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1. Targeting the conserved active site of splicing machines with specific and selective small molecule modulators

Author: Ilaria Silvestri, Jacopo Manigrasso, Alessandro Andreani, Nicoletta Brindani, Caroline Mas, Jean-Baptiste Reiser, Pietro Vidossich, Gianfranco Martino, Andrew A. McCarthy, Marco De Vivo, and Marco Marcia
Subjects: Science
Abstract: Abstract The self-splicing group II introns are bacterial and organellar ancestors of the nuclear spliceosome and retro-transposable elements of pharmacological and biotechnological importance. Integrating enzymatic, crystallographic, and simulation studies, we demonstrate how these introns recognize small molecules through their conserved active site. These RNA-binding small molecules selectively inhibit the two steps of splicing by adopting distinctive poses at different stages of catalysis, and by preventing crucial active site conformational changes that are essential for splicing progression. Our data exemplify the enormous power of RNA binders to mechanistically probe vital cellular pathways. Most importantly, by proving that the evolutionarily-conserved RNA core of splicing machines can recognize small molecules specifically, our work provides a solid basis for the rational design of splicing modulators not only against bacterial and organellar introns, but also against the human spliceosome, which is a validated drug target for the treatment of congenital diseases and cancers.
Published: 2024
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2. Structural and biochemical characterisation of the Providencia stuartii arginine decarboxylase shows distinct polymerisation and regulation

Author: Matthew Jessop, Karine Huard, Ambroise Desfosses, Guillaume Tetreau, Diego Carriel, Maria Bacia-Verloop, Caroline Mas, Philippe Mas, Angélique Fraudeau, Jacques-Philippe Colletier, and Irina Gutsche
Subjects: Biology (General), QH301-705.5
Abstract: Jessop et. al. investigate the expression, activity, structure and supramolecular assembly of the arginine decarboxylase from Providencia stuartii, compare its polymers with those formed by the Escherichia coli lysine decarboxylase, and analyse the evolutionary conservation of the structural determinants of the polymerisation of these enzymes in enterobacteria.
Published: 2022
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3. Structural and functional analysis of the Francisella lysine decarboxylase as a key actor in oxidative stress resistance

Author: Jan Felix, Claire Siebert, Julia Novion Ducassou, Jérôme Nigou, Pierre Simon Garcia, Angélique Fraudeau, Karine Huard, Caroline Mas, Céline Brochier-Armanet, Yohann Couté, Irina Gutsche, and Patricia Renesto
Subjects: Medicine, Science
Abstract: Abstract Francisella tularensis is one of the most virulent pathogenic bacteria causing the acute human respiratory disease tularemia. While the mechanisms underlying F. tularensis pathogenesis are largely unknown, previous studies have shown that a F. novicida transposon mutant with insertions in a gene coding for a putative lysine decarboxylase was attenuated in mouse spleen, suggesting a possible role of its protein product as a virulence factor. Therefore, we set out to structurally and functionally characterize the F. novicida lysine decarboxylase, which we termed LdcF. Here, we investigate the genetic environment of ldcF as well as its evolutionary relationships with other basic AAT-fold amino acid decarboxylase superfamily members, known as key actors in bacterial adaptative stress response and polyamine biosynthesis. We determine the crystal structure of LdcF and compare it with the most thoroughly studied lysine decarboxylase, E. coli LdcI. We analyze the influence of ldcF deletion on bacterial growth under different stress conditions in dedicated growth media, as well as in infected macrophages, and demonstrate its involvement in oxidative stress resistance. Finally, our mass spectrometry-based quantitative proteomic analysis enables identification of 80 proteins with expression levels significantly affected by ldcF deletion, including several DNA repair proteins potentially involved in the diminished capacity of the F. novicida mutant to deal with oxidative stress. Taken together, we uncover an important role of LdcF in F. novicida survival in host cells through participation in oxidative stress response, thereby singling out this previously uncharacterized protein as a potential drug target.
Published: 2021
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4. Structure and Dynamics of the Unassembled Nucleoprotein of Rabies Virus in Complex with Its Phosphoprotein Chaperone Module

Author: Francine C. A. Gérard, Jean-Marie Bourhis, Caroline Mas, Anaïs Branchard, Duc Duy Vu, Sylvia Varhoshkova, Cédric Leyrat, and Marc Jamin
Subjects: rabies virus, Mononegavirales, phosphoprotein, nucleocapsid assembly, X-ray crystallography, small-angle X-ray scattering, Microbiology, QR1-502
Abstract: As for all non-segmented negative RNA viruses, rabies virus has its genome packaged in a linear assembly of nucleoprotein (N), named nucleocapsid. The formation of new nucleocapsids during virus replication in cells requires the production of soluble N protein in complex with its phosphoprotein (P) chaperone. In this study, we reconstituted a soluble heterodimeric complex between an armless N protein of rabies virus (RABV), lacking its N-terminal subdomain (NNT-ARM), and a peptide encompassing the N0 chaperon module of the P protein. We showed that the chaperone module undergoes a disordered−order transition when it assembles with N0 and measured an affinity in the low nanomolar range using a competition assay. We solved the crystal structure of the complex at a resolution of 2.3 Å, unveiling the details of the conserved interfaces. MD simulations showed that both the chaperon module of P and RNA-mediated polymerization reduced the ability of the RNA binding cavity to open and close. Finally, by reconstituting a complex with full-length P protein, we demonstrated that each P dimer could independently chaperon two N0 molecules.
Published: 2022
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5. A plant-like mechanism coupling m6A reading to polyadenylation safeguards transcriptome integrity and developmental gene partitioning in Toxoplasma

Author: Dayana C Farhat, Matthew W Bowler, Guillaume Communie, Dominique Pontier, Lucid Belmudes, Caroline Mas, Charlotte Corrao, Yohann Couté, Alexandre Bougdour, Thierry Lagrange, Mohamed-Ali Hakimi, and Christopher Swale
Subjects: Toxoplasma gondii, epitranscriptomic, RNA processing, Arabidopsis thaliana, Medicine, Science, Biology (General), QH301-705.5
Abstract: Correct 3’end processing of mRNAs is one of the regulatory cornerstones of gene expression. In a parasite that must adapt to the regulatory requirements of its multi-host life style, there is a need to adopt additional means to partition the distinct transcriptional signatures of the closely and tandemly arranged stage-specific genes. In this study, we report our findings in T. gondii of an m6A-dependent 3’end polyadenylation serving as a transcriptional barrier at these loci. We identify the core polyadenylation complex within T. gondii and establish CPSF4 as a reader for m6A-modified mRNAs, via a YTH domain within its C-terminus, a feature which is shared with plants. We bring evidence of the specificity of this interaction both biochemically, and by determining the crystal structure at high resolution of the T. gondii CPSF4-YTH in complex with an m6A-modified RNA. We show that the loss of m6A, both at the level of its deposition or its recognition is associated with an increase in aberrantly elongated chimeric mRNAs emanating from impaired transcriptional termination, a phenotype previously noticed in the plant model Arabidopsis thaliana. Nanopore direct RNA sequencing shows the occurrence of transcriptional read-through breaching into downstream repressed stage-specific genes, in the absence of either CPSF4 or the m6A RNA methylase components in both T. gondii and A. thaliana. Taken together, our results shed light on an essential regulatory mechanism coupling the pathways of m6A metabolism directly to the cleavage and polyadenylation processes, one that interestingly seem to serve, in both T. gondii and A. thaliana, as a guardian against aberrant transcriptional read-throughs.
Published: 2021
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6. Classification of the human phox homology (PX) domains based on their phosphoinositide binding specificities

Author: Mintu Chandra, Yanni K.-Y. Chin, Caroline Mas, J. Ryan Feathers, Blessy Paul, Sanchari Datta, Kai-En Chen, Xinying Jia, Zhe Yang, Suzanne J. Norwood, Biswaranjan Mohanty, Andrea Bugarcic, Rohan D. Teasdale, W. Mike Henne, Mehdi Mobli, and Brett M. Collins
Subjects: Science
Abstract: Phox homology (PX) domains are membrane interacting domains that bind to various lipids. Here authors screen all human PX domains systematically for their phospholipid preferences and define four classes and provide the basis for defining and predicting functional PX-membrane interactions.
Published: 2019
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7. microRNA-122 amplifies hepatitis C virus translation by shaping the structure of the internal ribosomal entry site

Author: Philipp Schult, Hanna Roth, Rebecca L. Adams, Caroline Mas, Lionel Imbert, Christian Orlik, Alessia Ruggieri, Anna M. Pyle, and Volker Lohmann
Subjects: Science
Abstract: The liver-specific microRNA-122 is an essential proviral host factor of Hepatitis C virus replication. Here the authors show that microRNA-122 functions as an RNA chaperone that guides the formation of a functional internal ribosome entry site by preventing energetically more favorable secondary structures within the HCV RNA genome.
Published: 2018
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8. Binding Mechanism Elucidation of the Acute Respiratory Disease Causing Agent Adenovirus of Serotype 7 to Desmoglein-2

Author: Marc-André Hograindleur, Gregory Effantin, Daphna Fenel, Caroline Mas, André Lieber, Guy Schoehn, Pascal Fender, and Emilie Vassal-Stermann
Subjects: adenoviruses, desmoglein-2, virus-host interactions, cryo-electron microscopy, acute respiratory distress syndromes, Microbiology, QR1-502
Abstract: The study of viruses causing acute respiratory distress syndromes (ARDS) is more essential than ever at a time when a virus can create a global pandemic in a matter of weeks. Among human adenoviruses, adenovirus of serotype 7 (HAdV7) is one of the most virulent serotypes. This virus regularly re-emerges in Asia and has just been the cause of several deaths in the United States. A critical step of the virus life cycle is the attachment of the knob domain of the fiber (HAd7K) to the cellular receptor desmoglein-2 (DSG2). Complexes between the fiber knob and two extracellular domains of DSG2 have been produced. Their characterization by biochemical and biophysical methods show that these two domains are sufficient for the interaction and that the trimeric HAd7K could accommodate up to three DSG2 receptor molecules. The cryo-electron microscopy (cryo-EM) structure of these complexes at 3.1 Å resolution confirmed the biochemical data, and allowed the identification of the critical amino acid residues for this interaction, which shows similarities with other DSG2 interacting adenoviruses, despite a low homology in the primary sequences.
Published: 2020
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9. Analytical ultracentrifugation sedimentation velocity for the characterization of recombinant adeno-associated virus vectors sub-populations

Author: Sylvie Saleun, Caroline Mas, Aline Le Roy, Magalie Penaud-Budloo, Oumeya Adjali, Véronique Blouin, Christine Ebel, Laboratoire de Thérapie Génique Translationnelle des Maladies Génétiques / Translational Research in Gene Therapy - UMR_S 1089 (TARGET), Institut National de la Santé et de la Recherche Médicale (INSERM)-Nantes Université - UFR de Médecine et des Techniques Médicales (Nantes Univ - UFR MEDECINE), Nantes Université - pôle Santé, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes Université - pôle Santé, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ), Institut de biologie structurale (IBS - UMR 5075), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)
Subjects: AAV vector, AUC, Adeno-associated virus, [SDV]Life Sciences [q-bio], Sedimentation velocity, Analytical ultracentrifugation, Biophysics, Quality control, General Medicine
Abstract: Recombinant adeno-associated virus virus-derived vectors (rAAVs) are among the most used viral delivery system for in vivo gene therapies with a good safety profile. However, rAAV production methods often lead to a heterogeneous vector population, in particular with the presence of undesired empty particles. Analytical ultracentrifugation sedimentation velocity (AUC-SV) is considered as the gold analytical technique allowing the measurement of relative amounts of each vector subpopulation and components like particle aggregates, based on their sedimentation coefficients. This letter presents the principle and practice of AUC experiments for rAAVs characterization. We discuss our results in the framework of previously published works. In addition to classical detection at 260 nm, using interference optics in the ultracentrifuge can provide an independent estimate of weight percentages of the different populations of capsids, and of the genome size incorporated in rAAV particles.
Published: 2023

10. Realist evaluation of a community-based antiretroviral therapy (CBART) programme for key populations in Benue State in Nigeria

Author: Olujuwon Ibiloye, Tom Decroo, Caroline Masquillier, Prosper Okonkwo, Lutgarde Lynen, Plang Jwanle, Josefien van Olmen, and Sara van Belle
Subjects: Key population, Community-based antiretroviral therapy, HIV, Realist evaluation, Infectious and parasitic diseases, RC109-216
Abstract: Abstract Background World Health Organization recommended community-based ART (CBART) approaches to improve access to antiretroviral treatment (ART) and treatment outcomes among key populations living with (KPLHIV). Key populations (KP) are female sex workers, men who have sex with men, persons who inject drugs, and transgender people. How CBART for KP (KP-CBART) worked and why, for whom and in what circumstances it worked within KP communities or at community sites, are yet to be described. The aim of this study is to describe the different KP-CBART approaches or models in Nigeria, identifying the context conditions and mechanisms that are likely to produce the desired outcomes. Method Building on our previous study eliciting an initial programme theory for KP-CBART, we used a multiple case design and cross-case analysis to evaluate 3 KP-CBART approaches, namely: One Stop Shop clinic; community drop-in centre; and outreach venue. Between 2021 and 2023, we conducted a retrospective cohort study, 99 indepth interviews and 5 focused group discussions with various actors. Using realist evaluation, we synthesised context-mechanism-outcome configurations (CMOCs) and developed programme theory for each of the cases and an overall theory. Result The analysis showed the central importance of decentralizing ART service delivery to a safe place within the community for KPLHIV. The provision of ART in a KP friendly environment triggered a feeling of safety and trust in the healthcare workers among KPLHIV, resulting in KP-CBART acceptance and improved ART uptake, medication adherence and retention on ART. KP community engagement in ART delivery, peer support through support group meetings, and linkages with KP-led organizations improved self-efficacy, fostered solidarity and a sense of belonging among KP. These resources encouraged and motivated clients to engage with the KP-CBART model. However, fear of disclosure of HIV and KP status, and lack of trust between KP groups, demotivated and discouraged KPLHIV from initiating ART and continuing their treatment in KP-CBART. Conclusion To optimise access to ART and treatment outcomes for KPLHIV, policy makers and health practitioners should ensure the provision of a safe place for ART service delivery that can be trusted by the clients and the KP communities.
Published: 2024
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11. Protein Conformational Space at the Edge of Allostery: Turning a Nonallosteric Malate Dehydrogenase into an 'Allosterized' Enzyme Using Evolution-Guided Punctual Mutations

Author: Antonio Iorio, Céline Brochier-Armanet, Caroline Mas, Fabio Sterpone, Dominique Madern, Laboratoire de biochimie théorique [Paris] (LBT (UPR_9080)), Institut de biologie physico-chimique (IBPC (FR_550)), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie structurale (IBS - UMR 5075), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), ANR-16-CE11-0011,AlloAnc,Allostérie Ancestrale(2016), ANR-21-CE44-0034,AlloSpace,Au coeur de l'allostérie : un voyage à travers l'espace des séquences et conformations des enzymes(2021), ANR-11-LABX-0011,DYNAMO,Dynamique des membranes transductrices d'énergie : biogénèse et organisation supramoléculaire.(2011), and ANR-11-EQPX-0008,CACSICE,Centre d'analyse de systèmes complexes dans les environnements complexes(2011)
Subjects: Molecular dynamics and evolvability, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], L-Lactate Dehydrogenase, Lactate and malate dehydrogenase, evolution of allostery, Malates, Allosteric Regulation, Malate Dehydrogenase, Hidden conformational states of enzymes, Mutation, Genetics, Amino Acids, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Phylogeny
Abstract: We unveil the intimate relationship between protein dynamics and allostery by following the trajectories of model proteins in their conformational and sequence spaces. Starting from a nonallosteric hyperthermophilic malate dehydrogenase, we have tracked the role of protein dynamics in the evolution of the allosteric capacity. Based on a large phylogenetic analysis of the malate (MalDH) and lactate dehydrogenase (LDH) superfamily, we identified two amino acid positions that could have had a major role for the emergence of allostery in LDHs, which we targeted for investigation by site-directed mutagenesis. Wild-type MalDH and the single and double mutants were tested with respect to their substrate recognition profiles. The double mutant displayed a sigmoid-shaped profile typical of homotropic activation in LDH. By using molecular dynamics simulations, we showed that the mutations induce a drastic change in the protein sampling of its conformational landscape, making transiently T-like (inactive) conformers, typical of allosteric LDHs, accessible. Our data fit well with the seminal key concept linking protein dynamics and evolvability. We showed that the selection of a new phenotype can be achieved by a few key dynamics-enhancing mutations causing the enrichment of low-populated conformational substates.
Published: 2022

12. Altiratinib blocks Toxoplasma gondii and Plasmodium falciparum development by selectively targeting a spliceosome kinase

Author: Christopher Swale, Valeria Bellini, Matthew W. Bowler, Nardella Flore, Marie-Pierre Brenier-Pinchart, Dominique Cannella, Lucid Belmudes, Caroline Mas, Yohann Couté, Fabrice Laurent, Artur Scherf, Alexandre Bougdour, Mohamed-Ali Hakimi, Institute for Advanced Biosciences / Institut pour l'Avancée des Biosciences (Grenoble) (IAB), Centre Hospitalier Universitaire [Grenoble] (CHU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Etablissement français du sang - Auvergne-Rhône-Alpes (EFS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), European Molecular Biology Laboratory [Grenoble] (EMBL), Biologie des Interactions Hôte-Parasite - Biology of Host-Parasite Interactions, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), BioSanté (UMR BioSanté), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Integrated Structural Biology Grenoble (ISBG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-European Molecular Biology Laboratory [Grenoble] (EMBL)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Infectiologie et Santé Publique (UMR ISP), Université de Tours (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Fondation pour la Recherche Medicale (EQU202103012571), Roux-Cantarini Fellowship, ANR-11-LABX-0024,ParaFrap,Alliance française contre les maladies parasitaires(2011), ANR-18-CE15-0023,HostQuest,Stratégies de Persistence de Toxoplasma gondii : Conquérir la Cellule Hôte et Echapper à la Réponse Immune Innée(2018), ANR-21-CE35-0010,ApiNewDrug,Identification de nouvelles cibles thérapeutiques parmi des médicaments repositionnables pour traiter des maladies dues à des parasitaire apicomplexes(2021), ANR-20-CE18-0006,EpiKillMal,Cibler la méthylation de l'ADN pour contrer la chimiorésistance du paludisme(2020), ANR-10-INBS-0008,ProFI,Infrastructure Française de Protéomique(2010), ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017), European Project: 614880,Hosting Toxo, Laurent, Fabrice, Laboratoires d'excellence - Alliance française contre les maladies parasitaires - - ParaFrap2011 - ANR-11-LABX-0024 - LABX - VALID, APPEL À PROJETS GÉNÉRIQUE 2018 - Stratégies de Persistence de Toxoplasma gondii : Conquérir la Cellule Hôte et Echapper à la Réponse Immune Innée - - HostQuest2018 - ANR-18-CE15-0023 - AAPG2018 - VALID, Identification de nouvelles cibles thérapeutiques parmi des médicaments repositionnables pour traiter des maladies dues à des parasitaire apicomplexes - - ApiNewDrug2021 - ANR-21-CE35-0010 - AAPG2021 - VALID, Cibler la méthylation de l'ADN pour contrer la chimiorésistance du paludisme - - EpiKillMal2020 - ANR-20-CE18-0006 - AAPG2020 - VALID, Infrastructure Française de Protéomique - - ProFI2010 - ANR-10-INBS-0008 - INBS - VALID, CBH-EUR-GS - - CBH-EUR-GS2017 - ANR-17-EURE-0003 - EURE - VALID, and ERC Consolidator grant - Hosting Toxo - 614880 - INCOMING
Subjects: [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, General Medicine
Abstract: The Apicomplexa comprise a large phylum of single-celled, obligate intracellular protozoa that include Toxoplasma gondii , Plasmodium , and Cryptosporidium spp., which infect humans and animals and cause severe parasitic diseases. Available therapeutics against these diseases are limited by suboptimal efficacy and frequent side effects, as well as the emergence and spread of resistance. We use a drug repurposing strategy and identify altiratinib, a compound originally developed to treat glioblastoma, as a promising drug candidate with broad spectrum activity against apicomplexans. Altiratinib is parasiticidal and blocks the development of intracellular zoites in the nanomolar range and with a high selectivity index when used against T. gondii . We have identified Tg PRP4K of T. gondii as the primary target of altiratinib using genetic target deconvolution, which highlighted key residues within the kinase catalytic site that conferred drug resistance when mutated. We have further elucidated the molecular basis of the inhibitory mechanism and species selectivity of altiratinib for Tg PRP4K and for its Plasmodium falciparum counterpart, Pf CLK3. Our data identified structural features critical for binding of the other Pf CLK3 inhibitor, TCMDC-135051. Consistent with the splicing control activity of this kinase family, we have shown that altiratinib can cause global disruption of splicing, primarily through intron retention in both T. gondii and P. falciparum . Thus, our data establish parasitic PRP4K/CLK3 as a potential pan-apicomplexan target whose repertoire of inhibitors can be expanded by the addition of altiratinib.
Published: 2022

13. Altiratinib blocks

Author: Christopher, Swale, Valeria, Bellini, Matthew W, Bowler, Nardella, Flore, Marie-Pierre, Brenier-Pinchart, Dominique, Cannella, Lucid, Belmudes, Caroline, Mas, Yohann, Couté, Fabrice, Laurent, Artur, Scherf, Alexandre, Bougdour, and Mohamed-Ali, Hakimi
Subjects: Plasmodium falciparum, Spliceosomes, Animals, Cryptosporidiosis, Cryptosporidium, Humans, Angiogenesis Inhibitors, Malaria, Falciparum, Protein Kinase Inhibitors, Toxoplasma
Abstract: The Apicomplexa comprise a large phylum of single-celled, obligate intracellular protozoa that include
Published: 2022

14. Reproducibility and accuracy of microscale thermophoresis in the NanoTemper Monolith: a multi laboratory benchmark study

Author: Caroline Mas, Grzegorz Piszczek, Marjetka Podobnik, Kathryn Perez, Timothy Sharpe, Stephen H. McLaughlin, Roland Montserret, Stefan H. Knauer, Bruno Baron, Christopher M. Johnson, Quyen Nguyen, Mark A. Williams, Katja Pirc, Arthur Sedivy, Celeste Abreu, Tina Daviter, David Ortega-Alarcon, Daumantas Matulis, Rouba Nasreddine, Carlo Carolis, Thomas A. Jowitt, Stephan Uebel, David Staunton, Andrew P. Leech, Maria Garcia-Alai, June Southall, Alexander Fish, Jitka Holková, Alexander K. Buell, Michael Weyand, Jasmina Rokov-Plavec, Blanca López-Méndez, Sylvie Berger, Josef Houser, Natalia Rodrigo, Wojciech Bal, Chad A. Brautigam, Josef Hamacek, Reine Nehmé, Olga Abian, Christian Guenther, Ondrej Vanek, Susanne Schaefer, Sharon M. Kelly, Malgorzata Adamczyk, Di Wu, Pedro Tavares, University of Copenhagen = Københavns Universitet (KU), Biophysique Moléculaire (plateforme) - Molecular Biophysics (platform), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), University of Texas Southwestern Medical Center [Dallas], University of Manchester [Manchester], Universität Bayreuth, Max Planck Institute of Biochemistry (MPIB), Max-Planck-Gesellschaft, University of London [London], Vienna Biocenter Core Facilities, Partenaires INRAE, University of Zaragoza - Universidad de Zaragoza [Zaragoza], Charles University [Prague] (CU), Warsaw University of Technology [Warsaw], Institute of Biochemistry and Biophysics, Polish Academy of Sciences (PAN), Institut de Recherches SERVIER (IRS), Technical University of Denmark [Lyngby] (DTU), Centre for Genomic Regulation [Barcelona] (CRG), Universitat Pompeu Fabra [Barcelona] (UPF)-Centro Nacional de Analisis Genomico [Barcelona] (CNAG), The institute of cancer research [London], Netherlands Cancer Institute (NKI), Antoni van Leeuwenhoek Hospital, EMBL Hamburg, Centre de biophysique moléculaire (CBM), Université d'Orléans (UO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), MRC Laboratory of Molecular Biology [Cambridge, UK] (LMB), University of Cambridge [UK] (CAM)-Medical Research Council, University of Glasgow, University of York [York, UK], Integrated Structural Biology Grenoble (ISBG - UMS 3518 ), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-European Molecular Biology Laboratory [Grenoble] (EMBL)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Vilnius University [Vilnius], Institut de biologie et chimie des protéines [Lyon] (IBCP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie Organique et Analytique (ICOA), Université d'Orléans (UO)-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut de Chimie du CNRS (INC)-Institut National de la Santé et de la Recherche Médicale (INSERM), EMBL Heidelberg, National Institute of Chemistry, National Heart, Lung, and Blood Institute [Bethesda] (NHLBI), University of Zagreb, University of Bayreuth, University of Basel (Unibas), University of Oxford [Oxford], Faculdade de Ciências e Tecnologia [Faro] (FCT), Universidade do Algarve (UAlg), This research was funded by Fondo de Investigaciones Sanitarias from Instituto de Salud Carlos III and European Union (ERDF/ESF, 'Investing in your future' PI18/00349 and Diputación General de Aragón Digestive Pathology Group B25_17R to O.A. Spanish Ministry of Science, Innovation and Universities, FPI Predoctoral Research Contract BES-2017-080739 to D.O.A. This research was funded by project no 2015/17/B/NZ2/01160 (granted to MA), we also acknowledge financial support, from the Faculty of Chemistry at Warsaw University of Technology. As part of the Federal FTI strategy, this work was generously supported by the City of Vienna and the Austrian Ministry for Education, Science and Research., Frapart, Isabelle, University of Copenhagen = Københavns Universitet (UCPH), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Max-Planck-Institut für Biochemie = Max Planck Institute of Biochemistry (MPIB), Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Université d'Orléans (UO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Integrated Structural Biology Grenoble (ISBG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Orléans (UO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), and University of Oxford
Subjects: 0301 basic medicine, 030103 biophysics, Materials science, Thermophoresis, Interaction, Biophysics, [SDV.BBM.BP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Calorimetry, Benchmark, 03 medical and health sciences, Biomolècules, MST, TRIC, KD, [PHYS.PHYS.PHYS-INS-DET]Physics [physics]/Physics [physics]/Instrumentation and Detectors [physics.ins-det], Surface plasmon resonance, Monolith, Reliability (statistics), Reproducibility, geography, geography.geographical_feature_category, K D, Microscale thermophoresis, Intensity change, Temperature, Reproducibility of Results, Correction, General Medicine, Biofísica, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Benchmarking, 030104 developmental biology, [PHYS.PHYS.PHYS-INS-DET] Physics [physics]/Physics [physics]/Instrumentation and Detectors [physics.ins-det], Benchmark (computing), Original Article, Biological system, Laboratories
Abstract: Microscale thermophoresis (MST), and the closely related Temperature Related Intensity Change (TRIC), are synonyms for a recently developed measurement technique in the field of biophysics to quantify biomolecular interactions, using the (capillary-based) NanoTemper Monolith and (multiwell plate-based) Dianthus instruments. Although this technique has been extensively used within the scientific community due to its low sample consumption, ease of use, and ubiquitous applicability, MST/TRIC has not enjoyed the unambiguous acceptance from biophysicists afforded to other biophysical techniques like isothermal titration calorimetry (ITC) or surface plasmon resonance (SPR). This might be attributed to several facts, e.g., that various (not fully understood) effects are contributing to the signal, that the technique is licensed to only a single instrument developer, NanoTemper Technology, and that its reliability and reproducibility have never been tested independently and systematically. Thus, a working group of ARBRE-MOBIEU has set up a benchmark study on MST/TRIC to assess this technique as a method to characterize biomolecular interactions. Here we present the results of this study involving 32 scientific groups within Europe and two groups from the US, carrying out experiments on 40 Monolith instruments, employing a standard operation procedure and centrally prepared samples. A protein-small molecule interaction, a newly developed protein-protein interaction system and a pure dye were used as test systems. We characterized the instrument properties and evaluated instrument performance, reproducibility, the effect of different analysis tools, the influence of the experimenter during data analysis, and thus the overall reliability of this method. All authors acknowledge the COST Action project ARBRE-MOBIEU CA15126 under the auspices of whose Working Group 4 this study was carried out. ARBRE-MOBIEU COST Action CA15126 funded meetings in the Center for Protein Research, University of Copenhagen (ECOST-MEETING-CA15126-280618-098884) to organize this study and in the Vienna Biocenter Core Facilities GmbH (ECOST-MEETING-CA15126-121119-111544) to discuss the results of the benchmark. Ondřej Vaněk acknowledges support from the Ministry of Education, Youth and Sports of the Czech Republic (LTC17065 in frame of the COST Action CA15126). Jitka Holková and Josef Houser acknowledge CF Biomolecular Interactions and Crystallization of CIISB, Instruct-CZ Centre, supported by MEYS CR (LM2018127). Jasmina Rokov-Plavec acknowledges support from the Croatian Science Foundation (IP-2016-06-6272). Alexander K. Buell thanks the Novo Nordisk Foundation (grant number NNFSA170028392) for funding. Li Peng Lundgren acknowledges for preliminary MST/TRIC experiments (STMS 37745 in the frame of the COST Action CA15126) and the COST Action (CA15126) for a STMS (STMS 44783) for the data analysis. The Novo Nordisk Foundation Center for Protein Research is supported financially by the Novo Nordisk Foundation (Grant agreement NNF14CC0001). Katja Pirc and Marjetka Podobnik acknowledge the grant by the Slovenian Research Agency P1-0391 (Title: Molecular Interactions). This research was funded by Fondo de Investigaciones Sanitarias from Instituto de Salud Carlos III and European Union (ERDF/ESF, “Investing in your future” PI18/00349 and Diputación General de Aragón Digestive Pathology Group B25_17R to O.A. Spanish Ministry of Science, Innovation and Universities, FPI Predoctoral Research Contract BES-2017-080739 to D.O.A. This research was funded by project no 2015/17/B/NZ2/01160 (granted to MA)
Published: 2021

15. Structural and functional analysis of the Francisella lysine decarboxylase as a key actor in oxidative stress resistance

Author: Céline Brochier-Armanet, Yohann Couté, Pierre Simon Garcia, Angélique Fraudeau, Jan Felix, Patricia Renesto, Caroline Mas, Jérôme Nigou, Irina Gutsche, Karine Huard, Claire Siebert, Julia Novion Ducassou, Institut de biologie structurale (IBS - UMR 5075), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Translational microbial Evolution and Engineering (TIMC-TrEE), Translational Innovation in Medicine and Complexity / Recherche Translationnelle et Innovation en Médecine et Complexité - UMR 5525 (TIMC ), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), Etude de la dynamique des protéomes (EDyP), BioSanté (UMR BioSanté), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Institut de pharmacologie et de biologie structurale (IPBS), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), The platforms of the Grenoble Instruct center (ISBG, UMS 3518 CNRS-CEA-UJF-EMBL), ANR-10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010), ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010), ANR-10-INBS-0008,ProFI,Infrastructure Française de Protéomique(2010), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Brochier-Armanet, Céline, Infrastructure Française pour la Biologie Structurale Intégrée - - FRISBI2010 - ANR-10-INBS-0005 - INBS - VALID, Grenoble Alliance for Integrated Structural Cell Biology - - GRAL2010 - ANR-10-LABX-0049 - LABX - VALID, Infrastructure Française de Protéomique - - ProFI2010 - ANR-10-INBS-0008 - INBS - VALID, and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)
Subjects: Proteomics, 0301 basic medicine, DNA Repair, Carboxy-Lyases, Mutant, DETERMINANTS, SUSCEPTIBILITY, Virulence factor, Mice, Francisella tularensis, Tularemia, Cells, Cultured, Aromatic L-amino acid decarboxylase, [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Multidisciplinary, Virulence, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], biology, Lysine decarboxylase, Biological techniques, TULAREMIA, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Cell biology, Phylogenetics, ACID, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Francisella, Medicine, Microbiology techniques, [SDV.BBM.BS] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Science, 030106 microbiology, Proteomic analysis, Article, INTRACELLULAR SURVIVAL, 03 medical and health sciences, Bacterial Proteins, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Escherichia coli, Animals, VIBRIO-VULNIFICUS, BIOSYNTHESIS, Amino Acid Sequence, Structure determination, Gene, Mass spectrometry, Macrophages, TULARENSIS PATHOGENICITY ISLAND, Biology and Life Sciences, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, POLYAMINES, Oxidative Stress, 030104 developmental biology, VIRULENCE, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Sequence Alignment
Abstract: Francisella tularensis is one of the most virulent pathogenic bacteria causing the acute human respiratory disease tularemia. While the mechanisms underlying F. tularensis pathogenesis are largely unknown, previous studies have shown that a F. novicida transposon mutant with insertions in a gene coding for a putative lysine decarboxylase was attenuated in mouse spleen, suggesting a possible role of its protein product as a virulence factor. Therefore, we set out to structurally and functionally characterize the F. novicida lysine decarboxylase, which we termed LdcF. Here, we investigate the genetic environment of ldcF as well as its evolutionary relationships with other basic AAT-fold amino acid decarboxylase superfamily members, known as key actors in bacterial adaptative stress response and polyamine biosynthesis. We determine the crystal structure of LdcF and compare it with the most thoroughly studied lysine decarboxylase, E. coli LdcI. We analyze the influence of ldcF deletion on bacterial growth under different stress conditions in dedicated growth media, as well as in infected macrophages, and demonstrate its involvement in oxidative stress resistance. Finally, our mass spectrometry-based quantitative proteomic analysis enables identification of 80 proteins with expression levels significantly affected by ldcF deletion, including several DNA repair proteins potentially involved in the diminished capacity of the F. novicida mutant to deal with oxidative stress. Taken together, we uncover an important role of LdcF in F. novicida survival in host cells through participation in oxidative stress response, thereby singling out this previously uncharacterized protein as a potential drug target.
Published: 2021

16. Relationship between classic indicators of health behaviour and contraceptive choices in women in Flanders

Author: Nina Van Eekert, Naomi Biegel, Leen De Kort, Veronique Verhoeven, Thies Gehrmann, Caroline Masquillier, Sarah Ahannach, and Sarah Lebeer
Subjects: Contraceptive use, Local hormonal contraceptives, Hormone free contraceptives, Educational gradient, Health behaviour, Fundamental cause theory, Gynecology and obstetrics, RG1-991, Public aspects of medicine, RA1-1270
Abstract: Abstract Background In this study we shed light on ongoing trends in contraceptive use in Flanders (Belgium). Building on the fundamental cause theory and social diffusion of innovation theory, we examine socio-economic gradients in contraceptive use and the relationship to health behaviours. Methods Using the unique and recently collected (2020) ISALA data, we used multinomial logistic regression to model the uptake of contraceptives and its association to educational level and health behaviour (N:4316 women). Results Higher educated women, and women with a healthy lifestyle especially, tend to use non-hormonal contraceptives or perceived lower-dosage hormonal contraceptives that are still trustworthy from a medical point of view. Moreover, we identified a potentially vulnerable group in terms of health as our results indicate that women who do not engage in preventive health behaviours are more likely to use no, or no modern, contraceptive method. Discussion The fact that higher educated women and women with a healthy lifestyle are less likely to use hormonal contraceptive methods is in line with patient empowerment, as women no longer necessarily follow recommendations by healthcare professionals, and there is a growing demand for naturalness in Western societies. Conclusion The results of this study can therefore be used to inform policy makers and reproductive healthcare professionals, since up-to-date understanding of women’s contraceptive choices is clearly needed in order to develop effective strategies to prevent sexually transmitted infections and unplanned pregnancies, and in which women can take control over their sexuality and fertility in a comfortable and pleasurable way.
Published: 2024
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17. A drug repurposing screen identifies altiratinib as a selective inhibitor of a key regulatory splicing kinase and a potential therapeutic for toxoplasmosis and malaria

Author: Caroline Mas, Dominique Cannella, Artur Scherf, Christopher Swale, Lucid Belmudes, Fabrice Laurent, Mohamed-Ali Hakimi, Matthew W. Bowler, Marie-Pierre Brenier-Pinchart, Yohann Couté, Nardella Flore, Alexandre Bougdour, Valeria Bellini, Institute for Advanced Biosciences / Institut pour l'Avancée des Biosciences (Grenoble) (IAB), Centre Hospitalier Universitaire [Grenoble] (CHU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Etablissement français du sang - Auvergne-Rhône-Alpes (EFS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), European Molecular Biology Laboratory [Grenoble] (EMBL), Biologie des Interactions Hôte-Parasite - Biology of Host-Parasite Interactions, Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), BioSanté (UMR BioSanté), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Integrated Structural Biology Grenoble (ISBG - UMS 3518 ), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-European Molecular Biology Laboratory [Grenoble] (EMBL)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Infectiologie et Santé Publique (UMR ISP), Université de Tours-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), (FRM Equipe # EQU202103012571), ANR-11-LABX-0024,ParaFrap,Alliance française contre les maladies parasitaires(2011), ANR-18-CE15-0023,HostQuest,Stratégies de Persistence de Toxoplasma gondii : Conquérir la Cellule Hôte et Echapper à la Réponse Immune Innée(2018), ANR-21-CE35-0010,ApiNewDrug,Identification de nouvelles cibles thérapeutiques parmi des médicaments repositionnables pour traiter des maladies dues à des parasitaire apicomplexes(2021), ANR-20-CE18-0006,EpiKillMal,Cibler la méthylation de l'ADN pour contrer la chimiorésistance du paludisme(2020), ANR-10-INBS-0008,ProFI,Infrastructure Française de Protéomique(2010), ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017), European Project: 614880,Hosting Toxo, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Integrated Structural Biology Grenoble (ISBG), Université de Tours (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Chanteloup, Nathalie Katy, Laboratoires d'excellence - Alliance française contre les maladies parasitaires - - ParaFrap2011 - ANR-11-LABX-0024 - LABX - VALID, APPEL À PROJETS GÉNÉRIQUE 2018 - Stratégies de Persistence de Toxoplasma gondii : Conquérir la Cellule Hôte et Echapper à la Réponse Immune Innée - - HostQuest2018 - ANR-18-CE15-0023 - AAPG2018 - VALID, Identification de nouvelles cibles thérapeutiques parmi des médicaments repositionnables pour traiter des maladies dues à des parasitaire apicomplexes - - ApiNewDrug2021 - ANR-21-CE35-0010 - AAPG2021 - VALID, Cibler la méthylation de l'ADN pour contrer la chimiorésistance du paludisme - - EpiKillMal2020 - ANR-20-CE18-0006 - AAPG2020 - VALID, Infrastructure Française de Protéomique - - ProFI2010 - ANR-10-INBS-0008 - INBS - VALID, CBH-EUR-GS - - CBH-EUR-GS2017 - ANR-17-EURE-0003 - EURE - VALID, and ERC Consolidator grant - Hosting Toxo - 614880 - INCOMING
Subjects: 0303 health sciences, biology, drug repurposing, Kinase, kinase, Plasmodium falciparum, Intron, Toxoplasma gondii, Computational biology, biology.organism_classification, 3. Good health, Apicomplexa, 03 medical and health sciences, Drug repositioning, splicing, 0302 clinical medicine, CLK3, RNA splicing, parasitic diseases, Protozoa, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Altiratinib, [SDV.MP.PAR] Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract: Introductory paragraphThe apicomplexa comprise a large phylum of single-celled, obligate intracellular protozoa that infect humans and animals and cause severe parasitic diseases. Available therapeutics against these devastating diseases are limited by suboptimal efficacy and frequent side effects, as well as the emergence and spread of resistance. Here, we use a drug repurposing strategy and identify altiratinib, a compound originally developed to treat glioblastoma, as a promising drug candidate with broad spectrum activity against apicomplexans. Altiratinib is parasiticidal and blocks the development of intracellular zoites in the nanomolar range and with a high selectivity index. We have identified TgPRP4K of T. gondii as the primary target of altiratinib by genetic target deconvolution, highlighting key residues within the kinase catalytic site that, when mutated, confer resistance to the drug. We have further elucidated the molecular basis of the inhibitory mechanism and species selectivity of altiratinib for TgPRP4K as well as for its P. falciparum counterpart PfCLK3. Our data also point to structural features critical for binding of the other PfCLK3 inhibitor, TCMDC-135051. Consistent with the role of this kinase family in splicing in a broad spectrum of eukaryotes, we have shown that altiratinib causes global disruption of splicing, primarily through intron retention in both T. gondii and P. falciparum. Thus, our data establish parasitic PRP4K/CLK3 as a promising pan-apicomplexan target whose repertoire of inhibitors can be expanded by the addition of altiratinib.
Published: 2021

18. Structural Dynamics of the C-terminal X Domain of Nipah and Hendra Viruses Controls the Attachment to the C-terminal Tail of the Nucleocapsid Protein

Author: Jean-Marie Bourhis, Filip Yabukarski, Guillaume Communie, Robert Schneider, Valentina A. Volchkova, Mickaël Frénéat, Francine C. Gérard, Corinne Ducournau, Caroline Mas, Nicolas Tarbouriech, Malene Ringkjøbing Jensen, Viktor E. Volchkov, Martin Blackledge, Marc Jamin, Institut de biologie structurale (IBS - UMR 5075), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Bases moléculaires de la pathogénicité virale – Molecular Basis of Viral Pathogenicity (BMPV), 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)-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), Integrated Structural Biology Grenoble (ISBG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-European Molecular Biology Laboratory [Grenoble] (EMBL)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), the Fond de la Recherche Médicale (FRM) (grant 'Equipe 2017' DEQ20170336754), the FINOVI Fundation, ANR-12-BSV8-0025,NNViPol,Structure et fonction de la machine de transcription et réplication des virus à ARN non-segmenté de polarité négative(2012), ANR-18-CE11-0014,NiPah-C,Structure et fonctions de la protéine C du virus Nipah(2018), ANR-10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010), and ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017)
Subjects: Protein Folding, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], viruses, Nipah Virus, mononegavirales, Nucleocapsid Proteins, intrinsically disordered protein, phosphoprotein, Phosphoproteins, Virus Replication, Hendra Virus, Viral Proteins, Protein Domains, X-Ray Diffraction, Structural Biology, small-angle X-ray scattering, Scattering, Small Angle, Humans, Protein Multimerization, Molecular Biology
Abstract: International audience; To understand the dynamic interactions between the phosphoprotein (P) and the nucleoprotein (N) within the transcription/replication complex of the $Paramyxoviridae$ and to decipher their roles in regulating viral multiplication, we characterized the structural properties of the C-terminal X domain (P$_{XD}$) of Nipah (NiV) and Hendra virus (HeV) P protein. In crystals, isolated NiV P$_{XD}$ adopted a two-helix dimeric conformation, which was incompetent for binding its partners, but in complex with the C-terminal intrinsically disordered tail of the N protein (NTAIL), it folded into a canonical 3H bundle conformation. In solution, SEC-MALLS, SAXS and NMR spectroscopy experiments indicated that both NiV and HeV P$_{XD}$ were larger in size than expected for compact proteins of the same molecular mass and were in conformational exchange between a compact three-helix (3H) bundle and partially unfolded conformations, where helix $\alpha_3$ is detached from the other two. Some measurements also provided strong evidence for dimerization of NiV P$_{XD}$ in solution but not for HeV P$_{XD}$. Ensemble modeling of experimental SAXS data and statistical-dynamical modeling reconciled all these data, yielding a model where NiV and HeV P$_{XD}$ exchanged between different conformations, and where NiV but not HeV P$_{XD}$ formed dimers. Finally, recombinant NiV comprising a chimeric P carrying HeV P$_{XD}$ was rescued and compared with parental NiV. Experiments carried out in cellula demonstrated that the replacement of P$_{XD}$ did not significantly affect the replication dynamics while caused a slight virus attenuation, suggesting a possible role of the dimerization of NiV P$_{XD}$ in viral replication.
Published: 2021

19. Author response: A plant-like mechanism coupling m6A reading to polyadenylation safeguards transcriptome integrity and developmental gene partitioning in Toxoplasma

Author: Dayana C Farhat, Matthew W Bowler, Guillaume Communie, Dominique Pontier, Lucid Belmudes, Caroline Mas, Charlotte Corrao, Yohann Couté, Alexandre Bougdour, Thierry Lagrange, Mohamed-Ali Hakimi, and Christopher Swale
Published: 2021

20. Empowering communities through citizen science and participatory action research: implementation of a schistosomiasis communication campaign in Uganda

Author: Maxson Kenneth Anyolitho, Tine Huyse, Caroline Masquillier, Viola Nilah Nyakato, and Karolien Poels
Subjects: History of scholarship and learning. The humanities, AZ20-999, Social Sciences
Abstract: Abstract Schistosomiasis is a water-related disease strongly linked with high-risk water and sanitation practices perpetuating disease transmission. In Uganda, despite health education and sensitisation efforts through communication campaigns by the Ministry of Health to reduce schistosomiasis prevalence, common risky practices still pose a challenge, especially among endemic communities. Here, we steered away from the conventional top-down approach to communication campaigns and explored alternative methods. We employed citizen science (CS) and other participatory action research (PAR) techniques as a bottom-up approach to co-design and implement a communication campaign among communities of western Uganda, to achieve a more tangible outcome of behaviour change for preventing schistosomiasis. We collected qualitative data using data party, world café, prioritisation and ranking, focus group discussion, and key informant interviews from 378 purposively selected individuals and analysed it using a thematic analysis model. Community volunteers, community radios and local leaders were the most preferred channels for passing schistosomiasis information identified by participants. Lack of access to safe water and healthcare services, open defecation, and inadequate knowledge of schistosomiasis are some of the most pressing problems prioritised. Door-to-door visits by citizen scientists (CSs), community meetings, drama, and tournaments were the channels proposed by CSs and community groups during the co-design workshops. Over 1000 households and about 9000 community members were directly reached using the channels. Endemic communities prefer receiving schistosomiasis information using local channels instead of conventional ones. Combining citizen science with other PAR approaches empowers communities to interpret research findings in their contexts and take charge of the interventions. As such, clear and simple message coverage and a high audience turn-up can be achieved. A follow-up study is needed to evaluate the process and impact of the communication intervention on the citizen scientists and the community’s knowledge, attitudes, and practices regarding preventive measures.
Published: 2024
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21. Conducting co-creation for public health in low and middle-income countries: a systematic review and key informant perspectives on implementation barriers and facilitators

Author: Giuliana Raffaella Longworth, Oritseweyinmi Erikowa-Orighoye, Ebuka Miracle Anieto, Danielle Marie Agnello, Jorge Raul Zapata-Restrepo, Caroline Masquillier, and Maria Giné-Garriga
Subjects: Co-creation, LMICs, Implementation, Review, Facilitators, Barriers, Public aspects of medicine, RA1-1270
Abstract: Abstract Background There has been an increase in the use of co-creation for public health because of its claimed potential to increase an intervention’s impact, spark change and co-create knowledge. Still, little is reported on its use in low-and-middle-income countries (LMICs). This study offers a comprehensive overview of co-creation used in public-health-related interventions, including the interventions’ characteristics, and reported implementation barriers and facilitators. Methods We conducted a systematic review within the Scopus and PubMed databases, a Google Scholar search, and a manual search in two grey literature databases related to participatory research. We further conducted eight interviews with first authors, randomly selected from included studies, to validate and enrich the systematic review findings. Results Through our review, we identified a total of twenty-two studies conducted in twenty-four LMIC countries. Majority of the interventions were designed directly within the LMIC setting. Aside from one, all studies were published between 2019 and 2023. Most studies adopted a co-creation approach, while some reported on the use of co-production, co-design, and co-development, combined either with community-based participatory research, participatory action research or citizen science. Among the most reported implementation barriers, we found the challenge of understanding and accounting for systemic conditions, such as the individual’s socioeconomic status and concerns related to funding constraints and length of the process. Several studies described the importance of creating a safe space, relying on local resources, and involving existing stakeholders in the process from the development stage throughout, including future and potential implementors. High relevance was also given to the performance of a contextual and/or needs assessment and careful tailoring of strategies and methods. Conclusion This study provides a systematic overview of previously conducted studies and of reported implementation barriers and facilitators. It identifies implementation barriers such as the setting’s systemic conditions, the socioeconomic status and funding constrains along with facilitators such as the involvement of local stakeholders and future implementors throughout, the tailoring of the process to the population of interest and participants and contextual assessment. By incorporating review and interview findings, the study aims to provide practical insights and recommendations for guiding future research and policy.
Published: 2024
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22. A qualitative investigation of gender-based violence prevention and response using digital technologies in low resource settings and refugee populations

Author: Luissa Vahedi, Lindsay Stark, Rachel Ding, Caroline Masboungi, Dorcas Erskine, Catherine Poulton, and Ilana Seff
Subjects: Domestic violence, violence against women, digitalization, LMIC, online, remote services, Psychiatry, RC435-571
Abstract: ABSTRACTBackground: Governmental and non-governmental organizations across medical, legal, and psychosocial sectors providing care to survivors of gender-based violence (GBV) and their families rapidly digitalized services during the COVID-19 pandemic. GBV prevention/response services working with women and children who are forcibly displaced and/or living in low-and-middle income countries (LMIC) were no exception to the rapid digitalization trend. Literature is lacking a critical synthesis of best practices and lessons learned since digitalization replaced major operations involved in GBV prevention/response.Objective: This research qualitatively investigated how GBV service providers, located in a range of socio-political settings, navigated the process of digitalizing GBV prevention/response during the COVID-19 crisis.Method: Semi-structured key informant interviews (KII) with GBV service providers in varied sectors were implemented virtually (2020–2021) in Brazil, Guatemala, Iraq, and Italy (regarding forcibly displaced women/girls for the latter). Participants were recruited using purposive and snowball sampling. Interview guides covered a range of topics: perceived changes in violence and service provision, experiences with virtual services, system coordination, and challenges. The KIIs were conducted in Portuguese, Spanish, Arabic, and Italian. Interviews were audio-recorded, transcribed, and translated into English. The research team conducted thematic analysis within and between countries using a structured codebook of data driven and theory driven codes.Results: Major themes concerned the: (1) spectrum of services that were digitalized during the COVID-19 crisis; (2) gender digital divide as a barrier to equitable, safe, and effective service digitalization; (3) digital violence as an unintended consequence of increased digitalization across social/public services.Conclusion: Digitalization is a balancing act with respect to (1) the variety of remotely-delivered services that are possible and (2) the access/safety considerations related to the gender digital divide and digital violence.
Published: 2024
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23. Classification of the human phox homology (PX) domains based on their phosphoinositide binding specificities

Author: Mehdi Mobli, Suzanne J. Norwood, Brett M. Collins, Xinying Jia, Rohan D. Teasdale, Kai-En Chen, Sanchari Datta, W. Mike Henne, Mintu Chandra, Caroline Mas, Biswaranjan Mohanty, Yanni K.-Y. Chin, Zhe Yang, J. Ryan Feathers, Andrea Bugarcic, and Blessy Paul
Subjects: Models, Molecular, 0301 basic medicine, Protein family, Science, Endocytic cycle, General Physics and Astronomy, 02 engineering and technology, Calorimetry, Phosphatidylinositols, Article, General Biochemistry, Genetics and Molecular Biology, Homology (biology), 03 medical and health sciences, Protein Domains, Sequence Analysis, Protein, Organelle, Humans, Binding site, lcsh:Science, Sorting Nexins, Binding Sites, Multidisciplinary, Chemistry, Isothermal titration calorimetry, General Chemistry, PX domain, 021001 nanoscience & nanotechnology, 3. Good health, Transport protein, Interferometry, 030104 developmental biology, Biochemistry, lcsh:Q, 0210 nano-technology
Abstract: Phox homology (PX) domains are membrane interacting domains that bind to phosphatidylinositol phospholipids or phosphoinositides, markers of organelle identity in the endocytic system. Although many PX domains bind the canonical endosome-enriched lipid PtdIns3P, others interact with alternative phosphoinositides, and a precise understanding of how these specificities arise has remained elusive. Here we systematically screen all human PX domains for their phospholipid preferences using liposome binding assays, biolayer interferometry and isothermal titration calorimetry. These analyses define four distinct classes of human PX domains that either bind specifically to PtdIns3P, non-specifically to various di- and tri-phosphorylated phosphoinositides, bind both PtdIns3P and other phosphoinositides, or associate with none of the lipids tested. A comprehensive evaluation of PX domain structures reveals two distinct binding sites that explain these specificities, providing a basis for defining and predicting the functional membrane interactions of the entire PX domain protein family., Phox homology (PX) domains are membrane interacting domains that bind to various lipids. Here authors screen all human PX domains systematically for their phospholipid preferences and define four classes and provide the basis for defining and predicting functional PX-membrane interactions.
Published: 2019

24. Correction to: Reproducibility and accuracy of microscale thermophoresis in the NanoTemper Monolith: a multi laboratory benchmark study

Author: Di Wu, Reine Nehmé, David Ortega-Alarcon, Michael Weyand, June Southall, David Staunton, Carlo Carolis, Blanca López-Méndez, Christian Guenther, Quyen Nguyen, Maria Garcia-Alai, Alexander Fish, Josef Hamacek, Pedro Tavares, Thomas A. Jowitt, Caroline Mas, Stephan Uebel, Jitka Holková, Wojciech Bal, Bruno Baron, Katja Pirc, Olga Abian, Sylvie Berger, Roland Montserret, Sharon M. Kelly, Rouba Nasreddine, Marjetka Podobnik, Ondrej Vanek, Chad A. Brautigam, Timothy Sharpe, Natalia Rodrigo, Alexander K. Buell, Josef Houser, Mark A. Williams, Arthur Sedivy, Celeste Abreu, Kathryn Perez, Stephen H. McLaughlin, Andrew P. Leech, Malgorzata Adamczyk, Grzegorz Piszczek, Stefan H. Knauer, Jasmina Rokov-Plavec, Daumantas Matulis, Susanne Schaefer, Christopher M. Johnson, and Tina Daviter
Subjects: geography, Reproducibility, geography.geographical_feature_category, Materials science, Microscale thermophoresis, Nuclear engineering, Biophysics, Benchmark (computing), General Medicine, Monolith
Published: 2021

25. Divalent cations influence the dimerization mode of murine S100A9 protein by modulating its disulfide bond pattern

Author: Elisabetta Boeri Erba, Luca Signor, Caroline Mas, Georges Lutfalla, Adrien Picard, Theo Paris, Laure Yatime, Institut de biologie structurale (IBS - UMR 5075), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), LPHI - Laboratory of Pathogen Host Interactions (LPHI), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), ISBG UMS 3518, CNRS, CEA, Univ. Grenoble Alpes, EMBL, F-38000 Grenoble, France, ISBG, Instruct-ERIC (PID 6047), ANR-10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010), ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017), ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010), Laboratory of Pathogen Host Interactions [Montpellier] (LPHI), Integrated Structural Biology Grenoble (ISBG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-European Molecular Biology Laboratory [Grenoble] (EMBL)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Laboratory of Pathogen and Host Immunity [Montpellier] (LPHI), and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)
Subjects: Cations, Divalent, chemistry.chemical_element, Protomer, Zinc, Calcium, Divalent, Mice, 03 medical and health sciences, Protein Domains, Structural Biology, Animals, Calgranulin B, Disulfides, Receptor, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, Binding Sites, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], 030302 biochemistry & molecular biology, chemistry, Covalent bond, Intramolecular force, Biophysics, Protein quaternary structure, Dimerization
Abstract: S100A9, with its congener S100A8, belongs to the S100 family of calcium-binding proteins found exclusively in vertebrates. These two proteins are major constituents of neutrophils. In response to a pathological condition, they can be released extracellularly and become alarmins that induce both pro- and anti-inflammatory signals, through specific cell surface receptors. They also act as antimicrobial agents, mainly as a S100A8/A9 heterocomplex, through metal sequestration. The mechanisms whereby divalent cations modulate the extracellular functions of S100A8 and S100A9 are still unclear. Importantly, it has been proposed that these ions may affect both the ternary and quaternary structure of these proteins, thereby influencing their physiological properties. In the present study, we report the crystal structures of WT and C80A murine S100A9 (mS100A9), determined at 1.45 and 2.35 A resolution, respectively, in the presence of calcium and zinc. These structures reveal a canonical homodimeric form for the protein. They also unravel an intramolecular disulfide bridge that stabilizes the C-terminal tail in a rigid conformation, thus shaping a second Zn-binding site per S100A9 protomer. In solution, mS100A9 apparently binds only two zinc ions per homodimer, with an affinity in the micromolar range, and aggregates in the presence of excess zinc. Using mass spectrometry, we demonstrate that mS100A9 can form both non-covalent and covalent homodimers with distinct disulfide bond patterns. Interestingly, calcium and zinc seem to affect differentially the relative proportion of these forms. We discuss how the metal-dependent interconversion between mS100A9 homodimers may explain the versatility of physiological functions attributed to the protein.
Published: 2021

26. A plant-like mechanism coupling m6A reading to polyadenylation safeguards transcriptome integrity and developmental genes partitioning inToxoplasma

Author: Thierry Lagrange, Guillaume Communie, Alexandre Bougdour, Dominique Pontier, Yohann Couté, Dayana C. Farhat, Christopher Swale, Matthew W. Bowler, Caroline Mas, Lucid Belmudes, Charlotte Corrao, and Mohamed-Ali Hakimi
Subjects: 0303 health sciences, Polyadenylation, RNA, Biology, biology.organism_classification, Phenotype, Cell biology, Transcriptome, 03 medical and health sciences, 0302 clinical medicine, Gene expression, Arabidopsis thaliana, Polyadenylation Pathway, Gene, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract: Correct 3’end processing of mRNAs is regarded as one of the regulatory cornerstones of gene expression. In a parasite that must answer to the high regulatory requirements of its multi-host life style, there is a great need to adopt additional means to partition the distinct transcriptional signatures of the closely and tandemly-arranged stage specific genes. In this study, we report on our findings inT. gondiiof an m6A-dependent 3’end polyadenylation serving as a transcriptional barrier at theseloci. We identify the core polyadenylation complex withinT. gondiiand establish CPSF4 as a reader for m6A-modified mRNAs, via a YTH domain within its C-terminus, a feature which is shared with plants. We bring evidence of the specificity of this interaction both biochemically, and by determining the crystal structure at high resolution of theT. gondiiCPSF4-YTH in complex with an m6A modified RNA. We show that the loss of m6A, both at the level of its deposition or its recognition was associated with an increase in aberrantly elongated chimeric mRNAs emanating from impaired transcriptional termination, a phenotype previously noticed in the plant modelArabidopsis thaliana. We bring Nanopore direct RNA sequencing-based evidence of the occurrence of transcriptional read-through breaching into downstream repressed stage-specific genes, in the absence of either CPSF4 or the m6A RNA methylase components in bothT. gondiiandA. thaliana. Taken together, our results shed light on an essential regulatory mechanism coupling the pathways of m6A metabolism directly to the cleavage and polyadenylation processes, one that interestingly seem to serve, in bothT. gondiiandA. thaliana, as a guardian against aberrant transcriptional read-throughs.Highlightsm6A is recognized in apicomplexan and plants by CPSF4, a member of the cleavage and polyadenylation complex machinery.The structural insight behind the specificity of the binding of m6A by the CPSF4 YTH subunit are solved by high resolution crystal structures.The m6A-driven 3’end polyadenylation pathway protects transcriptome integrity by restricting transcriptional read-throughs and RNA chimera formation in apicomplexan parasites and plants.
Published: 2021

27. Structural insights into ring-building motif domains involved in bacterial sporulation

Author: Carlos Contreras-Martel, Cécile Morlot, Mónica Serrano, Christopher D. A. Rodrigues, Adriano O. Henriques, Elda Bauda, Helena Chan, Daphna Fenel, Emmanuelle Neumann, Caroline Mas, Adrien Favier, Bowen Liu, Anne-Marie Villard, Laure Bellard, Institut de biologie structurale (IBS - UMR 5075), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), University of Technology Sydney (UTS), Groupe Pneumocoque (IBS-PG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), and ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017)
Subjects: Cell, Biophysics, Germination, Bacillus subtilis, Endocytosis, Ring (chemistry), Protein Structure, Secondary, RBM, Secretion systems, Bacterial Proteins, Structural Biology, Ring-Building Motif, medicine, Homomeric, Secretion, Spores, Bacterial, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], 0601 Biochemistry and Cell Biology, 0608 Zoology, biology, Chemistry, QK, biology.organism_classification, QP, In vitro, Cell biology, QR, Membrane, medicine.anatomical_structure, Sporulation, SpoIIIAH, SpoIIIAG, YhcN
Abstract: International audience; Components of specialized secretion systems, which span the inner and outer membranes in Gram-negative bacteria, include ring-forming proteins whose oligomerization was proposed to be promoted by domains called RBM for "Ring-Building Motifs". During spore formation in Gram-positive bacteria, a transport system called the SpoIIIA-SpoIIQ complex also assembles in the double membrane that surrounds the forespore following its endocytosis by the mother cell. The presence of RBM domains in some of the SpoIIIA proteins led to the hypothesis that they would assemble into rings connecting the two membranes and form a conduit between the mother cell and forespore. Among them, SpoIIIAG forms homo-oligomeric rings in vitro but the oligomerization of other RBM-containing SpoIIIA proteins, including SpoIIIAH, remains to be demonstrated. In this work, we identified RBM domains in the YhcN/YlaJ family of proteins that are not related to the SpoIIIA-SpoIIQ complex. We solved the crystal structure of YhcN from Bacillus subtilis, which confirmed the presence of a RBM fold, flanked by additional secondary structures. As the protein did not show any oligomerization ability in vitro, we investigated the structural determinants of ring formation in SpoIIIAG, SpoIIIAH and YhcN. We showed that in vitro, the conserved core of RBM domains alone is not sufficient for oligomerization while the β-barrel forming region in SpoIIIAG forms rings on its own. This work suggests that some RBMs might indeed participate in the assembly of homomeric rings but others might have evolved toward other functions.
Published: 2022

28. Facilitating access to primary care for people living in socio-economically vulnerable circumstances in Belgium through community health workers: towards a conceptual model

Author: Caroline Masquillier and Theo Cosaert
Subjects: Community health workers, Access to primary care, People living in socio-economically vulnerable circumstances, Conceptual model, Primary care, Outreach, Medicine (General), R5-920
Abstract: Abstract Introduction Inspired by examples in low- and middle-income countries, 50 community health workers (CHWs) were introduced in Belgium to improve access to primary care for people living in socio-economically vulnerable circumstances. This article aims to explore the ways in which CHWs support people living in socio-economically vulnerable circumstances in their access to primary care. Methods The qualitative research focuses on the first year of implementation of this pioneer nationwide CHW programme in Belgium. To respond to the research aim, thirteen semi-structured in-depth interviews were held with people living in socio-economically vulnerable circumstances. In addition, a photovoice study was conducted with fifteen CHWs comprising four phases: (1) photovoice training; (2) participatory observation with each CHW individually; (3) an individual semi-structured in-depth interview; and (4) three focus group discussions. The transcripts and the observation notes were analysed in accordance with the abductive analysis procedures described by Timmermans and Tavory. Results The qualitative results show that the CHWs’ outreaching way of working allows them to reach people living at the crossroads of different vulnerabilities that are intertwined and reinforce each other. They experience complex care needs, while at the same time they face several barriers that interrupt the continuum of access to primary care – as conceptualised in the theoretical access-to-care framework of (Levesque et al. Int J Equity Health. 12:18, 2013). Building on the theoretical access-to-care framework described by (Levesque et al. Int J Equity Health. 12:18, 2013), the conceptual model outlines first the underlying mechanisms of CHW-facilitated access to primary care: (I) outreaching and pro-active way of working; (II) building trust; (III) providing unbiased support and guidance in a culturally sensitive manner; and (IV) tailoring the CHWs’ approach to the unique interplay of barriers at the individual and health system level along the access-to-care continuum as experienced by the individual. Further disentangling how CHWs provide support to the barriers in access to care across the continuum and at each step is outlined further in the process characteristics of this conceptual model. Furthermore, the qualitative results show that the way in which CHWs support people is also impacted by the broader health system, such as long waiting times and unwelcoming healthcare professionals after referral from a CHW. Discussion The conceptual model of CHW-facilitated access to primary care developed in this article explores the way in which CHWs support people living in socio-economically vulnerable circumstances in their access to primary care in Belgium. Through their outreaching method, they play a valuable bridging role between the Belgian healthcare system and people living in socio-economically vulnerable circumstances.
Published: 2023
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29. Binding Mechanism Elucidation of the Acute Respiratory Disease Causing Agent Adenovirus of Serotype 7 to Desmoglein-2

Author: André Lieber, Guy Schoehn, Grégory Effantin, Pascal Fender, Daphna Fenel, Emilie Vassal-Stermann, Caroline Mas, Marc-André Hograindleur, Institut de biologie structurale (IBS - UMR 5075), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Department of Medicine, Division of Medical Genetics, University of Washington [Seattle], ANR-18-CE11-0001,Ad-Cadh,Mécanisme d'interaction des adenovirus du sous-groupe B2 à la cadhérine desmosomale DSG2 et ses applications(2018), Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)
Subjects: Models, Molecular, 0301 basic medicine, Serotype, Protein Conformation, Adenoviridae Infections, [SDV]Life Sciences [q-bio], viruses, lcsh:QR1-502, lcsh:Microbiology, Homology (biology), 0302 clinical medicine, Receptors, Adenovirus, Receptor, Dodecahedron, Respiratory Distress Syndrome, Vaccines, Desmoglein 2, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Viral spreading, acute respiratory distress syndromes, 3. Good health, Infectious Diseases, Host-Pathogen Interactions, Receptors, Virus, Protein Binding, Desmoglein-2, Virulence, cryo-electron microscopy, Biology, Serogroup, Article, Virus, 03 medical and health sciences, Viral life cycle, Virology, Extracellular, Humans, Virus Like Particles, desmoglein-2, virus-host interactions, Adenoviruses, Human, Cryoelectron Microscopy, Structure, HEK293 Cells, 030104 developmental biology, adenoviruses, Mutation, Capsid Proteins, 030217 neurology & neurosurgery, Platonic solids
Abstract: The study of viruses causing acute respiratory distress syndromes (ARDS) is more essential than ever at a time when a virus can create a global pandemic in a matter of weeks. Among human adenoviruses, adenovirus of serotype 7 (HAdV7) is one of the most virulent serotypes. This virus regularly re-emerges in Asia and has just been the cause of several deaths in the United States. A critical step of the virus life cycle is the attachment of the knob domain of the fiber (HAd7K) to the cellular receptor desmoglein-2 (DSG2). Complexes between the fiber knob and two extracellular domains of DSG2 have been produced. Their characterization by biochemical and biophysical methods show that these two domains are sufficient for the interaction and that the trimeric HAd7K could accommodate up to three DSG2 receptor molecules. The cryo-electron microscopy (cryo-EM) structure of these complexes at 3.1 &Aring, resolution confirmed the biochemical data, and allowed the identification of the critical amino acid residues for this interaction, which shows similarities with other DSG2 interacting adenoviruses, despite a low homology in the primary sequences.
Published: 2020
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30. Structural Description of the Nipah Virus Phosphoprotein and Its Interaction with STAT1

Author: Valentina A. Volchkova, Caroline Mas, Malene Ringkjøbing Jensen, Eric Condamine, Martin Blackledge, Jean-Marie Bourhis, Guillaume Communie, Marc Jamin, Nicolas Tarbouriech, Filip Yabukarski, Viktor E. Volchkov, Institut de biologie structurale (IBS - UMR 5075), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Bases moléculaires de la pathogénicité virale – Molecular Basis of Viral Pathogenicity (BMPV), 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)-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), ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017), ANR-18-CE11-0014,NiPah-C,Structure et fonctions de la protéine C du virus Nipah(2018), 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)-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), and CCSD, Accord Elsevier
Subjects: Viral protein, Protein Conformation, [SDV.BBM.BS] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Biophysics, medicine.disease_cause, Virus Replication, Article, 03 medical and health sciences, Viral Proteins, 0302 clinical medicine, Transcription (biology), medicine, Binding site, Protein secondary structure, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Nipah Virus, Isothermal titration calorimetry, Nuclear magnetic resonance spectroscopy, Phosphoproteins, Amino acid, chemistry, Phosphoprotein, 030217 neurology & neurosurgery
Abstract: International audience; The structural characterization of modular proteins containing long intrinsically disordered regions intercalated with folded domains is complicated by their conformational diversity and flexibility and requires the integration of multiple experimental approaches. Nipah virus (NiV) phosphoprotein, an essential component of the viral RNA transcription/replication machine and a component of the viral arsenal that hijacks cellular components and counteracts host immune responses, is a prototypical model for such modular proteins. Curiously, the phosphoprotein of NiV is significantly longer than the corresponding protein of other paramyxoviruses. Here, we combine multiple biophysical methods, including x-ray crystallography, NMR spectroscopy, and small angle x-ray scattering, to characterize the structure of this protein and provide an atomistic representation of the full-length protein in the form of a conformational ensemble. We show that full-length NiV phosphoprotein is tetrameric, and we solve the crystal structure of its tetramerization domain. Using NMR spectroscopy and small angle x-ray scattering, we show that the long N-terminal intrinsically disordered region and the linker connecting the tetramerization domain to the C-terminal X domain exchange between multiple conformations while containing short regions of residual secondary structure. Some of these transient helices are known to interact with partners, whereas others represent putative binding sites for yet unidentified proteins. Finally, using NMR spectroscopy and isothermal titration calorimetry, we map a region of the phosphoprotein, comprising residues between 110 and 140 and common to the V and W proteins, that binds with weak affinity to STAT1 and confirm the involvement of key amino acids of the viral protein in this interaction. This provides new, to our knowledge, insights into how the phosphoprotein and the nonstructural V and W proteins of NiV perform their multiple functions.
Published: 2020

31. microRNA-122 amplifies hepatitis C virus translation by shaping the structure of the internal ribosomal entry site

Author: Christian Orlik, Anna Marie Pyle, Caroline Mas, Hanna Roth, Lionel Imbert, Rebecca L. Adams, Philipp Schult, Volker Lohmann, Alessia Ruggieri, Department of Infectious Diseases, University of Heidelberg, Medical Faculty, Department of Molecular, Cellular and Developmental Biology, Yale University [New Haven], Institut de biologie structurale (IBS - UMR 5075 ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Howard Hughes Medical Institute (HHMI), Universität Heidelberg [Heidelberg] = Heidelberg University, ANR-10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010), ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), and Universität Heidelberg [Heidelberg]
Subjects: 0301 basic medicine, Science, Genetic Vectors, General Physics and Astronomy, Hepacivirus, Biology, Internal Ribosome Entry Sites, Ribosome, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, Genes, Reporter, Transduction, Genetic, Cell Line, Tumor, microRNA, Protein biosynthesis, Humans, Luciferases, lcsh:Science, Multidisciplinary, Oligoribonucleotides, 030102 biochemistry & molecular biology, Base Sequence, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Lentivirus, RNA, Translation (biology), General Chemistry, Ribosomal RNA, 3. Good health, Cell biology, Internal ribosome entry site, MicroRNAs, 030104 developmental biology, Viral replication, Gene Expression Regulation, Protein Biosynthesis, Host-Pathogen Interactions, Hepatocytes, Nucleic Acid Conformation, RNA, Viral, lcsh:Q, Ribosomes, Signal Transduction
Abstract: The liver-specific microRNA-122 (miR-122) recognizes two conserved sites at the 5′ end of the hepatitis C virus (HCV) genome and contributes to stability, translation, and replication of the viral RNA. We show that stimulation of the HCV internal ribosome entry site (IRES) by miR-122 is essential for efficient viral replication. The mechanism relies on a dual function of the 5′ terminal sequence in the complementary positive (translation) and negative strand (replication), requiring different secondary structures. Predictions and experimental evidence argue for several alternative folds involving the miR-binding region (MBR) adjacent to the IRES and interfering with its function. Mutations in the MBR, designed to suppress these dysfunctional structures indeed stimulate translation independently of miR-122. Conversely, MBR mutants favoring alternative folds show impaired IRES activity. Our results therefore suggest that miR-122 binding assists the folding of a functional IRES in an RNA chaperone-like manner by suppressing energetically favorable alternative secondary structures., The liver-specific microRNA-122 is an essential proviral host factor of Hepatitis C virus replication. Here the authors show that microRNA-122 functions as an RNA chaperone that guides the formation of a functional internal ribosome entry site by preventing energetically more favorable secondary structures within the HCV RNA genome.
Published: 2018

32. Liste des collaborateurs

Author: Nelly, Achour-Frydman, primary, Olivier, Ami, additional, Françoise, Aubron, additional, Magalie, Barth, additional, Delphine, Beghin, additional, Claire, Bélanger, additional, Alexandra, Benachi, additional, Bernard, Benoit, additional, Guillaume, Benoist, additional, Florence, Biquard, additional, Dominique, Bonneau, additional, Claude, Bouderlique, additional, Pierre-Emmanuel, Bouet, additional, Françoise, Boussion, additional, Yves, Brossard, additional, Anne-Sophie, Cabaret, additional, Bruno, Carbonne, additional, Vanina, Castaigne, additional, Gihad, Chalouhi, additional, Paul, Chatel, additional, Bernard, Cimon, additional, Anne-Gaël, Cordier, additional, Valérie, Cormier-Daire, additional, Anne, Cortey, additional, Marie-Pierre, Cournot, additional, Évelyne, Cynober, additional, Albert, David, additional, Jocelyne, De Laveau-Coupet, additional, Benoît, Delorme, additional, Philippe, Descamps, additional, Alain, Diguet, additional, Julia, Dina, additional, Marc, Dommergues, additional, Guillaume, Ducarme, additional, Céline, Dupont-Bernabé, additional, Philippe, Duverger, additional, Sandra, El Sabbagh, additional, Élisabeth, Elefant, additional, René, Frydman, additional, Philippe, Gillard, additional, Stéphanie, Gouarin, additional, Liliane, Grangeot-Keros, additional, Agnès, Guichet, additional, Martine, Hérault, additional, Michel, Herlicoviez, additional, Véronique, Houfflin-Debarge, additional, Bertrand, Isidor, additional, François, Kotras, additional, Marc, Larsen, additional, Cédric, Le Caignec, additional, Martine, Le Merrer, additional, Magali, Leblanc, additional, Marc-David, Leclair, additional, Céline, Lefebvre-Lacœuille, additional, Catherine, Lépinard, additional, Ronaldo, Levy, additional, Didier, Loisel, additional, Dominique, Luton, additional, Laurent, Macchi, additional, Agnès, Mailloux, additional, Laurent, Mandelbrot, additional, Sylvie, Manouvrier-Hanu, additional, Anne-Élisabeth, Mas, additional, Marie-Caroline, Mas-Caradec, additional, Matthieu, Mezzadri, additional, Daniel, Moeglin, additional, Jean-Marc, Mouillie, additional, Isabelle, Ollivier, additional, Sophie, Patrier, additional, Philippe, Pézard, additional, Olivier, Picone, additional, Fabrice, Pierre, additional, Brigitte, Porcheron, additional, Patrice, Poulain, additional, Thierry, Rousseau, additional, Paul, Sagot, additional, Mariane, Saidi, additional, Loïc, Sentilhes, additional, Stéphane, Triau, additional, Christelle, Vauloup-Fellous, additional, Catherine, Vauzelle, additional, Éric, Verspyck, additional, Benjamin, Viaris De Lesegno, additional, Yves, Ville, additional, Edith, Vuillard, additional, Dominique, Weil, additional, and Norbert, Winer, additional
Published: 2011
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33. The role of community health workers in primary healthcare in the WHO-EU region: a scoping review

Author: Tijs Van Iseghem, Ilka Jacobs, Dorien Vanden Bossche, Peter Delobelle, Sara Willems, Caroline Masquillier, and Peter Decat
Subjects: Community health workers, Primary healthcare, WHO-EU region, Public aspects of medicine, RA1-1270
Abstract: Abstract Background Existing evidence on the role of community health workers (CHWs) in primary healthcare originates primarily from the United States, Canada and Australia, and from low- and middle-income countries. Little is known about the role of CHWs in primary healthcare in European countries. This scoping review aimed to contribute to filling this gap by providing an overview of literature reporting on the involvement of CHWs in primary healthcare in WHO-EU countries since 2001 with a focus on the role, training, recruitment and remuneration. Methods This systematic scoping review followed the guidelines of the Preferred Reporting Items for Systematic reviews and Meta-Analyses, extension for Scoping Reviews. All published peer-reviewed literature indexed in PubMed, Web of Science, and Embase databases from Jan 2001 to Feb 2023 were reviewed for inclusion. Included studies were screened on title, abstract and full text according to predetermined eligibility criteria. Studies were included if they were conducted in the WHO-EU region and provided information regarding the role, training, recruitment or remuneration of CHWs. Results Forty studies were included in this review, originating from eight countries. The involvement of CHWs in the WHO-EU regions was usually project-based, except in the United Kingdom. A substantial amount of literature with variability in the terminology used to describe CHWs, the areas of involvement, recruitment, training, and remuneration strategies was found. The included studies reported a trend towards recruitment from within the communities with some form of training and payment of CHWs. A salient finding was the social embeddedness of CHWs in the communities they served. Their roles can be classified into one or a combination of the following: educational; navigational and supportive. Conclusion Future research projects involving CHWs should detail their involvement and elaborate on CHWs’ role, training and recruitment procedures. In addition, further research on CHW programmes in the WHO-EU region is necessary to prepare for their integration into the broader national health systems.
Published: 2023
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34. The archaeal LDH-like malate dehydrogenase from Ignicoccus islandicus displays dual substrate recognition, hidden allostery and a non-canonical tetrameric oligomeric organization

Author: Jennifer Roche, Eric Girard, Caroline Mas, Dominique Madern, Institut de biologie structurale (IBS - UMR 5075 ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), ANR-16-CE11-0011,AlloAnc,Allostérie Ancestrale(2016), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0303 health sciences, 03 medical and health sciences, 0302 clinical medicine, L-Lactate Dehydrogenase, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Malate Dehydrogenase, Structural Biology, Archaeal Proteins, Protein Multimerization, Archaea, 030217 neurology & neurosurgery, Substrate Specificity, 030304 developmental biology
Abstract: International audience; The NAD(P)-dependent malate dehydrogenases (MalDHs) and NAD-dependent lactate dehydrogenases (LDHs) are homologous enzymes involved in central metabolism. They display a common protein fold and the same catalytic mechanism, yet have a stringent capacity to discriminate between their respective substrates. The MalDH/LDH superfamily is divided into several phylogenetically related groups. It has been shown that the canonical LDHs and LDH-like group of MalDHs are primarily tetrameric enzymes that diverged from a common ancestor. In order to gain understanding of the evolutionary history of the LDHs and MalDHs, the biochemical properties and crystallographic structure of the LDH-like MalDH from the hyperthermophilic archaeon Ignicoccus islandicus (I. isl) were determined. I. isl MalDH recognizes oxaloacetate as main substrate, but it is also able to use pyruvate. Surprisingly, with pyruvate, the enzymatic activity profile looks like that of allosteric LDHs, suggesting a hidden allosteric capacity in a MalDH. The I. isl MalDH tetrameric structure in the apo state is considerably different from those of canonical LDH-like MalDHs and LDHs, representing an alternative oligomeric organization. A comparison with MalDH and LDH counterparts provides strong evidence that the divergence between allosteric and non-allosteric members of the superfamily involves homologs with intermediate, atypical properties.
Published: 2019

35. The structure of the nucleoprotein of Influenza D shows that all Orthomyxoviridae nucleoproteins have a similar NPCORE, with or without a NPTAIL for nuclear transport

Author: Mariette F. Ducatez, Laura Tengo, Justine Oliva, Caroline Mas, Myriam Miloudi, Amélie Donchet, Guy Schoehn, Alice Labaronne, Thibaut Crépin, Francine C. A. Gérard, Rob W. H. Ruigrok, Institut de biologie structurale (IBS - UMR 5075 ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), Integrated Structural Biology Grenoble (ISBG - UMS 3518 ), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-European Molecular Biology Laboratory [Grenoble] (EMBL)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), AD, AL and MM were funded through the Labex GRAL (ANR-10-LABX-49-01), LT by the ANR RNAP-IAV (ANR-14-CE09-0017) and AD and JO are supported by a PhD scholarship of the French Ministry of Higher Education and Research. This work was supported by the Fondation de la Recherche Médicale (FRM, Equipe DEQ. 20170336754) and used the electron microscopy and the biophysical platforms of the Grenoble Instruct-ERIC Center (ISBG, UMS 3518 CNRS-CEA-UGA-EMBL) with support from FRISBI (ANR-10-INSB-0005) and GRAL, within the Grenoble Partnership for Structural Biology (PSB), as well as the Imagery platform of Centre de Physiopathologie de Toulouse Purpan. The IBS Electron Microscope facility is supported by the Rhône-Alpes Region, the Fonds Feder, the FRM and GIS-IBiSA., ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010), ANR-14-CE09-0017,RNAP-IAV,Interactions protéine-protéine et protéine-ARN au sein du complexe réplicatif du virus de la grippe de type A(2014), ANR-10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Centre National de la Recherche Scientifique (CNRS)-European Molecular Biology Laboratory [Grenoble] (EMBL)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie structurale (IBS - UMR 5075), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS), Integrated Structural Biology Grenoble (ISBG - UMS 3518), and Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-European Molecular Biology Laboratory [Grenoble] (EMBL)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)
Subjects: 0301 basic medicine, Stereochemistry, Viral protein, viruses, Orthomyxoviridae, lcsh:Medicine, medicine.disease_cause, Virus, 03 medical and health sciences, 0302 clinical medicine, Protein structure, medicine, NLS, lcsh:Science, Multidisciplinary, biology, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Chemistry, lcsh:R, biology.organism_classification, 3. Good health, Nucleoprotein, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], 030104 developmental biology, lcsh:Q, Nuclear transport, 030217 neurology & neurosurgery, Nuclear localization sequence
Abstract: This paper focuses on the nucleoprotein (NP) of the newly identified member of the Orthomyxoviridae family, Influenza D virus. To date several X-ray structures of NP of Influenza A (A/NP) and B (B/NP) viruses and of infectious salmon anemia (ISA/NP) virus have been solved. Here we purified, characterized and solved the X-ray structure of the tetrameric D/NP at 2.4 Å resolution. The crystal structure of its core is similar to NP of other Influenza viruses. However, unlike A/NP and B/NP which possess a flexible amino-terminal tail containing nuclear localization signals (NLS) for their nuclear import, D/NP possesses a carboxy-terminal tail (D/NPTAIL). We show that D/NPTAIL harbors a bipartite NLS and designed C-terminal truncated mutants to demonstrate the role of D/NPTAIL for nuclear transport.
Published: 2019

36. A plant-like mechanism coupling m6A reading to polyadenylation safeguards transcriptome integrity and developmental gene partitioning in Toxoplasma

Author: Lucid Belmudes, Guillaume Communie, Dayana C. Farhat, Thierry Lagrange, Alexandre Bougdour, Dominique Pontier, Yohann Couté, Matthew W. Bowler, Charlotte Corrao, Christopher Swale, Mohamed-Ali Hakimi, Caroline Mas, Institute for Advanced Biosciences / Institut pour l'Avancée des Biosciences (Grenoble) (IAB), Etablissement français du sang - Auvergne-Rhône-Alpes (EFS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre Hospitalier Universitaire [Grenoble] (CHU)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Laboratoire européen de biologie moléculaire - European Molecular Biology Laboratory (EMBL Grenoble), European Molecular Biology Laboratory [Grenoble] (EMBL), Institut Laue-Langevin (ILL), ILL, Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Etude de la dynamique des protéomes (EDyP), BioSanté (UMR BioSanté), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Integrated Structural Biology Grenoble (ISBG - UMS 3518 ), Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-European Molecular Biology Laboratory [Grenoble] (EMBL)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), ANR-10-INSB-0801 ProFI ANR-10-INSB-0801, ANR-11-LABX-0024,ParaFrap,Alliance française contre les maladies parasitaires(2011), ANR-18-CE15-0023,HostQuest,Stratégies de Persistence de Toxoplasma gondii : Conquérir la Cellule Hôte et Echapper à la Réponse Immune Innée(2018), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), ANR-18-EURE-0019,TULIP-GSR,The Toulouse-Perpignan(2018), Centre Hospitalier Universitaire [Grenoble] (CHU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Etablissement français du sang - Auvergne-Rhône-Alpes (EFS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Integrated Structural Biology Grenoble (ISBG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-European Molecular Biology Laboratory [Grenoble] (EMBL)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Rosalie, Martin, Laboratoires d'excellence - Alliance française contre les maladies parasitaires - - ParaFrap2011 - ANR-11-LABX-0024 - LABX - VALID, APPEL À PROJETS GÉNÉRIQUE 2018 - Stratégies de Persistence de Toxoplasma gondii : Conquérir la Cellule Hôte et Echapper à la Réponse Immune Innée - - HostQuest2018 - ANR-18-CE15-0023 - AAPG2018 - VALID, Towards a Unified theory of biotic Interactions: the roLe of environmental - - TULIP2010 - ANR-10-LABX-0041 - LABX - VALID, and The Toulouse-Perpignan - - TULIP-GSR2018 - ANR-18-EURE-0019 - EURE - VALID
Subjects: Models, Molecular, Polyadenylation, Arabidopsis thaliana, Arabidopsis, Transcriptome, 0302 clinical medicine, Gene expression, Biology (General), 0303 health sciences, Microbiology and Infectious Disease, Membrane Glycoproteins, biology, General Neuroscience, Cleavage And Polyadenylation Specificity Factor, Zinc Fingers, General Medicine, Phenotype, epitranscriptomic, Cell biology, EPITRANSCRIPTOMIC MODIFICATIONS, Medicine, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], RNA Splicing Factors, Toxoplasma, [SDV.MP.PAR] Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Research Article, QH301-705.5, Science, Toxoplasma gondii, Nerve Tissue Proteins, M6A, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Humans, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Genes, Developmental, RNA, Messenger, YTH DOMAIN, Gene, 030304 developmental biology, Binding Sites, General Immunology and Microbiology, Sequence Analysis, RNA, RNA, Methyltransferases, biology.organism_classification, RNA processing, Gene Expression Regulation, Reading, Other, 030217 neurology & neurosurgery
Abstract: Correct 3’end processing of mRNAs is one of the regulatory cornerstones of gene expression. In a parasite that must adapt to the regulatory requirements of its multi-host life style, there is a need to adopt additional means to partition the distinct transcriptional signatures of the closely and tandemly arranged stage-specific genes. In this study, we report our findings in T. gondii of an m6A-dependent 3’end polyadenylation serving as a transcriptional barrier at these loci. We identify the core polyadenylation complex within T. gondii and establish CPSF4 as a reader for m6A-modified mRNAs, via a YTH domain within its C-terminus, a feature which is shared with plants. We bring evidence of the specificity of this interaction both biochemically, and by determining the crystal structure at high resolution of the T. gondii CPSF4-YTH in complex with an m6A-modified RNA. We show that the loss of m6A, both at the level of its deposition or its recognition is associated with an increase in aberrantly elongated chimeric mRNAs emanating from impaired transcriptional termination, a phenotype previously noticed in the plant model Arabidopsis thaliana. Nanopore direct RNA sequencing shows the occurrence of transcriptional read-through breaching into downstream repressed stage-specific genes, in the absence of either CPSF4 or the m6A RNA methylase components in both T. gondii and A. thaliana. Taken together, our results shed light on an essential regulatory mechanism coupling the pathways of m6A metabolism directly to the cleavage and polyadenylation processes, one that interestingly seem to serve, in both T. gondii and A. thaliana, as a guardian against aberrant transcriptional read-throughs.
Published: 2021

37. Health-seeking behaviour regarding schistosomiasis treatment in the absence of a mass drug administration (MDA) program: the case of endemic communities along Lake Albert in Western Uganda

Author: Maxson Kenneth Anyolitho, Viola Nilah Nyakato, Tine Huyse, Karolien Poels, and Caroline Masquillier
Subjects: Health-seeking behaviour, Mass drug administration, Endemic, Communities, Lake Albert, Praziquantel, Public aspects of medicine, RA1-1270
Abstract: Abstract Introduction Schistosomiasis poses a serious public health problem and a social challenge affecting over 240 million people, the majority of whom live in sub-Saharan Africa. The World Health Organization (WHO) recommends praziquantel (PZQ) drug treatment through regular mass drug administration (MDA) accompanied by social mobilisation and health education and sensitisation. With social mobilisation and health education and sensitisation, there is bound to be increased demand for the PZQ, especially in the case of endemic communities. However, it is not clear where communities go for PZQ treatment in the absence of PZQ MDA. We explored the health-seeking behaviours regarding schistosomiasis treatment among communities along Lake Albert in Western Uganda when MDA had delayed, to inform a review of the implementation policy for the achievement of the WHO’s 2030 target of 75% coverage and uptake. Methods and materials We conducted a community-based qualitative study in Kagadi and Ntoroko, an endemic community in January and February 2020. We interviewed 12 individuals: local leaders, village health teams, and health workers, and conducted 28 focus group discussion sessions with 251 purposively selected community members. The audio recordings of the data were transcribed and analyzed using a thematic analysis model. Results Generally, participants seldom seek medication for schistosomiasis-related signs and symptoms from government hospitals and health centres II, III and IV. Instead, they rely on community volunteers such as VHTs, private facilities, such as clinics and drug shops nearby, or traditional sources (e.g. witch doctors and herbalists). Results show that factors influencing people to seek treatment from sources other than the government are: the absence of PZQ drugs in the government health facility; health workers’ negative attitude towards patients; long distances to the government hospitals and health facilities; poor and inaccessible roads; medication-related costs; and negative perceptions of the PZQ drug. Conclusions Availability and accessibility of PZQ seem to be a big challenge. PZQ uptake is further hampered by health systems and community-related and socio-cultural factors. Thus there is a need to bring schistosomiasis drug treatment and services closer to endemic communities, stock nearby facilities with PZQ and encourage endemic communities to take the drug. Contextualised awareness-raising campaigns are needed to debunk myths and misconceptions surrounding the drug.
Published: 2023
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38. Initial programme theory for community-based ART delivery for key populations in Benue State, Nigeria: a realist evaluation study

Author: Olujuwon Ibiloye, Tom Decroo, Josefien van Olmen, Caroline Masquillier, Prosper Okonkwo, Lutgarde Lynen, Plang Jwanle, and Sara Van Belle
Subjects: Key populations, HIV, Community-based antiretroviral therapy, ART, Realist evaluation, Programme theory, Public aspects of medicine, RA1-1270
Abstract: Abstract Background The community-based antiretroviral therapy delivery (CBART) model was implemented in Benue State in Nigeria to increase access of key populations living with HIV (KPLHIV) to antiretroviral treatment. Key populations (KP) are female sex workers, men who have sex with men, persons who inject drugs, and transgender people. Evidence shows that the CBART model for KP (KP-CBART) can improve HIV outcomes along the cascade of HIV care and treatment in sub-Saharan Africa. However, how KP-CBART works, for whom, why, and under what circumstances it generates specific outcomes are not yet clear. Therefore, the aim of this study is to identify the initial programme theory (IPT) of the KP-CBART in Benue State using a realist approach. Method The study design is exploratory and qualitative, exploring the implementation of KP-CBART. We reviewed the intervention logic framework & guidelines for the KP-CBART in Nigeria, conducted a desk review of KP-CBART in Sub-Saharan Africa (SSA) and interviewed programme managers in the Benue HIV programme between November 2021 and April 2022. Findings were synthesized using the Context-Mechanism-Outcome (CMO) heuristic tool to explain the relationship between the different types of CBART models, contextual factors, actors, mechanisms and outcomes. Using a generative causality logic (retroduction and abduction), we developed, following a realist approach, CMO configurations (CMOc), summarized as an empirically testable IPT. Result We developed 7 CMOc and an IPT of the KP-CBART. Where KPLHIV receive ART in a safe place while living in a setting of punitive laws, harassment, stigma and discrimination, KP will adhere to treatment and be retained in care because they feel safe and trust the healthcare providers. Where KPLHIV are involved in the design, planning and implementation of HIV services; medication adherence and retention in care will improve because KP clients perceive HIV services to be KP-friendly and participate in KP-CBART. Conclusion Implementation of CBART model where KPLHIV feel safe, trust healthcare providers, and participate in HIV service delivery can improve medication adherence and retention in care. This programme hypothesis will be tested and refined in the next phase of the realist evaluation of KP-CBART.
Published: 2023
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39. Insights into barriers and facilitators in PrEP uptake and use among migrant men and transwomen who have sex with men in Belgium

Author: Ella Van Landeghem, Stef Dielen, Aline Semaan, Anke Rotsaert, Jef Vanhamel, Caroline Masquillier, Edwin Wouters, Kristien Wouters, Bea Vuylsteke, Thijs Reyniers, and Christiana Nöstlinger
Subjects: HIV prevention, PrEP, Access to health care, Migrants, Belgium, Public aspects of medicine, RA1-1270
Abstract: Abstract Background PrEP uptake is low among non-Belgian men and transwomen who have sex with men, although the HIV epidemic among men who have sex with men in Belgium is diversifying in terms of nationalities and ethnicity. We lack an in-depth understanding of this gap. Methods We conducted a qualitative study using a grounded theory approach. The data consists of key informants interviews and in-depth interviews with migrant men or transwomen who have sex with men. Results We identified four underlying determinants which shape our participants’ experiences and contextualize the barriers to PrEP use. These include (1) the intersectional identities of being migrant and men and transwomen who have sex with men, (2) migration related stressors, (3) mental health and (4) socio-economic vulnerability. Identified barriers include: the accessibility of services; availability of information, social resources and providers’ attitudes. These barriers influence PrEP acceptance and mediated by individual agency this influences their PrEP uptake. Conclusion An interplay of several underlying determinants and barriers impacts on PrEP uptake among migrant men and transwomen who have sex with men, illustrating a social gradient in access to PrEP. We need equitable access to the full spectrum of HIV prevention and care for all priority populations, including undocumented migrants. We recommend social and structural conditions that foster exercising these rights, including adapting PrEP service delivery, mental health and social support.
Published: 2023
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40. A molecular code for endosomal recycling of phosphorylated cargos by the SNX27–retromer complex

Author: Blessy Paul, Rohan D. Teasdale, Mintu Chandra, Jocelyn Widagdo, Nathan J. Pavlos, Brett M. Collins, Zhe Yang, Maria Tello-Lafoz, Victor Anggono, Markus C. Kerr, Thomas Clairfeuille, Caroline Mas, Audrey S. M. Chan, and Isabel Mérida
Subjects: Models, Molecular, 0301 basic medicine, SNX27, Endosome, PDZ domain, PDZ Domains, Endosomes, 03 medical and health sciences, 0302 clinical medicine, Structural Biology, Humans, Amino Acid Sequence, Protein Interaction Maps, Phosphorylation, Sorting Nexins, Molecular Biology, Peptide sequence, Chemistry, Cell biology, Transport protein, Molecular Docking Simulation, Retromer complex, Protein Transport, Sorting nexin, HEK293 Cells, 030104 developmental biology, Receptors, Glutamate, Signal transduction, Sequence Alignment, 030217 neurology & neurosurgery, Protein Binding, Signal Transduction
Abstract: Recycling of internalized receptors from endosomal compartments is essential for the receptors' cell-surface homeostasis. Sorting nexin 27 (SNX27) cooperates with the retromer complex in the recycling of proteins containing type I PSD95-Dlg-ZO1 (PDZ)-binding motifs. Here we define specific acidic amino acid sequences upstream of the PDZ-binding motif required for high-affinity engagement of the human SNX27 PDZ domain. However, a subset of SNX27 ligands, such as the β2 adrenergic receptor and N-methyl-D-aspartate (NMDA) receptor, lack these sequence determinants. Instead, we identified conserved sites of phosphorylation that substitute for acidic residues and dramatically enhance SNX27 interactions. This newly identified mechanism suggests a likely regulatory switch for PDZ interaction and protein transport by the SNX27-retromer complex. Defining this SNX27 binding code allowed us to classify more than 400 potential SNX27 ligands with broad functional implications in signal transduction, neuronal plasticity and metabolite transport.
Published: 2016

41. Démonette-2, a derivational database for French with broad lexical coverage and fine-grained morphological descriptions

Author: Fiammetta Namer, Nabil Hathout, Dany Amiot, Lucie Barque, Olivier Bonami, Gilles Boyé, Basilio Calderone, Julie Cattini, Georgette Dal, Alexander Delaporte, Guillaume Duboisdindien, Achille Falaise, Natalia Grabar, Pauline Haas, Frédérique Henry, Mathilde Huguin, Nyoman Juniarta, Loïc Liégeois, Stéphanie Lignon, Lucie Macchi, Grigoriy Manucharian, Caroline Masson, Fabio Montermini, Nadejda Okinina, Franck Sajous, Daniele Sanacore, Mai Thi Tran, Juliette Thuilier, Yannick Toussaint, and Delphine Tribout
Subjects: Language and Literature
Abstract: Morphological databases play an important role in linguistic research today. While several exist for the study of inflectional morphology in French, there is still a lack of resources for derivational morphology. This article presents Démonette-2, a new release of the French derivational morphology database Démonette. Developed in the context of the Démonext project, this database provides a framework in which it is possible to integrate various existing derivational resources. Démonette is characterized by its relational nature, which makes it possible to describe an extensive set of word formation patterns, including suffixation, prefixation, and a variety of non-canonical derivational processes such as conversion and parasynthetic formations. It reconciles broad coverage and fine-grained descriptions and is suitable for different audiences: morphologists working in different theoretical frameworks, teachers, speech therapists, NLP specialists, etc. The article presents in detail the structure and content of Démonette, its evolution since the first version, and its query interface.
Published: 2023
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42. Explorer des corpus oraux à l’aide de la base de données Démonette-2 : usage de mots construits dans des interactions adulte(s)-enfant(s)

Author: Stéphanie Caët, Caroline Masson, Loïc Liégeois, Lucie Macchi, Christine Da Silva-Genest, and Nadejda Okinina
Subjects: Language and Literature
Abstract: Cet article illustre l’usage que l’on peut faire de la base de données Démonette-2 (Namer et al., ce numéro) pour explorer des corpus oraux d’interactions adulte(s)-enfant(s). Pour ce faire, nous poserons deux questions susceptibles d’être soulevées en acquisition du langage : (i) quelle est la fréquence de mots construits dans les productions spontanées d’adultes et d’enfants ? (ii) quelles sont les pratiques des adultes pour étayer la compréhension de mots construits ? Les corpus explorés, en français de France, transcrits au format CHAT de CLAN, contiennent des interactions parent(s)-enfant au développement typique et atypique, des interactions en crèche et des interactions orthophoniste-enfant, recueillies lors d’activités diverses (jeux, lecture, repas, activités métalinguistiques par exemple). Cet article intéressera des chercheurs travaillant sur corpus oraux ainsi que des professionnels du langage, notamment des orthophonistes.
Published: 2023
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43. How is equity captured for colorectal, breast and cervical cancer incidence and screening in the Republic of Ireland: A review

Author: Sophie Mulcahy Symmons, Paul Leavy, Laura Heavey, Caroline Mason Mohan, Amanda Drury, and Aoife De Brún
Subjects: Early detection of cancer, Cancer screening, Incidence, Cervical cancer, Breast cancer, Colorectal cancer, Medicine
Abstract: Introduction: Organised screening reduces the incidence and late-stage diagnosis of cancer. However, participation in screening is not consistent across populations. Variations can be measured using demographic factors on place of residence, race/ethnicity, occupation, gender/sex, religion, education, socio-economic position (SEP), and social capital (PROGRESS-Plus stratifiers). The Republic of Ireland has screening programmes for colorectal, breast, and cervical cancer but assessment of screening participation and cancer incidence is inconsistent. The review aimed to evaluate the use of stratifiers in breast, cervical and colorectal cancer incidence and screening literature, and assess variations in incidence and screening participation across subgroups in Ireland. Methods: PubMed was searched systematically and grey literature was identified via Google, Google Scholar, Lenus (Irish Health Research repository), and The Irish Longitudinal Study of Aging (TILDA) in June 2022. Studies were included if they captured stratifiers alongside incidence or screening participation data of the three cancers. Results: Thirty-six studies and reports were included. Place of residence, SEP, sex, and age were most frequently captured. Incidence and screening participation varied by age, place of residence, SEP, and sex. Discussion: PROGRESS-Plus is a useful equity lens to review health literature. Cancer incidence and screening participation studies lacked a comprehensive equity lens resulting in difficulties in identifying inequities and non-attenders. Place of residence, SEP and ethnicity should be prioritised in monitoring inequities. Integrating unique health identifiers should improve monitoring and enable evidence-based population-specific interventions to promote screening. Collaboration with community organisations would support engagement with vulnerable populations when data is limited.
Published: 2023
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44. Global health reciprocal innovation to address mental health and well-being: strategies used and lessons learnt

Author: Josefien van Olmen, Brandon A Kohrt, Dixon Chibanda, Caroline Masquillier, Janet M Turan, Ruth Verhey, Michael J Vinikoor, Austin Y Su, Mauricio Rangel-Gomez, Annika Sweetland, Robert Paulino-Ramírez, Chynere Best, and Paul Gaist
Subjects: Medicine (General), R5-920, Infectious and parasitic diseases, RC109-216
Published: 2023
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45. Reciprocal coproduction as a basis for the diffusion of global health innovations

Author: Josefien van Olmen, Caroline Masquillier, Albert Liu, James Dearing, Susan G Zieff, and Angela Rollins
Subjects: Medicine (General), R5-920, Infectious and parasitic diseases, RC109-216
Published: 2023
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46. Auxin sensing is a property of an unstructured domain in the Auxin Response Factor ETTIN of Arabidopsis thaliana

Author: Philippe J. Mas, Lars Østergaard, Sara Simonini, Caroline Mas, Darren J. Hart, Crop Genetics Department, John Innes Centre, Institut de biologie structurale (IBS - UMR 5075 ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), University of Zurich, and Østergaard, Lars
Subjects: 0301 basic medicine, lcsh:Medicine, Sequence alignment, Plasma protein binding, 580 Plants (Botany), Article, 03 medical and health sciences, 0302 clinical medicine, 10126 Department of Plant and Microbial Biology, Gene Expression Regulation, Plant, Auxin, Two-Hybrid System Techniques, Arabidopsis, Basic Helix-Loop-Helix Transcription Factors, Point Mutation, Arabidopsis thaliana, Protein Interaction Domains and Motifs, Short linear motif, heterocyclic compounds, 10211 Zurich-Basel Plant Science Center, lcsh:Science, Transcription factor, chemistry.chemical_classification, 1000 Multidisciplinary, Multidisciplinary, Indoleacetic Acids, biology, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Arabidopsis Proteins, Circular Dichroism, lcsh:R, fungi, Nuclear Proteins, food and beverages, Plants, Genetically Modified, biology.organism_classification, Recombinant Proteins, High-Throughput Screening Assays, Cell biology, DNA-Binding Proteins, Intrinsically Disordered Proteins, 030104 developmental biology, chemistry, lcsh:Q, Plant hormone, Sequence Alignment, 030217 neurology & neurosurgery, Protein Binding
Abstract: The plant hormone auxin regulates numerous aspects of the plant life cycle. Auxin signalling is mediated by auxin response factors (ARFs) that dimerise with modulating Aux/IAA repressors. ARF3 (ETTIN or ETT) is atypical as it does not interact with Aux/IAA repressors. It is proposed to be a non-canonical auxin sensor, regulating diverse functions essential for development. This sensing ability relies on a unique C-terminal ETT specific domain (ES domain). Alignments of ETT orthologues across the angiosperm phylum revealed that the length and sequence identities of ES domains are poorly conserved. Computational predictors suggested the ES domains to be intrinsically disordered, explaining their tolerance of insertions, deletions and mutations during evolution. Nevertheless, five highly conserved short linear motifs were identified suggesting functional significance. High-throughput library screening identified an almost full-length soluble ES domain that did not bind auxin directly, but exhibited a dose-dependent response in a yeast two-hybrid system against the Arabidopsis INDEHISCENT (IND) transcription factor. Circular dichroism confirmed the domain was disordered. The identification and purification of this domain opens the way to the future characterisation of the ETT auxin-sensing mechanism in planta and an improved understanding of auxin-mediated regulation.
Published: 2018

47. Structural characterization of the sporulation protein GerM from Bacillus subtilis

Author: Francisco Leisico, Ahmed M.T. Mohamed, Jennyfer Trouve, Carlos Contreras-Martel, Christopher D. A. Rodrigues, David Z. Rudner, Bowen Liu, Caroline Mas, Cécile Morlot, Institut de biologie structurale (IBS - UMR 5075 ), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), University of Technology Sydney (UTS), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Harvard Medical School [Boston] (HMS), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)
Subjects: 0301 basic medicine, Models, Molecular, Multiprotein complex, Hydrolases, Protein Conformation, Lipoproteins, 030106 microbiology, Cell, Biophysics, Bacillus subtilis, Flagellum, Crystallography, X-Ray, 03 medical and health sciences, Bacterial Proteins, Protein Domains, Structural Biology, medicine, Compartment (development), Secretion, Amino Acid Sequence, ComputingMilieux_MISCELLANEOUS, Spores, Bacterial, biology, Sequence Homology, Amino Acid, Chemistry, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Cell biology, 030104 developmental biology, medicine.anatomical_structure, Flagella, Function (biology), Bacteria
Abstract: © 2018 Elsevier Inc. The Gram-positive bacterium Bacillus subtilis responds to starvation by entering a morphological differentiation process leading to the formation of a highly resistant spore. Early in the sporulation process, the cell asymmetrically divides into a large compartment (the mother cell) and a smaller one (the forespore), which will maturate into a resistant spore. Proper development of the forespore requires the assembly of a multiprotein complex called the SpoIIIA-SpoIIQ complex or “A-Q complex”. This complex involves the forespore protein SpoIIQ and eight mother cell proteins (SpoIIIAA to SpoIIIAH), many of which share structural similarities with components of specialized secretion systems and flagella found in Gram-negative bacteria. The assembly of the A-Q complex across the two membranes that separate the mother cell and forespore was recently shown to require GerM. GerM is a lipoprotein composed of two GerMN domains, a family of domains with unknown function. Here, we report X-ray crystallographic structures of the first GerMN domain of GerM at 1.0 Å resolution, and of the soluble domain of GerM (the tandem of GerMN domains) at 2.1 Å resolution. These structures reveal that GerMN domains can adopt distinct conformations and that the core of these domains display structural similarities with ring-building motifs found in components of specialized secretion system and in SpoIIIA proteins. This work provides an additional piece towards the structural characterization of the A-Q complex.
Published: 2018

48. The structure of the nucleoprotein of Influenza D shows that all Orthomyxoviridae nucleoproteins have a similar NP

Author: Amélie, Donchet, Justine, Oliva, Alice, Labaronne, Laura, Tengo, Myriam, Miloudi, Francine, C A Gerard, Caroline, Mas, Guy, Schoehn, Rob, W H Ruigrok, Mariette, Ducatez, and Thibaut, Crépin
Subjects: Cell Nucleus, alpha Karyopherins, viruses, Active Transport, Cell Nucleus, Crystallography, X-Ray, Orthomyxoviridae, Recombinant Proteins, Article, HEK293 Cells, Nucleoproteins, Humans, Amino Acid Sequence, Protein Structure, Quaternary, Sequence Alignment, Thogotovirus, Protein Binding
Abstract: This paper focuses on the nucleoprotein (NP) of the newly identified member of the Orthomyxoviridae family, Influenza D virus. To date several X-ray structures of NP of Influenza A (A/NP) and B (B/NP) viruses and of infectious salmon anemia (ISA/NP) virus have been solved. Here we purified, characterized and solved the X-ray structure of the tetrameric D/NP at 2.4 Å resolution. The crystal structure of its core is similar to NP of other Influenza viruses. However, unlike A/NP and B/NP which possess a flexible amino-terminal tail containing nuclear localization signals (NLS) for their nuclear import, D/NP possesses a carboxy-terminal tail (D/NPTAIL). We show that D/NPTAIL harbors a bipartite NLS and designed C-terminal truncated mutants to demonstrate the role of D/NPTAIL for nuclear transport.
Published: 2018

49. A cross-cultural adaptation and validation of a scale to assess illness identity in adults living with a chronic illness in South Africa: a case of HIV

Author: Neo Phyllis Sematlane, Lucia Knight, Caroline Masquillier, and Edwin Wouters
Subjects: Immunologic diseases. Allergy, RC581-607
Abstract: Abstract The chronic illness trajectory and its outcomes are well explained by the concept of illness identity; the extent to which ill individuals have integrated their diagnosed chronic illness into their identity or sense of self. The capacity to measure illness identity in people living with HIV (PLHIV) is still relatively unexplored. However, this is potentially useful to help us understand how outcomes for PLHIV could be improved and sustained. This paper aims to explore the cross-cultural adaptation of a Belgian developed Illness Identity Questionnaire (IIQ) and validate the instrument using a sample of South African adults living with HIV. We followed a phased scale adaptation and validation process which included an investigation of conceptual, item, semantic and operational equivalence and also examined the psychometric properties of the IIQ. The concept of illness identity with its four factors; engulfment, rejection, acceptance and enrichment in PLHIV, was found to be relevant within this context. Five items from the original IIQ were excluded from the adapted IIQ due to either semantic insufficiency and/or inadequate measurement equivalence. The mode of administration of the IIQ was changed to accommodate current study participants. The original four factor 25-item model did not fit current data, however, a better contextualized, four-factor, 20-item model was identified and found valid in the current setting. The results showed adequate statistical fit; χ2/d.f. = 1.516, RMSEA = 0.076, SRMR = 0.0893, and CFI = 0.909. Convergent and discriminant validity were also tenable. The cross-cultural adaptation and validation of the IIQ was successful, resulting in the availability of an instrument capable of measuring illness identity in PLHIV in a high HIV prevalence and resource-constrained setting. This therefore addresses the paucity of information and expands on knowledge about illness identity.
Published: 2022
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50. Structural and functional characterization of an atypical activation domain in erythroid Krüppel-like factor (EKLF)

Author: Shefali Soni, Mathieu Lussier-Price, Geneviève Arseneault, James J. Bieker, Paola Di Lello, Julien Lafrance-Vanasse, Thomas Morse, James G. Omichinski, and Caroline Mas
Subjects: Models, Molecular, Protein Conformation, Protein subunit, Molecular Sequence Data, Kruppel-Like Transcription Factors, Plasma protein binding, Calorimetry, Kruppel-Like Factor 4, Transactivation, Protein structure, Humans, Amino Acid Sequence, Cloning, Molecular, CREB-binding protein, Nuclear Magnetic Resonance, Biomolecular, Transcription factor, Genetics, Binding Sites, Multidisciplinary, Sequence Homology, Amino Acid, biology, Biological Sciences, Cell biology, Pleckstrin homology domain, Mutagenesis, Site-Directed, Transcription factor II H, biology.protein, K562 Cells, Protein Binding, Transcription Factors
Abstract: Erythroid Krüppel-like factor (EKLF) plays an important role in erythroid development by stimulating β-globin gene expression. We have examined the details by which the minimal transactivation domain (TAD) of EKLF (EKLFTAD) interacts with several transcriptional regulatory factors. We report that EKLFTAD displays homology to the p53TAD and, like the p53TAD, can be divided into two functional subdomains (EKLFTAD1 and EKLFTAD2). Based on sequence analysis, we found that EKLFTAD2 is conserved in KLF2, KLF4, KLF5, and KLF15. In addition, we demonstrate that EKLFTAD2 binds the amino-terminal PH domain of the Tfb1/p62 subunit of TFIIH (Tfb1PH/p62PH) and four domains of CREB-binding protein/p300. The solution structure of the EKLFTAD2/Tfb1PH complex indicates that EKLFTAD2 binds Tfb1PH in an extended conformation, which is in contrast to the α-helical conformation seen for p53TAD2 in complex with Tfb1PH. These studies provide detailed mechanistic information into EKLFTAD functions as well as insights into potential interactions of the TADs of other KLF proteins. In addition, they suggest that not only have acidic TADs evolved so that they bind using different conformations on a common target, but that transitioning from a disordered to a more ordered state is not a requirement for their ability to bind multiple partners.
Published: 2011

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