@article{RN1839,

title = {A flexible and original architecture of two unrelated zinc fingers underlies the role of the multitask P1 in RYMV spread},

author = {V. Poignavent and F. Hoh and G. Terral and Y. Yang and F. X. Gillet and J. H. Kim and F. Allemand and E. Lacombe and C. Brugidou and S. Cianferani and H. Demene and F. Vignols},

url = {https://www.ncbi.nlm.nih.gov/pubmed/35798161},

doi = {10.1016/j.jmb.2022.167715},

issn = {1089-8638 (Electronic) 

0022-2836 (Linking)},

year  = {2022},

date = {2022-01-01},

journal = {J Mol Biol},

pages = {167715},

abstract = {Viruses of the sobemovirus genus are plant viruses, most of which generate very important agricultural and financial losses. Among them, the rice yellow mottle virus (RYMV) is one of the most damaging pathogens devastating rice fields in Africa. RYMV infectivity and propagation rely on its protein P1, identified as a key movement and potential long-distance RNA silencing suppressor. Here we describe P1's complete 3D structure and dynamics obtained by an integrative approach combining X-Ray crystallography and NMR spectroscopy. We show that P1 is organized in two semi-independent and topologically unrelated domains, each harboring an original zinc finger. The two domains exhibit different affinities for zinc and sensitivities to oxidoreduction conditions, making the C-terminal P1 region a potential labile sensor of the plant redox status. An additional level of regulation resides on the capacity of P1 to oligomerize through its N-terminal domain. Coupling P1 structure information with site-directed mutagenesis and plant functional assays, we identified key residues in each zinc domain essential for infectivity and spread in rice tissues. Altogether, our results provide the first complete structure of a sobemoviral P1 movement protein and highlight structural and dynamical properties that may serve RYMV functions to infect and invade its host plant.},

note = {Poignavent, Vianney 

Hoh, Francois 

Terral, Guillaume 

Yang, Yinshan 

Gillet, Francois-Xavier 

Kim, Jeong-Hyeon 

Allemand, Frederic 

Lacombe, Eric 

Brugidou, Christophe 

Cianferani, Sarah 

Demene, Helene 

Vignols, Florence 

eng 

Netherlands 

2022/07/08 06:00 

J Mol Biol. 2022 Jul 4:167715. doi: 10.1016/j.jmb.2022.167715.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1836,

title = {Upconversion in a d-f [RuYb3] Supramolecular Assembly},

author = {R. C. Knighton and L. K. Soro and W. Thor and J. M. Strub and S. Cianferani and Y. Mely and M. Lenertz and K. L. Wong and C. Platas-Iglesias and F. Przybilla and L. J. Charbonniere},

url = {https://www.ncbi.nlm.nih.gov/pubmed/35771602},

doi = {10.1021/jacs.2c05037},

issn = {1520-5126 (Electronic) 

0002-7863 (Linking)},

year  = {2022},

date = {2022-01-01},

journal = {J Am Chem Soc},

abstract = {We have prepared a hetero-tetrametallic assembly consisting of three ytterbium ions coordinated to a central [Ru(bpm)3](2+) (bpm = 2,2'-bipyrimidine) motif. Irradiation into the absorption band of the peripheral ytterbium ions at 980 nm engenders emission of the (3)MLCT state of the central [Ru(bpm)3](2+) core at 636 nm, which represents the first example of f –> d molecular upconversion (UC). Time-resolved measurements reveal a slow rise of the UC emission, which was modeled with a mathematical treatment of the observed kinetics according to a cooperative photosensitization mechanism using a virtual Yb centered doubly excited state followed by energy transfer to the Ru centered (1)MLCT state.},

note = {2021/02},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1829,

title = {Eusociality is linked to caste-specific differences in metabolism, immune system, and somatic maintenance-related processes in an ant species},

author = {M. Quque and C. Villette and F. Criscuolo and C. Sueur and F. Bertile and D. Heintz},

url = {https://www.ncbi.nlm.nih.gov/pubmed/34971425},

doi = {10.1007/s00018-021-04024-0},

issn = {1420-9071 (Electronic) 

1420-682X (Linking)},

year  = {2022},

date = {2022-01-01},

journal = {Cell Mol Life Sci},

volume = {79},

number = {1},

pages = {29},

abstract = {The social organization of many primate, bird and rodent species and the role of individuals within that organization are associated with specific individual physiological traits. However, this association is perhaps most pronounced in eusocial insects (e.g., termites, ants). In such species, genetically close individuals show significant differences in behavior, physiology, and life expectancy. Studies addressing the metabolic changes according to the social role are still lacking. We aimed at understanding how sociality could influence essential molecular processes in a eusocial insect, the black garden ant (Lasius niger) where queens can live up to ten times longer than workers. Using mass spectrometry-based analysis, we explored the whole metabolome of queens, nest-workers and foraging workers. A former proteomics study done in the same species allowed us to compare the findings of both approaches. Confirming the former results at the proteome level, we showed that queens had fewer metabolites related to immunity. Contrary to our predictions, we did not find any metabolite linked to reproduction in queens. Among the workers, foragers had a metabolic signature reflecting a more stressful environment and a more highly stimulated immune system. We also found that nest-workers had more digestion-related metabolites. Hence, we showed that specific metabolic signatures match specific social roles. Besides, we identified metabolites differently expressed among behavioral castes and involved in nutrient sensing and longevity pathways (e.g., sirtuins, FOXO). The links between such molecular pathways and aging being found in an increasing number of taxa, our results confirm and strengthen their potential universality.},

note = {2015/29},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1857,

title = {A Novel Family of Acid-Cleavable Linker Based on Cyclic Acetal Motifs for the Production of Antibody-Drug Conjugates with High Potency and Selectivity},

author = {T. Rady and L. Turelli and M. Nothisen and E. Tobaldi and S. Erb and F. Thoreau and O. Hernandez-Alba and S. Cianferani and F. Daubeuf and A. Wagner and G. Chaubet},

url = {https://www.ncbi.nlm.nih.gov/pubmed/36106863},

doi = {10.1021/acs.bioconjchem.2c00314},

issn = {1520-4812 (Electronic) 

1043-1802 (Linking)},

year  = {2022},

date = {2022-01-01},

journal = {Bioconjug Chem},

abstract = {Cleavable linkers have become the subject of intense study in the field of chemical biology, particularly because of their applications in the construction of antibody-drug conjugates (ADC), where they facilitate lysosomal cleavage and liberation of drugs from their carrier protein. Due to lysosomes' acidic nature, acid-labile motifs have attracted much attention, leading to the development of hydrazone and carbonate linkers among several other entities. Continuing our efforts in designing new moieties, we present here a family of cyclic acetals that exhibit excellent plasma stability and acid lability, notably in lysosomes. Incorporated in ADC, they led to potent constructs with picomolar potency in vitro and similar in vivo efficacy as the commercially available ADC Kadcyla in mouse xenograft models.},

note = {Rady, Tony 

Turelli, Lorenzo 

Nothisen, Marc 

Tobaldi, Elisabetta 

Erb, Stephane 

Thoreau, Fabien 

Hernandez-Alba, Oscar 

Cianferani, Sarah 

Daubeuf, Francois 

Wagner, Alain 

Chaubet, Guilhem 

eng 

2022/09/16 06:00 

Bioconjug Chem. 2022 Sep 15. doi: 10.1021/acs.bioconjchem.2c00314.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1831,

title = {Repeated Exposure of Macrophages to Synthetic Amorphous Silica Induces Adaptive Proteome Changes and a Moderate Cell Activation},

author = {A. Torres and V. Collin-Faure and H. Diemer and C. Moriscot and D. Fenel and B. Gallet and S. Cianferani and J. A. Sergent and T. Rabilloud},

url = {<Go to ISI>://WOS:000795447400001},

doi = {ARTN 1424 

10.3390/nano12091424},

year  = {2022},

date = {2022-01-01},

journal = {Nanomaterials},

volume = {12},

number = {9},

abstract = {Synthetic amorphous silica (SAS) is a nanomaterial used in a wide variety of applications, including the use as a food additive. Two types of SAS are commonly employed as a powder additive, precipitated silica and fumed silica. Numerous studies have investigated the effects of synthetic amorphous silica on mammalian cells. However, most of them have used an exposure scheme based on a single dose of SAS. In this study, we have used instead a repeated 10-day exposure scheme in an effort to better simulate the occupational exposure encountered in daily life by consumers and workers. As a biological model, we have used the murine macrophage cell line J774A.1, as macrophages are very important innate immune cells in the response to particulate materials. In order to obtain a better appraisal of the macrophage responses to this repeated exposure to SAS, we have used proteomics as a wide-scale approach. Furthermore, some of the biological pathways detected as modulated by the exposure to SAS by the proteomic experiments have been validated through targeted experiments. Overall, proteomics showed that precipitated SAS induced a more important macrophage response than fumed SAS at equal dose. Nevertheless, validation experiments showed that most of the responses detected by proteomics are indeed adaptive, as the cellular homeostasis appeared to be maintained at the end of the exposure. For example, the intracellular glutathione levels or the mitochondrial transmembrane potential at the end of the 10 days exposure were similar for SAS-exposed cells and for unexposed cells. Similarly, no gross lysosomal damage was observed after repeated exposure to SAS. Nevertheless, important functions of macrophages such as phagocytosis, TNF alpha, and interleukin-6 secretion were up-modulated after exposure, as was the expression of important membrane proteins such as the scavenger receptors, MHC-II, or the MAC-1 receptor. These results suggest that repeated exposure to low doses of SAS slightly modulates the immune functions of macrophages, which may alter the homeostasis of the immune system.},

note = {2009/55},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1856,

title = {Large-Scale Conformational Changes of FhaC Provide Insights Into the Two-Partner Secretion Mechanism},

author = {G. Sicoli and A. Konijnenberg and J. Guerin and S. Hessmann and E. Del Nero and O. Hernandez-Alba and S. Lecher and G. Rouaut and L. Mueggenburg and H. Vezin and S. Cianferani and F. Sobott and R. Schneider and F. Jacob-Dubuisson},

url = {<Go to ISI>://WOS:000837116500001},

doi = {ARTN 950871 

10.3389/fmolb.2022.950871},

year  = {2022},

date = {2022-01-01},

journal = {Frontiers in Molecular Biosciences},

volume = {9},

abstract = {The Two-Partner secretion pathway mediates protein transport across the outer membrane of Gram-negative bacteria. TpsB transporters belong to the Omp85 superfamily, whose members catalyze protein insertion into, or translocation across membranes without external energy sources. They are composed of a transmembrane beta barrel preceded by two periplasmic POTRA domains that bind the incoming protein substrate. Here we used an integrative approach combining in vivo assays, mass spectrometry, nuclear magnetic resonance and electron paramagnetic resonance techniques suitable to detect minor states in heterogeneous populations, to explore transient conformers of the TpsB transporter FhaC. This revealed substantial, spontaneous conformational changes on a slow time scale, with parts of the POTRA2 domain approaching the lipid bilayer and the protein's surface loops. Specifically, our data indicate that an amphipathic POTRA2 beta hairpin can insert into the beta barrel. We propose that these motions enlarge the channel and initiate substrate secretion. Our data propose a solution to the conundrum how TpsB transporters mediate protein secretion without the need for cofactors, by utilizing intrinsic protein dynamics.},

note = {3o8wy 

Times Cited:0 

Cited References Count:77},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1840,

title = {Structural and Biochemical Investigation of the Heterodimeric Murine tRNA-Guanine Transglycosylase},

author = {M. Sebastiani and C. Behrens and S. Dorr and H. D. Gerber and R. Benazza and O. Hernandez-Alba and S. Cianferani and G. Klebe and A. Heine and K. Reuter},

url = {https://www.ncbi.nlm.nih.gov/pubmed/35815944},

doi = {10.1021/acschembio.2c00368},

issn = {1554-8937 (Electronic) 

1554-8929 (Linking)},

year  = {2022},

date = {2022-01-01},

journal = {ACS Chem Biol},

abstract = {In tRNA(Asp), tRNA(Asn), tRNA(Tyr), and tRNA(His) of most bacteria and eukaryotes, the anticodon wobble position may be occupied by the modified nucleoside queuosine, which affects the speed and the accuracy of translation. Since eukaryotes are not able to synthesize queuosine de novo, they have to salvage queuine (the queuosine base) as a micronutrient from food and/or the gut microbiome. The heterodimeric Zn(2+) containing enzyme tRNA-guanine transglycosylase (TGT) catalyzes the insertion of queuine into the above-named tRNAs in exchange for the genetically encoded guanine. This enzyme has attracted medical interest since it was shown to be potentially useful for the treatment of multiple sclerosis. In addition, TGT inactivation via gene knockout leads to the suppressed cell proliferation and migration of certain breast cancer cells, which may render this enzyme a potential target for the design of compounds supporting breast cancer therapy. As a prerequisite to fully exploit the medical potential of eukaryotic TGT, we have determined and analyzed a number of crystal structures of the functional murine TGT with and without bound queuine. In addition, we have investigated the importance of two residues of its non-catalytic subunit on dimer stability and determined the Michaelis-Menten parameters of murine TGT with respect to tRNA and several natural and artificial nucleobase substrates. Ultimately, on the basis of available TGT crystal structures, we provide an entirely conclusive reaction mechanism for this enzyme, which in detail explains why the TGT-catalyzed insertion of some nucleobases into tRNA occurs reversibly while that of others is irreversible.},

note = {Sebastiani, Maurice 

Behrens, Christina 

Dorr, Stefanie 

Gerber, Hans-Dieter 

Benazza, Rania 

Hernandez-Alba, Oscar 

Cianferani, Sarah 

Klebe, Gerhard 

Heine, Andreas 

Reuter, Klaus 

eng 

2022/07/12 06:00 

ACS Chem Biol. 2022 Jul 11. doi: 10.1021/acschembio.2c00368.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ruedas2022b,

title = {Three-Dimensional Envelope and Subunit Interactions of the Plastid-Encoded RNA Polymerase from Sinapis alba},

author = {Rémi Ruedas and Soumiya Sankari Muthukumar and Sylvie Kieffer-Jaquinod and François-Xavier Gillet and Daphna Fenel and Grégory Effantin and Thomas Pfannschmidt and Yohann Couté and Robert Blanvillain and David Cobessi},

url = {https://www.mdpi.com/1422-0067/23/17/9922},

doi = {10.3390/ijms23179922},

issn = {1422-0067},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {International Journal of Molecular Sciences},

volume = {23},

issue = {17},

pages = {9922},

abstract = {RNA polymerases (RNAPs) are found in all living organisms. In the chloroplasts, the plastid-encoded RNA polymerase (PEP) is a prokaryotic-type multimeric RNAP involved in the selective transcription of plastid genome. One of its active states requires the assembly of nuclear-encoded PEP-Associated Proteins (PAPs) on the catalytic core, producing a complex of more than 900 kDa, regarded as essential for chloroplast biogenesis. In this study, sequence alignments of the catalytic core subunits across various chloroplasts of the green lineage and prokaryotes combined with structural data show that variations are observed at the surface of the core, whereas internal amino acids associated with the catalytic activity are conserved. A purification procedure compatible with a structural analysis was used to enrich the native PEP from Sinapis alba chloroplasts. A mass spectrometry (MS)-based proteomic analysis revealed the core components, the PAPs and additional proteins, such as FLN2 and pTAC18. MS coupled with crosslinking (XL-MS) provided the initial structural information in the form of protein clusters, highlighting the relative position of some subunits with the surfaces of their interactions. Using negative stain electron microscopy, the PEP three-dimensional envelope was calculated. Particles classification shows that the protrusions are very well-conserved, offering a framework for the future positioning of all the PAPs. Overall, the results show that PEP-associated proteins are firmly and specifically associated with the catalytic core, giving to the plastid transcriptional complex a singular structure compared to other RNAPs.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {SMYD3 Impedes Small Cell Lung Cancer Sensitivity to Alkylation Damage through RNF113A Methylation-Phosphorylation Cross-talk},

author = {Valentina Lukinović and Simone Hausmann and Gael S Roth and Clement Oyeniran and Tanveer Ahmad and Ning Tsao and Joshua R Brickner and Alexandre G Casanova and Florent Chuffart and Ana Morales Benitez and Jessica Vayr and Rebecca Rodell and Marianne Tardif and Pascal W T C Jansen and Yohann Couté and Michiel Vermeulen and Pierre Hainaut and Pawel K Mazur and Nima Mosammaparast and Nicolas Reynoird},

doi = {10.1158/2159-8290.CD-21-0205},

issn = {2159-8290},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {Cancer Discovery},

volume = {12},

issue = {9},

pages = {2158-2179},

abstract = {Small cell lung cancer (SCLC) is the most fatal form of lung cancer, with dismal survival, limited therapeutic options, and rapid development of chemoresistance. We identified the lysine methyltransferase SMYD3 as a major regulator of SCLC sensitivity to alkylation-based chemotherapy. RNF113A methylation by SMYD3 impairs its interaction with the phosphatase PP4, controlling its phosphorylation levels. This cross-talk between posttranslational modifications acts as a key switch in promoting and maintaining RNF113A E3 ligase activity, essential for its role in alkylation damage response. In turn, SMYD3 inhibition restores SCLC vulnerability to alkylating chemotherapy. Our study sheds light on a novel role of SMYD3 in cancer, uncovering this enzyme as a mediator of alkylation damage sensitivity and providing a rationale for small-molecule SMYD3 inhibition to improve responses to established chemotherapy. SIGNIFICANCE: SCLC rapidly becomes resistant to conventional chemotherapy, leaving patients with no alternative treatment options. Our data demonstrate that SMYD3 upregulation and RNF113A methylation in SCLC are key mechanisms that control the alkylation damage response. Notably, SMYD3 inhibition sensitizes cells to alkylating agents and promotes sustained SCLC response to chemotherapy. This article is highlighted in the In This Issue feature, p. 2007.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Villalta2022b,

title = {The giant mimivirus 1.2 Mb genome is elegantly organized into a 30-nm diameter helical protein shield},

author = {Alejandro Villalta and Alain Schmitt and Leandro F Estrozi and Emmanuelle R J Quemin and Jean-Marie Alempic and Audrey Lartigue and Vojtěch Pražák and Lucid Belmudes and Daven Vasishtan and Agathe M G Colmant and Flora A Honoré and Yohann Couté and Kay Grünewald and Chantal Abergel},

doi = {10.7554/eLife.77607},

issn = {2050-084X},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {eLife},

volume = {11},

pages = {e77607},

abstract = {Mimivirus is the prototype of the Mimiviridae family of giant dsDNA viruses. Little is known about the organization of the 1.2 Mb genome inside the membrane-limited nucleoid filling the textasciitilde0.5 µm icosahedral capsids. Cryo-electron microscopy, cryo-electron tomography, and proteomics revealed that it is encased into a textasciitilde30-nm diameter helical protein shell surprisingly composed of two GMC-type oxidoreductases, which also form the glycosylated fibrils decorating the capsid. The genome is arranged in 5- or 6-start left-handed super-helices, with each DNA-strand lining the central channel. This luminal channel of the nucleoprotein fiber is wide enough to accommodate oxidative stress proteins and RNA polymerase subunits identified by proteomics. Such elegant supramolecular organization would represent a remarkable evolutionary strategy for packaging and protecting the genome, in a state ready for immediate transcription upon unwinding in the host cytoplasm. The parsimonious use of the same protein in two unrelated substructures of the virion is unexpected for a giant virus with thousand genes at its disposal.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Barnault2022b,

title = {Hepatic inflammation elicits production of proinflammatory netrin-1 through exclusive activation of translation},

author = {Romain Barnault and Claire Verzeroli and Carole Fournier and Maud Michelet and Anna Rita Redavid and Ievgeniia Chicherova and Marie-Laure Plissonnier and Annie Adrait and Olga Khomich and Fleur Chapus and Mathieu Richaud and Maëva Hervieu and Veronika Reiterer and Federica Grazia Centonze and Julie Lucifora and Birke Bartosch and Michel Rivoire and Hesso Farhan and Yohann Couté and Valbona Mirakaj and Thomas Decaens and Patrick Mehlen and Benjamin Gibert and Fabien Zoulim and Romain Parent},

doi = {10.1002/hep.32446},

issn = {1527-3350},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

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

volume = {76},

issue = {5},

pages = {1345-1359},

abstract = {BACKGROUND AND AIMS: Netrin-1 displays protumoral properties, though the pathological contexts and processes involved in its induction remain understudied. The liver is a major model of inflammation-associated cancer development, leading to HCC. APPROACH AND RESULTS: A panel of cell biology and biochemistry approaches (reverse transcription quantitative polymerase chain reaction, reporter assays, run-on, polysome fractionation, cross linking immunoprecipitation, filter binding assay, subcellular fractionation, western blotting, immunoprecipitation, stable isotope labeling by amino acids in cell culture) on in vitro-grown primary hepatocytes, human liver cell lines, mouse samples and clinical samples was used. We identify netrin-1 as a hepatic inflammation-inducible factor and decipher its mode of activation through an exhaustive eliminative approach. We show that netrin-1 up-regulation relies on a hitherto unknown mode of induction, namely its exclusive translational activation. This process includes the transfer of NTN1 (netrin-1) mRNA to the endoplasmic reticulum and the direct interaction between the Staufen-1 protein and this transcript as well as netrin-1 mobilization from its cell-bound form. Finally, we explore the impact of a phase 2 clinical trial-tested humanized anti-netrin-1 antibody (NP137) in two distinct, toll-like receptor (TLR) 2/TLR3/TLR6-dependent, hepatic inflammatory mouse settings. We observe a clear anti-inflammatory activity indicating the proinflammatory impact of netrin-1 on several chemokines and Ly6C+ macrophages. CONCLUSIONS: These results identify netrin-1 as an inflammation-inducible factor in the liver through an atypical mechanism as well as its contribution to hepatic inflammation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Vilallongue2022b,

title = {Guidance landscapes unveiled by quantitative proteomics to control reinnervation in adult visual system},

author = {Noemie Vilallongue and Julia Schaeffer and Anne-Marie Hesse and Céline Delpech and Béatrice Blot and Antoine Paccard and Elise Plissonnier and Blandine Excoffier and Yohann Couté and Stephane Belin and Homaira Nawabi},

url = {https://www.nature.com/articles/s41467-022-33799-4},

doi = {10.1038/s41467-022-33799-4},

issn = {2041-1723},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {Nature Communications},

volume = {13},

issue = {1},

pages = {6040},

abstract = {Abstract In the injured adult central nervous system (CNS), activation of pro-growth molecular pathways in neurons leads to long-distance regeneration. However, most regenerative fibers display guidance defects, which prevent reinnervation and functional recovery. Therefore, the molecular characterization of the proper target regions of regenerative axons is essential to uncover the modalities of adult reinnervation. In this study, we use mass spectrometry (MS)-based quantitative proteomics to address the proteomes of major nuclei of the adult visual system. These analyses reveal that guidance-associated molecules are expressed in adult visual targets. Moreover, we show that bilateral optic nerve injury modulates the expression of specific proteins. In contrast, the expression of guidance molecules remains steady. Finally, we show that regenerative axons are able to respond to guidance cues ex vivo, suggesting that these molecules possibly interfere with brain target reinnervation in adult. Using a long-distance regeneration model, we further demonstrate that the silencing of specific guidance signaling leads to rerouting of regenerative axons in vivo. Altogether, our results suggest ways to modulate axon guidance of regenerative neurons to achieve circuit repair in adult.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Lacroux2022b,

title = {Proteomics unveil a central role for peroxisomes in butyrate assimilation of the heterotrophic Chlorophyte alga Polytomella sp.},

author = {Julien Lacroux and Ariane Atteia and Sabine Brugière and Yohann Couté and Olivier Vallon and Jean-Philippe Steyer and Robert Lis},

url = {https://www.frontiersin.org/articles/10.3389/fmicb.2022.1029828/full},

doi = {10.3389/fmicb.2022.1029828},

issn = {1664-302X},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {Frontiers in Microbiology},

volume = {13},

pages = {1029828},

abstract = {Volatile fatty acids found in effluents of the dark fermentation of biowastes can be used for mixotrophic growth of microalgae, improving productivity and reducing the cost of the feedstock. Microalgae can use the acetate in the effluents very well, but butyrate is poorly assimilated and can inhibit growth above 1 gC.L −1 . The non-photosynthetic chlorophyte alga Polytomella sp. SAG 198.80 was found to be able to assimilate butyrate fast. To decipher the metabolic pathways implicated in butyrate assimilation, quantitative proteomics study was developed comparing Polytomella sp. cells grown on acetate and butyrate at 1 gC.L −1 . After statistical analysis, a total of 1772 proteins were retained, of which 119 proteins were found to be overaccumulated on butyrate vs. only 46 on acetate, indicating that butyrate assimilation necessitates additional metabolic steps. The data show that butyrate assimilation occurs in the peroxisome via the β-oxidation pathway to produce acetyl-CoA and further tri/dicarboxylic acids in the glyoxylate cycle. Concomitantly, reactive oxygen species defense enzymes as well as the branched amino acid degradation pathway were strongly induced. Although no clear dedicated butyrate transport mechanism could be inferred, several membrane transporters induced on butyrate are identified as potential condidates. Metabolic responses correspond globally to the increased needs for central cofactors NAD, ATP and CoA, especially in the peroxisome and the cytosol.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Spontaneous Prophage Induction Contributes to the Production of Membrane Vesicles by the Gram-Positive Bacterium Lacticaseibacillus casei BL23},

author = {David Silva Barreira and Pierre Lapaquette and Julia Novion Ducassou and Yohann Couté and Jean Guzzo and Aurélie Rieu},

doi = {10.1128/mbio.02375-22},

issn = {2150-7511},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {mBio},

volume = {13},

issue = {5},

pages = {e0237522},

abstract = {The formation of membrane vesicles (MVs) by Gram-positive bacteria has gained increasing attention over the last decade. Recently, models of vesicle formation have been proposed and involve the digestion of the cell wall by prophage-encoded or stress-induced peptidoglycan (PG) hydrolases and the inhibition of PG synthesis by β-lactam antibiotics. The impact of these mechanisms on vesicle formation is largely dependent on the strain and growth conditions. To date, no information on the production of vesicles by the lactobacilli family has been reported. Here, we aimed to characterize the MVs released by the Gram-positive bacteria Lacticaseibacillus casei BL23 and also investigated the mechanisms involved in vesicle formation. Using electron microscopy, we established that the size of the majority of L. casei BL23 vesicles ranged from 50 to 100 nm. Furthermore, we showed that the vesicles were released consistently throughout the growth of the bacteria in standard culture conditions. The protein composition of the vesicles released in the supernatant was identified and a significant number of prophage proteins was detected. Moreover, using a mutant strain harboring a defective PLE2 prophage, we were able to show that the spontaneous and mitomycin-triggered induction of the prophage PLE2 contribute to the production of MVs by L. casei BL23. Finally, we also demonstrated the influence of prophages on the membrane integrity of bacteria. Overall, our results suggest a key role of the prophage PLE2 in the production of MVs by L. casei BL23 in the absence or presence of genotoxic stress. IMPORTANCE The last few decades have demonstrated that membrane vesicles (MVs) produced by microorganisms can have a wide variety of functions. This diversity places MVs at the crossroads of major research topics in current microbiology such as antibiotic resistance, horizontal gene transfer, cell communication, biofilm development, bacteriophage resistance, and pathogenesis. In particular, vesicles produced by probiotic strains have been shown to play a significant role in their beneficial effects. Thus, the study of vesicle biogenesis is a key element for promoting and improving their release. Overall, our results suggest a key role of spontaneous and mitomycin-triggered prophage induction in MV production by the Gram-positive bacteria Lacticaseibacillus casei BL23. This phenomenon is of great interest as prophage-induced MVs could potentially influence bacterial behavior, stress resistance, and vesicle functions.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Fancello2022b,

title = {An analysis of proteogenomics and how and when transcriptome-informed reduction of protein databases can enhance eukaryotic proteomics},

author = {Laura Fancello and Thomas Burger},

doi = {10.1186/s13059-022-02701-2},

issn = {1474-760X},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {Genome Biology},

volume = {23},

issue = {1},

pages = {132},

abstract = {BACKGROUND: Proteogenomics aims to identify variant or unknown proteins in bottom-up proteomics, by searching transcriptome- or genome-derived custom protein databases. However, empirical observations reveal that these large proteogenomic databases produce lower-sensitivity peptide identifications. Various strategies have been proposed to avoid this, including the generation of reduced transcriptome-informed protein databases, which only contain proteins whose transcripts are detected in the sample-matched transcriptome. These were found to increase peptide identification sensitivity. Here, we present a detailed evaluation of this approach. RESULTS: We establish that the increased sensitivity in peptide identification is in fact a statistical artifact, directly resulting from the limited capability of target-decoy competition to accurately model incorrect target matches when using excessively small databases. As anti-conservative false discovery rates (FDRs) are likely to hamper the robustness of the resulting biological conclusions, we advocate for alternative FDR control methods that are less sensitive to database size. Nevertheless, reduced transcriptome-informed databases are useful, as they reduce the ambiguity of protein identifications, yielding fewer shared peptides. Furthermore, searching the reference database and subsequently filtering proteins whose transcripts are not expressed reduces protein identification ambiguity to a similar extent, but is more transparent and reproducible. CONCLUSIONS: In summary, using transcriptome information is an interesting strategy that has not been promoted for the right reasons. While the increase in peptide identifications from searching reduced transcriptome-informed databases is an artifact caused by the use of an FDR control method unsuitable to excessively small databases, transcriptome information can reduce the ambiguity of protein identifications.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Abulfaraj2022b,

title = {Analysis of the Arabidopsis coilin mutant reveals a positive role of AtCOILIN in plant immunity},

author = {Aala A Abulfaraj and Hanna M Alhoraibi and Kiruthiga Mariappan and Jean Bigeard and Huoming Zhang and Marilia Almeida-Trapp and Olga Artyukh and Fatimah Abdulhakim and Sabiha Parween and Delphine Pflieger and Ikram Blilou and Heribert Hirt and Naganand Rayapuram},

doi = {10.1093/plphys/kiac280},

issn = {1532-2548},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {Plant Physiology},

volume = {190},

issue = {1},

pages = {745-761},

abstract = {Biogenesis of ribonucleoproteins occurs in dynamic subnuclear compartments called Cajal bodies (CBs). COILIN is a critical scaffolding component essential for CB formation, composition, and activity. We recently showed that Arabidopsis (Arabidopsis thaliana) AtCOILIN is phosphorylated in response to bacterial elicitor treatment. Here, we further investigated the role of AtCOILIN in plant innate immunity. Atcoilin mutants are compromised in defense responses to bacterial pathogens. Besides confirming a role of AtCOILIN in alternative splicing (AS), Atcoilin showed differential expression of genes that are distinct from those of AS, including factors involved in RNA biogenesis, metabolism, plant immunity, and phytohormones. Atcoilin mutant plants have reduced levels of defense phytohormones. As expected, the mutant plants were more sensitive to the necrotrophic fungal pathogen Botrytis cinerea. Our findings reveal an important role for AtCOILIN in innate plant immunity.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {The Toxoplasma effector GRA28 promotes parasite dissemination by inducing dendritic cell-like migratory properties in infected macrophages},

author = {Arne L Ten Hoeve and Laurence Braun and Matias E Rodriguez and Gabriela C Olivera and Alexandre Bougdour and Lucid Belmudes and Yohann Couté and Jeroen P J Saeij and Mohamed-Ali Hakimi and Antonio Barragan},

doi = {10.1016/j.chom.2022.10.001},

issn = {1934-6069},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {Cell Host & Microbe},

volume = {30},

issue = {11},

pages = {1570–1588.e7},

abstract = {Upon pathogen detection, macrophages normally stay sessile in tissues while dendritic cells (DCs) migrate to secondary lymphoid tissues. The obligate intracellular protozoan Toxoplasma gondii exploits the trafficking of mononuclear phagocytes for dissemination via unclear mechanisms. We report that, upon T. gondii infection, macrophages initiate the expression of transcription factors normally attributed to DCs, upregulate CCR7 expression with a chemotactic response, and perform systemic migration when adoptively transferred into mice. We show that parasite effector GRA28, released by the MYR1 secretory pathway, cooperates with host chromatin remodelers in the host cell nucleus to drive the chemotactic migration of parasitized macrophages. During in vivo challenge studies, bone marrow-derived macrophages infected with wild-type T. gondii outcompeted those challenged with MYR1- or GRA28-deficient strains in migrating and reaching secondary organs. This work reveals how an intracellular parasite hijacks chemotaxis in phagocytes and highlights a remarkable migratory plasticity in differentiated cells of the mononuclear phagocyte system.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Leisico2022b,

title = {Structure of the human heparan sulfate polymerase complex EXT1-EXT2},

author = {Francisco Leisico and Juneina Omeiri and Christine Le Narvor and Joël Beaudouin and Michael Hons and Daphna Fenel and Guy Schoehn and Yohann Couté and David Bonnaffé and Rabia Sadir and Hugues Lortat-Jacob and Rebekka Wild},

doi = {10.1038/s41467-022-34882-6},

issn = {2041-1723},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {Nature Communications},

volume = {13},

issue = {1},

pages = {7110},

abstract = {Heparan sulfates are complex polysaccharides that mediate the interaction with a broad range of protein ligands at the cell surface. A key step in heparan sulfate biosynthesis is catalyzed by the bi-functional glycosyltransferases EXT1 and EXT2, which generate the glycan backbone consisting of repeating N-acetylglucosamine and glucuronic acid units. The molecular mechanism of heparan sulfate chain polymerization remains, however, unknown. Here, we present the cryo-electron microscopy structure of human EXT1-EXT2, which reveals the formation of a tightly packed hetero-dimeric complex harboring four glycosyltransferase domains. A combination of in vitro and in cellulo mutational studies is used to dissect the functional role of the four catalytic sites. While EXT1 can catalyze both glycosyltransferase reactions, our results indicate that EXT2 might only have N-acetylglucosamine transferase activity. Our findings provide mechanistic insight into heparan sulfate chain elongation as a nonprocessive process and lay the foundation for future studies on EXT1-EXT2 function in health and disease.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Lupette2022b,

title = {Quantitative proteomic analyses reveal the impact of nitrogen starvation on the proteome of the model diatom Phaeodactylum tricornutum},

author = {Josselin Lupette and Marianne Tardif and Sabine Brugière and Yohann Couté and Juliette Salvaing and Eric Maréchal},

doi = {10.1002/pmic.202200155},

issn = {1615-9861},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {Proteomics},

volume = {22},

issue = {22},

pages = {e2200155},

abstract = {Diatoms are one of the largest groups in phytoplankton biodiversity. Understanding their response to nitrogen variations, present from micromolar to near-zero levels in oceans and fresh waters, is essential to comprehend their ecological success. Nitrogen starvation is used in biotechnological processes, to trigger the remodeling of carbon metabolism in the direction of fatty acids and triacylglycerol synthesis. We evaluated whole proteome changes in Phaeodactylum tricornutum after 7 days of cultivation with 5.5-mM nitrate (+N) or without any nitrogen source (-N). On a total of 3768 proteins detected in biological replicates, our analysis pointed to 384 differentially abundant proteins (DAP). Analysis of proteins of lower abundance in -N revealed an arrest of amino acid and protein syntheses, a remodeling of nitrogen metabolism, and a decrease of the proteasome abundance suggesting a decline in unselective whole-proteome decay. Analysis of proteins of higher abundance revealed the setting up of a general nitrogen scavenging system dependent on deaminases. The increase of a plastid palmitoyl-ACP desaturase appeared as a hallmark of carbon metabolism rewiring in the direction of fatty acid and triacylglycerol synthesis. This dataset is also valuable to select gene candidates for improved biotechnological properties.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Timcheva2022b,

title = {Chromatin-associated YTHDC1 coordinates heat-induced reprogramming of gene expression},

author = {Kalina Timcheva and Solenne Dufour and Leila Touat-Todeschini and Callum Burnard and Marie-Christine Carpentier and Florent Chuffart and Rémy Merret and Marion Helsmoortel and Sabrina Ferré and Aude Grézy and Yohann Couté and Sophie Rousseaux and Saadi Khochbin and Claire Vourc’h and Cécile Bousquet-Antonelli and Rosemary Kiernan and Daphné Seigneurin-Berny and André Verdel},

url = {https://linkinghub.elsevier.com/retrieve/pii/S2211124722016722},

doi = {10.1016/j.celrep.2022.111784},

issn = {22111247},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {Cell Reports},

volume = {41},

issue = {11},

pages = {111784},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Etourneau2022b,

title = {Challenging Targets or Describing Mismatches? A Comment on Common Decoy Distribution by Madej et al},

author = {Lucas Etourneau and Thomas Burger},

doi = {10.1021/acs.jproteome.2c00279},

issn = {1535-3907},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {Journal of Proteome Research},

volume = {21},

issue = {12},

pages = {2840-2845},

abstract = {In their recent article, Madej et al. (Madej, D.; Wu, L.; Lam, H.Common Decoy Distributions Simplify False Discovery Rate Estimation in Shotgun Proteomics. J. Proteome Res.2022, 21 (2), 339-348) proposed an original way to solve the recurrent issue of controlling for the false discovery rate (FDR) in peptide-spectrum-match (PSM) validation. Briefly, they proposed to derive a single precise distribution of decoy matches termed the Common Decoy Distribution (CDD) and to use it to control for FDR during a target-only search. Conceptually, this approach is appealing as it takes the best of two worlds, i.e., decoy-based approaches (which leverage a large-scale collection of empirical mismatches) and decoy-free approaches (which are not subject to the randomness of decoy generation while sparing an additional database search). Interestingly, CDD also corresponds to a middle-of-the-road approach in statistics with respect to the two main families of FDR control procedures: Although historically based on estimating the false-positive distribution, FDR control has recently been demonstrated to be possible thanks to competition between the original variables (in proteomics, target sequences) and their fictional counterparts (in proteomics, decoys). Discriminating between these two theoretical trends is of prime importance for computational proteomics. In addition to highlighting why proteomics was a source of inspiration for theoretical biostatistics, it provides practical insights into the improvements that can be made to FDR control methods used in proteomics, including CDD.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Lai2022b,

title = {Characterizing Nanoparticle Mass Distributions Using Charge-Independent Nanoresonator Mass Spectrometry},

author = {Szu-Hsueh Lai and Adrien Reynaud and Ning-Ning Zhang and Minjeong Kwak and Bogdan Vysotskyi and Sergio Dominguez-Medina and Thomas Fortin and Kavya Clement and Martial Defoort and Tae Geol Lee and Kun Liu and Sébastien Hentz and Christophe D Masselon},

url = {https://pubs.acs.org/doi/10.1021/acs.jpcc.2c06675},

doi = {10.1021/acs.jpcc.2c06675},

issn = {1932-7447, 1932-7455},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {The Journal of Physical Chemistry C},

volume = {126},

issue = {49},

pages = {20946-20953},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Targeted Proteomics Analysis of Staphylococcal Superantigenic Toxins in Menstrual Fluid from Women with Menstrual Toxic Shock Syndrome (mTSS)},

author = {Marie Courçon and Cédric Badiou and Mathilde Louwagie and Sibyle Etievant and Michel Jaquinod and Gérard Lina and Virginie Brun},

url = {https://www.mdpi.com/2072-6651/14/12/886},

doi = {10.3390/toxins14120886},

issn = {2072-6651},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {Toxins},

volume = {14},

issue = {12},

pages = {886},

abstract = {Menstrual toxic shock syndrome (mTSS) is a rare life-threatening febrile illness that occurs in women using intravaginal menstrual protection. It is caused by toxic shock syndrome toxin 1 (TSST-1) produced by Staphylococcus aureus, triggering a sudden onset of rash and hypotension, subsequently leading to multiple organ failure. Detecting TSST-1 and S. aureus virulence factors in menstrual fluid could accelerate the diagnosis and improve therapeutic management of mTSS. However, menstrual fluid is a highly complex matrix, making detection of bacterial toxins challenging. Here, we present a mass-spectrometry-based proteomics workflow for the targeted, quantitative analysis of four S. aureus superantigenic toxins in menstrual fluids (TSST-1, SEA, SEC, and SED). This method was applied to characterize toxin levels in menstrual fluids collected from patients with mTSS and healthy women. Toxins were detectable in samples from patients with mTSS and one healthy donor at concentrations ranging from 0 to 0.46 µg/mL for TSST-1, and 0 to 1.07 µg/mL for SEC. SEA and SED were never detected in clinical specimens, even though many S. aureus strains were positive for the corresponding genes. The method presented here could be used to explore toxin production in vivo in users of intravaginal devices to improve the diagnosis, understanding, and prevention of mTSS.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Caron2022b,

title = {Loss of SET1/COMPASS methyltransferase activity reduces lifespan and fertility in Caenorhabditis elegans},

author = {Matthieu Caron and Loïc Gely and Steven Garvis and Annie Adrait and Yohann Couté and Francesca Palladino and Paola Fabrizio},

doi = {10.26508/lsa.202101140},

issn = {2575-1077},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {Life Science Alliance},

volume = {5},

issue = {3},

pages = {e202101140},

abstract = {Changes in histone post-translational modifications are associated with aging through poorly defined mechanisms. Histone 3 lysine 4 (H3K4) methylation at promoters is deposited by SET1 family methyltransferases acting within conserved multiprotein complexes known as COMPASS. Previous work yielded conflicting results about the requirement for H3K4 methylation during aging. Here, we reassessed the role of SET1/COMPASS-dependent H3K4 methylation in Caenorhabditis elegans lifespan and fertility by generating set-2(syb2085) mutant animals that express a catalytically inactive form of SET-2, the C. elegans SET1 homolog. We show that set-2(syb2085) animals retain the ability to form COMPASS, but have a marked global loss of H3K4 di- and trimethylation (H3K4me2/3). Reduced H3K4 methylation was accompanied by loss of fertility, as expected; however, in contrast to earlier studies, set-2(syb2085) mutants displayed a significantly shortened, not extended, lifespan and had normal intestinal fat stores. Other commonly used set-2 mutants were also short-lived, as was a cfp-1 mutant that lacks the SET1/COMPASS chromatin-targeting component. These results challenge previously held views and establish that WT H3K4me2/3 levels are essential for normal lifespan in C. elegans.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ielasi2022b,

title = {Human histone pre-mRNA assembles histone or canonical mRNA-processing complexes by overlapping 3'-end sequence elements},

author = {Francesco S Ielasi and Sara Ternifi and Emeline Fontaine and Domenico Iuso and Yohann Couté and Andrés Palencia},

doi = {10.1093/nar/gkac878},

issn = {1362-4962},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {Nucleic Acids Research},

volume = {50},

issue = {21},

pages = {12425-12443},

abstract = {Human pre-mRNA processing relies on multi-subunit macromolecular complexes, which recognize specific RNA sequence elements essential for assembly and activity. Canonical pre-mRNA processing proceeds via the recognition of a polyadenylation signal (PAS) and a downstream sequence element (DSE), and produces polyadenylated mature mRNAs, while replication-dependent (RD) histone pre-mRNA processing requires association with a stem-loop (SL) motif and a histone downstream element (HDE), and produces cleaved but non-polyadenylated mature mRNAs. H2AC18 mRNA, a specific H2A RD histone pre-mRNA, can be processed to give either a non-polyadenylated mRNA, ending at the histone SL, or a polyadenylated mRNA. Here, we reveal how H2AC18 captures the two human pre-mRNA processing complexes in a mutually exclusive mode by overlapping a canonical PAS (AAUAAA) sequence element with a HDE. Disruption of the PAS sequence on H2AC18 pre-mRNA prevents recruitment of the canonical complex in vitro, without affecting the histone machinery. This shows how the relative position of cis-acting elements in histone pre-mRNAs allows the selective recruitment of distinct human pre-mRNA complexes, thereby expanding the capability to regulate 3' processing and polyadenylation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Binda2022b,

title = {SMA-linked SMN mutants prevent phase separation properties and SMN interactions with FMRP family members},

author = {Olivier Binda and Franceline Juillard and Julia Novion Ducassou and Constance Kleijwegt and Geneviève Paris and Andréanne Didillon and Faouzi Baklouti and Armelle Corpet and Yohann Couté and Jocelyn Côté and Patrick Lomonte},

doi = {10.26508/lsa.202201429},

issn = {2575-1077},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {Life Science Alliance},

volume = {6},

issue = {1},

pages = {e202201429},

abstract = {Although recent advances in gene therapy provide hope for spinal muscular atrophy (SMA) patients, the pathology remains the leading genetic cause of infant mortality. SMA is a monogenic pathology that originates from the loss of the SMN1 gene in most cases or mutations in rare cases. Interestingly, several SMN1 mutations occur within the TUDOR methylarginine reader domain of SMN. We hypothesized that in SMN1 mutant cases, SMA may emerge from aberrant protein-protein interactions between SMN and key neuronal factors. Using a BioID proteomic approach, we have identified and validated a number of SMN-interacting proteins, including fragile X mental retardation protein (FMRP) family members (FMRFM). Importantly, SMA-linked SMNTUDOR mutant forms (SMNST) failed to interact with FMRFM In agreement with the recent work, we define biochemically that SMN forms droplets in vitro and these droplets are stabilized by RNA, suggesting that SMN could be involved in the formation of membraneless organelles, such as Cajal nuclear bodies. Finally, we found that SMN and FMRP co-fractionate with polysomes, in an RNA-dependent manner, suggesting a potential role in localized translation in motor neurons.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1866,

title = {Surface charge influences protein corona, cell uptake and biological effects of carbon dots},

author = {Y. Arezki and F. Delalande and C. Schaeffer-Reiss and S. Cianferani and M. Rapp and L. Lebeau and F. Pons and C. Ronzani},

url = {https://www.ncbi.nlm.nih.gov/pubmed/36168840},

doi = {10.1039/d2nr03611h},

issn = {2040-3372 (Electronic) 

2040-3364 (Linking)},

year  = {2022},

date = {2022-01-01},

journal = {Nanoscale},

abstract = {Carbon dots are emerging nanoparticles (NPs) with tremendous applications, especially in the biomedical field. Herein is reported the first quantitative proteomic analysis of the protein corona formed on CDs with different surface charge properties. Four CDs were synthesized from citric acid and various amine group-containing passivation reagents, resulting in cationic NPs with increasing zeta (zeta)-potential and density of positive charges. After CD contact with serum, we show that protein corona identity is influenced by CD surface charge properties, which in turn impacts CD uptake and viability loss in macrophages. In particular, CDs with high zeta-potential (>+30 mV) and charge density (>2 mumol mg(-1)) are the most highly internalized, and their cell uptake is strongly correlated with a corona enriched in vitronectin, fibulin, fetuin, adiponectin and alpha-glycoprotein. On the contrary, CDs with a lower zeta-potential (+11 mV) and charge density (0.01 mumol mg(-1)) are poorly internalized, while having a corona with a very different protein signature characterized by a high abundance of apolipoproteins (APOA1, APOB and APOC), albumin and hemoglobin. These data illustrate how corona characterization may contribute to a better understanding of CD cellular fate and biological effects, and provide useful information for the development of CDs for biomedical applications.},

note = {Arezki, Yasmin 

Delalande, Francois 

Schaeffer-Reiss, Christine 

Cianferani, Sarah 

Rapp, Mickael 

Lebeau, Luc 

Pons, Francoise 

Ronzani, Carole 

eng 

England 

2022/09/29 06:00 

Nanoscale. 2022 Sep 28. doi: 10.1039/d2nr03611h.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1678,

title = {Wnt5a Promotes Lysosomal Cholesterol Egress and Protects Against Atherosclerosis},

author = {S. Awan and M. Lambert and A. Imtiaz and F. Alpy and C. Tomasetto and M. Oulad-Abdelghani and C. Schaeffer and C. Moritz and D. Julien-David and S. Najib and L. O. Martinez and R. L. Matz and X. Collet and R. Silva-Rojas and J. Bohm and J. Herz and J. Terrand and P. Boucher},

url = {https://www.ncbi.nlm.nih.gov/pubmed/34886684},

doi = {10.1161/CIRCRESAHA.121.318881},

issn = {1524-4571 (Electronic) 

0009-7330 (Linking)},

year  = {2022},

date = {2022-01-01},

journal = {Circ Res},

volume = {130},

number = {2},

pages = {184-199},

abstract = {BACKGROUND: Impairment of cellular cholesterol trafficking is at the heart of atherosclerotic lesions formation. This involves egress of cholesterol from the lysosomes and 2 lysosomal proteins, the NPC1 (Niemann-Pick C1) and NPC2 that promotes cholesterol trafficking. However, movement of cholesterol out the lysosome and how disrupted cholesterol trafficking leads to atherosclerosis is unclear. As the Wnt ligand, Wnt5a inhibits the intracellular accumulation of cholesterol in multiple cell types, we tested whether Wnt5a interacts with the lysosomal cholesterol export machinery and studied its role in atherosclerotic lesions formation. METHODS: We generated mice deleted for the Wnt5a gene in vascular smooth muscle cells. To establish whether Wnt5a also protects against cholesterol accumulation in human vascular smooth muscle cells, we used a CRISPR/Cas9 guided nuclease approach to generate human vascular smooth muscle cells knockout for Wnt5a. RESULTS: We show that Wnt5a is a crucial component of the lysosomal cholesterol export machinery. By increasing lysosomal acid lipase expression, decreasing metabolic signaling by the mTORC1 (mechanistic target of rapamycin complex 1) kinase, and through binding to NPC1 and NPC2, Wnt5a senses changes in dietary cholesterol supply and promotes lysosomal cholesterol egress to the endoplasmic reticulum. Consequently, loss of Wnt5a decoupled mTORC1 from variations in lysosomal sterol levels, disrupted lysosomal function, decreased cholesterol content in the endoplasmic reticulum, and promoted atherosclerosis. CONCLUSIONS: These results reveal an unexpected function of the Wnt5a pathway as essential for maintaining cholesterol homeostasis in vivo.},

note = {2018_31},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1833,

title = {Probing the mechanism of the peroxiredoxin decamer interaction with its reductase sulfiredoxin from the single molecule to the solution scale},

author = {A. Beaussart and F. Canonico and H. Mazon and J. Hidalgo and S. Cianferani and H. Le Cordier and A. Kriznik and S. Rahuel-Clermont},

url = {https://www.ncbi.nlm.nih.gov/pubmed/35234779},

doi = {10.1039/d2nh00037g},

issn = {2055-6764 (Electronic) 

2055-6756 (Linking)},

year  = {2022},

date = {2022-01-01},

journal = {Nanoscale Horiz},

volume = {7},

number = {5},

pages = {515-525},

abstract = {Peroxiredoxins from the Prx1 subfamily (Prx) are highly regulated multifunctional proteins involved in oxidative stress response, redox signaling and cell protection. Prx is a homodimer that associates into a decamer. The monomer C-terminus plays intricate roles in Prx catalytic functions, decamer stability and interaction with its redox partner, the small reductase sulfiredoxin (Srx), that regulates the switching between Prx cellular functions. As only static structures of covalent Prx-Srx complexes have been reported, whether Srx binding dissociates the decameric assembly and how Prx subunit flexibility impacts complex formation are unknown. Here, we assessed the non-covalent interaction mechanism and dynamics in the solution of Saccharomyces cerevisiae Srx with the ten subunits of Prx Tsa1 at the decamer level via a combination of multiscale biophysical approaches including native mass spectrometry. We show that the ten subunits of the decamer can be saturated by ten Srx molecules and that the Tsa1 decamer in complex with Srx does not dissociate in solution. Furthermore, the binding events of atomic force microscopy (AFM) tip-grafted Srx molecules to Tsa1 individual subunits were relevant to the interactions between free molecules in solution. Combined with protein engineering and rapid kinetics, the observation of peculiar AFM force-distance signatures revealed that Tsa1 C-terminus flexibility controls Tsa1/Srx two-step binding and dynamics and determines the force-induced dissociation of Srx from each subunit of the decameric complex in a sequential or concerted mode. This combined approach from the solution to the single-molecule level offers promising prospects for understanding oligomeric protein interactions with their partners.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1864,

title = {A novel nuclear receptor subfamily enlightens the origin of heterodimerization},

author = {B. Beinsteiner and G. V. Markov and M. Bourguet and A. G. McEwen and S. Erb and A. K. M. Patel and F. Z. El Khaloufi El Khaddar and C. Lecroisey and G. Holzer and K. Essabri and I. Hazemann and A. Hamiche and S. Cianferani and D. Moras and V. Laudet and I. M. L. Billas},

url = {https://www.ncbi.nlm.nih.gov/pubmed/36199108},

doi = {10.1186/s12915-022-01413-0},

issn = {1741-7007 (Electronic) 

1741-7007 (Linking)},

year  = {2022},

date = {2022-01-01},

journal = {BMC Biol},

volume = {20},

number = {1},

pages = {217},

abstract = {BACKGROUND: Nuclear receptors are transcription factors of central importance in human biology and associated diseases. Much of the knowledge related to their major functions, such as ligand and DNA binding or dimerization, derives from functional studies undertaken in classical model animals. It has become evident, however, that a deeper understanding of these molecular functions requires uncovering how these characteristics originated and diversified during evolution, by looking at more species. In particular, the comprehension of how dimerization evolved from ancestral homodimers to a more sophisticated state of heterodimers has been missing, due to a too narrow phylogenetic sampling. Here, we experimentally and phylogenetically define the evolutionary trajectory of nuclear receptor dimerization by analyzing a novel NR7 subgroup, present in various metazoan groups, including cnidarians, annelids, mollusks, sea urchins, and amphioxus, but lost in vertebrates, arthropods, and nematodes. RESULTS: We focused on NR7 of the cephalochordate amphioxus B. lanceolatum. We present a complementary set of functional, structural, and evolutionary analyses that establish that NR7 lies at a pivotal point in the evolutionary trajectory from homodimerizing to heterodimerizing nuclear receptors. The crystal structure of the NR7 ligand-binding domain suggests that the isolated domain is not capable of dimerizing with the ubiquitous dimerization partner RXR. In contrast, the full-length NR7 dimerizes with RXR in a DNA-dependent manner and acts as a constitutively active receptor. The phylogenetic and sequence analyses position NR7 at a pivotal point, just between the basal class I nuclear receptors that form monomers or homodimers on DNA and the derived class II nuclear receptors that exhibit the classical DNA-independent RXR heterodimers. CONCLUSIONS: Our data suggest that NR7 represents the "missing link" in the transition between class I and class II nuclear receptors and that the DNA independency of heterodimer formation is a feature that was acquired during evolution. Our studies define a novel paradigm of nuclear receptor dimerization that evolved from DNA-dependent to DNA-independent requirements. This new concept emphasizes the importance of DNA in the dimerization of nuclear receptors, such as the glucocorticoid receptor and other members of this pharmacologically important oxosteroid receptor subfamily. Our studies further underline the importance of studying emerging model organisms for supporting cutting-edge research.},

note = {Beinsteiner, Brice 

Markov, Gabriel V 

Bourguet, Maxime 

McEwen, Alastair G 

Erb, Stephane 

Patel, Abdul Kareem Mohideen 

El Khaloufi El Khaddar, Fatima Z 

Lecroisey, Claire 

Holzer, Guillaume 

Essabri, Karim 

Hazemann, Isabelle 

Hamiche, Ali 

Cianferani, Sarah 

Moras, Dino 

Laudet, Vincent 

Billas, Isabelle M L 

eng 

England 

2022/10/06 06:00 

BMC Biol. 2022 Oct 5;20(1):217. doi: 10.1186/s12915-022-01413-0.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1858,

title = {Functional genomics uncovers the transcription factor BNC2 as required for myofibroblastic activation in fibrosis},

author = {M. Bobowski-Gerard and C. Boulet and F. P. Zummo and J. Dubois-Chevalier and C. Gheeraert and M. Bou Saleh and J. M. Strub and A. Farce and M. Ploton and L. Guille and J. Vandel and A. Bongiovanni and N. Very and E. Woitrain and A. Deprince and F. Lalloyer and E. Bauge and L. Ferri and L. C. Ntandja-Wandji and A. K. Cotte and C. Grangette and E. Vallez and S. Cianferani and V. Raverdy and R. Caiazzo and V. Gnemmi and E. Leteurtre and B. Pourcet and R. Paumelle and K. Ravnskjaer and G. Lassailly and J. T. Haas and P. Mathurin and F. Pattou and L. Dubuquoy and B. Staels and P. Lefebvre and J. Eeckhoute},

url = {https://www.ncbi.nlm.nih.gov/pubmed/36088459},

doi = {10.1038/s41467-022-33063-9},

issn = {2041-1723 (Electronic) 

2041-1723 (Linking)},

year  = {2022},

date = {2022-01-01},

journal = {Nat Commun},

volume = {13},

number = {1},

pages = {5324},

abstract = {Tissue injury triggers activation of mesenchymal lineage cells into wound-repairing myofibroblasts, whose unrestrained activity leads to fibrosis. Although this process is largely controlled at the transcriptional level, whether the main transcription factors involved have all been identified has remained elusive. Here, we report multi-omics analyses unraveling Basonuclin 2 (BNC2) as a myofibroblast identity transcription factor. Using liver fibrosis as a model for in-depth investigations, we first show that BNC2 expression is induced in both mouse and human fibrotic livers from different etiologies and decreases upon human liver fibrosis regression. Importantly, we found that BNC2 transcriptional induction is a specific feature of myofibroblastic activation in fibrotic tissues. Mechanistically, BNC2 expression and activities allow to integrate pro-fibrotic stimuli, including TGFbeta and Hippo/YAP1 signaling, towards induction of matrisome genes such as those encoding type I collagen. As a consequence, Bnc2 deficiency blunts collagen deposition in livers of mice fed a fibrogenic diet. Additionally, our work establishes BNC2 as potentially druggable since we identified the thalidomide derivative CC-885 as a BNC2 inhibitor. Altogether, we propose that BNC2 is a transcription factor involved in canonical pathways driving myofibroblastic activation in fibrosis.},

note = {Bobowski-Gerard, Marie 

Boulet, Clemence 

Zummo, Francesco P 

Dubois-Chevalier, Julie 

Gheeraert, Celine 

Bou Saleh, Mohamed 

Strub, Jean-Marc 

Farce, Amaury 

Ploton, Maheul 

Guille, Loic 

Vandel, Jimmy 

Bongiovanni, Antonino 

Very, Ninon 

Woitrain, Eloise 

Deprince, Audrey 

Lalloyer, Fanny 

Bauge, Eric 

Ferri, Lise 

Ntandja-Wandji, Line-Carolle 

Cotte, Alexia K 

Grangette, Corinne 

Vallez, Emmanuelle 

Cianferani, Sarah 

Raverdy, Violeta 

Caiazzo, Robert 

Gnemmi, Viviane 

Leteurtre, Emmanuelle 

Pourcet, Benoit 

Paumelle, Rejane 

Ravnskjaer, Kim 

Lassailly, Guillaume 

Haas, Joel T 

Mathurin, Philippe 

Pattou, Francois 

Dubuquoy, Laurent 

Staels, Bart 

Lefebvre, Philippe 

Eeckhoute, Jerome 

eng 

ANR-10-INBS-08-03/Agence Nationale de la Recherche (French National Research Agency) 

ANR-21-CE17-0016/Agence Nationale de la Recherche (French National Research Agency) 

England 

2022/09/11 06:00 

Nat Commun. 2022 Sep 10;13(1):5324. doi: 10.1038/s41467-022-33063-9.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1865,

title = {Measuring the NQO2: Melatonin Complex by Native Nano-Electrospray Ionization Mass Spectrometry},

author = {J. A. Boutin and J. Stojko and G. Ferry and S. Cianferani},

url = {https://www.ncbi.nlm.nih.gov/pubmed/36180703},

doi = {10.1007/978-1-0716-2593-4_34},

issn = {1940-6029 (Electronic) 

1064-3745 (Linking)},

year  = {2022},

date = {2022-01-01},

journal = {Methods Mol Biol},

volume = {2550},

pages = {323-328},

abstract = {Melatonin exerts its effects through a series of target proteins/receptors and enzymes. Its antioxidant capacity might be due to its capacity to inhibit a quinone reductase (NQO2) at high concentration (50 muM). Demonstrating the existence of a complex between a compound and a protein is often not easy. It requires either that the compound is an inhibitor-and the complex translates by an inhibition of the catalytic activity-or the compound is radiolabeled-and the complex translates in standard binding approaches, such as in receptology. Outside these two cases, the detection of the protein:small molecule complexes by mass spectrometry has recently been made possible, thanks to the development of so-called native mass spectrometry. Using this approach, one can measure masses corresponding to an intact noncovalent complex between a compound and its target, usually after titration or competition experiments. In the present chapter, we detail the characterization of NQO2:melatonin interaction using native mass spectrometry.},

note = {Boutin, Jean A 

Stojko, Johann 

Ferry, Gilles 

Cianferani, Sarah 

eng 

2022/10/01 06:00 

Methods Mol Biol. 2022;2550:323-328. doi: 10.1007/978-1-0716-2593-4_34.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1826,

title = {Resistance to glycation in the zebra finch: Mass spectrometry-based analysis and its perspectives for evolutionary studies of aging},

author = {C. Brun and O. Hernandez-Alba and A. Hovasse and F. Criscuolo and C. Schaeffer-Reiss and F. Bertile},

url = {<Go to ISI>://WOS:000799037700003},

doi = {ARTN 111811 

10.1016/j.exger.2022.111811},

issn = {0531-5565},

year  = {2022},

date = {2022-01-01},

journal = {Experimental Gerontology},

volume = {164},

abstract = {In humans, hyperglycemia is associated with protein glycation, which may contribute to aging. Strikingly, birds usually outlive mammals of the same body mass, while exhibiting high plasma glucose levels. However, how birds succeed in escaping pro-aging effects of glycation remains unknown. Using a specific mass spectrometrybased approach in captive zebra finches of known age, we recorded high glycaemia values but no glycated hemoglobin form was found. Still, we showed that zebra finch hemoglobin can be glycated in vitro, albeit only to a limited extent compared to its human homologue. This may be due to peculiar structural features, as supported by the unusual presence of three different tetramer populations with balanced proportions and a still bound cofactor that could be inositol pentaphosphate. High levels of the glycated forms of zebra finch plasma serotransferrin, carbonic anhydrase 2, and albumin were measured. Glucose, age or body mass correlations with either plasma glycated proteins or hemoglobin isoforms suggest that those variables may be future molecular tools of choice to monitor glycation and its link with individual fitness. Our molecular advance may help determine how evolution succeeded in associating flying ability, high blood glucose and long lifespan in birds.},

note = {2014/28},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1869,

title = {Identification of driver genes for critical forms of COVID-19 in a deeply phenotyped young patient cohort},

author = {R. Carapito and R. Li and J. Helms and C. Carapito and S. Gujja and V. Rolli and R. Guimaraes and J. Malagon-Lopez and P. Spinnhirny and A. Lederle and R. Mohseninia and A. Hirschler and L. Muller and P. Bastard and A. Gervais and Q. Zhang and F. Danion and Y. Ruch and M. Schenck and O. Collange and T. N. Chamaraux-Tran and A. Molitor and A. Pichot and A. Bernard and O. Tahar and S. Bibi-Triki and H. G. Wu and N. Paul and S. Mayeur and A. Larnicol and G. Laumond and J. Frappier and S. Schmidt and A. Hanauer and C. Macquin and T. Stemmelen and M. Simons and X. Mariette and O. Hermine and S. Fafi-Kremer and B. Goichot and B. Drenou and K. Kuteifan and J. Pottecher and P. M. Mertes and S. Kailasan and M. J. Aman and E. Pin and P. Nilsson and A. Thomas and A. Viari and D. Sanlaville and F. Schneider and J. Sibilia and P. L. Tharaux and J. L. Casanova and Y. Hansmann and D. Lidar and M. Radosavljevic and J. R. Gulcher and F. Meziani and C. Moog and T. W. Chittenden and S. Bahram},

url = {<Go to ISI>://WOS:000745768200005},

doi = {ARTN eabj7521 

10.1126/scitranslmed.abj7521},

issn = {1946-6234},

year  = {2022},

date = {2022-01-01},

journal = {Science Translational Medicine},

volume = {14},

number = {628},

abstract = {The drivers of critical coronavirus disease 2019 (COVID-19) remain unknown. Given major confounding factors such as age and comorbidities, true mediators of this condition have remained elusive. We used a multi-omics analysis combined with artificial intelligence in a young patient cohort where major comorbidities were excluded at the onset. The cohort included 47 "critical" (in the intensive care unit under mechanical ventilation) and 25 "non-critical" (in a non-critical care ward) patients with COVID-19 and 22 healthy individuals. The analyses included whole-genome sequencing, whole-blood RNA sequencing, plasma and blood mononuclear cell proteomics, cytokine profiling, and high-throughput immunophenotyping. An ensemble of machine learning, deep learning, quantum annealing, and structural causal modeling were used. Patients with critical COVID-19 were characterized by exacerbated inflammation, perturbed lymphoid and myeloid compartments, increased coagulation, and viral cell biology. Among differentially expressed genes, we observed up-regulation of the metalloprotease ADAM9. This gene signature was validated in a second independent cohort of 81 critical and 73 recovered patients with COVID-19 and was further confirmed at the transcriptional and protein level and by proteolytic activity. Ex vivo ADAM9 inhibition decreased severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uptake and replication in human lung epithelial cells. In conclusion, within a young, otherwise healthy, cohort of individuals with COVID-19, we provide the landscape of biological perturbations in vivo where a unique gene signature differentiated critical from non-critical patients. We further identified ADAM9 as a driver of disease severity and a candidate therapeutic target.},

note = {2020/03},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1610,

title = {Proteomic analysis of Rhodospirillum rubrum after carbon monoxide exposure reveals an important effect on metallic cofactor biosynthesis},

author = {C. Cavazza and V. Collin-Faure and J. Perard and H. Diemer and S. Cianferani and T. Rabilloud and E. Darrouzet},

url = {https://www.ncbi.nlm.nih.gov/pubmed/34601154},

doi = {10.1016/j.jprot.2021.104389},

issn = {1876-7737 (Electronic) 

1874-3919 (Linking)},

year  = {2022},

date = {2022-01-01},

journal = {J Proteomics},

volume = {250},

pages = {104389},

abstract = {Some carboxydotrophs like Rhodospirillum rubrum are able to grow with CO as their sole source of energy using a Carbone monoxide dehydrogenase (CODH) and an Energy conserving hydrogenase (ECH) to perform anaerobically the so called water-gas shift reaction (WGSR) (CO + H2O –> CO2 + H2). Several studies have focused at the biochemical and biophysical level on this enzymatic system and a few OMICS studies on CO metabolism. Knowing that CO is toxic in particular due to its binding to heme iron atoms, and is even considered as a potential antibacterial agent, we decided to use a proteomic approach in order to analyze R. rubrum adaptation in term of metabolism and management of the toxic effect. In particular, this study allowed highlighting a set of proteins likely implicated in ECH maturation, and important perturbations in term of cofactor biosynthesis, especially metallic cofactors. This shows that even this CO tolerant microorganism cannot avoid completely CO toxic effects associated with its interaction with metallic ions. SIGNIFICANCE: This proteomic study highlights the fact that even in a microorganism able to handle carbon monoxide and in some way detoxifying it via the intrinsic action of the carbon monoxide dehydrogenase (CODH), CO has important effects on metal homeostasis, metal cofactors and metalloproteins. These effects are direct or indirect via transcription regulation, and amplified by the high interdependency of cofactors biosynthesis.},

note = {2018/14},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1827,

title = {Molecular Liver Fingerprint Reflects the Seasonal Physiology of the Grey Mouse Lemur (Microcebus murinus) during Winter},

author = {B. Chazarin and M. Benhaim-Delarbre and C. Brun and A. Anzeraey and F. Bertile and J. Terrien},

url = {<Go to ISI>://WOS:000785517200001},

doi = {ARTN 4254 

10.3390/ijms23084254},

year  = {2022},

date = {2022-01-01},

journal = {International Journal of Molecular Sciences},

volume = {23},

number = {8},

abstract = {Grey mouse lemurs (Microcebus murinus) are primates that respond to environmental energetic constraints through strong physiological seasonality. They notably fatten during early winter (EW), and mobilize their lipid reserves while developing glucose intolerance during late winter (LW), when food availability is low. To decipher how the hepatic mechanisms may support such metabolic flexibility, we analyzed the liver proteome of adult captive male mouse lemurs, whose seasonal regulations are comparable to their wild counterparts. We highlight profound hepatic changes that reflect fat accretion in EW at the whole-body level, without triggering an ectopic storage of fat in the liver, however. Moreover, molecular regulations are consistent with the decrease in liver glucose utilization in LW, and therefore with reduced tolerance to glucose. However, no major regulation was seen in insulin signaling/resistance pathways. Fat mobilization in LW appeared possibly linked to the reactivation of the reproductive system while enhanced liver detoxification may reflect an anticipation to return to summer levels of food intake. Overall, these results show that the physiology of mouse lemurs during winter relies on solid molecular foundations in liver processes to adapt fuel partitioning while opposing the development of a pathological state despite large lipid fluxes.},

note = {2011/34},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1860,

title = {Accounting for multiple imputation-induced variability for differential analysis in mass spectrometry-based label-free quantitative proteomics},

author = {M. Chion and C. Carapito and F. Bertrand},

url = {https://www.ncbi.nlm.nih.gov/pubmed/36037245},

doi = {10.1371/journal.pcbi.1010420},

issn = {1553-7358 (Electronic) 

1553-734X (Linking)},

year  = {2022},

date = {2022-01-01},

journal = {PLoS Comput Biol},

volume = {18},

number = {8},

pages = {e1010420},

abstract = {Imputing missing values is common practice in label-free quantitative proteomics. Imputation aims at replacing a missing value with a user-defined one. However, the imputation itself may not be optimally considered downstream of the imputation process, as imputed datasets are often considered as if they had always been complete. Hence, the uncertainty due to the imputation is not adequately taken into account. We provide a rigorous multiple imputation strategy, leading to a less biased estimation of the parameters' variability thanks to Rubin's rules. The imputation-based peptide's intensities' variance estimator is then moderated using Bayesian hierarchical models. This estimator is finally included in moderated t-test statistics to provide differential analyses results. This workflow can be used both at peptide and protein-level in quantification datasets. Indeed, an aggregation step is included for protein-level results based on peptide-level quantification data. Our methodology, named mi4p, was compared to the state-of-the-art limma workflow implemented in the DAPAR R package, both on simulated and real datasets. We observed a trade-off between sensitivity and specificity, while the overall performance of mi4p outperforms DAPAR in terms of F-Score.},

note = {Chion, Marie 

Carapito, Christine 

Bertrand, Frederic 

eng 

2022/08/30 06:00 

PLoS Comput Biol. 2022 Aug 29;18(8):e1010420. doi: 10.1371/journal.pcbi.1010420. eCollection 2022 Aug.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1854,

title = {Does size matter? A proteomics-informed comparison of the effects of polystyrene beads of different sizes on macrophages},

author = {V. Collin-Faure and B. Dalzon and J. Devcic and H. Diemer and S. Cianferani and T. Rabilloud},

url = {<Go to ISI>://WOS:000820824900001},

doi = {10.1039/d2en00214k},

issn = {2051-8153},

year  = {2022},

date = {2022-01-01},

journal = {Environmental Science-Nano},

volume = {9},

number = {8},

pages = {2827-2840},

abstract = {Plastics are one of the most preoccupying emerging pollutants. Macroplastics released into the environment degrade into microplastics and nanoplastics. Because of their small size, these micro and nano plastic particles can enter the food chain and, in addition to their ecotoxicological effects, contaminate humans with still unknown biological effects. Plastics being particulate pollutants, they are handled in the human body by scavenger cells such as macrophages, which are important players in the immune system. In order to get a better appraisal of the effects of plastic particles on macrophages, we have studied the effects of unmodified polystyrene particles of 0.1, 1 and 10 micrometers of diameter, by a combination of proteomics and targeted validation experiments. Proteomics showed important adaptive changes of the proteome in response to exposure to plastics, with more than one third of the detected proteins showing a significance change in their abundance in response to cell exposure to at least one plastic bead size. These changes affected for example mitochondrial, lysosomal or cytoskeletal proteins. Although an increase in the mitochondrial transmembrane potential was detected in response to 10 micrometer beads, no alteration in cell viability was observed. Similarly, no lysosomal dysfunction and no alteration in the phagocytic capability of the cells was observed in response to exposure to plastics. When the inflammatory response was examined, no increase in the secretion of tumor necrosis factor or interleukin 6 was observed. Oppositely, the secretion of these cytokines in response to lipopolysaccharide was observed after exposure to plastics, which suggested a decreased ability of macrophages to respond to bacterial infection. In conclusion, these results provide a better understanding of the responses of macrophages to exposure to polystyrene particles of different sizes.},

note = {3r2tj 

Times Cited:0 

Cited References Count:94},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1837,

title = {Multi-laboratory experiment PME11 for the standardization of phosphoproteome analysis},

author = {N. Colome and J. Abian and K. Aloria and J. M. Arizmendi and S. Barcelo-Batllori and S. Braga-Lagache and O. Burlet-Schiltz and M. Carrascal and J. I. Casal and E. Chicano-Galvez and C. Chiva and L. F. Clemente and F. Elortza and J. M. Estanyol and J. Fernandez-Irigoyen and P. Fernandez-Puente and M. J. Fidalgo and C. Froment and M. Fuentes and C. Fuentes-Almagro and M. Gay and A. Hainard and M. Heller and M. L. Hernandez and N. Ibarrola and I. Iloro and T. Kieselbach and A. Lario and M. Locard-Paulet and A. Marina-Ramirez and L. Martin and E. Morato-Lopez and J. Munoz and R. Navajas and M. A. Odena and L. Odriozola and E. Oliveira and A. Paradela and C. Pasquarello and V. Los Rios and C. Ruiz-Romero and E. Sabido and M. Sanchez Del Pino and J. Sancho and E. Santamaria and C. Schaeffer-Reiss and J. Schneider and C. Torre and M. L. Valero and M. Vilaseca and S. Wu and L. Wu and P. Ximenez de Embun and F. Canals and F. J. Corrales and Isciii ProteoRed and EuPa},

url = {https://www.ncbi.nlm.nih.gov/pubmed/34758407},

doi = {10.1016/j.jprot.2021.104409},

issn = {1876-7737 (Electronic) 

1874-3919 (Linking)},

year  = {2022},

date = {2022-01-01},

journal = {J Proteomics},

volume = {251},

pages = {104409},

abstract = {Global analysis of protein phosphorylation by mass spectrometry proteomic techniques has emerged in the last decades as a powerful tool in biological and biomedical research. However, there are several factors that make the global study of the phosphoproteome more challenging than measuring non-modified proteins. The low stoichiometry of the phosphorylated species and the need to retrieve residue specific information require particular attention on sample preparation, data acquisition and processing to ensure reproducibility, qualitative and quantitative robustness and ample phosphoproteome coverage in phosphoproteomic workflows. Aiming to investigate the effect of different variables in the performance of proteome wide phosphoprotein analysis protocols, ProteoRed-ISCIII and EuPA launched the Proteomics Multicentric Experiment 11 (PME11). A reference sample consisting of a yeast protein extract spiked in with different amounts of a phosphomix standard (Sigma/Merck) was distributed to 31 laboratories around the globe. Thirty-six datasets from 23 laboratories were analyzed. Our results indicate the suitability of the PME11 reference sample to benchmark and optimize phosphoproteomics strategies, weighing the influence of different factors, as well as to rank intra and inter laboratory performance.},

note = {2012/19},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1832,

title = {A Confinement-Driven Nucleation Mechanism of Metal Oxide Nanoparticles Obtained via Thermal Decomposition in Organic Media},

author = {G. Cotin and B. Heinrich and F. Perton and C. Kiefer and G. Francius and D. Mertz and B. Freis and B. Pichon and J. M. Strub and S. Cianferani and N. Ortiz Pena and D. Ihiawakrim and D. Portehault and O. Ersen and A. Khammari and M. Picher and F. Banhart and C. Sanchez and S. Begin-Colin},

url = {https://www.ncbi.nlm.nih.gov/pubmed/35426247},

doi = {10.1002/smll.202200414},

issn = {1613-6829 (Electronic) 

1613-6810 (Linking)},

year  = {2022},

date = {2022-01-01},

journal = {Small},

volume = {18},

number = {20},

pages = {e2200414},

abstract = {Thermal decomposition is a very efficient synthesis strategy to obtain nanosized metal oxides with controlled structures and properties. For the iron oxide nanoparticle synthesis, it allows an easy tuning of the nanoparticle's size, shape, and composition, which is often explained by the LaMer theory involving a clear separation between nucleation and growth steps. Here, the events before the nucleation of iron oxide nanocrystals are investigated by combining different complementary in situ characterization techniques. These characterizations are carried out not only on powdered iron stearate precursors but also on a preheated liquid reaction mixture. They reveal a new nucleation mechanism for the thermal decomposition method: instead of a homogeneous nucleation, the nucleation occurs within vesicle-like-nanoreactors confining the reactants. The different steps are: 1) the melting and coalescence of iron stearate particles, leading to "droplet-shaped nanostructures" acting as nanoreactors; 2) the formation of a hitherto unobserved iron stearate crystalline phase within the nucleation temperature range, simultaneously with stearate chains loss and Fe(III) to Fe(II) reduction; 3) the formation of iron oxide nuclei inside the nanoreactors, which are then ejected from them. This mechanism paves the way toward a better mastering of the metal oxide nanoparticles synthesis and the control of their properties.},

note = {2021/02},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1830,

title = {Upon heat stress processing of ribosomal RNA precursors into mature rRNAs is compromised after cleavage at primary P site in Arabidopsis thaliana},

author = {T. Darriere and E. Jobet and D. Zavala and M. L. Escande and N. Durut and A. Bures and F. Blanco-Herrera and E. A. Vidal and M. Rompais and C. Carapito and S. Gourbiere and J. Saez-Vasquez},

url = {https://www.ncbi.nlm.nih.gov/pubmed/35522061},

doi = {10.1080/15476286.2022.2071517},

issn = {1555-8584 (Electronic) 

1547-6286 (Linking)},

year  = {2022},

date = {2022-01-01},

journal = {RNA Biol},

volume = {19},

number = {1},

pages = {719-734},

abstract = {Transcription and processing of 45S rRNAs in the nucleolus are keystones of ribosome biogenesis. While these processes are severely impacted by stress conditions in multiple species, primarily upon heat exposure, we lack information about the molecular mechanisms allowing sessile organisms without a temperature-control system, like plants, to cope with such circumstances. We show that heat stress disturbs nucleolar structure, inhibits pre-rRNA processing and provokes imbalanced ribosome profiles in Arabidopsis thaliana plants. Notably, the accuracy of transcription initiation and cleavage at the primary P site in the 5'ETS (5' External Transcribed Spacer) are not affected but the levels of primary 45S and 35S transcripts are, respectively, increased and reduced. In contrast, precursors of 18S, 5.8S and 25S RNAs are rapidly undetectable upon heat stress. Remarkably, nucleolar structure, pre-rRNAs from major ITS1 processing pathway and ribosome profiles are restored after returning to optimal conditions, shedding light on the extreme plasticity of nucleolar functions in plant cells. Further genetic and molecular analysis to identify molecular clues implicated in these nucleolar responses indicate that cleavage rate at P site and nucleolin protein expression can act as a checkpoint control towards a productive pre-rRNA processing pathway.},

note = {2018/13},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1850,

title = {MS(2)Rescore: Data-driven rescoring dramatically boosts immunopeptide identification rates},

author = {A. Declercq and R. Bouwmeester and A. Hirschler and C. Carapito and S. Degroeve and L. Martens and R. Gabriels},

url = {https://www.ncbi.nlm.nih.gov/pubmed/35803561},

doi = {10.1016/j.mcpro.2022.100266},

issn = {1535-9484 (Electronic) 

1535-9476 (Linking)},

year  = {2022},

date = {2022-01-01},

journal = {Mol Cell Proteomics},

pages = {100266},

abstract = {Immunopeptidomics aims to identify Major Histocompatibility Complex-presented peptides on almost all cell that can be used in anti-cancer vaccine development. However, existing immunopeptidomics data analysis pipelines suffer from the non-tryptic nature of immunopeptides, complicating their identification. Previously, peak intensity predictions by MS(2)PIP and retention time predictions by DeepLC, have been shown to improve tryptic peptide identifications when rescoring peptide-spectrum matches with Percolator. However, as MS(2)PIP was tailored towards tryptic peptides, we have here retrained MS(2)PIP to include non-tryptic peptides. Interestingly, the new models not only greatly improve predictions for immunopeptides, but also yield further improvements for tryptic peptides. We show that the integration of new MS(2)PIP models, DeepLC, and Percolator in one software package, MS(2)Rescore, increases spectrum identification rate and unique identified peptides with 46% and 36% compared to standard Percolator rescoring at 1% FDR. Moreover, MS(2)Rescore also outperforms the current state-of-the-art in immunopeptide-specific identification approaches. Altogether, MS(2)Rescore thus allows substantially improved identification of novel epitopes from existing immunopeptidomics workflows.},

note = {Declercq, Arthur 

Bouwmeester, Robbin 

Hirschler, Aurelie 

Carapito, Christine 

Degroeve, Sven 

Martens, Lennart 

Gabriels, Ralf 

eng 

2022/07/09 06:00 

Mol Cell Proteomics. 2022 Jul 5:100266. doi: 10.1016/j.mcpro.2022.100266.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1867,

title = {A Combination of Native LC-MS Approaches for the Comprehensive Characterization of the Antibody-Drug Conjugate Trastuzumab Deruxtecan},

author = {E. Desligniere and H. Diemer and S. Erb and P. Coliat and X. Pivot and A. Detappe and O. Hernandez-Alba and S. Cianferani},

url = {https://www.ncbi.nlm.nih.gov/pubmed/36336868},

doi = {10.31083/j.fbl2710290},

issn = {2768-6698 (Electronic) 

2768-6698 (Linking)},

year  = {2022},

date = {2022-01-01},

journal = {Front Biosci (Landmark Ed)},

volume = {27},

number = {10},

pages = {290},

abstract = {BACKGROUND: Native mass spectrometry (nMS) approaches appear attractive to complement bottom-up strategies traditionally used in biopharmaceutical industries thanks to their quite straightforward and rapid workflows, especially through online hyphenation of non-denaturing liquid chromatography (LC) to nMS. The present work provides an overview of the state-of-the-art chromatographic tools available for the detailed characterization of monoclonal antibody (mAb) formats, exemplified on the antibody-drug conjugate (ADC) trastuzumab deruxtecan (T-DXd). METHODS: T-DXd was first characterized by conventional reversed phase LC (rpLC) and peptide mapping. Couplings of size exclusion chromatography (SEC), cation exchange chromatography (CEX), and hydrophobic interaction chromatography (HIC) to nMS were used to gain further insights into size, hydrophobic, and charge variants of T-DXd and its parental mAb trastuzumab, at intact and middle-up levels. RESULTS: SEC-nMS first offered a direct snapshot of the homogeneous conjugation of T-DXd, with an average drug-to-antibody ratio (DAR) of 8 in agreement with a conjugation on cysteines after reduction of all interchain disulfide bonds. Moreover, SEC-nMS afforded precise identification and quantification of aggregates and fragments. Middle-up level experiments performed after IdeS digestion confirmed that drug conjugation occurs in the Fab region of the mAb, as seen with rpLC. HIC separated two DAR8 species that could not be differentiated by nMS. Although middle-up HIC-nMS proved to be more informative for oxidized forms, the identification of minor variants was still difficult because of poor MS signal quality, showing how the coupling of HIC to nMS remains challenging. Lastly, middle-up CEX-nMS provided accurate determination and localization of post-translational modifications, with several acidic/basic variants within Fab and Fc regions of T-DXd that were also identified by peptide mapping. CONCLUSIONS: This study illustrates the strengths and drawbacks of each LC-nMS coupling. By combining SEC-, HIC-, and CEX-nMS, we were able to achieve a comprehensive characterization of T-DXd without extensive sample preparation prior to MS analysis.},

note = {Desligniere, Evolene 

Diemer, Helene 

Erb, Stephane 

Coliat, Pierre 

Pivot, Xavier 

Detappe, Alexandre 

Hernandez-Alba, Oscar 

Cianferani, Sarah 

eng 

ProFI; ANR-10-INBS-08-03/CNRS, the University of Strasbourg, the Agence Nationale de la Recherche, and the French Proteomic Infrastructure/ 

ANR-10-IDEX0002/IdEx Unistra/ 

ANR-20-SFRI0012/SFRI-STRAT'US project/ 

Singapore 

2022/11/08 06:00 

Front Biosci (Landmark Ed). 2022 Oct 26;27(10):290. doi: 10.31083/j.fbl2710290.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1677,

title = {Advanced IM-MS-based Approaches for Protein Analysis: Collision-induced Unfolding (CIU) and Hyphenation of Liquid Chromatography to IM-MS},

author = {E. Deslignière and O. Hernandez-Alba and S. Cianférani},

year  = {2022},

date = {2022-01-01},

journal = {in New developemnts in MS : ion -mobility Mass Spectrometry},

volume = {chapter 16},

pages = {436-460},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1834,

title = {Combination of IM-Based Approaches to Unravel the Coexistence of Two Conformers on a Therapeutic Multispecific mAb},

author = {E. Desligniere and S. Ollivier and A. Ehkirch and A. Martelet and D. Ropartz and N. Lechat and O. Hernandez-Alba and J. M. Menet and S. Clavier and H. Rogniaux and B. Genet and S. Cianferani},

url = {https://www.ncbi.nlm.nih.gov/pubmed/35604400},

doi = {10.1021/acs.analchem.2c00928},

issn = {1520-6882 (Electronic) 

0003-2700 (Linking)},

year  = {2022},

date = {2022-01-01},

journal = {Anal Chem},

volume = {94},

number = {22},

pages = {7981-7989},

abstract = {Multispecific antibodies, which target multiple antigens at once, are emerging as promising therapeutic entities to offer more effective treatment than conventional monoclonal antibodies (mAbs). However, these highly complex mAb formats pose significant analytical challenges. We report here on the characterization of a trispecific antibody (tsAb), which presents two isomeric forms clearly separated and identified with size exclusion chromatography coupled to native mass spectrometry (SEC-nMS). Previous studies showed that these isomers might originate from a proline cis/trans isomerization in one Fab subunit of the tsAb. We combined several innovative ion mobility (IM)-based approaches to confirm the isomeric nature of the two species and to gain new insights into the conformational landscape of both isomers. Preliminary SEC-nIM-MS measurements performed on a low IM resolution instrument provided the first hints of the coexistence of different conformers, while complementary collision-induced unfolding (CIU) experiments evidenced distinct gas-phase unfolding behaviors upon activation for the two isomers. As subtle conformational differences remained poorly resolved on our early generation IM platform, we performed high-resolution cyclic IM (cIM-MS) to unambiguously conclude on the coexistence of two conformers. The cis/trans equilibrium was further tackled by exploiting the IM(n) slicing capabilities of the cIM-MS instrument. Altogether, our results clearly illustrate the benefits of combining state-of-the-art nMS and IM-MS approaches to address challenging issues encountered in biopharma. As engineered antibody constructs become increasingly sophisticated, CIU and cIM-MS methodologies undoubtedly have the potential to integrate the drug development analytical toolbox to achieve in-depth conformational characterization of these products.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1859,

title = {Deciphering cellular and molecular determinants of human DPCD protein in complex with RUVBL1/RUVBL2 AAA-ATPases},

author = {R. Dos Santos Morais and P. E. Santo and M. Ley and C. Schelcher and Y. Abel and L. Plassart and E. Desligniere and M. E. Chagot and M. Quinternet and A. C. F. Paiva and S. Hessmann and N. Morellet and M. F. Sousa P and F. Vandermoere and E. Bertrand and B. Charpentier and T. M. Bandeiras and C. Plisson-Chastang and C. Verheggen and S. Cianferani and X. Manival},

url = {https://www.ncbi.nlm.nih.gov/pubmed/35901867},

doi = {10.1016/j.jmb.2022.167760},

issn = {1089-8638 (Electronic) 

0022-2836 (Linking)},

year  = {2022},

date = {2022-01-01},

journal = {J Mol Biol},

volume = {434},

number = {19},

pages = {167760},

abstract = {DPCD is a protein that may play a role in cilia formation and whose absence leads to primary ciliary dyskinesia (PCD), a rare disease caused by impairment of ciliated cells. Except for high-throughput studies that identified DPCD as a possible RUVBL1 (R1) and RUVBL2 (R2) partner, no in-depth cellular, biochemical, and structural investigation involving DPCD have been reported so far. R1 and R2 proteins are ubiquitous highly conserved AAA + family ATPases that assemble and mature a plethora of macromolecular complexes and are pivotal in numerous cellular processes, especially by guaranteeing a co-chaperoning function within R2TP or R2TP-like machineries. In the present study, we identified DPCD as a new R1R2 partner in vivo. We show that DPCD interacts directly with R1 and R2 in vitro and in cells. We characterized the physico-chemical properties of DPCD in solution and built a 3D model of DPCD. In addition, we used a variety of orthogonal biophysical techniques including small-angle X-ray scattering, structural mass spectrometry and electron microscopy to assess the molecular determinants of DPCD interaction with R1R2. Interestingly, DPCD disrupts the dodecameric state of R1R2 complex upon binding and this interaction occurs mainly via the DII domains of R1R2.},

note = {Dos Santos Morais, Raphael 

Santo, Paulo E 

Ley, Marie 

Schelcher, Cedric 

Abel, Yoann 

Plassart, Laura 

Desligniere, Evolene 

Chagot, Marie-Eve 

Quinternet, Marc 

Paiva, Ana C F 

Hessmann, Steve 

Morellet, Nelly 

M F Sousa, Pedro 

Vandermoere, Franck 

Bertrand, Edouard 

Charpentier, Bruno 

Bandeiras, Tiago M 

Plisson-Chastang, Celia 

Verheggen, Celine 

Cianferani, Sarah 

Manival, Xavier 

eng 

Netherlands 

2022/07/29 06:00 

J Mol Biol. 2022 Oct 15;434(19):167760. doi: 10.1016/j.jmb.2022.167760. Epub 2022 Jul 25.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1835,

title = {Insights into the atypical autokinase activity of the Pseudomonas aeruginosa GacS histidine kinase and its interaction with RetS},

author = {F. Fadel and V. Bassim and V. I. Francis and S. L. Porter and T. Botzanowski and P. Legrand and M. M. Perez and Y. Bourne and S. Cianferani and F. Vincent},

url = {https://www.ncbi.nlm.nih.gov/pubmed/35767996},

doi = {10.1016/j.str.2022.06.002},

issn = {1878-4186 (Electronic) 

0969-2126 (Linking)},

year  = {2022},

date = {2022-01-01},

journal = {Structure},

abstract = {Virulence in Pseudomonas aeruginosa (PA) depends on complex regulatory networks, involving phosphorelay systems based on two-component systems (TCSs). The GacS/GacA TCS is a master regulator of biofilm formation, swarming motility, and virulence. GacS is a membrane-associated unorthodox histidine kinase (HK) whose phosphorelay signaling pathway is inhibited by the RetS hybrid HK. Here we provide structural and functional insights into the interaction of GacS with RetS. The structure of the GacS-HAMP-H1 cytoplasmic regions reveals an unusually elongated homodimer marked by a 135 A long helical bundle formed by the HAMP, the signaling helix (S helix) and the DHp subdomain. The HAMP and S helix regions are essential for GacS signaling and contribute to the GacS/RetS binding interface. The structure of the GacS D1 domain together with the discovery of an unidentified functional ND domain, essential for GacS full autokinase activity, unveils signature motifs in GacS required for its atypical autokinase mechanism.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{boulan_crmp4-mediated_2021,

title = {CRMP4-mediated fornix development involves semaphorin-3E signaling pathway},

author = {Benoît Boulan and Charlotte Ravanello and Amandine Peyrel and Christophe Bosc and Christian Delphin and Florence Appaix and Eric Denarier and Alexandra Kraut and Muriel Jaquier-Sarlin and Alyson Fournier and Annie Andrieux and Sylvie Gory-Fauré and Jean-Christophe Deloulme},

url = {https://elifesciences.org/articles/70361},

doi = {10.7554/eLife.70361},

issn = {2050-084X},

year  = {2021},

date = {2021-12-01},

urldate = {2021-12-01},

journal = {eLife},

volume = {10},

pages = {e70361},

abstract = {Neurodevelopmental axonal pathfinding plays a central role in correct brain wiring and subsequent cognitive abilities. Within the growth cone, various intracellular effectors transduce axonal guidance signals by remodeling the cytoskeleton. Semaphorin-3E (Sema3E) is a guidance cue implicated in development of the fornix, a neuronal tract connecting the hippocampus to the hypothalamus. Microtubule-Associated Protein 6 (MAP6) has been shown to be involved in the Sema3E growth-promoting signaling pathway. In this study, we identified the Collapsin Response Mediator Protein 4 (CRMP4) as a MAP6 partner and a crucial effector in Sema3E growth-promoting activity. CRMP4-KO mice displayed abnormal fornix development reminiscent of that observed in Sema3E-KO mice. CRMP4 was shown to interact with the Sema3E tripartite receptor complex within Detergent- 

 Resistant 

 Membrane (DRM) domains, and DRM domain integrity was required to transduce Sema3E signaling through the Akt/GSK3 pathway. Finally, we showed that the cytoskeleton-binding domain of CRMP4 is required for Sema3E's growth-promoting activity, suggesting that CRMP4 plays a role at the interface between Sema3E receptors, located in DRM domains, and the cytoskeleton network. As the fornix is affected in many psychiatric diseases, such as schizophrenia, our results provide new insights to better understand the neurodevelopmental components of these diseases.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{ropers_multiomics_2021,

title = {Multiomics Study of Bacterial Growth Arrest in a Synthetic Biology Application},

author = {Delphine Ropers and Yohann Couté and Laëtitia Faure and Sabrina Ferré and Delphine Labourdette and Arieta Shabani and Lidwine Trouilh and Perrine Vasseur and Gwénaëlle Corre and Myriam Ferro and Marie-Ange Teste and Johannes Geiselmann and Hidde Jong},

doi = {10.1021/acssynbio.1c00115},

issn = {2161-5063},

year  = {2021},

date = {2021-11-01},

urldate = {2021-11-01},

journal = {ACS synthetic biology},

abstract = {We investigated the scalability of a previously developed growth switch based on external control of RNA polymerase expression. Our results indicate that, in liter-scale bioreactors operating in fed-batch mode, growth-arrested Escherichia coli cells are able to convert glucose to glycerol at an increased yield. A multiomics quantification of the physiology of the cells shows that, apart from acetate production, few metabolic side effects occur. However, a number of specific responses to growth slow-down and growth arrest are launched at the transcriptional level. These notably include the downregulation of genes involved in growth-associated processes, such as amino acid and nucleotide metabolism and translation. Interestingly, the transcriptional responses are buffered at the proteome level, probably due to the strong decrease of the total mRNA concentration after the diminution of transcriptional activity and the absence of growth dilution of proteins. Growth arrest thus reduces the opportunities for dynamically adjusting the proteome composition, which poses constraints on the design of biotechnological production processes but may also avoid the initiation of deleterious stress responses.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{jalabert_profiling_2021,

title = {Profiling of ob/ob mice skeletal muscle exosome-like vesicles demonstrates combined action of miRNAs, proteins and lipids to modulate lipid homeostasis in recipient cells},

author = {Audrey Jalabert and Laura Reininger and Emmanuelle Berger and Yohann Coute and Emmanuelle Meugnier and Alexis Forterre and Elizabeth Errazuriz-Cerda and Alain Geloen and Myriam Aouadi and Karim Bouzakri and Jennifer Rieusset and Sophie Rome},

doi = {10.1038/s41598-021-00983-3},

issn = {2045-2322},

year  = {2021},

date = {2021-11-01},

urldate = {2021-11-01},

journal = {Scientific Reports},

volume = {11},

number = {1},

pages = {21626},

abstract = {We have determined the lipid, protein and miRNA composition of skeletal muscle (SkM)-released extracellular vesicles (ELVs) from Ob/ob (OB) vs wild-type (WT) mice. The results showed that atrophic insulin-resistant OB-SkM released less ELVs than WT-SkM, highlighted by a RAB35 decrease and an increase in intramuscular cholesterol content. Proteomic analyses of OB-ELVs revealed a group of 37 proteins functionally connected, involved in lipid oxidation and with catalytic activities. OB-ELVs had modified contents for phosphatidylcholine (PC 34-4, PC 40-3 and PC 34-0), sphingomyelin (Sm d18:1/18:1) and ceramides (Cer d18:1/18:0) and were enriched in cholesterol, likely to alleviated intracellular accumulation. Surprisingly many ELV miRNAs had a nuclear addressing sequence, and targeted genes encoding proteins with nuclear activities. Interestingly, SkM-ELV miRNA did not target mitochondria. The most significant function targeted by the 7 miRNAs altered in OB-ELVs was lipid metabolism. In agreement, OB-ELVs induced lipid storage in recipient adipocytes and increased lipid up-take and fatty acid oxidation in recipient muscle cells. In addition, OB-ELVs altered insulin-sensitivity and induced atrophy in muscle cells, reproducing the phenotype of the releasing OB muscles. These data suggest for the first time, a cross-talk between muscle cells and adipocytes, through the SkM-ELV route, in favor of adipose tissue expansion.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}