ProFi Achievements
Publications
2018 |
Tascher, G; Gerbaix, M; Maes, P; Chazarin, B; Ghislin, S; Antropova, E; Vassilieva, G; Ouzren-Zarhloul, N; Gauquelin-Koch, G; Vico, L; Frippiat, JP.; Bertile, F Analysis of femurs from mice embarked on board BION-M1 biosatellite reveals a decrease in immune cell development, including B cells, after 1 wk of recovery on Earth Article de journal FASEB J., 33 (3), 2018. @article{625b, title = {Analysis of femurs from mice embarked on board BION-M1 biosatellite reveals a decrease in immune cell development, including B cells, after 1 wk of recovery on Earth}, author = {G Tascher and M Gerbaix and P Maes and B Chazarin and S Ghislin and E Antropova and G Vassilieva and N Ouzren-Zarhloul and G Gauquelin-Koch and L Vico and JP. Frippiat and F Bertile}, doi = {10.1096/fj.201801463R}, year = {2018}, date = {2018-12-06}, journal = {FASEB J.}, volume = {33}, number = {3}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Jonckheere, Julie; Deloulme, Jean-Christophe; Dall'Igna, Gaëlle; Chauliac, Nicolas; Pelluet, Albane; Nguon, Anne-Sophie; Lentini, Celia; Brocard, Jacques; Denarier, Eric; Brugière, Sabine; Couté, Yohann; Heinrich, Christophe; Porcher, Christophe; Holtzmann, Jérôme; Andrieux, Annie; Suaud-Chagny, Marie-Françoise; Gory-Fauré, Sylvie Short- and long-term efficacy of electroconvulsive stimulation in animal models of depression: The essential role of neuronal survival Article de journal Brain Stimulation, 11 (6), p. 1336–1347, 2018, ISSN: 1876-4754. @article{jonckheere_short-_2018, title = {Short- and long-term efficacy of electroconvulsive stimulation in animal models of depression: The essential role of neuronal survival}, author = {Julie Jonckheere and Jean-Christophe Deloulme and Gaëlle Dall'Igna and Nicolas Chauliac and Albane Pelluet and Anne-Sophie Nguon and Celia Lentini and Jacques Brocard and Eric Denarier and Sabine Brugière and Yohann Couté and Christophe Heinrich and Christophe Porcher and Jérôme Holtzmann and Annie Andrieux and Marie-Françoise Suaud-Chagny and Sylvie Gory-Fauré}, doi = {10.1016/j.brs.2018.08.001}, issn = {1876-4754}, year = {2018}, date = {2018-12-01}, journal = {Brain Stimulation}, volume = {11}, number = {6}, pages = {1336--1347}, abstract = {BACKGROUND: Severe and medication-resistant psychiatric diseases, such as major depressive disorder, bipolar disorder or schizophrenia, can be effectively and rapidly treated by electroconvulsive therapy (ECT). Despite extensive long-standing clinical use, the neurobiological mechanisms underlying the curative action of ECT remain incompletely understood. OBJECTIVE: Unravel biological basis of electroconvulsive stimulation (ECS) efficacy, the animal equivalent of ECT. METHODS: Using MAP6 KO mouse, a genetic model that constitutively exhibits features relevant to some aspects of depression; we analyzed the behavioral and biological consequences of ECS treatment alone (10 stimulations over a 2-week period) and associated with a continuation protocol (2 stimulations per week for 5 weeks). RESULTS: ECS treatment had a beneficial effect on constitutive behavioral defects. We showed that behavioral improvement is associated with a strong increase in the survival and integration of neurons born before ECS treatment. Retroviral infection revealed the larger number of integrated neurons to exhibit increased dendritic complexity and spine density, as well as remodeled synapses. Furthermore, our results show that ECS triggers a cortical increase in synaptogenesis. A sustained newborn neuron survival rate, induced by ECS treatment, is associated with the behavioral improvement, but relapse occurred 40 days after completing the ECS treatment. However, a 5-week continuation protocol following the initial ECS treatment led to persistent improvement of behavior correlated with sustained rate survival of newborn neurons. CONCLUSION: Altogether, these results reveal that increased synaptic connectivity and extended neuronal survival are key to the short and long-term efficacy of ECS.}, keywords = {}, pubstate = {published}, tppubtype = {article} } BACKGROUND: Severe and medication-resistant psychiatric diseases, such as major depressive disorder, bipolar disorder or schizophrenia, can be effectively and rapidly treated by electroconvulsive therapy (ECT). Despite extensive long-standing clinical use, the neurobiological mechanisms underlying the curative action of ECT remain incompletely understood. OBJECTIVE: Unravel biological basis of electroconvulsive stimulation (ECS) efficacy, the animal equivalent of ECT. METHODS: Using MAP6 KO mouse, a genetic model that constitutively exhibits features relevant to some aspects of depression; we analyzed the behavioral and biological consequences of ECS treatment alone (10 stimulations over a 2-week period) and associated with a continuation protocol (2 stimulations per week for 5 weeks). RESULTS: ECS treatment had a beneficial effect on constitutive behavioral defects. We showed that behavioral improvement is associated with a strong increase in the survival and integration of neurons born before ECS treatment. Retroviral infection revealed the larger number of integrated neurons to exhibit increased dendritic complexity and spine density, as well as remodeled synapses. Furthermore, our results show that ECS triggers a cortical increase in synaptogenesis. A sustained newborn neuron survival rate, induced by ECS treatment, is associated with the behavioral improvement, but relapse occurred 40 days after completing the ECS treatment. However, a 5-week continuation protocol following the initial ECS treatment led to persistent improvement of behavior correlated with sustained rate survival of newborn neurons. CONCLUSION: Altogether, these results reveal that increased synaptic connectivity and extended neuronal survival are key to the short and long-term efficacy of ECS. |
Albaret, Marie Alexandra; Vermot-Desroches, Claudine; Paré, Arnaud; Roca-Martinez, Jean-Xavier; Malet, Lucie; Esseily, Jad; Gerossier, Laetitia; Brière, Johan; Pion, Nathalie; Marcel, Virginie; Catez, Frédéric; Souza, Geneviève De; Vuillermoz, Boris; Doerflinger, Franck; Lavocat, Emilie; Subiger, Olivier; Rousset, Carine; Bresson, Corinne; Mandon, Elodie; Jawhari, Anass; Falson, Pierre; Jasmin, Mélissa; Couté, Yohann; Mertani, Hichem-Claude; Saintigny, Pierre; Diaz, Jean-Jacques Externalized Keratin 8: A Target at the Interface of Microenvironment and Intracellular Signaling in Colorectal Cancer Cells Article de journal Cancers, 10 (11), 2018, ISSN: 2072-6694. @article{albaret_externalized_2018, title = {Externalized Keratin 8: A Target at the Interface of Microenvironment and Intracellular Signaling in Colorectal Cancer Cells}, author = {Marie Alexandra Albaret and Claudine Vermot-Desroches and Arnaud Paré and Jean-Xavier Roca-Martinez and Lucie Malet and Jad Esseily and Laetitia Gerossier and Johan Brière and Nathalie Pion and Virginie Marcel and Frédéric Catez and Geneviève De Souza and Boris Vuillermoz and Franck Doerflinger and Emilie Lavocat and Olivier Subiger and Carine Rousset and Corinne Bresson and Elodie Mandon and Anass Jawhari and Pierre Falson and Mélissa Jasmin and Yohann Couté and Hichem-Claude Mertani and Pierre Saintigny and Jean-Jacques Diaz}, doi = {10.3390/cancers10110452}, issn = {2072-6694}, year = {2018}, date = {2018-11-01}, journal = {Cancers}, volume = {10}, number = {11}, abstract = {Accumulating evidence supports the remarkable presence at the membrane surface of cancer cells of proteins, which are normally expressed in the intracellular compartment. Although these proteins, referred to as externalized proteins, represent a highly promising source of accessible and druggable targets for cancer therapy, the mechanisms via which they impact cancer biology remain largely unexplored. The aim of this study was to expose an externalized form of cytokeratin 8 (eK8) as a key player of colorectal tumorigenesis and characterize its mode of action. To achieve this, we generated a unique antagonist monoclonal antibody (D-A10 MAb) targeting an eight-amino-acid-long domain of eK8, which enabled us to ascertain the pro-tumoral activity of eK8 in both KRAS-mutant and wild-type colorectal cancers (CRC). We showed that this pro-tumoral activity involves a bidirectional eK8-dependent control of caspase-mediated apoptosis in vivo and of the plasminogen-induced invasion process in cellulo. Furthermore, we demonstrated that eK8 is anchored at the plasma membrane supporting this dual function. We, therefore, identified eK8 as an innovative therapeutic target in CRC and provided a unique MAb targeting eK8 that displays anti-neoplastic activities that could be useful to treat CRC, including those harboring KRAS mutations.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Accumulating evidence supports the remarkable presence at the membrane surface of cancer cells of proteins, which are normally expressed in the intracellular compartment. Although these proteins, referred to as externalized proteins, represent a highly promising source of accessible and druggable targets for cancer therapy, the mechanisms via which they impact cancer biology remain largely unexplored. The aim of this study was to expose an externalized form of cytokeratin 8 (eK8) as a key player of colorectal tumorigenesis and characterize its mode of action. To achieve this, we generated a unique antagonist monoclonal antibody (D-A10 MAb) targeting an eight-amino-acid-long domain of eK8, which enabled us to ascertain the pro-tumoral activity of eK8 in both KRAS-mutant and wild-type colorectal cancers (CRC). We showed that this pro-tumoral activity involves a bidirectional eK8-dependent control of caspase-mediated apoptosis in vivo and of the plasminogen-induced invasion process in cellulo. Furthermore, we demonstrated that eK8 is anchored at the plasma membrane supporting this dual function. We, therefore, identified eK8 as an innovative therapeutic target in CRC and provided a unique MAb targeting eK8 that displays anti-neoplastic activities that could be useful to treat CRC, including those harboring KRAS mutations. |
Hahn, Friedrich; Hutterer, Corina; Henry, Christophe; Hamilton, Stuart T; Strojan, Hanife; Kraut, Alexandra; Schulte, Ulrike; Schütz, Martin; Kohrt, Stephan; Wangen, Christina; Pfizer, José; Couté, Yohann; Rawlinson, William D; Strobl, Stefan; Marschall, Manfred Novel cytomegalovirus-inhibitory compounds of the class pyrrolopyridines show a complex pattern of target binding that suggests an unusual mechanism of antiviral activity Article de journal Antiviral Research, 159 , p. 84–94, 2018, ISSN: 1872-9096. @article{hahn_novel_2018, title = {Novel cytomegalovirus-inhibitory compounds of the class pyrrolopyridines show a complex pattern of target binding that suggests an unusual mechanism of antiviral activity}, author = {Friedrich Hahn and Corina Hutterer and Christophe Henry and Stuart T Hamilton and Hanife Strojan and Alexandra Kraut and Ulrike Schulte and Martin Schütz and Stephan Kohrt and Christina Wangen and José Pfizer and Yohann Couté and William D Rawlinson and Stefan Strobl and Manfred Marschall}, doi = {10.1016/j.antiviral.2018.09.012}, issn = {1872-9096}, year = {2018}, date = {2018-11-01}, journal = {Antiviral Research}, volume = {159}, pages = {84--94}, abstract = {Human cytomegalovirus (HCMV) is a major human pathogen with seropositivity rates in the adult population ranging between 40% and 95%. HCMV infection is associated with severe pathology, such as life-threatening courses of infection in immunocompromised individuals and neonates. Current standard therapy with valganciclovir has the disadvantage of adverse side effects and viral drug resistance. A novel anti-HCMV drug, letermovir, has been approved recently, so that improved therapy options are available. Nevertheless, even more so far unexploited classes of compounds and molecular modes of action will be required for a next generation of antiherpesviral treatment strategies. In this study, we focused on the analysis of the antiviral potency of a novel class of compounds, i.e. pyrrolopyridine analogs, and identified both hit compounds and their target protein candidates. In essence, we provide novel evidence as follows: (i) screening hit SC88941 is highly active in inhibiting HCMV replication in primary human fibroblasts with an EC50 value of 0.20 ± 0.01 μM in the absence of cytotoxicity, (ii) inhibition occurs at the early-late stage of viral protein production and shows reinforcing effects upon LMV cotreatment, (iii) among the viruses analyzed, antiviral activity was most pronounced against β-herpesviruses (HCMV, HHV-6A) and intermediate against adenovirus (HAdV-2), (iv) induction of SC88941 resistance was not detectable, thus differed from the induction of ganciclovir resistance, (v) a linker-coupled model compound was used for mass spectrometry-based target identification, thus yielding several drug-binding target proteins and (vi) a first confocal imaging approach used for addressing intracellular effects of SC88941 indicated qualitative and quantitative alteration of viral protein expression and localization. Thus, our findings suggest a multifaceted pattern of compound-target binding in connection with an unusual mode of action, opening up further opportunities of antiviral drug development.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Human cytomegalovirus (HCMV) is a major human pathogen with seropositivity rates in the adult population ranging between 40% and 95%. HCMV infection is associated with severe pathology, such as life-threatening courses of infection in immunocompromised individuals and neonates. Current standard therapy with valganciclovir has the disadvantage of adverse side effects and viral drug resistance. A novel anti-HCMV drug, letermovir, has been approved recently, so that improved therapy options are available. Nevertheless, even more so far unexploited classes of compounds and molecular modes of action will be required for a next generation of antiherpesviral treatment strategies. In this study, we focused on the analysis of the antiviral potency of a novel class of compounds, i.e. pyrrolopyridine analogs, and identified both hit compounds and their target protein candidates. In essence, we provide novel evidence as follows: (i) screening hit SC88941 is highly active in inhibiting HCMV replication in primary human fibroblasts with an EC50 value of 0.20 ± 0.01 μM in the absence of cytotoxicity, (ii) inhibition occurs at the early-late stage of viral protein production and shows reinforcing effects upon LMV cotreatment, (iii) among the viruses analyzed, antiviral activity was most pronounced against β-herpesviruses (HCMV, HHV-6A) and intermediate against adenovirus (HAdV-2), (iv) induction of SC88941 resistance was not detectable, thus differed from the induction of ganciclovir resistance, (v) a linker-coupled model compound was used for mass spectrometry-based target identification, thus yielding several drug-binding target proteins and (vi) a first confocal imaging approach used for addressing intracellular effects of SC88941 indicated qualitative and quantitative alteration of viral protein expression and localization. Thus, our findings suggest a multifaceted pattern of compound-target binding in connection with an unusual mode of action, opening up further opportunities of antiviral drug development. |
Borges, Hélène; Guibert, Romain; Permiakova, Olga; Burger, Thomas Distinguishing between Spectral Clustering and Cluster Analysis of Mass Spectra Article de journal Journal of Proteome Research, 2018, ISSN: 1535-3907. @article{borges_distinguishing_2018, title = {Distinguishing between Spectral Clustering and Cluster Analysis of Mass Spectra}, author = {Hélène Borges and Romain Guibert and Olga Permiakova and Thomas Burger}, doi = {10.1021/acs.jproteome.8b00516}, issn = {1535-3907}, year = {2018}, date = {2018-11-01}, journal = {Journal of Proteome Research}, abstract = {The term "spectral clustering" is sometimes used to refer to the clustering of mass spectrometry data. However, it also classically refers to a family of popular clustering algorithms. To avoid confusion, a more specific term could advantageously be coined.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The term "spectral clustering" is sometimes used to refer to the clustering of mass spectrometry data. However, it also classically refers to a family of popular clustering algorithms. To avoid confusion, a more specific term could advantageously be coined. |
Dominguez-Medina, Sergio; Fostner, Shawn; Defoort, Martial; Sansa, Marc; Stark, Ann-Kathrin; Halim, Mohammad Abdul; Vernhes, Emeline; Gely, Marc; Jourdan, Guillaume; Alava, Thomas; Boulanger, Pascale; Masselon, Christophe; Hentz, Sébastien Neutral mass spectrometry of virus capsids above 100 megadaltons with nanomechanical resonators Article de journal Science (New York, N.Y.), 362 (6417), p. 918–922, 2018, ISSN: 1095-9203. @article{dominguez-medina_neutral_2018, title = {Neutral mass spectrometry of virus capsids above 100 megadaltons with nanomechanical resonators}, author = {Sergio Dominguez-Medina and Shawn Fostner and Martial Defoort and Marc Sansa and Ann-Kathrin Stark and Mohammad Abdul Halim and Emeline Vernhes and Marc Gely and Guillaume Jourdan and Thomas Alava and Pascale Boulanger and Christophe Masselon and Sébastien Hentz}, doi = {10.1126/science.aat6457}, issn = {1095-9203}, year = {2018}, date = {2018-11-01}, journal = {Science (New York, N.Y.)}, volume = {362}, number = {6417}, pages = {918--922}, abstract = {Measurement of the mass of particles in the mega- to gigadalton range is challenging with conventional mass spectrometry. Although this mass range appears optimal for nanomechanical resonators, nanomechanical mass spectrometers often suffer from prohibitive sample loss, extended analysis time, or inadequate resolution. We report on a system architecture combining nebulization of the analytes from solution, their efficient transfer and focusing without relying on electromagnetic fields, and the mass measurements of individual particles using nanomechanical resonator arrays. This system determined the mass distribution of textasciitilde30-megadalton polystyrene nanoparticles with high detection efficiency and effectively performed molecular mass measurements of empty or DNA-filled bacteriophage T5 capsids with masses up to 105 megadaltons using less than 1 picomole of sample and with an instrument resolution above 100.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Measurement of the mass of particles in the mega- to gigadalton range is challenging with conventional mass spectrometry. Although this mass range appears optimal for nanomechanical resonators, nanomechanical mass spectrometers often suffer from prohibitive sample loss, extended analysis time, or inadequate resolution. We report on a system architecture combining nebulization of the analytes from solution, their efficient transfer and focusing without relying on electromagnetic fields, and the mass measurements of individual particles using nanomechanical resonator arrays. This system determined the mass distribution of textasciitilde30-megadalton polystyrene nanoparticles with high detection efficiency and effectively performed molecular mass measurements of empty or DNA-filled bacteriophage T5 capsids with masses up to 105 megadaltons using less than 1 picomole of sample and with an instrument resolution above 100. |
Do, Le Duy; Gupton, Stéphanie L; Tanji, Kunikazu; Bastien, Joubert; Brugière, Sabine; Couté, Yohann; Quadrio, Isabelle; Rogemond, Véronique; Fabien, Nicole; Desestret, Virginie; Honnorat, Jérôme TRIM9 and TRIM67 Are New Targets in Paraneoplastic Cerebellar Degeneration Article de journal Cerebellum (London, England), 2018, ISSN: 1473-4230. @article{do_trim9_2018, title = {TRIM9 and TRIM67 Are New Targets in Paraneoplastic Cerebellar Degeneration}, author = {Le Duy Do and Stéphanie L Gupton and Kunikazu Tanji and Joubert Bastien and Sabine Brugière and Yohann Couté and Isabelle Quadrio and Véronique Rogemond and Nicole Fabien and Virginie Desestret and Jérôme Honnorat}, doi = {10.1007/s12311-018-0987-5}, issn = {1473-4230}, year = {2018}, date = {2018-10-01}, journal = {Cerebellum (London, England)}, abstract = {To describe autoantibodies (Abs) against tripartite motif-containing (TRIM) protein 9 and 67 in two patients with paraneoplastic cerebellar degeneration (PCD) associated with lung adenocarcinoma. Abs were characterized using immunohistochemistry, Western blotting, cultures of murine cortical, and hippocampal neurons, immunoprecipitation, mass spectrometry, knockout mice for Trim9 and 67, and cell-based assay. Control samples included sera from 63 patients with small cell lung cancer without any paraneoplastic neurological syndrome, 36 patients with lung adenocarcinoma and PNS, CSF from 100 patients with autoimmune encephalitis, and CSF from 165 patients with neurodegenerative diseases. We found Abs targeting TRIM9 and TRIM67 at high concentration in the serum and the cerebrospinal fluid (CSF) of a 78-year-old woman and a 65-year-old man. Both developed subacute severe cerebellar ataxia. Brain magnetic resonance imaging found no abnormality and no cerebellar atrophy. Both had CSF inflammation with mild pleiocytosis and a few oligoclonal bands. We identified a pulmonary adenocarcinoma, confirming the paraneoplastic neurological syndrome in both patients. They received immunomodulatory and cancer treatments without improvement of cerebellar ataxia, even though both were in remission of their cancer (for more than 10 years in one patient). Anti-TRIM9 and anti-TRIM67 Abs were specific to these two patients. All control serum and CSF samples tested were negative for anti-TRIM9 and 67. Anti-TRIM9 and anti-TRIM67 Abs appeared to be specific biomarkers of PCD and should be added to the panel of antigens tested when this is suspected.}, keywords = {}, pubstate = {published}, tppubtype = {article} } To describe autoantibodies (Abs) against tripartite motif-containing (TRIM) protein 9 and 67 in two patients with paraneoplastic cerebellar degeneration (PCD) associated with lung adenocarcinoma. Abs were characterized using immunohistochemistry, Western blotting, cultures of murine cortical, and hippocampal neurons, immunoprecipitation, mass spectrometry, knockout mice for Trim9 and 67, and cell-based assay. Control samples included sera from 63 patients with small cell lung cancer without any paraneoplastic neurological syndrome, 36 patients with lung adenocarcinoma and PNS, CSF from 100 patients with autoimmune encephalitis, and CSF from 165 patients with neurodegenerative diseases. We found Abs targeting TRIM9 and TRIM67 at high concentration in the serum and the cerebrospinal fluid (CSF) of a 78-year-old woman and a 65-year-old man. Both developed subacute severe cerebellar ataxia. Brain magnetic resonance imaging found no abnormality and no cerebellar atrophy. Both had CSF inflammation with mild pleiocytosis and a few oligoclonal bands. We identified a pulmonary adenocarcinoma, confirming the paraneoplastic neurological syndrome in both patients. They received immunomodulatory and cancer treatments without improvement of cerebellar ataxia, even though both were in remission of their cancer (for more than 10 years in one patient). Anti-TRIM9 and anti-TRIM67 Abs were specific to these two patients. All control serum and CSF samples tested were negative for anti-TRIM9 and 67. Anti-TRIM9 and anti-TRIM67 Abs appeared to be specific biomarkers of PCD and should be added to the panel of antigens tested when this is suspected. |
Völz, Ronny; Kim, Soon-Kap; Mi, Jianing; Mariappan, Kiruthiga G; Guo, Xiujie; Bigeard, Jean; Alejandro, Santiago; Pflieger, Delphine; Rayapuram, Naganand; Al-Babili, Salim; Hirt, Heribert The Trihelix transcription factor GT2-like 1 (GTL1) promotes salicylic acid metabolism, and regulates bacterial-triggered immunity Article de journal PLoS genetics, 14 (10), p. e1007708, 2018, ISSN: 1553-7404. @article{volz_trihelix_2018, title = {The Trihelix transcription factor GT2-like 1 (GTL1) promotes salicylic acid metabolism, and regulates bacterial-triggered immunity}, author = {Ronny Völz and Soon-Kap Kim and Jianing Mi and Kiruthiga G Mariappan and Xiujie Guo and Jean Bigeard and Santiago Alejandro and Delphine Pflieger and Naganand Rayapuram and Salim Al-Babili and Heribert Hirt}, doi = {10.1371/journal.pgen.1007708}, issn = {1553-7404}, year = {2018}, date = {2018-10-01}, journal = {PLoS genetics}, volume = {14}, number = {10}, pages = {e1007708}, abstract = {The Trihelix Transcription factor GT2-like 1 (GTL1) was previously shown to be a key regulator of ploidy-dependent trichome growth and drought tolerance. Here, we report that GTL1 plays an important role in coordinating plant immunity. We show that gtl1 mutants are compromised in the regulation of basal immunity, microbial pattern-triggered immunity (PTI) and effector-triggered RIN4-mediated immunity. Transcriptome analysis revealed that GTL1 positively regulates defense genes and inhibits factors that mediate growth and development. By performing hormonal measurements and chromatin-immunoprecipitation studies, we found GTL1 to coordinate genes involved in salicylic acid metabolism, transport and response. Interaction studies and comparative transcriptomics to known data sets revealed that GTL1 is part of the MPK4 pathway and regulates oppositely the expression of differentially expressed genes in mpk4 plants. We introduced the gtl1 mutation in the mpk4 mutant and thereby partially suppressed its dwarfism and the high resistance against a bacterial invader. Our data show that GTL1 is part of the MPK4 pathway and acts as a positive regulator of bacterial-triggered immunity and SA homeostasis.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The Trihelix Transcription factor GT2-like 1 (GTL1) was previously shown to be a key regulator of ploidy-dependent trichome growth and drought tolerance. Here, we report that GTL1 plays an important role in coordinating plant immunity. We show that gtl1 mutants are compromised in the regulation of basal immunity, microbial pattern-triggered immunity (PTI) and effector-triggered RIN4-mediated immunity. Transcriptome analysis revealed that GTL1 positively regulates defense genes and inhibits factors that mediate growth and development. By performing hormonal measurements and chromatin-immunoprecipitation studies, we found GTL1 to coordinate genes involved in salicylic acid metabolism, transport and response. Interaction studies and comparative transcriptomics to known data sets revealed that GTL1 is part of the MPK4 pathway and regulates oppositely the expression of differentially expressed genes in mpk4 plants. We introduced the gtl1 mutation in the mpk4 mutant and thereby partially suppressed its dwarfism and the high resistance against a bacterial invader. Our data show that GTL1 is part of the MPK4 pathway and acts as a positive regulator of bacterial-triggered immunity and SA homeostasis. |
Gervais, Virginie; Mari, Isabelle Muller Pierre-Olivier; Mourcet, Amandine; Movellan, Kumar Tekwani; Ramos, Pascal; Marcoux, Julien; Guillet, Valérie; Javaid, Sumaira; Burlet-Schiltz, Odile; Czaplicki, Georges; Milon, Alain; Giglia-Mari, Giuseppina Small molecule-based targeting of TTD-A dimerization to control TFIIH transcriptional activity represents a potential strategy for anticancer therapy Article de journal J Biol Chem., 293 (39), p. 14974-14988, 2018. @article{Gervais2018, title = {Small molecule-based targeting of TTD-A dimerization to control TFIIH transcriptional activity represents a potential strategy for anticancer therapy}, author = {Virginie Gervais and Isabelle Muller Pierre-Olivier Mari and Amandine Mourcet and Kumar Tekwani Movellan and Pascal Ramos and Julien Marcoux and Valérie Guillet and Sumaira Javaid and Odile Burlet-Schiltz and Georges Czaplicki and Alain Milon and Giuseppina Giglia-Mari}, doi = {10.1074/jbc.RA118.003444}, year = {2018}, date = {2018-09-28}, journal = {J Biol Chem.}, volume = {293}, number = {39}, pages = {14974-14988}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Shiota, Hitoshi; Barral, Sophie; Buchou, Thierry; Tan, Minjia; Couté, Yohann; Charbonnier, Guillaume; Reynoird, Nicolas; Boussouar, Fayçal; Gérard, Matthieu; Zhu, Mingrui; Bargier, Lisa; Puthier, Denis; Chuffart, Florent; Bourova-Flin, Ekaterina; Picaud, Sarah; Filippakopoulos, Panagis; Goudarzi, Afsaneh; Ibrahim, Ziad; Panne, Daniel; Rousseaux, Sophie; Zhao, Yingming; Khochbin, Saadi Nut Directs p300-Dependent, Genome-Wide Ħ4 Hyperacetylation in Male Germ Cells Article de journal Cell Reports, 24 (13), p. 3477–3487.e6, 2018, ISSN: 2211-1247. @article{shiota_nut_2018, title = {Nut Directs p300-Dependent, Genome-Wide Ħ4 Hyperacetylation in Male Germ Cells}, author = {Hitoshi Shiota and Sophie Barral and Thierry Buchou and Minjia Tan and Yohann Couté and Guillaume Charbonnier and Nicolas Reynoird and Fayçal Boussouar and Matthieu Gérard and Mingrui Zhu and Lisa Bargier and Denis Puthier and Florent Chuffart and Ekaterina Bourova-Flin and Sarah Picaud and Panagis Filippakopoulos and Afsaneh Goudarzi and Ziad Ibrahim and Daniel Panne and Sophie Rousseaux and Yingming Zhao and Saadi Khochbin}, doi = {10.1016/j.celrep.2018.08.069}, issn = {2211-1247}, year = {2018}, date = {2018-09-01}, journal = {Cell Reports}, volume = {24}, number = {13}, pages = {3477--3487.e6}, abstract = {Nuclear protein in testis (Nut) is a universal oncogenic driver in the highly aggressive NUT midline carcinoma, whose physiological function in male germ cells has been unclear. Here we show that expression of Nut is normally restricted to post-meiotic spermatogenic cells, where its presence triggers p300-dependent genome-wide histone H4 hyperacetylation, which is essential for the completion of histone-to-protamine exchange. Accordingly, the inactivation of Nut induces male sterility with spermatogenesis arrest at the histone-removal stage. Nut uses p300 and/or CBP to enhance acetylation of H4 at both K5 and K8, providing binding sites for the first bromodomain of Brdt, the testis-specific member of the BET family, which subsequently mediates genome-wide histone removal. Altogether, our data reveal the detailed molecular basis of the global histone hyperacetylation wave, which occurs before the final compaction of the male genome.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Nuclear protein in testis (Nut) is a universal oncogenic driver in the highly aggressive NUT midline carcinoma, whose physiological function in male germ cells has been unclear. Here we show that expression of Nut is normally restricted to post-meiotic spermatogenic cells, where its presence triggers p300-dependent genome-wide histone H4 hyperacetylation, which is essential for the completion of histone-to-protamine exchange. Accordingly, the inactivation of Nut induces male sterility with spermatogenesis arrest at the histone-removal stage. Nut uses p300 and/or CBP to enhance acetylation of H4 at both K5 and K8, providing binding sites for the first bromodomain of Brdt, the testis-specific member of the BET family, which subsequently mediates genome-wide histone removal. Altogether, our data reveal the detailed molecular basis of the global histone hyperacetylation wave, which occurs before the final compaction of the male genome. |
Nguyen, Minh Vu Chuong; Adrait, Annie; Baillet, Athan; Trocmé, Candice; Gottenberg, Jacques-Eric; Gaudin, Philippe Joint, Bone, Spine: Revue Du Rhumatisme, 2018, ISSN: 1778-7254. @article{nguyen_identification_2018, title = {Identification of cartilage oligomeric matrix protein as biomarker predicting abatacept response in rheumatoid arthritis patients with insufficient response to a first anti-TNFα treatment}, author = {Minh Vu Chuong Nguyen and Annie Adrait and Athan Baillet and Candice Trocmé and Jacques-Eric Gottenberg and Philippe Gaudin}, doi = {10.1016/j.jbspin.2018.09.005}, issn = {1778-7254}, year = {2018}, date = {2018-09-01}, journal = {Joint, Bone, Spine: Revue Du Rhumatisme}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Mato, José M; Elortza, Félix; Lu, Shelly C; Brun, Virginie; Paradela, Alberto; Corrales, Fernando J Liver cancer-associated changes to the proteome: what deserves clinical focus? Article de journal Expert Review of Proteomics, 15 (9), p. 749–756, 2018, ISSN: 1744-8387. @article{mato_liver_2018, title = {Liver cancer-associated changes to the proteome: what deserves clinical focus?}, author = {José M Mato and Félix Elortza and Shelly C Lu and Virginie Brun and Alberto Paradela and Fernando J Corrales}, doi = {10.1080/14789450.2018.1521277}, issn = {1744-8387}, year = {2018}, date = {2018-09-01}, journal = {Expert Review of Proteomics}, volume = {15}, number = {9}, pages = {749--756}, abstract = {INTRODUCTION: Hepatocellular carcinoma (HCC) is recognized as the fifth most common neoplasm and currently represents the second leading form of cancer-related death worldwide. Despite great progress has been done in the understanding of its pathogenesis, HCC represents a heavy societal and economic burden as most patients are still diagnosed at advanced stages and the 5-year survival rate remain below 20%. Early detection and revolutionary therapies that rely on the discovery of new molecular biomarkers and therapeutic targets are therefore urgently needed to develop precision medicine strategies for a more efficient management of patients. Areas covered: This review intends to comprehensively analyse the proteomics-based research conducted in the last few years to address some of the principal still open riddles in HCC biology, based on the identification of molecular drivers of tumor progression and metastasis. Expert commentary: The technical advances in mass spectrometry experienced in the last decade have significantly improved the analytical capacity of proteome wide studies. Large-scale protein and protein variant (post-translational modifications) identification and quantification have allowed detailed dissections of molecular mechanisms underlying HCC progression and are already paving the way for the identification of clinically relevant proteins and the development of their use on patient care.}, keywords = {}, pubstate = {published}, tppubtype = {article} } INTRODUCTION: Hepatocellular carcinoma (HCC) is recognized as the fifth most common neoplasm and currently represents the second leading form of cancer-related death worldwide. Despite great progress has been done in the understanding of its pathogenesis, HCC represents a heavy societal and economic burden as most patients are still diagnosed at advanced stages and the 5-year survival rate remain below 20%. Early detection and revolutionary therapies that rely on the discovery of new molecular biomarkers and therapeutic targets are therefore urgently needed to develop precision medicine strategies for a more efficient management of patients. Areas covered: This review intends to comprehensively analyse the proteomics-based research conducted in the last few years to address some of the principal still open riddles in HCC biology, based on the identification of molecular drivers of tumor progression and metastasis. Expert commentary: The technical advances in mass spectrometry experienced in the last decade have significantly improved the analytical capacity of proteome wide studies. Large-scale protein and protein variant (post-translational modifications) identification and quantification have allowed detailed dissections of molecular mechanisms underlying HCC progression and are already paving the way for the identification of clinically relevant proteins and the development of their use on patient care. |
Locard-Paulet, Marie; Parra, Julien; Albigot, Renaud; Mouton-Barbosa, Emmanuelle; Bardi, Laurent; Burlet-Schiltz, Odile; Marcoux, Julien VisioProt-MS: interactive 2D maps from intact protein mass spectrometry Article de journal Bioinformatics, 2018. @article{Locard-Paulet2018, title = {VisioProt-MS: interactive 2D maps from intact protein mass spectrometry}, author = {Marie Locard-Paulet and Julien Parra and Renaud Albigot and Emmanuelle Mouton-Barbosa and Laurent Bardi and Odile Burlet-Schiltz and Julien Marcoux}, doi = {10.1093/bioinformatics/bty680}, year = {2018}, date = {2018-08-06}, journal = {Bioinformatics}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Vinel, Claire; Lukjanenko, Laura; Batut, Aurélie; Deleruyelle, Simon; Pradère, Jean-Philippe; Gonidec, Sophie Le; Dortignac, Alizée; Geoffre, Nancy; Pereira, Ophélie; Karaz, Sonia; Lee, Umji; Camus, Mylène; Chaoui, Karima; Mouisel, Etienne; Bigot, Anne; Mouly, Vincent; Vigneau, Mathieu; Pagano, Allan F; Chopard, Angèle; Pillard, Fabien; Guyonnet, Sophie; Cesari, Matteo; Burlet-Schiltz, Odile; Pahor, Marco; Feige, Jérôme N; Vellas, Bruno; Valet, Philippe; Dray, Cédric The exerkine apelin reverses age-associated sarcopenia Article de journal Nat Med., 24 (9), p. 1360-71, 2018. @article{Vinel2018, title = {The exerkine apelin reverses age-associated sarcopenia}, author = {Claire Vinel and Laura Lukjanenko and Aurélie Batut and Simon Deleruyelle and Jean-Philippe Pradère and Sophie Le Gonidec and Alizée Dortignac and Nancy Geoffre and Ophélie Pereira and Sonia Karaz and Umji Lee and Mylène Camus and Karima Chaoui and Etienne Mouisel and Anne Bigot and Vincent Mouly and Mathieu Vigneau and Allan F. Pagano and Angèle Chopard and Fabien Pillard and Sophie Guyonnet and Matteo Cesari and Odile Burlet-Schiltz and Marco Pahor and Jérôme N. Feige and Bruno Vellas and Philippe Valet and Cédric Dray}, doi = {10.1038/s41591-018-0131-6}, year = {2018}, date = {2018-07-30}, journal = {Nat Med.}, volume = {24}, number = {9}, pages = {1360-71}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Jonik-Nowak, Beata; Menneteau, Thoma; Fesquet, Didier; Baldin, Véronique; Bonne-Andrea, Catherine; Méchali, Francisca; Fabre, Bertrand; Boisguerin, Prisca; de Rossi, Sylvain; Henriquet, Corinne; Pugnière, Martine; Ducoux-Petit, Manuelle; Burlet-Schiltz, Odile; Lamond, Angus I; Fort, Philippe; Boulon, Séverine; Bousquet, Mari-Pierre; Coux, Olivier PIP30/FAM192A is a novel regulator of the nuclear proteasome activator PA28γ Article de journal Proc Natl Acad Sci U S A., 115 (28), p. E6477-E6486, 2018. @article{Jonik-Nowak2018, title = {PIP30/FAM192A is a novel regulator of the nuclear proteasome activator PA28γ}, author = {Beata Jonik-Nowak and Thoma Menneteau and Didier Fesquet and Véronique Baldin and Catherine Bonne-Andrea and Francisca Méchali and Bertrand Fabre and Prisca Boisguerin and Sylvain de Rossi and Corinne Henriquet and Martine Pugnière and Manuelle Ducoux-Petit and Odile Burlet-Schiltz and Angus I. Lamond and Philippe Fort and Séverine Boulon and Mari-Pierre Bousquet and Olivier Coux}, doi = {10.1073/pnas.1722299115}, year = {2018}, date = {2018-07-10}, journal = {Proc Natl Acad Sci U S A.}, volume = {115}, number = {28}, pages = {E6477-E6486}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Gaud, Guillaume; Roncagalli, Romain; Chaoui, Karima; Bernard, Isabelle; andCéline Colacios, Julien Familiades; Kassem, Sahar; Monsarrat, Bernard; Burlet-Schiltz, Odile; de Peredo, Anne Gonzalez; Malissen, Bernard; Saoudi, Abdelhadi The costimulatory molecule CD226 signals through VAV1 to amplify TCR signals and promote IL-17 production by CD4+ T cells Article de journal 11 (538), p. eaar3083, 2018. @article{Gaud2018, title = {The costimulatory molecule CD226 signals through VAV1 to amplify TCR signals and promote IL-17 production by CD4+ T cells}, author = {Guillaume Gaud and Romain Roncagalli and Karima Chaoui and Isabelle Bernard and Julien Familiades andCéline Colacios and Sahar Kassem and Bernard Monsarrat and Odile Burlet-Schiltz and Anne Gonzalez de Peredo and Bernard Malissen and Abdelhadi Saoudi}, doi = {10.1126/scisignal.aar3083}, year = {2018}, date = {2018-07-10}, volume = {11}, number = {538}, pages = {eaar3083}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Behrens, Christina; Biela, Inna; andThomas Botzanowski, Stéphanie Petiot-Bécard; Cianférani, Sarah; Sager, Christoph P; Klebe, Gerhard; Heine, Andreas; Reuter, Klaus Homodimer Architecture of QTRT2, the Noncatalytic Subunit of the Eukaryotic tRNA-Guanine Transglycosylase Article de journal Biochemistry, 57 (26), p. 3953–3965, 2018. @article{Behrens2018, title = {Homodimer Architecture of QTRT2, the Noncatalytic Subunit of the Eukaryotic tRNA-Guanine Transglycosylase}, author = {Christina Behrens and Inna Biela and Stéphanie Petiot-Bécard andThomas Botzanowski and Sarah Cianférani and Christoph P. Sager and Gerhard Klebe and Andreas Heine and Klaus Reuter}, doi = {10.1021/acs.biochem.8b00294}, year = {2018}, date = {2018-06-04}, journal = {Biochemistry}, volume = {57}, number = {26}, pages = {3953–3965}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Fröhlich, Tony; Hahn, Friedrich; Belmudes, Lucid; Leidenberger, Maria; Friedrich, Oliver; Kappes, Barbara; Couté, Yohann; Marschall, Manfred; Tsogoeva, Svetlana B Synthesis of Artemisinin-Derived Dimers, Trimers and Dendrimers: Investigation of Their Antimalarial and Antiviral Activities Including Putative Mechanisms of Action Article de journal Chemistry (Weinheim an Der Bergstrasse, Germany), 24 (32), p. 8103–8113, 2018, ISSN: 1521-3765. @article{frohlich_synthesis_2018, title = {Synthesis of Artemisinin-Derived Dimers, Trimers and Dendrimers: Investigation of Their Antimalarial and Antiviral Activities Including Putative Mechanisms of Action}, author = {Tony Fröhlich and Friedrich Hahn and Lucid Belmudes and Maria Leidenberger and Oliver Friedrich and Barbara Kappes and Yohann Couté and Manfred Marschall and Svetlana B Tsogoeva}, doi = {10.1002/chem.201800729}, issn = {1521-3765}, year = {2018}, date = {2018-06-01}, journal = {Chemistry (Weinheim an Der Bergstrasse, Germany)}, volume = {24}, number = {32}, pages = {8103--8113}, abstract = {Generation of dimers, trimers and dendrimers of bioactive compounds is an approach that has recently been developed for the discovery of new potent drug candidates. Herein, we present the synthesis of new artemisinin-derived dimers and dendrimers and investigate their action against malaria parasite Plasmodium falciparum 3D7 strain and human cytomegalovirus (HCMV). Dimer 7 was the most active compound (EC50 1.4 nm) in terms of antimalarial efficacy and was even more effective than the standard drugs dihydroartemisinin (EC50 2.4 nm), artesunic acid (EC50 8.9 nm) and chloroquine (EC50 9.8 nm). Trimer 4 stood out as the most active agent against HCMV in vitro replication and exerted an EC50 value of 0.026 μm, representing an even higher activity than the two reference drugs ganciclovir (EC50 2.60 μm) and artesunic acid (EC50 5.41 μm). In addition, artemisinin-derived dimer 13 and trimer 15 were for the first time both immobilized on TOYOPEARL AF-Amino-650M beads and used for mass spectrometry-based target identification experiments using total lysates of HCMV-infected primary human fibroblasts. Two major groups of novel target candidates, namely cytoskeletal and mitochondrial proteins were obtained. Two putatively compound-binding viral proteins, namely major capsid protein (MCP) and envelope glycoprotein pUL132, which are both essential for HCMV replication, were identified.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Generation of dimers, trimers and dendrimers of bioactive compounds is an approach that has recently been developed for the discovery of new potent drug candidates. Herein, we present the synthesis of new artemisinin-derived dimers and dendrimers and investigate their action against malaria parasite Plasmodium falciparum 3D7 strain and human cytomegalovirus (HCMV). Dimer 7 was the most active compound (EC50 1.4 nm) in terms of antimalarial efficacy and was even more effective than the standard drugs dihydroartemisinin (EC50 2.4 nm), artesunic acid (EC50 8.9 nm) and chloroquine (EC50 9.8 nm). Trimer 4 stood out as the most active agent against HCMV in vitro replication and exerted an EC50 value of 0.026 μm, representing an even higher activity than the two reference drugs ganciclovir (EC50 2.60 μm) and artesunic acid (EC50 5.41 μm). In addition, artemisinin-derived dimer 13 and trimer 15 were for the first time both immobilized on TOYOPEARL AF-Amino-650M beads and used for mass spectrometry-based target identification experiments using total lysates of HCMV-infected primary human fibroblasts. Two major groups of novel target candidates, namely cytoskeletal and mitochondrial proteins were obtained. Two putatively compound-binding viral proteins, namely major capsid protein (MCP) and envelope glycoprotein pUL132, which are both essential for HCMV replication, were identified. |
Jacob, Laurent; Combes, Florence; Burger, Thomas PEPA test: fast and powerful differential analysis from relative quantitative proteomics data using shared peptides Article de journal Biostatistics (Oxford, England), 2018, ISSN: 1468-4357. @article{jacob_pepa_2018, title = {PEPA test: fast and powerful differential analysis from relative quantitative proteomics data using shared peptides}, author = {Laurent Jacob and Florence Combes and Thomas Burger}, doi = {10.1093/biostatistics/kxy021}, issn = {1468-4357}, year = {2018}, date = {2018-06-01}, journal = {Biostatistics (Oxford, England)}, abstract = {We propose a new hypothesis test for the differential abundance of proteins in mass-spectrometry based relative quantification. An important feature of this type of high-throughput analyses is that it involves an enzymatic digestion of the sample proteins into peptides prior to identification and quantification. Due to numerous homology sequences, different proteins can lead to peptides with identical amino acid chains, so that their parent protein is ambiguous. These so-called shared peptides make the protein-level statistical analysis a challenge and are often not accounted for. In this article, we use a linear model describing peptide-protein relationships to build a likelihood ratio test of differential abundance for proteins. We show that the likelihood ratio statistic can be computed in linear time with the number of peptides. We also provide the asymptotic null distribution of a regularized version of our statistic. Experiments on both real and simulated datasets show that our procedures outperforms state-of-the-art methods. The procedures are available via the pepa.test function of the DAPAR Bioconductor R package.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We propose a new hypothesis test for the differential abundance of proteins in mass-spectrometry based relative quantification. An important feature of this type of high-throughput analyses is that it involves an enzymatic digestion of the sample proteins into peptides prior to identification and quantification. Due to numerous homology sequences, different proteins can lead to peptides with identical amino acid chains, so that their parent protein is ambiguous. These so-called shared peptides make the protein-level statistical analysis a challenge and are often not accounted for. In this article, we use a linear model describing peptide-protein relationships to build a likelihood ratio test of differential abundance for proteins. We show that the likelihood ratio statistic can be computed in linear time with the number of peptides. We also provide the asymptotic null distribution of a regularized version of our statistic. Experiments on both real and simulated datasets show that our procedures outperforms state-of-the-art methods. The procedures are available via the pepa.test function of the DAPAR Bioconductor R package. |
Denadai-Souza, Alexandre; Bonnart, Chrystelle; Tapias, Núria Solà; Marcellin, Marlène; andLaurent Alric, Brendan Gilmore; Bonnet, Delphine; Burlet-Schiltz, Odile; Hollenberg, Morley D; Vergnolle, Nathalie; Deraison, Céline Functional Proteomic Profiling of Secreted Serine Proteases in Health and Inflammatory Bowel Disease Article de journal Sci Rep, 8 (1), p. 7834, 2018. @article{Denadai-Souza2018, title = {Functional Proteomic Profiling of Secreted Serine Proteases in Health and Inflammatory Bowel Disease}, author = {Alexandre Denadai-Souza and Chrystelle Bonnart and Núria Solà Tapias and Marlène Marcellin and Brendan Gilmore andLaurent Alric and Delphine Bonnet and Odile Burlet-Schiltz and Morley D. Hollenberg and Nathalie Vergnolle and Céline Deraison}, doi = {10.1038/s41598-018-26282-y}, year = {2018}, date = {2018-05-18}, journal = {Sci Rep}, volume = {8}, number = {1}, pages = {7834}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Lefebvre, Cyril; Boulon, Richard; Ducoux, Manuelle; Gavalda, Sabine; Laval, Françoise; Jamet, Stevie; Eynard, Nathalie; Lemassu, Anne; Cam, Kaymeuang; Bousquet, Marie-Pierre; Bardou, Fabienne; Burlet-Schiltz, Odile; Daffé, Mamadou; Quémard, Annaïck HadD, a novel fatty acid synthase type II protein, is essential for alpha- and epoxy-mycolic acid biosynthesis and mycobacterial fitness Article de journal Sci Rep, 8 (1), p. 6034, 2018. @article{Lefebvre2018, title = {HadD, a novel fatty acid synthase type II protein, is essential for alpha- and epoxy-mycolic acid biosynthesis and mycobacterial fitness}, author = {Cyril Lefebvre and Richard Boulon and Manuelle Ducoux and Sabine Gavalda and Françoise Laval and Stevie Jamet and Nathalie Eynard and Anne Lemassu and Kaymeuang Cam and Marie-Pierre Bousquet and Fabienne Bardou and Odile Burlet-Schiltz and Mamadou Daffé and Annaïck Quémard}, doi = {10.1038/s41598-018-24380-5}, year = {2018}, date = {2018-04-16}, journal = {Sci Rep}, volume = {8}, number = {1}, pages = {6034}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Cayrol, Corinne; Duval, Anaïs; Schmitt, Pauline; Roga, Stéphane; Stella, Mylène Camusand Alexandre; Burlet-Schiltz, Odile; Gonzalez de Peredo, Anne ; Girard, Jean-Philippe Environmental allergens induce allergic inflammation through proteolytic maturation of IL-33 Article de journal Nat Immunol, 19 (4), p. 375-385, 2018. @article{Cayrol2018, title = {Environmental allergens induce allergic inflammation through proteolytic maturation of IL-33}, author = {Corinne Cayrol and Anaïs Duval and Pauline Schmitt and Stéphane Roga and Mylène Camusand Alexandre Stella and Odile Burlet-Schiltz and Anne {Gonzalez de Peredo} and Jean-Philippe Girard}, doi = {10.1038/s41590-018-0067-5 }, year = {2018}, date = {2018-03-21}, journal = {Nat Immunol}, volume = {19}, number = {4}, pages = {375-385}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Garcia, Lény; Girod, Marion; Rompais, Magali; Dugourd, Philippe; Carapito, Christine; Lemoine, Jérôme Data-Independent Acquisition Coupled to Visible Laser-Induced Dissociation at 473 nm (DIA-LID) for Peptide-Centric Specific Analysis of Cysteine-Containing Peptide Subset Article de journal Anal Chem., 90 (6), p. 3928-3935, 2018. @article{Garcia2018, title = {Data-Independent Acquisition Coupled to Visible Laser-Induced Dissociation at 473 nm (DIA-LID) for Peptide-Centric Specific Analysis of Cysteine-Containing Peptide Subset}, author = {Lény Garcia and Marion Girod and Magali Rompais and Philippe Dugourd and Christine Carapito and Jérôme Lemoine}, doi = {10.1021/acs.analchem.7b04821}, year = {2018}, date = {2018-03-20}, journal = {Anal Chem.}, volume = {90}, number = {6}, pages = {3928-3935}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Dovgan, I; Erb, S; Hessmann, S; Ursuegui, S; Michel, C; Muller, C; Chaubet, G; Cianférani, S; Wagner, A Arginine-selective bioconjugation with 4-azidophenyl glyoxal: application to the single and dual functionalisation of native antibodies Article de journal Org Biomol Chem., 16 (8), p. 1305-1311, 2018. @article{RN1311, title = {Arginine-selective bioconjugation with 4-azidophenyl glyoxal: application to the single and dual functionalisation of native antibodies}, author = {I Dovgan and S Erb and S Hessmann and S Ursuegui and C Michel and C Muller and G Chaubet and S Cianférani and A Wagner}, doi = {10.1039/c7ob02844j}, year = {2018}, date = {2018-02-21}, journal = {Org Biomol Chem.}, volume = {16}, number = {8}, pages = {1305-1311}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Issa, N; Guillaumot, N; Lauret, E; Matt, N; Schaeffer-Reiss, C; Van Dorsselaer, A; Reichhart, J M; Veillard, F The Circulating Protease Persephone Is an Immune Sensor for Microbial Proteolytic Activities Upstream of the Drosophila Toll Pathway Article de journal Mol Cell, 69 (4), p. 539-550 e6, 2018. @article{RN1312, title = {The Circulating Protease Persephone Is an Immune Sensor for Microbial Proteolytic Activities Upstream of the Drosophila Toll Pathway}, author = {N Issa and N Guillaumot and E Lauret and N Matt and C Schaeffer-Reiss and A {Van Dorsselaer} and J M Reichhart and F Veillard}, doi = {10.1016/j.molcel.2018.01.029}, year = {2018}, date = {2018-02-15}, journal = {Mol Cell}, volume = {69}, number = {4}, pages = {539-550 e6}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Ehkirch, A; D'Atri, V; Rouvière, F; Hernandez-Alba, O; Goyon, A; Colas, O; Sarrut, M; Beck, A; Guillarme, D; Heinisch, S; Cianférani, S An online four-dimensional HICxSEC-IMxMS methodology for proof-of-concept characterization of antibody drug conjugates Article de journal Anal Chem., 90 (3), p. 1578-1586, 2018. @article{RN1307, title = {An online four-dimensional HICxSEC-IMxMS methodology for proof-of-concept characterization of antibody drug conjugates}, author = {A Ehkirch and V D'Atri and F Rouvière and O Hernandez-Alba and A Goyon and O Colas and M Sarrut and A Beck and D Guillarme and S Heinisch and S Cianférani}, doi = {10.1021/acs.analchem.7b02110}, year = {2018}, date = {2018-02-06}, journal = {Anal Chem.}, volume = {90}, number = {3}, pages = {1578-1586}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Lacombe, Maud; Marie-Desvergne, Caroline; Combes, Florence; Kraut, Alexandra; Bruley, Christophe; Vandenbrouck, Yves; Mossuz, Véronique Chamel; Couté, Yohann; Brun, Virginie Proteomic characterization of human exhaled breath condensate Article de journal Journal of Breath Research, 12 (2), p. 021001, 2018, ISSN: 1752-7163. @article{lacombe_proteomic_2018, title = {Proteomic characterization of human exhaled breath condensate}, author = {Maud Lacombe and Caroline Marie-Desvergne and Florence Combes and Alexandra Kraut and Christophe Bruley and Yves Vandenbrouck and Véronique Chamel Mossuz and Yohann Couté and Virginie Brun}, doi = {10.1088/1752-7163/aa9e71}, issn = {1752-7163}, year = {2018}, date = {2018-02-01}, journal = {Journal of Breath Research}, volume = {12}, number = {2}, pages = {021001}, abstract = {To improve biomedical knowledge and to support biomarker discovery studies, it is essential to establish comprehensive proteome maps for human tissues and biofluids, and to make them publicly accessible. In this study, we performed an in-depth proteomics characterization of exhaled breath condensate (EBC), a sample obtained non-invasively by condensation of exhaled air that contains submicron droplets of airway lining fluid. Two pooled samples of EBC, each obtained from 10 healthy donors, were processed using a straightforward protocol based on sample lyophilization, in-gel digestion and liquid chromatography tandem-mass spectrometry analysis. Two 'technical' control samples were processed in parallel to the pooled samples to correct for exogenous protein contamination. A total of 229 unique proteins were identified in EBC among which 153 proteins were detected in both EBC pooled samples. A detailed bioinformatics analysis of these 153 proteins showed that most of the proteins identified corresponded to proteins secreted in the respiratory tract (lung, bronchi). Eight proteins were salivary proteins. Our dataset is described and has been made accessible through the ProteomeXchange database (dataset identifier: PXD007591) and is expected to be useful for future MS-based biomarker studies using EBC as the diagnostic specimen.}, keywords = {}, pubstate = {published}, tppubtype = {article} } To improve biomedical knowledge and to support biomarker discovery studies, it is essential to establish comprehensive proteome maps for human tissues and biofluids, and to make them publicly accessible. In this study, we performed an in-depth proteomics characterization of exhaled breath condensate (EBC), a sample obtained non-invasively by condensation of exhaled air that contains submicron droplets of airway lining fluid. Two pooled samples of EBC, each obtained from 10 healthy donors, were processed using a straightforward protocol based on sample lyophilization, in-gel digestion and liquid chromatography tandem-mass spectrometry analysis. Two 'technical' control samples were processed in parallel to the pooled samples to correct for exogenous protein contamination. A total of 229 unique proteins were identified in EBC among which 153 proteins were detected in both EBC pooled samples. A detailed bioinformatics analysis of these 153 proteins showed that most of the proteins identified corresponded to proteins secreted in the respiratory tract (lung, bronchi). Eight proteins were salivary proteins. Our dataset is described and has been made accessible through the ProteomeXchange database (dataset identifier: PXD007591) and is expected to be useful for future MS-based biomarker studies using EBC as the diagnostic specimen. |
Grzela, R; Nusbaum, J; Fieulaine, S; Lavecchia, F; Desmadril, M; Nhiri, N; Van Dorsselaer, A; Cianférani, S; Jacquet, E; Meinnel, T; Giglione, C Peptide deformylases from Vibrio parahaemolyticus phage and bacteria display similar deformylase activity and inhibitor binding clefts Article de journal Biochim Biophys Acta., 1866 (2), p. 348-355, 2018. @article{RN1310, title = {Peptide deformylases from Vibrio parahaemolyticus phage and bacteria display similar deformylase activity and inhibitor binding clefts}, author = {R Grzela and J Nusbaum and S Fieulaine and F Lavecchia and M Desmadril and N Nhiri and A {Van Dorsselaer} and S Cianférani and E Jacquet and T Meinnel and C Giglione}, doi = {10.1016/j.bbapap.2017.10.007}, year = {2018}, date = {2018-02-01}, journal = {Biochim Biophys Acta.}, volume = {1866}, number = {2}, pages = {348-355}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
A, Métais; I, Lamsoul; A, Melet; S, Uttenweiler-Joseph; R, Poincloux; S, Stefanovic; A, Valière; de A, Gonzalez Peredo; A, Stella; O, Burlet-Schiltz; S, Zaffran; PG, Lutz; C, Moog-Lutz Asb2α-Filamin A Axis Is Essential for Actin Cytoskeleton Remodeling During Heart Development Article de journal Circ Res., 122 (6), p. 34-48, 2018. @article{A2018, title = {Asb2α-Filamin A Axis Is Essential for Actin Cytoskeleton Remodeling During Heart Development}, author = {Métais A and Lamsoul I and Melet A and Uttenweiler-Joseph S and Poincloux R and Stefanovic S and Valière A and Gonzalez de Peredo A and Stella A and Burlet-Schiltz O and Zaffran S and Lutz PG and Moog-Lutz C}, doi = {10.1161/CIRCRESAHA.117.312015}, year = {2018}, date = {2018-01-26}, journal = {Circ Res.}, volume = {122}, number = {6}, pages = {34-48}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Mori, M; Kovalenko, L; Malancona, S; Saladini, F; Forni, De D; Pires, M; Humbert, N; Real, E; Botzanowski, T; Cianférani, S; Giannini, A; Lang, MC. Dasso; Cugia, G; Poddesu, B; Lori, F; Zazzi, M; Harper, S; Summa, V; Mely, Y; Botta, M Structure-Based Identification of HIV-1 Nucleocapsid Protein Inhibitors Active against Wild-Type and Drug-Resistant HIV-1 Strains Article de journal ACS Chem Biol., 13 (1), p. 253-266, 2018. @article{RN1308, title = {Structure-Based Identification of HIV-1 Nucleocapsid Protein Inhibitors Active against Wild-Type and Drug-Resistant HIV-1 Strains}, author = {M Mori and L Kovalenko and S Malancona and F Saladini and D De Forni and M Pires and N Humbert and E Real and T Botzanowski and S Cianférani and A Giannini and MC. Dasso Lang and G Cugia and B Poddesu and F Lori and M Zazzi and S Harper and V Summa and Y Mely and M Botta}, doi = {10.1021/acschembio.7b00907}, year = {2018}, date = {2018-01-19}, journal = {ACS Chem Biol.}, volume = {13}, number = {1}, pages = {253-266}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Husson, G; Delangle, A; O'Hara, J; Cianférani, S; Gervais, A; Van Dorsselaer, A; Bracewell, D; Carapito, C Dual Data-Independent Acquisition Approach Combining Global HCP Profiling and Absolute Quantification of Key Impurities during Bioprocess Development Article de journal Anal Chem., 90 (2), p. 1241-1247, 2018. @article{RN1306, title = {Dual Data-Independent Acquisition Approach Combining Global HCP Profiling and Absolute Quantification of Key Impurities during Bioprocess Development}, author = {G Husson and A Delangle and J O'Hara and S Cianférani and A Gervais and A {Van Dorsselaer} and D Bracewell and C Carapito}, doi = {10.1021/acs.analchem.7b03965 }, year = {2018}, date = {2018-01-16}, journal = {Anal Chem.}, volume = {90}, number = {2}, pages = {1241-1247}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
L, Favre; A, Ortalo-Magné; C, Pichereaux; A, Gargaros; O, Burlet-Schiltz; V, Cotelle; G., Culioli Metabolome and proteome changes between biofilm and planktonic phenotypes of the marine bacterium Pseudoalteromonas lipolytica TC8 Article de journal Biofouling, 34 (2), p. 132-148, 2018. @article{L2018, title = {Metabolome and proteome changes between biofilm and planktonic phenotypes of the marine bacterium Pseudoalteromonas lipolytica TC8}, author = {Favre L and Ortalo-Magné A and Pichereaux C and Gargaros A and Burlet-Schiltz O and Cotelle V and Culioli G.}, doi = {10.1080/08927014.2017.1413551}, year = {2018}, date = {2018-01-10}, journal = {Biofouling}, volume = {34}, number = {2}, pages = {132-148}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Rayapuram, Naganand; Bigeard, Jean; Alhoraibi, Hanna; Bonhomme, Ludovic; Hesse, Anne-Marie; Vinh, Joëlle; Hirt, Heribert; Pflieger, Delphine Quantitative Phosphoproteomic Analysis Reveals Shared and Specific Targets ofArabidopsisMitogen-Activated Protein Kinases (MAPKs) MPK3, MPK4, and MPK6 Article de journal Molecular & cellular proteomics: MCP, 17 (1), p. 61–80, 2018, ISSN: 1535-9484. @article{rayapuram_quantitative_2018, title = {Quantitative Phosphoproteomic Analysis Reveals Shared and Specific Targets ofArabidopsisMitogen-Activated Protein Kinases (MAPKs) MPK3, MPK4, and MPK6}, author = {Naganand Rayapuram and Jean Bigeard and Hanna Alhoraibi and Ludovic Bonhomme and Anne-Marie Hesse and Joëlle Vinh and Heribert Hirt and Delphine Pflieger}, doi = {10.1074/mcp.RA117.000135}, issn = {1535-9484}, year = {2018}, date = {2018-01-01}, journal = {Molecular & cellular proteomics: MCP}, volume = {17}, number = {1}, pages = {61--80}, abstract = {In Arabidopsis, mitogen-activated protein kinases MPK3, MPK4, and MPK6 constitute essential relays for a variety of functions including cell division, development and innate immunity. Although some substrates of MPK3, MPK4 and MPK6 have been identified, the picture is still far from complete. To identify substrates of these MAPKs likely involved in cell division, growth and development we compared the phosphoproteomes of wild-type andmpk3,mpk4, andmpk6.To study the function of these MAPKs in innate immunity, we analyzed their phosphoproteomes following microbe-associated molecular pattern (MAMP) treatment. Partially overlapping substrates were retrieved for all three MAPKs, showing target specificity to one, two or all three MAPKs in different biological processes. More precisely, our results illustrate the fact that the entity to be defined as a specific or a shared substrate for MAPKs is not a phosphoprotein but a particular (S/T)P phosphorylation site in a given protein. One hundred fifty-two peptides were identified to be differentially phosphorylated in response to MAMP treatment and/or when compared between genotypes and 70 of them could be classified as putative MAPK targets. Biochemical analysis of a number of putative MAPK substrates by phosphorylation and interaction assays confirmed the global phosphoproteome approach. Our study also expands the set of MAPK substrates to involve other protein kinases, including calcium-dependent (CDPK) and sugar nonfermenting (SnRK) protein kinases.}, keywords = {}, pubstate = {published}, tppubtype = {article} } In Arabidopsis, mitogen-activated protein kinases MPK3, MPK4, and MPK6 constitute essential relays for a variety of functions including cell division, development and innate immunity. Although some substrates of MPK3, MPK4 and MPK6 have been identified, the picture is still far from complete. To identify substrates of these MAPKs likely involved in cell division, growth and development we compared the phosphoproteomes of wild-type andmpk3,mpk4, andmpk6.To study the function of these MAPKs in innate immunity, we analyzed their phosphoproteomes following microbe-associated molecular pattern (MAMP) treatment. Partially overlapping substrates were retrieved for all three MAPKs, showing target specificity to one, two or all three MAPKs in different biological processes. More precisely, our results illustrate the fact that the entity to be defined as a specific or a shared substrate for MAPKs is not a phosphoprotein but a particular (S/T)P phosphorylation site in a given protein. One hundred fifty-two peptides were identified to be differentially phosphorylated in response to MAMP treatment and/or when compared between genotypes and 70 of them could be classified as putative MAPK targets. Biochemical analysis of a number of putative MAPK substrates by phosphorylation and interaction assays confirmed the global phosphoproteome approach. Our study also expands the set of MAPK substrates to involve other protein kinases, including calcium-dependent (CDPK) and sugar nonfermenting (SnRK) protein kinases. |
Burger, Thomas Gentle Introduction to the Statistical Foundations of False Discovery Rate in Quantitative Proteomics Article de journal Journal of Proteome Research, 17 (1), p. 12–22, 2018, ISSN: 1535-3907. @article{burger_gentle_2018, title = {Gentle Introduction to the Statistical Foundations of False Discovery Rate in Quantitative Proteomics}, author = {Thomas Burger}, doi = {10.1021/acs.jproteome.7b00170}, issn = {1535-3907}, year = {2018}, date = {2018-01-01}, journal = {Journal of Proteome Research}, volume = {17}, number = {1}, pages = {12--22}, abstract = {The vocabulary of theoretical statistics can be difficult to embrace from the viewpoint of computational proteomics research, even though the notions it conveys are essential to publication guidelines. For example, "adjusted p-values", "q-values", and "false discovery rates" are essentially similar concepts, whereas "false discovery rate" and "false discovery proportion" must not be confused, even though "rate" and "proportion" are related in everyday language. In the interdisciplinary context of proteomics, such subtleties may cause misunderstandings. This article aims to provide an easy-to-understand explanation of these four notions (and a few other related ones). Their statistical foundations are dealt with from a perspective that largely relies on intuition, addressing mainly protein quantification but also, to some extent, peptide identification. In addition, a clear distinction is made between concepts that define an individual property (i.e., related to a peptide or a protein) and those that define a set property (i.e., related to a list of peptides or proteins).}, keywords = {}, pubstate = {published}, tppubtype = {article} } The vocabulary of theoretical statistics can be difficult to embrace from the viewpoint of computational proteomics research, even though the notions it conveys are essential to publication guidelines. For example, "adjusted p-values", "q-values", and "false discovery rates" are essentially similar concepts, whereas "false discovery rate" and "false discovery proportion" must not be confused, even though "rate" and "proportion" are related in everyday language. In the interdisciplinary context of proteomics, such subtleties may cause misunderstandings. This article aims to provide an easy-to-understand explanation of these four notions (and a few other related ones). Their statistical foundations are dealt with from a perspective that largely relies on intuition, addressing mainly protein quantification but also, to some extent, peptide identification. In addition, a clear distinction is made between concepts that define an individual property (i.e., related to a peptide or a protein) and those that define a set property (i.e., related to a list of peptides or proteins). |
Kennani, Sara El; Crespo, Marion; Govin, Jérôme; Pflieger, Delphine Proteomic Analysis of Histone Variants and Their PTMs: Strategies and Pitfalls Article de journal Proteomes, 6 (3), 2018, ISSN: 2227-7382. @article{el_kennani_proteomic_2018, title = {Proteomic Analysis of Histone Variants and Their PTMs: Strategies and Pitfalls}, author = {Sara El Kennani and Marion Crespo and Jérôme Govin and Delphine Pflieger}, doi = {10.3390/proteomes6030029}, issn = {2227-7382}, year = {2018}, date = {2018-01-01}, journal = {Proteomes}, volume = {6}, number = {3}, abstract = {Epigenetic modifications contribute to the determination of cell fate and differentiation. The molecular mechanisms underlying histone variants and post-translational modifications (PTMs) have been studied in the contexts of development, differentiation, and disease. Antibody-based assays have classically been used to target PTMs, but these approaches fail to reveal combinatorial patterns of modifications. In addition, some histone variants are so similar to canonical histones that antibodies have difficulty distinguishing between these isoforms. Mass spectrometry (MS) has progressively developed as a powerful technology for the study of histone variants and their PTMs. Indeed, MS analyses highlighted exquisitely complex combinations of PTMs, suggesting “crosstalk” between them, and also revealed that PTM patterns are often variant-specific. Even though the sensitivity and acquisition speed of MS instruments have considerably increased alongside the development of computational tools for the study of multiple PTMs, it remains challenging to correctly describe the landscape of histone PTMs, and in particular to confidently assign modifications to specific amino acids. Here, we provide an inventory of MS-based strategies and of the pitfalls inherent to histone PTM and variant characterization, while stressing the complex interplay between PTMs and histone sequence variations. We will particularly illustrate the roles played by MS-based analyses in identifying and quantifying histone variants and modifications.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Epigenetic modifications contribute to the determination of cell fate and differentiation. The molecular mechanisms underlying histone variants and post-translational modifications (PTMs) have been studied in the contexts of development, differentiation, and disease. Antibody-based assays have classically been used to target PTMs, but these approaches fail to reveal combinatorial patterns of modifications. In addition, some histone variants are so similar to canonical histones that antibodies have difficulty distinguishing between these isoforms. Mass spectrometry (MS) has progressively developed as a powerful technology for the study of histone variants and their PTMs. Indeed, MS analyses highlighted exquisitely complex combinations of PTMs, suggesting “crosstalk” between them, and also revealed that PTM patterns are often variant-specific. Even though the sensitivity and acquisition speed of MS instruments have considerably increased alongside the development of computational tools for the study of multiple PTMs, it remains challenging to correctly describe the landscape of histone PTMs, and in particular to confidently assign modifications to specific amino acids. Here, we provide an inventory of MS-based strategies and of the pitfalls inherent to histone PTM and variant characterization, while stressing the complex interplay between PTMs and histone sequence variations. We will particularly illustrate the roles played by MS-based analyses in identifying and quantifying histone variants and modifications. |
Kennani, Sara El; Adrait, Annie; Permiakova, Olga; Hesse, Anne-Marie; Ialy-Radio, Côme; Ferro, Myriam; Brun, Virginie; Cocquet, Julie; Govin, Jérôme; Pflieger, Delphine Systematic quantitative analysis of Ħ2A and Ħ2B variants by targeted proteomics Article de journal Epigenetics & Chromatin, 11 (1), p. 2, 2018, ISSN: 1756-8935. @article{el_kennani_systematic_2018, title = {Systematic quantitative analysis of Ħ2A and Ħ2B variants by targeted proteomics}, author = {Sara El Kennani and Annie Adrait and Olga Permiakova and Anne-Marie Hesse and Côme Ialy-Radio and Myriam Ferro and Virginie Brun and Julie Cocquet and Jérôme Govin and Delphine Pflieger}, doi = {10.1186/s13072-017-0172-y}, issn = {1756-8935}, year = {2018}, date = {2018-01-01}, journal = {Epigenetics & Chromatin}, volume = {11}, number = {1}, pages = {2}, abstract = {BACKGROUND: Histones organize DNA into chromatin through a variety of processes. Among them, a vast diversity of histone variants can be incorporated into chromatin and finely modulate its organization and functionality. Classically, the study of histone variants has largely relied on antibody-based assays. However, antibodies have a limited efficiency to discriminate between highly similar histone variants. RESULTS: In this study, we established a mass spectrometry-based analysis to address this challenge. We developed a targeted proteomics method, using selected reaction monitoring or parallel reaction monitoring, to quantify a maximum number of histone variants in a single multiplexed assay, even when histones are present in a crude extract. This strategy was developed on H2A and H2B variants, using 55 peptides corresponding to 25 different histone sequences, among which a few differ by a single amino acid. The methodology was then applied to mouse testis extracts in which almost all histone variants are expressed. It confirmed the abundance profiles of several testis-specific histones during successive stages of spermatogenesis and the existence of predicted H2A.L.1 isoforms. This methodology was also used to explore the over-expression pattern of H2A.L.1 isoforms in a mouse model of male infertility. CONCLUSIONS: Our results demonstrate that targeted proteomics is a powerful method to quantify highly similar histone variants and isoforms. The developed method can be easily transposed to the study of human histone variants, whose abundance can be deregulated in various diseases.}, keywords = {}, pubstate = {published}, tppubtype = {article} } BACKGROUND: Histones organize DNA into chromatin through a variety of processes. Among them, a vast diversity of histone variants can be incorporated into chromatin and finely modulate its organization and functionality. Classically, the study of histone variants has largely relied on antibody-based assays. However, antibodies have a limited efficiency to discriminate between highly similar histone variants. RESULTS: In this study, we established a mass spectrometry-based analysis to address this challenge. We developed a targeted proteomics method, using selected reaction monitoring or parallel reaction monitoring, to quantify a maximum number of histone variants in a single multiplexed assay, even when histones are present in a crude extract. This strategy was developed on H2A and H2B variants, using 55 peptides corresponding to 25 different histone sequences, among which a few differ by a single amino acid. The methodology was then applied to mouse testis extracts in which almost all histone variants are expressed. It confirmed the abundance profiles of several testis-specific histones during successive stages of spermatogenesis and the existence of predicted H2A.L.1 isoforms. This methodology was also used to explore the over-expression pattern of H2A.L.1 isoforms in a mouse model of male infertility. CONCLUSIONS: Our results demonstrate that targeted proteomics is a powerful method to quantify highly similar histone variants and isoforms. The developed method can be easily transposed to the study of human histone variants, whose abundance can be deregulated in various diseases. |
Adam, Céline; Guérois, Raphaël; Citarella, Anna; Verardi, Laura; Adolphe, Florine; Béneut, Claire; Sommermeyer, Vérane; Ramus, Claire; Govin, Jérôme; Couté, Yohann; Borde, Valérie The PHD finger protein Spp1 has distinct functions in the Set1 and the meiotic DSB formation complexes Article de journal PLoS genetics, 14 (2), p. e1007223, 2018, ISSN: 1553-7404. @article{adam_phd_2018, title = {The PHD finger protein Spp1 has distinct functions in the Set1 and the meiotic DSB formation complexes}, author = {Céline Adam and Raphaël Guérois and Anna Citarella and Laura Verardi and Florine Adolphe and Claire Béneut and Vérane Sommermeyer and Claire Ramus and Jérôme Govin and Yohann Couté and Valérie Borde}, doi = {10.1371/journal.pgen.1007223}, issn = {1553-7404}, year = {2018}, date = {2018-01-01}, journal = {PLoS genetics}, volume = {14}, number = {2}, pages = {e1007223}, abstract = {Histone H3K4 methylation is a feature of meiotic recombination hotspots shared by many organisms including plants and mammals. Meiotic recombination is initiated by programmed double-strand break (DSB) formation that in budding yeast takes place in gene promoters and is promoted by histone H3K4 di/trimethylation. This histone modification is recognized by Spp1, a PHD finger containing protein that belongs to the conserved histone H3K4 methyltransferase Set1 complex. During meiosis, Spp1 binds H3K4me3 and interacts with a DSB protein, Mer2, to promote DSB formation close to gene promoters. How Set1 complex- and Mer2- related functions of Spp1 are connected is not clear. Here, combining genome-wide localization analyses, biochemical approaches and the use of separation of function mutants, we show that Spp1 is present within two distinct complexes in meiotic cells, the Set1 and the Mer2 complexes. Disrupting the Spp1-Set1 interaction mildly decreases H3K4me3 levels and does not affect meiotic recombination initiation. Conversely, the Spp1-Mer2 interaction is required for normal meiotic recombination initiation, but dispensable for Set1 complex-mediated histone H3K4 methylation. Finally, we provide evidence that Spp1 preserves normal H3K4me3 levels independently of the Set1 complex. We propose a model where Spp1 works in three ways to promote recombination initiation: first by depositing histone H3K4 methylation (Set1 complex), next by "reading" and protecting histone H3K4 methylation, and finally by making the link with the chromosome axis (Mer2-Spp1 complex). This work deciphers the precise roles of Spp1 in meiotic recombination and opens perspectives to study its functions in other organisms where H3K4me3 is also present at recombination hotspots.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Histone H3K4 methylation is a feature of meiotic recombination hotspots shared by many organisms including plants and mammals. Meiotic recombination is initiated by programmed double-strand break (DSB) formation that in budding yeast takes place in gene promoters and is promoted by histone H3K4 di/trimethylation. This histone modification is recognized by Spp1, a PHD finger containing protein that belongs to the conserved histone H3K4 methyltransferase Set1 complex. During meiosis, Spp1 binds H3K4me3 and interacts with a DSB protein, Mer2, to promote DSB formation close to gene promoters. How Set1 complex- and Mer2- related functions of Spp1 are connected is not clear. Here, combining genome-wide localization analyses, biochemical approaches and the use of separation of function mutants, we show that Spp1 is present within two distinct complexes in meiotic cells, the Set1 and the Mer2 complexes. Disrupting the Spp1-Set1 interaction mildly decreases H3K4me3 levels and does not affect meiotic recombination initiation. Conversely, the Spp1-Mer2 interaction is required for normal meiotic recombination initiation, but dispensable for Set1 complex-mediated histone H3K4 methylation. Finally, we provide evidence that Spp1 preserves normal H3K4me3 levels independently of the Set1 complex. We propose a model where Spp1 works in three ways to promote recombination initiation: first by depositing histone H3K4 methylation (Set1 complex), next by "reading" and protecting histone H3K4 methylation, and finally by making the link with the chromosome axis (Mer2-Spp1 complex). This work deciphers the precise roles of Spp1 in meiotic recombination and opens perspectives to study its functions in other organisms where H3K4me3 is also present at recombination hotspots. |
Muyt, Arnaud De; Pyatnitskaya, Alexandra; Andréani, Jessica; Ranjha, Lepakshi; Ramus, Claire; Laureau, Raphaëlle; Fernandez-Vega, Ambra; Holoch, Daniel; Girard, Elodie; Govin, Jérome; Margueron, Raphaël; Couté, Yohann; Cejka, Petr; Guérois, Raphaël; Borde, Valérie A meiotic XPF-ERCC1-like complex recognizes joint molecule recombination intermediates to promote crossover formation Article de journal Genes & Development, 32 (3-4), p. 283–296, 2018, ISSN: 1549-5477. @article{de_muyt_meiotic_2018, title = {A meiotic XPF-ERCC1-like complex recognizes joint molecule recombination intermediates to promote crossover formation}, author = {Arnaud De Muyt and Alexandra Pyatnitskaya and Jessica Andréani and Lepakshi Ranjha and Claire Ramus and Raphaëlle Laureau and Ambra Fernandez-Vega and Daniel Holoch and Elodie Girard and Jérome Govin and Raphaël Margueron and Yohann Couté and Petr Cejka and Raphaël Guérois and Valérie Borde}, doi = {10.1101/gad.308510.117}, issn = {1549-5477}, year = {2018}, date = {2018-01-01}, journal = {Genes & Development}, volume = {32}, number = {3-4}, pages = {283--296}, abstract = {Meiotic crossover formation requires the stabilization of early recombination intermediates by a set of proteins and occurs within the environment of the chromosome axis, a structure important for the regulation of meiotic recombination events. The molecular mechanisms underlying and connecting crossover recombination and axis localization are elusive. Here, we identified the ZZS (Zip2-Zip4-Spo16) complex, required for crossover formation, which carries two distinct activities: one provided by Zip4, which acts as hub through physical interactions with components of the chromosome axis and the crossover machinery, and the other carried by Zip2 and Spo16, which preferentially bind branched DNA molecules in vitro. We found that Zip2 and Spo16 share structural similarities to the structure-specific XPF-ERCC1 nuclease, although it lacks endonuclease activity. The XPF domain of Zip2 is required for crossover formation, suggesting that, together with Spo16, it has a noncatalytic DNA recognition function. Our results suggest that the ZZS complex shepherds recombination intermediates toward crossovers as a dynamic structural module that connects recombination events to the chromosome axis. The identification of the ZZS complex improves our understanding of the various activities required for crossover implementation and is likely applicable to other organisms, including mammals.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Meiotic crossover formation requires the stabilization of early recombination intermediates by a set of proteins and occurs within the environment of the chromosome axis, a structure important for the regulation of meiotic recombination events. The molecular mechanisms underlying and connecting crossover recombination and axis localization are elusive. Here, we identified the ZZS (Zip2-Zip4-Spo16) complex, required for crossover formation, which carries two distinct activities: one provided by Zip4, which acts as hub through physical interactions with components of the chromosome axis and the crossover machinery, and the other carried by Zip2 and Spo16, which preferentially bind branched DNA molecules in vitro. We found that Zip2 and Spo16 share structural similarities to the structure-specific XPF-ERCC1 nuclease, although it lacks endonuclease activity. The XPF domain of Zip2 is required for crossover formation, suggesting that, together with Spo16, it has a noncatalytic DNA recognition function. Our results suggest that the ZZS complex shepherds recombination intermediates toward crossovers as a dynamic structural module that connects recombination events to the chromosome axis. The identification of the ZZS complex improves our understanding of the various activities required for crossover implementation and is likely applicable to other organisms, including mammals. |
Petosa, Carlo; Govin, Jérôme; Mietton, Flore [A new hope to fight invasive fungal infection] Article de journal Medecine Sciences: M/S, 34 (2), p. 123–125, 2018, ISSN: 1958-5381. @article{petosa_[new_2018, title = {[A new hope to fight invasive fungal infection]}, author = {Carlo Petosa and Jérôme Govin and Flore Mietton}, doi = {10.1051/medsci/20183402007}, issn = {1958-5381}, year = {2018}, date = {2018-01-01}, journal = {Medecine Sciences: M/S}, volume = {34}, number = {2}, pages = {123--125}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Garnaud, Cécile; García-Oliver, Encar; Wang, Yan; Maubon, Danièle; Bailly, Sébastien; Despinasse, Quentin; Champleboux, Morgane; Govin, Jérôme; Cornet, Muriel The Rim Pathway Mediates Antifungal Tolerance in Candida albicans through Newly Identified Rim101 Transcriptional Targets, Including Hsp90 and Ipt1 Article de journal Antimicrobial Agents and Chemotherapy, 62 (3), 2018, ISSN: 1098-6596. @article{garnaud_rim_2018, title = {The Rim Pathway Mediates Antifungal Tolerance in Candida albicans through Newly Identified Rim101 Transcriptional Targets, Including Hsp90 and Ipt1}, author = {Cécile Garnaud and Encar García-Oliver and Yan Wang and Danièle Maubon and Sébastien Bailly and Quentin Despinasse and Morgane Champleboux and Jérôme Govin and Muriel Cornet}, doi = {10.1128/AAC.01785-17}, issn = {1098-6596}, year = {2018}, date = {2018-01-01}, journal = {Antimicrobial Agents and Chemotherapy}, volume = {62}, number = {3}, abstract = {Invasive candidiasis (IC) is a major cause of morbidity and mortality despite antifungal treatment. Azoles and echinocandins are used as first-line therapies for IC. However, their efficacy is limited by yeast tolerance and the emergence of acquired resistance. Tolerance is a reversible stage created due to the yeast's capacity to counter antifungal drug exposure, leading to persistent growth. For Candida albicans, multiple stress signaling pathways have been shown to contribute to this adaptation. Among them, the pH-responsive Rim pathway, through its transcription factor Rim101p, was shown to mediate azole and echinocandin tolerance. The Rim pathway is fungus specific, is conserved among the members of the fungal kingdom, and plays a key role in pathogenesis and virulence. The present study aimed at confirming the role of Rim101p and investigating the implication of the other Rim proteins in antifungal tolerance in C. albicans, as well as the mechanisms underlying it. Time-kill curve experiments and colony formation tests showed that genetic inhibition of all the Rim factors enhances echinocandin and azole antifungal activity. Through RNA sequencing analysis of a rim101-/- mutant, a strain constitutively overexpressing RIM101, and control strains, we discovered novel Rim-dependent genes involved in tolerance, including HSP90, encoding a major molecular chaperone, and IPT1, involved in sphingolipid biosynthesis. Rim mutants were also hypersensitive to pharmacological inhibition of Hsp90. Taken together, these data suggest that Rim101 acts upstream of Hsp90 and that targeting the Rim pathway in combination with existing antifungal drugs may represent a promising antifungal strategy to indirectly but specifically target Hsp90 in yeasts.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Invasive candidiasis (IC) is a major cause of morbidity and mortality despite antifungal treatment. Azoles and echinocandins are used as first-line therapies for IC. However, their efficacy is limited by yeast tolerance and the emergence of acquired resistance. Tolerance is a reversible stage created due to the yeast's capacity to counter antifungal drug exposure, leading to persistent growth. For Candida albicans, multiple stress signaling pathways have been shown to contribute to this adaptation. Among them, the pH-responsive Rim pathway, through its transcription factor Rim101p, was shown to mediate azole and echinocandin tolerance. The Rim pathway is fungus specific, is conserved among the members of the fungal kingdom, and plays a key role in pathogenesis and virulence. The present study aimed at confirming the role of Rim101p and investigating the implication of the other Rim proteins in antifungal tolerance in C. albicans, as well as the mechanisms underlying it. Time-kill curve experiments and colony formation tests showed that genetic inhibition of all the Rim factors enhances echinocandin and azole antifungal activity. Through RNA sequencing analysis of a rim101-/- mutant, a strain constitutively overexpressing RIM101, and control strains, we discovered novel Rim-dependent genes involved in tolerance, including HSP90, encoding a major molecular chaperone, and IPT1, involved in sphingolipid biosynthesis. Rim mutants were also hypersensitive to pharmacological inhibition of Hsp90. Taken together, these data suggest that Rim101 acts upstream of Hsp90 and that targeting the Rim pathway in combination with existing antifungal drugs may represent a promising antifungal strategy to indirectly but specifically target Hsp90 in yeasts. |
He, Huan; Brenier-Pinchart, Marie-Pierre; Braun, Laurence; Kraut, Alexandra; Touquet, Bastien; Couté, Yohann; Tardieux, Isabelle; Hakimi, Mohamed-Ali; Bougdour, Alexandre Characterization of a Toxoplasma effector uncovers an alternative GSK3/β-catenin-regulatory pathway of inflammation Article de journal eLife, 7 , 2018, ISSN: 2050-084X. @article{he_characterization_2018, title = {Characterization of a Toxoplasma effector uncovers an alternative GSK3/β-catenin-regulatory pathway of inflammation}, author = {Huan He and Marie-Pierre Brenier-Pinchart and Laurence Braun and Alexandra Kraut and Bastien Touquet and Yohann Couté and Isabelle Tardieux and Mohamed-Ali Hakimi and Alexandre Bougdour}, doi = {10.7554/eLife.39887}, issn = {2050-084X}, year = {2018}, date = {2018-01-01}, journal = {eLife}, volume = {7}, abstract = {The intracellular parasite Toxoplasma gondii, hijacks evolutionarily conserved host processes by delivering effector proteins into the host cell that shift gene expression in a timely fashion. We identified a parasite dense granule protein as GRA18 that once released in the host cell cytoplasm forms versatile complexes with regulatory elements of the β-catenin destruction complex. By interacting with GSK3/PP2A-B56, GRA18 drives β-catenin up-regulation and the downstream effects on host cell gene expression. In the context of macrophages infection, GRA18 induces the expression of a specific set of genes commonly associated with an anti-inflammatory response that includes those encoding chemokines CCL17 and CCL22. Overall, this study adds another original strategy by which T. gondii tachyzoites reshuffle the host cell interactome through a GSK3/β-catenin axis to selectively reprogram immune gene expression.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The intracellular parasite Toxoplasma gondii, hijacks evolutionarily conserved host processes by delivering effector proteins into the host cell that shift gene expression in a timely fashion. We identified a parasite dense granule protein as GRA18 that once released in the host cell cytoplasm forms versatile complexes with regulatory elements of the β-catenin destruction complex. By interacting with GSK3/PP2A-B56, GRA18 drives β-catenin up-regulation and the downstream effects on host cell gene expression. In the context of macrophages infection, GRA18 induces the expression of a specific set of genes commonly associated with an anti-inflammatory response that includes those encoding chemokines CCL17 and CCL22. Overall, this study adds another original strategy by which T. gondii tachyzoites reshuffle the host cell interactome through a GSK3/β-catenin axis to selectively reprogram immune gene expression. |
Picard, Marion A L; Cosseau, Celine; Ferré, Sabrina; Quack, Thomas; Grevelding, Christoph G; Couté, Yohann; Vicoso, Beatriz Evolution of gene dosage on the Z-chromosome of schistosome parasites Article de journal eLife, 7 , 2018, ISSN: 2050-084X. @article{picard_evolution_2018, title = {Evolution of gene dosage on the Z-chromosome of schistosome parasites}, author = {Marion A L Picard and Celine Cosseau and Sabrina Ferré and Thomas Quack and Christoph G Grevelding and Yohann Couté and Beatriz Vicoso}, doi = {10.7554/eLife.35684}, issn = {2050-084X}, year = {2018}, date = {2018-01-01}, journal = {eLife}, volume = {7}, abstract = {XY systems usually show chromosome-wide compensation of X-linked genes, while in many ZW systems, compensation is restricted to a minority of dosage-sensitive genes. Why such differences arose is still unclear. Here, we combine comparative genomics, transcriptomics and proteomics to obtain a complete overview of the evolution of gene dosage on the Z-chromosome of Schistosoma parasites. We compare the Z-chromosome gene content of African (Schistosoma mansoni and S. haematobium) and Asian (S. japonicum) schistosomes and describe lineage-specific evolutionary strata. We use these to assess gene expression evolution following sex-linkage. The resulting patterns suggest a reduction in expression of Z-linked genes in females, combined with upregulation of the Z in both sexes, in line with the first step of Ohno's classic model of dosage compensation evolution. Quantitative proteomics suggest that post-transcriptional mechanisms do not play a major role in balancing the expression of Z-linked genes.}, keywords = {}, pubstate = {published}, tppubtype = {article} } XY systems usually show chromosome-wide compensation of X-linked genes, while in many ZW systems, compensation is restricted to a minority of dosage-sensitive genes. Why such differences arose is still unclear. Here, we combine comparative genomics, transcriptomics and proteomics to obtain a complete overview of the evolution of gene dosage on the Z-chromosome of Schistosoma parasites. We compare the Z-chromosome gene content of African (Schistosoma mansoni and S. haematobium) and Asian (S. japonicum) schistosomes and describe lineage-specific evolutionary strata. We use these to assess gene expression evolution following sex-linkage. The resulting patterns suggest a reduction in expression of Z-linked genes in females, combined with upregulation of the Z in both sexes, in line with the first step of Ohno's classic model of dosage compensation evolution. Quantitative proteomics suggest that post-transcriptional mechanisms do not play a major role in balancing the expression of Z-linked genes. |
Legendre, Matthieu; Fabre, Elisabeth; Poirot, Olivier; Jeudy, Sandra; Lartigue, Audrey; Alempic, Jean-Marie; Beucher, Laure; Philippe, Nadège; Bertaux, Lionel; Christo-Foroux, Eugène; Labadie, Karine; Couté, Yohann; Abergel, Chantal; Claverie, Jean-Michel Diversity and evolution of the emerging Pandoraviridae family Article de journal Nature Communications, 9 (1), p. 2285, 2018, ISSN: 2041-1723. @article{legendre_diversity_2018, title = {Diversity and evolution of the emerging Pandoraviridae family}, author = {Matthieu Legendre and Elisabeth Fabre and Olivier Poirot and Sandra Jeudy and Audrey Lartigue and Jean-Marie Alempic and Laure Beucher and Nadège Philippe and Lionel Bertaux and Eugène Christo-Foroux and Karine Labadie and Yohann Couté and Chantal Abergel and Jean-Michel Claverie}, doi = {10.1038/s41467-018-04698-4}, issn = {2041-1723}, year = {2018}, date = {2018-01-01}, journal = {Nature Communications}, volume = {9}, number = {1}, pages = {2285}, abstract = {With DNA genomes reaching 2.5 Mb packed in particles of bacterium-like shape and dimension, the first two Acanthamoeba-infecting pandoraviruses remained up to now the most complex viruses since their discovery in 2013. Our isolation of three new strains from distant locations and environments is now used to perform the first comparative genomics analysis of the emerging worldwide-distributed Pandoraviridae family. Thorough annotation of the genomes combining transcriptomic, proteomic, and bioinformatic analyses reveals many non-coding transcripts and significantly reduces the former set of predicted protein-coding genes. Here we show that the pandoraviruses exhibit an open pan-genome, the enormous size of which is not adequately explained by gene duplications or horizontal transfers. As most of the strain-specific genes have no extant homolog and exhibit statistical features comparable to intergenic regions, we suggest that de novo gene creation could contribute to the evolution of the giant pandoravirus genomes.}, keywords = {}, pubstate = {published}, tppubtype = {article} } With DNA genomes reaching 2.5 Mb packed in particles of bacterium-like shape and dimension, the first two Acanthamoeba-infecting pandoraviruses remained up to now the most complex viruses since their discovery in 2013. Our isolation of three new strains from distant locations and environments is now used to perform the first comparative genomics analysis of the emerging worldwide-distributed Pandoraviridae family. Thorough annotation of the genomes combining transcriptomic, proteomic, and bioinformatic analyses reveals many non-coding transcripts and significantly reduces the former set of predicted protein-coding genes. Here we show that the pandoraviruses exhibit an open pan-genome, the enormous size of which is not adequately explained by gene duplications or horizontal transfers. As most of the strain-specific genes have no extant homolog and exhibit statistical features comparable to intergenic regions, we suggest that de novo gene creation could contribute to the evolution of the giant pandoravirus genomes. |
Eymard-Vernain, Elise; Couté, Yohann; Adrait, Annie; Rabilloud, Thierry; Sarret, Géraldine; Lelong, Cécile The poly-gamma-glutamate of Bacillus subtilis interacts specifically with silver nanoparticles Article de journal PloS One, 13 (5), p. e0197501, 2018, ISSN: 1932-6203. @article{eymard-vernain_poly-gamma-glutamate_2018, title = {The poly-gamma-glutamate of Bacillus subtilis interacts specifically with silver nanoparticles}, author = {Elise Eymard-Vernain and Yohann Couté and Annie Adrait and Thierry Rabilloud and Géraldine Sarret and Cécile Lelong}, doi = {10.1371/journal.pone.0197501}, issn = {1932-6203}, year = {2018}, date = {2018-01-01}, journal = {PloS One}, volume = {13}, number = {5}, pages = {e0197501}, abstract = {For many years, silver nanoparticles, as with other antibacterial nanoparticles, have been extensively used in manufactured products. However, their fate in the environment is unclear and raises questions. We studied the fate of silver nanoparticles in the presence of bacteria under growth conditions that are similar to those found naturally in the environment (that is, bacteria in a stationary phase with low nutrient concentrations). We demonstrated that the viability and the metabolism of a gram-positive bacteria, Bacillus subtilis, exposed during the stationary phase is unaffected by 1 mg/L of silver nanoparticles. These results can be partly explained by a physical interaction of the poly-gamma-glutamate (PGA) secreted by Bacillus subtilis with the silver nanoparticles. The coating of the silver nanoparticles by the secreted PGA likely results in a loss of the bioavailability of nanoparticles and, consequently, a decrease of their biocidal effect.}, keywords = {}, pubstate = {published}, tppubtype = {article} } For many years, silver nanoparticles, as with other antibacterial nanoparticles, have been extensively used in manufactured products. However, their fate in the environment is unclear and raises questions. We studied the fate of silver nanoparticles in the presence of bacteria under growth conditions that are similar to those found naturally in the environment (that is, bacteria in a stationary phase with low nutrient concentrations). We demonstrated that the viability and the metabolism of a gram-positive bacteria, Bacillus subtilis, exposed during the stationary phase is unaffected by 1 mg/L of silver nanoparticles. These results can be partly explained by a physical interaction of the poly-gamma-glutamate (PGA) secreted by Bacillus subtilis with the silver nanoparticles. The coating of the silver nanoparticles by the secreted PGA likely results in a loss of the bioavailability of nanoparticles and, consequently, a decrease of their biocidal effect. |
Abulfaraj, Aala A; Mariappan, Kiruthiga; Bigeard, Jean; Manickam, Prabhu; Blilou, Ikram; Guo, Xiujie; Al-Babili, Salim; Pflieger, Delphine; Hirt, Heribert; Rayapuram, Naganand The Arabidopsis homolog of human G3BP1 is a key regulator of stomatal and apoplastic immunity Article de journal Life Science Alliance, 1 (2), p. e201800046, 2018, ISSN: 2575-1077. @article{abulfaraj_arabidopsis_2018, title = {The Arabidopsis homolog of human G3BP1 is a key regulator of stomatal and apoplastic immunity}, author = {Aala A Abulfaraj and Kiruthiga Mariappan and Jean Bigeard and Prabhu Manickam and Ikram Blilou and Xiujie Guo and Salim Al-Babili and Delphine Pflieger and Heribert Hirt and Naganand Rayapuram}, doi = {10.26508/lsa.201800046}, issn = {2575-1077}, year = {2018}, date = {2018-01-01}, journal = {Life Science Alliance}, volume = {1}, number = {2}, pages = {e201800046}, abstract = {Mammalian Ras-GTPase-activating protein SH3-domain-binding proteins (G3BPs) are a highly conserved family of RNA-binding proteins that link kinase receptor-mediated signaling to RNA metabolism. Mammalian G3BP1 is a multifunctional protein that functions in viral immunity. Here, we show that the Arabidopsis thaliana homolog of human G3BP1 negatively regulates plant immunity. Arabidopsis g3bp1 mutants showed enhanced resistance to the virulent bacterial pathogen Pseudomonas syringae pv. tomato. Pathogen resistance was mediated in Atg3bp1 mutants by altered stomatal and apoplastic immunity. Atg3bp1 mutants restricted pathogen entry into stomates showing insensitivity to bacterial coronatine-mediated stomatal reopening. AtG3BP1 was identified as a negative regulator of defense responses, which correlated with moderate up-regulation of salicylic acid biosynthesis and signaling without growth penalty.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Mammalian Ras-GTPase-activating protein SH3-domain-binding proteins (G3BPs) are a highly conserved family of RNA-binding proteins that link kinase receptor-mediated signaling to RNA metabolism. Mammalian G3BP1 is a multifunctional protein that functions in viral immunity. Here, we show that the Arabidopsis thaliana homolog of human G3BP1 negatively regulates plant immunity. Arabidopsis g3bp1 mutants showed enhanced resistance to the virulent bacterial pathogen Pseudomonas syringae pv. tomato. Pathogen resistance was mediated in Atg3bp1 mutants by altered stomatal and apoplastic immunity. Atg3bp1 mutants restricted pathogen entry into stomates showing insensitivity to bacterial coronatine-mediated stomatal reopening. AtG3BP1 was identified as a negative regulator of defense responses, which correlated with moderate up-regulation of salicylic acid biosynthesis and signaling without growth penalty. |
Sage, Eric; Sansa, Marc; Fostner, Shawn; Defoort, Martial; Gély, Marc; Naik, Akshay K; Morel, Robert; Duraffourg, Laurent; Roukes, Michael L; Alava, Thomas; Jourdan, Guillaume; Colinet, Eric; Masselon, Christophe; Brenac, Ariel; Hentz, Sébastien Single-particle mass spectrometry with arrays of frequency-addressed nanomechanical resonators Article de journal Nature Communications, 9 (1), p. 3283, 2018, ISSN: 2041-1723. @article{sage_single-particle_2018, title = {Single-particle mass spectrometry with arrays of frequency-addressed nanomechanical resonators}, author = {Eric Sage and Marc Sansa and Shawn Fostner and Martial Defoort and Marc Gély and Akshay K Naik and Robert Morel and Laurent Duraffourg and Michael L Roukes and Thomas Alava and Guillaume Jourdan and Eric Colinet and Christophe Masselon and Ariel Brenac and Sébastien Hentz}, doi = {10.1038/s41467-018-05783-4}, issn = {2041-1723}, year = {2018}, date = {2018-01-01}, journal = {Nature Communications}, volume = {9}, number = {1}, pages = {3283}, abstract = {One of the main challenges to overcome to perform nanomechanical mass spectrometry analysis in a practical time frame stems from the size mismatch between the analyte beam and the small nanomechanical detector area. We report here the demonstration of mass spectrometry with arrays of 20 multiplexed nanomechanical resonators; each resonator is designed with a distinct resonance frequency which becomes its individual address. Mass spectra of metallic aggregates in the MDa range are acquired with more than one order of magnitude improvement in analysis time compared to individual resonators. A 20 NEMS array is probed in 150 ms with the same mass limit of detection as a single resonator. Spectra acquired with a conventional time-of-flight mass spectrometer in the same system show excellent agreement. We also demonstrate how mass spectrometry imaging at the single-particle level becomes possible by mapping a 4-cm-particle beam in the MDa range and above.}, keywords = {}, pubstate = {published}, tppubtype = {article} } One of the main challenges to overcome to perform nanomechanical mass spectrometry analysis in a practical time frame stems from the size mismatch between the analyte beam and the small nanomechanical detector area. We report here the demonstration of mass spectrometry with arrays of 20 multiplexed nanomechanical resonators; each resonator is designed with a distinct resonance frequency which becomes its individual address. Mass spectra of metallic aggregates in the MDa range are acquired with more than one order of magnitude improvement in analysis time compared to individual resonators. A 20 NEMS array is probed in 150 ms with the same mass limit of detection as a single resonator. Spectra acquired with a conventional time-of-flight mass spectrometer in the same system show excellent agreement. We also demonstrate how mass spectrometry imaging at the single-particle level becomes possible by mapping a 4-cm-particle beam in the MDa range and above. |
Berthier, A; Vinod, M; Porez, G; Steenackers, A; Alexandre, J; Yamakawa, N; Gheeraert, C; Ploton, M; Maréchal, X; Dubois-Chevalier, J; Hovasse, A; Schaeffer-Reiss, C; Cianférani, S; Rolando, C; Bray, F; Duez, H; Eeckhoute, J; Lefebvre, T; Staels, B; Lefebvre, P Combinatorial regulation of hepatic cytoplasmic signaling and nuclear transcriptional events by the OGT/REV-ERBα complex. Article de journal Proc Natl Acad Sci U S A., 15 (47), p. E11033-E11042., 2018. @article{621, title = {Combinatorial regulation of hepatic cytoplasmic signaling and nuclear transcriptional events by the OGT/REV-ERBα complex.}, author = {A Berthier and M Vinod and G Porez and A Steenackers and J Alexandre and N Yamakawa and C Gheeraert and M Ploton and X Maréchal and J Dubois-Chevalier and A Hovasse and C Schaeffer-Reiss and S Cianférani and C Rolando and F Bray and H Duez and J Eeckhoute and T Lefebvre and B Staels and P Lefebvre}, doi = {10.1073/pnas.1805397115}, year = {2018}, date = {2018-01-01}, journal = {Proc Natl Acad Sci U S A.}, volume = {15}, number = {47}, pages = {E11033-E11042.}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Bibi-Triki, S; Husson, G; Maucourt, B; Vuilleumier, S; Carapito, C; Bringel, F N-terminome and proteogenomic analysis of the Methylobacterium extorquens DM4 reference strain for dichloromethane utilization. Article de journal J Proteomics., (179), p. 131-139, 2018. @article{606, title = {N-terminome and proteogenomic analysis of the Methylobacterium extorquens DM4 reference strain for dichloromethane utilization.}, author = {S Bibi-Triki and G Husson and B Maucourt and S Vuilleumier and C Carapito and F Bringel}, year = {2018}, date = {2018-01-01}, journal = {J Proteomics.}, number = {179}, pages = {131-139}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Boeuf, A; Schnell, G; Bernard, Q; Kern, A; Westermann, B; Ehret-Sabatier, L; Grillon, A; Schramm, F; Jaulhac, B; Boulanger, N Dissociating effect of salivary gland extract from Ixodes ricinus on human fibroblasts: Potential impact on Borrelia transmission. Article de journal Ticks Tick Borne Dis., pii: S1877-959X(18)30014-1. , 2018, (2012/29). @article{626, title = {Dissociating effect of salivary gland extract from Ixodes ricinus on human fibroblasts: Potential impact on Borrelia transmission.}, author = {A Boeuf and G Schnell and Q Bernard and A Kern and B Westermann and L Ehret-Sabatier and A Grillon and F Schramm and B Jaulhac and N Boulanger}, year = {2018}, date = {2018-01-01}, journal = {Ticks Tick Borne Dis.}, volume = {pii: S1877-959X(18)30014-1.}, note = {2012/29}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Carapito, R; Carapito, C; Morlon, A; Paul, N; Jacome, AS. Vaca; Alsaleh, G; Rolli, V; Tahar, O; Aouadi, I; Rompais, M; Delalande, F; Pichot, A; Georgel, P; Messer, L; Sibilia, J; Cianferani, S; Dorsselaer, Van A; Bahram, S Multi-OMICS analyses unveil STAT1 as a potential modifier gene in mevalonate kinase deficiency. Article de journal Ann Rheum Dis., 77 (11), p. 1675-1687., 2018. @article{616, title = {Multi-OMICS analyses unveil STAT1 as a potential modifier gene in mevalonate kinase deficiency.}, author = {R Carapito and C Carapito and A Morlon and N Paul and AS. Vaca Jacome and G Alsaleh and V Rolli and O Tahar and I Aouadi and M Rompais and F Delalande and A Pichot and P Georgel and L Messer and J Sibilia and S Cianferani and A Van Dorsselaer and S Bahram}, year = {2018}, date = {2018-01-01}, journal = {Ann Rheum Dis.}, volume = {77}, number = {11}, pages = {1675-1687.}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Cavallo, G; Poyer, S; Amalian, JA.; Dufour, F; Burel, A; Carapito, C; Charles, L; Lutz, JF. Cleavable Binary Dyads: Simplifying Data Extraction and Increasing Storage Density in Digital Polymers. Article de journal Angew Chem Int Ed Engl., 57 (21), p. 6266-6269., 2018. @article{605, title = {Cleavable Binary Dyads: Simplifying Data Extraction and Increasing Storage Density in Digital Polymers.}, author = {G Cavallo and S Poyer and JA. Amalian and F Dufour and A Burel and C Carapito and L Charles and JF. Lutz}, year = {2018}, date = {2018-01-01}, journal = {Angew Chem Int Ed Engl.}, volume = {57}, number = {21}, pages = {6266-6269.}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Chanon, S; Chazarin, B; Toubhans, B; Durand, C; Chery, I; Robert, M; Vieille-Marchiset, A; Swenson, J E; Zedrosser, A; Evans, A L; Brunberg, S; Arnemo, J M; Gauquelin-Koch, G; Storey, K B; Simon, C; Blanc, S; Bertile, F; Lefai, E Proteolysis inhibition by hibernating bear serum leads to increased protein content in human muscle cells Article de journal Sci Rep 2018, 8 (1), p. 5525, 2018, (2011/34). @article{597, title = {Proteolysis inhibition by hibernating bear serum leads to increased protein content in human muscle cells}, author = {S Chanon and B Chazarin and B Toubhans and C Durand and I Chery and M Robert and A Vieille-Marchiset and J E. Swenson and A Zedrosser and A L. Evans and S Brunberg and J M. Arnemo and G Gauquelin-Koch and K B. Storey and C Simon and S Blanc and F Bertile and E Lefai}, doi = {10.1038/s41598-018-23891-5}, year = {2018}, date = {2018-01-01}, journal = {Sci Rep 2018}, volume = {8}, number = {1}, pages = {5525}, note = {2011/34}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Chopard, C; Tong, PBV.; Tóth, P; Schatz, M; Yezid, H; Debaisieux, S; Mettling, C; Gross, A; Pugnière, M; Tu, A; Strub, JM.; Mesnard, JM.; Vitale, N; Beaumelle, B Cyclophilin A enables specific HIV-1 Tat palmitoylation and accumulation in uninfected cells. Article de journal Nat Commun., 2018, (2006/01). @article{608, title = {Cyclophilin A enables specific HIV-1 Tat palmitoylation and accumulation in uninfected cells.}, author = {C Chopard and PBV. Tong and P Tóth and M Schatz and H Yezid and S Debaisieux and C Mettling and A Gross and M Pugnière and A Tu and JM. Strub and JM. Mesnard and N Vitale and B Beaumelle}, year = {2018}, date = {2018-01-01}, journal = {Nat Commun.}, note = {2006/01}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Coulter, ME.; Dorobantu, CM.; Lodewijk, GA.; Delalande, F; Cianferani, S; Ganesh, VS.; Smith, RS.; Lim, ET.; Xu, CS.; Pang, S; Wong, ET.; Lidov, HGW.; Calicchio, ML.; Yang, E; Gonzalez, DM.; Schlaeger, TM.; Mochida, GH.; Hess, H; Lee, WA.; Lehtinen, MK.; Kirchhausen, T; Haussler, D; Jacobs, FMJ.; Gaudin, R; Walsh, CA. The ESCRT-III Protein CHMP1A Mediates Secretion of Sonic Hedgehog on a Distinctive Subtype of Extracellular Vesicles. Article de journal Cell Rep., 24 (4), p. 973-986.e8., 2018. @article{614, title = {The ESCRT-III Protein CHMP1A Mediates Secretion of Sonic Hedgehog on a Distinctive Subtype of Extracellular Vesicles.}, author = {ME. Coulter and CM. Dorobantu and GA. Lodewijk and F Delalande and S Cianferani and VS. Ganesh and RS. Smith and ET. Lim and CS. Xu and S Pang and ET. Wong and HGW. Lidov and ML. Calicchio and E Yang and DM. Gonzalez and TM. Schlaeger and GH. Mochida and H Hess and WA. Lee and MK. Lehtinen and T Kirchhausen and D Haussler and FMJ. Jacobs and R Gaudin and CA. Walsh}, year = {2018}, date = {2018-01-01}, journal = {Cell Rep.}, volume = {24}, number = {4}, pages = {973-986.e8.}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Criscuolo, F; Sorci, G; Behaim-Delarbre, M; Zahn, S; Faivre, B; Bertile, F Age-related response to an acute innate immune challenge in mice: proteomics reveals a telomere maintenance-related cost. Article de journal Proceedings of the Royal Society B, 285 , p. 20181877., 2018, (2012/28). @article{622, title = {Age-related response to an acute innate immune challenge in mice: proteomics reveals a telomere maintenance-related cost.}, author = {F Criscuolo and G Sorci and M Behaim-Delarbre and S Zahn and B Faivre and F Bertile}, year = {2018}, date = {2018-01-01}, journal = {Proceedings of the Royal Society B}, volume = {285}, pages = {20181877.}, note = {2012/28}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Dartevelle, P; Ehlinger, C; Zaet, A; Boehler, C; Rabineau, M; Westermann, B; Strub, JM.; Cianferani, S; Haïkel, Y; Metz-Boutigue, MH.; Marban, C D-Cateslytin: a new antifungal agent for the treatment of oral Candida albicans associated infections. Article de journal Sci Rep., 8 (1), p. 9235., 2018, (2009/25). @article{600, title = {D-Cateslytin: a new antifungal agent for the treatment of oral Candida albicans associated infections.}, author = {P Dartevelle and C Ehlinger and A Zaet and C Boehler and M Rabineau and B Westermann and JM. Strub and S Cianferani and Y Haïkel and MH. Metz-Boutigue and C Marban}, year = {2018}, date = {2018-01-01}, journal = {Sci Rep.}, volume = {8}, number = {1}, pages = {9235.}, note = {2009/25}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
D'Atri, V; Causon, T; Hernandez-Alba, O; Mutabazi, A; Veuthey, JL.; Cianferani, S; Guillarme, D Adding a new separation dimension to MS and LC-MS: What is the utility of ion mobility spectrometry? Article de journal J Sep Sci., 41 (1), p. 20-67., 2018, (0 (review)). @article{582, title = {Adding a new separation dimension to MS and LC-MS: What is the utility of ion mobility spectrometry?}, author = {V D'Atri and T Causon and O Hernandez-Alba and A Mutabazi and JL. Veuthey and S Cianferani and D Guillarme}, year = {2018}, date = {2018-01-01}, journal = {J Sep Sci.}, volume = {41}, number = {1}, pages = {20-67.}, note = {0 (review)}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Desplancq, D; Groysbeck, N; Chiper, M; Weiss, E; Frisch, B; Strub, JM.; Cianférani, S; Zafeiratos, S; Moeglin, E; Holy, X; a.L. Favier,; Decarlo, S; Schultz, P; Spehner, D; Zuber, G Cytosolic Diffusion and Peptide-assisted Nuclear Shuttling of Peptide-substituted circa 102 Gold Atom Nanoclusters in Living Cells Article de journal ACS Applied Nano Materials, 1 , p. 4236-4246, 2018, (2018/02). @article{619, title = {Cytosolic Diffusion and Peptide-assisted Nuclear Shuttling of Peptide-substituted circa 102 Gold Atom Nanoclusters in Living Cells}, author = {D Desplancq and N Groysbeck and M Chiper and E Weiss and B Frisch and JM. Strub and S Cianférani and S Zafeiratos and E Moeglin and X Holy and a.L. Favier and S Decarlo and P Schultz and D Spehner and G Zuber}, year = {2018}, date = {2018-01-01}, journal = {ACS Applied Nano Materials}, volume = {1}, pages = {4236-4246}, note = {2018/02}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Dovgan, I; Erb, S; Hessmann, S; Ursuegui, S; Michel, C; Muller, C; Chaubet, G; Cianférani, S; Wagner, A Arginine-selective bioconjugation with 4-azidophenyl glyoxal: application to the single and dual functionalisation of native antibodies. Article de journal Org Biomol Chem., in press (Feb 1. doi: 10.1039/c7ob02844j.), 2018, (2017/21). @article{595, title = {Arginine-selective bioconjugation with 4-azidophenyl glyoxal: application to the single and dual functionalisation of native antibodies.}, author = {I Dovgan and S Erb and S Hessmann and S Ursuegui and C Michel and C Muller and G Chaubet and S Cianférani and A Wagner}, year = {2018}, date = {2018-01-01}, journal = {Org Biomol Chem.}, volume = {in press}, number = {Feb 1. doi: 10.1039/c7ob02844j.}, note = {2017/21}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Ehkirch, A; D'Atri, V; Rouvière, F; Hernandez-Alba, O; Goyon, A; Colas, O; Sarrut, M; Beck, A; Guillarme, D; Heinisch, S; Cianférani, S An online four-dimensional HICxSEC-IMxMS methodology for proof-of-concept characterization of antibody drug conjugates. Article de journal Anal Chem., 90 (3), p. 1578-1586., 2018. @article{591, title = {An online four-dimensional HICxSEC-IMxMS methodology for proof-of-concept characterization of antibody drug conjugates.}, author = {A Ehkirch and V D'Atri and F Rouvière and O Hernandez-Alba and A Goyon and O Colas and M Sarrut and A Beck and D Guillarme and S Heinisch and S Cianférani}, year = {2018}, date = {2018-01-01}, journal = {Anal Chem.}, volume = {90}, number = {3}, pages = {1578-1586.}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Ehkirch, A; Goyon, A; Hernandez-Alba, O; Rouviere, F; D'Atri, V; Dreyfus, C; Haeuw, JF.; Diemer, H; Beck, A; Heinisch, S; Guillarme, D; Cianferani, S A Novel Online Four-Dimensional SEC×SEC-IM×MS Methodology for Characterization of Monoclonal Antibody Size Variants. Article de journal Anal Chem., Anal Chem. 2018 Nov 12. , p. doi: 10.1021/acs.analchem.8b03333., 2018, (2017/12). @article{620, title = {A Novel Online Four-Dimensional SEC×SEC-IM×MS Methodology for Characterization of Monoclonal Antibody Size Variants.}, author = {A Ehkirch and A Goyon and O Hernandez-Alba and F Rouviere and V D'Atri and C Dreyfus and JF. Haeuw and H Diemer and A Beck and S Heinisch and D Guillarme and S Cianferani}, year = {2018}, date = {2018-01-01}, journal = {Anal Chem.}, volume = {Anal Chem. 2018 Nov 12.}, pages = {doi: 10.1021/acs.analchem.8b03333.}, note = {2017/12}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Ehkirch, A; Hernandez-Alba, O; Colas, O; Beck, A; Guillarme, D; Cianférani, S Hyphenation of size exclusion chromatography to native ion mobility mass spectrometry for the analytical characterization of therapeutic antibodies and related products. Article de journal J Chromatogr B Analyt Technol Biomed Life Sci., (1086), p. 176-183., 2018, (2016/14). @article{604, title = {Hyphenation of size exclusion chromatography to native ion mobility mass spectrometry for the analytical characterization of therapeutic antibodies and related products.}, author = {A Ehkirch and O Hernandez-Alba and O Colas and A Beck and D Guillarme and S Cianférani}, year = {2018}, date = {2018-01-01}, journal = {J Chromatogr B Analyt Technol Biomed Life Sci.}, number = {1086}, pages = {176-183.}, note = {2016/14}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Ehrmann, FR.; Kalim, J; Pfaffeneder, T; Bernet, B; Hohn, C; Schäfer, E; Botzanowski, T; Cianférani, S; Heine, A; Reuter, K; Diederich, F; Klebe, G Swapping Interface Contacts in the Homodimeric tRNA Guanine Transglycosylase: An Option for Functional Regulation. Article de journal Angew Chem Int Ed Engl., 57 (32), p. 10085-10090., 2018, (2007/53). @article{599, title = {Swapping Interface Contacts in the Homodimeric tRNA Guanine Transglycosylase: An Option for Functional Regulation.}, author = {FR. Ehrmann and J Kalim and T Pfaffeneder and B Bernet and C Hohn and E Schäfer and T Botzanowski and S Cianférani and A Heine and K Reuter and F Diederich and G Klebe}, year = {2018}, date = {2018-01-01}, journal = {Angew Chem Int Ed Engl.}, volume = {57}, number = {32}, pages = {10085-10090.}, note = {2007/53}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Garcia, L; Girod, M; Rompais, M; Dugourd, P; Carapito, C; Lemoine, J Data-Independent Acquisition Coupled to Visible Laser-Induced Dissociation at 473 nm (DIA-LID) for Peptide-Centric Specific Analysis of Cysteine-Containing Peptide Subset. Article de journal Anal Chem., 90 (6), p. 3928-3935., 2018. @article{607, title = {Data-Independent Acquisition Coupled to Visible Laser-Induced Dissociation at 473 nm (DIA-LID) for Peptide-Centric Specific Analysis of Cysteine-Containing Peptide Subset.}, author = {L Garcia and M Girod and M Rompais and P Dugourd and C Carapito and J Lemoine}, year = {2018}, date = {2018-01-01}, journal = {Anal Chem.}, volume = {90}, number = {6}, pages = {3928-3935.}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Giroud, S; Evans, AL.; Chery, I; Bertile, F; Tascher, G; Bertrand-Michel, J; Gauquelin-Koch, G; Arnemo, JM.; Swenson, JE.; Lefai, E; Blanc, S; Simon, C Seasonal changes in eicosanoid metabolism in the brown bear. Article de journal Naturwissenschaften, 105 (9-10), p. 58, 2018, (2011/34). @article{610, title = {Seasonal changes in eicosanoid metabolism in the brown bear.}, author = {S Giroud and AL. Evans and I Chery and F Bertile and G Tascher and J Bertrand-Michel and G Gauquelin-Koch and JM. Arnemo and JE. Swenson and E Lefai and S Blanc and C Simon}, year = {2018}, date = {2018-01-01}, journal = {Naturwissenschaften}, volume = {105}, number = {9-10}, pages = {58}, note = {2011/34}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Grzela, R; Nusbaum, J; Fieulaine, S; Lavecchia, F; Desmadril, M; Nhiri, N; Dorsselaer, Van A; Cianferani, S; Jacquet, E; Meinnel, T; Giglione, C Peptide deformylases from Vibrio parahaemolyticus phage and bacteria display similar deformylase activity and inhibitor binding clefts. Article de journal Biochim Biophys Acta., 1866 (2), p. 348-355., 2018. @article{592, title = {Peptide deformylases from Vibrio parahaemolyticus phage and bacteria display similar deformylase activity and inhibitor binding clefts.}, author = {R Grzela and J Nusbaum and S Fieulaine and F Lavecchia and M Desmadril and N Nhiri and A Van Dorsselaer and S Cianferani and E Jacquet and T Meinnel and C Giglione}, year = {2018}, date = {2018-01-01}, journal = {Biochim Biophys Acta.}, volume = {1866}, number = {2}, pages = {348-355.}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Henri, J; Chagot, ME.; Bourguet, M; Abel, Y; Terral, G; Maurizy, C; Aigueperse, C; Georgescauld, F; Vandermoere, F; Saint-Fort, R; Behm-Ansmant, I; Charpentier, B; Pradet-Balade, B; Verheggen, C; Bertrand, E; Meyer, P; Cianférani, S; Manival, X; Quinternet, M Deep Structural Analysis of RPAP3 and PIH1D1, Two Components of the HSP90 Co-chaperone R2TP Complex. Article de journal Structure, 26 (9), p. 1196-1209.e8., 2018. @article{615, title = {Deep Structural Analysis of RPAP3 and PIH1D1, Two Components of the HSP90 Co-chaperone R2TP Complex.}, author = {J Henri and ME. Chagot and M Bourguet and Y Abel and G Terral and C Maurizy and C Aigueperse and F Georgescauld and F Vandermoere and R Saint-Fort and I Behm-Ansmant and B Charpentier and B Pradet-Balade and C Verheggen and E Bertrand and P Meyer and S Cianférani and X Manival and M Quinternet}, year = {2018}, date = {2018-01-01}, journal = {Structure}, volume = {26}, number = {9}, pages = {1196-1209.e8.}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Hernandez-Alba, O; Wagner-Rousset, E; Beck, A; Cianférani, S Native Mass Spectrometry, Ion Mobility, and Collision-Induced Unfolding for Conformational Characterization of IgG4 Monoclonal Antibodies. Article de journal Anal Chem., 90 (15), p. 8865-8872., 2018. @article{617, title = {Native Mass Spectrometry, Ion Mobility, and Collision-Induced Unfolding for Conformational Characterization of IgG4 Monoclonal Antibodies.}, author = {O Hernandez-Alba and E Wagner-Rousset and A Beck and S Cianférani}, year = {2018}, date = {2018-01-01}, journal = {Anal Chem.}, volume = {90}, number = {15}, pages = {8865-8872.}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Husson, G; Delangle, A; O'Hara, J; Cianferani, S; Gervais, A; Dorsselaer, Van A; Bracewell, D; Carapito, C Dual Data-Independent Acquisition Approach Combining Global HCP Profiling and Absolute Quantification of Key Impurities during Bioprocess Development. Article de journal Anal Chem., 90 (2), p. 1241-1247., 2018. @article{593, title = {Dual Data-Independent Acquisition Approach Combining Global HCP Profiling and Absolute Quantification of Key Impurities during Bioprocess Development.}, author = {G Husson and A Delangle and J O'Hara and S Cianferani and A Gervais and A Van Dorsselaer and D Bracewell and C Carapito}, year = {2018}, date = {2018-01-01}, journal = {Anal Chem.}, volume = {90}, number = {2}, pages = {1241-1247.}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Issa, N; Guillaumot, N; Lauret, E; Matt, N; Schaeffer-Reiss, C; Dorsselaer, Van A; Reichhart, J M; Veillard, F The Circulating Protease Persephone Is an Immune Sensor for Microbial Proteolytic Activities Upstream of the Drosophila Toll Pathway Article de journal Mol Cell, 69 (4), p. 539-550 e6., 2018, (2014/10). @article{596, title = {The Circulating Protease Persephone Is an Immune Sensor for Microbial Proteolytic Activities Upstream of the Drosophila Toll Pathway}, author = {N Issa and N Guillaumot and E Lauret and N Matt and C Schaeffer-Reiss and A Van Dorsselaer and J M Reichhart and F Veillard}, year = {2018}, date = {2018-01-01}, journal = {Mol Cell}, volume = {69}, number = {4}, pages = {539-550 e6.}, note = {2014/10}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Koniev, O; Dovgan, I; Renoux, B; Ehkirch, A; Eberova, J; S., Cianférani; Kolodych, S; Papot, S; Wagner, A Reduction-rebridging strategy for the preparation of ADPN-based antibody-drug conjugates. Article de journal Medchemcomm., 9 (5), p. 827-830., 2018. @article{612, title = {Reduction-rebridging strategy for the preparation of ADPN-based antibody-drug conjugates.}, author = {O Koniev and I Dovgan and B Renoux and A Ehkirch and J Eberova and Cianférani S. and S Kolodych and S Papot and A Wagner}, year = {2018}, date = {2018-01-01}, journal = {Medchemcomm.}, volume = {9}, number = {5}, pages = {827-830.}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Maurizy, C; Quinternet, M; Abel, Y; Verheggen, C; Santo, PE.; Bourguet, M; Paiva, A; Bragantini, B; Chagot, ME.; Robert, MC.; Abeza, C; Fabre, P; Fort, P; Vandermoere, F; Sousa, P; Rain, JC.; Charpentier, B; Cianférani, S; Bandeiras, TM.; Pradet-Balade, B; Manival, X; Bertrand, E The RPAP3-Cterminal domain identifies R2TP-like quaternary chaperones. Article de journal Nat Commun., 9 (1), p. 2093., 2018. @article{602, title = {The RPAP3-Cterminal domain identifies R2TP-like quaternary chaperones.}, author = {C Maurizy and M Quinternet and Y Abel and C Verheggen and PE. Santo and M Bourguet and A Paiva and B Bragantini and ME. Chagot and MC. Robert and C Abeza and P Fabre and P Fort and F Vandermoere and P Sousa and JC. Rain and B Charpentier and S Cianférani and TM. Bandeiras and B Pradet-Balade and X Manival and E Bertrand}, year = {2018}, date = {2018-01-01}, journal = {Nat Commun.}, volume = {9}, number = {1}, pages = {2093.}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Mons, C; Botzanowski, T; Nikolaev, A; Hellwig, P; Cianférani, S; Lescop, E; Bouton, C; Golinelli-Cohen, MP. The H2O2-Resistant Fe-S Redox Switch MitoNEET Acts as a pH Sensor To Repair Stress-Damaged Fe-S Protein. Article de journal Biochemistry, 57 (38), p. 5616-5628., 2018. @article{611, title = {The H2O2-Resistant Fe-S Redox Switch MitoNEET Acts as a pH Sensor To Repair Stress-Damaged Fe-S Protein.}, author = {C Mons and T Botzanowski and A Nikolaev and P Hellwig and S Cianférani and E Lescop and C Bouton and MP. Golinelli-Cohen}, year = {2018}, date = {2018-01-01}, journal = {Biochemistry}, volume = {57}, number = {38}, pages = {5616-5628.}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Mori, M; Kovalenko, L; Malancona, S; Saladini, F; Forni, De D; Pires, M; Humbert, N; Real, E; Botzanowski, T; Cianférani, S; Giannini, A; Lang, MC. Dasso; Cugia, G; Poddesu, B; Lori, F; Zazzi, M; Harper, S; Summa, V; Mely, Y; Botta, M Structure-Based Identification of HIV-1 Nucleocapsid Protein Inhibitors Active against Wild-Type and Drug-Resistant HIV-1 Strains. Article de journal ACS Chem Biol., 13 (1), p. 253-266., 2018. @article{594, title = {Structure-Based Identification of HIV-1 Nucleocapsid Protein Inhibitors Active against Wild-Type and Drug-Resistant HIV-1 Strains.}, author = {M Mori and L Kovalenko and S Malancona and F Saladini and D De Forni and M Pires and N Humbert and E Real and T Botzanowski and S Cianférani and A Giannini and MC. Dasso Lang and G Cugia and B Poddesu and F Lori and M Zazzi and S Harper and V Summa and Y Mely and M Botta}, year = {2018}, date = {2018-01-01}, journal = {ACS Chem Biol.}, volume = {13}, number = {1}, pages = {253-266.}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Muller, L; Fornecker, L; Chion, M; Dorsselaer, Van A; Cianférani, S; Rabilloud, T; Carapito, C Extended investigation of tube-gel sample preparation: a versatile and simple choice for high throughput quantitative proteomics. Article de journal Sci Rep., 8 (1), p. 8260, 2018, (2015/08). @article{598, title = {Extended investigation of tube-gel sample preparation: a versatile and simple choice for high throughput quantitative proteomics.}, author = {L Muller and L Fornecker and M Chion and A Van Dorsselaer and S Cianférani and T Rabilloud and C Carapito}, year = {2018}, date = {2018-01-01}, journal = {Sci Rep.}, volume = {8}, number = {1}, pages = {8260}, note = {2015/08}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Ploton, M; Mazuy, C; Gheeraert, C; Dubois, V; Berthier, A; Chevalier-Dubois, J; Diemer, H; Cianférani, S; Strub, JM.; Helleboid-Chapman, A; Eeckhoute, J; Staels, B; Lefebvre, P The Nuclear Bile Acid Receptor FXR is a PKA- and FOXA2-Sensitive Activator of Fasting Hepatic Gluconeogenesis Article de journal Journal of Hepatology, 2018, (2011/30). @article{609, title = {The Nuclear Bile Acid Receptor FXR is a PKA- and FOXA2-Sensitive Activator of Fasting Hepatic Gluconeogenesis}, author = {M Ploton and C Mazuy and C Gheeraert and V Dubois and A Berthier and J Chevalier-Dubois and H Diemer and S Cianférani and JM. Strub and A Helleboid-Chapman and J Eeckhoute and B Staels and P Lefebvre}, year = {2018}, date = {2018-01-01}, journal = {Journal of Hepatology}, note = {2011/30}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Prudent, R; Demoncheaux, N; Diemer, H; Collin-Faure, V; Kapur, R; Paublant, F; Lafanechère, L; Cianférani, S; Rabilloud, T A quantitative proteomic analysis of cofilin phosphorylation in myeloid cells and its modulation using the LIM kinase inhibitor Pyr1. Article de journal PLoS One., 13 (12), p. e0208979., 2018. @article{624, title = {A quantitative proteomic analysis of cofilin phosphorylation in myeloid cells and its modulation using the LIM kinase inhibitor Pyr1.}, author = {R Prudent and N Demoncheaux and H Diemer and V Collin-Faure and R Kapur and F Paublant and L Lafanechère and S Cianférani and T Rabilloud}, year = {2018}, date = {2018-01-01}, journal = {PLoS One.}, volume = {13}, number = {12}, pages = {e0208979.}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Salaam, J; Tabti, L; Bahamyirou, S; Lecointre, A; Alba, Hernandez O; Jeannin, O; Camerel, F; Cianférani, S; Bentouhami, E; Nonat, AM.; Charbonnière, LJ. Formation of Mono- and Polynuclear Luminescent Lanthanide Complexes based on the Coordination of Preorganized Phosphonated Pyridines. Article de journal Inorg Chem., 57 (10), p. 6095-6106., 2018. @article{603, title = {Formation of Mono- and Polynuclear Luminescent Lanthanide Complexes based on the Coordination of Preorganized Phosphonated Pyridines.}, author = {J Salaam and L Tabti and S Bahamyirou and A Lecointre and O Hernandez Alba and O Jeannin and F Camerel and S Cianférani and E Bentouhami and AM. Nonat and LJ. Charbonnière}, year = {2018}, date = {2018-01-01}, journal = {Inorg Chem.}, volume = {57}, number = {10}, pages = {6095-6106.}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Tascher, G; Gerbaix, M; Maes, P; Chazarin, B; Ghislin, S; Antropova, E; Vassilieva, G; Ouzren-Zarhloul, N; Gauquelin-Koch, G; Vico, L; Frippiat, JP.; Bertile, F Analysis of femurs from mice embarked on board BION-M1 biosatellite reveals a decrease in immune cell development, including B cells, after 1 wk of recovery on Earth. Article de journal FASEB J., Dec 6:fj201801463R. , 2018. @article{625, title = {Analysis of femurs from mice embarked on board BION-M1 biosatellite reveals a decrease in immune cell development, including B cells, after 1 wk of recovery on Earth.}, author = {G Tascher and M Gerbaix and P Maes and B Chazarin and S Ghislin and E Antropova and G Vassilieva and N Ouzren-Zarhloul and G Gauquelin-Koch and L Vico and JP. Frippiat and F Bertile}, year = {2018}, date = {2018-01-01}, journal = {FASEB J.}, volume = {Dec 6:fj201801463R.}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
van Tran, N; Muller, L; Ross, RL.; Lestini, R; Létoquart, J; Ulryck, N; Limbach, PA.; de Crécy-Lagard, V; Cianférani, S; Graille, M Evolutionary insights into Trm112-methyltransferase holoenzymes involved in translation between archaea and eukaryotes. Article de journal Nucleic Acids Res., 46 (16), p. 8483-8499., 2018. @article{618, title = {Evolutionary insights into Trm112-methyltransferase holoenzymes involved in translation between archaea and eukaryotes.}, author = {N van Tran and L Muller and RL. Ross and R Lestini and J Létoquart and N Ulryck and PA. Limbach and V de Crécy-Lagard and S Cianférani and M Graille}, year = {2018}, date = {2018-01-01}, journal = {Nucleic Acids Res.}, volume = {46}, number = {16}, pages = {8483-8499.}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Weinsanto, I; Laux-Biehlmann, A; Mouheiche, J; Maduna, T; Delalande, F; Chavant, V; Gabel, F; Darbon, P; Charlet, A; Poisbeau, P; Lamshöft, M; Dorsselaer, Van A; Cianferani, S; Parat, MO.; Goumon, Y Stable isotope-labelled morphine to study in vivo central and peripheral morphine glucuronidation and brain transport in tolerant mice. Article de journal Br J Pharmacol., 175 (19), p. 3844-3856., 2018. @article{613, title = {Stable isotope-labelled morphine to study in vivo central and peripheral morphine glucuronidation and brain transport in tolerant mice.}, author = {I Weinsanto and A Laux-Biehlmann and J Mouheiche and T Maduna and F Delalande and V Chavant and F Gabel and P Darbon and A Charlet and P Poisbeau and M Lamshöft and A Van Dorsselaer and S Cianferani and MO. Parat and Y Goumon}, year = {2018}, date = {2018-01-01}, journal = {Br J Pharmacol.}, volume = {175}, number = {19}, pages = {3844-3856.}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Weinsanto, I; Mouheiche, J; Laux-Biehlmann, A; Delalande, F; Marquette, A; Chavant, V; Gabel, F; Cianferani, S; Charlet, A; Parat, MO.; Goumon, Y Morphine Binds Creatine Kinase B and Inhibits Its Activity. Article de journal Front Cell Neurosci., p. 12:464, 2018. @article{623, title = {Morphine Binds Creatine Kinase B and Inhibits Its Activity.}, author = {I Weinsanto and J Mouheiche and A Laux-Biehlmann and F Delalande and A Marquette and V Chavant and F Gabel and S Cianferani and A Charlet and MO. Parat and Y Goumon}, year = {2018}, date = {2018-01-01}, journal = {Front Cell Neurosci.}, pages = {12:464}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Salvi, Daniel; Bournais, Sylvain; Moyet, Lucas; Bouchnak, Imen; Kuntz, Marcel; Bruley, Christophe; Rolland, Norbert AT_CHLORO: The First Step When Looking for Information About Subplastidial Localization of Proteins Article de journal Methods in Molecular Biology (Clifton, N.J.), 1829 , p. 395–406, 2018, ISSN: 1940-6029. @article{salvi_at_chloro:_2018, title = {AT_CHLORO: The First Step When Looking for Information About Subplastidial Localization of Proteins}, author = {Daniel Salvi and Sylvain Bournais and Lucas Moyet and Imen Bouchnak and Marcel Kuntz and Christophe Bruley and Norbert Rolland}, doi = {10.1007/978-1-4939-8654-5_26}, issn = {1940-6029}, year = {2018}, date = {2018-01-01}, journal = {Methods in Molecular Biology (Clifton, N.J.)}, volume = {1829}, pages = {395--406}, abstract = {Plastids contain several key subcompartments. The two limiting envelope membranes (inner and outer membrane of the plastid envelope with an intermembrane space between), an aqueous phase (stroma), and an internal membrane system terms (thylakoids) formed of flat compressed vesicles (grana) and more light structures (lamellae). The thylakoid vesicles delimit another discrete soluble compartment, the thylakoid lumen. AT_CHLORO ( http://at-chloro.prabi.fr/at_chloro/ ) is a unique database supplying information about the subplastidial localization of proteins. It was created from simultaneous proteomic analyses targeted to the main subcompartments of the chloroplast from Arabidopsis thaliana (i.e., envelope, stroma, thylakoid) and to the two subdomains of thylakoid membranes (i.e., grana and stroma lamellae). AT_CHLORO assembles several complementary information (MS-based experimental data, curated functional annotations and subplastidial localization, links to other public databases and references) which give a comprehensive overview of the current knowledge about the subplastidial localization and the function of chloroplast proteins, with a specific attention given to chloroplast envelope proteins.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Plastids contain several key subcompartments. The two limiting envelope membranes (inner and outer membrane of the plastid envelope with an intermembrane space between), an aqueous phase (stroma), and an internal membrane system terms (thylakoids) formed of flat compressed vesicles (grana) and more light structures (lamellae). The thylakoid vesicles delimit another discrete soluble compartment, the thylakoid lumen. AT_CHLORO ( http://at-chloro.prabi.fr/at_chloro/ ) is a unique database supplying information about the subplastidial localization of proteins. It was created from simultaneous proteomic analyses targeted to the main subcompartments of the chloroplast from Arabidopsis thaliana (i.e., envelope, stroma, thylakoid) and to the two subdomains of thylakoid membranes (i.e., grana and stroma lamellae). AT_CHLORO assembles several complementary information (MS-based experimental data, curated functional annotations and subplastidial localization, links to other public databases and references) which give a comprehensive overview of the current knowledge about the subplastidial localization and the function of chloroplast proteins, with a specific attention given to chloroplast envelope proteins. |
Govin, Jérôme; Barral, Sophie; Morozumi, Yuichi; Hoghoughi, Naghmeh; Buchou, Thierry; Rousseaux, Sophie; Khochbin, Saadi Characterization of Post-Meiotic Male Germ Cell Genome Organizational States Article de journal Methods in Molecular Biology (Clifton, N.J.), 1832 , p. 293–307, 2018, ISSN: 1940-6029. @article{govin_characterization_2018, title = {Characterization of Post-Meiotic Male Germ Cell Genome Organizational States}, author = {Jérôme Govin and Sophie Barral and Yuichi Morozumi and Naghmeh Hoghoughi and Thierry Buchou and Sophie Rousseaux and Saadi Khochbin}, doi = {10.1007/978-1-4939-8663-7_16}, issn = {1940-6029}, year = {2018}, date = {2018-01-01}, journal = {Methods in Molecular Biology (Clifton, N.J.)}, volume = {1832}, pages = {293--307}, abstract = {Dramatic and unique genome reorganizations accompany the differentiation of haploid male germ cells, characterized by a gradual loss of the vast majority of histones leading to a final tight compaction of the genome by protamines. Despite being essential for procreation and the life cycle, the mechanisms driving the transformation of nucleosomes into nucleoprotamines remain poorly understood. To address this issue, our laboratory has developed a number of specific approaches, ranging from the purification of spermatogenic cells at specific stages, the analysis of chromatin transitional states, the functional characterization of histone variants, histone-replacing proteins and their chaperones. This chapter will detail all related relevant techniques with a particular emphasis on methods allowing the functional studies of histone variants and the genome organizational states associated with the studied histones in spermatogenic cells undergoing histone-to-protamine exchange.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Dramatic and unique genome reorganizations accompany the differentiation of haploid male germ cells, characterized by a gradual loss of the vast majority of histones leading to a final tight compaction of the genome by protamines. Despite being essential for procreation and the life cycle, the mechanisms driving the transformation of nucleosomes into nucleoprotamines remain poorly understood. To address this issue, our laboratory has developed a number of specific approaches, ranging from the purification of spermatogenic cells at specific stages, the analysis of chromatin transitional states, the functional characterization of histone variants, histone-replacing proteins and their chaperones. This chapter will detail all related relevant techniques with a particular emphasis on methods allowing the functional studies of histone variants and the genome organizational states associated with the studied histones in spermatogenic cells undergoing histone-to-protamine exchange. |
D'Atri, V; Causon, T; Hernandez-Alba, O; Mutabazi, A; Veuthey, JL.; Cianférani, S; Guillarme, D Adding a new separation dimension to MS and LC-MS: What is the utility of ion mobility spectrometry? Article de journal J Sep Sci., 41 (1), p. 20-67, 2018. @article{RN1296, title = {Adding a new separation dimension to MS and LC-MS: What is the utility of ion mobility spectrometry?}, author = {V D'Atri and T Causon and O Hernandez-Alba and A Mutabazi and JL. Veuthey and S Cianférani and D Guillarme}, doi = {10.1002/jssc.201700919}, year = {2018}, date = {2018-01-01}, journal = {J Sep Sci.}, volume = {41}, number = {1}, pages = {20-67}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2017 |
Bouguenina, H; Salaun, D; Mangon, A; Muller, L; Baudelet, E; Camoin, L; Tachibana, T; Cianférani, S; Audebert, S; Verdier-Pinard, P; Badache, A EB1-binding-myomegalin protein complex promotes centrosomal microtubules functions Article de journal Proc Natl Acad Sci U S A., 114 (50), p. E10687-E10696, 2017. @article{RN1309, title = {EB1-binding-myomegalin protein complex promotes centrosomal microtubules functions}, author = {H Bouguenina and D Salaun and A Mangon and L Muller and E Baudelet and L Camoin and T Tachibana and S Cianférani and S Audebert and P Verdier-Pinard and A Badache}, doi = {10.1073/pnas.1705682114}, year = {2017}, date = {2017-12-12}, journal = {Proc Natl Acad Sci U S A.}, volume = {114}, number = {50}, pages = {E10687-E10696}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Erales, Jenny; Marchand, Virginie; Panthu, Baptiste; Gillot, Sandra; Belin, Stéphane; Ghayad, Sandra E; Garcia, Maxime; Laforêts, Florian; Marcel, Virginie; Baudin-Baillieu, Agnès; Bertin, Pierre; Couté, Yohann; Adrait, Annie; Meyer, Mélanie; Therizols, Gabriel; Yusupov, Marat; Namy, Olivier; Ohlmann, Théophile; Motorin, Yuri; Catez, Frédéric; Diaz, Jean-Jacques Evidence for rRNA 2'-O-methylation plasticity: Control of intrinsic translational capabilities of human ribosomes Article de journal Proceedings of the National Academy of Sciences of the United States of America, 114 (49), p. 12934–12939, 2017, ISSN: 1091-6490. @article{erales_evidence_2017, title = {Evidence for rRNA 2'-O-methylation plasticity: Control of intrinsic translational capabilities of human ribosomes}, author = {Jenny Erales and Virginie Marchand and Baptiste Panthu and Sandra Gillot and Stéphane Belin and Sandra E Ghayad and Maxime Garcia and Florian Laforêts and Virginie Marcel and Agnès Baudin-Baillieu and Pierre Bertin and Yohann Couté and Annie Adrait and Mélanie Meyer and Gabriel Therizols and Marat Yusupov and Olivier Namy and Théophile Ohlmann and Yuri Motorin and Frédéric Catez and Jean-Jacques Diaz}, doi = {10.1073/pnas.1707674114}, issn = {1091-6490}, year = {2017}, date = {2017-12-01}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {49}, pages = {12934--12939}, abstract = {Ribosomal RNAs (rRNAs) are main effectors of messenger RNA (mRNA) decoding, peptide-bond formation, and ribosome dynamics during translation. Ribose 2'-O-methylation (2'-O-Me) is the most abundant rRNA chemical modification, and displays a complex pattern in rRNA. 2'-O-Me was shown to be essential for accurate and efficient protein synthesis in eukaryotic cells. However, whether rRNA 2'-O-Me is an adjustable feature of the human ribosome and a means of regulating ribosome function remains to be determined. Here we challenged rRNA 2'-O-Me globally by inhibiting the rRNA methyl-transferase fibrillarin in human cells. Using RiboMethSeq, a nonbiased quantitative mapping of 2'-O-Me, we identified a repertoire of 2'-O-Me sites subjected to variation and demonstrate that functional domains of ribosomes are targets of 2'-O-Me plasticity. Using the cricket paralysis virus internal ribosome entry site element, coupled to in vitro translation, we show that the intrinsic capability of ribosomes to translate mRNAs is modulated through a 2'-O-Me pattern and not by nonribosomal actors of the translational machinery. Our data establish rRNA 2'-O-Me plasticity as a mechanism providing functional specificity to human ribosomes.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Ribosomal RNAs (rRNAs) are main effectors of messenger RNA (mRNA) decoding, peptide-bond formation, and ribosome dynamics during translation. Ribose 2'-O-methylation (2'-O-Me) is the most abundant rRNA chemical modification, and displays a complex pattern in rRNA. 2'-O-Me was shown to be essential for accurate and efficient protein synthesis in eukaryotic cells. However, whether rRNA 2'-O-Me is an adjustable feature of the human ribosome and a means of regulating ribosome function remains to be determined. Here we challenged rRNA 2'-O-Me globally by inhibiting the rRNA methyl-transferase fibrillarin in human cells. Using RiboMethSeq, a nonbiased quantitative mapping of 2'-O-Me, we identified a repertoire of 2'-O-Me sites subjected to variation and demonstrate that functional domains of ribosomes are targets of 2'-O-Me plasticity. Using the cricket paralysis virus internal ribosome entry site element, coupled to in vitro translation, we show that the intrinsic capability of ribosomes to translate mRNAs is modulated through a 2'-O-Me pattern and not by nonribosomal actors of the translational machinery. Our data establish rRNA 2'-O-Me plasticity as a mechanism providing functional specificity to human ribosomes. |
Arvin-Berod, Marie; Desroches-Castan, Agnès; Bonte, Simon; Brugière, Sabine; Couté, Yohann; Guyon, Laurent; Feige, Jean-Jacques; Baussanne, Isabelle; Demeunynck, Martine Indolizine-Based Scaffolds as Efficient and Versatile Tools: Application to the Synthesis of Biotin-Tagged Antiangiogenic Drugs Article de journal ACS Omega, 2 (12), p. 9221–9230, 2017, ISSN: 2470-1343. @article{arvin-berod_indolizine-based_2017, title = {Indolizine-Based Scaffolds as Efficient and Versatile Tools: Application to the Synthesis of Biotin-Tagged Antiangiogenic Drugs}, author = {Marie Arvin-Berod and Agnès Desroches-Castan and Simon Bonte and Sabine Brugière and Yohann Couté and Laurent Guyon and Jean-Jacques Feige and Isabelle Baussanne and Martine Demeunynck}, url = {https://doi.org/10.1021/acsomega.7b01184}, doi = {10.1021/acsomega.7b01184}, issn = {2470-1343}, year = {2017}, date = {2017-12-01}, urldate = {2018-02-22}, journal = {ACS Omega}, volume = {2}, number = {12}, pages = {9221--9230}, abstract = {We describe the design and optimization of polyfunctional scaffolds based on a fluorescent indolizine core derivatized with various orthogonal groups (amines, esters, oximes, alkynes, etc.). To show one application as tools in biology, the scaffold was used to prepare drug–biotin conjugates that were then immobilized onto avidin-agarose for affinity chromatography. More specifically, the antiangiogenic drug COB223, whose mechanism of action remained unclear, was chosen as a proof-of-concept drug. The drug-selective discrimination of proteins observed after elution of the cell lysates through the affinity columns, functionalized either with the biologically active COB223 or a structurally related inactive analogue (COB236), is a clear indication that the presence of the indolizine core does not limit drug–protein interaction and confirms the usefulness of the indolizine scaffold. Furthermore, the separation of COB223-interacting proteins from human placental extracts unveiled unanticipated protein targets belonging to the family of regulatory RNA-binding proteins, which opens the way to new hypotheses on the mode of action of this antiangiogenic drug.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We describe the design and optimization of polyfunctional scaffolds based on a fluorescent indolizine core derivatized with various orthogonal groups (amines, esters, oximes, alkynes, etc.). To show one application as tools in biology, the scaffold was used to prepare drug–biotin conjugates that were then immobilized onto avidin-agarose for affinity chromatography. More specifically, the antiangiogenic drug COB223, whose mechanism of action remained unclear, was chosen as a proof-of-concept drug. The drug-selective discrimination of proteins observed after elution of the cell lysates through the affinity columns, functionalized either with the biologically active COB223 or a structurally related inactive analogue (COB236), is a clear indication that the presence of the indolizine core does not limit drug–protein interaction and confirms the usefulness of the indolizine scaffold. Furthermore, the separation of COB223-interacting proteins from human placental extracts unveiled unanticipated protein targets belonging to the family of regulatory RNA-binding proteins, which opens the way to new hypotheses on the mode of action of this antiangiogenic drug. |
Cheng, Daian; Deobagkar-Lele, Mukta; Zvezdova, Ekaterina; Choi, Seeyoung; Uehara, Shoji; Baup, Delphine; Bennett, Sophia C; Bull, Katherine R; Crockford, Tanya L; Ferry, Helen; Warzecha, Claude; è, Marl; de Peredo, Anne Gonzalez; Lesourne, Renaud; Anzilotti, Consuelo; Love, Paul E; Cornall, Richard J Themis2 lowers the threshold for B cell activation during positive selection Article de journal Nature immunology, 18 (2), p. 205–213, 2017. @article{Cheng2017, title = {Themis2 lowers the threshold for B cell activation during positive selection}, author = {Daian Cheng and Mukta Deobagkar-Lele and Ekaterina Zvezdova and Seeyoung Choi and Shoji Uehara and Delphine Baup and Sophia C Bennett and Katherine R Bull and Tanya L Crockford and Helen Ferry and Claude Warzecha and Marl{è}ne Marcellin and Anne Gonzalez de Peredo and Renaud Lesourne and Consuelo Anzilotti and Paul E Love and Richard J Cornall}, doi = {10.1038/ni.3642}, year = {2017}, date = {2017-12-01}, journal = {Nature immunology}, volume = {18}, number = {2}, pages = {205--213}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Roitel, Olivier; Bonnard, Lionel; Stella, Alexandre; Schiltz, Odile; Maurice, Delphine; ë, Ga; Jacquenet, Sandrine; Favrot, Claude; Bihain, Bernard E; Couturier, Nicolas Detection of IgE-reactive proteins in hydrolysed dog foods Article de journal Veterinary dermatology, 28 (6), p. 589–e143, 2017. @article{Roitel2017, title = {Detection of IgE-reactive proteins in hydrolysed dog foods}, author = {Olivier Roitel and Lionel Bonnard and Alexandre Stella and Odile Schiltz and Delphine Maurice and Ga{ë}l Douchin and Sandrine Jacquenet and Claude Favrot and Bernard E Bihain and Nicolas Couturier}, doi = {10.1111/vde.12473}, year = {2017}, date = {2017-12-01}, journal = {Veterinary dermatology}, volume = {28}, number = {6}, pages = {589--e143}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Carapito, C; Duek, P; Macron, C; Seffals, M; Rondel, K; Delalande, F; Lindskog, C; Freour, T; Vandenbrouck, Y; Lane, L; Pineau, C Validating missing proteins in human sperm cells by targeted mass spectrometry- and antibody-based methods Article de journal J Proteome Res, 16 (12), p. 4340-4351, 2017. @article{RN1299, title = {Validating missing proteins in human sperm cells by targeted mass spectrometry- and antibody-based methods}, author = {C Carapito and P Duek and C Macron and M Seffals and K Rondel and F Delalande and C Lindskog and T Freour and Y Vandenbrouck and L Lane and C Pineau}, doi = {10.1021/acs.jproteome.7b00374}, year = {2017}, date = {2017-12-01}, journal = {J Proteome Res}, volume = {16}, number = {12}, pages = {4340-4351}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Grillon, A; Westermann, B; Cantero, P; Jaulhac, B; Voordouw, M J; Kapps, D; Collin, E; Barthel, C; Ehret-Sabatier, L; Boulanger, N Identification of Borrelia protein candidates in mouse skin for potential diagnosis of disseminated Lyme borreliosis Article de journal Sci Rep., 7 (1), p. 16719, 2017. @article{RN1297, title = {Identification of Borrelia protein candidates in mouse skin for potential diagnosis of disseminated Lyme borreliosis}, author = {A Grillon and B Westermann and P Cantero and B Jaulhac and M J Voordouw and D Kapps and E Collin and C Barthel and L Ehret-Sabatier and N Boulanger}, doi = {10.1038/s41598-017-16749-9}, year = {2017}, date = {2017-12-01}, journal = {Sci Rep.}, volume = {7}, number = {1}, pages = {16719}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Charbonnel, C; Niazi, Khan A; Elvira-Matelor, E; Nowak, E; Zytnicki, M; de Bures, A; Jobet, E; Opsomer, A; Shamandi, N; Nowotny, M; Carapito, C; Reichheld, J P; Vaucheret, H; Saez-Vasquez, J The siRNA suppressor RTL1 is redox-regulated through glutathionylation of a conserved cysteine in the doublestranded-RNA-binding domain Article de journal Nucleic Acids Res., 45 (20), p. 11891-11907, 2017. @article{RN1301, title = {The siRNA suppressor RTL1 is redox-regulated through glutathionylation of a conserved cysteine in the doublestranded-RNA-binding domain}, author = {C Charbonnel and A Khan Niazi and E Elvira-Matelor and E Nowak and M Zytnicki and A de Bures and E Jobet and A Opsomer and N Shamandi and M Nowotny and C Carapito and J P Reichheld and H Vaucheret and J Saez-Vasquez}, doi = {10.1093/nar/gkx820}, year = {2017}, date = {2017-11-16}, journal = {Nucleic Acids Res.}, volume = {45}, number = {20}, pages = {11891-11907}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Aillaud, Chrystelle; Bosc, Christophe; Peris, Leticia; Bosson, Anouk; Heemeryck, Pierre; Dijk, Juliette Van; Friec, Julien Le; Boulan, Benoit; Vossier, Frédérique; Sanman, Laura E; Syed, Salahuddin; Amara, Neri; Couté, Yohann; Lafanechère, Laurence; Denarier, Eric; Delphin, Christian; Pelletier, Laurent; Humbert, Sandrine; Bogyo, Matthew; Andrieux, Annie; Rogowski, Krzysztof; Moutin, Marie-Jo Vasohibins/SVBP are tubulin carboxypeptidases (TCP) that regulate neuron differentiation Article de journal Science (New York, N.Y.), 2017, ISSN: 1095-9203. @article{aillaud_vasohibins/svbp_2017, title = {Vasohibins/SVBP are tubulin carboxypeptidases (TCP) that regulate neuron differentiation}, author = {Chrystelle Aillaud and Christophe Bosc and Leticia Peris and Anouk Bosson and Pierre Heemeryck and Juliette Van Dijk and Julien Le Friec and Benoit Boulan and Frédérique Vossier and Laura E Sanman and Salahuddin Syed and Neri Amara and Yohann Couté and Laurence Lafanechère and Eric Denarier and Christian Delphin and Laurent Pelletier and Sandrine Humbert and Matthew Bogyo and Annie Andrieux and Krzysztof Rogowski and Marie-Jo Moutin}, doi = {10.1126/science.aao4165}, issn = {1095-9203}, year = {2017}, date = {2017-11-01}, journal = {Science (New York, N.Y.)}, abstract = {Reversible detyrosination of α-tubulin is crucial to microtubule dynamics and functions and defects have been implicated in cancer, brain disorganization, and cardiomyopathies. The identity of the tubulin tyrosine carboxypeptidase (TCP) responsible for detyrosination has remained unclear. We used chemical proteomics with a potent unique irreversible inhibitor to show that the major brain TCP is a complex of vasohibin-1 (VASH1) with the Small Vasohibin Binding Protein (SVBP). VASH1 and its homolog VASH2, when complexed with SVBP, exhibited robust and specific Tyr/Phe carboxypeptidase activity on microtubules. Knock down of vasohibins or SVBP and/or inhibitor addition in cultured neurons reduced detyrosinated α-tubulin levels and caused severe differentiation defects. Furthermore, knock down of vasohibins disrupted neuronal migration in developing mouse neocortex. Thus vasohibin/SVBP complexes represent long sought TCP enzymes.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Reversible detyrosination of α-tubulin is crucial to microtubule dynamics and functions and defects have been implicated in cancer, brain disorganization, and cardiomyopathies. The identity of the tubulin tyrosine carboxypeptidase (TCP) responsible for detyrosination has remained unclear. We used chemical proteomics with a potent unique irreversible inhibitor to show that the major brain TCP is a complex of vasohibin-1 (VASH1) with the Small Vasohibin Binding Protein (SVBP). VASH1 and its homolog VASH2, when complexed with SVBP, exhibited robust and specific Tyr/Phe carboxypeptidase activity on microtubules. Knock down of vasohibins or SVBP and/or inhibitor addition in cultured neurons reduced detyrosinated α-tubulin levels and caused severe differentiation defects. Furthermore, knock down of vasohibins disrupted neuronal migration in developing mouse neocortex. Thus vasohibin/SVBP complexes represent long sought TCP enzymes. |
Yamchi, Ahad; Ben, Cécile; Rossignol, Michel; Zareie, Sayed Reza; Mirlohi, Aghafakhr; Sayed-Tabatabaei, Badraldin Ebrahim; Pichereaux, Carole; Sarrafi, Ahmad; Rickauer, Martina; Gentzbittel, Laurent Cellular microbiology, p. e12796, 2017. @article{Yamchi2017, title = {Proteomics analysis of Medicago truncatula response to infection by the phytopathogenic bacterium Ralstonia solanacearum points to jasmonate and salicylate defence pathways.}, author = {Ahad Yamchi and Cécile Ben and Michel Rossignol and Sayed Reza Zareie and Aghafakhr Mirlohi and Badraldin Ebrahim Sayed-Tabatabaei and Carole Pichereaux and Ahmad Sarrafi and Martina Rickauer and Laurent Gentzbittel}, doi = {10.1111/cmi.12796}, year = {2017}, date = {2017-10-30}, journal = {Cellular microbiology}, pages = {e12796}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Montacié, C; Durut, N; Opsomer, A; Palm, D; Comella, P; Picart, C; Carpentier, M C; Pontvianne, F; Carapito, C; Schleiff, E; Saez-Vasquez, J Nucleolar proteome analysis and proteasomal activity assays reveal a link between nucleolus and 26S proteasome in A. thaliana Article de journal Front Plant Sci., 8 , p. 1815., 2017. @article{RN1302, title = {Nucleolar proteome analysis and proteasomal activity assays reveal a link between nucleolus and 26S proteasome in A. thaliana}, author = {C Montacié and N Durut and A Opsomer and D Palm and P Comella and C Picart and M C Carpentier and F Pontvianne and C Carapito and E Schleiff and J Saez-Vasquez}, doi = {10.3389/fpls.2017.01815}, year = {2017}, date = {2017-10-20}, journal = {Front Plant Sci.}, volume = {8}, pages = {1815.}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Terral, G; CHAMPION, T; Debaene, F; Colas, O; Bourguet, M; WAGNER-ROUSSET, E; Corvaia, N; Beck, A; Cianferani, S Epitope characterization of anti-JAM-A antibodies using orthogonal mass spectrometry and surface plasmon resonance approaches Article de journal MAbs., 9 (8), p. 1317-1326, 2017. @article{RN1294, title = {Epitope characterization of anti-JAM-A antibodies using orthogonal mass spectrometry and surface plasmon resonance approaches}, author = {G Terral and T CHAMPION and F Debaene and O Colas and M Bourguet and E WAGNER-ROUSSET and N Corvaia and A Beck and S Cianferani}, doi = {10.1080/19420862.2017.1380762}, year = {2017}, date = {2017-10-16}, journal = {MAbs.}, volume = {9}, number = {8}, pages = {1317-1326}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Radu, L; Schoenwetter, E; Braun, C; Marcoux, J; Koelmel, W; Schmitt, DR.; Kuper, J; Cianférani, S; Egly, JM.; Poterszman, A; Kisker, C The intricate network between the p34 and p44 subunits is central to the activity of the transcription/DNA repair factor TFIIH Article de journal Nucleic Acids Res., 45 (18), p. 10872-10883, 2017. @article{RN1293, title = {The intricate network between the p34 and p44 subunits is central to the activity of the transcription/DNA repair factor TFIIH}, author = {L Radu and E Schoenwetter and C Braun and J Marcoux and W Koelmel and DR. Schmitt and J Kuper and S Cianférani and JM. Egly and A Poterszman and C Kisker}, doi = {10.1093/nar/gkx743}, year = {2017}, date = {2017-10-13}, journal = {Nucleic Acids Res.}, volume = {45}, number = {18}, pages = {10872-10883}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Chiaradia, Laura; Lefebvre, Cyril; Parra, Julien; Marcoux, Julien; Burlet-Schiltz, Odile; Etienne, Gilles; Tropis, Maryelle; Daffé, Mamadou Dissecting the mycobacterial cell envelope and defining the composition of the native mycomembrane Article de journal Scientific Reports, 7 (1), p. 12807, 2017. @article{Chiaradia2017, title = {Dissecting the mycobacterial cell envelope and defining the composition of the native mycomembrane}, author = {Laura Chiaradia and Cyril Lefebvre and Julien Parra and Julien Marcoux and Odile Burlet-Schiltz and Gilles Etienne and Maryelle Tropis and Mamadou Daffé}, doi = {10.1038/s41598-017-12718-4}, year = {2017}, date = {2017-10-01}, journal = {Scientific Reports}, volume = {7}, number = {1}, pages = {12807}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Guéguéniat, J; Dupin, AF.; Stojko, J; Beaurepaire, L; Cianférani, S; Mackereth, CD.; Minvielle-Sébastia, L; Fribourg, S Distinct roles of Pcf11 zinc-binding domains in pre-mRNA 3'-end processing Article de journal Nucleic Acids Res., 45 (17), p. 10115-10131, 2017. @article{RN1292, title = {Distinct roles of Pcf11 zinc-binding domains in pre-mRNA 3'-end processing}, author = {J Guéguéniat and AF. Dupin and J Stojko and L Beaurepaire and S Cianférani and CD. Mackereth and L Minvielle-Sébastia and S Fribourg}, doi = {10.1093/nar/gkx674}, year = {2017}, date = {2017-09-29}, journal = {Nucleic Acids Res.}, volume = {45}, number = {17}, pages = {10115-10131}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
