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Lisboa J, Pereira C, Pinto RD, Rodrigues IS, Pereira LMG, Pinheiro B, Oliveira P, Pereira PJB, Azevedo JE, Durand D, Benz R, do Vale A, Dos Santos NMS. Unconventional structure and mechanisms for membrane interaction and translocation of the NF-κB-targeting toxin AIP56. Nat Commun 2023; 14:7431. [PMID: 37973928 PMCID: PMC10654918 DOI: 10.1038/s41467-023-43054-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 10/30/2023] [Indexed: 11/19/2023] Open
Abstract
Bacterial AB toxins are secreted key virulence factors that are internalized by target cells through receptor-mediated endocytosis, translocating their enzymatic domain to the cytosol from endosomes (short-trip) or the endoplasmic reticulum (long-trip). To accomplish this, bacterial AB toxins evolved a multidomain structure organized into either a single polypeptide chain or non-covalently associated polypeptide chains. The prototypical short-trip single-chain toxin is characterized by a receptor-binding domain that confers cellular specificity and a translocation domain responsible for pore formation whereby the catalytic domain translocates to the cytosol in an endosomal acidification-dependent way. In this work, the determination of the three-dimensional structure of AIP56 shows that, instead of a two-domain organization suggested by previous studies, AIP56 has three-domains: a non-LEE encoded effector C (NleC)-like catalytic domain associated with a small middle domain that contains the linker-peptide, followed by the receptor-binding domain. In contrast to prototypical single-chain AB toxins, AIP56 does not comprise a typical structurally complex translocation domain; instead, the elements involved in translocation are scattered across its domains. Thus, the catalytic domain contains a helical hairpin that serves as a molecular switch for triggering the conformational changes necessary for membrane insertion only upon endosomal acidification, whereas the middle and receptor-binding domains are required for pore formation.
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Affiliation(s)
- Johnny Lisboa
- Fish Immunology and Vaccinology Group, IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135, Porto, Portugal.
- Fish Immunology and Vaccinology Group, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal.
| | - Cassilda Pereira
- Fish Immunology and Vaccinology Group, IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135, Porto, Portugal
- Fish Immunology and Vaccinology Group, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal
| | - Rute D Pinto
- Fish Immunology and Vaccinology Group, IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135, Porto, Portugal
| | - Inês S Rodrigues
- Fish Immunology and Vaccinology Group, IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135, Porto, Portugal
- Fish Immunology and Vaccinology Group, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal
| | - Liliana M G Pereira
- Fish Immunology and Vaccinology Group, IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135, Porto, Portugal
| | - Bruno Pinheiro
- Fish Immunology and Vaccinology Group, IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135, Porto, Portugal
- Fish Immunology and Vaccinology Group, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal
- Doctoral Program in Molecular and Cell Biology (MCbiology), Instituto de Ciências Biomédicas Abel Salazar - Universidade do Porto, Porto, Portugal
| | - Pedro Oliveira
- EPIUnit, ICBAS-Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Pedro José Barbosa Pereira
- Biomolecular Structure Group, IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135, Porto, Portugal
- Macromolecular Structure Group, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal
| | - Jorge E Azevedo
- ICBAS-Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
- Organelle Biogenesis and Function, IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135, Porto, Portugal
- Organelle Biogenesis and Function, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal
| | - Dominique Durand
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Roland Benz
- Science Faculty, Constructor University, Bremen, Germany
| | - Ana do Vale
- Fish Immunology and Vaccinology Group, IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135, Porto, Portugal
- Fish Immunology and Vaccinology Group, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal
| | - Nuno M S Dos Santos
- Fish Immunology and Vaccinology Group, IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135, Porto, Portugal.
- Fish Immunology and Vaccinology Group, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal.
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Ginger L, Ledoux D, Bouchon M, Rautenbach I, Bagnard C, Lurier T, Foucras G, Germon P, Durand D, de Boyer des Roches A. Using behavioral observations in freestalls and at milking to improve pain detection in dairy cows after lipopolysaccharide-induced clinical mastitis. J Dairy Sci 2023:S0022-0302(23)00290-4. [PMID: 37268578 DOI: 10.3168/jds.2022-22533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/27/2023] [Indexed: 06/04/2023]
Abstract
This study aimed to determine the effect of lipopolysaccharide (LPS)-induced mastitis with or without nonsteroidal anti-inflammatory drug (NSAID) on dairy cows' clinical, physiological, and behavioral responses in the milking parlor and freestalls as well as the specificity (Sp) and sensitivity (Se) of behavioral responses in detecting cows with LPS-induced mastitis. Twenty-seven cows received an intramammary infusion of 25 µg of Escherichia coli LPS in 1 healthy quarter. Following LPS infusion, 14 cows received a placebo (LPS cows), and 13 cows received 3 mg/kg of body weight of ketoprofen i.m. (LPS+NSAID cows). Cow response to the challenge was monitored at regular intervals from 24 h before to 48 h postinfusion (hpi) through direct clinical observations, markers of inflammation in milk, and via point-in-time direct behavioral observations in the barn and at milking. In LPS cows, infusion induced a significant increase of plasma cortisol levels at 3 and 8 hpi, milk cortisol levels at 8 hpi, somatic cell counts from 8 to 48 hpi, IL-6 and IL-8 at 8 hpi, milk amyloid A (mAA) and haptoglobin at 8 and 24 hpi, rectal temperature at 8 hpi, and respiratory rate at 8 hpi. Their rumen motility rate decreased at 8 and 32 hpi. Compared with before the challenge, significantly more LPS cows stopped feeding/ruminating and pressed their tail between their legs at 3 and 5 hpi, increased feeding/ruminating at 24 hpi, and had the tendency to be less responsive, dropping their head, and dropping their ears at 5 hpi. At milking, compared with before challenge, significantly more LPS cows lifted their hooves at forestripping at 8 hpi. The 2 groups showed similar patterns of response for milk cortisol, somatic cell count, respiratory rate, mAA, haptoglobin, and IL-6, IL-1β, and IL-8. Compared with LPS cows, LPS+NSAID cows had significantly lower plasma cortisol levels at 3 hpi, their rectal temperature decreased at 8 hpi, their rumen motility rate increased at 8 and 32 hpi, and their heart rate increased at 32 hpi. Compared with LPS cows, a significantly larger proportion of LPS+NSAID cows were feeding/ruminating, a lower proportion had ears down at 5 hpi, and a larger proportion lied down at 24 hpi. At milking, whatever the phase of milking, for "hoof to belly," 9 out of 14 cows did not show this behavior before infusion (Sp = 64%) and 14/14 did not kick during pre-infusion milking (Sp = 100%). Regarding sensitivity, at maximum, 5 cows out of 14 (Se = 36%) displayed "hoof to belly" after infusion. For "lifting hoof," 14/14 did not show hoof-lifting before infusion (Sp = 100%) and 6/14 displayed it after infusion (Se = 43%) at forestripping only. In the freestall barn, 9 behaviors had a Sp >75% (at minimum, 10/14 did not show the behavior) whatever the time point but Se < 60% (at maximum, 8/14 displayed the behavior). Finally, "absence of feeding and ruminating" had Sp of 86% (12/14 ate/ruminated) and Se of 71% (10/14 did not eat/ruminate) at 5 hpi. This study shows that feeding/ruminating, tail position, and reactivity at forestripping could be used as behavioral indictors for early detection of mastitis-related pain in dairy cows.
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Affiliation(s)
- L Ginger
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, 63122 Saint-Genès-Champanelle, France
| | - D Ledoux
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, 63122 Saint-Genès-Champanelle, France
| | - M Bouchon
- INRAE, Herbipôle, 63122 Saint-Genès-Champanelle, France
| | - I Rautenbach
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, 63122 Saint-Genès-Champanelle, France
| | - C Bagnard
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, 63122 Saint-Genès-Champanelle, France
| | - T Lurier
- Université de Lyon, INRAE, VetAgro Sup, UMR EPIA, 69280 Marcy-l'Etoile, France; Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, 63122 Saint-Genès-Champanelle, France
| | - G Foucras
- Université de Toulouse, ENVT, INRAE, IHAP, 31076 Toulouse, France
| | - P Germon
- INRAE, UMR ISP, Université François Rabelais de Tours, 37380 Nouzilly, France
| | - D Durand
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, 63122 Saint-Genès-Champanelle, France
| | - A de Boyer des Roches
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR Herbivores, 63122 Saint-Genès-Champanelle, France.
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Leger C, Pitard I, Sadi M, Carvalho N, Brier S, Mechaly A, Hoos S, Vachette P, Durand D, Haouz A, Guijarro I, Ladant D, Chenal A. Dynamics and structural changes of calmodulin upon interaction with the antagonist calmidazolium. Biophys J 2023; 122:41a. [PMID: 36784142 DOI: 10.1016/j.bpj.2022.11.432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
- Corentin Leger
- Department of Structural Biology and Chemistry, Institut Pasteur, Paris, France
| | - Irène Pitard
- Department of Structural Biology and Chemistry, Institut Pasteur, Paris, France
| | - Mirko Sadi
- Department of Structural Biology and Chemistry, Institut Pasteur, Paris, France
| | - Nicolas Carvalho
- Department of Structural Biology and Chemistry, Institut Pasteur, Paris, France
| | - Sébastien Brier
- Biological NMR and HDX‑MS Technological Platform, Institut Pasteur, Paris, France
| | - Ariel Mechaly
- Plateforme de Cristallographie‑C2RT, Institut Pasteur, Paris, France
| | - Sylviane Hoos
- Plateforme de Biophysique Moléculaire, Institut Pasteur, Paris, France
| | - Patrice Vachette
- Institute for Integrative Biology of the Cell, Gif-sur-Yvette, France
| | - Dominique Durand
- Institute for Integrative Biology of the Cell, Gif-sur-Yvette, France
| | - Ahmed Haouz
- Plateforme de Cristallographie‑C2RT, Institut Pasteur, Paris, France
| | - Inaki Guijarro
- Biological NMR and HDX‑MS Technological Platform, Institut Pasteur, Paris, France
| | - Daniel Ladant
- Department of Structural Biology and Chemistry, Institut Pasteur, Paris, France
| | - Alexandre Chenal
- Department of Structural Biology and Chemistry, Institut Pasteur, Paris, France
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Voegele A, Sadi M, O'Brien DP, Gehan P, Hoos S, Brûlé S, Raynal B, Mechaly A, Haouz A, Rodriguez N, Vachette P, Durand D, Brier S, Ladant D, Chenal A. CyaA toxin translocation across host cell plasma membrane requires hijacking of calmodulin. Biophys J 2023; 122:370a. [PMID: 36783881 DOI: 10.1016/j.bpj.2022.11.2039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
| | | | | | | | - Sylviane Hoos
- Plateforme de Biophysique Moléculaire, Institut Pasteur, Paris, France
| | - Sébastien Brûlé
- Plateforme de Biophysique Moléculaire, Institut Pasteur, Paris, France
| | - Bertrand Raynal
- Plateforme de Biophysique Moléculaire, Institut Pasteur, Paris, France
| | - Ariel Mechaly
- Plateforme de Cristallographie, Institut Pasteur, Paris, France
| | - Ahmed Haouz
- Plateforme de Cristallographie, Institut Pasteur, Paris, France
| | | | | | | | - Sébastien Brier
- Biological NMR Technological Platform, Institut Pasteur, Paris, France
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Cargemel C, Marsin S, Adam Y, Chan-Yao-Chong M, Andreani J, Baconnais S, Legrand P, Ould Ali M, Gallay-Li De La Sierra I, Humbert A, Durand D, Aumont-Nicaise M, Velours C, Ochsenbein F, Le Cam E, Possoz C, Ha-Duong T, Walbott H, Ferat J, Quevillon-Cheruel S. DciA, the ancestral replicative helicase loader. Acta Cryst Sect A 2022. [DOI: 10.1107/s2053273322096292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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Léger C, Pitard I, Sadi M, Carvalho N, Brier S, Mechaly A, Raoux-Barbot D, Davi M, Hoos S, Weber P, Vachette P, Durand D, Haouz A, Guijarro JI, Ladant D, Chenal A. Dynamics and structural changes of calmodulin upon interaction with the antagonist calmidazolium. BMC Biol 2022; 20:176. [PMID: 35945584 PMCID: PMC9361521 DOI: 10.1186/s12915-022-01381-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/29/2022] [Indexed: 11/11/2022] Open
Abstract
Background Calmodulin (CaM) is an evolutionarily conserved eukaryotic multifunctional protein that functions as the major sensor of intracellular calcium signaling. Its calcium-modulated function regulates the activity of numerous effector proteins involved in a variety of physiological processes in diverse organs, from proliferation and apoptosis, to memory and immune responses. Due to the pleiotropic roles of CaM in normal and pathological cell functions, CaM antagonists are needed for fundamental studies as well as for potential therapeutic applications. Calmidazolium (CDZ) is a potent small molecule antagonist of CaM and one the most widely used inhibitors of CaM in cell biology. Yet, CDZ, as all other CaM antagonists described thus far, also affects additional cellular targets and its lack of selectivity hinders its application for dissecting calcium/CaM signaling. A better understanding of CaM:CDZ interaction is key to design analogs with improved selectivity. Here, we report a molecular characterization of CaM:CDZ complexes using an integrative structural biology approach combining SEC-SAXS, X-ray crystallography, HDX-MS, and NMR. Results We provide evidence that binding of a single molecule of CDZ induces an open-to-closed conformational reorientation of the two domains of CaM and results in a strong stabilization of its structural elements associated with a reduction of protein dynamics over a large time range. These CDZ-triggered CaM changes mimic those induced by CaM-binding peptides derived from physiological protein targets, despite their distinct chemical natures. CaM residues in close contact with CDZ and involved in the stabilization of the CaM:CDZ complex have been identified. Conclusion Our results provide molecular insights into CDZ-induced dynamics and structural changes of CaM leading to its inhibition and open the way to the rational design of more selective CaM antagonists. Graphical abstract Calmidazolium is a potent and widely used inhibitor of calmodulin, a major mediator of calcium-signaling in eukaryotic cells. Structural characterization of calmidazolium-binding to calmodulin reveals that it triggers open-to-closed conformational changes similar to those induced by calmodulin-binding peptides derived from enzyme targets. These results provide molecular insights into CDZ-induced dynamics and structural changes of CaM leading to its inhibition and open the way to the rational design of more selective CaM antagonists.![]() Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01381-5.
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Affiliation(s)
- Corentin Léger
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, CNRS UMR3528, Institut Pasteur, Paris, 75015, France
| | - Irène Pitard
- Biological NMR and HDX-MS Technological Platform, CNRS UMR3528, Université Paris Cité, Institut Pasteur, Paris, 75015, France
| | - Mirko Sadi
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, CNRS UMR3528, Institut Pasteur, Paris, 75015, France.,Université Paris Cité, Paris, France
| | - Nicolas Carvalho
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, CNRS UMR3528, Institut Pasteur, Paris, 75015, France.,Université Paris Cité, Paris, France
| | - Sébastien Brier
- Biological NMR and HDX-MS Technological Platform, CNRS UMR3528, Université Paris Cité, Institut Pasteur, Paris, 75015, France
| | - Ariel Mechaly
- Plate-forme de Cristallographie-C2RT, Université Paris Cité, CNRS UMR3528, Institut Pasteur, Paris, France
| | - Dorothée Raoux-Barbot
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, CNRS UMR3528, Institut Pasteur, Paris, 75015, France
| | - Maryline Davi
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, CNRS UMR3528, Institut Pasteur, Paris, 75015, France
| | - Sylviane Hoos
- Plateforme de Biophysique Moléculaire, Université Paris Cité, CNRS UMR3528, Institut Pasteur, Paris, France
| | - Patrick Weber
- Plate-forme de Cristallographie-C2RT, Université Paris Cité, CNRS UMR3528, Institut Pasteur, Paris, France
| | - Patrice Vachette
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Dominique Durand
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Ahmed Haouz
- Plate-forme de Cristallographie-C2RT, Université Paris Cité, CNRS UMR3528, Institut Pasteur, Paris, France
| | - J Iñaki Guijarro
- Biological NMR and HDX-MS Technological Platform, CNRS UMR3528, Université Paris Cité, Institut Pasteur, Paris, 75015, France
| | - Daniel Ladant
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, CNRS UMR3528, Institut Pasteur, Paris, 75015, France.
| | - Alexandre Chenal
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, CNRS UMR3528, Institut Pasteur, Paris, 75015, France.
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Durand D, Collin A, Merlot E, Baéza E, Guilloteau LA, Le Floc'h N, Thomas A, Fontagné-Dicharry S, Gondret F. Review: Implication of redox imbalance in animal health and performance at critical periods, insights from different farm species. Animal 2022; 16:100543. [PMID: 35623200 DOI: 10.1016/j.animal.2022.100543] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 04/15/2022] [Accepted: 04/25/2022] [Indexed: 11/01/2022] Open
Abstract
The process of oxidative stress occurs all over the production chain of animals and food products. This review summarises insights obtained in different farm species (pigs, ruminants, poultry, and fishes) to underpin the most critical periods for the venue of oxidative stress, namely birth/hatching and weaning/start-feeding phase. Common responses between species are also unravelled in periods of high physiological demands when animals are facing dietary deficiencies in specific nutrients, suggesting that nutritional recommendations must consider the modulation of responses to oxidative stress for optimising production performance and quality of food products. These conditions concern challenges such as heat stress, social stress, and inflammation. The magnitude of the responses is partly dependent on the prior experience of the animals before the challenge, reinforcing the importance of nutrition and other management practices during early periods to promote the development of antioxidant reserves in the animal. When these practices also improved the performance and health of the animal, this further confirms the central role played by oxidative stress in physiologically and environmentally induced perturbations. Difficulties in interpreting responses to oxidative stress arise from the fact that the indicators are only partly shared between studies, and their modulations may also be challenge-specific. A consensus about the best indicators to assess pro-oxidative and antioxidant pathways is of huge demand to propose a synthetic index measurable in a non-invasive way and interpretable along the productive life of the animals.
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Affiliation(s)
- D Durand
- INRAE, Université Clermont Auvergne, VetAgro Sup, UMR Herbivores, 63122 Saint-Genès-Champanelle, France.
| | - A Collin
- INRAE, Université de Tours, BOA, 37380 Nouzilly, France
| | - E Merlot
- PEGASE, INRAE, Institut Agro, 35590 Saint-Gilles, France
| | - E Baéza
- INRAE, Université de Tours, BOA, 37380 Nouzilly, France
| | | | - N Le Floc'h
- PEGASE, INRAE, Institut Agro, 35590 Saint-Gilles, France
| | - A Thomas
- INRAE, Université Clermont Auvergne, VetAgro Sup, UMR Herbivores, 63122 Saint-Genès-Champanelle, France
| | - S Fontagné-Dicharry
- INRAE, Université de Pau et des Pays de l'Adour, E2S UPPA, NUMEA, 64310 Saint-Pée-sur-Nivelle, France
| | - F Gondret
- PEGASE, INRAE, Institut Agro, 35590 Saint-Gilles, France
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8
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Cargemel C, Walbott H, Durand D, Legrand P, Ould Ali M, Ferat JL, Marsin S, Quevillon-Cheruel S. The apo-form of the Vibrio cholerae replicative helicase DnaB is a labile and inactive planar trimer of dimers. FEBS Lett 2022; 596:2031-2040. [PMID: 35568982 DOI: 10.1002/1873-3468.14403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/05/2022] [Accepted: 05/09/2022] [Indexed: 11/10/2022]
Abstract
To enable chromosomal replication, DNA is unwound by the ATPase molecular motor replicative helicase. The bacterial helicase DnaB is a ring-shaped homo-hexamer whose conformational dynamics are being studied through its different 3D structural states adopted along its functional cycle. Our findings describe a new crystal structure for the apo-DnaB from Vibrio cholerae, forming a planar hexamer with pseudo-symmetry, constituted by a trimer of dimers in which the C-terminal domains delimit a triskelion-shaped hole. This hexamer is labile and inactive. We suggest that it represents an intermediate state allowing the formation of the active NTP-bound hexamer from dimers.
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Affiliation(s)
- Claire Cargemel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Hélène Walbott
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Dominique Durand
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Pierre Legrand
- Synchrotron SOLEIL, L'Orme des Merisiers, 91192, Gif-sur-Yvette, France
| | - Malika Ould Ali
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Jean-Luc Ferat
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Stéphanie Marsin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Sophie Quevillon-Cheruel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
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Rengifo-Gonzalez JC, El Hage K, Clément MJ, Steiner E, Joshi V, Craveur P, Durand D, Pastré D, Bouhss A. The cooperative binding of TDP-43 to GU-rich RNA repeats antagonizes TDP-43 aggregation. eLife 2021; 10:67605. [PMID: 34490845 PMCID: PMC8523171 DOI: 10.7554/elife.67605] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 09/03/2021] [Indexed: 01/01/2023] Open
Abstract
TDP-43 is a nuclear RNA-binding protein that forms neuronal cytoplasmic inclusions in two major neurodegenerative diseases, ALS and FTLD. While the self-assembly of TDP-43 by its structured N-terminal and intrinsically disordered C-terminal domains has been widely studied, the mechanism by which mRNA preserves TDP-43 solubility in the nucleus has not been addressed. Here, we demonstrate that tandem RNA recognition motifs of TDP-43 bind to long GU-repeats in a cooperative manner through intermolecular interactions. Moreover, using mutants whose cooperativity is impaired, we found that the cooperative binding of TDP-43 to mRNA may be critical to maintain the solubility of TDP-43 in the nucleus and the miscibility of TDP-43 in cytoplasmic stress granules. We anticipate that the knowledge of a higher order assembly of TDP-43 on mRNA may clarify its role in intron processing and provide a means of interfering with the cytoplasmic aggregation of TDP-43.
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Affiliation(s)
- Juan Carlos Rengifo-Gonzalez
- Université Paris-Saclay, INSERM U1204, Univ Evry, Structure-Activité des Biomolécules Normales et Pathologiques (SABNP), Evry-Courcouronnes, France
| | - Krystel El Hage
- Université Paris-Saclay, INSERM U1204, Univ Evry, Structure-Activité des Biomolécules Normales et Pathologiques (SABNP), Evry-Courcouronnes, France
| | - Marie-Jeanne Clément
- Université Paris-Saclay, INSERM U1204, Univ Evry, Structure-Activité des Biomolécules Normales et Pathologiques (SABNP), Evry-Courcouronnes, France
| | - Emilie Steiner
- Université Paris-Saclay, INSERM U1204, Univ Evry, Structure-Activité des Biomolécules Normales et Pathologiques (SABNP), Evry-Courcouronnes, France
| | - Vandana Joshi
- Université Paris-Saclay, INSERM U1204, Univ Evry, Structure-Activité des Biomolécules Normales et Pathologiques (SABNP), Evry-Courcouronnes, France
| | | | - Dominique Durand
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - David Pastré
- Université Paris-Saclay, INSERM U1204, Univ Evry, Structure-Activité des Biomolécules Normales et Pathologiques (SABNP), Evry-Courcouronnes, France
| | - Ahmed Bouhss
- Université Paris-Saclay, INSERM U1204, Univ Evry, Structure-Activité des Biomolécules Normales et Pathologiques (SABNP), Evry-Courcouronnes, France
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10
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Durand D, Faure M, Lamberton P, Lemosquet S, de Boyer des Roches A. A multiparametric approach to assessing residual pain experienced by dairy cows undergoing digestive tract surgery under multimodal analgesia. Animal 2021; 15:100338. [PMID: 34418866 DOI: 10.1016/j.animal.2021.100338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 07/15/2021] [Accepted: 07/16/2021] [Indexed: 11/17/2022] Open
Abstract
This study assessed residual pain responses of dairy cows undergoing fistulation surgery under multimodal analgesia using a multiparametric method combining behavioural and physiological indicators. A longitudinal study was conducted on five dairy cows, each acting as her own control. The surgery consisted of implanting a ruminal and a duodenal cannula in each cow. The multimodal drug protocol consisted of a combination of N-Methyl-D aspartic Acid antagonists, α2-agonists, and local anaesthetic during surgery, and non-steroidal anti-inflammatory drugs (NSAIDs) and opioid treatment postsurgery. Cow responses to surgery were monitored by direct behavioural observation, physiological assay indicators, and milk production from day (D) -6 days before surgery (D-6) to D13 postsurgery. From the data recorded, the variables that contributed most to the discrimination of days pre- and postsurgery were identified using factorial discriminant analysis. Components 1 and 2 of the factorial discriminant analysis explained 68.2% and 17.9%, respectively, of the total variance. Component 1 was mainly explained by haptoglobin (contribution to axis: 0.885), oxidative stress (ratio of oxidized gluthatione to reduced glutathione (GSH/GSSG), -0.746; vitamin E, -0.683; vitamin A, -0.597; malondialdehyde (MDA), 0.416), and behavioural indicators (general attitude, 0.594). On this axis, the higher the score, the higher were the apathy and haptoglobin and MDA concentrations, and the lower were the GSH/GSSG ratio and concentrations of vitamins A and E. This axis opposed cows on D-6 to cows on D3 and D5; cows on D1 and D13 were intermediate. Component 2 was mainly explained by the Hypothalamic-pituitary-adrenal axis (non-esterified fatty acid (NEFA), 0.686; cortisol, 0.669), milk yield (-0.725), oxidative stress (MDA, -0.584; nitric oxide (NO), 0.454), and behavioural indicators of pain (ear position, 0.467; leg postures, 0.431). On this axis, the higher the score, the higher the NEFA, cortisol, and nitric oxide concentrations; the more the ear and leg pain postures; and the lower the milk production and MDA concentrations. This axis opposed cows on D13 to cows on D1. These results suggest that cows may experience some pain only on D1, whereas on subsequent days, the inflammatory response and oxidative stress did not seem to be associated with pain. Our results should be considered for different surgeries to improve analgesia immediately after surgery, and to provide antioxidants along with NSAIDs to promote recovery.
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Affiliation(s)
- D Durand
- INRAE, Université Clermont Auvergne, VetAgro Sup, UMR Herbivores, 63122 Saint-Genès-Champanelle, France.
| | - M Faure
- INRAE, Université Clermont Auvergne, VetAgro Sup, UMR Herbivores, 63122 Saint-Genès-Champanelle, France
| | - P Lamberton
- PEGASE, INRAE, Institut Agro, 35590 Saint Gilles, France
| | - S Lemosquet
- PEGASE, INRAE, Institut Agro, 35590 Saint Gilles, France
| | - A de Boyer des Roches
- INRAE, Université Clermont Auvergne, VetAgro Sup, UMR Herbivores, 63122 Saint-Genès-Champanelle, France
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11
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Ellies-Oury MP, Durand D, Listrat A, Chavent M, Saracco J, Gruffat D. Certain relationships between Animal Performance, Sensory Quality and Nutritional Quality can be generalized between various experiments on animal of similar types. Livest Sci 2021. [DOI: 10.1016/j.livsci.2021.104554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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12
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Marsin S, Adam Y, Cargemel C, Andreani J, Baconnais S, Legrand P, Li de la Sierra-Gallay I, Humbert A, Aumont-Nicaise M, Velours C, Ochsenbein F, Durand D, Le Cam E, Walbott H, Possoz C, Quevillon-Cheruel S, Ferat JL. Study of the DnaB:DciA interplay reveals insights into the primary mode of loading of the bacterial replicative helicase. Nucleic Acids Res 2021; 49:6569-6586. [PMID: 34107018 PMCID: PMC8216460 DOI: 10.1093/nar/gkab463] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 05/07/2021] [Accepted: 05/17/2021] [Indexed: 01/04/2023] Open
Abstract
Replicative helicases are essential proteins that unwind DNA in front of replication forks. Their loading depends on accessory proteins and in bacteria, DnaC and DnaI are well characterized loaders. However, most bacteria do not express either of these two proteins. Instead, they are proposed to rely on DciA, an ancestral protein unrelated to DnaC/I. While the DciA structure from Vibrio cholerae shares no homology with DnaC, it reveals similarities with DnaA and DnaX, two proteins involved during replication initiation. As other bacterial replicative helicases, VcDnaB adopts a toroid-shaped homo-hexameric structure, but with a slightly open dynamic conformation in the free state. We show that VcDnaB can load itself on DNA in vitro and that VcDciA stimulates this function, resulting in an increased DNA unwinding. VcDciA interacts with VcDnaB with a 3/6 stoichiometry and we show that a determinant residue, which discriminates DciA- and DnaC/I-helicases, is critical in vivo. Our work is the first step toward the understanding of the ancestral mode of loading of bacterial replicative helicases on DNA. It sheds light on the strategy employed by phage helicase loaders to hijack bacterial replicative helicases and may explain the recurrent domestication of dnaC/I through evolution in bacteria.
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Affiliation(s)
| | | | | | - Jessica Andreani
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Sonia Baconnais
- Genome Integrity and Cancer UMR 9019 CNRS, Université Paris Saclay, Gustave Roussy 114 rue Edouard Vaillant, 94805 Villejuif, France
| | - Pierre Legrand
- Synchrotron SOLEIL, L’Orme des Merisiers, 91192 Gif-sur-Yvette, France
| | - Ines Li de la Sierra-Gallay
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Adeline Humbert
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Magali Aumont-Nicaise
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Christophe Velours
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Françoise Ochsenbein
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Dominique Durand
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Eric Le Cam
- Genome Integrity and Cancer UMR 9019 CNRS, Université Paris Saclay, Gustave Roussy 114 rue Edouard Vaillant, 94805 Villejuif, France
| | - Hélène Walbott
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Christophe Possoz
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
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13
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Voegele A, Sadi M, O'Brien DP, Gehan P, Raoux‐Barbot D, Davi M, Hoos S, Brûlé S, Raynal B, Weber P, Mechaly A, Haouz A, Rodriguez N, Vachette P, Durand D, Brier S, Ladant D, Chenal A. A High-Affinity Calmodulin-Binding Site in the CyaA Toxin Translocation Domain is Essential for Invasion of Eukaryotic Cells. Adv Sci (Weinh) 2021; 8:2003630. [PMID: 33977052 PMCID: PMC8097335 DOI: 10.1002/advs.202003630] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/10/2020] [Indexed: 06/12/2023]
Abstract
The molecular mechanisms and forces involved in the translocation of bacterial toxins into host cells are still a matter of intense research. The adenylate cyclase (CyaA) toxin from Bordetella pertussis displays a unique intoxication pathway in which its catalytic domain is directly translocated across target cell membranes. The CyaA translocation region contains a segment, P454 (residues 454-484), which exhibits membrane-active properties related to antimicrobial peptides. Herein, the results show that this peptide is able to translocate across membranes and to interact with calmodulin (CaM). Structural and biophysical analyses reveal the key residues of P454 involved in membrane destabilization and calmodulin binding. Mutational analysis demonstrates that these residues play a crucial role in CyaA translocation into target cells. In addition, calmidazolium, a calmodulin inhibitor, efficiently blocks CyaA internalization. It is proposed that after CyaA binding to target cells, the P454 segment destabilizes the plasma membrane, translocates across the lipid bilayer and binds calmodulin. Trapping of CyaA by the CaM:P454 interaction in the cytosol may assist the entry of the N-terminal catalytic domain by converting the stochastic motion of the polypeptide chain through the membrane into an efficient vectorial chain translocation into host cells.
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Affiliation(s)
- Alexis Voegele
- Biochemistry of Macromolecular Interactions UnitDepartment of Structural Biology and ChemistryInstitut PasteurCNRS UMR3528Paris75015France
- Université de ParisSorbonne Paris CitéParis75006France
| | - Mirko Sadi
- Biochemistry of Macromolecular Interactions UnitDepartment of Structural Biology and ChemistryInstitut PasteurCNRS UMR3528Paris75015France
- Université de ParisSorbonne Paris CitéParis75006France
| | - Darragh Patrick O'Brien
- Biochemistry of Macromolecular Interactions UnitDepartment of Structural Biology and ChemistryInstitut PasteurCNRS UMR3528Paris75015France
| | - Pauline Gehan
- Sorbonne UniversitéÉcole normale supérieurePSL UniversityCNRSLaboratoire des biomoléculesLBMParis75005France
| | - Dorothée Raoux‐Barbot
- Biochemistry of Macromolecular Interactions UnitDepartment of Structural Biology and ChemistryInstitut PasteurCNRS UMR3528Paris75015France
| | - Maryline Davi
- Biochemistry of Macromolecular Interactions UnitDepartment of Structural Biology and ChemistryInstitut PasteurCNRS UMR3528Paris75015France
| | - Sylviane Hoos
- Plateforme de Biophysique MoléculaireInstitut PasteurUMR 3528 CNRSParis75015France
| | - Sébastien Brûlé
- Plateforme de Biophysique MoléculaireInstitut PasteurUMR 3528 CNRSParis75015France
| | - Bertrand Raynal
- Plateforme de Biophysique MoléculaireInstitut PasteurUMR 3528 CNRSParis75015France
| | - Patrick Weber
- Institut PasteurPlate‐forme de cristallographie‐C2RTUMR‐3528 CNRSParis75015France
| | - Ariel Mechaly
- Institut PasteurPlate‐forme de cristallographie‐C2RTUMR‐3528 CNRSParis75015France
| | - Ahmed Haouz
- Institut PasteurPlate‐forme de cristallographie‐C2RTUMR‐3528 CNRSParis75015France
| | - Nicolas Rodriguez
- Sorbonne UniversitéÉcole normale supérieurePSL UniversityCNRSLaboratoire des biomoléculesLBMParis75005France
| | - Patrice Vachette
- Université Paris‐SaclayCEACNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐Yvette91198France
| | - Dominique Durand
- Université Paris‐SaclayCEACNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐Yvette91198France
| | - Sébastien Brier
- Biological NMR Technological PlateformCenter for Technological Resources and ResearchDepartment of Structural Biology and ChemistryInstitut PasteurCNRS UMR3528Paris75015France
| | - Daniel Ladant
- Biochemistry of Macromolecular Interactions UnitDepartment of Structural Biology and ChemistryInstitut PasteurCNRS UMR3528Paris75015France
| | - Alexandre Chenal
- Biochemistry of Macromolecular Interactions UnitDepartment of Structural Biology and ChemistryInstitut PasteurCNRS UMR3528Paris75015France
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14
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Pinet L, Wang YH, Deville C, Lescop E, Guerlesquin F, Badache A, Bontems F, Morellet N, Durand D, Assrir N, van Heijenoort C. Structural and dynamic characterization of the C-terminal tail of ErbB2: Disordered but not random. Biophys J 2021; 120:1869-1882. [PMID: 33741354 DOI: 10.1016/j.bpj.2021.03.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 02/26/2021] [Accepted: 03/03/2021] [Indexed: 01/23/2023] Open
Abstract
ErbB2 (or HER2) is a receptor tyrosine kinase overexpressed in some breast cancers and associated with poor prognosis. Treatments targeting the receptor extracellular and kinase domains have greatly improved disease outcome in the last 20 years. In parallel, the structures of these domains have been described, enabling better mechanistic understanding of the receptor function and targeted inhibition. However, the ErbB2 disordered C-terminal cytoplasmic tail (CtErbB2) remains very poorly characterized in terms of structure, dynamics, and detailed functional mechanism. Yet, it is where signal transduction is triggered via phosphorylation of tyrosine residues and carried out via interaction with adaptor proteins. Here, we report the first description, to our knowledge, of the ErbB2 disordered tail at atomic resolution using NMR, complemented by small-angle x-ray scattering. We show that although no part of CtErbB2 has any fully populated secondary or tertiary structure, it contains several transient α-helices and numerous transient polyproline II helices, populated up to 20 and 40%, respectively, and low but significant compaction. The presence of some structural elements suggests, along the lines of the results obtained for EGFR (ErbB1), that they may have a functional role in ErbB2's autoregulation processes. In addition, the transient formation of polyproline II helices is compliant with previously suggested interactions with SH3 domains. All in all, our in-depth structural study opens perspectives in the mechanistic understanding of ErbB2.
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Affiliation(s)
- Louise Pinet
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Gif-sur-Yvette, France; Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Ying-Hui Wang
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Gif-sur-Yvette, France; SGS Taiwan LTD, New Taipei City, Taiwan
| | - Célia Deville
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Gif-sur-Yvette, France; IGBMC, University of Strasbourg, CNRS UMR, Illkirch, France
| | - Ewen Lescop
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Françoise Guerlesquin
- LISM, Institut de Microbiologie de la Méditerranée, CNRS and Aix-Marseille University, Marseille, France
| | - Ali Badache
- Centre de Recherche en Cancérologie de Marseille, Aix-Marseille Univ, INSERM, Institut Paoli-Calmettes, CNRS, Marseille, France
| | - François Bontems
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Gif-sur-Yvette, France; Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France
| | - Nelly Morellet
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Dominique Durand
- I2BC, Université Paris-Saclay, CNRS UMR 9198, Gif-sur-Yvette, France
| | - Nadine Assrir
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Carine van Heijenoort
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Gif-sur-Yvette, France.
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15
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Chan-Yao-Chong M, Marsin S, Quevillon-Cheruel S, Durand D, Ha-Duong T. Structural ensemble and biological activity of DciA intrinsically disordered region. J Struct Biol 2020; 212:107573. [PMID: 32679070 DOI: 10.1016/j.jsb.2020.107573] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/17/2020] [Accepted: 07/06/2020] [Indexed: 11/19/2022]
Abstract
DciA is a newly discovered bacterial protein involved in loading the replicative helicase DnaB onto DNA at the initiation step of chromosome replication. Its three-dimensional structure is composed of a folded N-terminal domain (residues 1-111) resembling K Homology domains and a long disordered C-terminal tail (residues 112-157) which structure-activity relationship remains to be elucidated. In the present study on Vibrio cholerae DciA, we emphasize the importance of its disordered region to load DnaB onto DNA using surface plasmon resonance (SPR) and isothermal titration microcalorimetry (ITC). Then we characterize the conformational ensemble of the full-length protein using a combination of circular dichroism (CD), small angle X-ray scattering (SAXS), and molecular dynamics (MD) simulations. The atomic-level structural ensemble generated by MD simulations is in very good agreement with SAXS data. From initial conformations of the C-terminal tail without any secondary structure, our simulations bring to light several transient helical structures in this segment, which might be molecular recognition features (MoRFs) for the binding to DnaB and its recruitment and loading onto DNA.
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Affiliation(s)
| | - Stéphanie Marsin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, 91198 Gif-sur-Yvette, France
| | - Sophie Quevillon-Cheruel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, 91198 Gif-sur-Yvette, France
| | - Dominique Durand
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell, 91198 Gif-sur-Yvette, France.
| | - Tâp Ha-Duong
- Université Paris-Saclay, CNRS, BioCIS, 92290 Châtenay-Malabry, France.
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16
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Ferry M, Dannoux-Papin A, Legand S, Exposito E, Durand D, Ngono-Ravache Y, Esnouf S. Alkaline hydrolysis of radio-oxidized aliphatic polymers. Radiat Phys Chem Oxf Engl 1993 2020. [DOI: 10.1016/j.radphyschem.2020.108783] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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17
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Villot C, Martin C, Bodin J, Durand D, Graulet B, Ferlay A, Mialon M, Trevisi E, Silberberg M. Combinations of non-invasive indicators to detect dairy cows submitted to high-starch-diet challenge. Animal 2020; 14:388-398. [PMID: 31311612 PMCID: PMC6974427 DOI: 10.1017/s1751731119001629] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 06/04/2019] [Accepted: 06/20/2019] [Indexed: 11/07/2022] Open
Abstract
High-starch diets (HSDs) fed to high-producing ruminants are often responsible for rumen dysfunction and could impair animal health and production. Feeding HSDs are often characterized by transient rumen pH depression, accurate monitoring of which requires costly or invasive methods. Numerous clinical signs can be followed to monitor such diet changes but no specific indicator is able to make a statement at animal level on-farm. The aim of this pilot study was to assess a combination of non-invasive indicators in dairy cows able to monitor a HSD in experimental conditions. A longitudinal study was conducted in 11 primiparous dairy cows fed with two different diets during three successive periods: a 4-week control period (P1) with a low-starch diet (LSD; 13% starch), a 4-week period with an HSD (P2, 35% starch) and a 3-week recovery period (P3) again with the LSD. Animal behaviour was monitored throughout the experiment, and faeces, urine, saliva, milk and blood were sampled simultaneously in each animal at least once a week for analysis. A total of 136 variables were screened by successive statistical approaches including: partial least squares-discriminant analysis, multivariate analysis and mixed-effect models. Finally, 16 indicators were selected as the most representative of a HSD challenge. A generalized linear mixed model analysis was applied to highlight parsimonious combinations of indicators able to identify animals under our experimental conditions. Eighteen models were established and the combination of milk urea nitrogen, blood bicarbonate and feed intake was the best to detect the different periods of the challenge with both 100% of specificity and sensitivity. Other indicators such as the number of drinking acts, fat:protein ratio in milk, urine, and faecal pH, were the most frequently used in the proposed models. Finally, the established models highlight the necessity for animals to have more than 1 week of recovery diet to return to their initial control state after a HSD challenge. This pilot study demonstrates the interest of using combinations of non-invasive indicators to monitor feed changes from a LSD to a HSD to dairy cows in order to improve prevention of rumen dysfunction on-farm. However, the adjustment and robustness of the proposed combinations of indicators need to be challenged using a greater number of animals as well as different acidogenic conditions before being applied on-farm.
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Affiliation(s)
- C. Villot
- Université Clermont Auvergne, INRA, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France
- Lallemand SAS, F-31702 Blagnac, France
- Valorex, Le Messayais, F-35210 Combourtillé, France
- Terrena, La Noëlle, F-44150 Ancenis, France
| | - C. Martin
- Université Clermont Auvergne, INRA, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France
| | - J. Bodin
- BR3 Consultants, F-69007 Lyon, France
| | - D. Durand
- Université Clermont Auvergne, INRA, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France
| | - B. Graulet
- Université Clermont Auvergne, INRA, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France
| | - A. Ferlay
- Université Clermont Auvergne, INRA, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France
| | - M.M. Mialon
- Université Clermont Auvergne, INRA, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France
| | - E. Trevisi
- Department of Agriculture, Food and Environmental Science CEO of CERZOO, DIANA, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy
| | - M. Silberberg
- Université Clermont Auvergne, INRA, VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France
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18
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Andueza D, Listrat A, Durand D, Normand J, Mourot B, Gruffat D. Prediction of beef meat fatty acid composition by visible-near-infrared spectroscopy was improved by preliminary freeze-drying. Meat Sci 2019; 158:107910. [DOI: 10.1016/j.meatsci.2019.107910] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/24/2019] [Accepted: 08/07/2019] [Indexed: 11/29/2022]
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Durand D, Vassieux L, Dodet JF, Millot I. Digital media: How to adapt digital media to promote health of young people? Eur J Public Health 2019. [DOI: 10.1093/eurpub/ckz185.100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
A priority of the French government health section is to promote strategies to develop teenager and young adult abilities to manage their own health. Interventions must be based on digital tools on how to improve it. The Pass’santé Jeunes (PSJ) is a regional measure based on a global, positive, community approaches, and on peers interventions. Managed by the Agence Régionale de Santé since 2013, and lead by the Instance Regional d’Education et de Promotion pour la Santé, this program consists of the provision of two portals: Pass’santé Jeunes and Pass’santé pro.
This project aims to renew prevention approaches with youths, and to develop a common culture around efficient intervention strategies with professionals for linkage in digital practices. This initiative has been developed and collaborated with the targeted public, parents, and professionals. We queried the opinions of a youth panel, and requested advice of experts to assure relevance and veracity of the information. Websites were then created for professionals to locate information to support their missions.
Analysis of the actual uses of the PSJ were conducted by the University of Burgundy in 2016. Results showed much of the research leaning toward the creation of a prevention tool. For alignment with internet use by youths, we adapted the variety of media (quizzes, videos, apps...). In 2018, the average monthly audience of both sites increased significantly.Greater utilization of these resources is explained by increased awareness by professionals and prevention missions of health students.
In the health sector, challenges exist in understanding digital practices of youth and professionals, therefore it is important to play a key liaison role. First identified as an informational medium, these devices are now real resources for meeting and circulating knowledge.Prospects for 2020 are to redirect these tools to the 0-8 years age group, adapt them to situations of disability, and expand to the pregnancy period.
Key messages
In line with digital practices of youth, the PSJ relies on innovative communication supports, available in different formats (videos, quizzes, games, apps...). Beyond an informational tool for the young, the PSJ turns out to be a tool of knowledge brockering. It facilitates networking, implementation of activities, and improving health practices.
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Affiliation(s)
- D Durand
- Instance Régionale d’Education et de Promotion pour la Santé - Bourgogne-Franche-Comté, Dijon, France
| | - L Vassieux
- Instance Régionale d’Education et de Promotion pour la Santé - Bourgogne-Franche-Comté, Dijon, France
| | - J-F Dodet
- Agence Régionale de Santé - Bourgogne-Franche-Comté, Dijon, France
| | - I Millot
- Instance Régionale d’Education et de Promotion pour la Santé - Bourgogne-Franche-Comté, Dijon, France
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20
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Kretov DA, Clément MJ, Lambert G, Durand D, Lyabin DN, Bollot G, Bauvais C, Samsonova A, Budkina K, Maroun RC, Hamon L, Bouhss A, Lescop E, Toma F, Curmi PA, Maucuer A, Ovchinnikov LP, Pastré D. YB-1, an abundant core mRNA-binding protein, has the capacity to form an RNA nucleoprotein filament: a structural analysis. Nucleic Acids Res 2019; 47:3127-3141. [PMID: 30605522 PMCID: PMC6451097 DOI: 10.1093/nar/gky1303] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 12/17/2018] [Accepted: 12/20/2018] [Indexed: 12/20/2022] Open
Abstract
The structural rearrangements accompanying mRNA during translation in mammalian cells remain poorly understood. Here, we discovered that YB-1 (YBX1), a major partner of mRNAs in the cytoplasm, forms a linear nucleoprotein filament with mRNA, when part of the YB-1 unstructured C-terminus has been truncated. YB-1 possesses a cold-shock domain (CSD), a remnant of bacterial cold shock proteins that have the ability to stimulate translation under the low temperatures through an RNA chaperone activity. The structure of the nucleoprotein filament indicates that the CSD of YB-1 preserved its chaperone activity also in eukaryotes and shows that mRNA is channeled between consecutive CSDs. The energy benefit needed for the formation of stable nucleoprotein filament relies on an electrostatic zipper mediated by positively charged amino acid residues in the YB-1 C-terminus. Thus, YB-1 displays a structural plasticity to unfold structured mRNAs into extended linear filaments. We anticipate that our findings will shed the light on the scanning of mRNAs by ribosomes during the initiation and elongation steps of mRNA translation.
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Affiliation(s)
- Dmitry A Kretov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russian Federation.,SABNP, University of Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Marie-Jeanne Clément
- SABNP, University of Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Guillaume Lambert
- SABNP, University of Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Dominique Durand
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Dmitry N Lyabin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russian Federation
| | | | - Cyril Bauvais
- Synsight, a/s IncubAlliance 86 rue de Paris Orsay 91400, France
| | - Anastasiia Samsonova
- SABNP, University of Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Karina Budkina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russian Federation.,SABNP, University of Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Rachid C Maroun
- SABNP, University of Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Loic Hamon
- SABNP, University of Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Ahmed Bouhss
- SABNP, University of Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Ewen Lescop
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, 91198 Gif sur Yvette cedex, France
| | - Flavio Toma
- SABNP, University of Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Patrick A Curmi
- SABNP, University of Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Alexandre Maucuer
- SABNP, University of Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Lev P Ovchinnikov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russian Federation
| | - David Pastré
- SABNP, University of Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
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21
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Ramos D, Caamaño M, Lemasson A, Rejmund M, Audouin L, Álvarez-Pol H, Frankland JD, Fernández-Domínguez B, Galiana-Baldó E, Piot J, Ackermann D, Biswas S, Clement E, Durand D, Farget F, Fregeau MO, Galaviz D, Heinz A, Henriques AI, Jacquot B, Jurado B, Kim YH, Morfouace P, Ralet D, Roger T, Schmitt C, Teubig P, Tsekhanovich I. First Direct Measurement of Isotopic Fission-Fragment Yields of ^{239}U. Phys Rev Lett 2019; 123:092503. [PMID: 31524478 DOI: 10.1103/physrevlett.123.092503] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Indexed: 06/10/2023]
Abstract
A direct and complete measurement of isotopic fission-fragment yields of ^{239}U has been performed for the first time. The ^{239}U fissioning system was produced with an average excitation energy of 8.3 MeV in one-neutron transfer reactions between a ^{238}U beam and a ^{9}Be target at Coulomb barrier energies. The fission fragments were detected and isotopically identified using the VAMOS++ spectrometer at the GANIL facility. The measurement allows us to directly evaluate the fission models at excitation energies of fast neutrons, which are relevant for next-generation nuclear reactors. The present data, in agreement with model calculations, do not support the recently reported anomaly in the fission-fragment yields of ^{239}U, and they confirm the persistence of spherical shell effects in the Sn region at excitation energies exceeding the fission barrier by a few mega-electron volts.
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Affiliation(s)
- D Ramos
- IPN Orsay, Université de Paris-Saclay, CNRS/IN2P3, F-91406 Orsay Cedex, France
- GANIL, CEA/DRF-CNRS/IN2P3, BP 55027, F-14076 Caen Cedex 5, France
| | - M Caamaño
- IGFAE, Universidade de Santiago de Compostela, E-15706 Santiago de Compostela, Spain
| | - A Lemasson
- GANIL, CEA/DRF-CNRS/IN2P3, BP 55027, F-14076 Caen Cedex 5, France
| | - M Rejmund
- GANIL, CEA/DRF-CNRS/IN2P3, BP 55027, F-14076 Caen Cedex 5, France
| | - L Audouin
- IPN Orsay, Université de Paris-Saclay, CNRS/IN2P3, F-91406 Orsay Cedex, France
| | - H Álvarez-Pol
- IGFAE, Universidade de Santiago de Compostela, E-15706 Santiago de Compostela, Spain
| | - J D Frankland
- GANIL, CEA/DRF-CNRS/IN2P3, BP 55027, F-14076 Caen Cedex 5, France
| | - B Fernández-Domínguez
- IGFAE, Universidade de Santiago de Compostela, E-15706 Santiago de Compostela, Spain
| | - E Galiana-Baldó
- IGFAE, Universidade de Santiago de Compostela, E-15706 Santiago de Compostela, Spain
- LIP Lisboa, 1649-003 Lisbon, Portugal
| | - J Piot
- GANIL, CEA/DRF-CNRS/IN2P3, BP 55027, F-14076 Caen Cedex 5, France
| | - D Ackermann
- GANIL, CEA/DRF-CNRS/IN2P3, BP 55027, F-14076 Caen Cedex 5, France
| | - S Biswas
- GANIL, CEA/DRF-CNRS/IN2P3, BP 55027, F-14076 Caen Cedex 5, France
| | - E Clement
- GANIL, CEA/DRF-CNRS/IN2P3, BP 55027, F-14076 Caen Cedex 5, France
| | - D Durand
- LPC Caen, Université de Caen Basse-Normandie-ENSICAEN-CNRS/IN2P3, F-14050 Caen Cedex, France
| | - F Farget
- LPC Caen, Université de Caen Basse-Normandie-ENSICAEN-CNRS/IN2P3, F-14050 Caen Cedex, France
| | - M O Fregeau
- GANIL, CEA/DRF-CNRS/IN2P3, BP 55027, F-14076 Caen Cedex 5, France
| | - D Galaviz
- LIP Lisboa, 1649-003 Lisbon, Portugal
| | - A Heinz
- Chalmers University of Technology, SE-41296 Göteborg, Sweden
| | - A I Henriques
- CENBG, IN2P3/CNRS-Université de Bordeaux, F-33175 Gradignan Cedex, France
| | - B Jacquot
- GANIL, CEA/DRF-CNRS/IN2P3, BP 55027, F-14076 Caen Cedex 5, France
| | - B Jurado
- CENBG, IN2P3/CNRS-Université de Bordeaux, F-33175 Gradignan Cedex, France
| | - Y H Kim
- GANIL, CEA/DRF-CNRS/IN2P3, BP 55027, F-14076 Caen Cedex 5, France
| | - P Morfouace
- GANIL, CEA/DRF-CNRS/IN2P3, BP 55027, F-14076 Caen Cedex 5, France
| | - D Ralet
- CSNSM, CNRS/IN2P3, Université de Paris-Saclay, F-91405 Orsay, France
| | - T Roger
- GANIL, CEA/DRF-CNRS/IN2P3, BP 55027, F-14076 Caen Cedex 5, France
| | - C Schmitt
- IPHC Strasbourg, Université de Strasbourg-CNRS/IN2P3, F-67037 Strasbourg Cedex 2, France
| | - P Teubig
- LIP Lisboa, 1649-003 Lisbon, Portugal
| | - I Tsekhanovich
- CENBG, IN2P3/CNRS-Université de Bordeaux, F-33175 Gradignan Cedex, France
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22
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Missoury S, Plancqueel S, Li de la Sierra-Gallay I, Zhang W, Liger D, Durand D, Dammak R, Collinet B, van Tilbeurgh H. The structure of the TsaB/TsaD/TsaE complex reveals an unexpected mechanism for the bacterial t6A tRNA-modification. Nucleic Acids Res 2019; 47:9464-9465. [PMID: 31428791 PMCID: PMC6755083 DOI: 10.1093/nar/gkz719] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Sophia Missoury
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Stéphane Plancqueel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Ines Li de la Sierra-Gallay
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Wenhua Zhang
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Dominique Liger
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Dominique Durand
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Raoudha Dammak
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Bruno Collinet
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France.,Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR7590 CNRS/Sorbonne-Université, UPMC, Paris, France
| | - Herman van Tilbeurgh
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
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23
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Furtak-Wrona K, Cornaton M, Durand D, Dauvois V, Roujou JL, Esnouf S, Ferry M. Temperature and LET effects on radiation-induced modifications in non-perfect polyethylenes. Polym Degrad Stab 2019. [DOI: 10.1016/j.polymdegradstab.2019.02.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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24
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Chan-Yao-Chong M, Durand D, Ha-Duong T. Molecular Dynamics Simulations Combined with Nuclear Magnetic Resonance and/or Small-Angle X-ray Scattering Data for Characterizing Intrinsically Disordered Protein Conformational Ensembles. J Chem Inf Model 2019; 59:1743-1758. [PMID: 30840442 DOI: 10.1021/acs.jcim.8b00928] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The concept of intrinsically disordered proteins (IDPs) has emerged relatively slowly, but over the past 20 years, it has become an intense research area in structural biology. Indeed, because of their considerable flexibility and structural heterogeneity, the determination of IDP conformational ensemble is particularly challenging and often requires a combination of experimental measurements and computational approaches. With the improved accuracy of all-atom force fields and the increasing computing performances, molecular dynamics (MD) simulations have become more and more reliable to generate realistic conformational ensembles. And the combination of MD simulations with experimental approaches, such as nuclear magnetic resonance (NMR) and/or small-angle X-ray scattering (SAXS) allows one to converge toward a more accurate and exhaustive description of IDP structures. In this Review, we discuss the state of the art of MD simulations of IDP conformational ensembles, with a special focus on studies that back-calculated and directly compared theoretical and experimental NMR or SAXS observables, such as chemical shifts (CS), 3J-couplings (3Jc), residual dipolar couplings (RDC), or SAXS intensities. We organize the review in three parts. In the first section, we discuss the studies which used NMR and/or SAXS data to test and validate the development of force fields or enhanced sampling techniques. In the second part, we explore different methods for the refinement of MD-derived structural ensembles, such as NMR or SAXS data-restrained MD simulations or ensemble reweighting to better fit experiments. Finally, we survey some recent studies combining MD simulations with NMR and/or SAXS measurements to investigate the relationship between IDP conformational ensemble and biological activity, as well as their implication in human diseases. From this review, we noticed that quite a few studies compared MD-generated conformational ensembles with both NMR and SAXS measurements to validate IDP structures at both local and global levels. Yet, beside the IDP propensity to form local secondary structures, their dynamic extension or compactness also appears important for their activity. Thus, we believe that a close synergy between MD simulations, NMR, and SAXS experiments would be greatly appropriate to address the challenges of characterizing the disordered structures of proteins and their complexes, relative to their biological functions.
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Affiliation(s)
- Maud Chan-Yao-Chong
- BioCIS, Université Paris-Sud, CNRS , Université Paris-Saclay , 92290 Châtenay-Malabry , France.,Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud , Université Paris-Saclay , 91198 , Gif-sur-Yvette cedex, France
| | - Dominique Durand
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud , Université Paris-Saclay , 91198 , Gif-sur-Yvette cedex, France
| | - Tâp Ha-Duong
- BioCIS, Université Paris-Sud, CNRS , Université Paris-Saclay , 92290 Châtenay-Malabry , France
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25
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Lisboa J, Celma L, Sanchez D, Marquis M, Andreani J, Guérois R, Ochsenbein F, Durand D, Marsin S, Cuniasse P, Radicella JP, Quevillon-Cheruel S. The C-terminal domain of HpDprA is a DNA-binding winged helix domain that does not bind double-stranded DNA. FEBS J 2019; 286:1941-1958. [PMID: 30771270 DOI: 10.1111/febs.14788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 11/21/2018] [Accepted: 02/14/2019] [Indexed: 12/15/2022]
Abstract
DNA-processing protein A, a ubiquitous multidomain DNA-binding protein, plays a crucial role during natural transformation in bacteria. Here, we carried out the structural analysis of DprA from the human pathogen Helicobacter pylori by combining data issued from the 1.8-Å resolution X-ray structure of the Pfam02481 domain dimer (RF), the NMR structure of the carboxy terminal domain (CTD), and the low-resolution structure of the full-length DprA dimer obtained in solution by SAXS. In particular, we sought a molecular function for the CTD, a domain that we show here is essential for transformation in H. pylori. Albeit its structural homology to winged helix DNA-binding motifs, we confirmed that the isolated CTD does not interact with ssDNA nor with dsDNA. The key R52 and K137 residues of RF are crucial for these two interactions. Search for sequences harboring homology to either HpDprA or Rhodopseudomonas palustris DprA CTDs led to the identification of conserved patches in the two CTD. Our structural study revealed the similarity of the structures adopted by these residues in RpDprA CTD and HpDprA CTD. This argues for a conserved, but yet to be defined, CTD function, distinct from DNA binding.
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Affiliation(s)
- Johnny Lisboa
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France
| | - Louisa Celma
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France
| | - Dyana Sanchez
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France
| | - Mathilde Marquis
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France
| | - Jessica Andreani
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France
| | - Raphael Guérois
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France
| | - Françoise Ochsenbein
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France
| | - Dominique Durand
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France
| | - Stéphanie Marsin
- Institute of Cellular and Molecular Radiobiology, Institut François Jacob, CEA, Universités Paris Diderot and Paris-Sud, Fontenay aux Roses, France
| | - Philippe Cuniasse
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France
| | - J Pablo Radicella
- Institute of Cellular and Molecular Radiobiology, Institut François Jacob, CEA, Universités Paris Diderot and Paris-Sud, Fontenay aux Roses, France
| | - Sophie Quevillon-Cheruel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France
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26
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Chan-Yao-Chong M, Deville C, Pinet L, van Heijenoort C, Durand D, Ha-Duong T. Structural Characterization of N-WASP Domain V Using MD Simulations with NMR and SAXS Data. Biophys J 2019; 116:1216-1227. [PMID: 30878202 DOI: 10.1016/j.bpj.2019.02.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 02/14/2019] [Accepted: 02/19/2019] [Indexed: 11/19/2022] Open
Abstract
Because of their large conformational heterogeneity, structural characterization of intrinsically disordered proteins (IDPs) is very challenging using classical experimental methods alone. In this study, we use NMR and small-angle x-ray scattering (SAXS) data with multiple molecular dynamics (MD) simulations to describe the conformational ensemble of the fully disordered verprolin homology domain of the neural Aldrich syndrome protein involved in the regulation of actin polymerization. First, we studied several back-calculation software of SAXS scattering intensity and optimized the adjustable parameters to accurately calculate the SAXS intensity from an atomic structure. We also identified the most appropriate force fields for MD simulations of this IDP. Then, we analyzed four conformational ensembles of neural Aldrich syndrome protein verprolin homology domain, two generated with the program flexible-meccano with or without NMR-derived information as input and two others generated by MD simulations with two different force fields. These four conformational ensembles were compared to available NMR and SAXS data for validation. We found that MD simulations with the AMBER-03w force field and the TIP4P/2005s water model are able to correctly describe the conformational ensemble of this 67-residue IDP at both local and global level.
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Affiliation(s)
- Maud Chan-Yao-Chong
- BioCIS, University Paris-Sud, CNRS UMR 8076, University Paris-Saclay, Châtenay-Malabry, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Célia Deville
- IGBMC, University of Strasbourg, CNRS UMR 7104, Illkirch, France
| | - Louise Pinet
- ICSN, CNRS UPR 2301, University Paris-Saclay, Gif-sur-Yvette, France
| | | | - Dominique Durand
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.
| | - Tâp Ha-Duong
- BioCIS, University Paris-Sud, CNRS UMR 8076, University Paris-Saclay, Châtenay-Malabry, France.
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Patrick O'Brien D, Durand D, Cannella S, Voegele A, Vachette P, Brier S, Ladant D, Chenal A. Conformational Disorder is Required for Toxin Secretion, Folding and Cell Intoxication. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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28
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Ziegler CS, Bouchab L, Tramier M, Durand D, Fieschi F, Dupré-Crochet S, Mérola F, Nüße O, Erard M. Quantitative live-cell imaging and 3D modeling reveal critical functional features in the cytosolic complex of phagocyte NADPH oxidase. J Biol Chem 2019; 294:3824-3836. [PMID: 30630949 DOI: 10.1074/jbc.ra118.006864] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/08/2019] [Indexed: 01/18/2023] Open
Abstract
Phagocyte NADPH oxidase produces superoxide anions, a precursor of reactive oxygen species (ROS) critical for host responses to microbial infections. However, uncontrolled ROS production contributes to inflammation, making NADPH oxidase a major drug target. It consists of two membranous (Nox2 and p22phox) and three cytosolic subunits (p40phox, p47phox, and p67phox) that undergo structural changes during enzyme activation. Unraveling the interactions between these subunits and the resulting conformation of the complex could shed light on NADPH oxidase regulation and help identify inhibition sites. However, the structures and the interactions of flexible proteins comprising several well-structured domains connected by intrinsically disordered protein segments are difficult to investigate by conventional techniques such as X-ray crystallography, NMR, or cryo-EM. Here, we developed an analytical strategy based on FRET-fluorescence lifetime imaging (FLIM) and fluorescence cross-correlation spectroscopy (FCCS) to structurally and quantitatively characterize NADPH oxidase in live cells. We characterized the inter- and intramolecular interactions of its cytosolic subunits by elucidating their conformation, stoichiometry, interacting fraction, and affinities in live cells. Our results revealed that the three subunits have a 1:1:1 stoichiometry and that nearly 100% of them are present in complexes in living cells. Furthermore, combining FRET data with small-angle X-ray scattering (SAXS) models and published crystal structures of isolated domains and subunits, we built a 3D model of the entire cytosolic complex. The model disclosed an elongated complex containing a flexible hinge separating two domains ideally positioned at one end of the complex and critical for oxidase activation and interactions with membrane components.
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Affiliation(s)
- Cornelia S Ziegler
- From the Laboratoire de Chimie Physique, CNRS, Université Paris-Sud, Université Paris-Saclay, 91405, Orsay France
| | - Leïla Bouchab
- From the Laboratoire de Chimie Physique, CNRS, Université Paris-Sud, Université Paris-Saclay, 91405, Orsay France
| | - Marc Tramier
- the Université Rennes, CNRS, Institut de Génétique et Développement de Rennes - UMR 6290, BIOSIT - UMS 3480, F-35000 Rennes, France
| | - Dominique Durand
- the Institute for Integrative Biology of the Cell, CEA, CNRS UMR 9198, Université Paris-Sud, Université Paris-Saclay, 91190 Gif-sur-Yvette, France, and
| | - Franck Fieschi
- the Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, F-38044 Grenoble, France
| | - Sophie Dupré-Crochet
- From the Laboratoire de Chimie Physique, CNRS, Université Paris-Sud, Université Paris-Saclay, 91405, Orsay France
| | - Fabienne Mérola
- From the Laboratoire de Chimie Physique, CNRS, Université Paris-Sud, Université Paris-Saclay, 91405, Orsay France
| | - Oliver Nüße
- From the Laboratoire de Chimie Physique, CNRS, Université Paris-Sud, Université Paris-Saclay, 91405, Orsay France,
| | - Marie Erard
- From the Laboratoire de Chimie Physique, CNRS, Université Paris-Sud, Université Paris-Saclay, 91405, Orsay France,
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29
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Mantovani G, Ramos D, Caamaño M, Lemasson A, Rejmund M, Audoin L, Álvarez Pol H, Frankland J, Fernández-Domínguez B, Galiana-Baldó E, Piot J, Gramegna F, Marchi T, Cicerchia M, Ackermann D, Biswas S, Clement E, Durand D, Farget F, Fregeau M, Galaviz D, Heinz A, Henriques A, Jacquot B, Jurado B, Kim Y, Morfouace P, Ralet D, Roger T, Schmitt C, Teubig P, Tsekhanovich I. Study of High-Energy Fission in Inverse Kinematics. EPJ Web Conf 2019. [DOI: 10.1051/epjconf/201922301037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Fission at low excitation energy, is a process in which both macroscopic and microscopic aspects are involved. Some features in the total kinetic energy and in the N/Z distributions of the fragments, commonly associated with shell effects, came out in a series of recent experiments with high excitation energy fusionfission reactions in inverse kinematics. In the latest experiment of this campaign, a study of high-energy fission and quasi-fission between a 238U beam and a series of light targets was carried out by using the aforementioned technique, in order to probe the role of the shell structure in these processes.
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30
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Voegele A, O'Brien DP, Subrini O, Sapay N, Cannella SE, Enguéné VYN, Hessel A, Karst J, Hourdel V, Perez ACS, Davi M, Veneziano R, Chopineau J, Vachette P, Durand D, Brier S, Ladant D, Chenal A. Translocation and calmodulin-activation of the adenylate cyclase toxin (CyaA) of Bordetella pertussis. Pathog Dis 2018; 76:5188676. [PMID: 30452651 DOI: 10.1093/femspd/fty085] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 11/16/2018] [Indexed: 01/19/2023] Open
Abstract
The adenylate cyclase toxin (CyaA) is a multi-domain protein secreted by Bordetella pertussis, the causative agent of whooping cough. CyaA is involved in the early stages of respiratory tract colonization by Bordetella pertussis. CyaA is produced and acylated in the bacteria, and secreted via a dedicated secretion system. The cell intoxication process involves a unique mechanism of transport of the CyaA toxin catalytic domain (ACD) across the plasma membrane of eukaryotic cells. Once translocated, ACD binds to and is activated by calmodulin and produces high amounts of cAMP, subverting the physiology of eukaryotic cells. Here, we review our work on the identification and characterization of a critical region of CyaA, the translocation region, required to deliver ACD into the cytosol of target cells. The translocation region contains a segment that exhibits membrane-active properties, i.e. is able to fold upon membrane interaction and permeabilize lipid bilayers. We proposed that this region is required to locally destabilize the membrane, decreasing the energy required for ACD translocation. To further study the translocation process, we developed a tethered bilayer lipid membrane (tBLM) design that recapitulate the ACD transport across a membrane separating two hermetic compartments. We showed that ACD translocation is critically dependent on calcium, membrane potential, CyaA acylation and on the presence of calmodulin in the trans compartment. Finally, we describe how calmodulin-binding triggers key conformational changes in ACD, leading to its activation and production of supraphysiological concentrations of cAMP.
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Affiliation(s)
- Alexis Voegele
- Département de Biologie Structurale et Chimie, Institut Pasteur, CNRS UMR 3528, 28 Rue du Dr Roux, 75724 Paris, CEDEX 15, France.,Université Paris Diderot Paris VII, 75013 Paris, France
| | - Darragh P O'Brien
- Département de Biologie Structurale et Chimie, Institut Pasteur, CNRS UMR 3528, 28 Rue du Dr Roux, 75724 Paris, CEDEX 15, France.,University of Oxford, United Kingdom
| | - Orso Subrini
- Département de Biologie Structurale et Chimie, Institut Pasteur, CNRS UMR 3528, 28 Rue du Dr Roux, 75724 Paris, CEDEX 15, France
| | - Nicolas Sapay
- Bioaster Technology Research Institute, 69007 Lyon, France
| | - Sara E Cannella
- Département de Biologie Structurale et Chimie, Institut Pasteur, CNRS UMR 3528, 28 Rue du Dr Roux, 75724 Paris, CEDEX 15, France.,University of Oxford, United Kingdom
| | - Véronique Yvette Ntsogo Enguéné
- Département de Biologie Structurale et Chimie, Institut Pasteur, CNRS UMR 3528, 28 Rue du Dr Roux, 75724 Paris, CEDEX 15, France
| | - Audrey Hessel
- Département de Biologie Structurale et Chimie, Institut Pasteur, CNRS UMR 3528, 28 Rue du Dr Roux, 75724 Paris, CEDEX 15, France
| | - Johanna Karst
- Département de Biologie Structurale et Chimie, Institut Pasteur, CNRS UMR 3528, 28 Rue du Dr Roux, 75724 Paris, CEDEX 15, France
| | - Véronique Hourdel
- Département de Biologie Structurale et Chimie, Institut Pasteur, CNRS UMR 3528, 28 Rue du Dr Roux, 75724 Paris, CEDEX 15, France
| | - Ana Cristina Sotomayor Perez
- Département de Biologie Structurale et Chimie, Institut Pasteur, CNRS UMR 3528, 28 Rue du Dr Roux, 75724 Paris, CEDEX 15, France
| | - Marilyne Davi
- Département de Biologie Structurale et Chimie, Institut Pasteur, CNRS UMR 3528, 28 Rue du Dr Roux, 75724 Paris, CEDEX 15, France
| | - Rémi Veneziano
- ICGM, UMR 5253 Univ Montpellier, CNRS, ENSCM, Montpellier 34095, France.,Department of Bioengineering, Volgenau School of Engineering, George Mason University, Fairfax, VA 22030-4422, USA
| | - Joel Chopineau
- ICGM, UMR 5253 Univ Montpellier, CNRS, ENSCM, Montpellier 34095, France
| | - Patrice Vachette
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex 91198, France
| | - Dominique Durand
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex 91198, France
| | - Sébastien Brier
- Département de Biologie Structurale et Chimie, Institut Pasteur, CNRS UMR 3528, 28 Rue du Dr Roux, 75724 Paris, CEDEX 15, France
| | - Daniel Ladant
- Département de Biologie Structurale et Chimie, Institut Pasteur, CNRS UMR 3528, 28 Rue du Dr Roux, 75724 Paris, CEDEX 15, France
| | - Alexandre Chenal
- Département de Biologie Structurale et Chimie, Institut Pasteur, CNRS UMR 3528, 28 Rue du Dr Roux, 75724 Paris, CEDEX 15, France
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31
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Hardouin P, Velours C, Bou-Nader C, Assrir N, Laalami S, Putzer H, Durand D, Golinelli-Pimpaneau B. Dissociation of the Dimer of the Intrinsically Disordered Domain of RNase Y upon Antibody Binding. Biophys J 2018; 115:2102-2113. [PMID: 30447990 DOI: 10.1016/j.bpj.2018.10.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 09/17/2018] [Accepted: 10/17/2018] [Indexed: 12/12/2022] Open
Abstract
Although RNase Y acts as the key enzyme initiating messenger RNA decay in Bacillus subtilis and likely in many other Gram-positive bacteria, its three-dimensional structure remains unknown. An antibody belonging to the rare immunoglobulin G (IgG) 2b λx isotype was raised against a 12-residue conserved peptide from the N-terminal noncatalytic domain of B. subtilis RNase Y (BsRNaseY) that is predicted to be intrinsically disordered. Here, we show that this domain can be produced as a stand-alone protein called Nter-BsRNaseY that undergoes conformational changes between monomeric and dimeric forms. Circular dichroism and size exclusion chromatography coupled with multiangle light scattering or with small angle x-ray scattering indicate that the Nter-BsRNaseY dimer displays an elongated form and a high content of α-helices, in agreement with the existence of a central coiled-coil structure appended with flexible ends, and that the monomeric state of Nter-BsRNaseY is favored upon binding the fragment antigen binding (Fab) of the antibody. The dissociation constants of the IgG/BsRNaseY, IgG/Nter-BsRNaseY, and IgG/peptide complexes indicate that the affinity of the IgG for Nter-BsRNaseY is in the nM range and suggest that the peptide is less accessible in BsRNaseY than in Nter-BsRNaseY. The crystal structure of the Fab in complex with the peptide antigen shows that the peptide adopts an elongated U-shaped conformation in which the unique hydrophobic residue of the peptide, Leu6, is completely buried. The peptide/Fab complex may mimic the interaction of a microdomain of the N-terminal domain of BsRNaseY with one of its cellular partners within the degradosome complex. Altogether, our results suggest that BsRNaseY may become accessible for protein interaction upon dissociation of its N-terminal domain into the monomeric form.
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Affiliation(s)
- Pierre Hardouin
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Université Pierre et Marie Curie, Paris CEDEX 05, France
| | - Christophe Velours
- Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette CEDEX, France
| | - Charles Bou-Nader
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Université Pierre et Marie Curie, Paris CEDEX 05, France
| | - Nadine Assrir
- Structural Chemistry and Biology Team, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Soumaya Laalami
- CNRS UMR8261-Université Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
| | - Harald Putzer
- CNRS UMR8261-Université Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, Paris, France
| | - Dominique Durand
- Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette CEDEX, France
| | - Béatrice Golinelli-Pimpaneau
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Université Pierre et Marie Curie, Paris CEDEX 05, France.
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32
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Celma L, Cuniasse P, Durand D, Lisboa J, Sanchez D, Marsin S, Quevillon-Cheruel S, Radicella P. HpDprA domains involved in interaction with DNA. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s2053273318092124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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33
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O'Brien DP, Perez ACS, Karst J, Cannella SE, Enguéné VYN, Hessel A, Raoux-Barbot D, Voegele A, Subrini O, Davi M, Guijarro JI, Raynal B, Baron B, England P, Hernandez B, Ghomi M, Hourdel V, Malosse C, Chamot-Rooke J, Vachette P, Durand D, Brier S, Ladant D, Chenal A. Calcium-dependent disorder-to-order transitions are central to the secretion and folding of the CyaA toxin of Bordetella pertussis, the causative agent of whooping cough. Toxicon 2018; 149:37-44. [DOI: 10.1016/j.toxicon.2018.01.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 11/20/2017] [Accepted: 01/10/2018] [Indexed: 02/07/2023]
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34
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Missoury S, Plancqueel S, Li de la Sierra-Gallay I, Zhang W, Liger D, Durand D, Dammak R, Collinet B, van Tilbeurgh H. The structure of the TsaB/TsaD/TsaE complex reveals an unexpected mechanism for the bacterial t6A tRNA-modification. Nucleic Acids Res 2018; 46:5850-5860. [PMID: 29741707 PMCID: PMC6009658 DOI: 10.1093/nar/gky323] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/09/2018] [Accepted: 04/17/2018] [Indexed: 12/25/2022] Open
Abstract
The universal N6-threonylcarbamoyladenosine (t6A) modification at position A37 of ANN-decoding tRNAs is essential for translational fidelity. In bacteria the TsaC enzyme first synthesizes an l-threonylcarbamoyladenylate (TC-AMP) intermediate. In cooperation with TsaB and TsaE, TsaD then transfers the l-threonylcarbamoyl-moiety from TC-AMP onto tRNA. We determined the crystal structure of the TsaB-TsaE-TsaD (TsaBDE) complex of Thermotoga maritima in presence of a non-hydrolysable AMPCPP. TsaE is positioned at the entrance of the active site pocket of TsaD, contacting both the TsaB and TsaD subunits and prohibiting simultaneous tRNA binding. AMPCPP occupies the ATP binding site of TsaE and is sandwiched between TsaE and TsaD. Unexpectedly, the binding of TsaE partially denatures the active site of TsaD causing loss of its essential metal binding sites. TsaE interferes in a pre- or post-catalytic step and its binding to TsaBD is regulated by ATP hydrolysis. This novel binding mode and activation mechanism of TsaE offers good opportunities for antimicrobial drug development.
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Affiliation(s)
- Sophia Missoury
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Stéphane Plancqueel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Ines Li de la Sierra-Gallay
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Wenhua Zhang
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Dominique Liger
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Dominique Durand
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Raoudha Dammak
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Bruno Collinet
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR7590 CNRS/Sorbonne-Université, UPMC, Paris, France
| | - Herman van Tilbeurgh
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
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35
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Dorval G, Gribouval O, Martinez-Barquero V, Machuca E, Tête MJ, Baudouin V, Benoit S, Chabchoub I, Champion G, Chauveau D, Chehade H, Chouchane C, Cloarec S, Cochat P, Dahan K, Dantal J, Delmas Y, Deschênes G, Dolhem P, Durand D, Ekinci Z, El Karoui K, Fischbach M, Grunfeld JP, Guigonis V, Hachicha M, Hogan J, Hourmant M, Hummel A, Kamar N, Krummel T, Lacombe D, Llanas B, Mesnard L, Mohsin N, Niaudet P, Nivet H, Parvex P, Pietrement C, de Pontual L, Noble CP, Ribes D, Ronco P, Rondeau E, Sallee M, Tsimaratos M, Ulinski T, Salomon R, Antignac C, Boyer O. Clinical and genetic heterogeneity in familial steroid-sensitive nephrotic syndrome. Pediatr Nephrol 2018; 33:473-483. [PMID: 29058154 DOI: 10.1007/s00467-017-3819-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Revised: 09/05/2017] [Accepted: 09/07/2017] [Indexed: 10/18/2022]
Abstract
BACKGROUND Familial steroid-sensitive nephrotic syndrome (SSNS) is a rare condition. The disease pathophysiology remains elusive. However, bi-allelic mutations in the EMP2 gene were identified, and specific variations in HLA-DQA1 were linked to a high risk of developing the disease. METHODS Clinical data were analyzed in 59 SSNS families. EMP2 gene was sequenced in families with a potential autosomal recessive (AR) inheritance. Exome sequencing was performed in a subset of 13 families with potential AR inheritance. Two variations in HLA-DQA1 were genotyped in the whole cohort. RESULTS Transmission was compatible with an AR (n = 33) or autosomal dominant (AD, n = 26) inheritance, assuming that familial SSNS is a monogenic trait. Clinical features did not differ between AR and AD groups. All patients, including primary (n = 7) and secondary steroid resistant nephrotic syndrone (SRNS), (n = 13) were sensitive to additional immunosuppressive therapy. Both HLA-DQA1 variations were found to be highly linked to the disease (OR = 4.34 and OR = 4.89; p < 0.001). Exome sequencing did not reveal any pathogenic mutation, neither did EMP2 sequencing. CONCLUSIONS Taken together, these results highlight the clinical and genetic heterogeneity in familial SSNS. Clinical findings sustain an immune origin in all patients, whatever the initial steroid-sensitivity. The absence of a variant shared by two families and the HLA-DQA1 variation enrichments suggest a complex mode of inheritance.
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Affiliation(s)
- Guillaume Dorval
- INSERM UMR1163, Laboratory of Hereditary Kidney Diseases, Imagine Institute, 24 Boulevard du Montparnasse, 75015, Paris, France. .,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France.
| | - Olivier Gribouval
- INSERM UMR1163, Laboratory of Hereditary Kidney Diseases, Imagine Institute, 24 Boulevard du Montparnasse, 75015, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Vanesa Martinez-Barquero
- INSERM UMR1163, Laboratory of Hereditary Kidney Diseases, Imagine Institute, 24 Boulevard du Montparnasse, 75015, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Eduardo Machuca
- INSERM UMR1163, Laboratory of Hereditary Kidney Diseases, Imagine Institute, 24 Boulevard du Montparnasse, 75015, Paris, France
| | - Marie-Josèphe Tête
- INSERM UMR1163, Laboratory of Hereditary Kidney Diseases, Imagine Institute, 24 Boulevard du Montparnasse, 75015, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Véronique Baudouin
- Department of Pediatric Nephrology, Assistance Publique-Hôpitaux de Paris, Robert Debré Hospital, Paris, France
| | - Stéphane Benoit
- Department of Nephrology, University Hospital of Tours, Tours, France
| | - Imen Chabchoub
- Department of Pediatrics, Sfax University, Sfax, Tunisia
| | - Gérard Champion
- Department of Pediatrics, University Hospital of Angers, Angers, France
| | - Dominique Chauveau
- Department of Nephrology and Organ Transplantation, University Hospital Rangueil, Toulouse, France
| | - Hassib Chehade
- Department of Pediatrics, Division of Pediatric Nephrology, Lausanne University Hospital, Lausanne, Switzerland
| | - Chokri Chouchane
- Department of Pediatrics, Monastir University, Monastir, Tunisia
| | - Sylvie Cloarec
- Department of Nephrology, University Hospital of Tours, Tours, France
| | - Pierre Cochat
- Department of Pediatric Nephrology, Claude-Bernard Lyon 1 University, Bron, France
| | - Karin Dahan
- Department of Human Genetics, Institute of Pathology and Genetics, Gosselies, Belgium
| | - Jacques Dantal
- Nephrology and Immunology Department, University Hospital of Nantes, Nantes, France
| | - Yahsou Delmas
- Department of Nephrology, University Hospital of Bordeaux, Bordeaux, France
| | - Georges Deschênes
- Department of Pediatric Nephrology, Assistance Publique-Hôpitaux de Paris, Robert Debré Hospital, Paris, France
| | - Phillippe Dolhem
- Department of Pediatrics, Saint-Quentin Hospital, Saint-Quentin, France
| | - Dominique Durand
- Department of Nephrology and Organ Transplantation, University Hospital Rangueil, Toulouse, France
| | | | - Khalil El Karoui
- Department of Nephrology, Assistance Publique-Hôpitaux de Paris, Necker-Enfants Malades Hospital, Paris, France
| | - Michel Fischbach
- Nephrology Dialysis Transplantation Children's Unit, University Hospital Hautepierre, Strasbourg, France
| | - Jean-Pierre Grunfeld
- Department of Nephrology, Assistance Publique-Hôpitaux de Paris, Necker-Enfants Malades Hospital, Paris, France
| | - Vincent Guigonis
- Department of Pediatrics, University Hospital of Limoges, Limoges, France
| | | | - Julien Hogan
- Department of Pediatric Nephrology, Assistance Publique-Hôpitaux de Paris, Armand Trousseau Hospital, Paris, France
| | - Maryvonne Hourmant
- Nephrology and Immunology Department, University Hospital of Nantes, Nantes, France
| | - Aurélie Hummel
- Department of Nephrology, Assistance Publique-Hôpitaux de Paris, Necker-Enfants Malades Hospital, Paris, France
| | - Nassim Kamar
- Department of Nephrology and Organ Transplantation, University Hospital Rangueil, Toulouse, France
| | - Thierry Krummel
- Department of Nephrology, University Hospital Hautepierre, Strasbourg, France
| | - Didier Lacombe
- Department of Genetics, University Hospital of Bordeaux, Bordeaux, France
| | - Brigitte Llanas
- Department of Pediatrics, University Hospital of Bordeaux, Bordeaux, France
| | - Laurent Mesnard
- Department of Nephrology and Dialysis, Assistance Publique-Hôpitaux de Paris, Tenon Hospital, Paris, France.,Sorbonne University, UPMC University Paris 06, Paris, France.,INSERM, UMR_S 1155, 75020, Paris, France
| | - Nabil Mohsin
- College of Medicine, Sultan Qaboos University, Muscat, Oman
| | - Patrick Niaudet
- Department of Pediatric Nephrology, Centre de référence du syndrome néphrotique idiopathique de l'enfant et l'adulte, Assistance Publique-Hôpitaux de Paris, Necker-Enfants Malades Hospital, Paris, France.,Centre de Référence Syndrome Néphrotique Idiopathique de l'enfant et de l'adulte, Paris, France
| | - Hubert Nivet
- Department of Nephrology, University Hospital of Tours, Tours, France
| | - Paloma Parvex
- Department of Pediatrics, Division of Pediatric Nephrology, Geneva University Hospital, Geneva, Switzerland
| | - Christine Pietrement
- Departement of Pediatrics, Nephrology Unit, University Hospital of Reims, Reims, France.,Faculty of Medicine, Laboratory of Biochemistry and Molecular Biology, UMR, CNRS/URCA n°7369, University of Champagne-Ardenne, Reims, France
| | - Loic de Pontual
- Department of Pediatrics, Assistance Publique-Hôpitaux de Paris, Jean Verdier Hospital, Bondy, France
| | - Claire Pouteil Noble
- Department of Nephrology and Transplantation, University Hospital of Lyon, Lyon, France
| | - David Ribes
- Department of Nephrology and Organ Transplantation, University Hospital Rangueil, Toulouse, France
| | - Pierre Ronco
- Department of Nephrology and Dialysis, Assistance Publique-Hôpitaux de Paris, Tenon Hospital, Paris, France.,Sorbonne University, UPMC University Paris 06, Paris, France.,INSERM, UMR_S 1155, 75020, Paris, France
| | - Eric Rondeau
- Department of Nephrology and Dialysis, Assistance Publique-Hôpitaux de Paris, Tenon Hospital, Paris, France
| | - Marion Sallee
- Department of Nephrology and Kidney Transplantation, The Conception Hospital, Marseille, France
| | - Michel Tsimaratos
- Department of Multidisciplinary Pediatrics Timone, Assistance Publique Hôpitaux de Marseille, Aix-Marseille University, Marseille, France
| | - Tim Ulinski
- Department of Pediatric Nephrology, Assistance Publique-Hôpitaux de Paris, Armand Trousseau Hospital, Paris, France
| | - Rémi Salomon
- INSERM UMR1163, Laboratory of Hereditary Kidney Diseases, Imagine Institute, 24 Boulevard du Montparnasse, 75015, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France.,Department of Pediatric Nephrology, Centre de référence du syndrome néphrotique idiopathique de l'enfant et l'adulte, Assistance Publique-Hôpitaux de Paris, Necker-Enfants Malades Hospital, Paris, France.,Centre de Référence Syndrome Néphrotique Idiopathique de l'enfant et de l'adulte, Paris, France
| | - Corinne Antignac
- INSERM UMR1163, Laboratory of Hereditary Kidney Diseases, Imagine Institute, 24 Boulevard du Montparnasse, 75015, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France.,Centre de Référence Syndrome Néphrotique Idiopathique de l'enfant et de l'adulte, Paris, France.,Department of Genetics, Assistance Publique-Hôpitaux de Paris, Necker-Enfants malades Hospital, Paris, France
| | - Olivia Boyer
- INSERM UMR1163, Laboratory of Hereditary Kidney Diseases, Imagine Institute, 24 Boulevard du Montparnasse, 75015, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France.,Department of Pediatric Nephrology, Centre de référence du syndrome néphrotique idiopathique de l'enfant et l'adulte, Assistance Publique-Hôpitaux de Paris, Necker-Enfants Malades Hospital, Paris, France.,Centre de Référence Syndrome Néphrotique Idiopathique de l'enfant et de l'adulte, Paris, France
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Johansen PO, Isaksen TE, Bye-Ingebrigtsen E, Haave M, Dahlgren TG, Kvalø SE, Greenacre M, Durand D, Rapp HT. Temporal changes in benthic macrofauna on the west coast of Norway resulting from human activities. Mar Pollut Bull 2018; 128:483-495. [PMID: 29571400 DOI: 10.1016/j.marpolbul.2018.01.063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 12/09/2017] [Accepted: 01/29/2018] [Indexed: 06/08/2023]
Abstract
Quantitative analyses of soft bottom invertebrate fauna from four Norwegian sill fjords show increased macrofaunal abundance, species richness, and a considerably changed benthic deep water macrofaunal composition in the inner parts of the fjord system. In retrospect, the analyses show significantly altered benthic macrofaunal community structure that was not reflected by the changes in the Shannon-Wiener diversity indices during regular monitoring. The observed changes are mainly due to an increased abundance of opportunistic species, especially of the polychaete Polydora sp. during the last 10-15 years which is correlated significantly to declining dissolved oxygen, rising temperature in the bottom water and increasing total organic matter in the sediment. Possible anthropogenic and climatic impact factors related to the observed macrofaunal changes and environmental consequences of the changes are discussed.
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Affiliation(s)
| | | | | | - Marte Haave
- Uni Research Environment, SAM-Marine, 5006 Bergen, Norway
| | - Thomas G Dahlgren
- Uni Research Environment, SAM-Marine, 5006 Bergen, Norway; Department of Marine Sciences, University of Gothenburg, 40530 Gothenburg, Sweden
| | | | | | | | - Hans Tore Rapp
- Uni Research Environment, SAM-Marine, 5006 Bergen, Norway; Department of Biology, KG Jebsen Centre for Deep Sea Research, University of Bergen, 5006 Bergen, Norway
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O'Brien DP, Durand D, Cannella S, Voegele A, Vachette P, Chamot Rooke J, Brier S, Ladant D, Chenal A. Structural Disorder in Action in a Bacterial Toxin: Secretion, Folding and Host Cell Hijacking. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.2374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Krivosic V, Philippakis E, Couturier A, Dupas B, Erginay A, Desmettre T, Streho M, Bonnin S, Mane V, Jouvaud S, Gualino V, Durand D, Tadayoni R. Erratum de l’article : « Un “circuit court” pour améliorer la prise en charge des patients atteints de dégénérescence maculaire liée à l’âge néovasculaire ». J Fr Ophtalmol 2018; 41:200. [DOI: 10.1016/j.jfo.2017.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 11/29/2017] [Indexed: 11/28/2022]
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Abstract
Summary
Objectives
: The field of neural engineering focuses on an area of research at the interface between neuroscience and engineering. The area of neural engineering was first associated with the brain machine interface but is much broader and encompasses experimental, computational, and theoretical aspects of neural interfacing, neuroelectronics, neuromechanical systems, neuroinformatics, neuroimaging, neural prostheses, artificial and biological neural circuits, neural control, neural tissue regeneration, neural signal processing, neural modelling and neuro-computation. One of the goals of neural engineering is to develop a selective interface for the peripheral nervous system.
Methods
: Nerve cuffs electrodes have been developed to either reshape or maintain the nerve into an elongated shape in order to increase the circumference to cross sectional ratio. It is then possible to place many electrodes around the nerve to achieve selectivity. This new cuff (flat interface nerve electrode: FINE) was applied to the hypoglossal nerve and the sciatic nerve in dogs and cats to estimate the selectivity of the interface.
Results
: By placing many contacts close to the axons, three different types of selectivity were achieved: 1) The FINE could generate a high degree of stimulation selectivity as estimated by the individual fascicle recording. 2) Similarly, recording selectivity was also demonstrated and blind source algorithms were applied to recover the signals. 3) Finally, by placing arrays of electrodes along the nerve, small fiber diameters could be excited before large fibers thereby reversing the recruitment order.
Conclusion
: Taking advantage of the fact that nerves are not round but oblong or flat allows a novel design for selective nerve interface with the peripheral nervous system. This new design has found applications in many disorders of the nervous system such as bladder incontinence, obstructive sleep apnea and stroke.
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Frotin M, Gros P, Attié D, Bernard D, Dauvois V, Delbart A, Durand D, Geerebaert Y, Legand S, Magnier P, Poilleux P, Semeniouk I. Sealed operation, and circulation and purification of gas in the HARPO TPC. EPJ Web Conf 2018. [DOI: 10.1051/epjconf/201817405002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
HARPO is a time projection chamber (TPC) demonstrator of a gamma-ray telescope and polarimeter in the MeV-GeV range, for a future space mission. We present the evolution of the TPC performance over a five month sealed-mode operation, by the analysis of cosmic-ray data, followed by the fast and complete recovery of the initial gas properties using a lightweight gas circulation and purification system.
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Hamdi H, Majdoub-Mathlouthi L, Durand D, Thomas A, Kraiem K. Effects of olive-cake supplementation on fatty acid composition, antioxidant status and lipid and meat-colour stability of Barbarine lambs reared on improved rangeland plus concentrates or indoors with oat hay plus concentrates. Anim Prod Sci 2018. [DOI: 10.1071/an16352] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The effects of feeding system (indoor vs rangeland) and olive-cake (OC) supplementation (control vs supplemented) on fatty acid (FA) composition, lipid oxidation status and meat-colour stability were studied. Lambs were fed indoor with hay (OH) or reared on improved rangeland (RL). All lambs received concentrate at a rate of 400 g/head.day. Twenty-four 6-month-old Barbarine lambs with an average weight of 24.3 ± 1.1 kg were assigned into the following four groups: OH without OC, OH with OC, RL without OC and RL with OC. Supplemented groups received 280 g/day of OC. Lambs were reared for ~3 months and then slaughtered at 33 kg. Feeding lambs on rangeland increased proportions of polyunsaturated fatty acids (PUFA, P < 0.05), n-3 PUFA (P < 0.01) and long-chain n-3 PUFA (P < 0.01) and decreased those of C16:0 and monounsaturated fatty acids (P = 0.052). Higher PUFA : saturated FA (SFA) (P < 0.001) and lower n-6 : n-3 PUFA (P < 0.01) ratios were found for RL lambs. The peroxidisability index was higher (P = 0.024) for RL lambs. Whereas, a lower malondialdehyde concentration (P < 0.001) was found for meat of RL group after 5-day storage, because of a higher vitamin E concentration (P < 0.001) and catalase activity (P = 0.002). Moreover, colour was more stable for meat of RL lamb. OC supplementation reduced only superoxide dismutase activity (P = 0.033) and did not have any effect on lipid peroxidation and colour stability. No interactions were noted between the feeding system and olive-cake supplementation. Meat lambs produced on rangeland had a healthier fatty acid composition. Lipids were more stable to oxidation than was meat produced indoor with hay and concentrate.
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O’Brien DP, Durand D, Voegele A, Hourdel V, Davi M, Chamot-Rooke J, Vachette P, Brier S, Ladant D, Chenal A. Calmodulin fishing with a structurally disordered bait triggers CyaA catalysis. PLoS Biol 2017; 15:e2004486. [PMID: 29287065 PMCID: PMC5764468 DOI: 10.1371/journal.pbio.2004486] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 01/11/2018] [Accepted: 12/07/2017] [Indexed: 11/18/2022] Open
Abstract
Once translocated into the cytosol of target cells, the catalytic domain (AC) of the adenylate cyclase toxin (CyaA), a major virulence factor of Bordetella pertussis, is potently activated by binding calmodulin (CaM) to produce supraphysiological levels of cAMP, inducing cell death. Using a combination of small-angle X-ray scattering (SAXS), hydrogen/deuterium exchange mass spectrometry (HDX-MS), and synchrotron radiation circular dichroism (SR-CD), we show that, in the absence of CaM, AC exhibits significant structural disorder, and a 75-residue-long stretch within AC undergoes a disorder-to-order transition upon CaM binding. Beyond this local folding, CaM binding induces long-range allosteric effects that stabilize the distant catalytic site, whilst preserving catalytic loop flexibility. We propose that the high enzymatic activity of AC is due to a tight balance between the CaM-induced decrease of structural flexibility around the catalytic site and the preservation of catalytic loop flexibility, allowing for fast substrate binding and product release. The CaM-induced dampening of AC conformational disorder is likely relevant to other CaM-activated enzymes. Calmodulin is a widespread and highly conserved protein that interacts with a wide variety of eukaryotic proteins and enzymes, controlling their activities in response to calcium. The adenylate cyclase toxin (CyaA) of Bordetella pertussis, the causative agent of whooping cough, is one such calmodulin target. Once transported across the plasma membrane of eukaryotic cells, the catalytic domain (AC) of CyaA is activated by calmodulin, producing high levels of cAMP, which can induce cell death. We use an integrative structural biology approach combining several biophysical techniques to characterize the structural rearrangements in AC upon calmodulin binding and to elucidate their relationship to CyaA activation. We show that a disordered stretch of 75 amino acid residues in AC serves as a bait for calmodulin capture. Binding induces significant folding within this region, a prerequisite for CyaA activation. Calmodulin binding promotes the stabilization of the distant catalytic site, whilst maintaining its catalytic loop in a flexible and exposed state. Both phenomena contribute to the high enzymatic activity of AC, allowing for fast substrate binding and cAMP release. The calmodulin-induced reduction of AC conformational disorder is likely relevant to other calmodulin-activated enzymes.
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Affiliation(s)
- Darragh P. O’Brien
- Institut Pasteur, UMR CNRS 3528, Chemistry and Structural Biology Department, Paris, France
| | - Dominique Durand
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
- * E-mail: (A.C.); (D.L.); (D.D.); (S.B.)
| | - Alexis Voegele
- Institut Pasteur, UMR CNRS 3528, Chemistry and Structural Biology Department, Paris, France
| | - Véronique Hourdel
- Institut Pasteur, USR CNRS 2000, Chemistry and Structural Biology Department, CITECH, Paris, France
| | - Marilyne Davi
- Institut Pasteur, UMR CNRS 3528, Chemistry and Structural Biology Department, Paris, France
| | - Julia Chamot-Rooke
- Institut Pasteur, USR CNRS 2000, Chemistry and Structural Biology Department, CITECH, Paris, France
| | - Patrice Vachette
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| | - Sébastien Brier
- Institut Pasteur, USR CNRS 2000, Chemistry and Structural Biology Department, CITECH, Paris, France
- * E-mail: (A.C.); (D.L.); (D.D.); (S.B.)
| | - Daniel Ladant
- Institut Pasteur, UMR CNRS 3528, Chemistry and Structural Biology Department, Paris, France
- * E-mail: (A.C.); (D.L.); (D.D.); (S.B.)
| | - Alexandre Chenal
- Institut Pasteur, UMR CNRS 3528, Chemistry and Structural Biology Department, Paris, France
- * E-mail: (A.C.); (D.L.); (D.D.); (S.B.)
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Ma M, Li de la Sierra-Gallay I, Lazar N, Pellegrini O, Durand D, Marchfelder A, Condon C, van Tilbeurgh H. The crystal structure of Trz1, the long form RNase Z from yeast. Nucleic Acids Res 2017; 45:6209-6216. [PMID: 28379452 PMCID: PMC5449637 DOI: 10.1093/nar/gkx216] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 04/03/2017] [Indexed: 01/25/2023] Open
Abstract
tRNAs are synthesized as precursor RNAs that have to undergo processing steps to become functional. Yeast Trz1 is a key endoribonuclease involved in the 3΄ maturation of tRNAs in all domains of life. It is a member of the β-lactamase family of RNases, characterized by an HxHxDH sequence motif involved in coordination of catalytic Zn-ions. The RNase Z family consists of two subfamilies: the short (250-400 residues) and the long forms (about double in size). Short form RNase Z enzymes act as homodimers: one subunit embraces tRNA with a protruding arm, while the other provides the catalytic site. The long form is thought to contain two fused β-lactamase domains within a single polypeptide. Only structures of short form RNase Z enzymes are known. Here we present the 3.1 Å crystal structure of the long-form Trz1 from Saccharomyces cerevisiae. Trz1 is organized into two β-lactamase domains connected by a long linker. The N-terminal domain has lost its catalytic residues, but retains the long flexible arm that is important for tRNA binding, while it is the other way around in the C-terminal domain. Trz1 likely evolved from a duplication and fusion of the gene encoding the monomeric short form RNase Z.
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Affiliation(s)
- Miao Ma
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, University of Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Ines Li de la Sierra-Gallay
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, University of Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Noureddine Lazar
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, University of Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | - Olivier Pellegrini
- UMR8261 (CNRS-University of Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Dominique Durand
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, University of Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
| | | | - Ciarán Condon
- UMR8261 (CNRS-University of Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Herman van Tilbeurgh
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS UMR 9198, University of Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette Cedex, France
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O'Brien DP, Brier S, Ladant D, Durand D, Chenal A, Vachette P. SEC-SAXS and HDX-MS: A powerful combination. The case of the calcium-binding domain of a bacterial toxin. Biotechnol Appl Biochem 2017; 65:62-68. [DOI: 10.1002/bab.1577] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/18/2017] [Accepted: 07/26/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Darragh P. O'Brien
- Institut Pasteur; UMR CNRS 3528; Chemistry and Structural Biology Department; Paris France
| | - Sébastien Brier
- Institut Pasteur; USR CNRS 2000; CITECH; Chemistry and Structural Biology Department; Paris France
| | - Daniel Ladant
- Institut Pasteur; UMR CNRS 3528; Chemistry and Structural Biology Department; Paris France
| | - Dominique Durand
- Institut de Biologie Intégrative de la Cellule, UMR 9198; Université Paris-Sud; Orsay France
| | - Alexandre Chenal
- Institut Pasteur; UMR CNRS 3528; Chemistry and Structural Biology Department; Paris France
| | - Patrice Vachette
- Institut de Biologie Intégrative de la Cellule, UMR 9198; Université Paris-Sud; Orsay France
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Trewhella J, Duff AP, Durand D, Gabel F, Guss JM, Hendrickson WA, Hura GL, Jacques DA, Kirby NM, Kwan AH, Pérez J, Pollack L, Ryan TM, Sali A, Schneidman-Duhovny D, Schwede T, Svergun DI, Sugiyama M, Tainer JA, Vachette P, Westbrook J, Whitten AE. 2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update. Acta Crystallogr D Struct Biol 2017; 73:710-728. [PMID: 28876235 PMCID: PMC5586245 DOI: 10.1107/s2059798317011597] [Citation(s) in RCA: 179] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 08/07/2017] [Indexed: 12/02/2022] Open
Abstract
In 2012, preliminary guidelines were published addressing sample quality, data acquisition and reduction, presentation of scattering data and validation, and modelling for biomolecular small-angle scattering (SAS) experiments. Biomolecular SAS has since continued to grow and authors have increasingly adopted the preliminary guidelines. In parallel, integrative/hybrid determination of biomolecular structures is a rapidly growing field that is expanding the scope of structural biology. For SAS to contribute maximally to this field, it is essential to ensure open access to the information required for evaluation of the quality of SAS samples and data, as well as the validity of SAS-based structural models. To this end, the preliminary guidelines for data presentation in a publication are reviewed and updated, and the deposition of data and associated models in a public archive is recommended. These guidelines and recommendations have been prepared in consultation with the members of the International Union of Crystallography (IUCr) Small-Angle Scattering and Journals Commissions, the Worldwide Protein Data Bank (wwPDB) Small-Angle Scattering Validation Task Force and additional experts in the field.
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Affiliation(s)
- Jill Trewhella
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Anthony P. Duff
- ANSTO, New Illawarra Road, Lucas Heights, NSW 2234, Australia
| | - Dominique Durand
- Institut de Biologie Intégrative de la Cellule, UMR 9198, Bâtiment 430, Université Paris-Sud, 91405 Orsay CEDEX, France
| | - Frank Gabel
- Université Grenoble Alpes, Commissariat à l’Energie Atomique (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale (IBS), and Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - J. Mitchell Guss
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Wayne A. Hendrickson
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Greg L. Hura
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - David A. Jacques
- University of Technology Sydney, ithree Institute, 15 Broadway, Ultimo, NSW 2007, Australia
| | - Nigel M. Kirby
- Australian Synchrotron, 800 Blackburn Road, Clayton, VIC 3168, Australia
| | - Ann H. Kwan
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Javier Pérez
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin BP48, 91192 Gif-sur-Yvette CEDEX, France
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853-2501, USA
| | - Timothy M. Ryan
- Australian Synchrotron, 800 Blackburn Road, Clayton, VIC 3168, Australia
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California San Francisco, San Francisco, California, USA
| | - Dina Schneidman-Duhovny
- School of Computer Science and Engineering, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Torsten Schwede
- Biozentrum, University of Basel and SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory (EMBL) Hamburg, c/o DESY, Nokestrasse 85, 22607 Hamburg, Germany
| | - Masaaki Sugiyama
- Research Reactor Institute, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan
| | - John A. Tainer
- Basic Science Research Division, Molecular and Cellular Oncology, MD Anderson Cancer Center, University of Texas, Houston, Texas, USA
| | - Patrice Vachette
- Institut de Biologie Intégrative de la Cellule, UMR 9198, Bâtiment 430, Université Paris-Sud, 91405 Orsay CEDEX, France
| | - John Westbrook
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, NJ 07102, USA
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Krivosic V, Philippakis E, Couturier A, Dupas B, Erginay A, Desmettre T, Streho M, Bonnin S, Mane V, Jouvaud S, Gualino V, Durand D, Tadayoni R. [A "fast track" to improve management of neovascular age related macular degeneration]. J Fr Ophtalmol 2017; 40:642-647. [PMID: 28865938 DOI: 10.1016/j.jfo.2017.03.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 02/20/2017] [Accepted: 03/06/2017] [Indexed: 11/17/2022]
Abstract
OBJECTIVE To evaluate the role of a fast track for management of patients with neovascular age- related macular degeneration (nARMD) treated by intravitreal injection of anti-VEGF. PATIENTS The records of 100 patients in the chronic maintenance phase of intravitreal anti-VEGF followed in the fast track and 63 patients followed in the standard protocol for at least 12 months were retrospectively analyzed. METHOD Patients in the fast track underwent visual acuity (VA) testing by ETDRS, optical coherence tomography (OCT) and a physician assessment. The injection was performed the same day whenever possible. The primary endpoint to evaluate patient adherence was the time between the ideal date of visit or injection prescribed by the physician and the actual date of administration. RESULTS The mean time between the ideal date of visit or injection prescribed by the physician and the actual date of administration was 4.1±7.5 days for the patients followed in the fast track and 5.6±18.7 days for the patients followed in the standard protocol. Mean VA remained stable for the patients followed in the fast track: 20/50 (20/800 to 20/20) at baseline vs. 20/50 (20/800 to 20/16) at the conclusion of follow-up. It dropped from 40/50 at baseline to 20/63 at the conclusion of follow-up for the patients followed in the standard protocol. CONCLUSION In the context of a fast track, it was possible to improve the adherence of nARMD patients and maintain their VA gain or stabilization achieved after the induction phase.
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Affiliation(s)
- V Krivosic
- Service d'ophtalmologie, hôpital Lariboisière, université Paris-Diderot, Sorbonne-Paris-Cité, AP - HP, 2, rue, Ambroise-Paré, 75010 Paris, France; Centre ophtalmologique de l'Odéon, 113, boulevard Saint-Germain, 75006 Paris, France.
| | - E Philippakis
- Service d'ophtalmologie, hôpital Lariboisière, université Paris-Diderot, Sorbonne-Paris-Cité, AP - HP, 2, rue, Ambroise-Paré, 75010 Paris, France
| | - A Couturier
- Service d'ophtalmologie, hôpital Lariboisière, université Paris-Diderot, Sorbonne-Paris-Cité, AP - HP, 2, rue, Ambroise-Paré, 75010 Paris, France
| | - B Dupas
- Service d'ophtalmologie, hôpital Lariboisière, université Paris-Diderot, Sorbonne-Paris-Cité, AP - HP, 2, rue, Ambroise-Paré, 75010 Paris, France
| | - A Erginay
- Service d'ophtalmologie, hôpital Lariboisière, université Paris-Diderot, Sorbonne-Paris-Cité, AP - HP, 2, rue, Ambroise-Paré, 75010 Paris, France
| | - T Desmettre
- Service d'ophtalmologie, hôpital Lariboisière, université Paris-Diderot, Sorbonne-Paris-Cité, AP - HP, 2, rue, Ambroise-Paré, 75010 Paris, France
| | - M Streho
- Service d'ophtalmologie, hôpital Lariboisière, université Paris-Diderot, Sorbonne-Paris-Cité, AP - HP, 2, rue, Ambroise-Paré, 75010 Paris, France
| | - S Bonnin
- Service d'ophtalmologie, hôpital Lariboisière, université Paris-Diderot, Sorbonne-Paris-Cité, AP - HP, 2, rue, Ambroise-Paré, 75010 Paris, France
| | - V Mane
- Service d'ophtalmologie, hôpital Lariboisière, université Paris-Diderot, Sorbonne-Paris-Cité, AP - HP, 2, rue, Ambroise-Paré, 75010 Paris, France
| | - S Jouvaud
- Service d'ophtalmologie, hôpital Lariboisière, université Paris-Diderot, Sorbonne-Paris-Cité, AP - HP, 2, rue, Ambroise-Paré, 75010 Paris, France
| | - V Gualino
- Service d'ophtalmologie, hôpital Lariboisière, université Paris-Diderot, Sorbonne-Paris-Cité, AP - HP, 2, rue, Ambroise-Paré, 75010 Paris, France
| | - D Durand
- Service d'ophtalmologie, hôpital Lariboisière, université Paris-Diderot, Sorbonne-Paris-Cité, AP - HP, 2, rue, Ambroise-Paré, 75010 Paris, France
| | - R Tadayoni
- Service d'ophtalmologie, hôpital Lariboisière, université Paris-Diderot, Sorbonne-Paris-Cité, AP - HP, 2, rue, Ambroise-Paré, 75010 Paris, France
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Arnold R, Augier C, Barabash AS, Basharina-Freshville A, Blondel S, Blot S, Bongrand M, Boursette D, Brudanin V, Busto J, Caffrey AJ, Calvez S, Cascella M, Cerna C, Cesar JP, Chapon A, Chauveau E, Chopra A, Dawson L, Duchesneau D, Durand D, Egorov V, Eurin G, Evans JJ, Fajt L, Filosofov D, Flack R, Garrido X, Gómez H, Guillon B, Guzowski P, Hodák R, Huber A, Hubert P, Hugon C, Jullian S, Klimenko A, Kochetov O, Konovalov SI, Kovalenko V, Lalanne D, Lang K, Lemière Y, Le Noblet T, Liptak Z, Liu XR, Loaiza P, Lutter G, Macko M, Macolino C, Mamedov F, Marquet C, Mauger F, Morgan B, Mott J, Nemchenok I, Nomachi M, Nova F, Nowacki F, Ohsumi H, Patrick C, Pahlka RB, Perrot F, Piquemal F, Povinec P, Přidal P, Ramachers YA, Remoto A, Reyss JL, Riddle CL, Rukhadze E, Saakyan R, Salazar R, Sarazin X, Shitov Y, Simard L, Šimkovic F, Smetana A, Smolek K, Smolnikov A, Söldner-Rembold S, Soulé B, Štefánik D, Štekl I, Suhonen J, Sutton CS, Szklarz G, Thomas J, Timkin V, Torre S, Tretyak VI, Tretyak VI, Umatov VI, Vanushin I, Vilela C, Vorobel V, Waters D, Xie F, Žukauskas A. Search for Neutrinoless Quadruple-β Decay of ^{150}Nd with the NEMO-3 Detector. Phys Rev Lett 2017; 119:041801. [PMID: 29341770 DOI: 10.1103/physrevlett.119.041801] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Indexed: 06/07/2023]
Abstract
We report the results of a first experimental search for lepton number violation by four units in the neutrinoless quadruple-β decay of ^{150}Nd using a total exposure of 0.19 kg yr recorded with the NEMO-3 detector at the Modane Underground Laboratory. We find no evidence of this decay and set lower limits on the half-life in the range T_{1/2}>(1.1-3.2)×10^{21} yr at the 90% C.L., depending on the model used for the kinematic distributions of the emitted electrons.
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Affiliation(s)
- R Arnold
- IPHC, ULP, CNRS/IN2P3, F-67037 Strasbourg, France
| | - C Augier
- LAL, Université Paris-Sud, CNRS/IN2P3, Université Paris-Saclay, F-91405 Orsay, France
| | - A S Barabash
- NRC "Kurchatov Institute," ITEP, 117218 Moscow, Russia
| | | | - S Blondel
- LAL, Université Paris-Sud, CNRS/IN2P3, Université Paris-Saclay, F-91405 Orsay, France
| | - S Blot
- University of Manchester, Manchester M13 9PL, United Kingdom
| | - M Bongrand
- LAL, Université Paris-Sud, CNRS/IN2P3, Université Paris-Saclay, F-91405 Orsay, France
| | - D Boursette
- LAL, Université Paris-Sud, CNRS/IN2P3, Université Paris-Saclay, F-91405 Orsay, France
| | - V Brudanin
- JINR, 141980 Dubna, Russia
- National Research Nuclear University MEPhI, 115409 Moscow, Russia
| | - J Busto
- Aix Marseille Université, CNRS, CPPM, F-13288 Marseille, France
| | - A J Caffrey
- Idaho National Laboratory, Idaho Falls, Idaho 83415, USA
| | - S Calvez
- LAL, Université Paris-Sud, CNRS/IN2P3, Université Paris-Saclay, F-91405 Orsay, France
| | | | - C Cerna
- CENBG, Université de Bordeaux, CNRS/IN2P3, F-33175 Gradignan, France
| | - J P Cesar
- University of Texas at Austin, Austin, Texas 78712, USA
| | - A Chapon
- LPC Caen, ENSICAEN, Université de Caen, CNRS/IN2P3, F-14050 Caen, France
| | - E Chauveau
- University of Manchester, Manchester M13 9PL, United Kingdom
| | - A Chopra
- UCL, London WC1E 6BT, United Kingdom
| | - L Dawson
- UCL, London WC1E 6BT, United Kingdom
| | - D Duchesneau
- LAPP, Université de Savoie, CNRS/IN2P3, F-74941 Annecy-le-Vieux, France
| | - D Durand
- LPC Caen, ENSICAEN, Université de Caen, CNRS/IN2P3, F-14050 Caen, France
| | | | - G Eurin
- LAL, Université Paris-Sud, CNRS/IN2P3, Université Paris-Saclay, F-91405 Orsay, France
- UCL, London WC1E 6BT, United Kingdom
| | - J J Evans
- University of Manchester, Manchester M13 9PL, United Kingdom
| | - L Fajt
- Institute of Experimental and Applied Physics, Czech Technical University in Prague, CZ-12800 Prague, Czech Republic
| | | | - R Flack
- UCL, London WC1E 6BT, United Kingdom
| | - X Garrido
- LAL, Université Paris-Sud, CNRS/IN2P3, Université Paris-Saclay, F-91405 Orsay, France
| | - H Gómez
- LAL, Université Paris-Sud, CNRS/IN2P3, Université Paris-Saclay, F-91405 Orsay, France
| | - B Guillon
- LPC Caen, ENSICAEN, Université de Caen, CNRS/IN2P3, F-14050 Caen, France
| | - P Guzowski
- University of Manchester, Manchester M13 9PL, United Kingdom
| | - R Hodák
- Institute of Experimental and Applied Physics, Czech Technical University in Prague, CZ-12800 Prague, Czech Republic
| | - A Huber
- CENBG, Université de Bordeaux, CNRS/IN2P3, F-33175 Gradignan, France
| | - P Hubert
- CENBG, Université de Bordeaux, CNRS/IN2P3, F-33175 Gradignan, France
| | - C Hugon
- CENBG, Université de Bordeaux, CNRS/IN2P3, F-33175 Gradignan, France
| | - S Jullian
- LAL, Université Paris-Sud, CNRS/IN2P3, Université Paris-Saclay, F-91405 Orsay, France
| | | | | | - S I Konovalov
- NRC "Kurchatov Institute," ITEP, 117218 Moscow, Russia
| | | | - D Lalanne
- LAL, Université Paris-Sud, CNRS/IN2P3, Université Paris-Saclay, F-91405 Orsay, France
| | - K Lang
- University of Texas at Austin, Austin, Texas 78712, USA
| | - Y Lemière
- LPC Caen, ENSICAEN, Université de Caen, CNRS/IN2P3, F-14050 Caen, France
| | - T Le Noblet
- LAPP, Université de Savoie, CNRS/IN2P3, F-74941 Annecy-le-Vieux, France
| | - Z Liptak
- University of Texas at Austin, Austin, Texas 78712, USA
| | - X R Liu
- UCL, London WC1E 6BT, United Kingdom
| | - P Loaiza
- LAL, Université Paris-Sud, CNRS/IN2P3, Université Paris-Saclay, F-91405 Orsay, France
| | - G Lutter
- CENBG, Université de Bordeaux, CNRS/IN2P3, F-33175 Gradignan, France
| | - M Macko
- CENBG, Université de Bordeaux, CNRS/IN2P3, F-33175 Gradignan, France
- FMFI, Comenius University, SK-842 48 Bratislava, Slovakia
| | - C Macolino
- LAL, Université Paris-Sud, CNRS/IN2P3, Université Paris-Saclay, F-91405 Orsay, France
| | - F Mamedov
- Institute of Experimental and Applied Physics, Czech Technical University in Prague, CZ-12800 Prague, Czech Republic
| | - C Marquet
- CENBG, Université de Bordeaux, CNRS/IN2P3, F-33175 Gradignan, France
| | - F Mauger
- LPC Caen, ENSICAEN, Université de Caen, CNRS/IN2P3, F-14050 Caen, France
| | - B Morgan
- University of Warwick, Coventry CV4 7AL, United Kingdom
| | - J Mott
- UCL, London WC1E 6BT, United Kingdom
| | | | - M Nomachi
- Osaka University, 1-1 Machikaneyama Toyonaka, Osaka 560-0043, Japan
| | - F Nova
- University of Texas at Austin, Austin, Texas 78712, USA
| | - F Nowacki
- IPHC, ULP, CNRS/IN2P3, F-67037 Strasbourg, France
| | - H Ohsumi
- Saga University, Saga 840-8502, Japan
| | - C Patrick
- UCL, London WC1E 6BT, United Kingdom
| | - R B Pahlka
- University of Texas at Austin, Austin, Texas 78712, USA
| | - F Perrot
- CENBG, Université de Bordeaux, CNRS/IN2P3, F-33175 Gradignan, France
| | - F Piquemal
- CENBG, Université de Bordeaux, CNRS/IN2P3, F-33175 Gradignan, France
- Laboratoire Souterrain de Modane, F-73500 Modane, France
| | - P Povinec
- FMFI, Comenius University, SK-842 48 Bratislava, Slovakia
| | - P Přidal
- Institute of Experimental and Applied Physics, Czech Technical University in Prague, CZ-12800 Prague, Czech Republic
| | - Y A Ramachers
- University of Warwick, Coventry CV4 7AL, United Kingdom
| | - A Remoto
- LAPP, Université de Savoie, CNRS/IN2P3, F-74941 Annecy-le-Vieux, France
| | - J L Reyss
- LSCE, CNRS, F-91190 Gif-sur-Yvette, France
| | - C L Riddle
- Idaho National Laboratory, Idaho Falls, Idaho 83415, USA
| | - E Rukhadze
- Institute of Experimental and Applied Physics, Czech Technical University in Prague, CZ-12800 Prague, Czech Republic
| | - R Saakyan
- UCL, London WC1E 6BT, United Kingdom
| | - R Salazar
- University of Texas at Austin, Austin, Texas 78712, USA
| | - X Sarazin
- LAL, Université Paris-Sud, CNRS/IN2P3, Université Paris-Saclay, F-91405 Orsay, France
| | - Yu Shitov
- JINR, 141980 Dubna, Russia
- Imperial College London, London SW7 2AZ, United Kingdom
| | - L Simard
- LAL, Université Paris-Sud, CNRS/IN2P3, Université Paris-Saclay, F-91405 Orsay, France
- Institut Universitaire de France, F-75005 Paris, France
| | - F Šimkovic
- FMFI, Comenius University, SK-842 48 Bratislava, Slovakia
| | - A Smetana
- Institute of Experimental and Applied Physics, Czech Technical University in Prague, CZ-12800 Prague, Czech Republic
| | - K Smolek
- Institute of Experimental and Applied Physics, Czech Technical University in Prague, CZ-12800 Prague, Czech Republic
| | | | | | - B Soulé
- CENBG, Université de Bordeaux, CNRS/IN2P3, F-33175 Gradignan, France
| | - D Štefánik
- FMFI, Comenius University, SK-842 48 Bratislava, Slovakia
| | - I Štekl
- Institute of Experimental and Applied Physics, Czech Technical University in Prague, CZ-12800 Prague, Czech Republic
| | - J Suhonen
- Jyväskylä University, FIN-40351 Jyväskylä, Finland
| | - C S Sutton
- MHC, South Hadley, Massachusetts 01075, USA
| | - G Szklarz
- LAL, Université Paris-Sud, CNRS/IN2P3, Université Paris-Saclay, F-91405 Orsay, France
| | - J Thomas
- UCL, London WC1E 6BT, United Kingdom
| | | | - S Torre
- UCL, London WC1E 6BT, United Kingdom
| | - Vl I Tretyak
- Institute for Nuclear Research, 03028 Kyiv, Ukraine
| | | | - V I Umatov
- NRC "Kurchatov Institute," ITEP, 117218 Moscow, Russia
| | - I Vanushin
- NRC "Kurchatov Institute," ITEP, 117218 Moscow, Russia
| | - C Vilela
- UCL, London WC1E 6BT, United Kingdom
| | - V Vorobel
- Charles University in Prague, Faculty of Mathematics and Physics, CZ-12116 Prague, Czech Republic
| | - D Waters
- UCL, London WC1E 6BT, United Kingdom
| | - F Xie
- UCL, London WC1E 6BT, United Kingdom
| | - A Žukauskas
- Charles University in Prague, Faculty of Mathematics and Physics, CZ-12116 Prague, Czech Republic
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Bahloul A, Pepermans E, Raynal B, Wolff N, Cordier F, England P, Nouaille S, Baron B, El-Amraoui A, Hardelin JP, Durand D, Petit C. Conformational switch of harmonin, a submembrane scaffold protein of the hair cell mechanoelectrical transduction machinery. FEBS Lett 2017; 591:2299-2310. [PMID: 28653419 PMCID: PMC5599985 DOI: 10.1002/1873-3468.12729] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Revised: 05/15/2017] [Accepted: 06/08/2017] [Indexed: 11/25/2022]
Abstract
Mutations in the gene encoding harmonin, a multi‐PDZ domain‐containing submembrane protein, cause Usher syndrome type 1 (congenital deafness and balance disorder, and early‐onset sight loss). The structure of the protein and biological activities of its three different classes of splice isoforms (a, b, and c) remain poorly understood. Combining biochemical and biophysical analyses, we show that harmonin‐a1 can switch between open and closed conformations through intramolecular binding of its C‐terminal PDZ‐binding motif to its N‐terminal supramodule NTD‐PDZ1 and through a flexible PDZ2‐PDZ3 linker. This conformational switch presumably extends to most harmonin isoforms, and it is expected to have an impact on the interaction with some binding partners, as shown here for cadherin‐related 23, another component of the hair cell mechanoelectrical transduction machinery.
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Affiliation(s)
- Amel Bahloul
- Unité de Génétique et Physiologie de l'Audition, Institut Pasteur, Paris, France.,UMRS1120, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France.,Sorbonne Universités, UPMC Université Paris 6, Paris, France
| | - Elise Pepermans
- Unité de Génétique et Physiologie de l'Audition, Institut Pasteur, Paris, France.,UMRS1120, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France.,Sorbonne Universités, UPMC Université Paris 6, Paris, France
| | - Bertrand Raynal
- Plateforme de Biophysique Moléculaire, Institut Pasteur, Paris, France
| | - Nicolas Wolff
- Unité de RMN des Biomolécules, Institut Pasteur, Paris, France
| | | | - Patrick England
- Plateforme de Biophysique Moléculaire, Institut Pasteur, Paris, France
| | - Sylvie Nouaille
- Unité de Génétique et Physiologie de l'Audition, Institut Pasteur, Paris, France.,UMRS1120, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France.,Sorbonne Universités, UPMC Université Paris 6, Paris, France
| | - Bruno Baron
- Plateforme de Biophysique Moléculaire, Institut Pasteur, Paris, France
| | - Aziz El-Amraoui
- Unité de Génétique et Physiologie de l'Audition, Institut Pasteur, Paris, France.,UMRS1120, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France.,Sorbonne Universités, UPMC Université Paris 6, Paris, France
| | - Jean-Pierre Hardelin
- Unité de Génétique et Physiologie de l'Audition, Institut Pasteur, Paris, France.,UMRS1120, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France.,Sorbonne Universités, UPMC Université Paris 6, Paris, France
| | - Dominique Durand
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Christine Petit
- Unité de Génétique et Physiologie de l'Audition, Institut Pasteur, Paris, France.,UMRS1120, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France.,Sorbonne Universités, UPMC Université Paris 6, Paris, France.,Collège de France, Paris, France
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Miranday JP, Busnel JP, Durand D, Bruneau CM. Réactivité en polycondensation. Mesure d’un effet de substitution sur unité multifonctionnelle. ACTA ACUST UNITED AC 2017. [DOI: 10.1051/jcp/1976730391] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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50
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Aymard P, Gimel JC, Nicolai T, Durand D. Experimental evidence for a two-step process in the aggregation of β-lactoglobulin at pH 7. ACTA ACUST UNITED AC 2017. [DOI: 10.1051/jcp/1996930987] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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