@article{650,

title = {Toxoplasma gondii ROP16 kinase silences the cyclin B1 gene promoter by hijacking host cell UHRF1-dependent epigenetic pathways},

author = {M Sabou and C Doderer-Lang and C Leyer and A Konjic and S Kubina and S Lennon and O Rohr and S Viville and S Cianférani and E Candolfi and AW. Pfaff and J Brunet},

doi = {10.1007/s00018-019-03267-2},

year  = {2019},

date = {2019-09-06},

journal = {Cell Mol Life Sci. 2019 Sep 6.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{648,

title = {VHH characterization. Comparison of recombinant with chemically synthesized anti-HER2 VHH},

author = {L Hartmann and T Botzanowski and M Galibert and M Jullian and E Chabrol and G Zeder-Lutz and V Kugler and J Stojko and JM. Strub and G Ferry and L Frankiewicz and K Puget and R Wagner and S Cianférani and JA. Boutin},

doi = {10.1002/pro.3712},

year  = {2019},

date = {2019-08-29},

journal = {Protein Sci.},

volume = {28},

number = {10},

pages = {1865-1879},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{647,

title = {Limited oxidative stress favors resistance to skeletal muscle atrophy in hibernating brown bears (Ursus arctos)},

author = {B Chazarin and A Ziemianin and A L Evans and E Meugnier and E Loizon and I Chery and J M Arnemo and J E Swenson and G Gauquelin-Koch and C Simon and S Blanc and E Lefai and F Bertile},

doi = {10.3390/antiox8090334},

year  = {2019},

date = {2019-08-22},

journal = {Antioxidants},

volume = {8},

number = {9},

pages = {334},

note = {2011/34},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{638,

title = {Physiologically relevant reconstitution of iron-sulfur cluster biosynthesis uncovers persulfide-processing functions of ferredoxin-2 and frataxin},

author = {S Gervason and D Larkem and AB. Mansour and T Botzanowski and CS. Müller and L Pecqueur and G Le Pavec and A Delaunay-Moisan and O Brun and J Agramunt and A Grandas and M Fontecave and V Schünemann and S Cianférani and C Sizun and MB. Tolédano and B D'Autréaux},

doi = {10.1038/s41467-019-11470-9},

year  = {2019},

date = {2019-08-08},

journal = {Nat Commun.},

volume = {10},

number = {1},

pages = {3566},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{646,

title = {Phosphomimetic substitution at Ser-33 of the chloroquine resistance transporter PfCRT reconstitutes drug responses in Plasmodium falciparum},

author = {CP. Sanchez and S Moliner Cubel and B Nyboer and M Jankowska-Döllken and C Schaeffer-Reiss and D Ayoub and G Planelles and M Lanzer},

doi = {10.1074/jbc.RA119.009464},

year  = {2019},

date = {2019-07-08},

journal = {J Biol Chem.},

pages = {pii: jbc.RA119.009464.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{644,

title = {Division of labour in the black garden ant (Lasius niger) leads to three distinct proteomes},

author = {M Quque and M Benhaim-Delarbre and JL. Deneubourg and C Sueur and F Criscuolo and F Bertile},

doi = {10.1016/j.jinsphys.2019.103907},

year  = {2019},

date = {2019-06-27},

journal = {J Insect Physiol.},

volume = {117},

pages = {103907},

note = {2015/29},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{639,

title = {A Proteomic View of Cellular Responses to Anticancer Quinoline-Copper Complexes},

author = {B Dalzon and J Bons and H Diemer and V Collin-Faure and C Marie-Desvergne and M Dubosson and S Cianferani and C Carapito and T Rabilloud},

doi = {10.3390/proteomes7020026},

year  = {2019},

date = {2019-06-24},

journal = {Proteomes},

volume = {7},

number = {2},

pages = {pii: E26},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{645,

title = {Metabolic reprogramming involving glycolysis in the hibernating brown bear skeletal muscle},

author = {B Chazarin and KB. Storey and A Ziemianin and S Chanon and M Plumel and I Chery and C Durand and AL. Evans and JM. Arnemo and A Zedrosser and JE. Swenson and G Gauquelin-Koch and C Simon and S Blanc and E Lefai and F Bertile},

doi = {10.1186/s12983-019-0312-2},

year  = {2019},

date = {2019-05-06},

journal = {Front Zool.},

volume = {16},

pages = {12},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{631,

title = {Circadian Analysis of the Mouse Cerebellum Proteome},

author = {M Plumel and S Dumont and P Maes and C Sandu and M P Felder-Scmittbuhl and E Challet and F Bertile},

doi = {10.3390/ijms20081852},

year  = {2019},

date = {2019-04-15},

journal = {International Journal of Molecular Sciences},

volume = {20},

number = {8},

pages = {1852},

note = {2012/26},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{630,

title = {Lipidomics Reveals Seasonal Shifts in a Large-Bodied Hibernator, the Brown Bear},

author = {S Giroud and I Chery and Bertile; F. and J Bertrand-Michel and G Tascher and G Gauquelin-Koch and J M Arnemo and J E Swenson and N V Singh and E Lefai and A L Evans and C Simon and S Blanc},

doi = {10.3389/fphys.2019.00389},

year  = {2019},

date = {2019-04-12},

journal = {Front Physiol.},

volume = {10},

pages = {389},

note = {2011/30},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30967366,

title = {Proteomic evidence of specific IGKV1-8 association with cystic lung light chain deposition disease},

author = {M Camus and S Hirschi and G Prevot and M P Chenard and H Mal and M Stern and M Reynaud-Gaubert and J Gilhodes and O Burlet-Schiltz and P Brousset and M Colombat},

doi = {10.1182/blood.2019898577},

year  = {2019},

date = {2019-04-09},

journal = {Blood},

volume = {133},

number = {26},

pages = {2741--2744},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid31200944,

title = {A transgenic mouse model reproduces human hereditary systemic amyloidosis},

author = {M Chabert and X Rousset and M Colombat and M Lacasa and H Kakanakou and M Bourderioux and P Brousset and O Burlet-Schiltz and J J Liepnieks and B Kluve-Beckerman and G Lambert and F P Châtelet and M D Benson and A D Kalopissis},

doi = {10.1016/j.kint.2019.03.013},

year  = {2019},

date = {2019-03-28},

journal = {Kidney Int.},

volume = {96},

number = {3},

pages = {628--641},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{640,

title = {A Combined N-terminomics and Shotgun Proteomics Approach to Investigate the Responses of Human Cells to Rapamycin and Zinc at the Mitochondrial Level},

author = {J Bons and C Macron and C Aude-Garcia and SA. Vaca-Jacome and M Rompais and S Cianférani and C Carapito and T Rabilloud},

doi = {10.1074/mcp.RA118.001269},

year  = {2019},

date = {2019-03-15},

journal = {Mol Cell Proteomics},

volume = {18},

number = {6},

pages = {1085-1095},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{632,

title = {Tube-Gel: A Fast and Effective Sample Preparation Method for High-Throughput Quantitative Proteomics},

author = {L Muller and L Fornecker and S Cianferani and C Carapito},

doi = {10.1007/978-1-4939-9164-8_8},

year  = {2019},

date = {2019-03-10},

journal = {Methods Mol Biol.},

volume = {1959},

pages = {123-127},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30862563,

title = {Analysis of durum wheat proteome changes under marine and fungal biostimulant treatments using large-scale quantitative proteomics: A useful dataset of durum wheat proteins},

author = {C Pichereaux and E A Laurent and A Gargaros and S Viudes and C Durieu and T Lamaze and P Grieu and O Burlet-Schiltz},

doi = {10.1016/j.jprot.2019.03.003},

year  = {2019},

date = {2019-03-09},

journal = {J Proteomics},

volume = {200},

pages = {28--39},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{629,

title = {In-Depth Proteome Analysis Highlights HepaRG Cells as a Versatile Cell System Surrogate for Primary Human Hepatocytes},

author = {G Tascher and A Burban and S Camus and M Plumel and S Chanon and R Le Guevel and V Shevchenko and A Van Dorsselaer and E Lefai and C Guguen-Guillouzo and F Bertile},

doi = {10.3390/cells8020192},

year  = {2019},

date = {2019-02-21},

journal = {Cells},

volume = {8},

number = {2},

pages = {192},

note = {2012/20},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{633,

title = {Cutting-edge multi-level analytical and structural characterization of antibody-drug conjugates: present and future},

author = {A Beck and V D'Atri and A Ehkirch and S Fekete and O Hernandez-Alba and R Gahoual and E Leize-Wagner and Y François and D Guillarme and S Cianférani},

doi = {10.1080/14789450.2019.1578215},

year  = {2019},

date = {2019-02-18},

journal = {Expert Rev Proteomics.},

volume = {16},

number = {4},

pages = {337-362.},

note = {review},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30084957,

title = {VisioProt-MS: interactive 2D maps from intact protein mass spectrometry},

author = {M Locard-Paulet and J Parra and R Albigot and E Mouton-Barbosa and L Bardi and O Burlet-Schiltz and J Marcoux},

doi = {10.1093/bioinformatics/bty680},

year  = {2019},

date = {2019-02-15},

journal = {Bioinformatics},

volume = {35},

number = {4},

pages = {679--681},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{637,

title = {An essential role for α4A-tubulin in platelet biogenesis},

author = {C Strassel and MM. Magiera and A Dupuis and M Batzenschlager and A Hovasse and I Pleines and P Guéguen and A Eckly and S Moog and L Mallo and Q Kimmerlin and S Chappaz and JM. Strub and N Kathiresan and H Salle and A Van Dorsselaer and C Ferec and JY. Py and C Gachet and C Schaeffer-Reiss and BT. Kile and C Janke and F Lanza},

doi = {10.26508/lsa.201900309},

year  = {2019},

date = {2019-02-13},

journal = {Life Sci Alliance},

volume = {2},

number = {1},

pages = {pii: e201900309.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{635,

title = {Studying the Fate of Tumor Extracellular Vesicles at High Spatiotemporal Resolution Using the Zebrafish Embryo},

author = {V Hyenne and S Ghoroghi and M Collot and J Bons and G Follain and S Harlepp and B Mary and J Bauer and L Mercier and I Busnelli and O Lefebvre and N Fekonja and MJ. Garcia-Leon and P Machado and F Delalande and AA. López and SG. Silva and FJ. Verweij and G Niel and F Djouad and H Peinado and C Carapito and AS. Klymchenko and JG. Goetz},

doi = {10.1016/j.devcel.2019.01.014},

year  = {2019},

date = {2019-02-07},

journal = {Dev Cell.},

volume = {48},

number = {4},

pages = {554-572.e7},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30700495,

title = {Mass Spectrometry-based Absolute Quantification of 20S Proteasome Status for Controlled Ex-vivo Expansion of Ħuman Adipose-derived Mesenchymal Stromal/Stem Cells},

author = {T Menneteau and B Fabre and L Garrigues and A Stella and D Zivkovic and F Roux-Dalvai and E Mouton-Barbosa and M Beau and M L Renoud and F Amalric and L Sensébé and A Gonzalez-de-Peredo and I Ader and O Burlet-Schiltz and M P Bousquet},

doi = {10.1074/mcp.RA118.000958},

year  = {2019},

date = {2019-01-30},

journal = {Mol. Cell Proteomics},

volume = {18},

number = {4},

pages = {744--759},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{628,

title = {Multi-omics dataset to decipher the complexity of drug resistance in diffuse large B-cell lymphoma},

author = {LM. Fornecker and L Muller and F Bertrand and N Paul and A Pichot and R Herbrecht and MP. Chenard and L Mauvieux and L Vallat and S Bahram and S Cianférani and R Carapito and C Carapito},

doi = {10.1038/s41598-018-37273-4},

year  = {2019},

date = {2019-01-29},

journal = {Sci Rep.},

volume = {9},

number = {1},

pages = {895},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid30697967,

title = {Muscle wasting in patients with end-stage renal disease or early-stage lung cancer: common mechanisms at work},

author = {J Aniort and A Stella and C Philipponnet and A Poyet and C Polge and A Claustre and L Combaret and D B?chet and D Attaix and S Boisgard and M Filaire and E Rosset and O Burlet-Schiltz and A E Heng and D Taillandier},

doi = {0.1002/jcsm.12376},

year  = {2019},

date = {2019-01-29},

journal = {J Cachexia Sarcopenia Muscle},

volume = {10},

number = {2},

pages = {323--337},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{634,

title = {Synthesis and biological evaluation of 2.4 nm thiolate-protected gold nanoparticles conjugated to Cetuximab for targeting glioblastoma cancer cells via the EGFR},

author = {N Groysbeck and A Stoessel and M Donzeau and EC. Silva and M Lehmann and JM. Strub and S Cianferani and K Dembélé and G Zuber},

doi = {10.1088/1361-6528/aaff0a},

year  = {2019},

date = {2019-01-16},

journal = {Nanotechnology},

volume = {30},

number = {18},

pages = {184005.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{627,

title = {Recurrent activating mutations of PPARγ associated with luminal bladder tumors},

author = {N Rochel and C Krucker and L Coutos-Thévenot and J Osz and R Zhang and E Guyon and W Zita and S Vanthong and O Hernandez-Alba and M Bourguet and K Al Badawy and F Dufour and C Peluso-Iltis and S Heckler-Beji and A Dejaegere and A Kamoun and A Reyniès and Y Neuzillet and S Rebouissou and C Béraud and H Lang and T Massfelder and Y Allory and S Cianférani and R H Stote and F Radvanyi and I Bernard-Pierrot},

doi = {10.1038/s41467-018-08157-y},

year  = {2019},

date = {2019-01-16},

journal = {Nature Communications},

volume = {10},

number = {1},

pages = {253},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{636,

title = {Cytosolic Isocitrate Dehydrogenase from Arabidopsis thaliana Is Regulated by Glutathionylation},

author = {AK. Niazi and L Bariat and C Riondet and C Carapito and A Mhamdi and G Noctor and JP. Reichheld},

doi = {10.3390/antiox8010016},

year  = {2019},

date = {2019-01-08},

journal = {Antioxidants (Basel)},

volume = {8},

number = {1},

pages = {pii: E16.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{desroches-castan_bone_2019,

title = {Bone Morphogenetic Protein 9 Is a Paracrine Factor Controlling Liver Sinusoidal Endothelial Cell Fenestration and Protecting Against Hepatic Fibrosis},

author = {Agnès Desroches-Castan and Emmanuelle Tillet and Nicolas Ricard and Marie Ouarné and Christine Mallet and Lucid Belmudes and Yohann Couté and Olivier Boillot and Jean-Yves Scoazec and Sabine Bailly and Jean-Jacques Feige},

doi = {10.1002/hep.30655},

issn = {1527-3350},

year  = {2019},

date = {2019-01-01},

journal = {Hepatology (Baltimore, Md.)},

volume = {70},

number = {4},

pages = {1392--1408},

abstract = {Bone morphogenetic protein 9 (BMP9) is a circulating factor produced by hepatic stellate cells that plays a critical role in vascular quiescence through its endothelial receptor activin receptor-like kinase 1 (ALK1). Mutations in the gene encoding ALK1 cause hereditary hemorrhagic telangiectasia type 2, a rare genetic disease presenting hepatic vessel malformations. Variations of both the circulating levels and the hepatic mRNA levels of BMP9 have been recently associated with various forms of hepatic fibrosis. However, the molecular mechanism that links BMP9 with liver diseases is still unknown. Here, we report that Bmp9 gene deletion in 129/Ola mice triggers hepatic perisinusoidal fibrosis that was detectable from 15 weeks of age. An inflammatory response appeared within the same time frame as fibrosis, whereas sinusoidal vessel dilation developed later on. Proteomic and mRNA analyses of primary liver sinusoidal endothelial cells (LSECs) both revealed that the expression of the LSEC-specifying transcription factor GATA-binding protein 4 was strongly reduced in Bmp9 gene knockout (Bmp9-KO) mice as compared with wild-type mice. LSECs from Bmp9-KO mice also lost the expression of several terminal differentiation markers (Lyve1, Stab1, Stab2, Ehd3, Cd209b, eNos, Maf, Plvap). They gained CD34 expression and deposited a basal lamina, indicating that they were capillarized. Another main characteristic of differentiated LSECs is the presence of permeable fenestrae. LSECs from Bmp9-KO mice had a significantly reduced number of fenestrae. This was already observable in 2-week-old pups. Moreover, we could show that addition of BMP9 to primary cultures of LSECs prevented the loss of their fenestrae and maintained the expression levels of Gata4 and Plvap. Conclusion: Taken together, our observations show that BMP9 is a key paracrine regulator of liver homeostasis, controlling LSEC fenestration and protecting against perivascular hepatic fibrosis.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{azevedo_uap56_2019,

title = {UAP56 associates with DRM2 and is localized to chromatin in Arabidopsis},

author = {Jacinthe Azevedo and Claire Picart and Laurent Dureau and Dominique Pontier and Sylvie Jaquinod-Kieffer and Mohamed-Ali Hakimi and Thierry Lagrange},

doi = {10.1002/2211-5463.12627},

issn = {2211-5463},

year  = {2019},

date = {2019-01-01},

journal = {FEBS open bio},

volume = {9},

number = {5},

pages = {973--985},

abstract = {Repeated sequence expression and transposable element mobilization are tightly controlled by multilayer processes, which include DNA 5'-cytosine methylation. The RNA-directed DNA methylation (RdDM) pathway, which uses siRNAs to guide sequence-specific directed DNA methylation, emerged specifically in plants. RdDM ensures DNA methylation maintenance on asymmetric CHH sites and specifically initiates de novo methylation in all cytosine sequence contexts through the action of DRM DNA methyltransferases, of which DRM2 is the most prominent. The RdDM pathway has been well described, but how DRM2 is recruited onto DNA targets and associates with other RdDM factors remains unknown. To address these questions, we developed biochemical approaches to allow the identification of factors that may escape genetic screens, such as proteins encoded by multigenic families. Through both conventional and affinity purification of DRM2, we identified DEAD box RNA helicases U2AF56 Associated Protein 56 (UAP56a/b), which are widespread among eukaryotes, as new DRM2 partners. We have shown that, similar to DRM2 and other RdDM actors, UAP56 has chromatin-associated protein properties. We confirmed this association both in vitro and in vivo in reproductive tissues. In addition, our experiments also suggest that UAP56 may exhibit differential distribution in cells depending on plant organ. While originally identified for its role in splicing, our study suggests that UAP56 may also have other roles, and our findings allow us to initiate discussion about its potential role in the RdDM pathway.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{vandenbrouck_bioinformatics_2019,

title = {Bioinformatics Tools and Workflow to Select Blood Biomarkers for Early Cancer Diagnosis: An Application to Pancreatic Cancer},

author = {Yves Vandenbrouck and David Christiany and Florence Combes and Valentin Loux and Virginie Brun},

doi = {10.1002/pmic.201800489},

issn = {1615-9861},

year  = {2019},

date = {2019-01-01},

journal = {Proteomics},

volume = {19},

number = {21-22},

pages = {e1800489},

abstract = {Secretome proteomics for the discovery of cancer biomarkers holds great potential to improve early cancer diagnosis. A knowledge-based approach relying on mechanistic criteria related to the type of cancer should help to identify candidates from available "omics" information. With the aim of accelerating the discovery process for novel biomarkers, a set of tools is developed and made available via a Galaxy-based instance to assist end-users biologists. These implemented tools proceed by a step-by-step strategy to mine transcriptomics and proteomics databases for information relating to tissue specificity, allow the selection of proteins that are part of the secretome, and combine this information with proteomics datasets to rank the most promising candidate biomarkers for early cancer diagnosis. Using pancreatic cancer as a case study, this strategy produces a list of 24 candidate biomarkers suitable for experimental assessment by MS-based proteomics. Among these proteins, three (SYCN, REG1B, and PRSS2) were previously reported as circulating candidate biomarkers of pancreatic cancer. Here, further refinement of this list allows to prioritize 14 candidate biomarkers along with their associated proteotypic peptides for further investigation, using targeted MS-based proteomics. The bioinformatics tools and the workflow implementing this strategy for the selection of candidate biomarkers are freely accessible at http://www.proteore.org.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{guillot_peptimapper:_2019,

title = {Peptimapper: proteogenomics workflow for the expert annotation of eukaryotic genomes},

author = {Laetitia Guillot and Ludovic Delage and Alain Viari and Yves Vandenbrouck and Emmanuelle Com and Andrés Ritter and Régis Lavigne and Dominique Marie and Pierre Peterlongo and Philippe Potin and Charles Pineau},

doi = {10.1186/s12864-019-5431-9},

issn = {1471-2164},

year  = {2019},

date = {2019-01-01},

journal = {BMC genomics},

volume = {20},

number = {1},

pages = {56},

abstract = {BACKGROUND: Accurate structural annotation of genomes is still a challenge, despite the progress made over the past decade. The prediction of gene structure remains difficult, especially for eukaryotic species, and is often erroneous and incomplete. We used a proteogenomics strategy, taking advantage of the combination of proteomics datasets and bioinformatics tools, to identify novel protein coding-genes and splice isoforms, assign correct start sites, and validate predicted exons and genes. 

RESULTS: Our proteogenomics workflow, Peptimapper, was applied to the genome annotation of Ectocarpus sp., a key reference genome for both the brown algal lineage and stramenopiles. We generated proteomics data from various life cycle stages of Ectocarpus sp. strains and sub-cellular fractions using a shotgun approach. First, we directly generated peptide sequence tags (PSTs) from the proteomics data. Second, we mapped PSTs onto the translated genomic sequence. Closely located hits (i.e., PSTs locations on the genome) were then clustered to detect potential coding regions based on parameters optimized for the organism. Third, we evaluated each cluster and compared it to gene predictions from existing conventional genome annotation approaches. Finally, we integrated cluster locations into GFF files to use a genome viewer. We identified two potential novel genes, a ribosomal protein L22 and an aryl sulfotransferase and corrected the gene structure of a dihydrolipoamide acetyltransferase. We experimentally validated the results by RT-PCR and using transcriptomics data. 

CONCLUSIONS: Peptimapper is a complementary tool for the expert annotation of genomes. It is suitable for any organism and is distributed through a Docker image available on two public bioinformatics docker repositories: Docker Hub and BioShaDock. This workflow is also accessible through the Galaxy framework and for use by non-computer scientists at https://galaxy.protim.eu . Data are available via ProteomeXchange under identifier PXD010618.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{legendre_pandoravirus_2019,

title = {Pandoravirus Celtis Illustrates the Microevolution Processes at Work in the Giant Pandoraviridae Genomes},

author = {Matthieu Legendre and Jean-Marie Alempic and Nadège Philippe and Audrey Lartigue and Sandra Jeudy and Olivier Poirot and Ngan Thi Ta and Sébastien Nin and Yohann Couté and Chantal Abergel and Jean-Michel Claverie},

doi = {10.3389/fmicb.2019.00430},

issn = {1664-302X},

year  = {2019},

date = {2019-01-01},

journal = {Frontiers in Microbiology},

volume = {10},

pages = {430},

abstract = {With genomes of up to 2.7 Mb propagated in $mu$m-long oblong particles and initially predicted to encode more than 2000 proteins, members of the Pandoraviridae family display the most extreme features of the known viral world. The mere existence of such giant viruses raises fundamental questions about their origin and the processes governing their evolution. A previous analysis of six newly available isolates, independently confirmed by a study including three others, established that the Pandoraviridae pan-genome is open, meaning that each new strain exhibits protein-coding genes not previously identified in other family members. With an average increment of about 60 proteins, the gene repertoire shows no sign of reaching a limit and remains largely coding for proteins without recognizable homologs in other viruses or cells (ORFans). To explain these results, we proposed that most new protein-coding genes were created de novo, from pre-existing non-coding regions of the G+C rich pandoravirus genomes. The comparison of the gene content of a new isolate, pandoravirus celtis, closely related (96% identical genome) to the previously described p. quercus is now used to test this hypothesis by studying genomic changes in a microevolution range. Our results confirm that the differences between these two similar gene contents mostly consist of protein-coding genes without known homologs, with statistical signatures close to that of intergenic regions. These newborn proteins are under slight negative selection, perhaps to maintain stable folds and prevent protein aggregation pending the eventual emergence of fitness-increasing functions. Our study also unraveled several insertion events mediated by a transposase of the hAT family, 3 copies of which are found in p. celtis and are presumably active. Members of the Pandoraviridae are presently the first viruses known to encode this type of transposase.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{do_trim9_2019,

title = {TRIM9 and TRIM67 Are New Targets in Paraneoplastic Cerebellar Degeneration},

author = {Le Duy Do and Stephanie L Gupton and Kunikazu Tanji and Joubert Bastien and Sabine Brugière and Yohann Couté and Isabelle Quadrio and Veronique Rogemond and Nicole Fabien and Virginie Desestret and Jerome Honnorat},

doi = {10.1007/s12311-018-0987-5},

issn = {1473-4230},

year  = {2019},

date = {2019-01-01},

journal = {Cerebellum (London, England)},

volume = {18},

number = {2},

pages = {245--254},

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}

}

@article{wieczorek_five_2019,

title = {Five simple yet essential steps to correctly estimate the rate of false differentially abundant proteins in mass spectrometry analyses},

author = {Samuel Wieczorek and Quentin Giai Gianetto and Thomas Burger},

url = {https://linkinghub.elsevier.com/retrieve/pii/S1874391919302131},

doi = {10.1016/j.jprot.2019.103441},

issn = {18743919},

year  = {2019},

date = {2019-01-01},

journal = {Journal of Proteomics},

volume = {207},

pages = {103441},

abstract = {Results from mass spectrometry based quantitative proteomics analysis correspond to a subset of proteins which are considered differentially abundant relative to a control. Their selection is delicate and often requires some statistical expertise in addition to a refined knowledge of the experimental data. To facilitate the selection process, we have considered differential analysis as a five-step process, and here we present the practical aspects of the different steps. Prostar software is used throughout this article for illustration, but the general methodology is applicable with many other tools. By applying the approach detailed here, researchers who may be less familiar with statistical considerations can be more confident in the results they present.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{wei_ribosomal_2019,

title = {Ribosomal Proteins Regulate MHC Class I Peptide Generation for Immunosurveillance},

author = {Jiajie Wei and Rigel J Kishton and Matthew Angel and Crystal S Conn and Nicole Dalla-Venezia and Virginie Marcel and Anne Vincent and Frédéric Catez and Sabrina Ferré and Lilia Ayadi and Virginie Marchand and Devin Dersh and James S Gibbs and Ivaylo P Ivanov and Nathan Fridlyand and Yohann Couté and Jean-Jacques Diaz and Shu-Bing Qian and Louis M Staudt and Nicholas P Restifo and Jonathan W Yewdell},

doi = {10.1016/j.molcel.2018.12.020},

issn = {1097-4164},

year  = {2019},

date = {2019-01-01},

journal = {Molecular Cell},

abstract = {The MHC class I antigen presentation system enables T cell immunosurveillance of cancers and viruses. A substantial fraction of the immunopeptidome derives from rapidly degraded nascent polypeptides (DRiPs). By knocking down each of the 80 ribosomal proteins, we identified proteins that modulate peptide generation without altering source protein expression. We show that 60S ribosomal proteins L6 (RPL6) and RPL28, which are adjacent on the ribosome, play opposite roles in generating an influenza A virus-encoded peptide. Depleting RPL6 decreases ubiquitin-dependent peptide presentation, whereas depleting RPL28 increases ubiquitin-dependent and -independent peptide presentation. 40S ribosomal protein S28 (RPS28) knockdown increases total peptide supply in uninfected cells by increasing DRiP synthesis from non-canonical translation of "untranslated" regions and non-AUG start codons and sensitizes tumor cells for T cell targeting. Our findings raise the possibility of modulating immunosurveillance by pharmaceutical targeting ribosomes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{kraut_protein_2019,

title = {Protein Biomarker Discovery in Non-depleted Serum by Spectral Library-Based Data-Independent Acquisition Mass Spectrometry},

author = {Alexandra Kraut and Mathilde Louwagie and Christophe Bruley and Christophe Masselon and Yohann Couté and Virginie Brun and Anne-Marie Hesse},

doi = {10.1007/978-1-4939-9164-8_9},

issn = {1940-6029},

year  = {2019},

date = {2019-01-01},

journal = {Methods in Molecular Biology (Clifton, N.J.)},

volume = {1959},

pages = {129--150},

abstract = {In discovery proteomics experiments, tandem mass spectrometry and data-dependent acquisition (DDA) are classically used to identify and quantify peptides and proteins through database searching. This strategy suffers from known limitations such as under-sampling and lack of reproducibility of precursor ion selection in complex proteomics samples, leading to somewhat inconsistent analytical results across large datasets. Data-independent acquisition (DIA) based on fragmentation of all the precursors detected in predetermined isolation windows can potentially overcome this limitation. DIA promises reproducible peptide and protein quantification with deeper proteome coverage and fewer missing values than DDA strategies. This approach is particularly attractive in the field of clinical biomarker discovery, where large numbers of samples must be analyzed. Here, we describe a DIA workflow for non-depleted serum analysis including a straightforward approach through which to construct a dedicated spectral library, and indications on how to optimize chromatographic and mass spectrometry analytical methods to produce high-quality DIA data and results.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{steingruber_cyclins_2019,

title = {Cyclins B1, T1, and H differ in their molecular mode of interaction with cytomegalovirus protein kinase pUL97},

author = {Mirjam Steingruber and Lena Keller and Eileen Socher and Sabrina Ferre and Anne-Marie Hesse and Yohann Couté and Friedrich Hahn and Nicole Büscher and Bodo Plachter and Heinrich Sticht and Manfred Marschall},

doi = {10.1074/jbc.RA118.007049},

issn = {1083-351X},

year  = {2019},

date = {2019-01-01},

journal = {The Journal of Biological Chemistry},

volume = {294},

number = {15},

pages = {6188--6203},

abstract = {Human cytomegalovirus (HCMV) is a common $beta$-herpesvirus causing life-long latent infections. HCMV replication interferes with cell cycle regulation in host cells because the HCMV-encoded cyclin-dependent kinase (CDK) ortholog pUL97 extensively phosphorylates the checkpoint regulator retinoblastoma protein. pUL97 also interacts with cyclins B1, T1, and H, and recent findings have strongly suggested that these interactions influence pUL97 substrate recognition. Interestingly, here we detected profound mechanistic differences among these pUL97-cyclin interactions. Our study revealed the following. (i) pUL97 interacts with cyclins B1 and H in a manner dependent on pUL97 activity and HCMV-specific cyclin modulation, respectively. (ii) The phosphorylated state of both proteins is an important determinant of the pUL97-cyclin B1 interaction. (iii) Activated phospho-Thr-315 cyclin H is up-regulated during HCMV replication. (iv) Thr-315 phosphorylation is independent of intracellular pUL97 or CDK7 activity. (v) pUL97-mediated in vitro phosphorylation is detectable for cyclin B1 but not H. (vi) Mutual transphosphorylation between pUL97 and CDK7 is not detectable, and an MS-based phosphosite analysis indicated that pUL97 might unexpectedly not be phosphorylated in its T-loop. (vii) The binary complexes pUL97-cyclin H and CDK7-cyclin H as well as the ternary complex pUL97-cyclin-H-CDK7 are detectable in an assembly-based CoIP approach. (viii) pUL97 self-interaction can be bridged by the transcriptional cyclins T1 or H but not by the classical cell cycle-regulating B1 cyclin. Combined, our findings unravel a number of cyclin type-specific differences in pUL97 interactions and suggest a multifaceted regulatory impact of cyclins on HCMV replication.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{siebert_francisella_2019,

title = {Francisella tularensis: FupA mutation contributes to fluoroquinolone resistance by increasing vesicle secretion and biofilm formation},

author = {Claire Siebert and Helena Lindgren and Sabrina Ferré and Corinne Villers and Sandrine Boisset and Julien Perard and Anders Sjöstedt and Max Maurin and Céline Brochier-Armanet and Yohann Couté and Patricia Renesto},

doi = {10.1080/22221751.2019.1615848},

issn = {2222-1751},

year  = {2019},

date = {2019-01-01},

journal = {Emerging Microbes & Infections},

volume = {8},

number = {1},

pages = {808--822},

abstract = {Francisella tularensis is the causative agent in tularemia for which the high prevalence of treatment failure and relapse is a major concern. Directed-evolution experiments revealed that acquisition of fluoroquinolone (FQ) resistance was linked to factors in addition to mutations in DNA gyrase. Here, using F. tularensis live vaccine strain (LVS) as a model, we demonstrated that FupA/B (Fer-Utilization Protein) expression is linked to FQ susceptibility, and that the virulent strain F. tularensis subsp. tularensis SCHU S4 deleted for the homologous FupA protein exhibited even higher FQ resistance. In addition to an increased FQ minimal inhibitory concentration, LVS$Delta$fupA/B displayed tolerance toward bactericidal compounds including ciprofloxacin and gentamicin. Interestingly, the FupA/B deletion was found to promote increased secretion of outer membrane vesicles (OMVs). Mass spectrometry-based quantitative proteomic characterization of vesicles from LVS and LVS∆fupA/B identified 801 proteins, including a subset of 23 proteins exhibiting differential abundance between both strains which may therefore contribute to the reduced antibiotic susceptibility of the FupA/B-deleted strain. We also demonstrated that OMVs are key structural elements of LVS$Delta$fupA/B biofilms providing protection against FQ. These results provide a new basis for understanding and tackling antibiotic resistance and/or persistence of Francisella and other pathogenic members of the Thiotrichales class.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{lupette_architecture_2019,

title = {The architecture of lipid droplets in the diatom Phaeodactylum tricornutum},

author = {Josselin Lupette and Antoine Jaussaud and Khawla Seddiki and Christian Morabito and Sabine Brugière and Hubert Schaller and Marcel Kuntz and Jean-Luc Putaux and Pierre-Henri Jouneau and Fabrice Rébeillé and Denis Falconet and Yohann Couté and Juliette Jouhet and Marianne Tardif and Juliette Salvaing and Eric Maréchal},

url = {http://www.sciencedirect.com/science/article/pii/S2211926418309160},

doi = {10.1016/j.algal.2019.101415},

issn = {2211-9264},

year  = {2019},

date = {2019-01-01},

journal = {Algal Research},

volume = {38},

pages = {101415},

abstract = {Diatoms are a major phylum of phytoplankton biodiversity and a resource considered for biotechnological developments, as feedstock for biofuels and applications ranging from food, human health or green chemistry. They contain a secondary plastid limited by four membranes, the outermost one being connected with the endoplasmic reticulum (ER). Upon nitrogen stress, diatoms reallocate carbon to triacylglycerol storage inside lipid droplets (LDs). The comprehensive glycerolipid and sterol composition and the architecture of diatom LDs are unknown. In Phaeodactylum tricornutum, LDs are in contact with plastid, mitochondria and uncharacterized endomembranes. We purified LDs from nitrogen-starved P. tricornutum cells to high purity level (99 mol% triacylglycerol of total glycerolipids). We used the Stramenopile Lipid Droplet Protein (StLDP) as a previously validated marker for the identity of P. tricornutum LD. Amphipathic lipids surrounding LDs consist of a betaine lipid, diacylglycerylhydroxymethyltrimethyl‑$beta$‑alanine (0.4 mol%); sulfoquinovosyldiacylglycerol (0.35 mol%); phosphatidylcholine (0.15 mol%) and one sterol, brassicasterol. By contrast with whole cell extracts, the betaine lipid from LDs only contains eicosapentaenoic acid paired with palmitoleic or palmitolenic acids. This polar lipid composition suggests a budding of LDs from the cytosolic leaflet of the plastid outermost membrane. LD pigments reveal a specific accumulation of $beta$‑carotene. The LD proteome obtained from three independent biological replicates, based on stringent filtering of extracted data, and following subtraction of proteins downregulated by nitrogen starvation, highlights a core proteome of 86 proteins, including StLDP. LD-associated proteins suggest connections with vesicular trafficking (coatomer, clathrin), cytoskeleton, plastid and mitochondria. Unsuspected LD-associated function includes protein synthesis (ribosomes), folding (chaperones), posttranslational modifications and quality control (ubiquitination and ERAD pathway), possibly preparing translation of specific mRNAs. The detection of histone proteins, as previously demonstrated in drosophila embryo LDs, also suggests the storage of nucleosome components, preparing cell division and chromatin packaging, when cells are not stressed anymore.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{bouchnak_unraveling_2019,

title = {Unraveling Hidden Components of the Chloroplast Envelope Proteome: Opportunities and Limits of Better MS Sensitivity},

author = {Imen Bouchnak and Sabine Brugière and Lucas Moyet and Sophie Le Gall and Daniel Salvi and Marcel Kuntz and Marianne Tardif and Norbert Rolland},

doi = {10.1074/mcp.RA118.000988},

issn = {1535-9484},

year  = {2019},

date = {2019-01-01},

journal = {Molecular & cellular proteomics: MCP},

volume = {18},

number = {7},

pages = {1285--1306},

abstract = {The chloroplast is a major plant cell organelle that fulfills essential metabolic and biosynthetic functions. Located at the interface between the chloroplast and other cell compartments, the chloroplast envelope system is a strategic barrier controlling the exchange of ions, metabolites and proteins, thus regulating essential metabolic functions (synthesis of hormones precursors, amino acids, pigments, sugars, vitamins, lipids, nucleotides etc.) of the plant cell. However, unraveling the contents of the chloroplast envelope proteome remains a difficult challenge; many proteins constituting this functional double membrane system remain to be identified. Indeed, the envelope contains only 1% of the chloroplast proteins (i.e. 0.4% of the whole cell proteome). In other words, most envelope proteins are so rare at the cell, chloroplast, or even envelope level, that they remained undetectable using targeted MS studies. Cross-contamination of chloroplast subcompartments by each other and by other cell compartments during cell fractionation, impedes accurate localization of many envelope proteins. The aim of the present study was to take advantage of technologically improved MS sensitivity to better define the proteome of the chloroplast envelope (differentiate genuine envelope proteins from contaminants). This MS-based analysis relied on an enrichment factor that was calculated for each protein identified in purified envelope fractions as compared with the value obtained for the same protein in crude cell extracts. Using this approach, a total of 1269 proteins were detected in purified envelope fractions, of which, 462 could be assigned an envelope localization by combining MS-based spectral count analyses with manual annotation using data from the literature and prediction tools. Many of such proteins being previously unknown envelope components, these data constitute a new resource of significant value to the broader plant science community aiming to define principles and molecular mechanisms controlling fundamental aspects of plastid biogenesis and functions.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{moulin_towards_2019,

title = {Towards a molecular understanding of the water purification properties of Moringa seed proteins},

author = {M Moulin and E Mossou and L Signor and S Kieffer-Jaquinod and H M Kwaambwa and F Nermark and P Gutfreund and E P Mitchell and M Haertlein and V T Forsyth and A R Rennie},

doi = {10.1016/j.jcis.2019.06.071},

issn = {1095-7103},

year  = {2019},

date = {2019-01-01},

journal = {Journal of Colloid and Interface Science},

volume = {554},

pages = {296--304},

abstract = {Seed extracts from Moringa oleifera are of wide interest for use in water purification where they can play an important role in flocculation; they also have potential as anti-microbial agents. Previous work has focused on the crude protein extract. Here we describe the detailed biophysical characterization of individual proteins from these seeds. The results provide new insights relating to the active compounds involved. One fraction, designated Mo-CBP3, has been characterized at a molecular level using a range of biochemical and biophysical techniques including liquid chromatography, X-ray diffraction, mass spectrometry, and neutron reflection. The interfacial behavior is of particular interest in considering water purification applications and interactions with both charged (e.g. silica) and uncharged (alumina) surfaces were studied. The reflection studies show that, in marked contrast to the crude extract, only a single layer of the purified Mo-CBP3 binds to a silica interface and that there is no binding to an alumina interface. These observations are consistent with the crystallographic structure of Mo-CBP3-4, which is one of the main isoforms of the Mo-CBP3 fraction. The results are put in context of previous studies of the properties of the crude extract. This work shows possible routes to development of separation processes that would be based on the specific properties of individual proteins.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{hajj_chehade_soluble_2019,

title = {A Soluble Metabolon Synthesizes the Isoprenoid Lipid Ubiquinone},

author = {Mahmoud Hajj Chehade and Ludovic Pelosi and Cameron David Fyfe and Laurent Loiseau and Bérengère Rascalou and Sabine Brugière and Katayoun Kazemzadeh and Chau-Duy-Tam Vo and Lidia Ciccone and Laurent Aussel and Yohann Couté and Marc Fontecave and Frédéric Barras and Murielle Lombard and Fabien Pierrel},

doi = {10.1016/j.chembiol.2018.12.001},

issn = {2451-9448},

year  = {2019},

date = {2019-01-01},

journal = {Cell Chemical Biology},

volume = {26},

number = {4},

pages = {482----492.e7},

abstract = {Ubiquinone (UQ) is a polyprenylated lipid that is conserved from bacteria to humans and is crucial to cellular respiration. How the cell orchestrates the efficient synthesis of UQ, which involves the modification of extremely hydrophobic substrates by multiple sequential enzymes, remains an unresolved issue. Here, we demonstrate that seven Ubi proteins form the Ubi complex, a stable metabolon that catalyzes the last six reactions of the UQ biosynthetic pathway in Escherichia coli. The SCP2 domain of UbiJ forms an extended hydrophobic cavity that binds UQ intermediates inside the 1-MDa Ubi complex. We purify the Ubi complex from cytoplasmic extracts and demonstrate that UQ biosynthesis occurs in this fraction, challenging the current thinking of a membrane-associated biosynthetic process. Collectively, our results document a rare case of stable metabolon and highlight how the supramolecular organization of soluble enzymes allows the modification of hydrophobic substrates in a hydrophilic environment.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{sentausa_insertion_2019,

title = {Insertion sequences drive the emergence of a highly adapted human pathogen},

author = {Erwin Sentausa and Pauline Basso and Alice Berry and Annie Adrait and Gwendoline Bellement and Yohann Couté and Stephen Lory and Sylvie Elsen and Ina Attrée},

doi = {10.1099/mgen.0.000265},

issn = {2057-5858},

year  = {2019},

date = {2019-01-01},

journal = {Microbial Genomics},

abstract = {Pseudomonas aeruginosa is a highly adaptive opportunistic pathogen that can have serious health consequences in patients with lung disorders. Taxonomic outliers of P. aeruginosa of environmental origin have recently emerged as infectious for humans. Here, we present the first genome-wide analysis of an isolate that caused fatal haemorrhagic pneumonia. In two clones, CLJ1 and CLJ3, sequentially recovered from a patient with chronic pulmonary disease, insertion of a mobile genetic element into the P. aeruginosa chromosome affected major virulence-associated phenotypes and led to increased resistance to the antibiotics used to combat the infection. Comparative genome, proteome and transcriptome analyses revealed that this ISL3-family insertion sequence disrupted the genes for flagellar components, type IV pili, O-specific antigens, translesion polymerase and enzymes producing hydrogen cyanide. Seven-fold more insertions were detected in the later isolate, CLJ3, than in CLJ1, some of which modified strain susceptibility to antibiotics by disrupting the genes for the outer-membrane porin OprD and the regulator of $beta$-lactamase expression AmpD. In the Galleria mellonella larvae model, the two strains displayed different levels of virulence, with CLJ1 being highly pathogenic. This study revealed insertion sequences to be major players in enhancing the pathogenic potential of a P. aeruginosa taxonomic outlier by modulating both its virulence and its resistance to antimicrobials, and explains how this bacterium adapts from the environment to a human host.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{braun_toxoplasma_2019,

title = {The Toxoplasma effector TEEGR promotes parasite persistence by modulating NF-$kappa$B signalling via EZH2},

author = {Laurence Braun and Marie-Pierre Brenier-Pinchart and Pierre-Mehdi Hammoudi and Dominique Cannella and Sylvie Kieffer-Jaquinod and Julien Vollaire and Véronique Josserand and Bastien Touquet and Yohann Couté and Isabelle Tardieux and Alexandre Bougdour and Mohamed-Ali Hakimi},

doi = {10.1038/s41564-019-0431-8},

issn = {2058-5276},

year  = {2019},

date = {2019-01-01},

journal = {Nature Microbiology},

volume = {4},

number = {7},

pages = {1208--1220},

abstract = {The protozoan parasite Toxoplasma gondii has co-evolved with its homeothermic hosts (humans included) strategies that drive its quasi-asymptomatic persistence in hosts, hence optimizing the chance of transmission to new hosts. Persistence, which starts with a small subset of parasites that escape host immune killing and colonize the so-called immune privileged tissues where they differentiate into a low replicating stage, is driven by the interleukin 12 (IL-12)-interferon-$gamma$ (IFN-$gamma$) axis. Recent characterization of a family of Toxoplasma effectors that are delivered into the host cell, in which they rewire the host cell gene expression, has allowed the identification of regulators of the IL-12-IFN-$gamma$ axis, including repressors. We now report on the dense granule-resident effector, called TEEGR (Toxoplasma E2F4-associated EZH2-inducing gene regulator) that counteracts the nuclear factor-$kappa$B (NF-$kappa$B) signalling pathway. Once exported into the host cell, TEEGR ends up in the nucleus where it not only complexes with the E2F3 and E2F4 host transcription factors to induce gene expression, but also promotes shaping of a non-permissive chromatin through its capacity to switch on EZH2. Remarkably, EZH2 fosters the epigenetic silencing of a subset of NF-$kappa$B-regulated cytokines, thereby strongly contributing to the host immune equilibrium that influences the host immune response and promotes parasite persistence in mice.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{darrieutort-laffite_rotator_2019,

title = {Rotator Cuff Tenocytes Differentiate into Hypertrophic Chondrocyte-Like Cells to Produce Calcium Deposits in an Alkaline Phosphatase-Dependent Manner},

author = {Christelle Darrieutort-Laffite and Paul Arnolfo and Thomas Garraud and Annie Adrait and Yohann Couté and Guy Louarn and Valérie Trichet and Pierre Layrolle and Benoit Le Goff and Frédéric Blanchard},

doi = {10.3390/jcm8101544},

issn = {2077-0383},

year  = {2019},

date = {2019-01-01},

journal = {Journal of Clinical Medicine},

volume = {8},

number = {10},

abstract = {Calcific tendonitis is a frequent cause of chronic shoulder pain. Its cause is currently poorly known. The objectives of this study were to better characterize the cells and mechanisms involved in depositing apatite crystals in human tendons. Histologic sections of cadaveric calcified tendons were analyzed, and human calcific deposits from patients undergoing lavage of their calcification were obtained to perform infrared spectroscopy and mass spectrometry-based proteomic characterizations. In vitro, the mineralization ability of human rotator cuff cells from osteoarthritis donors was assessed by alizarin red or Von Kossa staining. Calcifications were amorphous areas surrounded by a fibrocartilaginous metaplasia containing hypertrophic chondrocyte-like cells that expressed tissue non-specific alkaline phosphatase (TNAP) and ectonucleotide pyrophosphatase/phosphodiesterase 1 (ENPP1), which are two key enzymes of the mineralization process. Calcific deposits were composed of apatite crystals associated with proteins involved in bone and cartilage development and endochondral bone growth. In vitro, tenocyte-like cells extracted from the rotator cuff were able to mineralize in osteogenic cultures, and expressed TNAP, type X COLLAGEN, and MMP13, which are hypertrophic chondrocytes markers. The use of a TNAP inhibitor significantly prevented mineral deposits. We provide evidence that tenocytes have a propensity to differentiate into hypertrophic chondrocyte-like cells to produce TNAP-dependent calcium deposits. We believe that these results may pave the way to identifying regulating factors that might represent valuable targets in calcific tendonitis.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{bhalla_interactome_2019,

title = {Interactome of the yeast RNA polymerase III transcription machinery constitutes several chromatin modifiers and regulators of the genes transcribed by RNA polymerase II},

author = {Pratibha Bhalla and Dipti Vinayak Vernekar and Benoit Gilquin and Yohann Couté and Purnima Bhargava},

doi = {10.1016/j.gene.2018.12.037},

issn = {1879-0038},

year  = {2019},

date = {2019-01-01},

journal = {Gene},

volume = {702},

pages = {205--214},

abstract = {Eukaryotic transcription is a highly regulated fundamental life process. A large number of regulatory proteins and complexes, many of them with sequence-specific DNA-binding activity are known to influence transcription by RNA polymerase (pol) II with a fine precision. In comparison, only a few regulatory proteins are known for pol III, which transcribes genes encoding small, stable, non-translated RNAs. The pol III transcription is precisely regulated under various stress conditions. We used pol III transcription complex (TC) components TFIIIC (Tfc6), pol III (Rpc128) and TFIIIB (Brf1) as baits and mass spectrometry to identify their potential interactors in vivo. A large interactome constituting chromatin modifiers, regulators and factors of transcription by pol I and pol II supports the possibility of a crosstalk between the three transcription machineries. The association of proteins and complexes involved in various basic life processes like ribogenesis, RNA processing, protein folding and degradation, DNA damage response, replication and transcription underscores the possibility of the pol III TC serving as a signaling hub for communication between the transcription and other cellular physiological activities under normal growth conditions. We also found an equally large number of proteins and complexes interacting with the TC under nutrient starvation condition, of which at least 25% were non-identical under the two conditions. The data reveal the possibility of a large number of signaling cues for pol III transcription against adverse conditions, necessary for an efficient co-ordination of various cellular functions.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{jeudy_exploration_2019,

title = {Exploration of the propagation of transpovirons within Mimiviridae reveals a unique example of commensalism in the viral world},

author = {Sandra Jeudy and Lionel Bertaux and Jean-Marie Alempic and Audrey Lartigue and Matthieu Legendre and Lucid Belmudes and Sébastien Santini and Nadège Philippe and Laure Beucher and Emanuele G Biondi and Sissel Juul and Daniel J Turner and Yohann Couté and Jean-Michel Claverie and Chantal Abergel},

doi = {10.1038/s41396-019-0565-y},

issn = {1751-7370},

year  = {2019},

date = {2019-01-01},

journal = {The ISME journal},

abstract = {Acanthamoeba-infecting Mimiviridae are giant viruses with dsDNA genome up to 1.5 Mb. They build viral factories in the host cytoplasm in which the nuclear-like virus-encoded functions take place. They are themselves the target of infections by 20-kb-dsDNA virophages, replicating in the giant virus factories and can also be found associated with 7-kb-DNA episomes, dubbed transpovirons. Here we isolated a virophage (Zamilon vitis) and two transpovirons respectively associated to B- and C-clade mimiviruses. We found that the virophage could transfer each transpoviron provided the host viruses were devoid of a resident transpoviron (permissive effect). If not, only the resident transpoviron originally isolated from the corresponding virus was replicated and propagated within the virophage progeny (dominance effect). Although B- and C-clade viruses devoid of transpoviron could replicate each transpoviron, they did it with a lower efficiency across clades, suggesting an ongoing process of adaptive co-evolution. We analysed the proteomes of host viruses and virophage particles in search of proteins involved in this adaptation process. This study also highlights a unique example of intricate commensalism in the viral world, where the transpoviron uses the virophage to propagate and where the Zamilon virophage and the transpoviron depend on the giant virus to replicate, without affecting its infectious cycle.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{dellaglio_identification_2019,

title = {Identification of the Arabidopsis calmodulin-dependent NAD+ kinase that sustains the elicitor-induced oxidative burst},

author = {Elisa Dell'Aglio and Cecile Giustini and Alexandra Kraut and Yohann Couté and Alex Costa and Guillaume Decros and Yves Gibon and Christian Mazars and Michel Matringe and Giovanni Finazzi and Gilles Curien},

doi = {10.1104/pp.19.00912},

issn = {1532-2548},

year  = {2019},

date = {2019-01-01},

journal = {Plant Physiology},

abstract = {NADP(H) is an essential cofactor of multiple metabolic processes in all living organisms, and in plants, NADP(H) is required as the substrate of Ca2+-dependent NADPH oxidases, which catalyze a reactive oxygen species burst in response to various stimuli. While NADP+ production in plants has long been known to involve a calmodulin (CaM)/Ca2+- dependent NAD+ kinase, the nature of the enzyme catalyzing this activity has remained enigmatic, as has its role in plant physiology. Here, we used proteomic, biochemical, molecular and in vivo analyses to identify an Arabidopsis (Arabidopsis thaliana) protein that catalyzes NADP+ production exclusively in the presence of CaM/Ca2+. This enzyme, which we named NAD kinase-CaM dependent (NADKc), has a CaM-binding peptide located in its N-terminal region and displays peculiar biochemical properties as well as different domain organization compared to known plant NAD+ kinases. In response to a pathogen elicitor, activity of NADKc, which is associated with the mitochondrial periphery, contributes to an increase in the cellular NADP+ concentration and to the amplification of the elicitor-induced oxidative burst. Based on a phylogenetic analysis and enzymatic assays, we propose the CaM/Ca2+-dependent NAD+ kinase activity found in photosynthetic organisms is carried out by NADKc-related proteins. Thus, NADKc represents the missing link between Ca2+ signalling, metabolism and the oxidative burst.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{chapelle_dissecting_2019,

title = {Dissecting the Shared and Context-Dependent Pathways Mediated by the p140Cap Adaptor Protein in Cancer and in Neurons},

author = {Jennifer Chapelle and Oksana Sorokina and Colin McLean and Vincenzo Salemme and Annalisa Alfieri and Costanza Angelini and Alessandro Morellato and Annie Adrait and Elisabetta Menna and Michela Matteoli and Yohann Couté and Ugo Ala and Emilia Turco and Paola Defilippi and Douglas J Armstrong},

url = {https://www.frontiersin.org/article/10.3389/fcell.2019.00222/full},

doi = {10.3389/fcell.2019.00222},

issn = {2296-634X},

year  = {2019},

date = {2019-01-01},

journal = {Frontiers in Cell and Developmental Biology},

volume = {7},

pages = {222},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{sonego_usp1_2019,

title = {USP1 links platinum resistance to cancer cell dissemination by regulating Snail stability},

author = {Maura Sonego and Ilenia Pellarin and Alice Costa and Gian Luca Rampioni Vinciguerra and Michela Coan and Alexandra Kraut and Sara D'Andrea and Alessandra Dall'Acqua and Dan Cacsire Castillo-Tong and Daniela Califano and Simona Losito and Riccardo Spizzo and Yohann Couté and Andrea Vecchione and Barbara Belletti and Monica Schiappacassi and Gustavo Baldassarre},

doi = {10.1126/sciadv.aav3235},

issn = {2375-2548},

year  = {2019},

date = {2019-01-01},

journal = {Science Advances},

volume = {5},

number = {5},

pages = {eaav3235},

abstract = {Resistance to platinum-based chemotherapy is a common event in patients with cancer, generally associated with tumor dissemination and metastasis. Whether platinum treatment per se activates molecular pathways linked to tumor spreading is not known. Here, we report that the ubiquitin-specific protease 1 (USP1) mediates ovarian cancer cell resistance to platinum, by regulating the stability of Snail, which, in turn, promotes tumor dissemination. At the molecular level, we observed that upon platinum treatment, USP1 is phosphorylated by ATM and ATR and binds to Snail. Then, USP1 de-ubiquitinates and stabilizes Snail expression, conferring resistance to platinum, increased stem cell-like features, and metastatic ability. Consistently, knockout or pharmacological inhibition of USP1 increased platinum sensitivity and decreased metastatic dissemination in a Snail-dependent manner. Our findings identify Snail as a USP1 target and open the way to a novel strategy to overcome platinum resistance and more successfully treat patients with ovarian cancer.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{louwagie_ultrasensitive_2019,

title = {Ultrasensitive Quantification of Recombinant Proteins Using AAA-MS},

author = {Mathilde Louwagie and Sylvie Kieffer-Jaquinod and Virginie Brun},

doi = {10.1007/978-1-4939-9639-1_1},

issn = {1940-6029},

year  = {2019},

date = {2019-01-01},

journal = {Methods in Molecular Biology (Clifton, N.J.)},

volume = {2030},

pages = {1--10},

abstract = {Recombinant proteins are essential components of therapeutic, biotechnological, food, and household products. In some cases, recombinant proteins must be purified and their quantity and/or concentration precisely determined. In this chapter, we describe a protocol for the quantification of purified recombinant proteins. The protocol is based on a microwave-assisted acidic hydrolysis of the target protein followed by high-resolution mass spectrometry (HRMS) analysis of the hydrolytic products. Absolute quantification is obtained by adding controlled amounts of labeled amino acids that serve as standards.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}