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1. At the crossroads of epidemiology and biology: bridging the gap between SARS-CoV-2 viral strain properties and epidemic wave characteristics

Author

Poydenot, Florian, Lebreton, Alice, Haiech, Jacques, and Andreotti, Bruno

Subjects
Quantitative Biology - Populations and Evolution, Physics - Biological Physics
Abstract

The COVID-19 pandemic has given rise to numerous articles from different scientific fields (epidemiology, virology, immunology, airflow physics...) without any effort to link these different insights. In this review, we aim to establish relationships between epidemiological data and the characteristics of the virus strain responsible for the epidemic wave concerned. We have carried out this study on the Wuhan, Alpha, Delta and Omicron strains allowing us to illustrate the evolution of the relationships we have highlighted according to these different viral strains. We addressed the following questions: 1) How can the mean infectious dose (one quantum, by definition in epidemiology) be measured and expressed as an amount of viral RNA molecules (in genome units, GU) or as a number of replicative viral particles (in plaque-forming units, PFU)? 2) How many infectious quanta are exhaled by an infected person per unit of time? 3) How many infectious quanta are exhaled, on average, integrated over the whole contagious period? 4) How do these quantities relate to the epidemic reproduction rate R as measured in epidemiology, and to the viral load, as measured by molecular biological methods? 5) How has the infectious dose evolved with the different strains of SARS-CoV-2? We make use of state-of-the-art modelling, reviewed and explained in the appendix of the article (Supplemental Information, SI), to answer these questions using data from the literature in both epidemiology and virology. We have considered the modification of these relationships according to the vaccination status of the population. We hope that this work will allow a better integration of data from different fields (virology, epidemiology, and immunology) to anticipate the evolution of the epidemic in the case of COVID-19, but also in respiratory pathologies transmissible in an airborne manner., Comment: 26 pages, 5 figures; submitted to Biochimie

Published
2023

12. Fluorescent secreted bacterial effectors reveal active intravacuolar proliferation of Listeria monocytogenes in epithelial cells

Author

Peron Cane, Caroline, Carlos Fernandez, José, Leblanc, Julien, Wingertsmann, Laure, Gautier, Arnaud, Desprat, Nicolas, Lebreton, Alice, Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de physique de l'ENS - ENS Paris (LPENS), Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Sorbonne Université (SU)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Laboratoire des biomolécules (LBM UMR 7203), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Chimie Moléculaire de Paris Centre (FR 2769), Institut de Chimie du CNRS (INC)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), Université Paris Diderot - Paris 7 (UPD7), ABCD : Biophysique des Biomolécules, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Sorbonne Université (SU)-École normale supérieure - Paris (ENS Paris), ATIP-Avenir, Amorçage de jeune équipe de la Fondation pour la Recherche Médicale (FRM-AJE20131128944), Programme Émergences – Recherche médicale de la Mairie de Paris, ANR-10-IDEX-0001,PSL,Paris Sciences et Lettres(2010), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Département de Physique de l'ENS-PSL, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Chimie Moléculaire de Paris Centre (FR 2769), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Département de Physique de l'ENS-PSL, Lebreton, Alice, Initiative d'excellence - Paris Sciences et Lettres - - PSL2010 - ANR-10-IDEX-0001 - IDEX - VALID, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Laboratoire de physique de l'ENS - ENS Paris (LPENS (UMR_8023)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-École normale supérieure - Paris (ENS Paris)

Subjects
Physiology, Secretion Systems, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], Pathology and Laboratory Medicine, [SDV.BBM.BM] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Epithelium, Hemolysin Proteins, Cytosol, Bacterial secretion, Animal Cells, Phagosomes, Microbial Physiology, Medicine and Health Sciences, Listeriosis, Intravacuolar life, Bacterial Physiology, Biology (General), Heat-Shock Proteins, Virulence factors, Bacterial Pathogens, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Intracellular Pathogens, Medical Microbiology, Cellular Structures and Organelles, Pathogens, Cellular Types, Anatomy, Research Article, Listeria, Imaging Techniques, QH301-705.5, Bacterial Toxins, [SDV.BBM.BP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Research and Analysis Methods, Microbiology, Cell Line, Bacterial Proteins, Fluorescence Imaging, [SDV.BC.BC] Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], Humans, Live cell imaging, Microbial Pathogens, Secretion, Cell Proliferation, Fluorescent Dyes, Bacteria, Host-pathogen interactions, Macrophages, Organisms, Biology and Life Sciences, Epithelial Cells, Bacteriology, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Cell Biology, RC581-607, Listeria monocytogenes, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Biological Tissue, Vacuoles, Pore-forming toxin, Caco-2 Cells, Immunologic diseases. Allergy, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Physiological Processes
Abstract

Real-time imaging of bacterial virulence factor dynamics is hampered by the limited number of fluorescent tools suitable for tagging secreted effectors. Here, we demonstrated that the fluorogenic reporter FAST could be used to tag secreted proteins, and we implemented it to monitor infection dynamics in epithelial cells exposed to the human pathogen Listeria monocytogenes (Lm). By tracking individual FAST-labelled vacuoles after Lm internalisation into cells, we unveiled the heterogeneity of residence time inside entry vacuoles. Although half of the bacterial population escaped within 13 minutes after entry, 12% of bacteria remained entrapped over an hour inside long term vacuoles, and sometimes much longer, regardless of the secretion of the pore-forming toxin listeriolysin O (LLO). We imaged LLO-FAST in these long-term vacuoles, and showed that LLO enabled Lm to proliferate inside these compartments, reminiscent of what had been previously observed for Spacious Listeria-containing phagosomes (SLAPs). Unexpectedly, inside epithelial SLAP-like vacuoles (eSLAPs), Lm proliferated as fast as in the host cytosol. eSLAPs thus constitute an alternative replication niche in epithelial cells that might promote the colonization of host tissues., Author summary Bacterial pathogens secrete virulence factors to subvert their hosts; however, monitoring bacterial secretion in real-time remains challenging. Here, we developed a convenient method that enabled fluorescent imaging of secreted proteins in live microscopy, and applied it to the human pathogen Listeria monocytogenes. Listeria has been described to invade cells and proliferate in their cytosol; it is first internalized inside vacuoles, from where it escapes thanks to the secretion of virulence factors that disrupt membranes. Our work revealed the existence, in human epithelial cells, of a population of Listeria that failed to escape vacuoles but instead multiplied efficiently therein, despite—and in fact, thanks to—the active secretion of a toxin that permeates membranes. This intravacuolar niche may provide Listeria with an alternative strategy to colonize its host.

Published
2020

13. Endonucleolytic RNA cleavage by a eukaryotic exosome

Author

Lebreton, Alice, Tomecki, Rafal, Dziembowski, Andrzej, and Seraphin, Bertrand

Subjects
Exonucleases -- Structure -- Genetic aspects, RNA -- Structure -- Genetic aspects, Environmental issues, Science and technology, Zoology and wildlife conservation, Structure, Genetic aspects
Abstract

The exosome is a major eukaryotic nuclease located in both the nucleus and the cytoplasm that contributes to the processing, quality control and/or turnover of a large number of cellular [...]

Published
2008

14. An alternative replication niche for Listeria monocytogenes revealed by fluorescent tagging of bacterial secreted effectors

Author

Peron Cane, Caroline, Leblanc, Julien, Wingertsmann, Laure, Fernandez, José-Carlos, Gautier, Arnaud, Desprat, Nicolas, and Lebreton, Alice

Abstract

Tracking the dynamics of secreted virulence factors in real time is impaired by the paucity of appropriate fluorescent tools. Here, we took advantage of the fluorogenic reporter FAST to tag secreted proteins and monitor infection dynamics among a population of epithelial cells infected by Listeria monocytogenes ( Lm ). Thereby, we unveiled the heterogeneity of Lm residence time in internalisation vacuoles. Although half of the bacterial population escaped rapidly, a significant fraction remained entrapped several hours in Long Residence Vacuoles (LRVs), independently of the secretion of the pore-forming toxin listeriolysin O (LLO). Unexpectedly, LLO enabled Lm to proliferate inside these compartments as fast as in the cytosol. LRVs display similarities with the spacious Listeria -containing phagosomes described in macrophages, and could constitute an alternative replication niche for Lm in epithelial cells.

Published
2019
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15. A functional network involved in the recycling of nucleocytoplasmic pre-60S factors

Author

Lebreton, Alice, Saveanu, Cosmin, Decourty, Laurence, Rain, Jean-Christophe, Jacquier, Alain, and Fromont-Racine, Micheline

Subjects
Cytoplasm -- Research, Eukaryotes -- Research, Biological sciences
Abstract

Eukaryotic pre-ribosomes go through cytoplasmic maturation steps before entering translation. The nucleocytoplasmic proteins participating in these late stages of maturation are reimported to the nucleus. In this study, we describe a functional network focused on Rei1/Ybr267w, a strictly cytoplasmic pre-60S factor indirectly involved in nuclear 27S pre-ribosomal RNA processing. In the absence of Reil, the nuclear import of at least three other pre-60S factors is impaired. The accumulation in the cytoplasm of a small complex formed by the association of Arx1 with a novel factor, Alb1/YjI122w, inhibits the release of the putative antiassociation factor Tif6 from the premature large ribosomal subunits and its recycling to the nucleus. We propose a model in which Reil is a key factor for the coordinated dissociation and recycling of the last pre-60S factors before newly synthesized large ribosomal subunits enter translation.

Published
2006

16. Transformation of isopropylamine to L-alaninol by Pseudomonas sp. strain KIE171 involves N-glutamylated intermediates

Author

Azevedo Wasch, Susana I. de, Ploeg, Jan R. van der, Maire, Tere, Lebreton, Alice, Kiener, Andreas, and Leisinger, Thomas

Subjects
Pseudomonas -- Research, Microbial metabolism -- Research, Biological sciences
Abstract

The synthesis of L-alaninol from isopropylamine in Pseudomonas sp. strain KIE171 involves the intermediates gamma-glutamyl-isopropylamide and gamma-glutamyl-L-alaninol. L-alaninol is then further degraded by an unknown mechanism, which most likely involves two aldehyde dehydrogenases.

Published
2002

22. An RNA-Binding Protein Secreted by a Bacterial Pathogen Modulates RIG-I Signaling

Author

Pagliuso, Alessandro, primary, Tham, To Nam, additional, Allemand, Eric, additional, Robertin, Stevens, additional, Dupuy, Bruno, additional, Bertrand, Quentin, additional, Bécavin, Christophe, additional, Koutero, Mikael, additional, Najburg, Valérie, additional, Nahori, Marie-Anne, additional, Tangy, Frédéric, additional, Stavru, Fabrizia, additional, Bessonov, Sergey, additional, Dessen, Andréa, additional, Muchardt, Christian, additional, Lebreton, Alice, additional, Komarova, Anastassia V., additional, and Cossart, Pascale, additional

Published
2019
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24. Listeriolysin O promotes the intravacuolar growth of Listeria monocytogenes in epithelial cells

Author

Peron Cane, Caroline, Leblanc, Julien, Wingertsmann, Laure, Carlos Fernandez, José, Gautier, Arnaud, Desprat, Nicolas, Lebreton, Alice, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), ABCD : Biophysique des Biomolécules, Laboratoire de physique de l'ENS - ENS Paris (LPENS (UMR_8023)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Université Paris Diderot - Paris 7 (UPD7)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Université Paris Diderot - Paris 7 (UPD7), Laboratoire des biomolécules (LBM UMR 7203), Institut National de la Santé et de la Recherche Médicale (INSERM)-Chimie Moléculaire de Paris Centre (FR 2769), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Département de Chimie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), Université Paris Diderot - Paris 7 (UPD7), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ATIP-Avenir, Amorçage de jeune équipe de la Fondation pour la Recherche Médicale (FRM-AJE20131128944), Programme Émergences – Recherche médicale de la Mairie de Paris, ANR-10-IDEX-0001-02/10-LABX-0054,MEMOLIFE,Memory in living systems: an integrated approach(2010), ANR-10-IDEX-0001-02/10-IDEX-0001,PSL,Paris Sciences et Lettres(2010), École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Fédération de recherche du Département de physique de l'Ecole Normale Supérieure - ENS Paris (FRDPENS), Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris)-Université Paris Diderot - Paris 7 (UPD7)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Fédération de recherche du Département de physique de l'Ecole Normale Supérieure - ENS Paris (FRDPENS), Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris)-Université Paris Diderot - Paris 7 (UPD7)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Chimie Moléculaire de Paris Centre (FR 2769), Université Pierre et Marie Curie - Paris 6 (UPMC)-ESPCI ParisTech-Ecole Nationale Supérieure de Chimie de Paris- Chimie ParisTech-PSL (ENSCP)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris)-Université Pierre et Marie Curie - Paris 6 (UPMC)-ESPCI ParisTech-Ecole Nationale Supérieure de Chimie de Paris- Chimie ParisTech-PSL (ENSCP)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris)-Département de Chimie - ENS Paris, École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), and École normale supérieure - Paris (ENS Paris)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Ecole Nationale Supérieure de Chimie de Paris- Chimie ParisTech-PSL (ENSCP)-ESPCI ParisTech-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Ecole Nationale Supérieure de Chimie de Paris- Chimie ParisTech-PSL (ENSCP)-ESPCI ParisTech-Centre National de la Recherche Scientifique (CNRS)-Département de Chimie - ENS Paris

Subjects
[SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Bacterial secretion, Virulence factors, Host-pathogen interactions, Intravacuolar life, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Pore-forming toxin, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], Live cell imaging, Listeria monocytogenes, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology
Published
2019

25. Acute Renal Failure

Author

Kallanagowdar, Chandra, LeBreton, Alice, and Aviles, Diego H.

Published
2006

26. An RNA-Binding Protein Secreted by a Bacterial Pathogen Modulates RIG-I Signaling

Author

Pagliuso, Alessandro, Allemand, Eric, Robertin, Stevens, Dupuy, Bruno, Bertrand, Quentin, Becavin, Christophe, Koutero, Mikael, Najburg, Valerie, Nahori, Marie-Anne, Tangy, Frederic, Stavru, Fabrizia, Bessonov, Sergey, Dessen, Andrea, Muchardt, Christian, Lebreton, Alice, Komarova, Anastassia, V, Cossart, Pascale, Pagliuso, Alessandro, Allemand, Eric, Robertin, Stevens, Dupuy, Bruno, Bertrand, Quentin, Becavin, Christophe, Koutero, Mikael, Najburg, Valerie, Nahori, Marie-Anne, Tangy, Frederic, Stavru, Fabrizia, Bessonov, Sergey, Dessen, Andrea, Muchardt, Christian, Lebreton, Alice, Komarova, Anastassia, V, and Cossart, Pascale

Abstract

RNA-binding proteins (RBPs) perform key cellular activities by controlling the function of bound RNAs. The widely held assumption that RBPs are strictly intracellular has been challenged by the discovery of secreted RBPs. However, extracellular RBPs have been described in eukaryotes, while secreted bacterial RBPs have not been reported. Here, we show that the bacterial pathogen Listeria monocytogenes secretes a small RBP that we named Zea. We show that Zea binds a subset of L. monocytogenes RNAs, causing their accumulation in the extracellular medium. Furthermore, during L. monocytogenes infection, Zea binds RIG-I, the non-self-RNA innate immunity sensor, potentiating interferon-beta production. Mouse infection studies reveal that Zea affects L. monocytogenes virulence. Together, our results unveil that bacterial RNAs can be present extracellularly in association with RBPs, acting as social RNAs to trigger a host response during infection.

Published
2019

28. An RNA-binding protein secreted byListeria monocytogenesactivates RIG-I signaling

Author

Pagliuso, Alessandro, primary, Tham, To Nam, additional, Allemand, Eric, additional, Robertin, Stevens, additional, Dupuy, Bruno, additional, Bertrand, Quentin, additional, Bécavin, Christophe, additional, Koutero, Mikael, additional, Najburg, Valérie, additional, Nahori, Marie-Anne, additional, Stavru, Fabrizia, additional, Dessen, Andréa, additional, Muchard, Christian, additional, Lebreton, Alice, additional, Komarova, Anastassia V., additional, and Cossart, Pascale, additional

Published
2019
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29. Régulations post-transcriptionnelles de l'expression génique de la cellule hôte en réponse à l'infection bactérienne

Author

Lebreton, Alice, Institut National de la Recherche Agronomique (INRA), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Paris Diderot (Paris 7), Jonathan Weitzman, École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Lebreton, Alice, Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Translation, Host-pathogen interactions, Virulence factors, Interactions hôte-pathogène, [SDV]Life Sciences [q-bio], [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], [SDV.BBM.BM] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Listeria monocytogenes, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Facteurs de virulence, Expression génique, [SDV] Life Sciences [q-bio], Traduction, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Post-transcriptional regulations, [SDV.BC.BC] Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Régulations post-transcriptionnelles, Gene expression, mRNA stability, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Stabilité des ARN
Abstract

Listeria monocytogenes est un pathogène fréquent du bétail et l’agent de la listériose humaine, une maladie grave pour les femmes enceintes, les personnes âgées ou immunodéprimées. La prolifération de cette bactérie dans les cellules qu’elle infecte s’accompagne d’une reprogrammation de l’expression génique et des fonctions cellulaires.Après un doctorat sous la direction de Micheline Fromont-Racine (groupe d’Alain Jacquier) à l’Institut Pasteur sur la biogenèse des ribosomes, mes travaux de post-doctorat dans le groupe dirigé par Bertrand Séraphin au Centre de Génétique Moléculaire (Gif-sur-Yvette) ont mis en évidence une nouvelle activité enzymatique – une endonucléase – dans l’un des complexes de dégradation des ARN eucaryotes les plus étudiés, l’exosome.Recrutée à l’INRA en tant que chargée de recherche en 2008, j’ai rejoint jusqu’en 2014 l’équipe dirigée par Pascale Cossart à l’Institut Pasteur. J’y ai étudié comment la bactérie pathogène Listeria monocytogenes détourne la machinerie de répression chromatinienne des cellules qu’elle infecte, pour moduler certaines réponses immunitaires.Je dirige depuis octobre 2014 à l’Institut de Biologie de l’École Normale Supérieure (IBENS) une équipe de recherche qui étudie les mécanismes post-transcriptionnels régulant les ARNm eucaryotes en réponse à l’infection par Listeria monocytogenes. Nous travaillons sur quatre problématiques principales : L’infection conduit-elle à une dégradation globale ou spécifique des ARNm ? La machinerie et l’efficacité de la traduction sont-elles perturbées ? Quels effecteurs moléculaires de la bactérie ou de l’hôte sont impliqués dans ces processus ? Quelles en sont les conséquences patho-physiologiques ?Ces travaux, reposant sur des technologies haut débit adaptées à l’étude du devenir des ARNm, ainsi que sur des approches plus classiques de microbiologie cellulaire, permettront de mieux comprendre les impératifs de l’adaptation mutuelle entre la bactérie et son hôte, d’identifier de nouveaux facteurs de virulence, et d’explorer les voies de contrôle traductionnel eucaryotes dans un contexte d’infection.

Published
2015

32. Role of the BAHD1 Chromatin-Repressive Complex in Placental Development and Regulation of Steroid Metabolism

Author

Lakisic, Goran, primary, Lebreton, Alice, additional, Pourpre, Renaud, additional, Wendling, Olivia, additional, Libertini, Emanuele, additional, Radford, Elizabeth J., additional, Le Guillou, Morwenna, additional, Champy, Marie-France, additional, Wattenhofer-Donzé, Marie, additional, Soubigou, Guillaume, additional, Ait-Si-Ali, Slimane, additional, Feunteun, Jean, additional, Sorg, Tania, additional, Coppée, Jean-Yves, additional, Ferguson-Smith, Anne C., additional, Cossart, Pascale, additional, and Bierne, Hélène, additional

Published
2016
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35. Dynamics of pre-ribosomal factors along the large ribosomal subunit biogenesis in S. cerevisiae

Author

Lebreton, Alice, Génétique des Interactions Macromoléculaires, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Université Paris-Diderot - Paris VII, Micheline Fromont-Racine, and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)

Subjects
transport nucléo-cytoplasmique, [SDV.GEN]Life Sciences [q-bio]/Genetics, ribosome biogenesis, pre-ribosomal factor, assembly order, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, [SDV.BBM.MN]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular Networks [q-bio.MN], Saccharomyces cerevisiae, facteur pré-ribosomique, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], facteur navette, SILAC, shuttling factor, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], ordre d'assemblage, biogenèse des ribosomes, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], ribosomal RNA, nucleo-cytoplasmic transport, ARN ribosomique
Abstract

This work focuses on the dynamics of assembly, dissociation and recycling of proteins involved in the biogenesis of the large ribosomal subunit in Saccharomyces cerevisiae. It sheds some light on two control points in this metabolic pathway, localised in the nucleus and the cytoplasm respectively.We have shown that the nuclear protein Nsa2, which is very conserved throughout the eukaryotic kingdom, is required for the correct maturation of the 27SB ribosomal RNA precursor. Nsa2 is an unstable factor, regulated in correlation with the activity of ribosome biogenesis; it thus constitutes a good candidate for the integration of various signals resulting in the regulation of this metabolic pathway. Besides, using the SILAC technique, we could define groups of early or late acting factors relative to the Nsa2 action time.In the cytoplasm, we identified a protein network, which marks the end of ribosome biogenesis and triggers the entry of new ribosomal subunits into translation. The cytoplasmic protein Rei1 and the karyopherin Kap121 are both required for the recycling from the cytoplasm to the nucleus of a dimer of shuttling factors, Arx1-Alb1. This recycling enables the dissociation of the anti-association factor Tif6 from the large ribosomal subunit, which can consequently bind the small ribosomal subunit and enter translation.; Les travaux de ce mémoire portent sur la dynamique d'assemblage, de dissociation et de recyclage des protéines impliquées dans la biogenèse de la grande sous-unité ribosomique chez la levure Saccharomyces cerevisiae. Ils permettent une meilleure compréhension de deux points de contrôle de cette voie métabolique, l'un dans le noyau, l'autre dans le cytoplasme. Nous avons montré que la protéine nucléaire Nsa2, extrêmement conservée chez les Eucaryotes, est requise pour la maturation correcte de l'intermédiaire d'ARN ribosomique 27SB. Nsa2 est un facteur instable et régulé en fonction de l'activité de la biogenèse des ribosomes ; à ce titre, il pourrait centraliser différents signaux de contrôle de la voie métabolique. Par ailleurs, la technique de SILAC nous a permis de définir des groupes de facteurs pré-ribosomiques précoces ou tardifs par rapport au point d'action de Nsa2.Dans le cytoplasme, nous avons mis en évidence un réseau de protéines marquant la transition entre la fin de la biogenèse de la grande sous-unité et l'initiation de la traduction. La protéine cytoplasmique Rei1 et la karyophérine Kap121 sont requises pour le recyclage du dimère de facteurs navettes Arx1-Alb1, du cytoplasme vers le noyau. Ce recyclage conditionne la dissociation entre le facteur d'anti-association Tif6 et la grande sous-unité ribosomique, qui peut dès lors se lier à la petite sous-unité ribosomique et participer à la traduction.

Published
2006

44. RNA- and protein-mediated control of Listeria monocytogenesvirulence gene expression

Author

Lebreton, Alice and Cossart, Pascale

Abstract

ABSTRACTThe model opportunistic pathogen Listeria monocytogeneshas been the object of extensive research, aiming at understanding its ability to colonize diverse environmental niches and animal hosts. Bacterial transcriptomes in various conditions reflect this efficient adaptability. We review here our current knowledge of the mechanisms allowing L. monocytogenesto respond to environmental changes and trigger pathogenicity, with a special focus on RNA-mediated control of gene expression. We highlight how these studies have brought novel concepts in prokaryotic gene regulation, such as the ‘excludon’ where the 5′-UTR of a messenger also acts as an antisense regulator of an operon transcribed in opposite orientation, or the notion that riboswitches can regulate non-coding RNAs to integrate complex metabolic stimuli into regulatory networks. Overall, the Listeriamodel exemplifies that fine RNA tuners act together with master regulatory proteins to orchestrate appropriate transcriptional programmes.

Published
2017
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45. Cytoplasmic Recycling of 60S Preribosomal Factors Depends on the AAA Protein Drg1

Author

Pertschy, Brigitte, primary, Saveanu, Cosmin, additional, Zisser, Gertrude, additional, Lebreton, Alice, additional, Tengg, Martin, additional, Jacquier, Alain, additional, Liebminger, Eva, additional, Nobis, Berthold, additional, Kappel, Lisa, additional, van der Klei, Ida, additional, Högenauer, Gregor, additional, Fromont-Racine, Micheline, additional, and Bergler, Helmut, additional

Published
2007
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47. Sequential Protein Association with Nascent 60S Ribosomal Particles

Author

Saveanu, Cosmin, primary, Namane, Abdelkader, additional, Gleizes, Pierre-Emmanuel, additional, Lebreton, Alice, additional, Rousselle, Jean-Claude, additional, Noaillac-Depeyre, Jacqueline, additional, Gas, Nicole, additional, Jacquier, Alain, additional, and Fromont-Racine, Micheline, additional

Published
2003
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49. Exosome-mediated quality control: Substrate recruitment and molecular activity.

Author

Lebreton, Alice and Séraphin, Bertrand

Subjects
RIBONUCLEASES, MESSENGER RNA, DNA helicases, GENETIC regulation, EUKARYOTIC cells, GENETICS
Abstract

Abstract: The eukaryotic exosome is a multisubunit complex that is mainly responsible for 3′–5′ exonucleolytic degradation of RNAs, both in the nucleus and the cytoplasm. In this review we summarize the recent experiments that have provided information on the organisation, structure and activity of this large assembly. Interestingly, eukaryotic exosomes have been implicated in a large number of RNA degradation pathways including recently discovered RNA quality control mechanisms. A variety of cofactors have been shown to participate in substrate recruitment and/or assist exonucleolytic activities. Despite this avalanche of new results, further analyses will be required to improve our understanding of exosome regulation. [Copyright &y& Elsevier]

Published
2008
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50. Adaptations of intracellular bacteria to vacuolar or cytosolic niches

Author

Thomas Petit, Alice Lebreton, Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Programme Émergence(s) Recherche médicale de la mairie de Paris, ANR-20-CE15-0030,LiVaLife,Dynamique et contribution à l'infection des vies intravacuolaires de Listeria(2020), Lebreton, Alice, and Dynamique et contribution à l'infection des vies intravacuolaires de Listeria - - LiVaLife2020 - ANR-20-CE15-0030 - AAPG2020 - VALID

Subjects
Salmonella typhimurium, Microbiology (medical), vacuole, invasive bacteria, pathogenic bacteria, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], Listeria monocytogenes, Microbiology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Infectious Diseases, intracellular lifestyle, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Virology, Host-Pathogen Interactions, Vacuoles, [SDV.BC.BC] Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, cytosol, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology
Abstract

International audience; Invasive bacteria colonise their host tissues by establishing niches inside eukaryotic cells, where they grow either in the cytosol or inside a specialised vacuole. These two distinct intracellular lifestyles both present benefits but also impose various constraints on pathogenic microorganisms, in terms of nutrient acquisition, space requirements, exposure to immune responses, and ability to disseminate. Here we review the major characteristics of cytosolic and vacuolar lifestyles and the strategies used by bacteria to overcome challenges specific to each compartment. Recent research providing evidence that these scenarios are not mutually exclusive is presented, with the dual lifestyles of two foodborne pathogens, Listeria monocytogenes and Salmonella Typhimurium, discussed in detail. Finally, we elaborate on the conceptual implications of polyvalence from the perspective of host-pathogen interactions.

Published
2022

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