proof-of-concept study, we characterized EVs from primary SjS patients (pSS, n=12) at the phenotypic and proteomic levels, compared to EVs from healthy donor (HD, n=8) and systemic lupus erythematosus patients (SLE, n=12). Specific plasma EVs subpopulations, derived from neutrophils, endothelial, and epithelial cells, were found increased in pSS. We also identified a pSS proteomic signature in plasma EVs, including neutrophil-, epithelial-, and endothelial-related proteins, such as integrin alpha M (ITGAM), olfactomedin-4 (OLFM4), Ras-related protein RAB10, and CD36. Overall, our results support the relevance of plasma EVs as biomarkers in SjS.
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Affiliation(s)
- Juliette Ferrant
- Pôle Biologie, Centre Hospitalier Universitaire de Rennes, Rennes, France
- UMR, Université Rennes, INSERM, Établissement Français du Sang, Rennes, France
| | - Adeline Pontis
- Pôle Biologie, Centre Hospitalier Universitaire de Rennes, Rennes, France
| | - François Zimmermann
- Département de Médecine Interne et Immunologie Clinique, Centre Hospitalier Universitaire de Rennes, Rennes, France
| | - Florent Dingli
- Institut Curie, PSL Research University, CurieCoreTech Mass Spectrometry Proteomics, Paris, France
| | - Patrick Poullet
- Institut Curie, PSL Research University, INSERM, Mines Paris Tech, Bioinformatics core facility (CUBIC), Paris, France
| | - Damarys Loew
- Institut Curie, PSL Research University, CurieCoreTech Mass Spectrometry Proteomics, Paris, France
| | - Karin Tarte
- Pôle Biologie, Centre Hospitalier Universitaire de Rennes, Rennes, France
- UMR, Université Rennes, INSERM, Établissement Français du Sang, Rennes, France
| | - Erwan Dumontet
- Pôle Biologie, Centre Hospitalier Universitaire de Rennes, Rennes, France
- UMR, Université Rennes, INSERM, Établissement Français du Sang, Rennes, France
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23
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Duruflé H, Balliau T, Blanchet N, Chaubet A, Duhnen A, Pouilly N, Blein-Nicolas M, Mangin B, Maury P, Langlade NB, Zivy M. Sunflower Hybrids and Inbred Lines Adopt Different Physiological Strategies and Proteome Responses to Cope with Water Deficit. Biomolecules 2023; 13:1110. [PMID: 37509146 PMCID: PMC10377273 DOI: 10.3390/biom13071110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/03/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
Sunflower is a hybrid crop that is considered moderately drought-tolerant and adapted to new cropping systems required for the agro-ecological transition. Here, we studied the impact of hybridity status (hybrids vs. inbred lines) on the responses to drought at the molecular and eco-physiological level exploiting publicly available datasets. Eco-physiological traits and leaf proteomes were measured in eight inbred lines and their sixteen hybrids grown in the high-throughput phenotyping platform Phenotoul-Heliaphen. Hybrids and parental lines showed different growth strategies: hybrids grew faster in the absence of water constraint and arrested their growth more abruptly than inbred lines when subjected to water deficit. We identified 471 differentially accumulated proteins, of which 256 were regulated by drought. The amplitude of up- and downregulations was greater in hybrids than in inbred lines. Our results show that hybrids respond more strongly to water deficit at the molecular and eco-physiological levels. Because of presence/absence polymorphism, hybrids potentially contain more genes than their parental inbred lines. We propose that detrimental homozygous mutations and the lower number of genes in inbred lines lead to a constitutive defense mechanism that may explain the lower growth of inbred lines under well-watered conditions and their lower reactivity to water deficit.
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Affiliation(s)
- Harold Duruflé
- INRAE UMR441, CNRS UMR2594, LIPME, Université de Toulouse, 31077 Toulouse, France
- INRAE, ONF, BioForA, 45075 Orleans, France
| | - Thierry Balliau
- AgroParisTech, GQE-Le Moulon, PAPPSO, Université Paris-Saclay, INRAE, CNRS, 91190 Gif-sur-Yvette, France
| | - Nicolas Blanchet
- INRAE UMR441, CNRS UMR2594, LIPME, Université de Toulouse, 31077 Toulouse, France
| | - Adeline Chaubet
- INRAE UMR441, CNRS UMR2594, LIPME, Université de Toulouse, 31077 Toulouse, France
| | - Alexandra Duhnen
- INRAE UMR441, CNRS UMR2594, LIPME, Université de Toulouse, 31077 Toulouse, France
| | - Nicolas Pouilly
- INRAE UMR441, CNRS UMR2594, LIPME, Université de Toulouse, 31077 Toulouse, France
| | - Mélisande Blein-Nicolas
- AgroParisTech, GQE-Le Moulon, PAPPSO, Université Paris-Saclay, INRAE, CNRS, 91190 Gif-sur-Yvette, France
| | - Brigitte Mangin
- INRAE UMR441, CNRS UMR2594, LIPME, Université de Toulouse, 31077 Toulouse, France
| | - Pierre Maury
- INRAE, INP-ENSAT Toulouse, UMR AGIR, Université de Toulouse, 31000 Toulouse, France
| | | | - Michel Zivy
- AgroParisTech, GQE-Le Moulon, PAPPSO, Université Paris-Saclay, INRAE, CNRS, 91190 Gif-sur-Yvette, France
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24
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Chauvet L, Ménard O, Le Gouar Y, Henry G, Jardin J, Hennetier M, Croguennec T, Van Audenhaege M, Dupont D, Lemaire M, Le Huërou-Luron I, Deglaire A. Protein ingredient quality of infant formulas impacts their structure and kinetics of proteolysis under in vitro dynamic digestion. Food Res Int 2023; 169:112883. [PMID: 37254331 DOI: 10.1016/j.foodres.2023.112883] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/19/2023] [Accepted: 04/21/2023] [Indexed: 06/01/2023]
Abstract
Infant formula (IF) is a complex matrix requiring numerous ingredients and processing steps. The objective was to understand how the quality of protein ingredients impacts IF structure and, in turn, their kinetics of digestion. Four powdered IFs (A/B/C/D), based on commercial whey protein (WP) ingredients, with different protein denaturation levels and composition (A/B/C), and on caseins with different supramolecular organisations (C/D), were produced at a semi-industrial level after homogenization and spray-drying. Once reconstituted in water (13 %, wt/wt), the IF microstructure was analysed with asymmetrical flow field-flow fractionation coupled with multi-angle light scattering and differential refractometer, transmission electron microscopy and electrophoresis. The rehydrated IFs were subjected to simulated infant in vitro dynamic digestion (DIDGI®). Digesta were regularly sampled to follow structural changes (confocal microscopy, laser-light scattering) and proteolysis (OPA, SDS-PAGE, LC-MS/MS, cation-exchange chromatography). Before digestion, different microstructures were observed among IFs. IF-A, characterized by more denatured WPs, presented star-shaped mixed aggregates, with protein aggregates bounded to casein micelles, themselves adsorbed at the fat droplet interface. Non-micellar caseins, brought by non-micellar casein powder (IF-D) underwent rearrangement and aggregation at the interface of flocculated fat droplets, leading to a largely different microstructure of IF emulsion, with large aggregates of lipids and proteins. During digestion, IF-A more digested (degree of proteolysis + 16 %) at 180 min of intestinal phase than IF-C/D. The modification of the supramolecular organisation of caseins implied different kinetics of peptide release derived from caseins during the gastric phase (more abundant at G80 for IF-D). Bioactive peptide release kinetics were also different during digestion with IF-C presenting a maximal abundance for a large proportion of them. Overall, the present study highlights the importance of the structure and composition of the protein ingredients (WPs and caseins) selected for IF formulation on the final IF structure and, in turn, on proteolysis. Whether it has some physiological consequences remains to be investigated.
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Affiliation(s)
- Lucile Chauvet
- INRAE, Institut Agro, STLO, 35042 Rennes, France; Institut NuMeCan, INRAE, INSERM, Univ Rennes, Saint Gilles, France; SODIAAL International, Centre Recherche & Innovation, Rennes, France
| | | | | | | | | | - Marie Hennetier
- Université de Toulouse, Institut National Polytechnique de Toulouse - Ecole d'ingénieur de Purpan, Département Sciences Agronomique et Agroalimentaire, Toulouse, France
| | | | | | | | - Marion Lemaire
- SODIAAL International, Centre Recherche & Innovation, Rennes, France
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25
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Solier S, Müller S, Cañeque T, Versini A, Mansart A, Sindikubwabo F, Baron L, Emam L, Gestraud P, Pantoș GD, Gandon V, Gaillet C, Wu TD, Dingli F, Loew D, Baulande S, Durand S, Sencio V, Robil C, Trottein F, Péricat D, Näser E, Cougoule C, Meunier E, Bègue AL, Salmon H, Manel N, Puisieux A, Watson S, Dawson MA, Servant N, Kroemer G, Annane D, Rodriguez R. A druggable copper-signalling pathway that drives inflammation. Nature 2023; 617:386-394. [PMID: 37100912 PMCID: PMC10131557 DOI: 10.1038/s41586-023-06017-4] [Citation(s) in RCA: 71] [Impact Index Per Article: 71.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 03/27/2023] [Indexed: 04/28/2023]
Abstract
Inflammation is a complex physiological process triggered in response to harmful stimuli1. It involves cells of the immune system capable of clearing sources of injury and damaged tissues. Excessive inflammation can occur as a result of infection and is a hallmark of several diseases2-4. The molecular bases underlying inflammatory responses are not fully understood. Here we show that the cell surface glycoprotein CD44, which marks the acquisition of distinct cell phenotypes in the context of development, immunity and cancer progression, mediates the uptake of metals including copper. We identify a pool of chemically reactive copper(II) in mitochondria of inflammatory macrophages that catalyses NAD(H) redox cycling by activating hydrogen peroxide. Maintenance of NAD+ enables metabolic and epigenetic programming towards the inflammatory state. Targeting mitochondrial copper(II) with supformin (LCC-12), a rationally designed dimer of metformin, induces a reduction of the NAD(H) pool, leading to metabolic and epigenetic states that oppose macrophage activation. LCC-12 interferes with cell plasticity in other settings and reduces inflammation in mouse models of bacterial and viral infections. Our work highlights the central role of copper as a regulator of cell plasticity and unveils a therapeutic strategy based on metabolic reprogramming and the control of epigenetic cell states.
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Affiliation(s)
- Stéphanie Solier
- Equipe Labellisée Ligue Contre le Cancer, Institut Curie, CNRS, INSERM, PSL Research University, Paris, France
| | - Sebastian Müller
- Equipe Labellisée Ligue Contre le Cancer, Institut Curie, CNRS, INSERM, PSL Research University, Paris, France
| | - Tatiana Cañeque
- Equipe Labellisée Ligue Contre le Cancer, Institut Curie, CNRS, INSERM, PSL Research University, Paris, France
| | - Antoine Versini
- Equipe Labellisée Ligue Contre le Cancer, Institut Curie, CNRS, INSERM, PSL Research University, Paris, France
| | - Arnaud Mansart
- Paris Saclay University, UVSQ, INSERM, 2I, Montigny-le-Bretonneux, France
| | - Fabien Sindikubwabo
- Equipe Labellisée Ligue Contre le Cancer, Institut Curie, CNRS, INSERM, PSL Research University, Paris, France
| | - Leeroy Baron
- Equipe Labellisée Ligue Contre le Cancer, Institut Curie, CNRS, INSERM, PSL Research University, Paris, France
| | - Laila Emam
- Paris Saclay University, UVSQ, INSERM, 2I, Montigny-le-Bretonneux, France
| | - Pierre Gestraud
- CBIO-Centre for Computational Biology, Institut Curie, INSERM, Mines ParisTech, Paris, France
| | - G Dan Pantoș
- Department of Chemistry, University of Bath, Bath, UK
| | - Vincent Gandon
- Institut de Chimie Moléculaire et des Matériaux d'Orsay, CNRS, Paris Saclay University, Orsay, France
- Laboratoire de Chimie Moléculaire, CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France
| | - Christine Gaillet
- Equipe Labellisée Ligue Contre le Cancer, Institut Curie, CNRS, INSERM, PSL Research University, Paris, France
| | - Ting-Di Wu
- Institut Curie, PSL Research University, Paris, France
- Multimodal Imaging Center, Paris Saclay University, CNRS, INSERM, Orsay, France
| | - Florent Dingli
- CurieCoreTech Mass Spectrometry Proteomic, Institut Curie, PSL Research University, Paris, France
| | - Damarys Loew
- CurieCoreTech Mass Spectrometry Proteomic, Institut Curie, PSL Research University, Paris, France
| | - Sylvain Baulande
- ICGex Next-Generation Sequencing Platform, Institut Curie, PSL Research University, Paris, France
| | - Sylvère Durand
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France
| | - Valentin Sencio
- Université de Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, CIIL, Lille, France
| | - Cyril Robil
- Université de Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, CIIL, Lille, France
| | - François Trottein
- Université de Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, CIIL, Lille, France
| | - David Péricat
- Institut of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
| | - Emmanuelle Näser
- Institut of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
- Cytometry and Imaging Core facility, Institute of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
| | - Céline Cougoule
- Institut of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
| | - Etienne Meunier
- Institut of Pharmacology and Structural Biology, University of Toulouse, CNRS, Toulouse, France
| | | | - Hélène Salmon
- Institut Curie, INSERM, PSL Research University, Paris, France
| | - Nicolas Manel
- Institut Curie, INSERM, PSL Research University, Paris, France
| | - Alain Puisieux
- Equipe Labellisée Ligue Contre le Cancer, Institut Curie, CNRS, INSERM, PSL Research University, Paris, France
| | - Sarah Watson
- Department of Medical Oncology, Institut Curie, PSL Research University, Paris, France
| | - Mark A Dawson
- Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, Melbourne, Victoria, Australia
- Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia
| | - Nicolas Servant
- CBIO-Centre for Computational Biology, Institut Curie, INSERM, Mines ParisTech, Paris, France
| | - Guido Kroemer
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France
- Centre de Recherche des Cordeliers, University of Paris, Sorbonne University, INSERM, Institut Universitaire de France, Paris, France
- Institut du Cancer Paris CARPEM, Department of Biology, Hôpital Européen Georges Pompidou, AP-HP, Paris, France
| | - Djillali Annane
- Paris Saclay University, UVSQ, INSERM, 2I, Montigny-le-Bretonneux, France
- Department of Intensive Care, Hôpital Raymond Poincaré, AP-HP, Garches, France
| | - Raphaël Rodriguez
- Equipe Labellisée Ligue Contre le Cancer, Institut Curie, CNRS, INSERM, PSL Research University, Paris, France.
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26
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Oudart M, Avila-Gutierrez K, Moch C, Dossi E, Milior G, Boulay AC, Gaudey M, Moulard J, Lombard B, Loew D, Bemelmans AP, Rouach N, Chapat C, Cohen-Salmon M. The ribosome-associated protein RACK1 represses Kir4.1 translation in astrocytes and influences neuronal activity. Cell Rep 2023; 42:112456. [PMID: 37126448 DOI: 10.1016/j.celrep.2023.112456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 02/10/2023] [Accepted: 04/16/2023] [Indexed: 05/02/2023] Open
Abstract
The regulation of translation in astrocytes, the main glial cells in the brain, remains poorly characterized. We developed a high-throughput proteomics screen for polysome-associated proteins in astrocytes and focused on ribosomal protein receptor of activated protein C kinase 1 (RACK1), a critical factor in translational regulation. In astrocyte somata and perisynaptic astrocytic processes (PAPs), RACK1 preferentially binds to a number of mRNAs, including Kcnj10, encoding the inward-rectifying potassium (K+) channel Kir4.1. By developing an astrocyte-specific, conditional RACK1 knockout mouse model, we show that RACK1 represses production of Kir4.1 in hippocampal astrocytes and PAPs. Upregulation of Kir4.1 in the absence of RACK1 increases astrocytic Kir4.1-mediated K+ currents and volume. It also modifies neuronal activity attenuating burst frequency and duration. Reporter-based assays reveal that RACK1 controls Kcnj10 translation through the transcript's 5' untranslated region. Hence, translational regulation by RACK1 in astrocytes represses Kir4.1 expression and influences neuronal activity.
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Affiliation(s)
- Marc Oudart
- Center for Interdisciplinary Research in Biology, College de France, CNRS, INSERM, Université PSL, Labex Memolife, Paris, France
| | - Katia Avila-Gutierrez
- Center for Interdisciplinary Research in Biology, College de France, CNRS, INSERM, Université PSL, Labex Memolife, Paris, France
| | - Clara Moch
- Laboratoire de Biochimie, Ecole Polytechnique, CNRS, Université Paris-Saclay, Palaiseau, France
| | - Elena Dossi
- Center for Interdisciplinary Research in Biology, College de France, CNRS, INSERM, Université PSL, Labex Memolife, Paris, France
| | - Giampaolo Milior
- Center for Interdisciplinary Research in Biology, College de France, CNRS, INSERM, Université PSL, Labex Memolife, Paris, France
| | - Anne-Cécile Boulay
- Center for Interdisciplinary Research in Biology, College de France, CNRS, INSERM, Université PSL, Labex Memolife, Paris, France
| | - Mathis Gaudey
- Center for Interdisciplinary Research in Biology, College de France, CNRS, INSERM, Université PSL, Labex Memolife, Paris, France
| | - Julien Moulard
- Center for Interdisciplinary Research in Biology, College de France, CNRS, INSERM, Université PSL, Labex Memolife, Paris, France
| | - Bérangère Lombard
- CurieCoreTech Spectrométrie de Masse Protéomique, Institut Curie, University PSL, Paris, France
| | - Damarys Loew
- CurieCoreTech Spectrométrie de Masse Protéomique, Institut Curie, University PSL, Paris, France
| | - Alexis-Pierre Bemelmans
- CEA, Institut de Biologie François Jacob, Molecular Imaging Research Center (MIRCen), CNRS, Université Paris-Sud, Université Paris-Saclay, Fontenay-aux-Roses, France
| | - Nathalie Rouach
- Center for Interdisciplinary Research in Biology, College de France, CNRS, INSERM, Université PSL, Labex Memolife, Paris, France
| | - Clément Chapat
- Laboratoire de Biochimie, Ecole Polytechnique, CNRS, Université Paris-Saclay, Palaiseau, France
| | - Martine Cohen-Salmon
- Center for Interdisciplinary Research in Biology, College de France, CNRS, INSERM, Université PSL, Labex Memolife, Paris, France.
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27
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Amhaz S, Boëda B, Chouchène M, Colasse S, Dingli F, Loew D, Henri J, Prunier C, Levy L. The UAS thioredoxin-like domain of UBXN7 regulates E3 ubiquitin ligase activity of RNF111/Arkadia. BMC Biol 2023; 21:73. [PMID: 37024974 PMCID: PMC10080908 DOI: 10.1186/s12915-023-01576-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 03/24/2023] [Indexed: 04/08/2023] Open
Abstract
BACKGROUND E3 ubiquitin ligases play critical roles in regulating cellular signaling pathways by inducing ubiquitylation of key components. RNF111/Arkadia is a RING E3 ubiquitin ligase that activates TGF-β signaling by inducing ubiquitylation and proteasomal degradation of the transcriptional repressor SKIL/SnoN. In this study, we have sought to identify novel regulators of the E3 ubiquitin ligase activity of RNF111 by searching for proteins that specifically interacts with its RING domain. RESULTS We found that UBXN7, a member of the UBA-UBX family, directly interacts with the RING domain of RNF111 or its related E3 RNF165/ARK2C that shares high sequence homology with RNF111. We showed that UBXN7 docks on RNF111 or RNF165 RING domain through its UAS thioredoxin-like domain. Overexpression of UBXN7 or its UAS domain increases endogenous RNF111, while an UBXN7 mutant devoid of UAS domain has no effect. Conversely, depletion of UBXN7 decreases RNF111 protein level. As a consequence, we found that UBXN7 can modulate degradation of the RNF111 substrate SKIL in response to TGF-β signaling. We further unveiled this mechanism of regulation by showing that docking of the UAS domain of UBXN7 inhibits RNF111 ubiquitylation by preventing interaction of the RING domain with the E2 conjugating enzymes. By analyzing the interactome of the UAS domain of UBXN7, we identified that it also interacts with the RING domain of the E3 TOPORS and similarly regulates its E3 ubiquitin ligase activity by impairing E2 binding. CONCLUSIONS Taken together, our results demonstrate that UBXN7 acts as a direct regulator for the E3 ubiquitin ligases RNF111, RNF165, and TOPORS and reveal that a thioredoxin-like domain can dock on specific RING domains to regulate their E3 ubiquitin ligase activity.
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Affiliation(s)
- Sadek Amhaz
- Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, CRSA, 75012, Paris, France
| | - Batiste Boëda
- Cell Polarity, Migration and Cancer Unit, Institut Pasteur, UMR3691 CNRS, Université Paris Cité, F-75015, Paris, France
| | - Mouna Chouchène
- Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, CRSA, 75012, Paris, France
| | - Sabrina Colasse
- Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, CRSA, 75012, Paris, France
| | - Florent Dingli
- CurieCoreTech Mass Spectrometry Proteomics, Institut Curie, PSL Research University, Paris, France
| | - Damarys Loew
- CurieCoreTech Mass Spectrometry Proteomics, Institut Curie, PSL Research University, Paris, France
| | - Julien Henri
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative - UMR 7238, 75005, Paris, France
| | - Céline Prunier
- Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, CRSA, 75012, Paris, France.
| | - Laurence Levy
- Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, CRSA, 75012, Paris, France.
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28
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Termination factor Rho mediates transcriptional reprogramming of Bacillus subtilis stationary phase. PLoS Genet 2023; 19:e1010618. [PMID: 36735730 PMCID: PMC9931155 DOI: 10.1371/journal.pgen.1010618] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 02/15/2023] [Accepted: 01/14/2023] [Indexed: 02/04/2023] Open
Abstract
Transcription termination factor Rho is known for its ubiquitous role in suppression of pervasive, mostly antisense, transcription. In the model Gram-positive bacterium Bacillus subtilis, de-repression of pervasive transcription by inactivation of rho revealed the role of Rho in the regulation of post-exponential differentiation programs. To identify other aspects of the regulatory role of Rho during adaptation to starvation, we have constructed a B. subtilis strain (Rho+) that expresses rho at a relatively stable high level in order to compensate for its decrease in the wild-type cells entering stationary phase. The RNAseq analysis of Rho+, WT and Δrho strains (expression profiles can be visualized at http://genoscapist.migale.inrae.fr/seb_rho/) shows that Rho over-production enhances the termination efficiency of Rho-sensitive terminators, thus reducing transcriptional read-through and antisense transcription genome-wide. Moreover, the Rho+ strain exhibits global alterations of sense transcription with the most significant changes observed for the AbrB, CodY, and stringent response regulons, forming the pathways governing the transition to stationary phase. Subsequent physiological analyses demonstrated that maintaining rho expression at a stable elevated level modifies stationary phase-specific physiology of B. subtilis cells, weakens stringent response, and thereby negatively affects the cellular adaptation to nutrient limitations and other stresses, and blocks the development of genetic competence and sporulation. These results highlight the Rho-specific termination of transcription as a novel element controlling stationary phase. The release of this control by decreasing Rho levels during the transition to stationary phase appears crucial for the functionality of complex gene networks ensuring B. subtilis survival in stationary phase.
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29
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Ghouili E, Sassi K, Hidri Y, M’Hamed HC, Somenahally A, Xue Q, Jebara M, Nefissi Ouertani R, Riahi J, de Oliveira AC, Abid G, Muhovski Y. Effects of Date Palm Waste Compost Application on Root Proteome Changes of Barley ( Hordeum vulgare L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:526. [PMID: 36771612 PMCID: PMC9921465 DOI: 10.3390/plants12030526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/15/2023] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Proteomic analysis was performed to investigate the differentially abundant proteins (DAPs) in barley roots during the tillering stage. Bioinformatic tools were used to interpret the biological function, the pathway analysis and the visualisation of the network amongst the identified proteins. A total of 72 DAPs (33 upregulated and 39 downregulated) among a total of 2580 proteins were identified in response to compost treatment, suggesting multiple pathways of primary and secondary metabolism, such as carbohydrates and energy metabolism, phenylpropanoid pathway, glycolysis pathway, protein synthesis and degradation, redox homeostasis, RNA processing, stress response, cytoskeleton organisation, and phytohormone metabolic pathways. The expression of DAPs was further validated by qRT-PCR. The effects on barley plant development, such as the promotion of root growth and biomass increase, were associated with a change in energy metabolism and protein synthesis. The activation of enzymes involved in redox homeostasis and the regulation of stress response proteins suggest a protective effect of compost, consequently improving barley growth and stress acclimation through the reduction of the environmental impact of productive agriculture. Overall, these results may facilitate a better understanding of the molecular mechanism of compost-promoted plant growth and provide valuable information for the identification of critical genes/proteins in barley as potential targets of compost.
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Affiliation(s)
- Emna Ghouili
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, (L2AD, CBBC), P.O. Box 901, Hammam-Lif 2050, Tunisia
| | - Khaled Sassi
- Laboratory of Agronomy, National Agronomy Institute of Tunisia (INAT), University of Carthage, Avenue Charles Nicolle, Tunis-Mahrajène, P.O. Box 43, Tunis 1082, Tunisia
| | - Yassine Hidri
- Laboratory of Integrated Olive Production in the Humid, Sub-humid and Semi-arid Region (LR16IO3), Olive Tree Institute, Cité Mahragène, P.O. Box 208, Tunis 1082, Tunisia
| | - Hatem Cheikh M’Hamed
- Agronomy Laboratory, National Institute of Agronomic Research of Tunis (INRAT), Carthage University, Hedi Karray Street, Ariana 2049, Tunisia
| | - Anil Somenahally
- Department of Soil and Crop Sciences, Texas A&M University, 370 Olsen Blvd, College Station, TX 77843-2474, USA
| | - Qingwu Xue
- Texas A&M AgriLife Research and Extension Center, Amarillo, TX 79403-6603, USA
| | - Moez Jebara
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, (L2AD, CBBC), P.O. Box 901, Hammam-Lif 2050, Tunisia
| | - Rim Nefissi Ouertani
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj Cedria, P.O. Box 901, Hammam-Lif 2050, Tunisia
| | - Jouhaina Riahi
- Laboratory of Agronomy, National Agronomy Institute of Tunisia (INAT), University of Carthage, Avenue Charles Nicolle, Tunis-Mahrajène, P.O. Box 43, Tunis 1082, Tunisia
| | - Ana Caroline de Oliveira
- Biological Engineering Unit, Department of Life Sciences, Walloon Agricultural Research Centre, Chaussée de Charleroi, P.O. Box 234, 5030 Gembloux, Belgium
| | - Ghassen Abid
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, (L2AD, CBBC), P.O. Box 901, Hammam-Lif 2050, Tunisia
| | - Yordan Muhovski
- Biological Engineering Unit, Department of Life Sciences, Walloon Agricultural Research Centre, Chaussée de Charleroi, P.O. Box 234, 5030 Gembloux, Belgium
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30
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Brauer BL, Wiredu K, Gerber SA, Kettenbach AN. Evaluation of Quantification and Normalization Strategies for Phosphoprotein Phosphatase Affinity Proteomics: Application to Breast Cancer Signaling. J Proteome Res 2023; 22:47-61. [PMID: 36448918 PMCID: PMC10625046 DOI: 10.1021/acs.jproteome.2c00465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Accurate quantification of proteomics data is essential for revealing and understanding biological signaling processes. We have recently developed a chemical proteomic strategy termed phosphatase inhibitor beads and mass spectrometry (PIB-MS) to investigate endogenous phosphoprotein phosphatase (PPP) dephosphorylation signaling. Here, we compare the robustness and reproducibility of status quo quantification methods for optimal performance and ease of implementation. We then apply PIB-MS to an array of breast cancer cell lines to determine differences in PPP signaling between subtypes. Breast cancer, a leading cause of cancer death in women, consists of three main subtypes: estrogen receptor-positive (ER+), human epidermal growth factor receptor two positive (HER2+), and triple-negative (TNBC). Although there are effective treatment strategies for ER+ and HER2+ subtypes, tumors become resistant and progress. Furthermore, TNBC has few targeted therapies. Therefore, there is a need to identify new approaches for treating breast cancers. Using PIB-MS, we distinguished TNBC from non-TNBC based on subtype-specific PPP holoenzyme composition. In addition, we identified an increase in PPP interactions with Hippo pathway proteins in TNBC. These interactions suggest that phosphatases in TNBC play an inhibitory role on the Hippo pathway and correlate with increased expression of YAP/TAZ target genes both in TNBC cell lines and in TNBC patients.
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Affiliation(s)
- Brooke L. Brauer
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH
| | - Kwame Wiredu
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH
| | - Scott A. Gerber
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH
- Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH
| | - Arminja N. Kettenbach
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH
- Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH
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31
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Pinto MJ, Cottin L, Dingli F, Laigle V, Ribeiro LF, Triller A, Henderson F, Loew D, Fabre V, Bessis A. Microglial TNFα orchestrates protein phosphorylation in the cortex during the sleep period and controls homeostatic sleep. EMBO J 2023; 42:e111485. [PMID: 36385434 PMCID: PMC9811617 DOI: 10.15252/embj.2022111485] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 10/04/2022] [Accepted: 10/11/2022] [Indexed: 11/18/2022] Open
Abstract
Sleep intensity is adjusted by the length of previous awake time, and under tight homeostatic control by protein phosphorylation. Here, we establish microglia as a new cellular component of the sleep homeostasis circuit. Using quantitative phosphoproteomics of the mouse frontal cortex, we demonstrate that microglia-specific deletion of TNFα perturbs thousands of phosphorylation sites during the sleep period. Substrates of microglial TNFα comprise sleep-related kinases such as MAPKs and MARKs, and numerous synaptic proteins, including a subset whose phosphorylation status encodes sleep need and determines sleep duration. As a result, microglial TNFα loss attenuates the build-up of sleep need, as measured by electroencephalogram slow-wave activity and prevents immediate compensation for loss of sleep. Our data suggest that microglia control sleep homeostasis by releasing TNFα which acts on neuronal circuitry through dynamic control of phosphorylation.
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Affiliation(s)
- Maria J Pinto
- Institut de Biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERMUniversité PSLParisFrance
| | - Léa Cottin
- Institut de Biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERMUniversité PSLParisFrance
| | - Florent Dingli
- Centre de Recherche, Laboratoire de Spectrométrie de Masse ProtéomiqueInstitut Curie, PSL Research UniversityParisFrance
| | - Victor Laigle
- Centre de Recherche, Laboratoire de Spectrométrie de Masse ProtéomiqueInstitut Curie, PSL Research UniversityParisFrance
| | - Luís F Ribeiro
- Center for Neuroscience and Cell Biology (CNC), Institute for Interdisciplinary Research (IIIUC)University of CoimbraCoimbraPortugal
| | - Antoine Triller
- Institut de Biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERMUniversité PSLParisFrance
| | - Fiona Henderson
- Sorbonne Université, CNRS UMR 8246, INSERM U1130, Neuroscience Paris Seine – Institut de Biologie Paris Seine (NPS – IBPS)ParisFrance
| | - Damarys Loew
- Centre de Recherche, Laboratoire de Spectrométrie de Masse ProtéomiqueInstitut Curie, PSL Research UniversityParisFrance
| | - Véronique Fabre
- Sorbonne Université, CNRS UMR 8246, INSERM U1130, Neuroscience Paris Seine – Institut de Biologie Paris Seine (NPS – IBPS)ParisFrance
| | - Alain Bessis
- Institut de Biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERMUniversité PSLParisFrance
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Giai Gianetto Q. Statistical Analysis of Post-Translational Modifications Quantified by Label-Free Proteomics Across Multiple Biological Conditions with R: Illustration from SARS-CoV-2 Infected Cells. Methods Mol Biol 2023; 2426:267-302. [PMID: 36308693 DOI: 10.1007/978-1-0716-1967-4_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Protein post-translational modifications (PTMs) are essential elements of cellular communication. Their variations in abundance can affect cellular pathways, leading to cellular disorders and diseases. A widely used method for revealing PTM-mediated regulatory networks is their label-free quantitation (LFQ) by high-resolution mass spectrometry. The raw data resulting from such experiments are generally interpreted using specific software, such as MaxQuant, MassChroQ, or Proline for instance. They provide data matrices containing quantified intensities for each modified peptide identified. Statistical analyses are then necessary (1) to ensure that the quantified data are of good enough quality and sufficiently reproducible, (2) to highlight the modified peptides that are differentially abundant between the biological conditions under study. The objective of this chapter is therefore to provide a complete data analysis pipeline for analyzing the quantified values of modified peptides in presence of two or more biological conditions using the R software. We illustrate our pipeline starting from MaxQuant outputs dealing with the analysis of A549-ACE2 cells infected by SARS-CoV-2 at different time stamps, freely available on PRIDE (PXD020019).
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Affiliation(s)
- Quentin Giai Gianetto
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France.
- Institut Pasteur, Université Paris Cité, Proteomic Platform, Mass Spectrometry for Biology Unit, CNRS, UAR 2024, Paris, France.
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33
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Fibroblast growth factor-2 bound to specific dermal fibroblast-derived extracellular vesicles is protected from degradation. Sci Rep 2022; 12:22131. [PMID: 36550142 PMCID: PMC9780220 DOI: 10.1038/s41598-022-26217-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Fibroblast growth factor-2 (FGF2) has multiple roles in cutaneous wound healing but its natural low stability prevents the development of its use in skin repair therapies. Here we show that FGF2 binds the outer surface of dermal fibroblast (DF)-derived extracellular vesicles (EVs) and this association protects FGF2 from fast degradation. EVs isolated from DF cultured in the presence of FGF2 harbor FGF2 on their surface and FGF2 can bind purified EVs in absence of cells. Remarkably, FGF2 binding to EVs is restricted to a specific subpopulation of EVs, which do not express CD63 and CD81 markers. Treatment of DF with FGF2-EVs activated ERK and STAT signaling pathways and increased cell proliferation and migration. Local injection of FGF2-EVs improved wound healing in mice. We further demonstrated that binding to EVs protects FGF2 from both thermal and proteolytic degradation, thus maintaining FGF2 function. This suggests that EVs protect soluble factors from degradation and increase their stability and half-life. These results reveal a novel aspect of EV function and suggest EVs as a potential tool for delivering FGF2 in skin healing therapies.
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34
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Ghouili E, Abid G, Jebara M, Nefissi Ouertani R, de Oliveira AC, El Ayed M, Muhovski Y. Proteomic Analysis of Barley ( Hordeum vulgare L.) Leaves in Response to Date Palm Waste Compost Application. PLANTS (BASEL, SWITZERLAND) 2022; 11:3287. [PMID: 36501326 PMCID: PMC9737688 DOI: 10.3390/plants11233287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/26/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Composts are an emerging biofertilizers used in agronomy that can improve crop performance, but much less is known regarding their modes of action. The current study aimed to investigate the differentially abundant proteins (DAPs) in barley leaves associated with growth promotion induced by application of date palm waste compost. Morphophysiological measurements revealed that compost induced a significant increase in plant height, chlorophyll content, gas exchange parameters and plant biomass. LC-MS/MS analyses indicate that compost induced global changes in the proteome of barley leaves. A total of 62 DAPs (26 upregulated and 36 downregulated) among a total of 2233 proteins were identified in response to compost application. The expression of DAPs was further validated based on qRT-PCR. Compost application showed altered abundance of several proteins related to abiotic stress, plant defense, redox homeostasis, transport, tricarboxylic acid cycle, carbohydrate, amino acid, energy and protein metabolism. Furthermore, proteins related to metabolic processes of phytohormone, DNA methylation and secondary metabolites were induced. These results indicate that barley responds to compost application by complex metabolism pathways and may result in a positive alteration in a physiological and metabolic barley plant state which consequently could lead to improved growth and stress adaptation observed in compost-treated plants.
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Affiliation(s)
- Emna Ghouili
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, (L2AD, CBBC), P. B. 901, Hammam-Lif 2050, Tunisia
| | - Ghassen Abid
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, (L2AD, CBBC), P. B. 901, Hammam-Lif 2050, Tunisia
| | - Moez Jebara
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, (L2AD, CBBC), P. B. 901, Hammam-Lif 2050, Tunisia
| | - Rim Nefissi Ouertani
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj Cedria, BP 901, Hammam-Lif 2050, Tunisia
| | - Ana Caroline de Oliveira
- Biological Engineering Unit, Department of Life Sciences, Walloon Agricultural Research Centre, Chaussée de Charleroi, BP 234, 5030 Gembloux, Belgium
| | - Mohamed El Ayed
- Laboratory of Bioactive Substances, Centre of Biotechnology of Borj Cedria, BP 901, Hammam-Lif 2050, Tunisia
| | - Yordan Muhovski
- Biological Engineering Unit, Department of Life Sciences, Walloon Agricultural Research Centre, Chaussée de Charleroi, BP 234, 5030 Gembloux, Belgium
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35
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Diffendall GM, Barcons-Simon A, Baumgarten S, Dingli F, Loew D, Scherf A. Discovery of RUF6 ncRNA-interacting proteins involved in P. falciparum immune evasion. Life Sci Alliance 2022; 6:6/1/e202201577. [PMID: 36379669 PMCID: PMC9670795 DOI: 10.26508/lsa.202201577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 10/25/2022] [Accepted: 10/26/2022] [Indexed: 11/16/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are emerging regulators of immune evasion and transmission of Plasmodium falciparum RUF6 is an ncRNA gene family that is transcribed by RNA polymerase III but actively regulates the Pol II-transcribed var virulence gene family. Understanding how RUF6 ncRNA connects to downstream effectors is lacking. We developed an RNA-directed proteomic discovery (ChIRP-MS) protocol to identify in vivo RUF6 ncRNA-protein interactions. The RUF6 ncRNA interactome was purified with biotinylated antisense oligonucleotides. Quantitative label-free mass spectrometry identified several unique proteins linked to gene transcription including RNA Pol II subunits, nucleosome assembly proteins, and a homologue of DEAD box helicase 5 (DDX5). Affinity purification of Pf-DDX5 identified proteins originally found by our RUF6-ChIRP protocol, validating the technique's robustness for identifying ncRNA interactomes in P. falciparum Inducible displacement of nuclear Pf-DDX5 resulted in significant down-regulation of the active var gene. Our work identifies a RUF6 ncRNA-protein complex that interacts with RNA Pol II to sustain the var gene expression, including a helicase that may resolve G-quadruplex secondary structures in var genes to facilitate transcriptional activation and progression.
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Affiliation(s)
- Gretchen M Diffendall
- Universite Paris Cité, Institut Pasteur, Biology of Host-Parasite Interactions Unit, INSERM U1201, CNRS EMR9195, Paris, France,Sorbonne Université Ecole doctorale Complexité du Vivant ED515, Paris, France
| | - Anna Barcons-Simon
- Universite Paris Cité, Institut Pasteur, Biology of Host-Parasite Interactions Unit, INSERM U1201, CNRS EMR9195, Paris, France,Sorbonne Université Ecole doctorale Complexité du Vivant ED515, Paris, France,Biomedical Center, Division of Physiological Chemistry, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | | | - Florent Dingli
- Institut Curie, PSL Research University, Centre de Recherche, CurieCoreTech Mass Spectrometry Proteomics, Paris, France
| | - Damarys Loew
- Institut Curie, PSL Research University, Centre de Recherche, CurieCoreTech Mass Spectrometry Proteomics, Paris, France
| | - Artur Scherf
- Universite Paris Cité, Institut Pasteur, Biology of Host-Parasite Interactions Unit, INSERM U1201, CNRS EMR9195, Paris, France
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36
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Leduc A, Le Guillou S, Bianchi L, Correia LO, Gelé M, Pires J, Martin P, Leroux C, Le Provost F, Boutinaud M. Milk proteins as a feed restriction signature indicating the metabolic adaptation of dairy cows. Sci Rep 2022; 12:18886. [PMID: 36344510 PMCID: PMC9640695 DOI: 10.1038/s41598-022-21804-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 10/04/2022] [Indexed: 11/09/2022] Open
Abstract
Milk production in dairy cows is affected by numerous factors, including diet. Feed restriction is known to have little impact on milk total protein content but its effect on the fine protein composition is still poorly documented. The objective of this study was to describe the effects of two feed restriction trials of different intensities on the milk protein composition of Holstein cows. One restriction trial was of high intensity (H: 8 mid-lactation Holstein cows) and the second of moderate intensity (M: 19 peak lactation Holstein cows). Feed restriction decreased the milk protein yield for caseins under the M trial and of all six major milk proteins under the H trial. These decreased yields lead to lower concentrations of αs1-, αs2- and β-caseins during the H trial. The milk proteome, analyzed on 32 milk samples, was affected as a function of restriction intensity. Among the 345 proteins identified eight varied under the M trial and 160 under the H trial. Ontology analyses revealed their implication in carbohydrate, lipid and protein metabolisms as well as in the immune system. These proteins reflected adaptations of the animal and mammary gland physiology to feed restriction and constituted a signature of this change.
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Affiliation(s)
- A Leduc
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
- INRAE, Institut Agro Rennes Angers, PEGASE, 35590, Saint-Gilles, France
- Institut de L'Elevage, 75012, Paris, France
| | - S Le Guillou
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - L Bianchi
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - L Oliveira Correia
- INRAE, AgroParisTech, Micalis Institute, PAPPSO, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - M Gelé
- Institut de L'Elevage, 75012, Paris, France
| | - J Pires
- INRAE, UMRH, Vetagro Sup, Université Clermont Auvergne, 63122, Saint-Genès-Champanelle, France
| | - P Martin
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - C Leroux
- INRAE, UMRH, Vetagro Sup, Université Clermont Auvergne, 63122, Saint-Genès-Champanelle, France
| | - F Le Provost
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - M Boutinaud
- INRAE, Institut Agro Rennes Angers, PEGASE, 35590, Saint-Gilles, France.
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37
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da Luz BSR, de Rezende Rodovalho V, Nicolas A, Chabelskaya S, Jardin J, Briard-Bion V, Le Loir Y, de Carvalho Azevedo VA, Guédon É. Impact of Environmental Conditions on the Protein Content of Staphylococcus aureus and Its Derived Extracellular Vesicles. Microorganisms 2022; 10:microorganisms10091808. [PMID: 36144410 PMCID: PMC9506334 DOI: 10.3390/microorganisms10091808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/01/2022] [Accepted: 09/04/2022] [Indexed: 12/03/2022] Open
Abstract
Staphylococcus aureus, a major opportunistic pathogen in humans, produces extracellular vesicles (EVs) that are involved in cellular communication, the delivery of virulence factors, and modulation of the host immune system response. However, to date, the impact of culture conditions on the physicochemical and functional properties of S. aureus EVs is still largely unexplored. Here, we use a proteomic approach to provide a complete protein characterization of S. aureus HG003, a NCTC8325 derivative strain and its derived EVs under four growth conditions: early- and late-stationary growth phases, and in the absence and presence of a sub-inhibitory concentration of vancomycin. The HG003 EV protein composition in terms of subcellular localization, COG and KEGG categories, as well as their relative abundance are modulated by the environment and differs from that of whole-cell (WC). Moreover, the environmental conditions that were tested had a more pronounced impact on the EV protein composition when compared to the WC, supporting the existence of mechanisms for the selective packing of EV cargo. This study provides the first general picture of the impact of different growth conditions in the proteome of S. aureus EVs and its producing-cells and paves the way for future studies to understand better S. aureus EV production, composition, and roles.
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Affiliation(s)
- Brenda Silva Rosa da Luz
- INRAE, Institut Agro, STLO, F-35000 Rennes, France
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Vinícius de Rezende Rodovalho
- INRAE, Institut Agro, STLO, F-35000 Rennes, France
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
| | | | - Svetlana Chabelskaya
- BRM (Bacterial Regulatory RNAs and Medicine) UMR_S 1230, Inserm 1230, University of Rennes 1, 35000 Rennes, France
| | | | | | - Yves Le Loir
- INRAE, Institut Agro, STLO, F-35000 Rennes, France
| | - Vasco Ariston de Carvalho Azevedo
- Laboratory of Cellular and Molecular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Éric Guédon
- INRAE, Institut Agro, STLO, F-35000 Rennes, France
- Correspondence:
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38
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Label-Free Quantitative Proteomics Reveal the Involvement of PRT6 in Arabidopsis thaliana Seed Responsiveness to Ethylene. Int J Mol Sci 2022; 23:ijms23169352. [PMID: 36012613 PMCID: PMC9409418 DOI: 10.3390/ijms23169352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/11/2022] [Accepted: 08/16/2022] [Indexed: 11/17/2022] Open
Abstract
In Arabidopsis thaliana, the breaking of seed dormancy in wild type (Col-0) by ethylene at 100 μL L-1 required at least 30 h application. A mutant of the proteolytic N-degron pathway, lacking the E3 ligase PROTEOLYSIS 6 (PRT6), was investigated for its role in ethylene-triggered changes in proteomes during seed germination. Label-free quantitative proteomics was carried out on dormant wild type Col-0 and prt6 seeds treated with (+) or without (-) ethylene. After 16 h, 1737 proteins were identified, but none was significantly different in protein levels in response to ethylene. After longer ethylene treatment (30 h), 2552 proteins were identified, and 619 Differentially Expressed Proteins (DEPs) had significant differences in protein abundances between ethylene treatments and genotypes. In Col, 587 DEPs were enriched for those involved in signal perception and transduction, reserve mobilization and new material generation, which potentially contributed to seed germination. DEPs up-regulated by ethylene in Col included S-adenosylmethionine synthase 1, methionine adenosyltransferase 3 and ACC oxidase involved in ethylene synthesis and of Pyrabactin Resistance1 acting as an ABA receptor, while DEPs down-regulated by ethylene in Col included aldehyde oxidase 4 involved in ABA synthesis. In contrast, in prt6 seeds, ethylene did not result in strong proteomic changes with only 30 DEPs. Taken together, the present work demonstrates that the proteolytic N-degron pathway is essential for ethylene-mediated reprogramming of seed proteomes during germination.
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39
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Luciano AK, Korobkina E, Lyons SP, Haley JA, Fluharty S, Jung SM, Kettenbach AN, Guertin DA. Proximity labeling of endogenous RICTOR identifies mTOR Complex 2 regulation by ADP ribosylation factor ARF1. J Biol Chem 2022; 298:102379. [PMID: 35973513 PMCID: PMC9513271 DOI: 10.1016/j.jbc.2022.102379] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 07/22/2022] [Accepted: 08/09/2022] [Indexed: 01/08/2023] Open
Abstract
Mechanistic target of rapamycin (mTOR) complex 2 (mTORC2) regulates metabolism, cell proliferation, and cell survival. mTORC2 activity is stimulated by growth factors, and it phosphorylates the hydrophobic motif site of the AGC kinases AKT, SGK, and PKC. However, the proteins that interact with mTORC2 to control its activity and localization remain poorly defined. To identify mTORC2-interacting proteins in living cells, we tagged endogenous RICTOR, an essential mTORC2 subunit, with the modified BirA biotin ligase BioID2 and performed live-cell proximity labeling. We identified 215 RICTOR-proximal proteins, including proteins with known mTORC2 pathway interactions, and 135 proteins (63%) not previously linked to mTORC2 signaling, including nuclear and cytoplasmic proteins. Our imaging and cell fractionation experiments suggest nearly 30% of RICTOR is in the nucleus, hinting at potential nuclear functions. We also identified 29 interactors containing RICTOR-dependent, insulin-stimulated phosphorylation sites, thus providing insight into mTORC2-dependent insulin signaling dynamics. Finally, we identify the endogenous ADP ribosylation factor 1 (ARF1) GTPase as an mTORC2-interacting protein. Through gain-of-function and loss-of-function studies, we provide functional evidence that ARF1 may negatively regulate mTORC2. In summary, we present a new method of studying endogenous mTORC2, a resource of RICTOR/mTORC2 protein interactions in living cells, and a potential mechanism of mTORC2 regulation by the ARF1 GTPase.
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Affiliation(s)
- Amelia K Luciano
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605
| | - Ekaterina Korobkina
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605
| | - Scott P Lyons
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755
| | - John A Haley
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605
| | - Shelagh Fluharty
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605
| | - Su Myung Jung
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605
| | - Arminja N Kettenbach
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755; Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Hanover, NH 03755
| | - David A Guertin
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605; Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605.
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40
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Peslerbes M, Fellenberg A, Jardin J, Deglaire A, Ibáñez RA. Manufacture of Whey Protein Hydrolysates Using Plant Enzymes: Effect of Processing Conditions and Simulated Gastrointestinal Digestion on Angiotensin-I-Converting Enzyme (ACE) Inhibitory Activity. Foods 2022; 11:foods11162429. [PMID: 36010429 PMCID: PMC9407499 DOI: 10.3390/foods11162429] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/03/2022] [Accepted: 08/08/2022] [Indexed: 11/19/2022] Open
Abstract
Hydrolysis of proteins leads to the release of bioactive peptides with positive impact on human health. Peptides exhibiting antihypertensive properties (i.e., inhibition of angiotensin-I-converting enzyme) are commonly found in whey protein hydrolysates made with enzymes of animal, plant or microbial origin. However, bioactive properties can be influenced by processing conditions and gastrointestinal digestion. In this study, we evaluated the impact of three plant enzymes (papain, bromelain and ficin) in the manufacture of whey protein hydrolysates with varying level of pH, enzyme-to-substrate ratio and time of hydrolysis, based on a central composite design, to determine the degree of hydrolysis and antihypertensive properties. Hydrolysates made on laboratory scales showed great variation in the type of enzyme used, their concentrations and the pH level of hydrolysis. However, low degrees of hydrolysis in papain and bromelain treatments were associated with increased antihypertensive properties, when compared to ficin. Simulated gastrointestinal digestion performed for selected hydrolysates showed an increase in antihypertensive properties of hydrolysates made with papain and bromelain, which was probably caused by further release of peptides. Several peptides with reported antihypertensive properties were found in all treatments. These results suggest plant enzymes used in this study can be suitable candidates to develop ingredients with bioactive properties.
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Affiliation(s)
- Marie Peslerbes
- Departamento de Ciencias Animales, Facultad de Agronomia e Ingenieria Forestal, Pontificia Universidad Catolica de Chile, Macul, Santiago 7820436, Chile
- École Supérieure D’agricultures Angers Loire, 49000 Angers, France
| | - Angélica Fellenberg
- Departamento de Ciencias Animales, Facultad de Agronomia e Ingenieria Forestal, Pontificia Universidad Catolica de Chile, Macul, Santiago 7820436, Chile
- Correspondence: (A.F.); (R.A.I.); Tel.: +56-2-2354-4147 (A.F.); +1-608-262-3268 (R.A.I)
| | | | | | - Rodrigo A. Ibáñez
- Departamento de Ciencias Animales, Facultad de Agronomia e Ingenieria Forestal, Pontificia Universidad Catolica de Chile, Macul, Santiago 7820436, Chile
- Center for Dairy Research, University of Wisconsin-Madison, Madison, WI 53706, USA
- Correspondence: (A.F.); (R.A.I.); Tel.: +56-2-2354-4147 (A.F.); +1-608-262-3268 (R.A.I)
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41
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Plancade S, Berland M, Blein-Nicolas M, Langella O, Bassignani A, Juste C. A combined test for feature selection on sparse metaproteomics data-an alternative to missing value imputation. PeerJ 2022; 10:e13525. [PMID: 35769140 PMCID: PMC9235818 DOI: 10.7717/peerj.13525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 05/11/2022] [Indexed: 01/18/2023] Open
Abstract
One of the difficulties encountered in the statistical analysis of metaproteomics data is the high proportion of missing values, which are usually treated by imputation. Nevertheless, imputation methods are based on restrictive assumptions regarding missingness mechanisms, namely "at random" or "not at random". To circumvent these limitations in the context of feature selection in a multi-class comparison, we propose a univariate selection method that combines a test of association between missingness and classes, and a test for difference of observed intensities between classes. This approach implicitly handles both missingness mechanisms. We performed a quantitative and qualitative comparison of our procedure with imputation-based feature selection methods on two experimental data sets, as well as simulated data with various scenarios regarding the missingness mechanisms and the nature of the difference of expression (differential intensity or differential presence). Whereas we observed similar performances in terms of prediction on the experimental data set, the feature ranking and selection from various imputation-based methods were strongly divergent. We showed that the combined test reaches a compromise by correlating reasonably with other methods, and remains efficient in all simulated scenarios unlike imputation-based feature selection methods.
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Affiliation(s)
- Sandra Plancade
- UR875 MIAT, Université fédérale de Toulouse, INRAE, Castanet-Tolosan, France
| | - Magali Berland
- Université Paris-Saclay, INRAE, MGP, Jouy en Josas, France
| | - Mélisande Blein-Nicolas
- Université Paris-Saclay, CNRS, INRAE, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette, France,Université Paris-Saclay, CNRS, INRAE, AgroParisTech, PAPPSO, Gif-sur-Yvette, France
| | - Olivier Langella
- Université Paris-Saclay, CNRS, INRAE, AgroParisTech, GQE-Le Moulon, Gif-sur-Yvette, France,Université Paris-Saclay, CNRS, INRAE, AgroParisTech, PAPPSO, Gif-sur-Yvette, France
| | - Ariane Bassignani
- Université Paris-Saclay, INRAE, MGP, Jouy en Josas, France,Université Paris-Saclay, CNRS, INRAE, AgroParisTech, PAPPSO, Gif-sur-Yvette, France
| | - Catherine Juste
- Micalis Institute, Université Paris-Saclay, INRAE, AgroParis Tech, Jouy-en-Josas, France
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42
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Baudouin E, Puyaubert J, Meimoun P, Blein-Nicolas M, Davanture M, Zivy M, Bailly C. Dynamics of Protein Phosphorylation during Arabidopsis Seed Germination. Int J Mol Sci 2022; 23:ijms23137059. [PMID: 35806063 PMCID: PMC9266807 DOI: 10.3390/ijms23137059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/16/2022] [Accepted: 06/22/2022] [Indexed: 11/16/2022] Open
Abstract
Seed germination is critical for early plantlet development and is tightly controlled by environmental factors. Nevertheless, the signaling networks underlying germination control remain elusive. In this study, the remodeling of Arabidopsis seed phosphoproteome during imbibition was investigated using stable isotope dimethyl labeling and nanoLC-MS/MS analysis. Freshly harvested seeds were imbibed under dark or constant light to restrict or promote germination, respectively. For each light regime, phosphoproteins were extracted and identified from dry and imbibed (6 h, 16 h, and 24 h) seeds. A large repertoire of 10,244 phosphopeptides from 2546 phosphoproteins, including 110 protein kinases and key regulators of seed germination such as Delay Of Germination 1 (DOG1), was established. Most phosphoproteins were only identified in dry seeds. Early imbibition led to a similar massive downregulation in dormant and non-dormant seeds. After 24 h, 411 phosphoproteins were specifically identified in non-dormant seeds. Gene ontology analyses revealed their involvement in RNA and protein metabolism, transport, and signaling. In addition, 489 phosphopeptides were quantified, and 234 exhibited up or downregulation during imbibition. Interaction networks and motif analyses revealed their association with potential signaling modules involved in germination control. Our study provides evidence of a major role of phosphosignaling in the regulation of Arabidopsis seed germination.
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Affiliation(s)
- Emmanuel Baudouin
- Laboratoire de Biologie du Développement, UMR 7622, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, CNRS, F-75005 Paris, France; (J.P.); (P.M.); (C.B.)
- Correspondence: ; Tel.: +33-1-44-27-59-87
| | - Juliette Puyaubert
- Laboratoire de Biologie du Développement, UMR 7622, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, CNRS, F-75005 Paris, France; (J.P.); (P.M.); (C.B.)
| | - Patrice Meimoun
- Laboratoire de Biologie du Développement, UMR 7622, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, CNRS, F-75005 Paris, France; (J.P.); (P.M.); (C.B.)
| | - Mélisande Blein-Nicolas
- PAPPSO, Génétique Quantitative et Evolution (GQE), Université Paris-Saclay, INRAE, CNRS, AgroParisTech, F-91190 Gif-sur-Yvette, France; (M.B.-N.); (M.D.); (M.Z.)
| | - Marlène Davanture
- PAPPSO, Génétique Quantitative et Evolution (GQE), Université Paris-Saclay, INRAE, CNRS, AgroParisTech, F-91190 Gif-sur-Yvette, France; (M.B.-N.); (M.D.); (M.Z.)
| | - Michel Zivy
- PAPPSO, Génétique Quantitative et Evolution (GQE), Université Paris-Saclay, INRAE, CNRS, AgroParisTech, F-91190 Gif-sur-Yvette, France; (M.B.-N.); (M.D.); (M.Z.)
| | - Christophe Bailly
- Laboratoire de Biologie du Développement, UMR 7622, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, CNRS, F-75005 Paris, France; (J.P.); (P.M.); (C.B.)
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Vit G, Duro J, Rajendraprasad G, Hertz EPT, Holland LKK, Weisser MB, McEwan BC, Lopez‐Mendez B, Sotelo‐Parrilla P, Jeyaprakash AA, Montoya G, Mailand N, Maeda K, Kettenbach A, Barisic M, Nilsson J. Chemogenetic profiling reveals PP2A-independent cytotoxicity of proposed PP2A activators iHAP1 and DT-061. EMBO J 2022; 41:e110611. [PMID: 35695070 PMCID: PMC9289710 DOI: 10.15252/embj.2022110611] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 01/01/2023] Open
Abstract
Protein phosphatase 2A (PP2A) is an abundant phosphoprotein phosphatase that acts as a tumor suppressor. For this reason, compounds able to activate PP2A are attractive anticancer agents. The compounds iHAP1 and DT-061 have recently been reported to selectively stabilize specific PP2A-B56 complexes to mediate cell killing. We were unable to detect direct effects of iHAP1 and DT-061 on PP2A-B56 activity in biochemical assays and composition of holoenzymes. Therefore, we undertook genome-wide CRISPR-Cas9 synthetic lethality screens to uncover biological pathways affected by these compounds. We found that knockout of mitotic regulators is synthetic lethal with iHAP1 while knockout of endoplasmic reticulum (ER) and Golgi components is synthetic lethal with DT-061. Indeed we showed that iHAP1 directly blocks microtubule assembly both in vitro and in vivo and thus acts as a microtubule poison. In contrast, DT-061 disrupts both the Golgi apparatus and the ER and lipid synthesis associated with these structures. Our work provides insight into the biological pathways perturbed by iHAP1 and DT-061 causing cellular toxicity and argues that these compounds cannot be used for dissecting PP2A-B56 biology.
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Affiliation(s)
- Gianmatteo Vit
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Joana Duro
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Girish Rajendraprasad
- Cell Division and CytoskeletonDanish Cancer Society Research CenterCopenhagenDenmark
| | - Emil P T Hertz
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Lya Katrine Kauffeldt Holland
- Cell Death and Metabolism UnitCenter for Autophagy, Recycling and Disease (CARD)Danish Cancer Society Research Center (DCRC)CopenhagenDenmark
| | - Melanie Bianca Weisser
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Brennan C McEwan
- Department of Biochemistry and Cell BiologyGeisel School of Medicine at Dartmouth CollegeHanoverNHUSA,Norris Cotton Cancer CenterLebanonNHUSA
| | - Blanca Lopez‐Mendez
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | | | | | - Guillermo Montoya
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Niels Mailand
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Kenji Maeda
- Cell Death and Metabolism UnitCenter for Autophagy, Recycling and Disease (CARD)Danish Cancer Society Research Center (DCRC)CopenhagenDenmark
| | - Arminja Kettenbach
- Department of Biochemistry and Cell BiologyGeisel School of Medicine at Dartmouth CollegeHanoverNHUSA
| | - Marin Barisic
- Cell Division and CytoskeletonDanish Cancer Society Research CenterCopenhagenDenmark,Department of Cellular and Molecular MedicineFaculty of Health SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Jakob Nilsson
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
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Sano N, Lounifi I, Cueff G, Collet B, Clément G, Balzergue S, Huguet S, Valot B, Galland M, Rajjou L. Multi-Omics Approaches Unravel Specific Features of Embryo and Endosperm in Rice Seed Germination. FRONTIERS IN PLANT SCIENCE 2022; 13:867263. [PMID: 35755645 PMCID: PMC9225960 DOI: 10.3389/fpls.2022.867263] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 04/29/2022] [Indexed: 06/15/2023]
Abstract
Seed germination and subsequent seedling growth affect the final yield and quality of the crop. Seed germination is defined as a series of processes that begins with water uptake by a quiescent dry seed and ends with the elongation of embryonic axis. Rice is an important cereal crop species, and during seed germination, two tissues function in a different manner; the embryo grows into a seedling as the next generation and the endosperm is responsible for nutritional supply. Toward understanding the integrated roles of each tissue at the transcriptional, translational, and metabolic production levels during germination, an exhaustive "multi-omics" analysis was performed by combining transcriptomics, label-free shotgun proteomics, and metabolomics on rice germinating embryo and endosperm, independently. Time-course analyses of the transcriptome and metabolome in germinating seeds revealed a major turning point in the early phase of germination in both embryo and endosperm, suggesting that dramatic changes begin immediately after water imbibition in the rice germination program at least at the mRNA and metabolite levels. In endosperm, protein profiles mostly showed abundant decreases corresponding to 90% of the differentially accumulated proteins. An ontological classification revealed the shift from the maturation to the germination process where over-represented classes belonged to embryonic development and cellular amino acid biosynthetic processes. In the embryo, 19% of the detected proteins are differentially accumulated during germination. Stress response, carbohydrate, fatty acid metabolism, and transport are the main functional classes representing embryo proteome change. Moreover, proteins specific to the germinated state were detected by both transcriptomic and proteomic approaches and a major change in the network operating during rice germination was uncovered. In particular, concomitant changes of hormonal metabolism-related proteins (GID1L2 and CNX1) implicated in GAs and ABA metabolism, signaling proteins, and protein turnover events emphasized the importance of such biological networks in rice seeds. Using metabolomics, we highlighted the importance of an energetic supply in rice seeds during germination. In both embryo and endosperm, starch degradation, glycolysis, and subsequent pathways related to these cascades, such as the aspartate-family pathway, are activated during germination. A relevant number of accumulated proteins and metabolites, especially in embryos, testifies the pivotal role of energetic supply in the preparation of plant growth. This article summarizes the key genetic pathways in embryo and endosperm during rice seed germination at the transcriptional, translational, and metabolite levels and thereby, emphasizes the value of combined multi-omics approaches to uncover the specific feature of tissues during germination.
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Affiliation(s)
- Naoto Sano
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Imen Lounifi
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
- MBCC Group, Master Builders Construction Chemical, Singapore, Singapore
| | - Gwendal Cueff
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Boris Collet
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Gilles Clément
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Sandrine Balzergue
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, Beaucouzé, France
| | - Stéphanie Huguet
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Benoît Valot
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, PAPPSO, Plateforme d'Analyse de Proteomique Paris-Sud-Ouest, Gif-sur-Yvette, France
- Chrono-Environnement Research Team UMR/CNRS-6249, Bourgogne-Franche-Comté University, Besançon, France
| | - Marc Galland
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Loïc Rajjou
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
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45
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Vibert J, Saulnier O, Collin C, Petit F, Borgman KJE, Vigneau J, Gautier M, Zaidi S, Pierron G, Watson S, Gruel N, Hénon C, Postel-Vinay S, Deloger M, Raynal V, Baulande S, Laud-Duval K, Hill V, Grossetête S, Dingli F, Loew D, Torrejon J, Ayrault O, Orth MF, Grünewald TGP, Surdez D, Coulon A, Waterfall JJ, Delattre O. Oncogenic chimeric transcription factors drive tumor-specific transcription, processing, and translation of silent genomic regions. Mol Cell 2022; 82:2458-2471.e9. [PMID: 35550257 DOI: 10.1016/j.molcel.2022.04.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 02/20/2022] [Accepted: 04/14/2022] [Indexed: 12/11/2022]
Abstract
Many cancers are characterized by gene fusions encoding oncogenic chimeric transcription factors (TFs) such as EWS::FLI1 in Ewing sarcoma (EwS). Here, we find that EWS::FLI1 induces the robust expression of a specific set of novel spliced and polyadenylated transcripts within otherwise transcriptionally silent regions of the genome. These neogenes (NGs) are virtually undetectable in large collections of normal tissues or non-EwS tumors and can be silenced by CRISPR interference at regulatory EWS::FLI1-bound microsatellites. Ribosome profiling and proteomics further show that some NGs are translated into highly EwS-specific peptides. More generally, we show that hundreds of NGs can be detected in diverse cancers characterized by chimeric TFs. Altogether, this study identifies the transcription, processing, and translation of novel, specific, highly expressed multi-exonic transcripts from otherwise silent regions of the genome as a new activity of aberrant TFs in cancer.
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Affiliation(s)
- Julien Vibert
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France; INSERM U830, Integrative Functional Genomics of Cancer Lab, PSL Research University, Institut Curie Research Center, Paris, France; Department of Translational Research, PSL Research University, Institut Curie Research Center, Paris, France
| | - Olivier Saulnier
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - Céline Collin
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - Floriane Petit
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - Kyra J E Borgman
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR 3664, Laboratoire Dynamique du Noyau, 75005 Paris, France; Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005 Paris, France
| | - Jérômine Vigneau
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - Maud Gautier
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - Sakina Zaidi
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - Gaëlle Pierron
- Unité de Génétique Somatique, Service d'oncogénétique, Institut Curie, Centre Hospitalier, Paris, France
| | - Sarah Watson
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France; Medical Oncology Department, PSL Research University, Institut Curie Hospital, Paris, France
| | - Nadège Gruel
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France; Department of Translational Research, PSL Research University, Institut Curie Research Center, Paris, France
| | - Clémence Hénon
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France
| | - Sophie Postel-Vinay
- ATIP-Avenir group, Inserm Unit U981, Gustave Roussy, Villejuif, France; Drug Development Department, DITEP, Gustave Roussy, Villejuif, France
| | - Marc Deloger
- Bioinformatics and Computational Systems Biology of Cancer, PSL Research University, Mines Paris Tech, INSERM U900, Paris, France
| | - Virginie Raynal
- Institut Curie Genomics of Excellence (ICGex) Platform, PSL Research University, Institut Curie Research Center, Paris, France
| | - Sylvain Baulande
- Institut Curie Genomics of Excellence (ICGex) Platform, PSL Research University, Institut Curie Research Center, Paris, France
| | - Karine Laud-Duval
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - Véronique Hill
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - Sandrine Grossetête
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - Florent Dingli
- Laboratoire de Spectrométrie de Masse Protéomique, PSL Research University, Institut Curie Research Center, Paris, France
| | - Damarys Loew
- Laboratoire de Spectrométrie de Masse Protéomique, PSL Research University, Institut Curie Research Center, Paris, France
| | - Jacob Torrejon
- Institut Curie, CNRS UMR3347, INSERM, PSL Research University, Orsay, France; CNRS UMR 3347, INSERM U1021, Université Paris Sud, Université Paris-Saclay, Orsay, France
| | - Olivier Ayrault
- Institut Curie, CNRS UMR3347, INSERM, PSL Research University, Orsay, France; CNRS UMR 3347, INSERM U1021, Université Paris Sud, Université Paris-Saclay, Orsay, France
| | - Martin F Orth
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Thomas G P Grünewald
- Division of Translational Pediatric Sarcoma Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany; Hopp-Children's Cancer Center (KiTZ), Heidelberg, Germany; Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Didier Surdez
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France
| | - Antoine Coulon
- Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR 3664, Laboratoire Dynamique du Noyau, 75005 Paris, France; Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005 Paris, France
| | - Joshua J Waterfall
- INSERM U830, Integrative Functional Genomics of Cancer Lab, PSL Research University, Institut Curie Research Center, Paris, France; Department of Translational Research, PSL Research University, Institut Curie Research Center, Paris, France.
| | - Olivier Delattre
- INSERM U830, Équipe Labellisée LNCC, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, SIREDO Oncology Center, Institut Curie Research Center, Paris, France; Institut Curie, PSL Research University, Sorbonne Université, CNRS UMR 3664, Laboratoire Dynamique du Noyau, 75005 Paris, France.
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46
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Kage F, Vicente-Manzanares M, McEwan BC, Kettenbach AN, Higgs HN. Myosin II proteins are required for organization of calcium-induced actin networks upstream of mitochondrial division. Mol Biol Cell 2022; 33:ar63. [PMID: 35427150 PMCID: PMC9561854 DOI: 10.1091/mbc.e22-01-0005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The formin INF2 polymerizes a calcium-activated cytoplasmic network of actin filaments, which we refer to as calcium-induced actin polymerization (CIA). CIA plays important roles in multiple cellular processes, including mitochondrial dynamics and vesicle transport. Here, we show that nonmuscle myosin II (NMII) is activated within 60 s of calcium stimulation and rapidly recruited to the CIA network. Knockout of any individual NMII in U2OS cells affects the organization of the CIA network, as well as three downstream effects: endoplasmic-reticulum-to-mitochondrial calcium transfer, mitochondrial Drp1 recruitment, and mitochondrial division. Interestingly, while NMIIC is the least abundant NMII in U2OS cells (>200-fold less than NMIIA and >10-fold less than NMIIB), its knockout is equally deleterious to CIA. On the basis of these results, we propose that myosin II filaments containing all three NMII heavy chains exert organizational and contractile roles in the CIA network. In addition, NMIIA knockout causes a significant decrease in myosin regulatory light chain levels, which might have additional effects.
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Affiliation(s)
- Frieda Kage
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth College, Hanover NH 03755, USA
| | - Miguel Vicente-Manzanares
- Centro de Investigacion del Cancer/Instituto de Biologia Molecular y Celular del Cancer, Centro Mixto Universidad de Salamanca, 37007 Salamanca, Spain
| | - Brennan C. McEwan
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth College, Hanover NH 03755, USA
- Program in Cancer Biology, Geisel School of Medicine at Dartmouth College, Hanover NH 03755, USA
| | - Arminja N. Kettenbach
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth College, Hanover NH 03755, USA
- Program in Cancer Biology, Geisel School of Medicine at Dartmouth College, Hanover NH 03755, USA
| | - Henry N. Higgs
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth College, Hanover NH 03755, USA
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47
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Zang L, Tarkowski ŁP, Morère-Le Paven MC, Zivy M, Balliau T, Clochard T, Bahut M, Balzergue S, Pelletier S, Landès C, Limami AM, Montrichard F. The Nitrate Transporter MtNPF6.8 Is a Master Sensor of Nitrate Signal in the Primary Root Tip of Medicago truncatula. FRONTIERS IN PLANT SCIENCE 2022; 13:832246. [PMID: 35371178 PMCID: PMC8971838 DOI: 10.3389/fpls.2022.832246] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/22/2022] [Indexed: 06/12/2023]
Abstract
Nitrate is not only an essential nutrient for plants, but also a signal involved in plant development. We have previously shown in the model legume Medicago truncatula, that the nitrate signal, which restricts primary root growth, is mediated by MtNPF6.8, a nitrate transporter. Nitrate signal also induces changes in reactive oxygen species accumulation in the root tip due to changes in cell wall peroxidase (PODs) activity. Thus, it was interesting to determine the importance of the role of MtNPF6.8 in the regulation of the root growth by nitrate and identify the POD isoforms responsible for the changes in POD activity. For this purpose, we compared in M. truncatula a npf6.8 mutant and nitrate insensitive line deficient in MtNPF6.8 and the corresponding wild and sensitive genotype for their transcriptomic and proteomic responses to nitrate. Interestingly, only 13 transcripts and no protein were differently accumulated in the primary root tip of the npf6.8-3 mutant line in response to nitrate. The sensitivity of the primary root tip to nitrate appeared therefore to be strongly linked to the integrity of MtNPF6.8 which acts as a master mediator of the nitrate signal involved in the control of the root system architecture. In parallel, 7,259 and 493 genes responded, respectively, at the level of transcripts or proteins in the wild type, 196 genes being identified by both their transcript and protein. By focusing on these 196 genes, a concordance of expression was observed for most of them with 143 genes being up-regulated and 51 being down-regulated at the two gene expression levels. Their ontology analysis uncovered a high enrichment in POD genes, allowing the identification of POD candidates involved in the changes in POD activity previously observed in response to nitrate.
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Affiliation(s)
- Lili Zang
- Institut Agro, INRAE, IRHS, SFR QUASAV, Université d’Angers, Angers, France
| | | | | | - Michel Zivy
- PAPPSO, GQE – Le Moulon, INRA, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Thierry Balliau
- PAPPSO, GQE – Le Moulon, INRA, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Thibault Clochard
- Institut Agro, INRAE, IRHS, SFR QUASAV, Université d’Angers, Angers, France
| | | | - Sandrine Balzergue
- Institut Agro, INRAE, IRHS, SFR QUASAV, Université d’Angers, Angers, France
| | - Sandra Pelletier
- Institut Agro, INRAE, IRHS, SFR QUASAV, Université d’Angers, Angers, France
| | - Claudine Landès
- Institut Agro, INRAE, IRHS, SFR QUASAV, Université d’Angers, Angers, France
| | - Anis M. Limami
- Institut Agro, INRAE, IRHS, SFR QUASAV, Université d’Angers, Angers, France
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48
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Seetharaman S, Vianay B, Roca V, Farrugia AJ, De Pascalis C, Boëda B, Dingli F, Loew D, Vassilopoulos S, Bershadsky A, Théry M, Etienne-Manneville S. Microtubules tune mechanosensitive cell responses. NATURE MATERIALS 2022; 21:366-377. [PMID: 34663953 DOI: 10.1038/s41563-021-01108-x] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 08/20/2021] [Indexed: 05/05/2023]
Abstract
Mechanotransduction is a process by which cells sense the mechanical properties of their surrounding environment and adapt accordingly to perform cellular functions such as adhesion, migration and differentiation. Integrin-mediated focal adhesions are major sites of mechanotransduction and their connection with the actomyosin network is crucial for mechanosensing as well as for the generation and transmission of forces onto the substrate. Despite having emerged as major regulators of cell adhesion and migration, the contribution of microtubules to mechanotransduction still remains elusive. Here, we show that talin- and actomyosin-dependent mechanosensing of substrate rigidity controls microtubule acetylation (a tubulin post-translational modification) by promoting the recruitment of α-tubulin acetyltransferase 1 (αTAT1) to focal adhesions. Microtubule acetylation tunes the mechanosensitivity of focal adhesions and Yes-associated protein (YAP) translocation. Microtubule acetylation, in turn, promotes the release of the guanine nucleotide exchange factor GEF-H1 from microtubules to activate RhoA, actomyosin contractility and traction forces. Our results reveal a fundamental crosstalk between microtubules and actin in mechanotransduction that contributes to mechanosensitive cell adhesion and migration.
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Affiliation(s)
- Shailaja Seetharaman
- Cell Polarity, Migration and Cancer Unit, Institut Pasteur, UMR3691 CNRS, Equipe Labellisée Ligue Contre le Cancer, Paris, France
- Université Paris Descartes, Paris, France
| | - Benoit Vianay
- Paris University, INSERM, CEA, Hôpital Saint Louis, Institut Universitaire d'Hematologie, Paris, France
| | - Vanessa Roca
- Cell Polarity, Migration and Cancer Unit, Institut Pasteur, UMR3691 CNRS, Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Aaron J Farrugia
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Chiara De Pascalis
- Cell Polarity, Migration and Cancer Unit, Institut Pasteur, UMR3691 CNRS, Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Batiste Boëda
- Cell Polarity, Migration and Cancer Unit, Institut Pasteur, UMR3691 CNRS, Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Florent Dingli
- PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Institut Curie, Paris, France
| | - Damarys Loew
- PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Institut Curie, Paris, France
| | | | - Alexander Bershadsky
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Manuel Théry
- Paris University, INSERM, CEA, Hôpital Saint Louis, Institut Universitaire d'Hematologie, Paris, France
| | - Sandrine Etienne-Manneville
- Cell Polarity, Migration and Cancer Unit, Institut Pasteur, UMR3691 CNRS, Equipe Labellisée Ligue Contre le Cancer, Paris, France.
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Seetharaman S, Vianay B, Roca V, Farrugia AJ, De Pascalis C, Boëda B, Dingli F, Loew D, Vassilopoulos S, Bershadsky A, Théry M, Etienne-Manneville S. Microtubules tune mechanosensitive cell responses. NATURE MATERIALS 2022; 21:366-377. [PMID: 34663953 DOI: 10.1101/2020.07.22.205203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 08/20/2021] [Indexed: 05/24/2023]
Abstract
Mechanotransduction is a process by which cells sense the mechanical properties of their surrounding environment and adapt accordingly to perform cellular functions such as adhesion, migration and differentiation. Integrin-mediated focal adhesions are major sites of mechanotransduction and their connection with the actomyosin network is crucial for mechanosensing as well as for the generation and transmission of forces onto the substrate. Despite having emerged as major regulators of cell adhesion and migration, the contribution of microtubules to mechanotransduction still remains elusive. Here, we show that talin- and actomyosin-dependent mechanosensing of substrate rigidity controls microtubule acetylation (a tubulin post-translational modification) by promoting the recruitment of α-tubulin acetyltransferase 1 (αTAT1) to focal adhesions. Microtubule acetylation tunes the mechanosensitivity of focal adhesions and Yes-associated protein (YAP) translocation. Microtubule acetylation, in turn, promotes the release of the guanine nucleotide exchange factor GEF-H1 from microtubules to activate RhoA, actomyosin contractility and traction forces. Our results reveal a fundamental crosstalk between microtubules and actin in mechanotransduction that contributes to mechanosensitive cell adhesion and migration.
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Affiliation(s)
- Shailaja Seetharaman
- Cell Polarity, Migration and Cancer Unit, Institut Pasteur, UMR3691 CNRS, Equipe Labellisée Ligue Contre le Cancer, Paris, France
- Université Paris Descartes, Paris, France
| | - Benoit Vianay
- Paris University, INSERM, CEA, Hôpital Saint Louis, Institut Universitaire d'Hematologie, Paris, France
| | - Vanessa Roca
- Cell Polarity, Migration and Cancer Unit, Institut Pasteur, UMR3691 CNRS, Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Aaron J Farrugia
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Chiara De Pascalis
- Cell Polarity, Migration and Cancer Unit, Institut Pasteur, UMR3691 CNRS, Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Batiste Boëda
- Cell Polarity, Migration and Cancer Unit, Institut Pasteur, UMR3691 CNRS, Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Florent Dingli
- PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Institut Curie, Paris, France
| | - Damarys Loew
- PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Institut Curie, Paris, France
| | | | - Alexander Bershadsky
- Mechanobiology Institute, National University of Singapore, Singapore, Singapore
| | - Manuel Théry
- Paris University, INSERM, CEA, Hôpital Saint Louis, Institut Universitaire d'Hematologie, Paris, France
| | - Sandrine Etienne-Manneville
- Cell Polarity, Migration and Cancer Unit, Institut Pasteur, UMR3691 CNRS, Equipe Labellisée Ligue Contre le Cancer, Paris, France.
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50
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Simulated dynamic digestion reveals different peptide releases from human milk processed by means of holder or high temperature-short time pasteurization. Food Chem 2022; 369:130998. [PMID: 34507088 DOI: 10.1016/j.foodchem.2021.130998] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 08/25/2021] [Accepted: 08/29/2021] [Indexed: 11/20/2022]
Abstract
High Temperature-Short Time (HTST) pasteurization was proposed as an alternative to Holder pasteurization (HOP) to increase the retention of specific human milk (HM) bioactive proteins. The present study explored whether HTST and HOP differently affect peptide release during simulated preterm infant gastrointestinal digestion. Raw (RHM), HOP- and HTST- pasteurized HM were digested using an in vitro dynamic system, and the identified peptides were analyzed by mass spectrometry and multivariate statistics. Before digestion, 158 peptides were identified in either RHM, HTST- or HOP- HM, mostly (84.4%) originating from β-casein (CASB). During gastric digestion, HOP-HM presented a greater number and more abundant specific CASB peptides. A delayed release of peptides was observed in RHM during the intestinal phase, with respect to both pasteurized HM. Although limited to gastric digestion, the HM peptidomic profile differed according to the pasteurization type, and the pattern of the HTST peptides showed a greater similarity with RHM.
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