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72 results on '"Thibault Chaze"'

1. Proteomic landscape of tunneling nanotubes reveals CD9 and CD81 tetraspanins as key regulators

Author: Roberto Notario Manzano, Thibault Chaze, Eric Rubinstein, Esthel Penard, Mariette Matondo, Chiara Zurzolo, and Christel Brou
Subjects: tunneling nanotubes, tetraspanins, extracellular vesicles, Medicine, Science, Biology (General), QH301-705.5
Abstract: Tunneling nanotubes (TNTs) are open actin- and membrane-based channels, connecting remote cells and allowing direct transfer of cellular material (e.g. vesicles, mRNAs, protein aggregates) from the cytoplasm to the cytoplasm. Although they are important especially, in pathological conditions (e.g. cancers, neurodegenerative diseases), their precise composition and their regulation were still poorly described. Here, using a biochemical approach allowing to separate TNTs from cell bodies and from extracellular vesicles and particles (EVPs), we obtained the full composition of TNTs compared to EVPs. We then focused on two major components of our proteomic data, the CD9 and CD81 tetraspanins, and further investigated their specific roles in TNT formation and function. We show that these two tetraspanins have distinct non-redundant functions: CD9 participates in stabilizing TNTs, whereas CD81 expression is required to allow the functional transfer of vesicles in the newly formed TNTs, possibly by regulating docking to or fusion with the opposing cell.
Published: 2024
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2. Mtfp1 ablation enhances mitochondrial respiration and protects against hepatic steatosis

Author: Cecilia Patitucci, Juan Diego Hernández-Camacho, Elodie Vimont, Sonny Yde, Thomas Cokelaer, Thibault Chaze, Quentin Giai Gianetto, Mariette Matondo, Anastasia Gazi, Ivan Nemazanyy, David A. Stroud, Daniella H. Hock, Erminia Donnarumma, and Timothy Wai
Subjects: Science
Abstract: Abstract Hepatic steatosis is the result of imbalanced nutrient delivery and metabolism in the liver and is the first hallmark of Metabolic dysfunction-associated steatotic liver disease (MASLD). MASLD is the most common chronic liver disease and involves the accumulation of excess lipids in hepatocytes, inflammation, and cancer. Mitochondria play central roles in liver metabolism yet the specific mitochondrial functions causally linked to MASLD remain unclear. Here, we identify Mitochondrial Fission Process 1 protein (MTFP1) as a key regulator of mitochondrial and metabolic activity in the liver. Deletion of Mtfp1 in hepatocytes is physiologically benign in mice yet leads to the upregulation of oxidative phosphorylation (OXPHOS) activity and mitochondrial respiration, independently of mitochondrial biogenesis. Consequently, liver-specific knockout mice are protected against high fat diet-induced steatosis and metabolic dysregulation. Additionally, Mtfp1 deletion inhibits mitochondrial permeability transition pore opening in hepatocytes, conferring protection against apoptotic liver damage in vivo and ex vivo. Our work uncovers additional functions of MTFP1 in the liver, positioning this gene as an unexpected regulator of OXPHOS and a therapeutic candidate for MASLD.
Published: 2023
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3. Using a multiomics approach to unravel a septic shock specific signature in skeletal muscle

Author: Baptiste Duceau, Michael Blatzer, Jean Bardon, Thibault Chaze, Quentin Giai Gianetto, Florence Castelli, François Fenaille, Lucie Duarte, Thomas Lescot, Christophe Tresallet, Bruno Riou, Mariette Matondo, Olivier Langeron, Pierre Rocheteau, Fabrice Chrétien, and Adrien Bouglé
Subjects: Medicine, Science
Abstract: Abstract Sepsis is defined as a dysregulated host response to infection leading to organs failure. Among them, sepsis induces skeletal muscle (SM) alterations that contribute to acquired-weakness in critically ill patients. Proteomics and metabolomics could unravel biological mechanisms in sepsis-related organ dysfunction. Our objective was to characterize a distinctive signature of septic shock in human SM by using an integrative multi-omics approach. Muscle biopsies were obtained as part of a multicenter non-interventional prospective study. Study population included patients in septic shock (S group, with intra-abdominal source of sepsis) and two critically ill control populations: cardiogenic shock (C group) and brain dead (BD group). The proteins and metabolites were extracted and analyzed by High-Performance Liquid Chromatography-coupled to tandem Mass Spectrometry, respectively. Fifty patients were included, 19 for the S group (53% male, 64 ± 17 years, SAPS II 45 ± 14), 12 for the C group (75% male, 63 ± 4 years, SAPS II 43 ± 15), 19 for the BD group (63% male, 58 ± 10 years, SAPS II 58 ± 9). Biopsies were performed in median 3 days [interquartile range 1–4]) after intensive care unit admission. Respectively 31 patients and 40 patients were included in the proteomics and metabolomics analyses of 2264 proteins and 259 annotated metabolites. Enrichment analysis revealed that mitochondrial pathways were significantly decreased in the S group at protein level: oxidative phosphorylation (adjusted p = 0.008); branched chained amino acids degradation (adjusted p = 0.005); citrate cycle (adjusted p = 0.005); ketone body metabolism (adjusted p = 0.003) or fatty acid degradation (adjusted p = 0.008). Metabolic reprogramming was also suggested (i) by the differential abundance of the peroxisome proliferator-activated receptors signaling pathway (adjusted p = 0.007), and (ii) by the accumulation of fatty acids like octanedioic acid dimethyl or hydroxydecanoic. Increased polyamines and depletion of mitochondrial thioredoxin or mitochondrial peroxiredoxin indicated a high level of oxidative stress in the S group. Coordinated alterations in the proteomic and metabolomic profiles reveal a septic shock signature in SM, highlighting a global impairment of mitochondria-related metabolic pathways, the depletion of antioxidant capacities, and a metabolic shift towards lipid accumulation. ClinicalTrial registration: NCT02789995. Date of first registration 03/06/2016.
Published: 2022
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4. Mitochondrial Fission Process 1 controls inner membrane integrity and protects against heart failure

Author: Erminia Donnarumma, Michael Kohlhaas, Elodie Vimont, Etienne Kornobis, Thibault Chaze, Quentin Giai Gianetto, Mariette Matondo, Maryse Moya-Nilges, Christoph Maack, and Timothy Wai
Subjects: Science
Abstract: Mitochondria power the beating heart. Here, Donnarumma et al. show that loss of the inner mitochondrial membrane protein MTFP1 in cardiomyocytes reduces bioenergetic efficiency and cell death resistance leading to heart failure in mice.
Published: 2022
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5. Impact of the gut microbiota on the m6A epitranscriptome of mouse cecum and liver

Author: Sabrina Jabs, Anne Biton, Christophe Bécavin, Marie-Anne Nahori, Amine Ghozlane, Alessandro Pagliuso, Giulia Spanò, Vincent Guérineau, David Touboul, Quentin Giai Gianetto, Thibault Chaze, Mariette Matondo, Marie-Agnès Dillies, and Pascale Cossart
Subjects: Science
Abstract: The intestinal microbiota modulates host physiology and gene expression via unclear mechanisms. Here, Jabs et al. show that variations in the gut microbiota correlate with N6-methyladenosine modifications of host mRNAs in the cecum and liver of mice.
Published: 2020
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6. Experimental evolution links post-transcriptional regulation to Leishmania fitness gain.

Author: Laura Piel, K Shanmugha Rajan, Giovanni Bussotti, Hugo Varet, Rachel Legendre, Caroline Proux, Thibaut Douché, Quentin Giai-Gianetto, Thibault Chaze, Thomas Cokelaer, Barbora Vojtkova, Nadav Gordon-Bar, Tirza Doniger, Smadar Cohen-Chalamish, Praveenkumar Rengaraj, Céline Besse, Anne Boland, Jovana Sadlova, Jean-François Deleuze, Mariette Matondo, Ron Unger, Petr Volf, Shulamit Michaeli, Pascale Pescher, and Gerald F Späth
Subjects: Immunologic diseases. Allergy, RC581-607, Biology (General), QH301-705.5
Abstract: The protozoan parasite Leishmania donovani causes fatal human visceral leishmaniasis in absence of treatment. Genome instability has been recognized as a driver in Leishmania fitness gain in response to environmental change or chemotherapy. How genome instability generates beneficial phenotypes despite potential deleterious gene dosage effects is unknown. Here we address this important open question applying experimental evolution and integrative systems approaches on parasites adapting to in vitro culture. Phenotypic analyses of parasites from early and late stages of culture adaptation revealed an important fitness tradeoff, with selection for accelerated growth in promastigote culture (fitness gain) impairing infectivity (fitness costs). Comparative genomics, transcriptomics and proteomics analyses revealed a complex regulatory network associated with parasite fitness gain, with genome instability causing highly reproducible, gene dosage-independent and -dependent changes. Reduction of flagellar transcripts and increase in coding and non-coding RNAs implicated in ribosomal biogenesis and protein translation were not correlated to dosage changes of the corresponding genes, revealing a gene dosage-independent, post-transcriptional mechanism of regulation. In contrast, abundance of gene products implicated in post-transcriptional regulation itself correlated to corresponding gene dosage changes. Thus, RNA abundance during parasite adaptation is controled by direct and indirect gene dosage changes. We correlated differential expression of small nucleolar RNAs (snoRNAs) with changes in rRNA modification, providing first evidence that Leishmania fitness gain in culture may be controlled by post-transcriptional and epitranscriptomic regulation. Our findings propose a novel model for Leishmania fitness gain in culture, where differential regulation of mRNA stability and the generation of modified ribosomes may potentially filter deleterious from beneficial gene dosage effects and provide proteomic robustness to genetically heterogenous, adapting parasite populations. This model challenges the current, genome-centric approach to Leishmania epidemiology and identifies the Leishmania transcriptome and non-coding small RNome as potential novel sources for the discovery of biomarkers that may be associated with parasite phenotypic adaptation in clinical settings.
Published: 2022
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7. Cryptococcus extracellular vesicles properties and their use as vaccine platforms

Author: Juliana Rizzo, Sarah Sze Wah Wong, Anastasia D. Gazi, Frédérique Moyrand, Thibault Chaze, Pierre‐Henri Commere, Sophie Novault, Mariette Matondo, Gérard Péhau‐Arnaudet, Flavia C. G. Reis, Matthijn Vos, Lysangela R. Alves, Robin C. May, Leonardo Nimrichter, Marcio L. Rodrigues, Vishukumar Aimanianda, and Guilhem Janbon
Subjects: Cryo‐EM, cryptococcus, extracellular vesicles, fungal infections, mannoproteins, vaccine, Cytology, QH573-671
Abstract: Abstract Whereas extracellular vesicle (EV) research has become commonplace in different biomedical fields, this field of research is still in its infancy in mycology. Here we provide a robust set of data regarding the structural and compositional aspects of EVs isolated from the fungal pathogenic species Cryptococcus neoformans, C. deneoformans and C. deuterogattii. Using cutting‐edge methodological approaches including cryogenic electron microscopy and cryogenic electron tomography, proteomics, and flow cytometry, we revisited cryptococcal EV features and suggest a new EV structural model, in which the vesicular lipid bilayer is covered by mannoprotein‐based fibrillar decoration, bearing the capsule polysaccharide as its outer layer. About 10% of the EV population is devoid of fibrillar decoration, adding another aspect to EV diversity. By analysing EV protein cargo from the three species, we characterized the typical Cryptococcus EV proteome. It contains several membrane‐bound protein families, including some Tsh proteins bearing a SUR7/PalI motif. The presence of known protective antigens on the surface of Cryptococcus EVs, resembling the morphology of encapsulated virus structures, suggested their potential as a vaccine. Indeed, mice immunized with EVs obtained from an acapsular C. neoformans mutant strain rendered a strong antibody response in mice and significantly prolonged their survival upon C. neoformans infection.
Published: 2021
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8. CYP450 core involvement in multiple resistance strains of Aedes aegypti from French Guiana highlighted by proteomics, molecular and biochemical studies.

Author: Yanouk Epelboin, Lanjiao Wang, Quentin Giai Gianetto, Valérie Choumet, Pascal Gaborit, Jean Issaly, Amandine Guidez, Thibaut Douché, Thibault Chaze, Mariette Matondo, and Isabelle Dusfour
Subjects: Medicine, Science
Abstract: Insecticide resistance is a worldwide threat for vector control around the world, and Aedes aegypti, the main vector of several arboviruses, is a particular concern. To better understand the mechanisms of resistance, four isofemale strains originally from French Guiana were isolated and analysed using combined approaches. The activity of detoxification enzymes involved in insecticide resistance was assayed, and mutations located at positions 1016 and 1534 of the sodium voltage-gated channel gene, which have been associated with pyrethroid resistance in Aedes aegypti populations in Latin America, were monitored. Resistance to other insecticide families (organophosphates and carbamates) was evaluated. A large-scale proteomic analysis was performed to identify proteins involved in insecticide resistance. Our results revealed a metabolic resistance and resistance associated with a mutation of the sodium voltage-gated channel gene at position 1016. Metabolic resistance was mediated through an increase of esterase activity in most strains but also through the shifts in the abundance of several cytochrome P450 (CYP450s). Overall, resistance to deltamethrin was linked in the isofemale strains to resistance to other class of insecticides, suggesting that cross- and multiple resistance occur through selection of mechanisms of metabolic resistance. These results give some insights into resistance to deltamethrin and into multiple resistance phenomena in populations of Ae. aegypti.
Published: 2021
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9. Characterization of Extracellular Vesicles Produced by Aspergillus fumigatus Protoplasts

Author: Juliana Rizzo, Thibault Chaze, Kildare Miranda, Robert W. Roberson, Olivier Gorgette, Leonardo Nimrichter, Mariette Matondo, Jean-Paul Latgé, Anne Beauvais, and Marcio L. Rodrigues
Subjects: Aspergillus fumigatus, conidia, protoplasts, extracellular vesicles, Aspergillus, Microbiology, QR1-502
Abstract: ABSTRACT Extracellular vesicles (EVs) are membranous compartments produced by yeast and mycelial forms of several fungal species. One of the difficulties in perceiving the role of EVs during the fungal life, and particularly in cell wall biogenesis, is caused by the presence of a thick cell wall. One alternative to have better access to these vesicles is to use protoplasts. This approach has been investigated here with Aspergillus fumigatus, one of the most common opportunistic fungal pathogens worldwide. Analysis of regenerating protoplasts by scanning electron microscopy and fluorescence microscopy indicated the occurrence of outer membrane projections in association with surface components and the release of particles with properties resembling those of fungal EVs. EVs in culture supernatants were characterized by transmission electron microscopy and nanoparticle tracking analysis. Proteomic and glycome analysis of EVs revealed the presence of a complex array of enzymes related to lipid/sugar metabolism, pathogenic processes, and cell wall biosynthesis. Our data indicate that (i) EV production is a common feature of different morphological stages of this major fungal pathogen and (ii) protoplastic EVs are promising tools for undertaking studies of vesicle functions in fungal cells. IMPORTANCE Fungal cells use extracellular vesicles (EVs) to export biologically active molecules to the extracellular space. In this study, we used protoplasts of Aspergillus fumigatus, a major fungal pathogen, as a model to evaluate the role of EV production in cell wall biogenesis. Our results demonstrated that wall-less A. fumigatus exports plasma membrane-derived EVs containing a complex combination of proteins and glycans. Our report is the first to characterize fungal EVs in the absence of a cell wall. Our results suggest that protoplasts represent a promising model for functional studies of fungal vesicles.
Published: 2020
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10. Differentiation-dependent susceptibility of human muscle cells to Zika virus infection.

Author: Vincent Legros, Patricia Jeannin, Julien Burlaud-Gaillard, Thibault Chaze, Quentin Giai Gianetto, Gillian Butler-Browne, Vincent Mouly, Jim Zoladek, Philippe V Afonso, Mariela-Natacha Gonzàlez, Mariette Matondo, Ingo Riederer, Philippe Roingeard, Antoine Gessain, Valérie Choumet, and Pierre-Emmanuel Ceccaldi
Subjects: Arctic medicine. Tropical medicine, RC955-962, Public aspects of medicine, RA1-1270
Abstract: Muscle cells are potential targets of many arboviruses, such as Ross River, Dengue, Sindbis, and chikungunya viruses, that may be involved in the physiopathological course of the infection. During the recent outbreak of Zika virus (ZIKV), myalgia was one of the most frequently reported symptoms. We investigated the susceptibility of human muscle cells to ZIKV infection. Using an in vitro model of human primary myoblasts that can be differentiated into myotubes, we found that myoblasts can be productively infected by ZIKV. In contrast, myotubes were shown to be resistant to ZIKV infection, suggesting a differentiation-dependent susceptibility. Infection was accompanied by a caspase-independent cytopathic effect, associated with paraptosis-like cytoplasmic vacuolization. Proteomic profiling was performed 24h and 48h post-infection in cells infected with two different isolates. Proteome changes indicate that ZIKV infection induces an upregulation of proteins involved in the activation of the Interferon type I pathway, and a downregulation of protein synthesis. This work constitutes the first observation of primary human muscle cells susceptibility to ZIKV infection, and differentiation-dependent restriction of infection from myoblasts to myotubes. Since myoblasts constitute the reservoir of stem cells involved in reparation/regeneration in muscle tissue, the infection of muscle cells and the viral-induced alterations observed here could have consequences in ZIKV infection pathogenesis.
Published: 2020
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11. Phosphorylation-Dependent Assembly of a 14-3-3 Mediated Signaling Complex during Red Blood Cell Invasion by Plasmodium falciparum Merozoites

Author: Kunal R. More, Inderjeet Kaur, Quentin Giai Gianetto, Brandon M. Invergo, Thibault Chaze, Ravi Jain, Christéle Huon, Petra Gutenbrunner, Hendrik Weisser, Mariette Matondo, Jyoti S. Choudhary, Gordon Langsley, Shailja Singh, and Chetan E. Chitnis
Subjects: host cell invasion, host-parasite interaction, malaria, signaling, Microbiology, QR1-502
Abstract: ABSTRACT Red blood cell (RBC) invasion by Plasmodium merozoites requires multiple steps that are regulated by signaling pathways. Exposure of P. falciparum merozoites to the physiological signal of low K+, as found in blood plasma, leads to a rise in cytosolic Ca2+, which mediates microneme secretion, motility, and invasion. We have used global phosphoproteomic analysis of merozoites to identify signaling pathways that are activated during invasion. Using quantitative phosphoproteomics, we found 394 protein phosphorylation site changes in merozoites subjected to different ionic environments (high K+/low K+), 143 of which were Ca2+ dependent. These included a number of signaling proteins such as catalytic and regulatory subunits of protein kinase A (PfPKAc and PfPKAr) and calcium-dependent protein kinase 1 (PfCDPK1). Proteins of the 14-3-3 family interact with phosphorylated target proteins to assemble signaling complexes. Here, using coimmunoprecipitation and gel filtration chromatography, we demonstrate that Pf14-3-3I binds phosphorylated PfPKAr and PfCDPK1 to mediate the assembly of a multiprotein complex in P. falciparum merozoites. A phospho-peptide, P1, based on the Ca2+-dependent phosphosites of PKAr, binds Pf14-3-3I and disrupts assembly of the Pf14-3-3I-mediated multiprotein complex. Disruption of the multiprotein complex with P1 inhibits microneme secretion and RBC invasion. This study thus identifies a novel signaling complex that plays a key role in merozoite invasion of RBCs. Disruption of this signaling complex could serve as a novel approach to inhibit blood-stage growth of malaria parasites. IMPORTANCE Invasion of red blood cells (RBCs) by Plasmodium falciparum merozoites is a complex process that is regulated by intricate signaling pathways. Here, we used phosphoproteomic profiling to identify the key proteins involved in signaling events during invasion. We found changes in the phosphorylation of various merozoite proteins, including multiple kinases previously implicated in the process of invasion. We also found that a phosphorylation-dependent multiprotein complex including signaling kinases assembles during the process of invasion. Disruption of this multiprotein complex impairs merozoite invasion of RBCs, providing a novel approach for the development of inhibitors to block the growth of blood-stage malaria parasites.
Published: 2020
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12. Listeria monocytogenes Exploits Mitochondrial Contact Site and Cristae Organizing System Complex Subunit Mic10 To Promote Mitochondrial Fragmentation and Cellular Infection

Author: Filipe Carvalho, Anna Spier, Thibault Chaze, Mariette Matondo, Pascale Cossart, and Fabrizia Stavru
Subjects: Listeria monocytogenes, MICOS complex, Mic10, mitochondrial fission, proteomics, Microbiology, QR1-502
Abstract: ABSTRACT Mitochondrial function adapts to cellular demands and is affected by the ability of the organelle to undergo fusion and fission in response to physiological and nonphysiological cues. We previously showed that infection with the human bacterial pathogen Listeria monocytogenes elicits transient mitochondrial fission and a drop in mitochondrion-dependent energy production through a mechanism requiring the bacterial pore-forming toxin listeriolysin O (LLO). Here, we performed quantitative mitochondrial proteomics to search for host factors involved in L. monocytogenes-induced mitochondrial fission. We found that Mic10, a critical component of the mitochondrial contact site and cristae organizing system (MICOS) complex, is significantly enriched in mitochondria isolated from cells infected with wild-type but not with LLO-deficient L. monocytogenes. Increased mitochondrial Mic10 levels did not correlate with upregulated transcription, suggesting a posttranscriptional mechanism. We then showed that Mic10 is necessary for L. monocytogenes-induced mitochondrial network fragmentation and that it contributes to L. monocytogenes cellular infection independently of MICOS proteins Mic13, Mic26, and Mic27. In conclusion, investigation of L. monocytogenes infection allowed us to uncover a role for Mic10 in mitochondrial fission. IMPORTANCE Pathogenic bacteria can target host cell organelles to take control of key cellular processes and promote their intracellular survival, growth, and persistence. Mitochondria are essential, highly dynamic organelles with pivotal roles in a wide variety of cell functions. Mitochondrial dynamics and function are intimately linked. Our previous research showed that Listeria monocytogenes infection impairs mitochondrial function and triggers fission of the mitochondrial network at an early infection stage, in a process that is independent of the presence of the main mitochondrial fission protein Drp1. Here, we analyzed how mitochondrial proteins change in response to L. monocytogenes infection and found that infection raises the levels of Mic10, a mitochondrial inner membrane protein involved in formation of cristae. We show that Mic10 is important for L. monocytogenes-dependent mitochondrial fission and infection of host cells. Our findings thus offer new insight into the mechanisms used by L. monocytogenes to hijack mitochondria to optimize host infection.
Published: 2020
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13. The transpeptidase PBP2 governs initial localization and activity of the major cell-wall synthesis machinery in E. coli

Author: Gizem Özbaykal, Eva Wollrab, Francois Simon, Antoine Vigouroux, Baptiste Cordier, Andrey Aristov, Thibault Chaze, Mariette Matondo, and Sven van Teeffelen
Subjects: cell-wall insertion, single-enzyme dynamics, MreB cytoskeleton, bacterial morphogenesis, Rod complex, Medicine, Science, Biology (General), QH301-705.5
Abstract: Bacterial shape is physically determined by the peptidoglycan cell wall. The cell-wall-synthesis machinery responsible for rod shape in Escherichia coli is the processive 'Rod complex'. Previously, cytoplasmic MreB filaments were thought to govern formation and localization of Rod complexes based on local cell-envelope curvature. Using single-particle tracking of the transpeptidase and Rod-complex component PBP2, we found that PBP2 binds to a substrate different from MreB. Depletion and localization experiments of other putative Rod-complex components provide evidence that none of those provide the sole rate-limiting substrate for PBP2 binding. Consistently, we found only weak correlations between MreB and envelope curvature in the cylindrical part of cells. Residual correlations do not require curvature-based Rod-complex initiation but can be attributed to persistent rotational motion. We therefore speculate that the local cell-wall architecture provides the cue for Rod-complex initiation, either through direct binding by PBP2 or through an unknown intermediate.
Published: 2020
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14. Comparison of a human neuronal model proteome upon Japanese encephalitis or West Nile Virus infection and potential role of mosquito saliva in neuropathogenesis.

Author: Benoit Besson, Justine Basset, Sandrine Gatellier, Hélène Chabrolles, Thibault Chaze, Véronique Hourdel, Mariette Matondo, Nathalie Pardigon, and Valérie Choumet
Subjects: Medicine, Science
Abstract: Neurotropic flavivirus Japanese encephalitis virus (JEV) and West Nile virus (WNV) are amongst the leading causes of encephalitis. Using label-free quantitative proteomics, we identified proteins differentially expressed upon JEV (gp-3, RP9) or WNV (IS98) infection of human neuroblastoma cells. Data are available via ProteomeXchange with identifier PXD016805. Both viruses were associated with the up-regulation of immune response (IFIT1/3/5, ISG15, OAS, STAT1, IRF9) and the down-regulation of SSBP2 and PAM, involved in gene expression and in neuropeptide amidation respectively. Proteins associated to membranes, involved in extracellular matrix organization and collagen metabolism represented major clusters down-regulated by JEV and WNV. Moreover, transcription regulation and mRNA processing clusters were also heavily regulated by both viruses. The proteome of neuroblastoma cells infected by JEV or WNV was significantly modulated in the presence of mosquito saliva, but distinct patterns were associated to each virus. Mosquito saliva favored modulation of proteins associated with gene regulation in JEV infected neuroblastoma cells while modulation of proteins associated with protein maturation, signal transduction and ion transporters was found in WNV infected neuroblastoma cells.
Published: 2020
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15. Class-A penicillin binding proteins do not contribute to cell shape but repair cell-wall defects

Author: Antoine Vigouroux, Baptiste Cordier, Andrey Aristov, Laura Alvarez, Gizem Özbaykal, Thibault Chaze, Enno Rainer Oldewurtel, Mariette Matondo, Felipe Cava, David Bikard, and Sven van Teeffelen
Subjects: peptidoglycan cell wall, cell envelope, cell-wall repair, CRISPRi, single-molecule tracking, penicillin-binding proteins, Medicine, Science, Biology (General), QH301-705.5
Abstract: Cell shape and cell-envelope integrity of bacteria are determined by the peptidoglycan cell wall. In rod-shaped Escherichia coli, two conserved sets of machinery are essential for cell-wall insertion in the cylindrical part of the cell: the Rod complex and the class-A penicillin-binding proteins (aPBPs). While the Rod complex governs rod-like cell shape, aPBP function is less well understood. aPBPs were previously hypothesized to either work in concert with the Rod complex or to independently repair cell-wall defects. First, we demonstrate through modulation of enzyme levels that aPBPs do not contribute to rod-like cell shape but are required for mechanical stability, supporting their independent activity. By combining measurements of cell-wall stiffness, cell-wall insertion, and PBP1b motion at the single-molecule level, we then present evidence that PBP1b, the major aPBP, contributes to cell-wall integrity by repairing cell wall defects.
Published: 2020
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16. Infection Reveals a Modification of SIRT2 Critical for Chromatin Association

Author: Jorge M. Pereira, Christine Chevalier, Thibault Chaze, Quentin Gianetto, Francis Impens, Mariette Matondo, Pascale Cossart, and Mélanie A. Hamon
Subjects: Biology (General), QH301-705.5
Abstract: Summary: Sirtuin 2 is a nicotinamide-adenine-dinucleotide-dependent deacetylase that regulates cell processes such as carcinogenesis, cell cycle, DNA damage, and infection. Subcellular localization of SIRT2 is crucial for its function but is poorly understood. Infection with the bacterial pathogen Listeria monocytogenes, which relocalizes SIRT2 from the cytoplasm to the chromatin, provides an ideal stimulus for the molecular study of this process. In this report, we provide a map of SIRT2 post-translational modification sites and focus on serine 25 phosphorylation. We show that infection specifically induces dephosphorylation of S25, an event essential for SIRT2 chromatin association. Furthermore, we identify a nuclear complex formed by the phosphatases PPM1A and PPM1B, with SIRT2 essential for controlling H3K18 deacetylation and SIRT2-mediated gene repression during infection and necessary for a productive Listeria infection. This study reveals a molecular mechanism regulating SIRT2 function and localization, paving the way for understanding other SIRT2-regulated cellular processes. : Sirtuins are enzymes critical for various processes, including genomic stability, metabolism, and aging. Through study of Listeria monocytogenes, a bacterial pathogen that exploits SIRT2 for productive infection, Pereira et al. uncover a SIRT2 modification necessary for chromatin association and function. Keywords: chromatin, sirtuin, Listeria monocytogenes, phosphorylation, PPM1, histone acetylation, H3K18, infection, subcellular localization
Published: 2018
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17. Proteomic analysis of plasma extracellular vesicles reveals mitochondrial stress upon HTLV-1 infection

Author: Patricia Jeannin, Thibault Chaze, Quentin Giai Gianetto, Mariette Matondo, Olivier Gout, Antoine Gessain, and Philippe V. Afonso
Subjects: Medicine, Science
Abstract: Abstract Extracellular vesicles (EVs) can participate in intercellular communication and pathogenesis. EVs contain many cargos, including proteins, and the composition of EVs differs between cell-types and activation levels. Thus, plasma EVs can be used as a biomarker of systemic response to infection and/or disease progression. In this study, we aimed at describing alterations in the protein content of plasma EVs upon infection with the human T-lymphotropic retrovirus type 1 (HTLV-1). HTLV-1 is the etiological agent of a lymphoproliferative disease (ATL) and a series of inflammatory diseases, including a neurodegenerative inflammatory disease (HAM/TSP). We found that plasma EVs are more abundant and smaller in HTLV-1 asymptomatic carriers or HAM/TSP patients when compared to uninfected healthy donors. Moreover, EVs from HTLV-1 infected donors contain markers of metabolic and mitochondrial stress.
Published: 2018
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18. RadD Contributes to R-Loop Avoidance in Sub-MIC Tobramycin

Author: Veronica Negro, Evelyne Krin, Sebastian Aguilar Pierlé, Thibault Chaze, Quentin Giai Gianetto, Sean P. Kennedy, Mariette Matondo, Didier Mazel, and Zeynep Baharoglu
Subjects: DNA repair, R-loop, antibiotic resistance, Microbiology, QR1-502
Abstract: ABSTRACT We have previously identified Vibrio cholerae mutants in which the stress response to subinhibitory concentrations of aminoglycoside is altered. One gene identified, VC1636, encodes a putative DNA/RNA helicase, recently named RadD in Escherichia coli. Here we combined extensive genetic characterization and high-throughput approaches in order to identify partners and molecular mechanisms involving RadD. We show that double-strand DNA breaks (DSBs) are formed upon subinhibitory tobramycin treatment in the absence of radD and recBCD and that formation of these DSBs can be overcome by RNase H1 overexpression. Loss of RNase H1, or of the transcription-translation coupling factor EF-P, is lethal in the radD deletion mutant. We propose that R-loops are formed upon sublethal aminoglycoside treatment, leading to the formation of DSBs that can be repaired by the RecBCD homologous recombination pathway, and that RadD counteracts such R-loop accumulation. We discuss how R-loops that can occur upon translation-transcription uncoupling could be the link between tobramycin treatment and DNA break formation. IMPORTANCE Bacteria frequently encounter low concentrations of antibiotics. Active antibiotics are commonly detected in soil and water at concentrations much below lethal concentration. Although sub-MICs of antibiotics do not kill bacteria, they can have a major impact on bacterial populations by contributing to the development of antibiotic resistance through mutations in originally sensitive bacteria or acquisition of DNA from resistant bacteria. It was shown that concentrations as low as 100-fold below the MIC can actually lead to the selection of antibiotic-resistant cells. We seek to understand how bacterial cells react to such antibiotic concentrations using E. coli, the Gram-negative bacterial paradigm, and V. cholerae, the causative agent of cholera. Our findings shed light on the processes triggered at the DNA level by antibiotics targeting translation, how damage occurs, and what the bacterial strategies are to respond to such DNA damage.
Published: 2019
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19. The Oxygen Sensor PHD2 Controls Dendritic Spines and Synapses via Modification of Filamin A

Author: Inmaculada Segura, Christian Lange, Ellen Knevels, Anastasiya Moskalyuk, Rocco Pulizzi, Guy Eelen, Thibault Chaze, Cicerone Tudor, Cyril Boulegue, Matthew Holt, Dirk Daelemans, Mariette Matondo, Bart Ghesquière, Michele Giugliano, Carmen Ruiz de Almodovar, Mieke Dewerchin, and Peter Carmeliet
Subjects: Biology (General), QH301-705.5
Abstract: Neuronal function is highly sensitive to changes in oxygen levels, but how hypoxia affects dendritic spine formation and synaptogenesis is unknown. Here we report that hypoxia, chemical inhibition of the oxygen-sensing prolyl hydroxylase domain proteins (PHDs), and silencing of Phd2 induce immature filopodium-like dendritic protrusions, promote spine regression, reduce synaptic density, and decrease the frequency of spontaneous action potentials independently of HIF signaling. We identified the actin cross-linker filamin A (FLNA) as a target of PHD2 mediating these effects. In normoxia, PHD2 hydroxylates the proline residues P2309 and P2316 in FLNA, leading to von Hippel-Lindau (VHL)-mediated ubiquitination and proteasomal degradation. In hypoxia, PHD2 inactivation rapidly upregulates FLNA protein levels because of blockage of its proteasomal degradation. FLNA upregulation induces more immature spines, whereas Flna silencing rescues the immature spine phenotype induced by PHD2 inhibition.
Published: 2016
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20. Serum Proteome Analysis for Profiling Predictive Protein Markers Associated with the Severity of Skin Lesions Induced by Ionizing Radiation

Author: Thibault Chaze, Louis Hornez, Christophe Chambon, Iman Haddad, Joelle Vinh, Jean-Philippe Peyrat, Marc Benderitter, and Olivier Guipaud
Subjects: 2D-DIGE, biomarkers, cutaneous radiation syndrome, ionizing radiation, mass spectrometry, proteomics, radiotherapy, serum proteome, SELDI-TOF, skin, Microbiology, QR1-502
Abstract: The finding of new diagnostic and prognostic markers of local radiation injury, and particularly of the cutaneous radiation syndrome, is crucial for its medical management, in the case of both accidental exposure and radiotherapy side effects. Especially, a fast high-throughput method is still needed for triage of people accidentally exposed to ionizing radiation. In this study, we investigated the impact of localized irradiation of the skin on the early alteration of the serum proteome of mice in an effort to discover markers associated with the exposure and severity of impending damage. Using two different large-scale quantitative proteomic approaches, 2D-DIGE-MS and SELDI-TOF-MS, we performed global analyses of serum proteins collected in the clinical latency phase (days 3 and 7) from non-irradiated and locally irradiated mice exposed to high doses of 20, 40 and 80 Gy which will develop respectively erythema, moist desquamation and necrosis. Unsupervised and supervised multivariate statistical analyses (principal component analysis, partial-least square discriminant analysis and Random Forest analysis) using 2D-DIGE quantitative protein data allowed us to discriminate early between non-irradiated and irradiated animals, and between uninjured/slightly injured animals and animals that will develop severe lesions. On the other hand, despite a high number of animal replicates, PLS-DA and Random Forest analyses of SELDI-TOF-MS data failed to reveal sets of MS peaks able to discriminate between the different groups of animals. Our results show that, unlike SELDI-TOF-MS, the 2D-DIGE approach remains a powerful and promising method for the discovery of sets of proteins that could be used for the development of clinical tests for triage and the prognosis of the severity of radiation-induced skin lesions. We propose a list of 15 proteins which constitutes a set of candidate proteins for triage and prognosis of skin lesion outcomes.
Published: 2013
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21. Evidence for the Sialylation of PilA, the PI-2a Pilus-Associated Adhesin of Streptococcus agalactiae Strain NEM316.

Author: Eric Morello, Adeline Mallet, Yoan Konto-Ghiorghi, Thibault Chaze, Michel-Yves Mistou, Giulia Oliva, Liliana Oliveira, Anne-Marie Di Guilmi, Patrick Trieu-Cuot, and Shaynoor Dramsi
Subjects: Medicine, Science
Abstract: Streptococcus agalactiae (or Group B Streptococcus, GBS) is a commensal bacterium present in the intestinal and urinary tracts of approximately 30% of humans. We and others previously showed that the PI-2a pilus polymers, made of the backbone pilin PilB, the tip adhesin PilA and the cell wall anchor protein PilC, promote adhesion to host epithelia and biofilm formation. Affinity-purified PI-2a pili from GBS strain NEM316 were recognized by N-acetylneuraminic acid (NeuNAc, also known as sialic acid) specific lectins such as Elderberry Bark Lectin (EBL) suggesting that pili are sialylated. Glycan profiling with twenty different lectins combined with monosaccharide composition by HPLC suggested that affinity-purified PI-2a pili are modified by N-glycosylation and decorated with sialic acid attached to terminal galactose. Analysis of various relevant mutants in the PI-2a pilus operon by flow-cytometry and electron microscopy analyses pointed to PilA as the pilus subunit modified by glycosylation. Double labeling using PilB antibody and EBL lectin, which specifically recognizes N-acetylneuraminic acid attached to galactose in α-2, 6, revealed a characteristic binding of EBL at the tip of the pilus structures, highly reminiscent of PilA localization. Expression of a secreted form of PilA using an inducible promoter showed that this recombinant PilA binds specifically to EBL lectin when produced in the native GBS context. In silico search for potentially glycosylated asparagine residues in PilA sequence pointed to N427 and N597, which appear conserved and exposed in the close homolog RrgA from S. pneumoniae, as likely candidates. Conversion of these two asparagyl residues to glutamyl resulted in a higher instability of PilA. Our results provide the first evidence that the tip PilA adhesin can be glycosylated, and suggest that this modification is critical for PilA stability and may potentially influence interactions with the host.
Published: 2015
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22. Pneumococcus triggers NFkB degradation in COMMD2 aggresome-like bodies

Author: Michael G. Connor, Lisa Sanchez, Christine Chevalier, Filipe Carvalho, Matthew G. Eldridge, Thibault Chaze, Mariette Matondo, Caroline M. Weight, Robert S. Heyderman, Jost Enninga, Melanie A. Hamon, Chromatine et Infection - Chromatin and Infection, Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Dynamique des Interactions Hôte-Pathogène - Dynamics of Host-Pathogen Interactions, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Spectrométrie de Masse pour la Biologie – Mass Spectrometry for Biology (UTechS MSBio), Institut Pasteur [Paris] (IP)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), and University College of London [London] (UCL)
Subjects: [SDV]Life Sciences [q-bio]
Abstract: NF-kB driven cellular immunity is essential for both pro- and anti-inflammatory responses to microbes, which makes it one of the most frequently targeted pathways by bacteria during pathogenesis. How NF-kB tunes the epithelial response to Streptococcus pneumoniae across the spectrum of commensal to pathogenic host phenotypic outcomes is not fully understood. In this study, we compare a commensal-like 6B ST90 strain to an invasive TIGR4 isolate and demonstrate that TIGR4 both blunts and antagonizes NF-kB activation. We identified, through comparative mass spectrometry of the p65 interactome, that the 6B ST90 isolate drives a non-canonical NF-kB RelB cascade, whereas TIGR4 induces p65 degradation though aggrephagy. Mechanistically, we show that during TIGR4 challenge a novel interaction of COMMD2 with p65 and p62 is established to mediate degradation of p65. With these results, we establish a role for COMMD2 in negative NF-kB regulation, and present a paradigm for diverging NF-kB responses to pneumococcus. Thus, our studies reveal for the first time a new bacterial pathogenesis mechanism to repress host inflammatory response though COMMD2 mediated turnover of p65.
Published: 2023

23. Proteomic landscape of tunneling nanotubes reveals CD9 and CD81 tetraspanins as key regulators

Author: Roberto Notario Manzano, Thibault Chaze, Eric Rubinstein, Mariette Matondo, Chiara Zurzolo, and Christel Brou
Abstract: SummaryTunneling nanotubes (TNTs) are open actin- and membrane-based channels, connecting remote cells and allowing direct transfer of cellular material (e.g. vesicles, mRNAs, protein aggregates) from cytoplasm to cytoplasm. Although they are important especially in pathological conditions (e.g., cancers, neurodegenerative diseases), their precise composition and their regulation were still poorly described. Here, using a biochemical approach allowing to separate TNTs from cell bodies and from extracellular vesicles and particles (EVPs), we obtained the full composition of TNTs compared to EVPs. We then focused to two major components of our proteomic data, the CD9 and CD81 tetraspanins, and further investigated their specific roles in TNT formation and function. We show that these two tetraspanins have distinct functions: CD9 participates in the initiation of TNTs, whereas CD81 expression is required to allow the functional transfer of vesicle in the newly formed TNTs, possibly by regulating fusion with the opposing cell.
Published: 2022
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24. A balance between actin and Eps8/IRSp53 utilization in branched versus linear actin networks determines tunneling nanotube formation

Author: J. Michael Henderson, Nina Ljubojevic, Thibault Chaze, Daryl Castaneda, Aude Battistella, Quentin Giai Gianetto, Mariette Matondo, Stéphanie Descroix, Patricia Bassereau, and Chiara Zurzolo
Abstract: Tunneling nanotubes (TNTs) connect distant cells and mediate cargo transfer for intercellular communication in physiological and pathological contexts. How cells generate these actin-mediated protrusions to span lengths beyond those attainable by canonical filopodia remains unknown. Through a combination of micropatterning, microscopy and optical tweezer-based approaches, we demonstrate that TNTs forming through the outward extension of actin (not through cellular dislodgement) achieve distances greater than the mean length of filopodia, and that branched Arp2/3-dependent pathways attenuate the extent to which actin polymerizes in nanotubes, limiting TNT occurrence. Proteomic analysis using Epidermal growth factor receptor kinase substrate 8 (Eps8) as a positive effector of TNTs showed that upon Arp2/3 inhibition, proteins enhancing filament turnover and depolymerization were reduced and Eps8 instead exhibited heightened interactions with the inverted Bin/Amphiphysin/Rvs (I-BAR) domain protein IRSp53 that provides a direct connection with linear actin polymerases. Our data reveals how common protrusion players (Eps8 and IRSp53) form TNTs, and that when competing pathways overutilizing such proteins and monomeric actin in Arp2/3 networks are inhibited, processes promoting linear actin growth dominate to favour TNT formation. Thus, this work reinforces a general principle for actin network control for cellular protrusions where simple shifts in the balance between processes that inhibit actin growth versus those that promote growth dictate protrusion formation and the ultimate length scales protrusions achieve.
Published: 2022
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25. Single locus phosphoproteomics reveals phosphorylation of RPA-1 is required for generation of single-strand DNA following a break at a subtelomeric locus

Author: Emilia McLaughlin, Annick Dujeancourt-Henry, Thibault Chaze, Quentin Giai Gianetto, Mariette Matondo, Michael D Urbaniak, Lucy Glover, Biologie moléculaire des Trypanosomes - Trypanosome Molecular Biology, Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Plateforme de Protéomique / Proteomics platform, Université Paris Cité (UPCité)-Spectrométrie de Masse pour la Biologie – Mass Spectrometry for Biology (UTechS MSBio), Institut Pasteur [Paris] (IP)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut Pasteur [Paris] (IP)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Work in the LG laboratory is has received financial support from the Institut Pasteur (G5 Junior group). EJM is part of the Pasteur - Paris University (PPU) International PhD Program. This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 665807 and from the Foundation Recherché Médicale grant number FDT202012010602. Funding for open access charge: Institut Pasteur G5 funding., EJM, MM, MU and LG designed the experiments. EJM, ADH, TC performed the experiments,EJM, QGG and MU performed the statistical analysis. EJM and LG wrote the manuscript, all authors edited the manuscript. We would also like to thank Sebastian Hutchinson for his guidance with the analysis of the VSG-sequencing, and European Project: 665807,H2020,H2020-MSCA-COFUND-2014,PASTEURDOC(2015)
Subjects: Phosphoproteomics, [SDV]Life Sciences [q-bio], DNA damage, Trypanosoma brucei
Abstract: Damage to the genetic material of the cell poses a universal threat to all forms of life. Central to the DNA damage response (DDR) is a phosphorylation signalling cascade that leads to the co-ordination of the cellular response to a DNA break. Identifying the proteins that are phosphorylated is crucial to understanding the mechanisms underlying this DDR. We have used SILAC-based quantitative phosphoproteomics to profile changes in phosphorylation site abundance following a single double strand break (DSB) at a chromosome internal locus and the subtelomeric bloodstream form expression site in Trypanosoma brucei. We report >6500 phosphorylation sites, including a core set of 211 DSB responsive phosphorylation sites. Along with phosphorylation of canonical DNA damage factors, we find that there is a striking distinction between the proteins phosphorylated in response to a chromosome internal DSB and one at the active BES and describe a single phosphorylation event on Replication factor A (RPA) 1 that is required for efficient resection at a bloodstream form expression site.
Published: 2022
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26. Author Reply to Peer Reviews of Mitochondrial fission process 1 (MTFP1) controls bioenergetic efficiency and prevents inflammatory cardiomyopathy and heart failure in mice

Author: Timothy Wai, Christoph Maack, Maryse Moya-Nilges, Mariette Matondo, Quentin Giai Gianetto, Thibault Chaze, Etienne Kornobis, Elodie Vimont, Michael Kohlhaas, and Erminia Donnarumma
Published: 2021
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27. Mitochondrial fission process 1 (MTFP1) controls bioenergetic efficiency and prevents inflammatory cardiomyopathy and heart failure in mice

Author: Timothy Wai, Erminia Donnarumma, Christoph Maack, Thibault Chaze, Quentin Giai Gianetto, Mariette Matondo, Elodie Vimont, Etienne Kornobis, Michael Kohlhaas, Maryse Moya-Nilges, Biologie mitochondriale – Mitochondrial biology, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), University Clinic Würzburg, Biomics (plateforme technologique), Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Plateforme de Spectrométrie de Masse Protéomique - Mass Spectrometry Proteomics Platform (MSPP), and Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM)
Subjects: uncoupling, Programmed cell death, permeability transition pore, Cardiac fibrosis, Chemistry, oxidative phosphorylation, Cardiomyopathy, Oxidative phosphorylation, Mitochondrion, medicine.disease, Cell biology, mitochondria, Mitochondrial permeability transition pore, Knockout mouse, medicine, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Mitochondrial fission, cardiomyopathy
Abstract: Mitochondria are paramount to the metabolism and survival of cardiomyocytes. Here we show that Mitochondrial Fission Process 1 (MTFP1) is essential for cardiac structure and function. Constitutive knockout of cardiomyocyte MTFP1 in mice resulted in adult-onset dilated cardiomyopathy (DCM) characterized by sterile inflammation and cardiac fibrosis that progressed to heart failure and middle-aged death. Failing hearts from cardiomyocyte-restricted knockout mice displayed a general decline in mitochondrial gene expression and oxidative phosphorylation (OXPHOS) activity. Pre-DCM, we observed no defects in mitochondrial morphology, content, gene expression, OXPHOS assembly nor phosphorylation dependent respiration. However, knockout cardiac mitochondria displayed reduced membrane potential and increased non-phosphorylation dependent respiration, which could be rescued by pharmacological inhibition of the adenine nucleotide translocase ANT. Primary cardiomyocytes from pre-symptomatic knockout mice exhibited normal excitation-contraction coupling but increased sensitivity to programmed cell death (PCD), which was accompanied by an opening of the mitochondrial permeability transition pore (mPTP). Intriguingly, mouse embryonic fibroblasts deleted for Mtfp1 recapitulated PCD sensitivity and mPTP opening, both of which could be rescued by pharmacological or genetic inhibition of the mPTP regulator Cyclophilin D. Collectively, our data demonstrate that contrary to previous in vitro studies, the loss of the MTFP1 promotes mitochondrial uncoupling and increases cell death sensitivity, causally mediating pathogenic cardiac remodeling.
Published: 2021
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28. Listeriolysin S: A bacteriocin from

Author: Jazmín, Meza-Torres, Mickaël, Lelek, Juan J, Quereda, Martin, Sachse, Giulia, Manina, Dmitry, Ershov, Jean-Yves, Tinevez, Lilliana, Radoshevich, Claire, Maudet, Thibault, Chaze, Quentin, Giai Gianetto, Mariette, Matondo, Marc, Lecuit, Isabelle, Martin-Verstraete, Christophe, Zimmer, Hélène, Bierne, Olivier, Dussurget, Pascale, Cossart, and Javier, Pizarro-Cerdá
Subjects: Cytoplasm, Cell Membrane, Biological Sciences, microfluidic microscopy, Listeria monocytogenes, Microbiology, contact-dependent inhibition (CDI), Hemolysin Proteins, Adenosine Triphosphate, Bacteriocins, bacteriocin, Listeria monocytogenes (Lm), Listeriolysin S (LLS)
Abstract: Significance Listeria monocytogenes (Lm) is a bacterial pathogen that causes listeriosis, a foodborne disease characterized by gastroenteritis, meningitis, bacteremia, and abortions in pregnant women. The most severe human listeriosis outbreaks are associated with a subset of Lm hypervirulent clones that encode the bacteriocin Listeriolysin S (LLS), which modifies the gut microbiota and allows efficient Lm gut colonization and invasion of deeper organs. Our present work identifies the killing mechanism displayed by LLS to outcompete gut commensal bacteria, demonstrating that it induces membrane permeabilization and membrane depolarization of target bacteria. Moreover, we show that LLS is a thiazole/oxazole–modified microcin that displays a contact-dependent inhibition mechanism., Listeriolysin S (LLS) is a thiazole/oxazole–modified microcin (TOMM) produced by hypervirulent clones of Listeria monocytogenes. LLS targets specific gram-positive bacteria and modulates the host intestinal microbiota composition. To characterize the mechanism of LLS transfer to target bacteria and its bactericidal function, we first investigated its subcellular distribution in LLS-producer bacteria. Using subcellular fractionation assays, transmission electron microscopy, and single-molecule superresolution microscopy, we identified that LLS remains associated with the bacterial cell membrane and cytoplasm and is not secreted to the bacterial extracellular space. Only living LLS-producer bacteria (and not purified LLS-positive bacterial membranes) display bactericidal activity. Applying transwell coculture systems and microfluidic-coupled microscopy, we determined that LLS requires direct contact between LLS-producer and -target bacteria in order to display bactericidal activity, and thus behaves as a contact-dependent bacteriocin. Contact-dependent exposure to LLS leads to permeabilization/depolarization of the target bacterial cell membrane and adenosine triphosphate (ATP) release. Additionally, we show that lipoteichoic acids (LTAs) can interact with LLS and that LTA decorations influence bacterial susceptibility to LLS. Overall, our results suggest that LLS is a TOMM that displays a contact-dependent inhibition mechanism.
Published: 2021

29. Mass‐spectrometry analysis of the human pineal proteome during night and day and in autism

Author: Guillaume, Dumas, Hany, Goubran-Botros, Mariette, Matondo, Cécile, Pagan, Cyril, Boulègue, Thibault, Chaze, Julia, Chamot-Rooke, Erik, Maronde, Thomas, Bourgeron, Génétique humaine et fonctions cognitives - Human Genetics and Cognitive Functions (GHFC (UMR_3571 / U-Pasteur_1)), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Precision Psychiatry and Social Physiology laboratory [Montreal] (PPHP), CRSN/Faculté de médecine Université de Montréal-CHU Sainte Justine [Montréal], Spectrométrie de Masse pour la Biologie – Mass Spectrometry for Biology (UTechS MSBio), Institut Pasteur [Paris] (IP)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université Sorbonne Paris Cité (USPC), Service de Biochimie et de Biologie Moléculaire [AP-HP Hôpital Lariboisière] (Inserm U942), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Lariboisière-Fernand-Widal [APHP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institute for Anatomy II, Goethe-Universität Frankfurt am Main, This work was supported by the Institut Pasteur, the CNRS, the INSERM, the AP-HP, the University Paris Diderot, the Cognacq-Jay foundation, the Bettencourt-Schueller foundation, the Orange foundation, the FondaMental foundation, the Fondation de France, the Conny-Maeva foundation, the Eranet-Neuron ANR (ALTRUISM), and the Labex GenMed and BioPsy. GD is funded by the Institute for Data Valorization (IVADO), Montreal, and the Fonds de recherche du Québec (FRQ)., ANR-11-IDEX-0004,SUPER,Sorbonne Universités à Paris pour l'Enseignement et la Recherche(2011), ANR-10-LABX-0013,GENMED,Medical Genomics(2010), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Institut Pasteur [Paris]-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), PORTELETTE, Virginie, Sorbonne Universités à Paris pour l'Enseignement et la Recherche - - SUPER2011 - ANR-11-IDEX-0004 - IDEX - VALID, and Medical Genomics - - GENMED2010 - ANR-10-LABX-0013 - LABX - VALID
Subjects: Proteomics, chaperon proteins, circadian rhythm, Spectrometry, Mass, Electrospray Ionization, endocrine system, Time Factors, antioxidant, Proteome, pineal gland, autism spectrum disorders, autism spectrum disorder, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, energy production, Tandem Mass Spectrometry, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Humans, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Protein Interaction Maps, Autistic Disorder, [SDV.BC] Life Sciences [q-bio]/Cellular Biology, mass spectrometry, Proteins, Original Articles, mass spectometry, Case-Control Studies, Original Article, hormones, hormone substitutes, and hormone antagonists
Abstract: International audience; The human pineal gland regulates day‐night dynamics of multiple physiological processes, especially through the secretion of melatonin. Using mass spectrometry‐based proteomics and dedicated analysis tools, we identify proteins in the human pineal gland and analyze systematically their variation throughout the day, and, compare these changes in the pineal proteome between control specimens and donors diagnosed with autism. Results reveal diverse regulated clusters of proteins with, among others, catabolic carbohydrate process and cytoplasmic membrane‐bounded vesicle‐related proteins differing between day and night and/or control versus autism pineal glands. These data show novel and unexpected processes happening in the human pineal gland during the day/night rhythm as well as specific differences between autism donor pineal glands and those from controls.
Published: 2020
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30. Characterization of Extracellular Vesicles Produced by Aspergillus fumigatus Protoplasts

Author: Thibault Chaze, Leonardo Nimrichter, Mariette Matondo, Olivier Gorgette, Anne Beauvais, Juliana Rizzo, Robert W. Roberson, Jean-Paul Latgé, Kildare Miranda, Marcio L. Rodrigues, Instituto de Microbiologia Paulo de Góes [Rio de Janeiro] (IMPG), Universidade Federal do Rio de Janeiro (UFRJ), Département de Mycologie - Department of Mycology, Institut Pasteur [Paris] (IP), Spectrométrie de Masse pour la Biologie – Mass Spectrometry for Biology (UTechS MSBio), Institut Pasteur [Paris] (IP)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Arizona State University [Tempe] (ASU), Microscopie ultrastructurale (plate-forme), University of Crete [Heraklion] (UOC), Fiocruz Paraná - Instituto Carlos Chagas / Carlos Chagas Institute [Curitiba, Brésil] (ICC), Fundação Oswaldo Cruz / Oswaldo Cruz Foundation (FIOCRUZ), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), M.L.R. was supported by grants from the Brazilian Ministry of Health (grant 440015/2018-9), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq, grants 405520/2018-2 and 301304/2017-3), and Fiocruz (grants VPPCB-007-FIO-18 and VPPIS-001-FIO18). We also acknowledge support from the Instituto Nacional de Ciência e Tecnologia de Inovação em Doenças de Populações Negligenciadas (INCT-IDPN). J.R. developed part of this work as a Ph.D. student supported by FAPERJ (E-26/201.991/2015) and is currently a postdoctoral fellow at Institut Pasteur (Paris, France), funded by the CAPES-Cofecub Program (88887.142840/2017-00). This research was partly supported by funds provided to J.-P.L. by the Laboratoire d'Excellence 'Integrative Biology of Emerging Infectious Diseases' (grant ANR-10-LABX-62-IBEID), la Fondation pour la Recherche Médicale (DEQ20150331722 LATGE Equipe FRM 2015)., We are grateful to Leandro Honorato (Instituto de Microbiologia Paulo de Goes, UFRJ, Brazil) and Luna Sobrino Joffe (Stony Brook University, USA) for help with protoplast purification, Flavia Reis (Fiocruz, Brazil) for help with NTA, Fernando P. de Almeida for the help with superresolution microscopy (CENABIO/UFRJ, Brazil), and Vishukumar Aimanianda (Institut Pasteur, France) for discussions and for providing some of the antibodies for this study., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), Instituto de Microbiologia Paulo de Góes (IMPG), Institut Pasteur [Paris], Institut Pasteur [Paris]-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), and Fundação Oswaldo Cruz (FIOCRUZ)
Subjects: Proteomics, Molecular Biology and Physiology, lcsh:QR1-502, conidia, Microbiology, lcsh:Microbiology, Aspergillus fumigatus, Fungal Proteins, Cell wall, 03 medical and health sciences, Microscopy, Electron, Transmission, protoplasts, Cell Wall, Extracellular, Molecular Biology, 030304 developmental biology, 0303 health sciences, Organelle Biogenesis, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], biology, 030306 microbiology, Chemistry, Vesicle, biology.organism_classification, Glycome, QR1-502, Yeast, Cell biology, Aspergillus, Microscopy, Fluorescence, Microscopy, Electron, Scanning, extracellular vesicles, Bacterial outer membrane, Biogenesis, Research Article
Abstract: Fungal cells use extracellular vesicles (EVs) to export biologically active molecules to the extracellular space. In this study, we used protoplasts of Aspergillus fumigatus, a major fungal pathogen, as a model to evaluate the role of EV production in cell wall biogenesis. Our results demonstrated that wall-less A. fumigatus exports plasma membrane-derived EVs containing a complex combination of proteins and glycans. Our report is the first to characterize fungal EVs in the absence of a cell wall. Our results suggest that protoplasts represent a promising model for functional studies of fungal vesicles., Extracellular vesicles (EVs) are membranous compartments produced by yeast and mycelial forms of several fungal species. One of the difficulties in perceiving the role of EVs during the fungal life, and particularly in cell wall biogenesis, is caused by the presence of a thick cell wall. One alternative to have better access to these vesicles is to use protoplasts. This approach has been investigated here with Aspergillus fumigatus, one of the most common opportunistic fungal pathogens worldwide. Analysis of regenerating protoplasts by scanning electron microscopy and fluorescence microscopy indicated the occurrence of outer membrane projections in association with surface components and the release of particles with properties resembling those of fungal EVs. EVs in culture supernatants were characterized by transmission electron microscopy and nanoparticle tracking analysis. Proteomic and glycome analysis of EVs revealed the presence of a complex array of enzymes related to lipid/sugar metabolism, pathogenic processes, and cell wall biosynthesis. Our data indicate that (i) EV production is a common feature of different morphological stages of this major fungal pathogen and (ii) protoplastic EVs are promising tools for undertaking studies of vesicle functions in fungal cells. IMPORTANCE Fungal cells use extracellular vesicles (EVs) to export biologically active molecules to the extracellular space. In this study, we used protoplasts of Aspergillus fumigatus, a major fungal pathogen, as a model to evaluate the role of EV production in cell wall biogenesis. Our results demonstrated that wall-less A. fumigatus exports plasma membrane-derived EVs containing a complex combination of proteins and glycans. Our report is the first to characterize fungal EVs in the absence of a cell wall. Our results suggest that protoplasts represent a promising model for functional studies of fungal vesicles.
Published: 2020
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31. Revisiting Cryptococcus extracellular vesicles properties and their use as vaccine platforms

Author: Flavia C. G. Reis, Lysangela R. Alves, Guilhem Janbon, Marcio L. Rodrigues, Juliana Rizzo, Sophie Novault, Mariette Matondo, Robin C. May, Gérard Pehau-Arnaudet, Leonardo Nimrichter, Pierre-Henri Commere, Matthijn Vos, Vishukumar Aimanianda, Sarah Sze Wah Wong, Frédérique Moyrand, Anastasia D. Gazi, Thibault Chaze, Biologie des ARN des Pathogènes fongiques - RNA Biology of Fungal Pathogens, Institut Pasteur [Paris], Mycologie moléculaire - Molecular Mycology, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Plateforme BioImagerie Ultrastructurale – Ultrastructural BioImaging Platform (UTechS UBI), Spectrométrie de Masse pour la Biologie – Mass Spectrometry for Biology (UTechS MSBio), Institut Pasteur [Paris]-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Cytometrie et Biomarqueurs – Cytometry and Biomarkers (UTechS CB), Fundação Oswaldo Cruz (FIOCRUZ), Réseau International des Instituts Pasteur (RIIP), Plateforme technologique Nanoimagerie / Nanoimaging Technological Platform, University of Birmingham [Birmingham], Universidade Federal do Rio de Janeiro (UFRJ), This work was supported by a CAPES COFECUB grant n°39712ZK (to GJ, MLR, LA and 1039 LN). JR was supported by the CAPES-COFECUB Franco-Brazilian Research Exchange Program (88887.357947/2019-00) and by a Pasteur-Roux-Cantarini fellowship of Institut Pasteur. SSWW was supported by CEFIPRA/ANR-DFG-AfuINF grant and Pasteur-Roux- Cantarini postdoctoral fellowship. VA was supported by ANR-DFG AfuINF and Indo-French Centre for the Promotion of Advanced Research (CEFIPRA, Grant No5403-1) grants. Jean-Marie Winter from the NanoImaging Core at Institut Pasteur is acknowledged for his support image acquisition. The NanoImaging Core was created with the help of a grant from the French Government’s ‘Investissements d’Avenir’ program (EQUIPEX CACSICE – 'Centre d’analyse de systèmes complexes dans les environnements complexes', ANR-11-EQPX-0008). The Falcon II equipping the F20 microscope at the UBI used during this study was also financed by the Equipex CACSICE (grant number ANR-11-EQPX-0008). M.L.R. is supported by grants from the Brazilian Ministry of Health (grant 440015/2018-9), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq, grants 405520/2018-2 and 1052 301304/2017-3), and Fiocruz (grants VPPC B-00 7-FIO-18 and VPPIS-001-F IO18)MLR, J R, and FCGR also acknowledge support from Coordenac ão de Aperfeicoa mento de Pessoal de Nível Superior ( CAPES , finance code 001 ) and the Instituto Nacional de Ciencia e Tecnologia de Inovacão em Doencas de Populacões Negligenciadas (INCT-IDPN). MLR is currently on leave of an associate professor position at the Instituto de Microbiologia Paulo de Góes of the Universidade Federal do Rio de Janeiro. We thank Adèle Trottier for her help in the preparation of EV samples, ANR-16-CE92-0039,AfuInf,Protéome and polysaccharidome d'Aspergillus fumigatus lors des étapes précoces de l'infection(2016), ANR-11-EQPX-0008,CACSICE,Centre d'analyse de systèmes complexes dans les environnements complexes(2011), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), and Institut de Chimie du CNRS (INC)-Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: Cryo-electron microscopy, Population, Cryptococcus, Proteomics, 03 medical and health sciences, vaccine, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Lipid bilayer, education, mannoproteins, Cryo-EM, 030304 developmental biology, Cryptococcus neoformans, 0303 health sciences, education.field_of_study, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], biology, 030306 microbiology, Chemistry, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Extracellular vesicle, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, Cell biology, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, fungal infections, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Proteome, extracellular vesicles
Abstract: Whereas extracellular vesicle (EV) research has become commonplace in different biomedical fields, this field of research is still in its infancy in mycology. Here we provide a robust set of data regarding the structural and compositional aspects of EVs isolated from the fungal pathogenic species Cryptococcus neoformans, C. deneoformans and C. deuterogattii. Using cutting-edge methodological approaches including cryogenic electron microscopy and cryogenic electron tomography, proteomics, and flow cytometry, we revisited cryptococcal EV features and suggest a new EV structural model, in which the vesicular lipid bilayer is covered by mannoprotein-based fibrillar decoration, bearing the capsule polysaccharide as its outer layer. About 10% of the EV population is devoid of fibrillar decoration, adding another aspect to EV diversity. By analyzing EV protein cargo from the three species, we characterized the typical Cryptococcus EV proteome. It contains several membrane-bound protein families, including some Tsh proteins bearing a SUR7/PalI motif. The presence of known protective antigens on the surface of Cryptococcus EVs, resembling the morphology of encapsulated virus structures, suggested their potential as a vaccine. Indeed, mice immunized with EVs obtained from an acapsular C. neoformans mutant strain rendered a strong antibody response in mice and significantly prolonged their survival upon C. neoformans infection.
Published: 2020
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32. Impact of the gut microbiota on the m 6 A epitranscriptome of mouse cecum and liver

Author: Pascale Cossart, Marie-Agnès Dillies, Sabrina Jabs, Amine Ghozlane, Quentin Giai Gianetto, Vincent Guérineau, Christophe Bécavin, David Touboul, Alessandro Pagliuso, Giulia Spanò, Mariette Matondo, Marie-Anne Nahori, Thibault Chaze, Anne Biton, Interactions Bactéries-Cellules (UIBC), Institut National de la Recherche Agronomique (INRA)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie des Substances Naturelles (ICSN), Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Spectrométrie de Masse pour la Biologie – Mass Spectrometry for Biology (UTechS MSBio), Institut Pasteur [Paris] (IP)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), We thank Marion Bérard and the Gnotobiology platform of the Institut Pasteur for support in conducting gnotobiology experiments, the Pasteur Biomics platforms for Transcriptomics and Epigenetics and Metagenomics for providing RNA sequencing and 16S rRNA sequencing services, Cédric Fund, Biomics Platform, C2RT, Institut Pasteur, Paris, France, supported by France Génomique (ANR-10-INBS-09-09) and IBISA, Carla Saleh and Olivier Dussurget for helpful discussions, Hugo Varet (Institut Pasteur Bionformatics and Statistics Hub) for advice concerning statistical analysis, Stevenn Volant for help with analysis of 16S sequencing data. This work was supported by grants to P.C.: European Research Council (ERC) Advanced Grant BacCellEpi (670823), ANR Investissement d’Avenir Programme (10-LABX-62-IBEID), ERANET-Infect-ERA PROANTILIS (ANR-13-IFEC-0004-02) and the Fondation Le Roch-Les Mousquetaires. S.J. was supported by a Danone Research fellowship and European Research Council (ERC) Advanced Grant BacCellEpi (670823)., ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-13-IFEC-0004,PROANTILIS,Subversive pro- and anti-inflammation trade-offs promote infection by Listeria monocytogenes(2013), European Project: 670823,H2020,ERC-2014-ADG,BacCellEpi(2015), Nahori, marie-anne, Organisation et montée en puissance d'une Infrastructure Nationale de Génomique - - France-Génomique2010 - ANR-10-INBS-0009 - INBS - VALID, Integrative Biology of Emerging Infectious Diseases - - IBEID2010 - ANR-10-LABX-0062 - LABX - VALID, ERA-NET Infect-ERA - Subversive pro- and anti-inflammation trade-offs promote infection by Listeria monocytogenes - - PROANTILIS2013 - ANR-13-IFEC-0004 - IFEC - VALID, Bacterial, cellular and epigenetic factors that control enteropathogenicity - BacCellEpi - - H20202015-10-01 - 2018-09-30 - 670823 - VALID, Institut National de la Recherche Agronomique (INRA)-Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur [Paris]-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Adenosine, Methyltransferase, Science, [SDV]Life Sciences [q-bio], General Physics and Astronomy, Biology, Gut flora, Methylation, digestive system, Article, General Biochemistry, Genetics and Molecular Biology, Microbiology, Transcriptome, Mice, 03 medical and health sciences, Cecum, 0302 clinical medicine, fluids and secretions, Gene expression, medicine, Animals, RNA, Messenger, lcsh:Science, Multidisciplinary, Bacteria, Methyltransferases, General Chemistry, biology.organism_classification, Commensalism, Gastrointestinal Microbiome, Mice, Inbred C57BL, [SDV] Life Sciences [q-bio], stomatognathic diseases, 030104 developmental biology, medicine.anatomical_structure, Liver, Female, lcsh:Q, Microbiome, 030217 neurology & neurosurgery, Akkermansia muciniphila
Abstract: The intestinal microbiota modulates host physiology and gene expression via mechanisms that are not fully understood. Here we examine whether host epitranscriptomic marks are affected by the gut microbiota. We use methylated RNA-immunoprecipitation and sequencing (MeRIP-seq) to identify N6-methyladenosine (m6A) modifications in mRNA of mice carrying conventional, modified, or no microbiota. We find that variations in the gut microbiota correlate with m6A modifications in the cecum, and to a lesser extent in the liver, affecting pathways related to metabolism, inflammation and antimicrobial responses. We analyze expression levels of several known writer and eraser enzymes, and find that the methyltransferase Mettl16 is downregulated in absence of a microbiota, and one of its target mRNAs, encoding S-adenosylmethionine synthase Mat2a, is less methylated. We furthermore show that Akkermansia muciniphila and Lactobacillus plantarum affect specific m6A modifications in mono-associated mice. Our results highlight epitranscriptomic modifications as an additional level of interaction between commensal bacteria and their host., The intestinal microbiota modulates host physiology and gene expression via unclear mechanisms. Here, Jabs et al. show that variations in the gut microbiota correlate with N6-methyladenosine modifications of host mRNAs in the cecum and liver of mice.
Published: 2020
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33. The transpeptidase PBP2 governs initial localization and activity of the major cell-wall synthesis machinery in E. coli

Author: Baptiste Cordier, Andrey Aristov, Eva Wollrab, Mariette Matondo, Gizem Özbaykal, Thibault Chaze, Antoine Vigouroux, Sven van Teeffelen, François Simon, Morphogénèse et Croissance microbiennes / Microbial Morphogenesis and Growth, Institut Pasteur [Paris], Université Paris Diderot, Sorbonne Paris Cité, Paris, France, Université Paris Diderot - Paris 7 (UPD7), Biologie de Synthèse - Synthetic biology, Université Paris-Descartes, Sorbonne Paris Cité, 75014 Paris, France, Spectrométrie de Masse pour la Biologie – Mass Spectrometry for Biology (UTechS MSBio), Institut Pasteur [Paris]-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), H2020 European Research Council 679980French National Research Agency ANR-10-LABX-62-IBEIDVolkswagenRégion Ile-de-FranceCampus France, ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), European Project: 679980,H2020,ERC-2015-STG,RCSB(2016), Institut Pasteur [Paris] (IP), and Institut Pasteur [Paris] (IP)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: genetic structures, QH301-705.5, MreB cytoskeleton, Science, infectious disease, bacterial morphogenesis, Curvature, medicine.disease_cause, MreB, General Biochemistry, Genetics and Molecular Biology, Cell wall synthesis, Cell wall, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Cell Wall, physics of living systems, Escherichia coli, medicine, Penicillin-Binding Proteins, Rod complex, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Biology (General), single-enzyme dynamics, 030304 developmental biology, Microbiology and Infectious Disease, 0303 health sciences, General Immunology and Microbiology, Escherichia coli Proteins, General Neuroscience, microbiology, E. coli, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, General Medicine, chemistry, Cytoplasm, Direct binding, Biophysics, Medicine, Peptidoglycan, sense organs, cell-wall insertion, 030217 neurology & neurosurgery, Subcellular Fractions, Research Article
Abstract: International audience; Bacterial shape is physically determined by the peptidoglycan cell wall. The cell-wall-synthesis machinery responsible for rod shape in Escherichia coli is the processive 'Rod complex'. Previously, cytoplasmic MreB filaments were thought to govern formation and localization of Rod complexes based on local cell-envelope curvature. Using single-particle tracking of the transpeptidase and Rod-complex component PBP2, we found that PBP2 binds to a substrate different from MreB. Depletion and localization experiments of other putative Rod-complex components provide evidence that none of those provide the sole rate-limiting substrate for PBP2 binding. Consistently, we found only weak correlations between MreB and envelope curvature in the cylindrical part of cells. Residual correlations do not require curvature-based Rod-complex initiation but can be attributed to persistent rotational motion. We therefore speculate that the local cell-wall architecture provides the cue for Rod-complex initiation, either through direct binding by PBP2 or through an unknown intermediate.
Published: 2020
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34. Listeria monocytogenes Exploits Mitochondrial Contact Site and Cristae Organizing System Complex Subunit Mic10 To Promote Mitochondrial Fragmentation and Cellular Infection

Author: Mariette Matondo, Anna Spier, Fabrizia Stavru, Filipe Carvalho, Thibault Chaze, and Pascale Cossart
Subjects: listeria monocytogenes, Mitochondrion, Biology, medicine.disease_cause, Mitochondrial Dynamics, Microbiology, Host-Microbe Biology, Mitochondrial Proteins, 03 medical and health sciences, proteomics, Listeria monocytogenes, Virology, Organelle, medicine, Humans, Inner mitochondrial membrane, 030304 developmental biology, 0303 health sciences, mic10, MICOS complex, mitochondrial fission, 030302 biochemistry & molecular biology, Listeriolysin O, Membrane Proteins, micos complex, HCT116 Cells, QR1-502, Cell biology, Mitochondria, Up-Regulation, Mitochondrial fission, Intracellular, Research Article
Abstract: Pathogenic bacteria can target host cell organelles to take control of key cellular processes and promote their intracellular survival, growth, and persistence. Mitochondria are essential, highly dynamic organelles with pivotal roles in a wide variety of cell functions. Mitochondrial dynamics and function are intimately linked. Our previous research showed that Listeria monocytogenes infection impairs mitochondrial function and triggers fission of the mitochondrial network at an early infection stage, in a process that is independent of the presence of the main mitochondrial fission protein Drp1. Here, we analyzed how mitochondrial proteins change in response to L. monocytogenes infection and found that infection raises the levels of Mic10, a mitochondrial inner membrane protein involved in formation of cristae. We show that Mic10 is important for L. monocytogenes-dependent mitochondrial fission and infection of host cells. Our findings thus offer new insight into the mechanisms used by L. monocytogenes to hijack mitochondria to optimize host infection., Mitochondrial function adapts to cellular demands and is affected by the ability of the organelle to undergo fusion and fission in response to physiological and nonphysiological cues. We previously showed that infection with the human bacterial pathogen Listeria monocytogenes elicits transient mitochondrial fission and a drop in mitochondrion-dependent energy production through a mechanism requiring the bacterial pore-forming toxin listeriolysin O (LLO). Here, we performed quantitative mitochondrial proteomics to search for host factors involved in L. monocytogenes-induced mitochondrial fission. We found that Mic10, a critical component of the mitochondrial contact site and cristae organizing system (MICOS) complex, is significantly enriched in mitochondria isolated from cells infected with wild-type but not with LLO-deficient L. monocytogenes. Increased mitochondrial Mic10 levels did not correlate with upregulated transcription, suggesting a posttranscriptional mechanism. We then showed that Mic10 is necessary for L. monocytogenes-induced mitochondrial network fragmentation and that it contributes to L. monocytogenes cellular infection independently of MICOS proteins Mic13, Mic26, and Mic27. In conclusion, investigation of L. monocytogenes infection allowed us to uncover a role for Mic10 in mitochondrial fission.
Published: 2020

35. Phosphorylation-Dependent Assembly of a 14-3-3 Mediated Signaling Complex During Red Blood Cell Invasion by Plasmodium falciparum Merozoites

Author: Jyoti S. Choudhary, Brandon M. Invergo, Christèle Huon, Petra Gutenbrunner, Mariette Matondo, Inderjeet Kaur, Kunal R. More, Chetan E. Chitnis, Shailja Singh, Ravi Jain, Hendrik Weisser, Thibault Chaze, Gordon Langsley, Quentin Giai Gianetto, Biologie de Plasmodium et Vaccins - Malaria Parasite Biology and Vaccines, Institut Pasteur [Paris], International Centre for Genetic Engineering and Biotechnology [New Delhi] (ICGEB), Spectrométrie de Masse pour la Biologie – Mass Spectrometry for Biology (UTechS MSBio), Institut Pasteur [Paris]-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, The Wellcome Trust Sanger Institute [Cambridge], Jawaharlal Nehru University (JNU), Biologie cellulaire comparative des Apicomplexes, [Institut Cochin] Departement Infection, immunité, inflammation, Institut Cochin (IC UM3 (UMR 8104 / U1016)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut Cochin (IC UM3 (UMR 8104 / U1016)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), This work was supported by a MolSigMal grant (ANR-17-CE15-0010) from Agence Nationale de la Recherche (ANR) to C.E.C. and internal funds from the Institut Pasteur. G.L. acknowledges support from the Labex ParaFrap (ANR-11-LABX-0024). K.R.M. received a short-term fellowship from the European Molecular Biology Organization (EMBO)., ANR-17-CE15-0010,MolSigMal,Evènements moléculaires de la signalisation induite par l'invasion des globules rouges par les parasites paludéens(2017), ANR-11-LABX-0024,ParaFrap,Alliance française contre les maladies parasitaires(2011), Institut Pasteur [Paris] (IP), Institut Pasteur [Paris] (IP)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut Cochin (IC UM3 (UMR 8104 / U1016)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), PORTELETTE, Virginie, Evènements moléculaires de la signalisation induite par l'invasion des globules rouges par les parasites paludéens - - MolSigMal2017 - ANR-17-CE15-0010 - AAPG2017 - VALID, and Laboratoires d'excellence - Alliance française contre les maladies parasitaires - - ParaFrap2011 - ANR-11-LABX-0024 - LABX - VALID
Subjects: Proteomics, Erythrocytes, Multiprotein complex, [SDV.BBM.BS] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Plasmodium falciparum, Protozoan Proteins, malaria, Microbiology, Host-Microbe Biology, Microneme, 03 medical and health sciences, 0302 clinical medicine, hemic and lymphatic diseases, Virology, parasitic diseases, Humans, Protein phosphorylation, Phosphorylation, Protein kinase A, host cell invasion, 030304 developmental biology, 0303 health sciences, biology, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Merozoites, Kinase, Chemistry, Phosphoproteomics, hemic and immune systems, biology.organism_classification, host-parasite interaction, QR1-502, 3. Good health, Cell biology, 14-3-3 Proteins, Signal transduction, signaling, 030217 neurology & neurosurgery, circulatory and respiratory physiology, Signal Transduction, Research Article
Abstract: Invasion of red blood cells (RBCs) by Plasmodium falciparum merozoites is a complex process that is regulated by intricate signaling pathways. Here, we used phosphoproteomic profiling to identify the key proteins involved in signaling events during invasion. We found changes in the phosphorylation of various merozoite proteins, including multiple kinases previously implicated in the process of invasion. We also found that a phosphorylation-dependent multiprotein complex including signaling kinases assembles during the process of invasion. Disruption of this multiprotein complex impairs merozoite invasion of RBCs, providing a novel approach for the development of inhibitors to block the growth of blood-stage malaria parasites., Red blood cell (RBC) invasion by Plasmodium merozoites requires multiple steps that are regulated by signaling pathways. Exposure of P. falciparum merozoites to the physiological signal of low K+, as found in blood plasma, leads to a rise in cytosolic Ca2+, which mediates microneme secretion, motility, and invasion. We have used global phosphoproteomic analysis of merozoites to identify signaling pathways that are activated during invasion. Using quantitative phosphoproteomics, we found 394 protein phosphorylation site changes in merozoites subjected to different ionic environments (high K+/low K+), 143 of which were Ca2+ dependent. These included a number of signaling proteins such as catalytic and regulatory subunits of protein kinase A (PfPKAc and PfPKAr) and calcium-dependent protein kinase 1 (PfCDPK1). Proteins of the 14-3-3 family interact with phosphorylated target proteins to assemble signaling complexes. Here, using coimmunoprecipitation and gel filtration chromatography, we demonstrate that Pf14-3-3I binds phosphorylated PfPKAr and PfCDPK1 to mediate the assembly of a multiprotein complex in P. falciparum merozoites. A phospho-peptide, P1, based on the Ca2+-dependent phosphosites of PKAr, binds Pf14-3-3I and disrupts assembly of the Pf14-3-3I-mediated multiprotein complex. Disruption of the multiprotein complex with P1 inhibits microneme secretion and RBC invasion. This study thus identifies a novel signaling complex that plays a key role in merozoite invasion of RBCs. Disruption of this signaling complex could serve as a novel approach to inhibit blood-stage growth of malaria parasites.
Published: 2020
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36. Author response: The transpeptidase PBP2 governs initial localization and activity of the major cell-wall synthesis machinery in E. coli

Author: Andrey Aristov, Baptiste Cordier, Thibault Chaze, Mariette Matondo, Gizem Özbaykal, Antoine Vigouroux, Eva Wollrab, François Simon, and Sven van Teeffelen
Subjects: Chemistry, Cell wall synthesis, Cell biology
Published: 2020
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37. Author response: Class-A penicillin binding proteins do not contribute to cell shape but repair cell-wall defects

Author: Felipe Cava, Mariette Matondo, Thibault Chaze, Gizem Özbaykal, Enno R. Oldewurtel, Sven van Teeffelen, Baptiste Cordier, Antoine Vigouroux, Andrey Aristov, David Bikard, and Laura Alvarez
Subjects: Cell wall, Penicillin binding proteins, Chemistry, Cell shape, Cell biology
Published: 2020
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38. Differentiation-dependent susceptibility of human muscle cells to Zika virus infection

Author: Gillian Butler-Browne, Jim Zoladek, Ingo Riederer, Quentin Giai Gianetto, Philippe Roingeard, Patricia Jeannin, Julien Burlaud-Gaillard, Pierre-Emmanuel Ceccaldi, Mariette Matondo, Valérie Choumet, Thibault Chaze, Vincent Legros, Vincent Mouly, Philippe V. Afonso, Antoine Gessain, Mariela-Natacha Gonzàlez, Epidémiologie et Physiopathologie des Virus Oncogènes (EPVO (UMR_3569 / U-Pasteur_3)), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Morphogénèse et antigénicité du VIH et du virus des Hépatites (MAVIVH - U1259 Inserm - CHRU Tours), Université de Tours-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre Hospitalier Régional Universitaire de Tours (CHRU TOURS), Plateforme IBISA de Microscopie Electronique [CHRU de Tours] (UNIV Tours), Centre Hospitalier Régional Universitaire de Tours (CHRU TOURS)-Université de Tours, Spectrométrie de Masse pour la Biologie – Mass Spectrometry for Biology (UTechS MSBio), Centre National de la Recherche Scientifique (CNRS)-Centre de Ressources et de Recherche Technologique - Center for Technological Resources and Research (C2RT), Institut Pasteur [Paris]-Institut Pasteur [Paris], Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut de Myologie, Centre National de la Recherche Scientifique (CNRS)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Association française contre les myopathies (AFM-Téléthon)-Sorbonne Université (SU), Centre de recherche en myologie, Association française contre les myopathies (AFM-Téléthon)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Fundação Oswaldo Cruz (FIOCRUZ), Réseau International des Instituts Pasteur (RIIP), Environnement et Risques infectieux - Environment and Infectious Risks (ERI), Institut Pasteur [Paris], This work was supported by a Pasteur-Fiocruz grant. VL was supported by a fellowship from the 'Fondation pour la Recherche Médicale' (FRM), IR and MG by CNPq/Ciências sem Fronteiras program, CNPq/Brazilian National Institute of Science and Technology on Neuroimmunomodulation (INCT-NIM). FOCEM - Mercosur Structural Convergence Fund 03/11. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript., Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Epidémiologie et Physiopathologie des Virus Oncogènes / Oncogenic Virus Epidemiology and Pathophysiology (EPVO (UMR_3569 / U-Pasteur_3)), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Centre Hospitalier Régional Universitaire de Tours (CHRU Tours)-Université de Tours (UT), Institut Pasteur [Paris] (IP)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Centre de recherche en Myologie – U974 SU-INSERM, Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Institut Pasteur [Paris] (IP), Matondo, Mariette, Institut Pasteur [Paris]-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Association française contre les myopathies (AFM-Téléthon)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), UMRS974, Université Pierre et Marie Curie - Paris 6 (UPMC), Centre de Recherche en Myologie, Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Fundação Oswaldo Cruz / Oswaldo Cruz Foundation (FIOCRUZ)
Subjects: Proteomics, Pulmonology, RC955-962, Apoptosis, Pathology and Laboratory Medicine, Zika virus, 0302 clinical medicine, Medical Conditions, Animal Cells, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Arctic medicine. Tropical medicine, MESH: Proteins, Chikungunya, ComputingMilieux_MISCELLANEOUS, [SDV.MHEP.ME] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Zika Virus Infection, Stem Cells, MESH: Proteomics, 3. Good health, Medical Microbiology, Arboviral Infections, Viral Pathogens, Interferon Type I, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Public aspects of medicine, Cellular Types, MESH: Zika Virus, Microbiology, 03 medical and health sciences, Respiratory Disorders, MESH: Zika Virus Infection, Humans, Microbial Pathogens, MESH: Humans, Flaviviruses, MESH: Host-Pathogen Interactions, Public Health, Environmental and Occupational Health, Organisms, Biology and Life Sciences, Chikungunya Infection, Proteins, medicine.disease, Tropical Diseases, Virology, MESH: Cell Line, 030104 developmental biology, Biological Tissue, Interferon type I, Developmental Biology, 0301 basic medicine, RNA viruses, MESH: Cell Death, MESH: Interferon Type I, MESH: Muscle Cells, Viral Diseases, [SDV]Life Sciences [q-bio], Muscle Fibers, Skeletal, medicine.disease_cause, Virus Replication, Dengue fever, Myoblasts, Cytopathogenic Effect, Viral, Medicine and Health Sciences, Morphogenesis, Myocyte, Cytopathic effect, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, MESH: Muscle Fibers, Skeletal, Cell Death, Myogenesis, Cell Differentiation, Muscle Differentiation, Infectious Diseases, Cell Processes, Viruses, Host-Pathogen Interactions, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Disease Susceptibility, Stem cell, RA1-1270, Pathogens, Anatomy, medicine.drug, Research Article, Neglected Tropical Diseases, MESH: Cell Differentiation, 030231 tropical medicine, Muscle Tissue, MESH: Disease Susceptibility, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, MESH: Stem Cells, Biology, Cell Line, medicine, MESH: Myoblasts, Muscle Cells, MESH: Virus Replication, Cell Biology, Zika Virus, biology.organism_classification, MESH: Cytopathogenic Effect, Viral, Respiratory Infections
Abstract: Muscle cells are potential targets of many arboviruses, such as Ross River, Dengue, Sindbis, and chikungunya viruses, that may be involved in the physiopathological course of the infection. During the recent outbreak of Zika virus (ZIKV), myalgia was one of the most frequently reported symptoms. We investigated the susceptibility of human muscle cells to ZIKV infection. Using an in vitro model of human primary myoblasts that can be differentiated into myotubes, we found that myoblasts can be productively infected by ZIKV. In contrast, myotubes were shown to be resistant to ZIKV infection, suggesting a differentiation-dependent susceptibility. Infection was accompanied by a caspase-independent cytopathic effect, associated with paraptosis-like cytoplasmic vacuolization. Proteomic profiling was performed 24h and 48h post-infection in cells infected with two different isolates. Proteome changes indicate that ZIKV infection induces an upregulation of proteins involved in the activation of the Interferon type I pathway, and a downregulation of protein synthesis. This work constitutes the first observation of primary human muscle cells susceptibility to ZIKV infection, and differentiation-dependent restriction of infection from myoblasts to myotubes. Since myoblasts constitute the reservoir of stem cells involved in reparation/regeneration in muscle tissue, the infection of muscle cells and the viral-induced alterations observed here could have consequences in ZIKV infection pathogenesis., Author summary Muscle cells are potential targets of many arboviruses, such as Ross River, Dengue, Sindbis, and chikungunya viruses, and may be involved in the disease manifestation. During the recent outbreak of Zika virus (ZIKV), myalgia was one of the most frequently reported symptoms. We investigated the susceptibility of human muscle cells to ZIKV infection. Using an in vitro model of human muscle stem cells (myoblasts) that can be differentiated into differentiated muscle cells (myotubes), we found that myoblasts can be infected by ZIKV. In contrast, myotubes were shown to be resistant to ZIKV infection. Infection induced the death of infected cells. Protein levels 24h and 48h post-infection indicate that ZIKV infection induces an upregulation of proteins involved in the activation of the Interferon type I pathway, and a downregulation of protein synthesis. This work constitutes the first observation of primary human muscle cells susceptibility to ZIKV infection, muscle stem cells being susceptible while differentiated muscle cells are resistant. Since myoblasts constitute the reservoir of stem cells involved in reparation/regeneration in muscle tissue, the infection of muscle cells and the viral-induced alterations observed here could have consequences during ZIKV infection.
Published: 2020
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39. Class-A penicillin binding proteins do not contribute to cell shape but repair cell- wall defects

Author: Mariette Matondo, Enno R. Oldewurtel, Sven van Teeffelen, Antoine Vigouroux, Baptiste Cordier, Gizem Özbaykal, Felipe Cava, Andrey Aristov, Laura Alvarez, Thibault Chaze, David Bikard, Biologie de Synthèse - Synthetic biology, Institut Pasteur [Paris], Morphogénèse et Croissance microbiennes / Microbial Morphogenesis and Growth, Université Paris Descartes - Paris 5 (UPD5), Université Sorbonne Paris Cité (USPC), Department of Molecular Biology [Umeå], Umeå University, Université Paris Diderot - Paris 7 (UPD7), Spectrométrie de Masse pour la Biologie – Mass Spectrometry for Biology (UTechS MSBio), Institut Pasteur [Paris]-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), This work was supported by the European Research Council (ERC) under the Europe Union’s Horizon 2020 research and innovation program [Grant Agreement No. (679980)], the French Government’s Investissement d’Avenir program Laboratoire d’Excellence ‘Integrative Biology of Emerging Infectious Diseases’ (ANR-10-LABX-62-IBEID), the Mairie de Paris ‘Emergence(s)’ program, and the Volkswagen Foundation. Research in the Cava lab is supported by MIMS, the Knut and Alice Wallenberg Foundation (KAW), the Swedish Research Council and the Kempe Foundation., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), European Project: 679980,H2020,ERC-2015-STG,RCSB(2016), European Project: 677823,H2020,ERC-2015-STG,CRISPAIR(2016), Centre National de la Recherche Scientifique (CNRS)-Centre de Ressources et de Recherche Technologique - Center for Technological Resources and Research (C2RT), Institut Pasteur [Paris]-Institut Pasteur [Paris], ANR-10-LABX-62-IBEID,IBEID,Laboratoire d'Excellence 'Integrative Biology of Emerging Infectious Diseases'(2010), Institut Pasteur [Paris] (IP), and Institut Pasteur [Paris] (IP)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Penicillin binding proteins, cell envelope, QH301-705.5, Science, infectious disease, Cell, Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy), medicine.disease_cause, General Biochemistry, Genetics and Molecular Biology, Cell wall, 03 medical and health sciences, chemistry.chemical_compound, Cell Wall, cell biology, medicine, Escherichia coli, Biology (General), Medicinsk bioteknologi (med inriktning mot cellbiologi (inklusive stamcellsbiologi), molekylärbiologi, mikrobiologi, biokemi eller biofarmaci), 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, Microbiology and Infectious Disease, General Immunology and Microbiology, 030306 microbiology, single-molecule tracking, penicillin-binding proteins, General Neuroscience, Escherichia coli Proteins, microbiology, E. coli, CRISPRi, General Medicine, Cell Biology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, peptidoglycan cell wall, medicine.anatomical_structure, Enzyme, chemistry, Biophysics, cell-wall repair, Medicine, Peptidoglycan, sense organs, Cell envelope, Cell wall repair, Research Article
Abstract: International audience; Cell shape and cell-envelope integrity of bacteria are determined by the peptidoglycan cell wall. In rod-shaped Escherichia coli, two conserved sets of machinery are essential for cell-wall insertion in the cylindrical part of the cell: the Rod complex and the class-A penicillin-binding proteins (aPBPs). While the Rod complex governs rod-like cell shape, aPBP function is less well understood. aPBPs were previously hypothesized to either work in concert with the Rod complex or to independently repair cell-wall defects. First, we demonstrate through modulation of enzyme levels that aPBPs do not contribute to rod-like cell shape but are required for mechanical stability, supporting their independent activity. By combining measurements of cell-wall stiffness, cell-wall insertion, and PBP1b motion at the single-molecule level, we then present evidence that PBP1b, the major aPBP, contributes to cell-wall integrity by repairing cell wall defects.
Published: 2020
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40. Network shifts away from branched actin formation promote the uniquely long growth of tunneling nanotubes

Author: J. Michael Henderson, Nina Ljubojevic, Thibault Chaze, Quentin Giai Gianetto, Stéphanie Descroix, Patricia M. Bassereau, and Chiara Zurzolo
Subjects: Biophysics
Published: 2022
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41. Cell-wall synthases contribute to bacterial cell-envelope integrity by actively repairing defects

Author: Andrey Aristov, Enno R. Oldewurtel, David Bikard, Baptiste Cordier, Thibault Chaze, Mariette Matondo, Gizem Özbaykal, Antoine Vigouroux, and Sven van Teeffelen
Subjects: 0303 health sciences, 030306 microbiology, Cell, medicine.disease_cause, Bacterial cell structure, Cell biology, Cell wall, 03 medical and health sciences, chemistry.chemical_compound, medicine.anatomical_structure, chemistry, Mechanical stability, medicine, Peptidoglycan, Cell shape, Escherichia coli, Function (biology), 030304 developmental biology
Abstract: AbstracCell shape and cell-envelope integrity of bacteria are determined by the peptidoglycan cell wall. In rod-shapedEscherichia coli, two conserved sets of machinery are essential for cell-wall insertion in the cylindrical part of the cell, the Rod complex and the class-A penicillin-binding proteins (aPBPs). While the Rod complex governs rod-like cell shape, aPBP function is less well understood. aPBPs were previously hypothesized to either work in concert with the Rod complex or to independently repair cell-wall defects. First, we demonstrate through modulation of enzyme levels that class-A PBPs do not contribute to rod-like cell shape but are required for mechanical stability, supporting their independent activity. By combining measurements of cell-wall stiffness, cell-wall insertion, and PBP1b motion at the single-molecule level we then demonstrate that PBP1b, the major class-A PBP, contributes to cell-wall integrity by localizing and inserting peptidoglycan in direct response to local cell-wall defects.
Published: 2019
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42. RadD Contributes to R-Loop Avoidance in Sub-MIC Tobramycin

Author: Quentin Giai Gianetto, Didier Mazel, Sean Kennedy, Mariette Matondo, Thibault Chaze, Zeynep Baharoglu, Evelyne Krin, Sebastian Aguilar Pierlé, Veronica Negro, Plasticité du Génome Bactérien - Bacterial Genome Plasticity (PGB), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Collège doctoral [Sorbonne universités], Sorbonne Université (SU), Spectrométrie de Masse pour la Biologie – Mass Spectrometry for Biology (UTechS MSBio), Institut Pasteur [Paris]-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Work in the Mazel lab is funded by the Institut Pasteur, the Centre National de la Recherche Scientifique (CNRS-UMR3525), the French National Research Agency (ANR Unibac ANR-17-CE13-0010-01), and the French Government’s Investissement d’Avenir program, Laboratoire d’Excellence 'Integrative Biology of Emerging Infectious Diseases'(grant no. ANR-10-LABX-62-IBEID). V.N. was funded by fellowships from DIM Malinf 140051 (Conseil régional d’Île-de-France) and FRM grant DBF20160635736. S.A.P. was supported by a postdoctoral fellowship from the Roux Foundation (Institut Pasteur), the FRM grant DBF20160635736, and the ANR Unibac ANR-17-CE13-0010-01, We thank Christophe Thomas for his help with protein purification, Melis Asal and Ricardo Albino Camacho for their participation in strain constructions, and Julie Lambert for UV tests. We thank Micheline Fromont for the yeast strains and plasmids and for her help with the two-hybrid experiment. We are grateful to Bénédicte Michel for the gift of several E. coli strains. We thank Melanie Blokesch for the Vibrio cholerae WT strain used in this study. We thank Sébastien Fleurier for advice for TUNEL experiments., ANR-17-CE13-0010,UniBac,Etude de l'émergence de la résistance aux antibiotiques et de la diversification génétique chez les bactéries à l'échelle de cellules uniques.(2017), ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Collège Doctoral, and Institut Pasteur [Paris] (IP)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: DNA, Bacterial, Molecular Biology and Physiology, antibiotic resistance, DNA repair, DNA damage, [SDV]Life Sciences [q-bio], Microbial Sensitivity Tests, medicine.disease_cause, Microbiology, 03 medical and health sciences, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Virology, Escherichia coli, medicine, DNA Breaks, Double-Stranded, Vibrio cholerae, 030304 developmental biology, Adenosine Triphosphatases, RecBCD, 0303 health sciences, Microbial Viability, biology, 030306 microbiology, Chemistry, Escherichia coli Proteins, Aminoglycoside, biology.organism_classification, QR1-502, Anti-Bacterial Agents, 3. Good health, Homologous Recombination Pathway, Tobramycin, R-loop, R-Loop Structures, Bacteria, Research Article
Abstract: Bacteria frequently encounter low concentrations of antibiotics. Active antibiotics are commonly detected in soil and water at concentrations much below lethal concentration. Although sub-MICs of antibiotics do not kill bacteria, they can have a major impact on bacterial populations by contributing to the development of antibiotic resistance through mutations in originally sensitive bacteria or acquisition of DNA from resistant bacteria. It was shown that concentrations as low as 100-fold below the MIC can actually lead to the selection of antibiotic-resistant cells. We seek to understand how bacterial cells react to such antibiotic concentrations using E. coli, the Gram-negative bacterial paradigm, and V. cholerae, the causative agent of cholera. Our findings shed light on the processes triggered at the DNA level by antibiotics targeting translation, how damage occurs, and what the bacterial strategies are to respond to such DNA damage., We have previously identified Vibrio cholerae mutants in which the stress response to subinhibitory concentrations of aminoglycoside is altered. One gene identified, VC1636, encodes a putative DNA/RNA helicase, recently named RadD in Escherichia coli. Here we combined extensive genetic characterization and high-throughput approaches in order to identify partners and molecular mechanisms involving RadD. We show that double-strand DNA breaks (DSBs) are formed upon subinhibitory tobramycin treatment in the absence of radD and recBCD and that formation of these DSBs can be overcome by RNase H1 overexpression. Loss of RNase H1, or of the transcription-translation coupling factor EF-P, is lethal in the radD deletion mutant. We propose that R-loops are formed upon sublethal aminoglycoside treatment, leading to the formation of DSBs that can be repaired by the RecBCD homologous recombination pathway, and that RadD counteracts such R-loop accumulation. We discuss how R-loops that can occur upon translation-transcription uncoupling could be the link between tobramycin treatment and DNA break formation.
Published: 2019
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43. CYP450 core involvement in multiple resistance strains of Aedes aegypti from French Guiana highlighted by proteomics, molecular and biochemical studies

Author: Jean Issaly, Thibaut Douché, Quentin Giai Gianetto, Mariette Matondo, Valérie Choumet, Yanouk Epelboin, Lanjiao Wang, Amandine Guidez, Pascal Gaborit, Thibault Chaze, Isabelle Dusfour, Unité d'entomologie médicale, Vectopôle Amazonien Emile Abonnenc [Cayenne, Guyane française], Institut Pasteur de la Guyane, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut Pasteur de la Guyane, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Spectrométrie de Masse pour la Biologie – Mass Spectrometry for Biology (UTechS MSBio), Institut Pasteur [Paris]-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Plateforme de Protéomique / Proteomics platform, Institut Pasteur [Paris]-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris]-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Environnement et Risques infectieux - Environment and Infectious Risks (ERI), Institut Pasteur [Paris], Département de Santé Globale - Department Global Health, This study was funded by the European Funds for Regional Development and CNES under FEDER 'CONTROLE', project n° Synergie: GY0010695 awarded to YE, LW, PG, JI, AG, and ID. This study was also funded by 'an Investissement d’Avenir grant of the Agence Nationale de la Recherche' (CEBA: ANR-10-LABX-25-01) in which the Institut Pasteur de la Guyane is partner awarded to YE, LW, PG, JI, AG, and ID., ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010), Institut Pasteur [Paris] (IP)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), and Institut Pasteur [Paris] (IP)
Subjects: Proteomics, Insecticides, Proteome, Hydrolases, Oligonucleotides, Voltage-Gated Sodium Channels, Disease Vectors, Toxicology, Pathology and Laboratory Medicine, medicine.disease_cause, Mosquitoes, Biochemistry, Esterase, Insecticide Resistance, chemistry.chemical_compound, Medical Conditions, 0302 clinical medicine, Cytochrome P-450 Enzyme System, Aedes, Pyrethrins, Medicine and Health Sciences, Intestinal Mucosa, 2. Zero hunger, Genetics, 0303 health sciences, Mutation, Multidisciplinary, Organic Compounds, Esterases, Eukaryota, Agriculture, Organophosphates, French Guiana, Enzymes, 3. Good health, Insects, Chemistry, Infectious Diseases, Gene Knockdown Techniques, Inactivation, Metabolic, Physical Sciences, Insect Proteins, Medicine, Female, Agrochemicals, Detoxification, Research Article, Ethers, Genotype, Arthropoda, Death Rates, Science, 030231 tropical medicine, Aedes aegypti, Aedes Aegypti, Biology, Polymorphism, Single Nucleotide, 03 medical and health sciences, Population Metrics, Nitriles, medicine, Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Gene, 030304 developmental biology, Population Biology, Resistance (ecology), Organic Chemistry, Organisms, Chemical Compounds, Biology and Life Sciences, Proteins, Cytochrome P450, biology.organism_classification, Invertebrates, Insect Vectors, Species Interactions, Deltamethrin, chemistry, Vector (epidemiology), Enzymology, biology.protein, Zoology, Entomology
Abstract: Insecticide resistance is a worldwide threat for vector control around the world, and Aedes aegypti, the main vector of several arboviruses, is a particular concern. To better understand the mechanisms of resistance, four isofemale strains originally from French Guiana were isolated and analysed using combined approaches. The activity of detoxification enzymes involved in insecticide resistance was assayed, and mutations located at positions 1016 and 1534 of the sodium voltage-gated channel gene, which have been associated with pyrethroid resistance in Aedes aegypti populations in Latin America, were monitored. Resistance to other insecticide families (organophosphates and carbamates) was evaluated. A large-scale proteomic analysis was performed to identify proteins involved in insecticide resistance. Our results revealed a metabolic resistance and resistance associated with a mutation of the sodium voltage-gated channel gene at position 1016. Metabolic resistance was mediated through an increase of esterase activity in most strains but also through the shifts in the abundance of several cytochrome P450 (CYP450s). Overall, resistance to deltamethrin was linked in the isofemale strains to resistance to other class of insecticides, suggesting that cross- and multiple resistance occur through selection of mechanisms of metabolic resistance. These results give some insights into resistance to deltamethrin and into multiple resistance phenomena in populations of Ae. aegypti.
Published: 2021
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44. MUB40 Binds to Lactoferrin and Stands as a Specific Neutrophil Marker

Author: Friederike Jönsson, Mariette Matondo, Dorothée Selimoglu-Buet, Benoit S. Marteyn, Bruno Baron, Naelle Lombion, Philippe J. Sansonetti, Jean-Yves Tinevez, Giulia Nigro, Thierry Lazure, Yves Marie Coïc, Valérie Lapierre, David J. Thornton, Katharina Nothelfer, Mark C. Anderson, Louise Injarabian, Thibault Chaze, Françoise Baleux, Ellen T. Arena, Eric Solary, Judith Souphron, Pascale Vonaesch, Caroline Ridley, Pathogénie microbienne moléculaire, Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Plateforme de Protéomique / Proteomics platform, Spectrométrie de Masse pour la Biologie – Mass Spectrometry for Biology (UTechS MSBio), Institut Pasteur [Paris]-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris]-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Chimie des Biomolécules - Chemistry of Biomolecules, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Institut de biochimie et génétique cellulaires (IBGC), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), Anticorps en thérapie et pathologie - Antibodies in Therapy and Pathology, Laboratoire de thérapie cellulaire, Département de médecine oncologique [Gustave Roussy], Institut Gustave Roussy (IGR)-Institut Gustave Roussy (IGR), Hématopoïèse normale et pathologique, Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Gustave Roussy (IGR)-Université Paris-Sud - Paris 11 (UP11), University of Manchester [Manchester], Biophysique Moléculaire (Plate-forme), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Imagopole (CITECH), Institut Pasteur [Paris], AP-HP Hôpital Bicêtre (Le Kremlin-Bicêtre), Département d'Immunologie - Department of Immunology, Chaire Microbiologie et Maladies infectieuses, Collège de France (CdF (institution)), This work was supported by the Fondation Laurette Fugain (LF-2015-15) (B.S.M.) and ANR JCJC grants (ANR-17-CE15-0012) (B.S.M.) - (ANR-16-CE15-0012-01) (F.J.)., ANR-17-CE15-0012,NEUTROXIA,Effet de l'exposition des neutrophiles à l'oxygène sur leur activation et leur mort : une lame à double tranchant(2017), ANR-16-CE15-0012,PlanA,Rôle des plaquettes et leurs interactions dans les réactions anaphylactiques(2016), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Pasteur [Paris] (IP)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud - Paris 11 (UP11)-Institut Gustave Roussy (IGR)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Pasteur [Paris] (IP), and Collège de France - Chaire Microbiologie et Maladies infectieuses
Subjects: 0301 basic medicine, MESH: Inflammation, Clinical Biochemistry, Cell, Arthritis, MESH: Rabbits, Peptide, MESH: Neutrophils, Biochemistry, MESH: Shigella, MUB, Drug Discovery, MESH: Animals, chemistry.chemical_classification, MESH: Middle Aged, Lactoferrin, MESH: Peptides, imaging, neutrophil, MESH: Fluorescent Dyes, 3. Good health, lactoferrin, medicine.anatomical_structure, Molecular Medicine, biomarker, [SDV.IMM]Life Sciences [q-bio]/Immunology, MESH: Carbocyanines, medicine.symptom, MESH: Dysentery, Bacillary, Inflammation, Biology, MESH: Guinea Pigs, Guinea pig, 03 medical and health sciences, Immune system, MESH: Mice, Inbred C57BL, medicine, Secretion, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, MESH: Mice, Pharmacology, MESH: Humans, MUB(40), MESH: Adult, medicine.disease, Molecular biology, MESH: Lactoferrin, 030104 developmental biology, chemistry, biology.protein, MESH: Biomarkers, MESH: Female
Abstract: Neutrophils represent the most abundant immune cells recruited to inflamed tissues. A lack of dedicated tools has hampered their detection and study. We show that a synthesized peptide, MUB40, binds to lactoferrin, the most abundant protein stored in neutrophil-specific and tertiary granules. Lactoferrin is specifically produced by neutrophils among other leukocytes, making MUB40 a specific neutrophil marker. Naive mammalian neutrophils (human, guinea pig, mouse, rabbit) were labeled by fluorescent MUB40 conjugates (-Cy5, Dylight405). A peptidase-resistant retro-inverso MUB40 (RI-MUB40) was synthesized and its lactoferrin-binding property validated. Neutrophil lactoferrin secretion during in vitro Shigella infection was assessed with RI-MUB40-Cy5 using live cell microscopy. Systemically administered RI-MUB40-Cy5 accumulated at sites of inflammation in a mouse arthritis inflammation model in vivo and showed usefulness as a potential tool for inflammation detection using non-invasive imaging. Improving neutrophil detection with the universal and specific MUB40 marker will aid the study of broad ranges of inflammatory diseases. MUB40 is a universal and specific marker of mammalian neutrophils. MUB40 interacts with lactoferrin, stored in specific (β1), tertiary (β2), and secretome (γ) granules secreted upon stimulation. Neutrophil detection in inflamed or infected tissues is facilitated by MUB40 peptides conjugated to fluorophores. Neutrophilic inflammation detection may be envisaged by combining MUB40 with non-invasive imaging.
Published: 2018
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45. Proteomic analysis of plasma extracellular vesicles reveals mitochondrial stress upon HTLV-1 infection

Author: Philippe V. Afonso, Antoine Gessain, Quentin Giai Gianetto, Olivier Gout, Mariette Matondo, Patricia Jeannin, Thibault Chaze, Epidémiologie et Physiopathologie des Virus Oncogènes (EPVO (UMR_3569 / U-Pasteur_3)), Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Institut Pasteur [Paris], Spectrométrie de Masse pour la Biologie – Mass Spectrometry for Biology (UTechS MSBio), Institut Pasteur [Paris]-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Fondation Ophtalmologique Adolphe de Rothschild [Paris], This work was supported by Ville de Paris [Programme Emergence(s)] and Ligue Contre le Cancer/Comité de Paris (RS18/75-5)., We would like to thank Camille Roesch (Izon) for her help in measuring the samples composition, Epidémiologie et Physiopathologie des Virus Oncogènes, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique ( CNRS ), Spectrométrie de Masse pour la Biologie – Mass Spectrometry for Biology ( UTechS MSBio ), Centre de Bioinformatique, Biostatistique et Biologie Intégrative ( C3BI ), Institut Pasteur [Paris], Institut Pasteur [Paris] (IP)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris]-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Centre de Ressources et de Recherche Technologique - Center for Technological Resources and Research (C2RT), and Institut Pasteur [Paris]-Institut Pasteur [Paris]
Subjects: Adult, Male, Proteomics, 0301 basic medicine, Science, Disease, Mitochondrion, [ SDV.MP.VIR ] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Mass Spectrometry, Article, Mitochondrial Proteins, Pathogenesis, Extracellular Vesicles, Young Adult, 03 medical and health sciences, Retrovirus, Stress, Physiological, immune system diseases, hemic and lymphatic diseases, Humans, Aged, Human T-lymphotropic virus 1, Multidisciplinary, biology, Proteins, virus diseases, Neurodegenerative Diseases, Middle Aged, biology.organism_classification, HTLV-I Infections, Lymphoproliferative Disorders, 3. Good health, Mitochondria, 030104 developmental biology, Viral infection, Carrier State, Immunology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Chromatography, Gel, Biomarker (medicine), Medicine, Female, HTLV-1 Infection, Lysosomes, Asymptomatic carrier, Biomarkers, Intracellular
Abstract: Extracellular vesicles (EVs) can participate in intercellular communication and pathogenesis. EVs contain many cargos, including proteins, and the composition of EVs differs between cell-types and activation levels. Thus, plasma EVs can be used as a biomarker of systemic response to infection and/or disease progression. In this study, we aimed at describing alterations in the protein content of plasma EVs upon infection with the human T-lymphotropic retrovirus type 1 (HTLV-1). HTLV-1 is the etiological agent of a lymphoproliferative disease (ATL) and a series of inflammatory diseases, including a neurodegenerative inflammatory disease (HAM/TSP). We found that plasma EVs are more abundant and smaller in HTLV-1 asymptomatic carriers or HAM/TSP patients when compared to uninfected healthy donors. Moreover, EVs from HTLV-1 infected donors contain markers of metabolic and mitochondrial stress.
Published: 2018
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46. Infection reveals a modification of SIRT2 critical for chromatin association

Author: Quentin Giai Gianetto, Pascale Cossart, Mariette Matondo, Jorge M. Pereira, Christine Chevalier, Melanie Hamon, Thibault Chaze, Francis Impens, Interactions Bactéries-Cellules ( UIBC ), Institut National de la Recherche Agronomique ( INRA ) -Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale ( INSERM ), Chromatine et Infection, Institut Pasteur [Paris], Spectrométrie de Masse structurale et protéomique, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique ( CNRS ), Ghent University [Belgium] ( UGENT ), Work in the M.A.H. laboratory received financial support from Institut Pasteur and the National Research Agency (ANR-EPIBACTIN). Work in the P.C. laboratory received financial support from Institut Pasteur, INSERM, INRA, the National Research Agency (ANR, ERANET Infect-ERA PROANTILIS ANR-13-IFEC-0004-02), the French Government’s Investissement d’Avenir program, the Laboratoire d’Excellence 'Integrative Biology of Emerging Infectious Diseases' (ANR-10-LABX-62-IBEID), the European Research Council (ERC, H2020-ERC-2014-ADG 670823-BacCellEpi), the Fondation le Roch les Mousquetaires, and the Fondation Balzan. P.C. is a Senior International Research Scholar of the Howard Hughes Medical Institute., We thank B. Lüscher for providing the SIRT2 isoform 2 plasmid, ANR-13-IFEC-0004,PROANTILIS,Subversive pro- and anti-inflammation trade-offs promote infection by Listeria monocytogenes ( 2013 ), ANR-10-LABX-62-IBEID,IBEID,Laboratoire d'Excellence 'Integrative Biology of Emerging Infectious Diseases' ( 2010 ), European Project : 670823,H2020,ERC-2014-ADG,BacCellEpi ( 2015 ), Interactions Bactéries-Cellules (UIBC), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur [Paris]-Institut National de la Recherche Agronomique (INRA), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Ghent University [Belgium] (UGENT), We thank B. Lüscher for providing the SIRT2 isoform 2 plasmid., ANR-13-IFEC-0004,PROANTILIS,Subversive pro- and anti-inflammation trade-offs promote infection by Listeria monocytogenes(2013), ANR-10-LABX-62-IBEID,IBEID,Laboratoire d'Excellence 'Integrative Biology of Emerging Infectious Diseases'(2010), European Project: 670823,H2020,ERC-2014-ADG,BacCellEpi(2015), vicente, marie-therese, ERA-NET Infect-ERA - Subversive pro- and anti-inflammation trade-offs promote infection by Listeria monocytogenes - - PROANTILIS2013 - ANR-13-IFEC-0004 - IFEC - VALID, Integrative Biology of Emerging Infectious Diseases - - IBEID2010 - ANR-10-LABX-0062 - LABX - VALID, Bacterial, cellular and epigenetic factors that control enteropathogenicity - BacCellEpi - - H20202015-10-01 - 2018-09-30 - 670823 - VALID, Institut National de la Recherche Agronomique (INRA)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Chromatine et Infection - Chromatin and Infection, Institut Pasteur [Paris] (IP), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Universiteit Gent = Ghent University (UGENT), ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), Institut National de la Recherche Agronomique (INRA)-Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Universiteit Gent = Ghent University [Belgium] (UGENT), Cossart, Pascale, and Hamon, Mélanie A.
Subjects: 0301 basic medicine, nucleocytoplasmic transport, listeria-monocytogenes, protein deacetylases, tubulin deacetylase, predict prognosis, gene-expression, phosphatase, phosphorylation, sirtuins, target, [ SDV.MP.BAC ] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, PPM1B, Mice, Sirtuin 2, 0302 clinical medicine, subcellular localization, Listeriosis, LISTERIA-MONOCYTOGENES, PHOSPHORYLATION, lcsh:QH301-705.5, GENE-EXPRESSION, Mice, Knockout, biology, histone acetylation, Cell cycle, 3. Good health, Chromatin, Cell biology, Protein Phosphatase 2C, sirtuin, TARGET, 030220 oncology & carcinogenesis, Sirtuin, Phosphorylation, H3K18, PHOSPHATASE, DNA damage, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, SIRT2, PROTEIN DEACETYLASES, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Animals, Humans, [SDV.BC] Life Sciences [q-bio]/Cellular Biology, TUBULIN DEACETYLASE, NUCLEOCYTOPLASMIC TRANSPORT, [ SDV.BC.BC ] Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], Biology and Life Sciences, Subcellular localization, Listeria monocytogenes, infection, 030104 developmental biology, lcsh:Biology (General), PREDICT PROGNOSIS, SIRTUINS, biology.protein, chromatin, PPM1, Protein Processing, Post-Translational, HeLa Cells
Abstract: Summary Sirtuin 2 is a nicotinamide-adenine-dinucleotide-dependent deacetylase that regulates cell processes such as carcinogenesis, cell cycle, DNA damage, and infection. Subcellular localization of SIRT2 is crucial for its function but is poorly understood. Infection with the bacterial pathogen Listeria monocytogenes, which relocalizes SIRT2 from the cytoplasm to the chromatin, provides an ideal stimulus for the molecular study of this process. In this report, we provide a map of SIRT2 post-translational modification sites and focus on serine 25 phosphorylation. We show that infection specifically induces dephosphorylation of S25, an event essential for SIRT2 chromatin association. Furthermore, we identify a nuclear complex formed by the phosphatases PPM1A and PPM1B, with SIRT2 essential for controlling H3K18 deacetylation and SIRT2-mediated gene repression during infection and necessary for a productive Listeria infection. This study reveals a molecular mechanism regulating SIRT2 function and localization, paving the way for understanding other SIRT2-regulated cellular processes., Graphical Abstract, Highlights • Infection induces modification of the host deacetylase SIRT2 to target it to chromatin • Dephosphorylation of serine 25 on SIRT2 controls its subcellular localization • PPM1A and PPM1B form a nuclear complex to dephosphorylate serine 25 • The phosphorylation state of serine 25 is crucial for Listeria infection, Sirtuins are enzymes critical for various processes, including genomic stability, metabolism, and aging. Through study of Listeria monocytogenes, a bacterial pathogen that exploits SIRT2 for productive infection, Pereira et al. uncover a SIRT2 modification necessary for chromatin association and function.
Published: 2018
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47. MUB

Author: Mark C, Anderson, Thibault, Chaze, Yves-Marie, Coïc, Louise, Injarabian, Friederike, Jonsson, Naelle, Lombion, Dorothée, Selimoglu-Buet, Judith, Souphron, Caroline, Ridley, Pascale, Vonaesch, Bruno, Baron, Ellen T, Arena, Jean-Yves, Tinevez, Giulia, Nigro, Katharina, Nothelfer, Eric, Solary, Valérie, Lapierre, Thierry, Lazure, Mariette, Matondo, David, Thornton, Philippe J, Sansonetti, Françoise, Baleux, and Benoit S, Marteyn
Subjects: Adult, Inflammation, Neutrophils, Guinea Pigs, Carbocyanines, Middle Aged, Mice, Inbred C57BL, Lactoferrin, Mice, Animals, Humans, Female, Rabbits, Shigella, Peptides, Biomarkers, Dysentery, Bacillary, Fluorescent Dyes
Abstract: Neutrophils represent the most abundant immune cells recruited to inflamed tissues. A lack of dedicated tools has hampered their detection and study. We show that a synthesized peptide, MUB
Published: 2017

48. Serum Proteome Analysis for Profiling Predictive Protein Markers Associated with the Severity of Skin Lesions Induced by Ionizing Radiation

Author: Joëlle Vinh, Christophe Chambon, Jean-Philippe Peyrat, Marc Benderitter, Louis Hornez, Iman Haddad, Thibault Chaze, Olivier Guipaud, Radiobiologie et épidémiologie (DRPH/SRBE), Institut de Radioprotection et de Sûreté Nucléaire (IRSN), Laboratoire d'Oncologie Moléculaire Humaine, Lille, France, Centre Oscat Lambré, Unité de Nutrition Humaine (UNH), Institut National de la Recherche Agronomique (INRA)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Clermont Université, Neurobiologie et diversité cellulaire (NDC), ESPCI ParisTech-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Oncologie Moléculaire Humaine, CRLCC Oscar Lambret, Laboratoire de Radiopathologie et Thérapies Expérimentales [IRSN, Fontenay-aux-Roses] (PRP-HOM - SRBE), Université d'Auvergne - Clermont-Ferrand I (UdA)-Clermont Université-Institut National de la Recherche Agronomique (INRA), Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Centre Régional de Lutte contre le Cancer Oscar Lambret [Lille] (UNICANCER/Lille), Université Lille Nord de France (COMUE)-UNICANCER-Université Lille Nord de France (COMUE)-UNICANCER, Service de RadioBiologie et d'Epidémiologie (IRSN/DRPH/SRBE), Université de Lille-UNICANCER-Université de Lille-UNICANCER, and Laboratoire de Radiopathologie et de Thérapies Expérimentales (IRSN/PRP-HOM/SRBE/LRTE)
Subjects: Pathology, medicine.medical_specialty, skin, Necrosis, Erythema, medicine.medical_treatment, serum proteome, Clinical Biochemistry, lcsh:QR1-502, Biology, Proteomics, Biochemistry, Article, lcsh:Microbiology, Ionizing radiation, 03 medical and health sciences, 0302 clinical medicine, proteomics, Structural Biology, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], medicine, 2D-DIGE, biomarkers, cutaneous radiation syndrome, ionizing radiation, mass spectrometry, radiotherapy, SELDI-TOF, Molecular Biology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Triage, Blood proteins, 3. Good health, Radiation therapy, Moist desquamation, 030220 oncology & carcinogenesis, medicine.symptom
Abstract: The finding of new diagnostic and prognostic markers of local radiation injury, and particularly of the cutaneous radiation syndrome, is crucial for its medical management, in the case of both accidental exposure and radiotherapy side effects. Especially, a fast high-throughput method is still needed for triage of people accidentally exposed to ionizing radiation. In this study, we investigated the impact of localized irradiation of the skin on the early alteration of the serum proteome of mice in an effort to discover markers associated with the exposure and severity of impending damage. Using two different large-scale quantitative proteomic approaches, 2D-DIGE-MS and SELDI-TOF-MS, we performed global analyses of serum proteins collected in the clinical latency phase (days 3 and 7) from non-irradiated and locally irradiated mice exposed to high doses of 20, 40 and 80 Gy which will develop respectively erythema, moist desquamation and necrosis. Unsupervised and supervised multivariate statistical analyses (principal component analysis, partial-least square discriminant analysis and Random Forest analysis) using 2D-DIGE quantitative protein data allowed us to discriminate early between non-irradiated and irradiated animals, and between uninjured/slightly injured animals and animals that will develop severe lesions. On the other hand, despite a high number of animal replicates, PLS-DA and Random Forest analyses of SELDI-TOF-MS data failed to reveal sets of MS peaks able to discriminate between the different groups of animals. Our results show that, unlike SELDI-TOF-MS, the 2D-DIGE approach remains a powerful and promising method for the discovery of sets of proteins that could be used for the development of clinical tests for triage and the prognosis of the severity of radiation-induced skin lesions. We propose a list of 15 proteins which constitutes a set of candidate proteins for triage and prognosis of skin lesion outcomes.
Published: 2013
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49. Properties of probiotic bacteria explored by proteomic approaches

Author: Thibault Chaze, Gwénaël Jan, Michel-Yves Mistou, Maarten van de Guchte, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Science et Technologie du Lait et de l'Oeuf (STLO), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and ANR Grant Glycopath. ANR-Alia Grant 'Surfing'
Subjects: Proteomics, Microbiology (medical), [SDV]Life Sciences [q-bio], In silico, Computational biology, Microbiology, law.invention, Bacterial protein, 03 medical and health sciences, Probiotic, Bacterial Proteins, law, proteomique, Animals, Humans, Probiotic bacteria, Computer Simulation, santé, 030304 developmental biology, 0303 health sciences, Bacteria, biology, 030306 microbiology, Probiotics, probiotique, biology.organism_classification, Crosstalk (biology), Infectious Diseases, protéine, identification
Abstract: The study of health-beneficial effects that probiotic bacteria can exert on humans and animals is at its beginning. Pending scientific questions include the identification of molecular markers of the health-promoting activity of specific strains, which may be used to select novel probiotic strains and to gain understanding of the mechanisms underlying their effects. In that perspective, the role of bacterial proteins must be evaluated, placing proteomics-based approaches at the core of the field. Until now, most proteomic analyses focused on the dynamics of abundant cytoplasmic proteins during adaptation of bacteria to conditions mimicking the gastro-intestinal tract environment. The development of in silico and experimental procedures allowing identification and quantification of surface-exposed and secreted proteins should boost our understanding of bacteria-host crosstalk.
Published: 2012
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50. Proteome dynamics during contractile and metabolic differentiation of bovine foetal muscle

Author: Bruno Meunier, Brigitte Picard, Thibault Chaze, Catherine Jurie, Christophe Chambon, Unité de Recherches sur les Herbivores (URH), Institut National de la Recherche Agronomique (INRA), and Qualité des Produits Animaux (QuaPA)
Subjects: Myosin light-chain kinase, CONTRACTILE AND METABOLIC DIFFERENTIATION, Enolase, Context (language use), Biology, Proteomics, SF1-1100, BOS TAURUS, MYOGENESIS, 03 medical and health sciences, Myosin, 030304 developmental biology, IN VIVO, 2. Zero hunger, 0303 health sciences, Dihydrolipoamide dehydrogenase, Myogenesis, 0402 animal and dairy science, 04 agricultural and veterinary sciences, 040201 dairy & animal science, Animal culture, Biochemistry, [SDV.SA.SPA]Life Sciences [q-bio]/Agricultural sciences/Animal production studies, Proteome, PROTEOMICS, Animal Science and Zoology
Abstract: International audience; Contractile and metabolic properties of bovine muscles play an important role in meat sensorial quality, particularly tenderness. Earlier studies based on Myosin heavy chain isoforms analyses and measurements of glycolytic and oxidative enzyme activities have demonstrated that the third trimester of foetal life in bovine is characterized by contractile and metabolic differentiation. In order to complete this data and to obtain a precise view of this phase and its regulation, we performed a proteomic analysis of Semitendinosus muscle from Charolais foetuses analysed at three stages of the third trimester of gestation (180, 210 and 260 days). The results complete the knowledge of important changes in the profiles of proteins from metabolic and contractile pathways. They provide new insights about proteins such as Aldehyde dehydrogenase family, Enolase, Dihydrolipoyl dehydrogenase, Troponin T or Myosin light chains isoforms. These data have agronomical applications not only for the management of beef sensorial quality but also in medical context, as bovine myogenesis appears very similar to human one.
Published: 2009
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