@article{ngo_popn_2020,

title = {The PopN gate-keeper complex acts on the ATPase PscN to regulate the T3SS secretion switch from early to middle substrates in Pseudomonas aeruginosa},

author = {Tuan-Dung Ngo and Caroline Perdu and Bakhos Jneid and Michel Ragno and Julia Novion Ducassou and Alexandra Kraut and Yohann Couté and Charles Stopford and Ina Attree and Arne Rietsch and Eric Faudry},

url = {http://www.sciencedirect.com/science/article/pii/S0022283620306008},

doi = {10.1016/j.jmb.2020.10.024},

issn = {0022-2836},

year  = {2020},

date = {2020-01-01},

journal = {Journal of Molecular Biology},

abstract = {Pseudomonas aeruginosa is an opportunistic bacterium of which the main virulence factor is the Type III Secretion System. The ATPase of this machinery, PscN (SctN), is thought to be localized at the base of the secretion apparatus and to participate in the recognition, chaperone dissociation and unfolding of exported T3SS proteins. In this work, a protein-protein interaction ELISA revealed the interaction of PscN with a wide range of exported T3SS proteins including the needle, translocator, gate-keeper and effector. These interactions were further confirmed by Microscale Thermophoresis that also indicated a preferential interaction of PscN with secreted proteins or protein-chaperone complex rather than with chaperones alone, in line with the release of the chaperones in the bacterial cytoplasm after the dissociation from their exported proteins. Moreover, we suggest a new role of the gate-keeper complex and the ATPase in the regulation of early substrates recognition by the T3SS. This finding sheds a new light on the mechanism of secretion switching from early to middle substrates in P. aeruginosa.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{lamboux_blood_2020,

title = {The blood copper isotopic composition is a prognostic indicator of the hepatic injury in Wilson disease},

author = {Aline Lamboux and Eduardo Couchonnal-Bedoya and Olivier Guillaud and Chloé Laurencin and Laurence Lion-François and Abdelouahed Belmalih and Elisabeth Mintz and Virginie Brun and Muriel Bost and Alain Lachaux and Vincent Balter},

doi = {10.1039/d0mt00167h},

issn = {1756-591X},

year  = {2020},

date = {2020-01-01},

journal = {Metallomics: Integrated Biometal Science},

abstract = {Wilson disease (WD) is an autosomal recessive disorder of copper (Cu) metabolism. The gene responsible for WD, ATP7B, is involved in the cellular transport of Cu, and mutations in the ATP7B gene induce accumulation of Cu in the liver and ultimately in the brain. In a pilot study, the natural variations of copper stable isotope ratios (65Cu/63Cu) in the serum of WD patients have been shown to differ from that of healthy controls. In the present study, we challenged these first results by measuring the 65Cu/63Cu ratios in the blood of treated (n = 25), naïve patients (n = 11) and age matched healthy controls (n = 75). The results show that naïve patients and healthy controls exhibit undistinguishable 65Cu/63Cu ratios, implying that the Cu isotopic ratio cannot serve as a reliable diagnostic biomarker. The type of treatment (d-penicillamine vs. triethylenetetramine) does not affect the 65Cu/63Cu ratios in WD patients, which remain constant regardless of the type and duration of the treatment. In addition, the 65Cu/63Cu ratios do not vary in naïve patients after the onset of the treatment. However, the 65Cu/63Cu ratios decrease with the degree of liver fibrosis and the gradient of the phenotypic presentation, i.e. presymptomatic, hepatic and neurologic. To get insights into the mechanisms at work, we study the effects of the progress of the WD on the organism by measuring the Cu concentrations and the 65Cu/63Cu ratios in the liver, feces and plasma of 12 and 45 week old Atp7b-/- mice. The evolution of the 65Cu/63Cu ratios is marked by a decrease in all tissues. The results show that 63Cu accumulates in the liver preferentially to 65Cu due to the preferential cellular entry of 63Cu and the impairment of the 63Cu exit by ceruloplasmin. The hepatic accumulation of monovalent 63Cu+ is likely to fuel the production of free radicals, which is potentially an explanation of the pathogenicity of WD. Altogether, the results suggest that the blood 65Cu/63Cu ratio recapitulates WD progression and is a potential prognostic biomarker of WD.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{roblin_unusual_2020,

title = {The unusual structure of Ruminococcin C1 antimicrobial peptide confers clinical properties},

author = {Clarisse Roblin and Steve Chiumento and Olivier Bornet and Matthieu Nouailler and Christina S Müller and Katy Jeannot and Christian Basset and Sylvie Kieffer-Jaquinod and Yohann Couté and Stéphane Torelli and Laurent Le Pape and Volker Schünemann and Hamza Olleik and Bruno De La Villeon and Philippe Sockeel and Eric Di Pasquale and Cendrine Nicoletti and Nicolas Vidal and Leonora Poljak and Olga Iranzo and Thierry Giardina and Michel Fons and Estelle Devillard and Patrice Polard and Marc Maresca and Josette Perrier and Mohamed Atta and Françoise Guerlesquin and Mickael Lafond and Victor Duarte},

doi = {10.1073/pnas.2004045117},

issn = {1091-6490},

year  = {2020},

date = {2020-01-01},

journal = {Proceedings of the National Academy of Sciences of the United States of America},

abstract = {The emergence of superbugs developing resistance to antibiotics and the resurgence of microbial infections have led scientists to start an antimicrobial arms race. In this context, we have previously identified an active RiPP, the Ruminococcin C1, naturally produced by Ruminococcus gnavus E1, a symbiont of the healthy human intestinal microbiota. This RiPP, subclassified as a sactipeptide, requires the host digestive system to become active against pathogenic Clostridia and multidrug-resistant strains. Here we report its unique compact structure on the basis of four intramolecular thioether bridges with reversed stereochemistry introduced posttranslationally by a specific radical-SAM sactisynthase. This structure confers to the Ruminococcin C1 important clinical properties including stability to digestive conditions and physicochemical treatments, a higher affinity for bacteria than simulated intestinal epithelium, a valuable activity at therapeutic doses on a range of clinical pathogens, mediated by energy resources disruption, and finally safety for human gut tissues.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{sokolovska_using_2020,

title = {Using Unlabeled Data to Discover Bivariate Causality with Deep Restricted Boltzmann Machines},

author = {Nataliya Sokolovska and Olga Permiakova and Sofia K Forslund and Jean-Daniel Zucker},

doi = {10.1109/TCBB.2018.2879504},

issn = {1557-9964},

year  = {2020},

date = {2020-01-01},

journal = {IEEE/ACM transactions on computational biology and bioinformatics},

volume = {17},

number = {1},

pages = {358--364},

abstract = {An important question in microbiology is whether treatment causes changes in gut flora, and whether it also affects metabolism. The reconstruction of causal relations purely from non-temporal observational data is challenging. We address the problem of causal inference in a bivariate case, where the joint distribution of two variables is observed. We consider, in particular, data on discrete domains. The state-of-the-art causal inference methods for continuous data suffer from high computational complexity. Some modern approaches are not suitable for categorical data, and others need to estimate and fix multiple hyper-parameters. In this contribution, we introduce a novel method of causal inference which is based on the widely used assumption that if X causes Y, then P(X) and P(Y$backslash$textbarX) are independent. We propose to explore a semi-supervised approach where P(Y$backslash$textbarX) and P(X) are estimated from labeled and unlabeled data respectively, whereas the marginal probability is estimated potentially from much more (cheap unlabeled) data than the conditional distribution. We validate the proposed method on the standard cause-effect pairs. We illustrate by experiments on several benchmarks of biological network reconstruction that the proposed approach is very competitive in terms of computational time and accuracy compared to the state-of-the-art methods. Finally, we apply the proposed method to an original medical task where we study whether drugs confound human metagenome.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{674,

title = {Software requirements for the analysis and interpretation of native ion mobility mass spectrometry data},

author = {T M Allison and P E Barran and J L P Benesch and S Cianferani and M T Degiacomi and V Gabelica and R Grandori and E G Marklund and T Menneteau and L G Migas and A Politis and M Sharon and F Sobott and K Thalassinos},

url = {https://www.ncbi.nlm.nih.gov/pubmed/32649184},

doi = {10.1021/acs.analchem.9b05792},

issn = {1520-6882 (Electronic) 0003-2700 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {Anal Chem},

note = {review, pas de projet LSMBO},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{673b,

title = {Computational strategies and challenges for using native ion mobility mass spectrometry in biophysics and structural biology},

author = {T M Allison and P E Barran and S Cianferani and M T Degiacomi and V Gabelica and R Grandori and E G Marklund and T Menneteau and L G Migas and A Politis and M Sharon and F Sobott and K Thalassinos and J L P Benesch},

url = {https://www.ncbi.nlm.nih.gov/pubmed/32667808},

doi = {10.1021/acs.analchem.9b05791},

issn = {1520-6882 (Electronic) 0003-2700 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {Anal Chem},

note = {review pas de projet LSMBO},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{663b,

title = {Middle Level IM-MS and CIU Experiments for Improved Therapeutic Immunoglobulin Subclass Fingerprinting},

author = {T Botzanowski and O Hernandez-Alba and M Malissard and E Wagner-Rousset and E Desligniere and O Colas and J F Haeuw and A Beck and S Cianferani},

url = {https://www.ncbi.nlm.nih.gov/pubmed/32453570},

doi = {10.1021/acs.analchem.0c00293},

issn = {1520-6882 (Electronic) 0003-2700 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {Anal Chem},

volume = {92},

number = {13},

pages = {8827-8835},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{679b,

title = {NCKAP1L defects lead to a novel syndrome combining immunodeficiency, lymphoproliferation, and hyperinflammation},

author = {C N Castro and M Rosenzwajg and R Carapito and M Shahrooei and M Konantz and A Khan and Z Miao and M Gross and T Tranchant and M Radosavljevic and N Paul and T Stemmelen and F Pitoiset and A Hirschler and B Nespola and A Molitor and V Rolli and A Pichot and L E Faletti and B Rinaldi and S Friant and M Mednikov and H Karauzum and M J Aman and C Carapito and C Lengerke and V Ziaee and W Eyaid and S Ehl and F Alroqi and N Parvaneh and S Bahram},

url = {https://www.ncbi.nlm.nih.gov/pubmed/32766723},

doi = {10.1084/jem.20192275},

issn = {1540-9538 (Electronic) 0022-1007 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {J Exp Med},

volume = {217},

number = {12},

note = {????},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{659,

title = {VHH characterization.Recombinant VHHs: Production, characterization and affinity},

author = {E Chabrol and J Stojko and A Nicolas and T Botzanowski and B Fould and M Antoine and S Cianferani and G Ferry and J A Boutin},

url = {https://www.ncbi.nlm.nih.gov/pubmed/31676284},

doi = {10.1016/j.ab.2019.113491},

issn = {1096-0309 (Electronic) 0003-2697 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {Anal Biochem},

volume = {589},

pages = {113491},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{678,

title = {Optimal conditions for tandem mass spectrometric sequencing of information-containing nitrogen-substituted polyurethanes},

author = {L Charles and T Mondal and V Greff and M Razzini and V Monnier and A Burel and C Carapito and J F Lutz},

url = {https://www.ncbi.nlm.nih.gov/pubmed/32311797},

doi = {10.1002/rcm.8815},

issn = {1097-0231 (Electronic) 0951-4198 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {Rapid Commun Mass Spectrom},

volume = {34},

number = {14},

pages = {e8815},

note = {????},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{666,

title = {Abeta(1-42) tetramer and octamer structures reveal edge conductivity pores as a mechanism for membrane damage},

author = {S Ciudad and E Puig and T Botzanowski and M Meigooni and A S Arango and J Do and M Mayzel and M Bayoumi and S Chaignepain and G Maglia and S Cianferani and V Orekhov and E Tajkhorshid and B Bardiaux and N Carulla},

url = {https://www.ncbi.nlm.nih.gov/pubmed/32541820},

doi = {10.1038/s41467-020-16566-1},

issn = {2041-1723 (Electronic) 2041-1723 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {Nat Commun},

volume = {11},

number = {1},

pages = {3014},

note = {2018/12},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{667,

title = {On the use of DNA as a linker in antibody-drug conjugates: synthesis, stability and in vitro potency},

author = {I Dovgan and A Ehkirch and V Lehot and I Kuhn and O Koniev and S Kolodych and A Hentz and M Ripoll and S Ursuegui and M Nothisen and S Cianferani and A Wagner},

url = {https://www.ncbi.nlm.nih.gov/pubmed/32376903},

doi = {10.1038/s41598-020-64518-y},

issn = {2045-2322 (Electronic) 2045-2322 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {Sci Rep},

volume = {10},

number = {1},

pages = {7691},

note = {2019-05},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{668b,

title = {Glycan-Mediated Technology for Obtaining Homogeneous Site-Specific Conjugated Antibody-Drug Conjugates: Synthesis and Analytical Characterization by Using Complementary Middle-up LC/HRMS Analysis},

author = {B L Duivelshof and E Desligniere and O Hernandez-Alba and A Ehkirch and H Toftevall and J Sjogren and S Cianferani and A Beck and D Guillarme and V D'Atri},

url = {https://www.ncbi.nlm.nih.gov/pubmed/32407621},

doi = {10.1021/acs.analchem.0c00282},

issn = {1520-6882 (Electronic) 0003-2700 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {Anal Chem},

volume = {92},

number = {12},

pages = {8170-8177},

note = {pas de manips au LSMBO},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{655,

title = {Homogeneous antibody-drug conjugates: DAR 2 anti-HER2 obtained by conjugation on isolated light chain followed by mAb assembly},

author = {M Farras and J Miret and M Camps and R Roman and O Martinez and X Pujol and S Erb and A Ehkirch and S Cianferani and A Casablancas and J J Cairo},

url = {https://www.ncbi.nlm.nih.gov/pubmed/31876436},

doi = {10.1080/19420862.2019.1702262},

issn = {1942-0870 (Electronic) 1942-0862 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {MAbs},

volume = {12},

number = {1},

pages = {1702262},

note = {2018/06},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{656,

title = {Analysis of ADCs by Native Mass Spectrometry},

author = {O Hernandez-Alba and A Ehkirch and A Beck and S Cianferani},

url = {https://www.ncbi.nlm.nih.gov/pubmed/31643058},

doi = {10.1007/978-1-4939-9929-3_13},

issn = {1940-6029 (Electronic) 1064-3745 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {Methods Mol Biol},

volume = {2078},

pages = {197-211},

note = {review},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{658,

title = {(Thia)calixarenephosphonic Acids as Potent Inhibitors of the Nucleic Acid Chaperone Activity of the HIV-1 Nucleocapsid Protein with a New Binding Mode and Multitarget Antiviral Activity},

author = {N Humbert and L Kovalenko and F Saladini and A Giannini and M Pires and T Botzanowski and S Cherenok and C Boudier and K K Sharma and E Real and O A Zaporozhets and S Cianferani and C Seguin-Devaux and F Poggialini and M Botta and M Zazzi and V I Kalchenko and M Mori and Y Mely},

url = {https://www.ncbi.nlm.nih.gov/pubmed/32045204},

doi = {10.1021/acsinfecdis.9b00290},

issn = {2373-8227 (Electronic) 2373-8227 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {ACS Infect Dis},

volume = {6},

number = {4},

pages = {687-702},

abstract = {The nucleocapsid protein (NC) is a highly conserved protein that plays key roles in HIV-1 replication through its nucleic acid chaperone properties mediated by its two zinc fingers and basic residues. NC is a promising target for antiviral therapy, particularly to control viral strains resistant to currently available drugs. Since calixarenes with antiviral properties have been described, we explored the ability of calixarene hydroxymethylphosphonic or sulfonic acids to inhibit NC chaperone properties and exhibit antiviral activity. By using fluorescence-based assays, we selected four calixarenes inhibiting NC chaperone activity with submicromolar IC50 values. These compounds were further shown by mass spectrometry, isothermal titration calorimetry, and fluorescence anisotropy to bind NC with no zinc ejection and to compete with nucleic acids for the binding to NC. Molecular dynamic simulations further indicated that these compounds interact via their phosphonate or sulfonate groups with the basic surface of NC but not with the hydrophobic plateau at the top of the folded fingers. Cellular studies showed that the most soluble compound CIP201 inhibited the infectivity of wild-type and drug-resistant HIV-1 strains at low micromolar concentrations, primarily targeting the early steps of HIV-1 replication. Moreover, CIP201 was also found to inhibit the flipping and polymerization activity of reverse transcriptase. Calixarenes thus form a class of noncovalent NC inhibitors, endowed with a new binding mode and multitarget antiviral activity.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{675,

title = {Effectiveness of Resistive Vibration Exercise and Whey Protein Supplementation Plus Alkaline Salt on the Skeletal Muscle Proteome Following 21 Days of Bed Rest in Healthy Males},

author = {H C Kenny and G Tascher and A Ziemianin and F Rudwill and A Zahariev and I Chery and G Gauquelin-Koch and M P Barielle and M Heer and S Blanc and D J O'Gorman and F Bertile},

url = {https://www.ncbi.nlm.nih.gov/pubmed/32609523},

doi = {10.1021/acs.jproteome.0c00256},

issn = {1535-3907 (Electronic) 1535-3893 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {J Proteome Res},

volume = {19},

number = {8},

pages = {3438-3451},

note = {2011/34},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{661,

title = {Growth and differentiation factor 15 is secreted by skeletal muscle during exercise and promotes lipolysis in humans},

author = {C Laurens and A Parmar and E Murphy and D Carper and B Lair and P Maes and J Vion and N Boulet and C Fontaine and M Marquès and D Larrouy and I Harant and C Thalamas and E Montastier and S Caspar-Baugil and V Bourlier and G Tavernier and J L Grolleau and A Bouloumié and D Langin and N Viguerie and F Bertile and S Blanc and I De Glisezinski and D O’Gorman and C Moro},

year  = {2020},

date = {2020-01-01},

journal = {JCI Insight},

volume = {5},

number = {6},

pages = {E131870},

note = {2016/26},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{664b,

title = {Effects of topical corticosteroids and lidocaine on Borrelia burgdorferi sensu lato in mouse skin: potential impact to human clinical trials},

author = {B Lefeuvre and P Cantero and L Ehret-Sabatier and C Lenormand and C Barthel and C Po and N Parveen and A Grillon and B Jaulhac and N Boulanger},

url = {https://www.ncbi.nlm.nih.gov/pubmed/32601348},

doi = {10.1038/s41598-020-67440-5},

issn = {2045-2322 (Electronic) 2045-2322 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {Sci Rep},

volume = {10},

number = {1},

pages = {10552},

note = {2012/30},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{665b,

title = {MicroRNAs facilitate skeletal muscle maintenance and metabolic suppression in hibernating brown bears},

author = {B E Luu and E Lefai and S Giroud and J E Swenson and B Chazarin and G Gauquelin-Koch and J M Arnemo and A L Evans and F Bertile and K B Storey},

url = {https://www.ncbi.nlm.nih.gov/pubmed/31643088},

doi = {10.1002/jcp.29294},

issn = {1097-4652 (Electronic) 0021-9541 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {J Cell Physiol},

volume = {235},

number = {4},

pages = {3984-3993},

note = {2011/34},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{662,

title = {Phenotypic Adaption of Pseudomonas aeruginosa by Hacking Siderophores Produced by Other Microorganisms},

author = {Q Perraud and P Cantero and B Roche and V Gasser and V P Normant and L Kuhn and P Hammann and G L A Mislin and L Ehret-Sabatier and I J Schalk},

url = {https://www.ncbi.nlm.nih.gov/pubmed/32024770},

doi = {10.1074/mcp.RA119.001829},

issn = {1535-9484 (Electronic) 1535-9476 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {Mol Cell Proteomics},

volume = {19},

number = {4},

pages = {589-607},

note = {2015/28},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{669b,

title = {Probing Protein Interaction Networks by Combining MS-Based Proteomics and Structural Data Integration},

author = {G Postic and J Marcoux and V Reys and J Andreani and Y Vandenbrouck and M P Bousquet and E Mouton-Barbosa and S Cianferani and O Burlet-Schiltz and R Guerois and G Labesse and P Tuffery},

url = {https://www.ncbi.nlm.nih.gov/pubmed/32338910},

doi = {10.1021/acs.jproteome.0c00066},

issn = {1535-3907 (Electronic) 1535-3893 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {J Proteome Res},

volume = {19},

number = {7},

pages = {2807-2820},

note = {pas de projet, pas de manips au labo},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{670b,

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 Cianferani and E Candolfi and A W Pfaff and J Brunet},

url = {https://www.ncbi.nlm.nih.gov/pubmed/31492965},

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

issn = {1420-9071 (Electronic) 1420-682X (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {Cell Mol Life Sci},

volume = {77},

number = {11},

pages = {2141-2156},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{671b,

title = {Investigating Ugi / Passerini multicomponent reactions for the Site-Selective Conjugation of Native Trastuzumab},

author = {C Sornay and S Hessmann and S Erb and I Dovgan and A Ehkirch and T Botzanowski and S Cianferani and A Wagner and G Chaubet},

url = {https://www.ncbi.nlm.nih.gov/pubmed/32588934},

doi = {10.1002/chem.202002432},

issn = {1521-3765 (Electronic) 0947-6539 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {Chemistry},

note = {2018/30},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{677,

title = {Tenascin-C Orchestrates an Immune-Suppressive Tumor Microenvironment in Oral Squamous Cell Carcinoma},

author = {C Spenle and T Loustau and D Murdamoothoo and W Erne and S Beghelli-de Forest Divonne and R Veber and L Petti and P Bourdely and M Morgelin and E M Brauchle and G Cremel and V Randrianarisoa and A Camara and S Rekima and S Schaub and K Nouhen and T Imhof and U Hansen and N Paul and R Carapito and N Pythoud and A Hirschler and C Carapito and H Dumortier and C G Mueller and M Koch and K Schenke-Layland and S Kon and A Sudaka and F Anjuere and E Van Obberghen-Schilling and G Orend},

url = {https://www.ncbi.nlm.nih.gov/pubmed/32665262},

doi = {10.1158/2326-6066.CIR-20-0074},

issn = {2326-6074 (Electronic) 2326-6066 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {Cancer Immunol Res},

note = {????},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{672b,

title = {Ethynylation of Cysteine Residues: From Peptides to Proteins in Vitro and in Living Cells},

author = {R Tessier and R K Nandi and B G Dwyer and D Abegg and C Sornay and J Ceballos and S Erb and S Cianferani and A Wagner and G Chaubet and A Adibekian and J Waser},

url = {https://www.ncbi.nlm.nih.gov/pubmed/32233093},

doi = {10.1002/anie.202002626},

issn = {1521-3773 (Electronic) 1433-7851 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {Angew Chem Int Ed Engl},

volume = {59},

number = {27},

pages = {10961-10970},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{676,

title = {Phylogenomic Classification and Biosynthetic Potential of the Fossil Fuel-Biodesulfurizing Rhodococcus Strain IGTS8},

author = {D Thompson and V Cognat and M Goodfellow and S Koechler and D Heintz and C Carapito and A Van Dorsselaer and H Mahmoud and V Sangal and W Ismail},

url = {https://www.ncbi.nlm.nih.gov/pubmed/32733398},

doi = {10.3389/fmicb.2020.01417},

issn = {1664-302X (Print) 1664-302X (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {Front Microbiol},

volume = {11},

pages = {1417},

note = {???},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{642,

title = {Determination of size variants by CE-SDS for approved therapeutic antibodies: Key implications of subclasses and light chain specificities},

author = {E Wagner and O Colas and S Chenu and A Goyon and A Murisier and S Cianferani and Y Francois and S Fekete and D Guillarme and V D'Atri and A Beck},

url = {https://www.ncbi.nlm.nih.gov/pubmed/32113118},

doi = {10.1016/j.jpba.2020.113166},

issn = {1873-264X (Electronic) 0731-7085 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {J Pharm Biomed Anal},

volume = {184},

pages = {113166},

note = {pas de manip MS},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{660,

title = {Drug Loading and Distribution of ADCs After Reduction or IdeS Digestion and Reduction},

author = {E Wagner-Rousset and O Colas and Y N Francois and S Heinisch and D Guillarme and S Cianferani and A Beck},

url = {https://www.ncbi.nlm.nih.gov/pubmed/31643057},

doi = {10.1007/978-1-4939-9929-3_12},

issn = {1940-6029 (Electronic) 1064-3745 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {Methods Mol Biol},

volume = {2078},

pages = {187-195},

note = {pas de manip MS LSMBO},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{641b,

title = {Quantification of biomarkers for beef meat qualities using a combination of Parallel Reaction Monitoring- and antibody-based proteomics},

author = {M Bonnet and J Soulat and J Bons and S Leger and L De Koning and C Carapito and B Picard},

url = {https://www.ncbi.nlm.nih.gov/pubmed/32078991},

doi = {10.1016/j.foodchem.2020.126376},

issn = {1873-7072 (Electronic) 0308-8146 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {Food Chem},

volume = {317},

pages = {126376},

abstract = {We and others have identified biomarker candidates of tenderness or marbling, two major attributes of bovine meat-eating qualities for consumers' satisfaction. In this study, Reverse Phase Protein Arrays (RPPA) and targeted mass spectrometry assays using Parallel Reaction Monitoring (PRM) were developed to test whether 10 proteins pass the sequential qualification and verification steps of the challenging biomarker discovery pipeline. At least MYH1, TPI1, ALDH1A1 and CRYAB were qualified by RPPA or PRM as being differentially abundant according to marbling values of longissimus thoracis and semimembranosus muscles. Significant mathematical relationships between the individual abundance of each of the four proteins and marbling values were verified by linear or logistic regressions. Four proteins, TNNT1, MDH1, PRDX6 and ENO3 were qualified and verified for tenderness, and the abundance of MDH1 explained 49% of the tenderness variability. The present PRM and RPPA results pave the way for development of useful meat industrial multiplex-proteins assays.},

note = {???},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{643b,

title = {Alterations in rat adipose tissue transcriptome and proteome in response to prolonged fasting.},

author = {M Ibrahim and D Ayoub and T Wasselin and A Van Dorsselaer and Y Le Maho and T Raclot and F Bertile},

year  = {2020},

date = {2020-01-01},

journal = {Biological Chemistry},

volume = {401},

number = {3},

pages = {389-405},

note = {2009/41},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{691,

title = {Molecular determinants of MED1 interaction with the DNA bound VDR-RXR heterodimer},

author = {A Y Belorusova and M Bourguet and S Hessmann and S Chalhoub and B Kieffer and S Cianferani and N Rochel},

url = {https://www.ncbi.nlm.nih.gov/pubmed/32990725},

doi = {10.1093/nar/gkaa775},

issn = {1362-4962 (Electronic) 0305-1048 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {Nucleic Acids Res},

volume = {48},

number = {19},

pages = {11199-11213},

abstract = {The MED1 subunit of the Mediator complex is an essential coactivator of nuclear receptor-mediated transcriptional activation. While structural requirements for ligand-dependent binding of classical coactivator motifs of MED1 to numerous nuclear receptor ligand-binding domains have been fully elucidated, the recognition of the full-length or truncated coactivator by full nuclear receptor complexes remain unknown. Here we present structural details of the interaction between a large part of MED1 comprising its structured N-terminal and the flexible receptor-interacting domains and the mutual heterodimer of the vitamin D receptor (VDR) and the retinoid X receptor (RXR) bound to their cognate DNA response element. Using a combination of structural and biophysical methods we show that the ligand-dependent interaction between VDR and the second coactivator motif of MED1 is crucial for complex formation and we identify additional, previously unseen, interaction details. In particular, we identified RXR regions involved in the interaction with the structured N-terminal domain of MED1, as well as VDR regions outside the classical coactivator binding cleft affected by coactivator recruitment. These findings highlight important roles of each receptor within the heterodimer in selective recognition of MED1 and contribute to our understanding of the nuclear receptor-coregulator complexes.},

note = {Belorusova, Anna Y 

Bourguet, Maxime 

Hessmann, Steve 

Chalhoub, Sandra 

Kieffer, Bruno 

Cianferani, Sarah 

Rochel, Natacha 

eng 

Research Support, Non-U.S. Gov't 

England 

2020/09/30 06:00 

Nucleic Acids Res. 2020 Nov 4;48(19):11199-11213. doi: 10.1093/nar/gkaa775.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{654,

title = {Skin Interface, a Key Player for Borrelia Multiplication and Persistence in Lyme Borreliosis},

author = {Q Bernard and A Grillon and C Lenormand and L Ehret-Sabatier and N Boulanger},

url = {https://www.ncbi.nlm.nih.gov/pubmed/32007396},

doi = {10.1016/j.pt.2019.12.017},

issn = {1471-5007 (Electronic) 

1471-4922 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {Trends Parasitol},

volume = {36},

number = {3},

pages = {304-314},

abstract = {The skin plays a key role in vector-borne diseases because it is the site where the arthropod coinoculates pathogens and its saliva. Lyme borreliosis, particularly well investigated in this context, is a multisystemic infectious disease caused by Borrelia burgdorferi sensu lato and transmitted by the hard tick Ixodes. Numerous in vitro studies were conducted to better understand the role of specific skin cells and tick saliva in host defense, vector feeding, and pathogen transmission. The skin was also evidenced in various animal models as the site of bacterial multiplication and persistence. We present the achievements in this field as well as the gaps that impede comprehensive knowledge of the disease pathophysiology and the development of efficient diagnostic tools and vaccines in humans.},

note = {2012/30},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{680,

title = {Specific shifts in the endocannabinoid system in hibernating brown bears},

author = {C Boyer and L Cussonneau and C Brun and C Deval and J P Pais Barros and S Chanon and N Bernoud-Hubac and P Daira and A L Evans and J M Arnemo and J E Swenson and G Gauquelin-Koch and C Simon and S Blanc and L Combaret and F Bertile and E Lefai},

url = {https://www.ncbi.nlm.nih.gov/pubmed/33292302},

doi = {10.1186/s12983-020-00380-y},

issn = {1742-9994 (Print) 1742-9994 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {Front Zool},

volume = {17},

number = {1},

pages = {35},

abstract = {In small hibernators, global downregulation of the endocannabinoid system (ECS), which is involved in modulating neuronal signaling, feeding behavior, energy metabolism, and circannual rhythms, has been reported to possibly drive physiological adaptation to the hibernating state. In hibernating brown bears (Ursus arctos), we hypothesized that beyond an overall suppression of the ECS, seasonal shift in endocannabinoids compounds could be linked to bear's peculiar features that include hibernation without arousal episodes and capacity to react to external disturbance. We explored circulating lipids in serum and the ECS in plasma and metabolically active tissues in free-ranging subadult Scandinavian brown bears when both active and hibernating. In winter bear serum, in addition to a 2-fold increase in total fatty acid concentration, we found significant changes in relative proportions of circulating fatty acids, such as a 2-fold increase in docosahexaenoic acid C22:6 n-3 and a decrease in arachidonic acid C20:4 n-6. In adipose and muscle tissues of hibernating bears, we found significant lower concentrations of 2-arachidonoylglycerol (2-AG), a major ligand of cannabinoid receptors 1 (CB1) and 2 (CB2). Lower mRNA level for genes encoding CB1 and CB2 were also found in winter muscle and adipose tissue, respectively. The observed reduction in ECS tone may promote fatty acid mobilization from body fat stores, and favor carbohydrate metabolism in skeletal muscle of hibernating bears. Additionally, high circulating level of the endocannabinoid-like compound N-oleoylethanolamide (OEA) in winter could favor lipolysis and fatty acid oxidation in peripheral tissues. We also speculated on a role of OEA in the conservation of an anorexigenic signal and in the maintenance of torpor during hibernation, while sustaining the capacity of bears to sense stimuli from the environment.},

note = {2011/34},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{694,

title = {The longer the worse: a combined proteomic and targeted study of the long-termversusshort-term effects of silver nanoparticles on macrophages},

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

url = {<Go to ISI>://WOS:000549099000010},

doi = {10.1039/c9en01329f},

issn = {2051-8153},

year  = {2020},

date = {2020-01-01},

journal = {Environmental Science-Nano},

volume = {7},

number = {7},

pages = {2032-2046},

abstract = {Despite considerable research effort devoted to the study of the effects of silver nanoparticles on mammalian cells in recent years, data on the potential long term effects of this nanomaterial remain scarce, and centered on epithelial cells. The aim of this study was to explore the effects of silver nanoparticles on macrophages. To this end, RAW 264.7 murine macrophages were exposed to either 1 mu g ml(-1)silver nanoparticles for 20 days,i.e.a chronic exposure scheme, or to 20 mu g ml(-1)silver nanoparticles for 24 hours,i.e.an acute exposure scheme. A proteomic study was then conducted to study and compare the cellular responses to both exposure schemes. They proved to be essentially different, and stronger for the chronic exposure scheme. Targeted validation studies showed effects of chronic exposure to silver nanoparticles on detoxifying enzymes such as flavin reductase, which was increased, and on central metabolism enzymes such as triose phosphate isomerase, the activity of which decreased under chronic exposure to silver nanoparticles. Chronic exposure to silver nanoparticles also induced a decrease of reduced glutathione content, a decreased phagocytic activity and reduced macrophage responses to lipopolysaccharide, as exemplified by nitric oxide and interleukin 6 production. Overall, chronic exposure to silver nanoparticles induced stronger effects than acute exposure on macrophages in the metabolic (glutathione level, mitochondrial potential) and functional (phagocytosis, cytokine production) parameters tested.},

note = {2014/29},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{690,

title = {Toward Automation of Collision-Induced Unfolding Experiments through Online Size Exclusion Chromatography Coupled to Native Mass Spectrometry},

author = {E Desligniere and A Ehkirch and T Botzanowski and A Beck and O Hernandez-Alba and S Cianferani},

url = {https://www.ncbi.nlm.nih.gov/pubmed/32886492},

doi = {10.1021/acs.analchem.0c01426},

issn = {1520-6882 (Electronic) 0003-2700 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {Anal Chem},

volume = {92},

number = {19},

pages = {12900-12908},

abstract = {Ion mobility (IM)-based collision-induced unfolding (CIU) has gained increasing attention to probe gas-phase unfolding of proteins and their noncovalent complexes, notably for biotherapeutics. CIU detects subtle conformational changes of proteins and emerges as an attractive alternative to circumvent poor IM resolution. However, CIU still lacks in automation for buffer exchange and data acquisition, precluding its wide adoption. We present here an automated workflow for CIU experiments, from sample preparation to data interpretation using online size exclusion chromatography coupled to native IM mass spectrometry (SEC-CIU). Online automated SEC-CIU experiments offer several benefits over nanoESI-CIU, among which are (i) improved and fast desalting compared to manual buffer exchange used for classical CIU experiments; (ii) drastic reduction of the overall data collection time process; and (iii) maintaining the number of unfolding transitions. We then evaluate the potential of SEC-CIU to distinguish monoclonal antibody (mAb) subclasses, illustrating the efficiency of our method for rapid mAb subclass identification at both intact and middle levels. Finally, we demonstrate that CIU data acquisition time can be further reduced either by setting up a scheduled CIU method relying on diagnostic trap collision voltages or by implementing mAb-multiplexed SEC-CIU analyses to maximize information content in a single experiment. Altogether, our results confirm the suitability of SEC-CIU to automate CIU experiments, particularly for the fast characterization of next-generation mAb-based products.},

note = {Desligniere, Evolene 

Ehkirch, Anthony 

Botzanowski, Thomas 

Beck, Alain 

Hernandez-Alba, Oscar 

Cianferani, Sarah 

eng 

Research Support, Non-U.S. Gov't 

2020/09/05 06:00 

Anal Chem. 2020 Oct 6;92(19):12900-12908. doi: 10.1021/acs.analchem.0c01426. Epub 2020 Sep 18.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{681b,

title = {Transcriptional Changes Involved in Atrophying Muscles during Prolonged Fasting in Rats},

author = {M Ibrahim and T Wasselin and E Challet and A Van Dorsselaer and Y Le Maho and T Raclot and F Bertile},

url = {https://www.ncbi.nlm.nih.gov/pubmed/32825252},

doi = {10.3390/ijms21175984},

issn = {1422-0067 (Electronic) 1422-0067 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {Int J Mol Sci},

volume = {21},

number = {17},

abstract = {Food deprivation resulting in muscle atrophy may be detrimental to health. To better understand how muscle mass is regulated during such a nutritional challenge, the current study deciphered muscle responses during phase 2 (P2, protein sparing) and phase 3 (P3, protein mobilization) of prolonged fasting in rats. This was done using transcriptomics analysis and a series of biochemistry measurements. The main findings highlight changes for plasma catabolic and anabolic stimuli, as well as for muscle transcriptome, energy metabolism, and oxidative stress. Changes were generally consistent with the intense use of lipids as fuels during P2. They also reflected increased muscle protein degradation and repressed synthesis, in a more marked manner during P3 than P2 compared to the fed state. Nevertheless, several unexpected changes appeared to be in favor of muscle protein synthesis during fasting, notably at the level of the phosphatidylinositol-3-kinase (PI3K)/protein kinase B (AKT)/mammalian target of rapamycin (mTOR) signaling pathway, transcription and translation processes, and the response to oxidative stress. Such mechanisms might promote protein sparing during P2 and prepare the restoration of the protein compartment during P3 in anticipation of food intake for optimizing the effects of an upcoming refeeding, thereby promoting body maintenance and survival. Future studies should examine relevance of such targets for improving nitrogen balance during catabolic diseases.},

note = {Ibrahim, Marianne 

Wasselin, Thierry 

Challet, Etienne 

Van Dorsselaer, Alain 

Le Maho, Yvon 

Raclot, Thierry 

Bertile, Fabrice 

eng 

ANR-05-BLAN-0069/Agence Nationale de la Recherche 

ANR-10-INSB-08-03/Proteomics French Infrastructure (ProFI) 

Switzerland 

2020/08/23 06:00 

Int J Mol Sci. 2020 Aug 20;21(17). pii: ijms21175984. doi: 10.3390/ijms21175984.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{693,

title = {The catalytic activity of the translation termination factor methyltransferase Mtq2-Trm112 complex is required for large ribosomal subunit biogenesis},

author = {C Lacoux and L Wacheul and K Saraf and N Pythoud and E Huvelle and S Figaro and M Graille and C Carapito and D L J Lafontaine and V Heurgue-Hamard},

url = {https://www.ncbi.nlm.nih.gov/pubmed/33166396},

doi = {10.1093/nar/gkaa972},

issn = {1362-4962 (Electronic) 0305-1048 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {Nucleic Acids Res},

volume = {48},

number = {21},

pages = {12310-12325},

abstract = {The Mtq2-Trm112 methyltransferase modifies the eukaryotic translation termination factor eRF1 on the glutamine side chain of a universally conserved GGQ motif that is essential for release of newly synthesized peptides. Although this modification is found in the three domains of life, its exact role in eukaryotes remains unknown. As the deletion of MTQ2 leads to severe growth impairment in yeast, we have investigated its role further and tested its putative involvement in ribosome biogenesis. We found that Mtq2 is associated with nuclear 60S subunit precursors, and we demonstrate that its catalytic activity is required for nucleolar release of pre-60S and for efficient production of mature 5.8S and 25S rRNAs. Thus, we identify Mtq2 as a novel ribosome assembly factor important for large ribosomal subunit formation. We propose that Mtq2-Trm112 might modify eRF1 in the nucleus as part of a quality control mechanism aimed at proof-reading the peptidyl transferase center, where it will subsequently bind during translation termination.},

note = {Lacoux, Caroline 

Wacheul, Ludivine 

Saraf, Kritika 

Pythoud, Nicolas 

Huvelle, Emmeline 

Figaro, Sabine 

Graille, Marc 

Carapito, Christine 

Lafontaine, Denis L J 

Heurgue-Hamard, Valerie 

eng 

Research Support, Non-U.S. Gov't 

England 

2020/11/10 06:00 

Nucleic Acids Res. 2020 Dec 2;48(21):12310-12325. doi: 10.1093/nar/gkaa972.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{692,

title = {Precise Alkoxyamine Design to Enable Automated Tandem Mass Spectrometry Sequencing of Digital Poly(phosphodiester)s},

author = {K Launay and J A Amalian and E Laurent and L Oswald and A Al Ouahabi and A Burel and F Dufour and C Carapito and J L Clement and J F Lutz and L Charles and D Gigmes},

url = {https://www.ncbi.nlm.nih.gov/pubmed/32964618},

doi = {10.1002/anie.202010171},

issn = {1521-3773 (Electronic) 1433-7851 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {Angew Chem Int Ed Engl},

abstract = {A major step towards reliable reading of information coded in the sequence of long poly(phosphodiester)s was previously achieved by introducing an alkoxyamine spacer between information sub-segments. However, MS/MS decoding had to be performed manually to safely identify useful fragments of low abundance compared to side-products from the amide-based alkoxyamine used. Here, alternative alkoxyamines were designed to prevent side-reactions and enable automated MS/MS sequencing. Different styryl-TEMPO spacers were prepared to increase radical delocalization and stiffness of the structure. Their dissociation behavior was investigated by EPR and best results were obtained with spacers containing in-chain benzyl ring, with no side-reaction during synthesis or sequencing. Automated decoding of these polymers was performed using the MS-DECODER software, which interprets fragmentation data recorded for each sub-segment and re-align them in their original order based on location tags.},

note = {Launay, Kevin 

Amalian, Jean-Arthur 

Laurent, Eline 

Oswald, Laurence 

Al Ouahabi, Abdelaziz 

Burel, Alexandre 

Dufour, Florent 

Carapito, Christine 

Clement, Jean-Louis 

Lutz, Jean-Francois 

Charles, Laurence 

Gigmes, Didier 

eng 

ANR-16-CE29-0004-01/Agence Nationale de la Recherche 

ANR-16-CE29-0004-02/Agence Nationale de la Recherche 

Germany 

2020/09/24 06:00 

Angew Chem Int Ed Engl. 2020 Sep 22. doi: 10.1002/anie.202010171.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{689b,

title = {The Importance of Charge in Perturbing the Aromatic Glue Stabilizing the Protein-Protein Interface of Homodimeric tRNA-Guanine Transglycosylase},

author = {A Nguyen and D Nguyen and T X Phong Nguyen and M Sebastiani and S Dorr and O Hernandez-Alba and F Debaene and S Cianferani and A Heine and G Klebe and K Reuter},

url = {https://www.ncbi.nlm.nih.gov/pubmed/33166460},

doi = {10.1021/acschembio.0c00700},

issn = {1554-8937 (Electronic) 1554-8929 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {ACS Chem Biol},

volume = {15},

number = {11},

pages = {3021-3029},

abstract = {Bacterial tRNA-guanine transglycosylase (Tgt) is involved in the biosynthesis of the modified tRNA nucleoside queuosine present in the anticodon wobble position of tRNAs specific for aspartate, asparagine, histidine, and tyrosine. Inactivation of the tgt gene leads to decreased pathogenicity of Shigella bacteria. Therefore, Tgt constitutes a putative target for Shigellosis drug therapy. Since it is only active as homodimer, interference with dimer-interface formation may, in addition to active-site inhibition, provide further means to disable this protein. A cluster of four aromatic residues seems important to stabilize the homodimer. We mutated residues of this aromatic cluster and analyzed each mutated variant with respect to the dimer and thermal stability or enzyme activity by applying native mass spectrometry, a thermal shift assay, enzyme kinetics, and X-ray crystallography. Our structural studies indicate a strong influence of pH on the homodimer stability. Apparently, protonation of a histidine within the aromatic cluster supports the collapse of an essential structural motif within the dimer interface at slightly acidic pH.},

note = {Nguyen, Andreas 

Nguyen, Dzung 

Phong Nguyen, Tran Xuan 

Sebastiani, Maurice 

Dorr, Stefanie 

Hernandez-Alba, Oscar 

Debaene, Francois 

Cianferani, Sarah 

Heine, Andreas 

Klebe, Gerhard 

Reuter, Klaus 

eng 

Research Support, Non-U.S. Gov't 

2020/11/10 06:00 

ACS Chem Biol. 2020 Nov 20;15(11):3021-3029. doi: 10.1021/acschembio.0c00700. Epub 2020 Nov 9.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{688,

title = {Structures of B. subtilis Maturation RNases Captured on 50S Ribosome with Pre-rRNAs},

author = {S Oerum and T Dendooven and M Catala and L Gilet and C Degut and A Trinquier and M Bourguet and P Barraud and S Cianferani and B F Luisi and C Condon and C Tisne},

url = {https://www.ncbi.nlm.nih.gov/pubmed/32991829},

doi = {10.1016/j.molcel.2020.09.008},

issn = {1097-4164 (Electronic) 1097-2765 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {Mol Cell},

volume = {80},

number = {2},

pages = {227-236 e5},

abstract = {The pathways for ribosomal RNA (rRNA) maturation diverge greatly among the domains of life. In the Gram-positive model bacterium, Bacillus subtilis, the final maturation steps of the two large ribosomal subunit (50S) rRNAs, 23S and 5S pre-rRNAs, are catalyzed by the double-strand specific ribonucleases (RNases) Mini-RNase III and RNase M5, respectively. Here we present a protocol that allowed us to solve the 3.0 and 3.1 A resolution cryoelectron microscopy structures of these RNases poised to cleave their pre-rRNA substrates within the B. subtilis 50S particle. These data provide the first structural insights into rRNA maturation in bacteria by revealing how these RNases recognize and process double-stranded pre-rRNA. Our structures further uncover how specific ribosomal proteins act as chaperones to correctly fold the pre-rRNA substrates and, for Mini-III, anchor the RNase to the ribosome. These r-proteins thereby serve a quality-control function in the process from accurate ribosome assembly to rRNA processing.},

note = {Oerum, Stephanie 

Dendooven, Tom 

Catala, Marjorie 

Gilet, Laetitia 

Degut, Clement 

Trinquier, Aude 

Bourguet, Maxime 

Barraud, Pierre 

Cianferani, Sarah 

Luisi, Ben F 

Condon, Ciaran 

Tisne, Carine 

eng 

206171/Z/17/Z/WT_/Wellcome Trust/United Kingdom 

202905/Z/16/Z/WT_/Wellcome Trust/United Kingdom 

Research Support, Non-U.S. Gov't 

2020/09/30 06:00 

Mol Cell. 2020 Oct 15;80(2):227-236.e5. doi: 10.1016/j.molcel.2020.09.008. Epub 2020 Sep 28.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{687,

title = {Structural basis for DNA recognition and allosteric control of the retinoic acid receptors RAR-RXR},

author = {J Osz and A G McEwen and M Bourguet and F Przybilla and C Peluso-Iltis and P Poussin-Courmontagne and Y Mely and S Cianferani and C M Jeffries and D I Svergun and N Rochel},

url = {https://www.ncbi.nlm.nih.gov/pubmed/32974652},

doi = {10.1093/nar/gkaa697},

issn = {1362-4962 (Electronic) 0305-1048 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {Nucleic Acids Res},

volume = {48},

number = {17},

pages = {9969-9985},

abstract = {Retinoic acid receptors (RARs) as a functional heterodimer with retinoid X receptors (RXRs), bind a diverse series of RA-response elements (RAREs) in regulated genes. Among them, the non-canonical DR0 elements are bound by RXR-RAR with comparable affinities to DR5 elements but DR0 elements do not act transcriptionally as independent RAREs. In this work, we present structural insights for the recognition of DR5 and DR0 elements by RXR-RAR heterodimer using x-ray crystallography, small angle x-ray scattering, and hydrogen/deuterium exchange coupled to mass spectrometry. We solved the crystal structures of RXR-RAR DNA-binding domain in complex with the Rarb2 DR5 and RXR-RXR DNA-binding domain in complex with Hoxb13 DR0. While cooperative binding was observed on DR5, the two molecules bound non-cooperatively on DR0 on opposite sides of the DNA. In addition, our data unveil the structural organization and dynamics of the multi-domain RXR-RAR DNA complexes providing evidence for DNA-dependent allosteric communication between domains. Differential binding modes between DR0 and DR5 were observed leading to differences in conformation and structural dynamics of the multi-domain RXR-RAR DNA complexes. These results reveal that the topological organization of the RAR binding element confer regulatory information by modulating the overall topology and structural dynamics of the RXR-RAR heterodimers.},

note = {Osz, Judit 

McEwen, Alastair G 

Bourguet, Maxime 

Przybilla, Frederic 

Peluso-Iltis, Carole 

Poussin-Courmontagne, Pierre 

Mely, Yves 

Cianferani, Sarah 

Jeffries, Cy M 

Svergun, Dmitri I 

Rochel, Natacha 

eng 

Research Support, Non-U.S. Gov't 

England 

2020/09/26 06:00 

Nucleic Acids Res. 2020 Sep 25;48(17):9969-9985. doi: 10.1093/nar/gkaa697.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{683b,

title = {Proteomic as an Exploratory Approach to Develop Vaccines Against Tick-Borne Diseases Using Lyme Borreliosis as a Test Case},

author = {E Talagrand-Reboul and B Westermann and M A Raess and G Schnell and P Cantero and C Barthel and L Ehret-Sabatier and B Jaulhac and N Boulanger},

url = {https://www.ncbi.nlm.nih.gov/pubmed/32825641},

doi = {10.3390/vaccines8030463},

issn = {2076-393X (Print) 2076-393X (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {Vaccines (Basel)},

volume = {8},

number = {3},

abstract = {Tick-borne diseases affecting humans and animals are on the rise worldwide. Vaccines constitute an effective control measure, but very few are available. We selected Lyme borreliosis, a bacterial infection transmitted by the hard tick Ixodes, to validate a new concept to identify vaccine candidates. This disease is the most common tick-borne disease in the Northern Hemisphere. Although attempts to develop a vaccine exist, none have been successfully marketed. In tick-borne diseases, the skin constitutes a very specific environment encountered by the pathogen during its co-inoculation with tick saliva. In a mouse model, we developed a proteomic approach to identify vaccine candidates in skin biopsies. We identified 30 bacterial proteins after syringe inoculation or tick inoculation of bacteria. Discovery proteomics using mass spectrometry might be used in various tick-borne diseases to identify pathogen proteins with early skin expression. It should help to better develop sub-unit vaccines based on a cocktail of several antigens, associated with effective adjuvant and delivery systems of antigens. In all vector-borne diseases, the skin deserves further investigation to better define its role in the elaboration of protective immunity against pathogens.},

note = {2012-31},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{685,

title = {How Reversible Are the Effects of Fumed Silica on Macrophages? A Proteomics-Informed View},

author = {A Torres and B Dalzon and V Collin-Faure and H Diemer and D Fenel and G Schoehn and S Cianferani and M Carriere and T Rabilloud},

url = {https://www.ncbi.nlm.nih.gov/pubmed/33003391},

doi = {10.3390/nano10101939},

issn = {2079-4991 (Print) 2079-4991 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {Nanomaterials (Basel)},

volume = {10},

number = {10},

abstract = {Synthetic amorphous silica is one of the most used nanomaterials, and numerous toxicological studies have studied its effects. Most of these studies have used an acute exposure mode to investigate the effects immediately after exposure. However, this exposure modality does not allow the investigation of the persistence of the effects, which is a crucial aspect of silica toxicology, as exemplified by crystalline silica. In this paper, we extended the investigations by studying not only the responses immediately after exposure but also after a 72 h post-exposure recovery phase. We used a pyrolytic silica as the test nanomaterial, as this variant of synthetic amorphous silica has been shown to induce a more persistent inflammation in vivo than precipitated silica. To investigate macrophage responses to pyrolytic silica, we used a combination of proteomics and targeted experiments, which allowed us to show that most of the cellular functions that were altered immediately after exposure to pyrolytic silica at a subtoxic dose, such as energy metabolism and cell morphology, returned to normal at the end of the recovery period. However, some alterations, such as the inflammatory responses and some aldehyde detoxification proteins, were persistent. At the proteomic level, other alterations, such as proteins implicated in the endosomal/lysosomal pathway, were also persistent but resulted in normal function, thus suggesting cellular adaptation.},

note = {Torres, Anaelle 

Dalzon, Bastien 

Collin-Faure, Veronique 

Diemer, Helene 

Fenel, Daphna 

Schoehn, Guy 

Cianferani, Sarah 

Carriere, Marie 

Rabilloud, Thierry 

eng 

PNREST 2015/032/Agence Nationale de Securite Sanitaire de l'Alimentation, de l'Environnement et du Travail 

ANR-16-CE34-0011; ANR-11-LABX-0064; ANR-10-INBS-05-02; ANR-17-EURE-0003; ANR-10-INBS-08-03/Agence Nationale de la Recherche 

Switzerland 

2020/10/03 06:00 

Nanomaterials (Basel). 2020 Sep 29;10(10). pii: nano10101939. doi: 10.3390/nano10101939.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Lesne2020,

title = {Conformational maps of human 20S proteasomes reveal PA28- and immuno-dependent inter-ring crosstalks.},

author = {Jean Lesne and Marie Locard-Paulet and Julien Parra and Dušan Zivković and Thomas Menneteau and Marie-Pierre Bousquet and Odile Burlet-Schiltz and Julien Marcoux},

year  = {2020},

date = {2020-01-01},

journal = {Nature communications},

volume = {11},

number = {1},

pages = {6140},

abstract = {Hydrogen-Deuterium eXchange coupled to Mass Spectrometry (HDX-MS) is now common practice in structural biology. However, it is most of the time applied to rather small oligomeric complexes. Here, we report on the use of HDX-MS to investigate conformational differences between the human standard 20S (std20S) and immuno 20S (i20s) proteasomes alone or in complex with PA28$alpha$$beta$ or PA28$gamma$ activators. Their solvent accessibility is analyzed through a dedicated bioinformatic pipeline including stringent statistical analysis and 3D visualization. These data confirm the existence of allosteric differences between the std20S and i20S at the surface of the $alpha$-ring triggered from inside the catalytic $beta$-ring. Additionally, binding of the PA28 regulators to the 20S proteasomes modify solvent accessibility due to conformational changes of the $beta$-rings. This work is not only a proof-of-concept that HDX-MS can be used to get structural insights on large multi-protein complexes in solution, it also demonstrates that the binding of the std20S or i20S subtype to any of its PA28 activator triggers allosteric changes that are specific to this 20S/PA28 pair.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Sorroche2020,

title = {The ex planta signal activity of a Medicago ribosomal uL2 protein suggests a moonlighting role in controlling secondary rhizobial infection.},

author = {Fernando Sorroche and Violette Morales and Saïda Mouffok and Carole Pichereaux and Marie A Garnerone and Lan Zou and Badrish Soni and Marie-Anne Carpéné and Audrey Gargaros and Fabienne Maillet and Odile Burlet-Schiltz and Verena Poinsot and Patrice Polard and Clare Gough and Jacques Batut},

year  = {2020},

date = {2020-01-01},

journal = {PloS one},

volume = {15},

number = {10},

pages = {e0235446},

abstract = {We recently described a regulatory loop, which we termed autoregulation of infection (AOI), by which Sinorhizobium meliloti, a Medicago endosymbiont, downregulates the root susceptibility to secondary infection events via ethylene. AOI is initially triggered by so-far unidentified Medicago nodule signals named signal 1 and signal 1' whose transduction in bacteroids requires the S. meliloti outer-membrane-associated NsrA receptor protein and the cognate inner-membrane-associated adenylate cyclases, CyaK and CyaD1/D2, respectively. Here, we report on advances in signal 1 identification. Signal 1 activity is widespread as we robustly detected it in Medicago nodule extracts as well as in yeast and bacteria cell extracts. Biochemical analyses indicated a peptidic nature for signal 1 and, together with proteomic analyses, a universally conserved Medicago ribosomal protein of the uL2 family was identified as a candidate signal 1. Specifically, MtRPuL2A (MtrunA17Chr7g0247311) displays a strong signal activity that requires S. meliloti NsrA and CyaK, as endogenous signal 1. We have shown that MtRPuL2A is active in signaling only in a non-ribosomal form. A Medicago truncatula mutant in the major symbiotic transcriptional regulator MtNF-YA1 lacked most signal 1 activity, suggesting that signal 1 is under developmental control. Altogether, our results point to the MtRPuL2A ribosomal protein as the candidate for signal 1. Based on the Mtnf-ya1 mutant, we suggest a link between root infectiveness and nodule development. We discuss our findings in the context of ribosomal protein moonlighting.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{LeMoigne2020,

title = {A TLR2-Activating Fraction From Mycobacterium abscessus Rough Variant Demonstrates Vaccine and Diagnostic Potential.},

author = {Vincent Le Moigne and Anne-Laure Roux and Aude Jobart-Malfait and Landry Blanc and Karima Chaoui and Odile Burlet-Schiltz and Jean-Louis Gaillard and Stéphane Canaan and Jérôme Nigou and Jean-Louis Herrmann},

year  = {2020},

date = {2020-01-01},

journal = {Frontiers in cellular and infection microbiology},

volume = {10},

pages = {432},

abstract = {Mycobacterium abscessus is a prevalent pathogenic mycobacterium in cystic fibrosis (CF) patients and one of the most highly drug resistant mycobacterial species to antimicrobial agents. It possesses the property to transition from a smooth (S) to a rough (R) morphotype, thereby influencing the host innate immune response. This transition from the S to the R morphotype takes place in patients with an exacerbation of the disease and a persistence of M. abscessus. We have previously shown that the exacerbation of the Toll-like receptor 2 (TLR2)-mediated inflammatory response, following this S to R transition, is essentially due to overproduction of bacilli cell envelope surface compounds, which we were able to extract by mechanical treatment and isolation by solvent partition in a fraction called interphase. Here, we set up a purification procedure guided by bioactivity to isolate a fraction from the R variant of M. abscessus cells which exhibits a high TLR2 stimulating activity, referred to as TLR2-enriched fraction (TLR2eF). As expected, TLR2eF was found to contain several lipoproteins and proteins known to be stimuli for TLR2. Vaccination with TLR2eF showed no protection toward an M. abscessus aerosol challenge, but provided mild protection in $Delta$F508 mice and their FVB littermates when intravenously challenged by M. abscessus. Interestingly however, antibodies against TLR2eF compounds were detected during disease in CF patients. In conclusion, we show the potential for compounds in TLR2eF as vaccine and diagnostic candidates, in order to enhance diagnosis, prevent and/or treat M. abscessus-related infections.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Locard-Paulet2020,

title = {LymphoAtlas: a dynamic and integrated phosphoproteomic resource of TCR signaling in primary T cells reveals ITSN2 as a regulator of effector functions.},

author = {Marie Locard-Paulet and Guillaume Voisinne and Carine Froment and Marisa Goncalves Menoita and Youcef Ounoughene and Laura Girard and Claude Gregoire and Daiki Mori and Manuel Martinez and Hervé Luche and Jerôme Garin and Marie Malissen and Odile Burlet-Schiltz and Bernard Malissen and Anne Peredo and Romain Roncagalli},

year  = {2020},

date = {2020-01-01},

journal = {Molecular systems biology},

volume = {16},

number = {7},

pages = {e9524},

abstract = {T-cell receptor (TCR) ligation-mediated protein phosphorylation regulates the activation, cellular responses, and fates of T cells. Here, we used time-resolved high-resolution phosphoproteomics to identify, quantify, and characterize the phosphorylation dynamics of thousands of phosphorylation sites in primary T cells during the first 10 min after TCR stimulation. Bioinformatic analysis of the data revealed a coherent orchestration of biological processes underlying T-cell activation. In particular, functional modules associated with cytoskeletal remodeling, transcription, translation, and metabolic processes were mobilized within seconds after TCR engagement. Among proteins whose phosphorylation was regulated by TCR stimulation, we demonstrated, using a fast-track gene inactivation approach in primary lymphocytes, that the ITSN2 adaptor protein regulated T-cell effector functions. This resource, called LymphoAtlas, represents an integrated pipeline to further decipher the organization of the signaling network encoding T-cell activation. LymphoAtlas is accessible to the community at: https://bmm-lab.github.io/LymphoAtlas.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Thouvenel2020,

title = {The final assembly of trehalose polyphleates takes place within the outer layer of the mycobacterial cell envelope.},

author = {Laurie Thouvenel and Gautier Prevot and Laura Chiaradia and Julien Parra and Emmanuelle Mouton-Barbosa and Marie Locard-Paulet and Julien Marcoux and Maryelle Tropis and Odile Burlet-Schiltz and Mamadou Daffé and Christophe Guilhot and Gilles Etienne and Christian Chalut},

year  = {2020},

date = {2020-01-01},

journal = {The Journal of biological chemistry},

volume = {295},

number = {32},

pages = {11184--11194},

abstract = {Trehalose polyphleates (TPP) are high-molecular-weight, surface-exposed glycolipids present in a broad range of nontuberculous mycobacteria. These compounds consist of a trehalose core bearing polyunsaturated fatty acyl substituents (called phleic acids) and a straight-chain fatty acid residue and share a common basic structure with trehalose-based glycolipids produced by Mycobacterium tuberculosis TPP production starts in the cytosol with the formation of a diacyltrehalose intermediate. An acyltransferase, called PE, subsequently catalyzes the transfer of phleic acids onto diacyltrehalose to form TPP, and an MmpL transporter promotes the export of TPP or its precursor across the plasma membrane. PE is predicted to be an anchored membrane protein, but its topological organization is unknown, raising questions about the subcellular localization of the final stage of TPP biosynthesis and the chemical nature of the substrates that are translocated by the MmpL transporter. Here, using genetic, biochemical, and proteomic approaches, we established that PE of Mycobacterium smegmatis is exported to the cell envelope following cleavage of its signal peptide and that this process is required for TPP biosynthesis, indicating that the last step of TPP formation occurs in the outer layers of the mycobacterial cell envelope. These results provide detailed insights into the molecular mechanisms controlling TPP formation and transport to the cell surface, enabling us to propose an updated model of the TPP biosynthetic pathway. Because the molecular mechanisms of glycolipid production are conserved among mycobacteria, these findings obtained with PE from M. smegmatis may offer clues to glycolipid formation in M. tuberculosis.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Le2020,

title = {The protein kinase PknB negatively regulates biosynthesis and trafficking of mycolic acids in mycobacteria.},

author = {Nguyen-Hung Le and Marie Locard-Paulet and Alexandre Stella and Nicolas Tomas and Virginie Molle and Odile Burlet-Schiltz and Mamadou Daffé and Hedia Marrakchi},

year  = {2020},

date = {2020-01-01},

journal = {Journal of lipid research},

volume = {61},

number = {8},

pages = {1180--1191},

abstract = {Mycobacterium tuberculosis is the causative agent of tuberculosis and remains one of the most widespread and deadliest bacterial pathogens in the world. A distinguishing feature of mycobacteria that sets them apart from other bacteria is the unique architecture of their cell wall, characterized by various species-specific lipids, most notably mycolic acids (MAs). Therefore, targeted inhibition of enzymes involved in MA biosynthesis, transport, and assembly has been extensively explored in drug discovery. Additionally, more recent evidence suggests that many enzymes in the MA biosynthesis pathway are regulated by kinase-mediated phosphorylation, thus opening additional drug-development opportunities. However, how phosphorylation regulates MA production remains unclear. Here, we used genetic strategies combined with lipidomics and phosphoproteomics approaches to investigate the role of protein phosphorylation in Mycobacterium The results of this analysis revealed that the Ser/Thr protein kinase PknB regulates the export of MAs and promotes the remodeling of the mycobacterial cell envelope. In particular, we identified the essential MmpL3 as a substrate negatively regulated by PknB. Taken together, our findings add to the understanding of how PknB activity affects the mycobacterial MA biosynthesis pathway and reveal the essential role of protein phosphorylation/dephosphorylation in governing lipid metabolism, paving the way for novel antimycobacterial strategies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}