M3i

Dufossez Robin, Ursuegui Sylvain, Baudrey Stephanie, Pernod Ketty, Mouftakhir Safae, Oulad-Abdelghani Mustapha, Mosser Michel, Chaubet Guilhem, Ryckelynck Michael, Wagner Alain

Droplet Surface Immunoassay by Relocation (D-SIRe) for High-Throughput Analysis of Cytosolic Proteins at the Single-Cell Level Article de journal

Dans: Anal Chem, vol. 95, iss. 9, p. 4470-4478, 2023, ISSN: 1520-6882.

Résumé | Liens | BibTeX | Étiquettes: RYCKELYNCK, Unité ARN

@article{pmid36821722,

title = {Droplet Surface Immunoassay by Relocation (D-SIRe) for High-Throughput Analysis of Cytosolic Proteins at the Single-Cell Level},

author = {Robin Dufossez and Sylvain Ursuegui and Stephanie Baudrey and Ketty Pernod and Safae Mouftakhir and Mustapha Oulad-Abdelghani and Michel Mosser and Guilhem Chaubet and Michael Ryckelynck and Alain Wagner},

doi = {10.1021/acs.analchem.2c05168},

issn = {1520-6882},

year  = {2023},

date = {2023-02-01},

urldate = {2023-02-01},

journal = {Anal Chem},

volume = {95},

issue = {9},

pages = {4470-4478},

abstract = {Enzyme-linked immunosorbent assay (ELISA) is a central analytic method in biological science for the detection of proteins. Introduction of droplet-based microfluidics allowed the development of miniaturized, less-consuming, and more sensitive ELISA assays by coencapsulating the biological sample and antibody-functionalized particles. We report herein an alternative in-droplet immunoassay format, which avoids the use of particles. It exploits the oil/aqueous-phase interface as a protein capture and detection surface. This is achieved using tailored perfluorinated surfactants bearing azide-functionalized PEG-based polar headgroups, which spontaneously react when meeting at the droplet formation site, with strained alkyne-functionalized antibodies solubilized in the water phase. The resulting antibody-functionalized inner surface can then be used to capture a target protein. This surface capture process leads to concomitant relocation at the surface of a labeled detection antibody and in turn to a drastic change in the shape of the fluorescence signal from a convex shape (not captured) to a characteristic concave shape (captured). This novel droplet surface immunoassay by fluorescence relocation (D-SIRe) proved to be fast and sensitive at 2.3 attomoles of analyte per droplet. It was further demonstrated to allow detection of cytosolic proteins at the single bacteria level.},

keywords = {RYCKELYNCK, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

Fermer

Lee Seungjae, Jee David, Srivastava Sid, Yang Acong, Ramidi Abhinav, Shang Renfu, Bortolamiol-Becet Diane, Pfeffer Sébastien, Gu Shuo, Wen Jiayu, Lai Eric C

Promiscuous splicing-derived hairpins are dominant substrates of tailing-mediated defense of miRNA biogenesis in mammals Article de journal

Dans: Cell Rep, vol. 42, no. 2, p. 112111, 2023, ISSN: 2211-1247.

Résumé | Liens | BibTeX | Étiquettes: PFEFFER, Unité ARN

Giegé Richard, Eriani Gilbert

The tRNA identity landscape for aminoacylation and beyond Article de journal

Dans: Nucleic Acids Res, vol. 51, no. 4, p. 1528–1570, 2023, ISSN: 1362-4962.

Résumé | Liens | BibTeX | Étiquettes: ERIANI, GIEGE, Unité ARN

Husser Claire, Baudrey Stéphanie, Ryckelynck Michael

High-Throughput Development and Optimization of RNA-Based Fluorogenic Biosensors of Small Molecules Using Droplet-Based Microfluidics Chapitre d'ouvrage

Dans: Günter Mayer, Marcus M. Menger (Ed.): vol. 2570, p. 243–269, Günter Mayer, Marcus M. Menger, 2023, ISSN: 1940-6029.

Résumé | Liens | BibTeX | Étiquettes: RYCKELYNCK, Unité ARN

Gosset-Erard Clarisse, Didierjean Mévie, Pansanel Jérome, Lechner Antony, Wolff Philippe, Kuhn Lauriane, Aubriet Frédéric, Leize-Wagner Emmanuelle, Chaimbault Patrick, François Yannis-Nicolas

Nucleos'ID: A New Search Engine Enabling the Untargeted Identification of RNA Post-transcriptional Modifications from Tandem Mass Spectrometry Analyses of Nucleosides Article de journal

Dans: Anal Chem, vol. 95, iss. 2, p. 1608-1617, 2023, ISSN: 1520-6882.

Résumé | Liens | BibTeX | Étiquettes: ARN-MS, PPSE, Unité ARN

@article{pmid36598775,

title = {Nucleos'ID: A New Search Engine Enabling the Untargeted Identification of RNA Post-transcriptional Modifications from Tandem Mass Spectrometry Analyses of Nucleosides},

author = {Clarisse Gosset-Erard and Mévie Didierjean and Jérome Pansanel and Antony Lechner and Philippe Wolff and Lauriane Kuhn and Frédéric Aubriet and Emmanuelle Leize-Wagner and Patrick Chaimbault and Yannis-Nicolas François},

doi = {10.1021/acs.analchem.2c04722},

issn = {1520-6882},

year  = {2023},

date = {2023-01-01},

urldate = {2023-01-01},

journal = {Anal Chem},

volume = {95},

issue = {2},

pages = {1608-1617},

abstract = {As RNA post-transcriptional modifications are of growing interest, several methods were developed for their characterization. One of them established for their identification, at the nucleosidic level, is the hyphenation of separation methods, such as liquid chromatography or capillary electrophoresis, to tandem mass spectrometry. However, to our knowledge, no software is yet available for the untargeted identification of RNA post-transcriptional modifications from MS/MS data-dependent acquisitions. Thus, very long and tedious manual data interpretations are required. To meet the need of easier and faster data interpretation, a new user-friendly search engine, called Nucleos'ID, was developed for CE-MS/MS and LC-MS/MS users. Performances of this new software were evaluated on CE-MS/MS data from nucleoside analyses of already well-described  transfer RNA and  total tRNA extract. All samples showed great true positive, true negative, and false discovery rates considering the database size containing all modified and unmodified nucleosides referenced in the literature. The true positive and true negative rates obtained were above 0.94, while the false discovery rates were between 0.09 and 0.17. To increase the level of sample complexity, untargeted identification of several RNA modifications from  70S ribosome was achieved by the Nucleos'ID search following CE-MS/MS analysis.},

keywords = {ARN-MS, PPSE, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

Fermer

Ponce José R Jaramillo, Théobald-Dietrich Anne, Bénas Philippe, Paulus Caroline, Sauter Claude, Frugier Magali

Solution x-ray scattering highlights discrepancies in Plasmodium multi-aminoacyl-tRNA synthetase complexes Article de journal

Dans: Protein Sci, p. e4564, 2023, ISSN: 1469-896X.

Résumé | Liens | BibTeX | Étiquettes: FRUGIER, SAUTER, Unité ARN

L. Urzhumtseva, V. Lunin, A. Urzhumtsev

Algorithms and programs for the shell decomposition of oscillating functions in space Article de journal

Dans: J Appl Cryst, vol. 56, no. 1, p. 302-311, 2023.

Résumé | Liens | BibTeX | Étiquettes: Unité ARN, Urzhumtseva

@article{nokey,

title = {Algorithms and programs for the shell decomposition of oscillating functions in space},

author = {Urzhumtseva L. and Lunin V. and Urzhumtsev A.},

url = {https://onlinelibrary.wiley.com/doi/abs/10.1107/S160057672201144X},

doi = {10.1107/S160057672201144X},

year  = {2023},

date = {2023-01-01},

urldate = {2023-01-01},

journal = {J Appl Cryst},

volume = {56},

number = {1},

pages = {302-311},

abstract = {Real-space refinement of atomic models in macromolecular crystallography and cryo-electron microscopy fits a model to a map obtained with experimental data. To do so, the atomic model is converted into a map of limited resolution and then this map is compared quantitatively with the experimental one. For an appropriate comparison, the atomic contributions comprising the model map should reflect the resolution of the experimental map and the atomic displacement parameter (ADP) values. Such contributions are spherically symmetric oscillating functions, different for chemically different kinds of atoms, different ADPs and different resolution values, and their derivatives with respect to atomic parameters rule the model refinement. For given parameter values, every contribution may be calculated numerically using two Fourier transforms, which is highly time consuming and makes calculation of the respective derivatives problematic. Alternatively, for an atom of each required type its contribution can be expressed in an analytical form as a sum of specially designed terms. Each term is different from zero essentially inside a spherical shell, and changing the ADP value does not change its form but rather changes the value of one of its arguments. In general, these terms become a convenient tool for the decomposition of oscillating spherically symmetric functions. This work describes the algorithms and respective software, named dec3D, to carry out such a shell decomposition for density contributions of different kinds of atoms and ions.},

keywords = {Unité ARN, Urzhumtseva},

pubstate = {published},

tppubtype = {article}

}

Fermer

Giuliodori Anna Maria, Belardinelli Riccardo, Duval Melodie, Garofalo Raffaella, Schenckbecher Emma, Hauryliuk Vasili, Ennifar Eric, Marzi Stefano

CspA stimulates translation in the cold of its own mRNA by promoting ribosome progression Article de journal

Dans: Front Microbiol, vol. 14, p. 1118329, 2023, ISSN: 1664-302X.

Résumé | Liens | BibTeX | Étiquettes: ENNIFAR, ROMBY, Unité ARN

Giuliodori Anna Maria, Londei Paola, Marzi Stefano

Editorial: Interview with the translational apparatus: stories of intriguing circuits and mechanisms to regulate translation in bacteria, volume II Divers

2023, ISSN: 1664-302X.

Liens | BibTeX | Étiquettes: MARZI, ROMBY, Unité ARN

Bahena-Ceron R., Ponce J. R. Jaramillo, Kanazawa H., Antoine L., Wolff P., Marchand V., Klaholz B., Motorin Y, Romby P., Marzi S.

Methods to Analyze Post-transcriptional Modifications Applied to Stable RNAs in Staphylococcus aureus Chapitre d'ouvrage

Dans: Springer, (Ed.): RNA Structure and Function, vol. 14, p. 233-258, 2023.

Résumé | Liens | BibTeX | Étiquettes: ROMBY, ROMBY MARZI, Unité ARN

Westhof E

Data, data, burning deep, in the forests of the net Article de journal

Dans: Biochem Biophys Res Commun, vol. 633, p. 42-44, 2022, ISSN: 1090-2104.

Résumé | Liens | BibTeX | Étiquettes: Unité ARN, WESTHOF

Urzhumtsev Alexandre G, Urzhumtseva Ludmila M, Lunin Vladimir Y

Direct calculation of cryo-EM and crystallographic model maps for real-space refinement Article de journal

Dans: Acta Crystallogr D Struct Biol, vol. 78, no. Pt 12, p. 1451–1468, 2022, ISSN: 2059-7983.

Résumé | Liens | BibTeX | Étiquettes: Unité ARN

@article{pmid36458616,

title = {Direct calculation of cryo-EM and crystallographic model maps for real-space refinement},

author = {Alexandre G Urzhumtsev and Ludmila M Urzhumtseva and Vladimir Y Lunin},

doi = {10.1107/S2059798322010907},

issn = {2059-7983},

year = {2022},

date = {2022-12-01},

urldate = {2022-12-01},

journal = {Acta Crystallogr D Struct Biol},

volume = {78},

number = {Pt 12},

pages = {1451--1468},

abstract = {This work addresses the problem of the calculation of limited-resolution maps from an atomic model in cryo-electron microscopy and in X-ray and neutron crystallography, including cases where the resolution varies from one molecular region to another. Such maps are necessary in real-space refinement for comparison with the experimental maps. For an appropriate numeric comparison, the calculated maps should reproduce not only the structural features contained in the experimental maps but also the principal map distortions. These model maps can be obtained with no use of Fourier transforms but, similar to density distributions, as a sum of individual atomic contributions. Such contributions, referred to as atomic density images, are atomic densities morphed to reflect distortions of the experimental map, in particular the loss of resolution. They are described by functions composed of a central peak surrounded by Fourier ripples. For practical calculations, atomic images should be cut at some distance. It is shown that to reach a reasonable accuracy such a distance should be significantly larger than the distance customarily applied when calculating density distributions. This is a consequence of the slow rate with which the amplitude of the Fourier ripples decreases. Such a large distance means that at least a few ripples should be included in calculations in order to obtain a map that is sufficiently accurate. Oscillating functions describing these atomic contributions depend, for a given atomic type, on the resolution and on the atomic displacement parameter values. To express both the central peak and the Fourier ripples of the atomic images, these functions are represented by the sums of especially designed terms, each concentrated in a spherical shell and depending analytically on the atomic parameters. In this work, the strength of the dependence of the accuracy of resulting map on the accuracy of the atomic displacement parameters and on the truncation distance, i.e. the number of ripples included in atomic density images, is analyzed. This analysis is completed by practical aspects of the calculation of maps of inhomogeneous resolution. Tests show that the calculation of limited-resolution maps from an atomic model as a sum of atomic contributions requires a large truncation radius extending beyond the central peak of an atomic image and the first Fourier ripples. The article discusses the practical details of such calculations expressing atomic contributions as analytic functions of the atomic coordinates, the atomic displacement parameters and the local resolution.},

keywords = {Unité ARN},

pubstate = {published},

tppubtype = {article}

}

Fermer

This work addresses the problem of the calculation of limited-resolution maps from an atomic model in cryo-electron microscopy and in X-ray and neutron crystallography, including cases where the resolution varies from one molecular region to another. Such maps are necessary in real-space refinement for comparison with the experimental maps. For an appropriate numeric comparison, the calculated maps should reproduce not only the structural features contained in the experimental maps but also the principal map distortions. These model maps can be obtained with no use of Fourier transforms but, similar to density distributions, as a sum of individual atomic contributions. Such contributions, referred to as atomic density images, are atomic densities morphed to reflect distortions of the experimental map, in particular the loss of resolution. They are described by functions composed of a central peak surrounded by Fourier ripples. For practical calculations, atomic images should be cut at some distance. It is shown that to reach a reasonable accuracy such a distance should be significantly larger than the distance customarily applied when calculating density distributions. This is a consequence of the slow rate with which the amplitude of the Fourier ripples decreases. Such a large distance means that at least a few ripples should be included in calculations in order to obtain a map that is sufficiently accurate. Oscillating functions describing these atomic contributions depend, for a given atomic type, on the resolution and on the atomic displacement parameter values. To express both the central peak and the Fourier ripples of the atomic images, these functions are represented by the sums of especially designed terms, each concentrated in a spherical shell and depending analytically on the atomic parameters. In this work, the strength of the dependence of the accuracy of resulting map on the accuracy of the atomic displacement parameters and on the truncation distance, i.e. the number of ripples included in atomic density images, is analyzed. This analysis is completed by practical aspects of the calculation of maps of inhomogeneous resolution. Tests show that the calculation of limited-resolution maps from an atomic model as a sum of atomic contributions requires a large truncation radius extending beyond the central peak of an atomic image and the first Fourier ripples. The article discusses the practical details of such calculations expressing atomic contributions as analytic functions of the atomic coordinates, the atomic displacement parameters and the local resolution.

Fermer

Neyroud Anne Sophie, Rudinger-Thirion Joëlle, Frugier Magali, Riley Lisa G, Bidet Maud, Akloul Linda, Simpson Andrea, Gilot David, Christodoulou John, Ravel Célia, Sinclair Andrew H, Belaud-Rotureau Marc-Antoine, Tucker Elena J, Jaillard Sylvie

LARS2 variants can present as premature ovarian insufficiency in the absence of overt hearing loss Article de journal

Dans: Eur J Hum Genet, vol. 31, iss. 4, p. 453-460, 2022, ISSN: 1476-5438.

Résumé | Liens | BibTeX | Étiquettes: FRUGIER, Unité ARN

@article{pmid36450801,

title = {LARS2 variants can present as premature ovarian insufficiency in the absence of overt hearing loss},

author = {Anne Sophie Neyroud and Joëlle Rudinger-Thirion and Magali Frugier and Lisa G Riley and Maud Bidet and Linda Akloul and Andrea Simpson and David Gilot and John Christodoulou and Célia Ravel and Andrew H Sinclair and Marc-Antoine Belaud-Rotureau and Elena J Tucker and Sylvie Jaillard},

doi = {10.1038/s41431-022-01252-1},

issn = {1476-5438},

year  = {2022},

date = {2022-12-01},

urldate = {2022-12-01},

journal = {Eur J Hum Genet},

volume = {31},

issue = {4},

pages = {453-460},

abstract = {Premature ovarian insufficiency (POI) affects 1 in 100 women and is a leading cause of female infertility. There are over 80 genes in which variants can cause POI, with these explaining only a minority of cases. Whole exome sequencing (WES) can be a useful tool for POI patient management, allowing clinical care to be personalized to underlying cause. We performed WES to investigate two French sisters, whose only clinical complaint was POI. Surprisingly, they shared one known and one novel likely pathogenic variant in the Perrault syndrome gene, LARS2. Using amino-acylation studies, we established that the novel missense variant significantly impairs LARS2 function. Perrault syndrome is characterized by sensorineural hearing loss in addition to POI. This molecular diagnosis alerted the sisters to the significance of their difficulty in following conversation. Subsequent audiology assessment revealed a mild bilateral hearing loss. We describe the first cases presenting with perceived isolated POI and causative variants in a Perrault syndrome gene. Our study expands the phenotypic spectrum associated with LARS2 variants and highlights the clinical benefit of having a genetic diagnosis, with prediction of potential co-morbidity and prompt and appropriate medical care, in this case by an audiologist for early detection of hearing loss.},

keywords = {FRUGIER, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

Fermer

Mráziková Klaudia, Kruse Holger, Mlýnský Vojtěch, Auffinger Pascal, Šponer Jiří

Multiscale Modeling of Phosphate···π Contacts in RNA U-Turns Exposes Differences between Quantum-Chemical and AMBER Force Field Descriptions Article de journal

Dans: J Chem Inf Model, vol. 62, iss. 23, p. 6182-6200, 2022, ISSN: 1549-960X.

Résumé | Liens | BibTeX | Étiquettes: ENNIFAR, Unité ARN

@article{pmid36454943,

title = {Multiscale Modeling of Phosphate···π Contacts in RNA U-Turns Exposes Differences between Quantum-Chemical and AMBER Force Field Descriptions},

author = {Klaudia Mráziková and Holger Kruse and Vojtěch Mlýnský and Pascal Auffinger and Jiří Šponer},

doi = {10.1021/acs.jcim.2c01064},

issn = {1549-960X},

year  = {2022},

date = {2022-12-01},

urldate = {2022-12-01},

journal = {J Chem Inf Model},

volume = {62},

issue = {23},

pages = {6182-6200},

abstract = {Phosphate···π, also called anion···π, contacts occur between nucleobases and anionic phosphate oxygens (OP2) in r(GNRA) and r(UNNN) U-turn motifs (N = A,G,C,U; R = A,G). These contacts were investigated using state-of-the-art quantum-chemical methods (QM) to characterize their physicochemical properties and to serve as a reference to evaluate AMBER force field (AFF) performance. We found that phosphate···π interaction energies calculated with the AFF for dimethyl phosphate···nucleobase model systems are less stabilizing in comparison with double-hybrid DFT and that minimum contact distances are larger for all nucleobases. These distance stretches are also observed in large-scale AFF vs QM/MM computations and classical molecular dynamics (MD) simulations on several r(gcGNRAgc) tetraloop hairpins when compared to experimental data extracted from X-ray/cryo-EM structures (res. ≤ 2.5 Å) using the WebFR3D bioinformatic tool. MD simulations further revealed shifted OP2/nucleobase positions. We propose that discrepancies between the QM and AFF result from a combination of missing polarization in the AFF combined with too large AFF Lennard-Jones (LJ) radii of nucleobase carbon atoms in addition to an exaggerated short-range repulsion of the  LJ repulsive term. We compared these results with earlier data gathered on lone pair···π contacts in CpG Z-steps occurring in r(UNCG) tetraloops. In both instances, charge transfer calculations do not support any significant  → π* donation effects. We also investigated thiophosphate···π contacts that showed reduced stabilizing interaction energies when compared to phosphate···π contacts. Thus, we challenge suggestions that the experimentally observed enhanced thermodynamic stability of phosphorothioated r(GNRA) tetraloops can be explained by larger London dispersion.},

keywords = {ENNIFAR, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

Fermer

Girardi Erika, Messmer Melanie, Lopez Paula, Fender Aurelie, Chicher Johana, Chane-Woon-Ming Beatrice, Hammann Philippe, Pfeffer Sebastien

Proteomics-based determination of double stranded RNA interactome reveals known and new factors involved in Sindbis virus infection Article de journal

Dans: RNA, vol. 29, iss. 3, p. 361-375, 2022, ISSN: 1469-9001.

Résumé | Liens | BibTeX | Étiquettes: PFEFFER, PPSE, Unité ARN

@article{pmid36617674,

title = {Proteomics-based determination of double stranded RNA interactome reveals known and new factors involved in Sindbis virus infection},

author = {Erika Girardi and Melanie Messmer and Paula Lopez and Aurelie Fender and Johana Chicher and Beatrice Chane-Woon-Ming and Philippe Hammann and Sebastien Pfeffer},

doi = {10.1261/rna.079270.122},

issn = {1469-9001},

year  = {2022},

date = {2022-12-01},

urldate = {2022-12-01},

journal = {RNA},

volume = {29},

issue = {3},

pages = {361-375},

abstract = {Viruses are obligate intracellular parasites, which depend on the host cellular machineries to replicate their genome and complete their infectious cycle. Long double stranded (ds)RNA is a common viral by-product originating during RNA virus replication and is universally sensed as a danger signal to trigger the antiviral response. As a result, viruses hide dsRNA intermediates into viral replication factories and have evolved strategies to hijack cellular proteins for their benefit. The characterization of the host factors associated with viral dsRNA and involved in viral replication remains a major challenge to develop new antiviral drugs against RNA viruses. Here, we performed anti-dsRNA immunoprecipitation followed by mass spectrometry analysis to fully characterize the dsRNA interactome in Sindbis virus (SINV) infected human cells. Among the identified proteins, we characterized SFPQ (Splicing factor, proline-glutamine rich) as a new dsRNA-associated proviral factor upon SINV infection. We showed that SFPQ depletion reduces SINV infection in human HCT116 and SK-N-BE(2) cells, suggesting that SFPQ enhances viral production. We demonstrated that the cytoplasmic fraction of SFPQ partially colocalizes with dsRNA upon SINV infection. In agreement, we proved by RNA-IP that SFPQ can bind dsRNA and viral RNA. Furthermore, we showed that overexpression of a wild type, but not an RNA binding mutant SFPQ, increased viral infection, suggesting that RNA binding is essential for its positive effect on the virus. Overall, this study provides the community with a compendium of dsRNA-associated factors during viral infection and identifies SFPQ as a new proviral dsRNA binding protein.},

keywords = {PFEFFER, PPSE, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

Fermer

Xu Rui, Lou Yanyan, Tidu Antonin, Bulet Philippe, Heinekamp Thorsten, Martin Franck, Brakhage Axel, Li Zi, Liégeois Samuel, Ferrandon Dominique

The Toll pathway mediates Drosophila resilience to Aspergillus mycotoxins through specific Bomanins Article de journal

Dans: EMBO Rep, p. e56036, 2022, ISSN: 1469-3178.

Résumé | Liens | BibTeX | Étiquettes: ERIANI, ferrandon, M3i, MARTIN, Unité ARN

Belinite Margarita, Khusainov Iskander, Marzi Stefano

30S Ribosomal Subunit Purification and Its Biochemical and Cryo-EM Analysis Article de journal

Dans: Bio Protoc, vol. 12, no. 20, 2022, ISSN: 2331-8325.

Résumé | Liens | BibTeX | Étiquettes: ROMBY, Unité ARN

Bonaventure B., Rebendenne A., Valadão A. L Chaves, Arnaud-Arnould M., Gracias S., de Gracia F. Garcia, McKellar J., Labaronne E., Tauziet M., Vivet-Boudou V., Bernard E., Briant L., Gros N., Djilli W., Courgnaud V., Parrinello H., Rialle S., Blaise M., Lacroix L., Lavigne M., Paillart J. -C., Ricci E. P, Schulz R., Jouvenet N., Moncorgé O., Goujon C.

The DEAD box RNA helicase DDX42 is an intrinsic inhibitor of positive-strand RNA viruses Article de journal

Dans: EMBO Rep, p. e54061, 2022, ISSN: 1469-3178.

Résumé | Liens | BibTeX | Étiquettes: MARQUET, PAILLART, Unité ARN

@article{pmid36161446,

title = {The DEAD box RNA helicase DDX42 is an intrinsic inhibitor of positive-strand RNA viruses},

author = {B. Bonaventure and A. Rebendenne and A.L Chaves Valadão and M. Arnaud-Arnould and S. Gracias and F. Garcia de Gracia and J. McKellar and E. Labaronne and M. Tauziet and V. Vivet-Boudou and E. Bernard and L. Briant and N. Gros and W. Djilli and V. Courgnaud and H. Parrinello and S. Rialle and M. Blaise and L. Lacroix and M. Lavigne and J.-C. Paillart and E. P Ricci and R. Schulz and N. Jouvenet and O. Moncorgé and C. Goujon},

url = {https://pubmed.ncbi.nlm.nih.gov/36161446/},

doi = {10.15252/embr.202154061},

issn = {1469-3178},

year  = {2022},

date = {2022-09-01},

urldate = {2022-09-01},

journal = {EMBO Rep},

pages = {e54061},

abstract = {Genome-wide screens are powerful approaches to unravel regulators of viral infections. Here, a CRISPR screen identifies the RNA helicase DDX42 as an intrinsic antiviral inhibitor of HIV-1. Depletion of endogenous DDX42 increases HIV-1 DNA accumulation and infection in cell lines and primary cells. DDX42 overexpression inhibits HIV-1 infection, whereas expression of a dominant-negative mutant increases infection. Importantly, DDX42 also restricts LINE-1 retrotransposition and infection with other retroviruses and positive-strand RNA viruses, including CHIKV and SARS-CoV-2. However, DDX42 does not impact the replication of several negative-strand RNA viruses, arguing against an unspecific effect on target cells, which is confirmed by RNA-seq analysis. Proximity ligation assays show DDX42 in the vicinity of viral elements, and cross-linking RNA immunoprecipitation confirms a specific interaction of DDX42 with RNAs from sensitive viruses. Moreover, recombinant DDX42 inhibits HIV-1 reverse transcription in vitro. Together, our data strongly suggest a direct mode of action of DDX42 on viral ribonucleoprotein complexes. Our results identify DDX42 as an intrinsic viral inhibitor, opening new perspectives to target the life cycle of numerous RNA viruses.},

keywords = {MARQUET, PAILLART, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

Fermer

Tong Xiaoling, Han Min-Jin, Lu Kunpeng, Tai Shuaishuai, Liang Shubo, Liu Yucheng, Hu Hai, Shen Jianghong, Long Anxing, Zhan Chengyu, Ding Xin, Liu Shuo, Gao Qiang, Zhang Bili, Zhou Linli, Tan Duan, Yuan Yajie, Guo Nangkuo, Li Yan-Hong, Wu Zhangyan, Liu Lulu, Li Chunlin, Lu Yaru, Gai Tingting, Zhang Yahui, Yang Renkui, Qian Heying, Liu Yanqun, Luo Jiangwen, Zheng Lu, Lou Jinghou, Peng Yunwu, Zuo Weidong, Song Jiangbo, He Songzhen, Wu Songyuan, Zou Yunlong, Zhou Lei, Cheng Lan, Tang Yuxia, Cheng Guotao, Yuan Lianwei, He Weiming, Xu Jiabao, Fu Tao, Xiao Yang, Lei Ting, Xu Anying, Yin Ye, Wang Jian, Monteiro Antónia, Westhof E, Lu Cheng, Tian Zhixi, Wang Wen, Xiang Zhonghuai, Dai Fangyin

High-resolution silkworm pan-genome provides genetic insights into artificial selection and ecological adaptation Article de journal

Dans: Nat Commun, vol. 13, no. 1, p. 5619, 2022, ISSN: 2041-1723.

Résumé | Liens | BibTeX | Étiquettes: Unité ARN, WESTHOF

@article{pmid36153338,

title = {High-resolution silkworm pan-genome provides genetic insights into artificial selection and ecological adaptation},

author = {Xiaoling Tong and Min-Jin Han and Kunpeng Lu and Shuaishuai Tai and Shubo Liang and Yucheng Liu and Hai Hu and Jianghong Shen and Anxing Long and Chengyu Zhan and Xin Ding and Shuo Liu and Qiang Gao and Bili Zhang and Linli Zhou and Duan Tan and Yajie Yuan and Nangkuo Guo and Yan-Hong Li and Zhangyan Wu and Lulu Liu and Chunlin Li and Yaru Lu and Tingting Gai and Yahui Zhang and Renkui Yang and Heying Qian and Yanqun Liu and Jiangwen Luo and Lu Zheng and Jinghou Lou and Yunwu Peng and Weidong Zuo and Jiangbo Song and Songzhen He and Songyuan Wu and Yunlong Zou and Lei Zhou and Lan Cheng and Yuxia Tang and Guotao Cheng and Lianwei Yuan and Weiming He and Jiabao Xu and Tao Fu and Yang Xiao and Ting Lei and Anying Xu and Ye Yin and Jian Wang and Antónia Monteiro and E Westhof and Cheng Lu and Zhixi Tian and Wen Wang and Zhonghuai Xiang and Fangyin Dai},

doi = {10.1038/s41467-022-33366-x},

issn = {2041-1723},

year  = {2022},

date = {2022-09-01},

urldate = {2022-09-01},

journal = {Nat Commun},

volume = {13},

number = {1},

pages = {5619},

abstract = {The silkworm Bombyx mori is an important economic insect for producing silk, the "queen of fabrics". The currently available genomes limit the understanding of its genetic diversity and the discovery of valuable alleles for breeding. Here, we deeply re-sequence 1,078 silkworms and assemble long-read genomes for 545 representatives. We construct a high-resolution pan-genome dataset representing almost the entire genomic content in the silkworm. We find that the silkworm population harbors a high density of genomic variants and identify 7308 new genes, 4260 (22%) core genes, and 3,432,266 non-redundant structure variations (SVs). We reveal hundreds of genes and SVs that may contribute to the artificial selection (domestication and breeding) of silkworm. Further, we focus on four genes responsible, respectively, for two economic (silk yield and silk fineness) and two ecologically adaptive traits (egg diapause and aposematic coloration). Taken together, our population-scale genomic resources will promote functional genomics studies and breeding improvement for silkworm.},

keywords = {Unité ARN, WESTHOF},

pubstate = {published},

tppubtype = {article}

}

Fermer

Hayek Hassan, Eriani Gilbert, Allmang Christine

eIF3 Interacts with Selenoprotein mRNAs Article de journal

Dans: Biomolecules, vol. 12, no. 9, 2022, ISSN: 2218-273X.

Résumé | Liens | BibTeX | Étiquettes: ERIANI, Unité ARN

Diallo Idrissa, Ho Jeffrey, Lambert Marine, Benmoussa Abderrahim, Husseini Zeinab, Lalaouna David, Massé Eric, Provost Patrick

A tRNA-derived fragment present in E. coli OMVs regulates host cell gene expression and proliferation Article de journal

Dans: PLoS Pathog, vol. 18, no. 9, p. e1010827, 2022, ISSN: 1553-7374.

Résumé | Liens | BibTeX | Étiquettes: ROMBY, Unité ARN

Danne Camille, Michaudel Chloé, Skerniskyte Jurate, Planchais Julien, Magniez Aurélie, Agus Allison, Michel Marie-Laure, Lamas Bruno, Costa Gregory Da, Spatz Madeleine, Oeuvray Cyriane, Galbert Chloé, Poirier Maxime, Wang Yazhou, Lapière Alexia, Rolhion Nathalie, Ledent Tatiana, Pionneau Cédric, Chardonnet Solenne, Bellvert Floriant, Cahoreau Edern, Rocher Amandine, Arguello Rafael Rose, Peyssonnaux Carole, Louis Sabine, Richard Mathias L, Langella Philippe, El-Benna Jamel, Marteyn Benoit, Sokol Harry

CARD9 in neutrophils protects from colitis and controls mitochondrial metabolism and cell survival Article de journal

Dans: Gut, vol. 72, iss. 6, p. 1081-1092, 2022, ISSN: 1468-3288.

Résumé | Liens | BibTeX | Étiquettes: MARTEYN, Unité ARN

@article{pmid36167663,

title = {CARD9 in neutrophils protects from colitis and controls mitochondrial metabolism and cell survival},

author = {Camille Danne and Chloé Michaudel and Jurate Skerniskyte and Julien Planchais and Aurélie Magniez and Allison Agus and Marie-Laure Michel and Bruno Lamas and Gregory Da Costa and Madeleine Spatz and Cyriane Oeuvray and Chloé Galbert and Maxime Poirier and Yazhou Wang and Alexia Lapière and Nathalie Rolhion and Tatiana Ledent and Cédric Pionneau and Solenne Chardonnet and Floriant Bellvert and Edern Cahoreau and Amandine Rocher and Rafael Rose Arguello and Carole Peyssonnaux and Sabine Louis and Mathias L Richard and Philippe Langella and Jamel El-Benna and Benoit Marteyn and Harry Sokol},

doi = {10.1136/gutjnl-2022-326917},

issn = {1468-3288},

year  = {2022},

date = {2022-09-01},

urldate = {2022-09-01},

journal = {Gut},

volume = {72},

issue = {6},

pages = {1081-1092},

abstract = {OBJECTIVES: Inflammatory bowel disease (IBD) results from a combination of genetic predisposition, dysbiosis of the gut microbiota and environmental factors, leading to alterations in the gastrointestinal immune response and chronic inflammation. Caspase recruitment domain 9 (), one of the IBD susceptibility genes, has been shown to protect against intestinal inflammation and fungal infection. However, the cell types and mechanisms involved in the CARD9 protective role against inflammation remain unknown.



DESIGN: We used dextran sulfate sodium (DSS)-induced and adoptive transfer colitis models in total and conditional CARD9 knock-out mice to uncover which cell types play a role in the CARD9 protective phenotype. The impact of  deletion on neutrophil function was assessed by an in vivo model of fungal infection and various functional assays, including endpoint dilution assay, apoptosis assay by flow cytometry, proteomics and real-time bioenergetic profile analysis (Seahorse).



RESULTS: Lymphocytes are not intrinsically involved in the CARD9 protective role against colitis. CARD9 expression in neutrophils, but not in epithelial or CD11c+cells, protects against DSS-induced colitis. In the absence of CARD9, mitochondrial dysfunction increases mitochondrial reactive oxygen species production leading to the premature death of neutrophilsthrough apoptosis, especially in oxidative environment. The decreased functional neutrophils in tissues might explain the impaired containment of fungi and increased susceptibility to intestinal inflammation.



CONCLUSION: These results provide new insight into the role of CARD9 in neutrophil mitochondrial function and its involvement in intestinal inflammation, paving the way for new therapeutic strategies targeting neutrophils.},

keywords = {MARTEYN, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

Fermer

Jakob C., Paul-Stansilaus R., Schwemmle M., Marquet R., Bolte H.

The influenza A virus genome packaging network - complex, flexible and yet unsolved Article de journal

Dans: Nucleic Acids Res, vol. 50, iss. 16, p. 9023-9038, 2022, ISSN: 1362-4962.

Résumé | Liens | BibTeX | Étiquettes: MARQUET, Unité ARN

@article{pmid35993811,

title = {The influenza A virus genome packaging network - complex, flexible and yet unsolved},

author = {C. Jakob and R. Paul-Stansilaus and M. Schwemmle and R. Marquet and H. Bolte},

doi = {10.1093/nar/gkac688},

issn = {1362-4962},

year  = {2022},

date = {2022-08-01},

urldate = {2022-08-01},

journal = {Nucleic Acids Res},

volume = {50},

issue = {16},

pages = {9023-9038},

abstract = {The genome of influenza A virus (IAV) consists of eight unique viral RNA segments. This genome organization allows genetic reassortment between co-infecting IAV strains, whereby new IAVs with altered genome segment compositions emerge. While it is known that reassortment events can create pandemic IAVs, it remains impossible to anticipate reassortment outcomes with pandemic prospects. Recent research indicates that reassortment is promoted by a viral genome packaging mechanism that delivers the eight genome segments as a supramolecular complex into the virus particle. This finding holds promise of predicting pandemic IAVs by understanding the intermolecular interactions governing this genome packaging mechanism. Here, we critically review the prevailing mechanistic model postulating that IAV genome packaging is orchestrated by a network of intersegmental RNA-RNA interactions. Although we find supporting evidence, including segment-specific packaging signals and experimentally proposed RNA-RNA interaction networks, this mechanistic model remains debatable due to a current shortage of functionally validated intersegmental RNA-RNA interactions. We speculate that identifying such functional intersegmental RNA-RNA contacts might be hampered by limitations of the utilized probing techniques and the inherent complexity of the genome packaging mechanism. Nevertheless, we anticipate that improved probing strategies combined with a mutagenesis-based validation could facilitate their discovery.},

keywords = {MARQUET, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

Fermer

Mair Stefan, Erharter Kevin, Renard Eva, Brillet Karl, Brunner Melanie, Lusser Alexandra, Kreutz Christoph, Ennifar Eric, Micura Ronald

Towards a comprehensive understanding of RNA deamination: synthesis and properties of xanthosine-modified RNA Article de journal

Dans: Nucleic Acids Res, vol. 50, iss. 11, p. 6038-6051, 2022, ISSN: 1362-4962.

Résumé | Liens | BibTeX | Étiquettes: ENNIFAR, Unité ARN

@article{pmid35687141,

title = {Towards a comprehensive understanding of RNA deamination: synthesis and properties of xanthosine-modified RNA},

author = {Stefan Mair and Kevin Erharter and Eva Renard and Karl Brillet and Melanie Brunner and Alexandra Lusser and Christoph Kreutz and Eric Ennifar and Ronald Micura},

doi = {10.1093/nar/gkac477},

issn = {1362-4962},

year  = {2022},

date = {2022-06-01},

urldate = {2022-06-01},

journal = {Nucleic Acids Res},

volume = {50},

issue = {11},

pages = {6038-6051},

abstract = {Nucleobase deamination, such as A-to-I editing, represents an important posttranscriptional modification of RNA. When deamination affects guanosines, a xanthosine (X) containing RNA is generated. However, the biological significance and chemical consequences on RNA are poorly understood. We present a comprehensive study on the preparation and biophysical properties of X-modified RNA. Thermodynamic analyses revealed that base pairing strength is reduced to a level similar to that observed for a G•U replacement. Applying NMR spectroscopy and X-ray crystallography, we demonstrate that X can form distinct wobble geometries with uridine depending on the sequence context. In contrast, X pairing with cytidine occurs either through wobble geometry involving protonated C or in Watson-Crick-like arrangement. This indicates that the different pairing modes are of comparable stability separated by low energetic barriers for switching. Furthermore, we demonstrate that the flexible pairing properties directly affect the recognition of X-modified RNA by reverse transcription enzymes. Primer extension assays and PCR-based sequencing analysis reveal that X is preferentially read as G or A and that the ratio depends on the type of reverse transcriptase. Taken together, our results elucidate important properties of X-modified RNA paving the way for future studies on its biological significance.},

keywords = {ENNIFAR, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

Fermer

Vilimova Monika, Pfeffer Sébastien

Post-transcriptional regulation of polycistronic microRNAs Article de journal

Dans: Wiley Interdiscip Rev RNA, vol. 14, iss. 2, p. e1749, 2022, ISSN: 1757-7012.

Résumé | Liens | BibTeX | Étiquettes: PFEFFER, Unité ARN

@article{pmid35702737,

title = {Post-transcriptional regulation of polycistronic microRNAs},

author = {Monika Vilimova and Sébastien Pfeffer},

doi = {10.1002/wrna.1749},

issn = {1757-7012},

year  = {2022},

date = {2022-06-01},

urldate = {2022-06-01},

journal = {Wiley Interdiscip Rev RNA},

volume = {14},

issue = {2},

pages = {e1749},

abstract = {An important proportion of microRNA (miRNA) genes tend to lie close to each other within animal genomes. Such genomic organization is generally referred to as miRNA clusters. Even though many miRNA clusters have been greatly studied, most attention has been usually focused on functional impacts of clustered miRNA co-expression. However, there is also another compelling aspect about these miRNA clusters, their polycistronic nature. Being transcribed on a single RNA precursor, polycistronic miRNAs benefit from common transcriptional regulation allowing their coordinated expression. And yet, numerous reports have revealed striking discrepancies in the accumulation of mature miRNAs produced from the same cluster. Indeed, the larger polycistronic transcripts can act as platforms providing unforeseen post-transcriptional regulatory mechanisms controlling individual miRNA processing, thus leading to differential miRNA expression, and sometimes even challenging the general assumption that polycistronic miRNAs are co-expressed. In this review, we aim to address the current knowledge about how miRNA polycistrons are post-transcriptionally regulated. In particular, we will focus on the mechanisms occurring at the level of the primary transcript, which are highly relevant for individual miRNA processing and as such have a direct repercussion on miRNA function within the cell. This article is categorized under: RNA Processing > Processing of Small RNAs Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.},

keywords = {PFEFFER, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

Fermer

McKellar Stuart W, Ivanova Ivayla, Arede Pedro, Zapf Rachel L, Mercier Noémie, Chu Liang-Cui, Mediati Daniel G, Pickering Amy C, Briaud Paul, Foster Robert G, Kudla Grzegorz, Fitzgerald J Ross, Caldelari Isabelle, Carroll Ronan K, Tree Jai J, Granneman Sander

RNase III CLASH in MRSA uncovers sRNA regulatory networks coupling metabolism to toxin expression Article de journal

Dans: Nat Commun, vol. 13, no. 1, p. 3560, 2022, ISSN: 2041-1723.

Résumé | Liens | BibTeX | Étiquettes: ROMBY, Unité ARN

Roovers Martine L, Labar Geoffray, Wolff Philippe, Feller Andre, Elder Dany Van, Soin Romuald, Gueydan Cyril, Kruys Veronique, Droogmans Louis

The Bacillus subtilis open reading frame ysgA encodes the SPOUT methyltransferase RlmP forming 2'-O-methylguanosine at position 2553 in the A-loop of 23S rRNA Article de journal

Dans: RNA, vol. 28, iss. 9, p. 1185-1196, 2022, ISSN: 1469-9001.

Résumé | Liens | BibTeX | Étiquettes: ARN-MS, ENNIFAR, Unité ARN

Verdikt Roxane, Bendoumou Maryam, Bouchat Sophie, Nestola Lorena, Pasternak Alexander O, Darcis Gilles, Avettand-Fenoel Véronique, Vanhulle Caroline, Aït-Ammar Amina, Santangelo Marion, Plant Estelle, Douce Valentin Le, Delacourt Nadège, Cicilionytė Aurelija, Necsoi Coca, Corazza Francis, Passaes Caroline Pereira Bittencourt, Schwartz Christian, Bizet Martin, Fuks François, Sáez-Cirión Asier, Rouzioux Christine, Wit Stéphane De, Berkhout Ben, Gautier Virginie, Rohr Olivier, Lint Carine Van

Novel role of UHRF1 in the epigenetic repression of the latent HIV-1 Article de journal

Dans: EBioMedicine, vol. 79, p. 103985, 2022, ISSN: 2352-3964.

Résumé | Liens | BibTeX | Étiquettes: ROHR, Unité ARN

@article{pmid35429693,

title = {Novel role of UHRF1 in the epigenetic repression of the latent HIV-1},

author = {Roxane Verdikt and Maryam Bendoumou and Sophie Bouchat and Lorena Nestola and Alexander O Pasternak and Gilles Darcis and Véronique Avettand-Fenoel and Caroline Vanhulle and Amina Aït-Ammar and Marion Santangelo and Estelle Plant and Valentin Le Douce and Nadège Delacourt and Aurelija Cicilionytė and Coca Necsoi and Francis Corazza and Caroline Pereira Bittencourt Passaes and Christian Schwartz and Martin Bizet and François Fuks and Asier Sáez-Cirión and Christine Rouzioux and Stéphane De Wit and Ben Berkhout and Virginie Gautier and Olivier Rohr and Carine Van Lint},

doi = {10.1016/j.ebiom.2022.103985},

issn = {2352-3964},

year  = {2022},

date = {2022-05-01},

urldate = {2022-05-01},

journal = {EBioMedicine},

volume = {79},

pages = {103985},

abstract = {BACKGROUND: The multiplicity, heterogeneity, and dynamic nature of human immunodeficiency virus type-1 (HIV-1) latency mechanisms are reflected in the current lack of functional cure for HIV-1. Accordingly, all classes of latency-reversing agents (LRAs) have been reported to present variable ex vivo potencies. Here, we investigated the molecular mechanisms underlying the potency variability of one LRA: the DNA methylation inhibitor 5-aza-2'-deoxycytidine (5-AzadC).nnMETHODS: We employed epigenetic interrogation methods (electrophoretic mobility shift assays, chromatin immunoprecipitation, Infinium array) in complementary HIV-1 infection models (latently-infected T-cell line models, primary CD4 T-cell models and ex vivo cultures of PBMCs from HIV individuals). Extracellular staining of cell surface receptors and intracellular metabolic activity were measured in drug-treated cells. HIV-1 expression in reactivation studies was explored by combining the measures of capsid p24 protein, green fluorescence protein signal, intracellular and extracellular viral RNA and viral DNA.nnFINDINGS: We uncovered specific demethylation CpG signatures induced by 5-AzadC in the HIV-1 promoter. By analyzing the binding modalities to these CpG, we revealed the recruitment of the epigenetic integrator Ubiquitin-like with PHD and RING finger domain 1 (UHRF1) to the HIV-1 promoter. We showed that UHRF1 redundantly binds to the HIV-1 promoter with different binding modalities where DNA methylation was either non-essential, essential or enhancing UHRF1 binding. We further demonstrated the role of UHRF1 in the epigenetic repression of the latent viral promoter by a concerted control of DNA and histone methylations.nnINTERPRETATION: A better understanding of the molecular mechanisms of HIV-1 latency allows for the development of innovative antiviral strategies. As a proof-of-concept, we showed that pharmacological inhibition of UHRF1 in ex vivo HIV patient cell cultures resulted in potent viral reactivation from latency. Together, we identify UHRF1 as a novel actor in HIV-1 epigenetic silencing and highlight that it constitutes a new molecular target for HIV-1 cure strategies.nnFUNDING: Funding was provided by the Belgian National Fund for Scientific Research (F.R.S.-FNRS, Belgium), the « Fondation Roi Baudouin », the NEAT (European AIDS Treatment Network) program, the Internationale Brachet Stiftung, ViiV Healthcare, the Télévie, the Walloon Region (« Fonds de Maturation »), « Les Amis des Instituts Pasteur à Bruxelles, asbl », the University of Brussels (Action de Recherche Concertée ULB grant), the Marie Skodowska Curie COFUND action, the European Union's Horizon 2020 research and innovation program under grant agreement No 691119-EU4HIVCURE-H2020-MSCA-RISE-2015, the French Agency for Research on AIDS and Viral Hepatitis (ANRS), the Sidaction and the "Alsace contre le Cancer" Foundation. This work is supported by 1UM1AI164562-01, co-funded by National Heart, Lung and Blood Institute, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Neurological Disorders and Stroke, National Institute on Drug Abuse and the National Institute of Allergy and Infectious Diseases.},

keywords = {ROHR, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

Fermer

BACKGROUND: The multiplicity, heterogeneity, and dynamic nature of human immunodeficiency virus type-1 (HIV-1) latency mechanisms are reflected in the current lack of functional cure for HIV-1. Accordingly, all classes of latency-reversing agents (LRAs) have been reported to present variable ex vivo potencies. Here, we investigated the molecular mechanisms underlying the potency variability of one LRA: the DNA methylation inhibitor 5-aza-2'-deoxycytidine (5-AzadC).nnMETHODS: We employed epigenetic interrogation methods (electrophoretic mobility shift assays, chromatin immunoprecipitation, Infinium array) in complementary HIV-1 infection models (latently-infected T-cell line models, primary CD4 T-cell models and ex vivo cultures of PBMCs from HIV individuals). Extracellular staining of cell surface receptors and intracellular metabolic activity were measured in drug-treated cells. HIV-1 expression in reactivation studies was explored by combining the measures of capsid p24 protein, green fluorescence protein signal, intracellular and extracellular viral RNA and viral DNA.nnFINDINGS: We uncovered specific demethylation CpG signatures induced by 5-AzadC in the HIV-1 promoter. By analyzing the binding modalities to these CpG, we revealed the recruitment of the epigenetic integrator Ubiquitin-like with PHD and RING finger domain 1 (UHRF1) to the HIV-1 promoter. We showed that UHRF1 redundantly binds to the HIV-1 promoter with different binding modalities where DNA methylation was either non-essential, essential or enhancing UHRF1 binding. We further demonstrated the role of UHRF1 in the epigenetic repression of the latent viral promoter by a concerted control of DNA and histone methylations.nnINTERPRETATION: A better understanding of the molecular mechanisms of HIV-1 latency allows for the development of innovative antiviral strategies. As a proof-of-concept, we showed that pharmacological inhibition of UHRF1 in ex vivo HIV patient cell cultures resulted in potent viral reactivation from latency. Together, we identify UHRF1 as a novel actor in HIV-1 epigenetic silencing and highlight that it constitutes a new molecular target for HIV-1 cure strategies.nnFUNDING: Funding was provided by the Belgian National Fund for Scientific Research (F.R.S.-FNRS, Belgium), the « Fondation Roi Baudouin », the NEAT (European AIDS Treatment Network) program, the Internationale Brachet Stiftung, ViiV Healthcare, the Télévie, the Walloon Region (« Fonds de Maturation »), « Les Amis des Instituts Pasteur à Bruxelles, asbl », the University of Brussels (Action de Recherche Concertée ULB grant), the Marie Skodowska Curie COFUND action, the European Union's Horizon 2020 research and innovation program under grant agreement No 691119-EU4HIVCURE-H2020-MSCA-RISE-2015, the French Agency for Research on AIDS and Viral Hepatitis (ANRS), the Sidaction and the "Alsace contre le Cancer" Foundation. This work is supported by 1UM1AI164562-01, co-funded by National Heart, Lung and Blood Institute, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Neurological Disorders and Stroke, National Institute on Drug Abuse and the National Institute of Allergy and Infectious Diseases.

Fermer

Libre C, Seissler T, Guerrero S, Batisse J, Verriez C, Stupfler B, Gilmer O, Cabrera-Rodriguez R, Weber M, Valenzuela-Fernandez A, Cimarelli A, Etienne L, Marquet R, Paillart J C

A Conserved uORF Regulates APOBEC3G Translation and Is Targeted by HIV-1 Vif Protein to Repress the Antiviral Factor Article de journal

Dans: Biomedicines, vol. 10, no. 1, p. 13, 2022.

Résumé | Liens | BibTeX | Étiquettes: MARQUET, PAILLART, Unité ARN

@article{Libre2022,

title = {A Conserved uORF Regulates APOBEC3G Translation and Is Targeted by HIV-1 Vif Protein to Repress the Antiviral Factor},

author = {C Libre and T Seissler and S Guerrero and J Batisse and C Verriez and B Stupfler and O Gilmer and R Cabrera-Rodriguez and M Weber and A Valenzuela-Fernandez and A Cimarelli and L Etienne and R Marquet and J C Paillart},

url = {https://www.mdpi.com/2227-9059/10/1/13},

doi = {10.1101/2021.01.13.426487},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {Biomedicines},

volume = {10},

number = {1},

pages = {13},

abstract = {The HIV-1 Vif protein is essential for viral fitness and pathogenicity. Vif decreases expression of cellular cytosine deaminases APOBEC3G (A3G), A3F, A3D and A3H, which inhibit HIV-1 replication by inducing hypermutations during reverse transcription. Vif counteracts A3G by several non-redundant mechanisms (transcription, translation and protein degradation) that concur in reducing the levels of A3G in cell and in preventing its incorporation into viral particles. How Vif affects A3G translation remains unclear. Here, we uncovered the importance of a short conserved uORF (upstream ORF) located within two critical stem-loop structures of the 5-untranslated region (5-UTR) of A3G mRNA. Extensive mutagenesis of A3G 5-UTR, combined with an analysis of their translational effect in transfected cells, indicated that the uORF represses A3G translation and that A3G mRNA is translated through a dual leaky-scanning and re-initiation mechanism. Interestingly, the uORF is also mandatory for the Vif-mediated repression of A3G translation. Furthermore, we showed that the redirection of A3G mRNA into stress granules was dependent not only on Vif, but also on the uORF. Overall, we discovered that A3G translation is regulated by a small uORF conserved in the human population and that Vif uses this specific motif to repress its translation.},

keywords = {MARQUET, PAILLART, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

Fermer

Desgranges E., Barrientos L., Herrgott L., Marzi S., Toledo-Arana A., Moreau K., Vandenesch F., Romby P., Caldelari I.

The 3'UTR-derived sRNA RsaG coordinates redox homeostasis and metabolism adaptation in response to glucose-6-phosphate uptake in Staphylococcus aureus Article de journal

Dans: Mol Microbiol, 2022, ISBN: 34783400, (1365-2958 (Electronic) 0950-382X (Linking) Journal Article).

Résumé | Liens | BibTeX | Étiquettes: ROMBY, Unité ARN

@article{nokey,

title = {The 3'UTR-derived sRNA RsaG coordinates redox homeostasis and metabolism adaptation in response to glucose-6-phosphate uptake in Staphylococcus aureus},

author = {E. Desgranges and L. Barrientos and L. Herrgott and S. Marzi and A. Toledo-Arana and K. Moreau and F. Vandenesch and P. Romby and I. Caldelari},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=34783400},

doi = {10.1111/mmi.14845},

isbn = {34783400},

year  = {2022},

date = {2022-01-01},

urldate = {2021-01-01},

journal = {Mol Microbiol},

abstract = {Staphylococcus aureus RsaG is a 3' untranslated region (3'UTR) derived sRNA from the conserved uhpT gene encoding a glucose-6-phosphate (G6P) transporter expressed in response to extracellular G6P. The transcript uhpT-RsaG undergoes degradation from 5' to 3' end by the action of the exoribonucleases J1/J2, which are blocked by a stable hairpin structure at the 5' end of RsaG, leading to its accumulation. RsaG together with uhpT are induced when bacteria are internalized into host cells or in presence of mucus-secreting cells. Using MS2 affinity purification coupled with RNA sequencing, several RNAs were identified as targets including mRNAs encoding the transcriptional factors Rex, CcpA, SarA and the sRNA RsaI. Our data suggested that RsaG contributes to the control of redox homeostasis and adjusts metabolism to changing environmental conditions. RsaG uses different molecular mechanisms to stabilize, to degrade, or to repress translation of its mRNA targets. While RsaG is conserved only in closely related species, the uhpT 3'UTR of the ape pathogen S. simiae harbors a sRNA, whose sequence is highly different, and which does not respond to G6P levels. Our results hypothesized that the 3'UTRs from UhpT transporter encoding mRNAs could have rapidly evolved to enable adaptation to host niches.},

note = {1365-2958 (Electronic) 

0950-382X (Linking) 

Journal Article},

keywords = {ROMBY, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

Fermer

Camara A., Lavanant A. C., Abe J., Desforges H. L., Alexandre Y. O., Girardi E., Igamberdieva Z., Asano K., Tanaka M., Hehlgans T., Pfeffer K., Pfeffer S., Mueller S. N., Stein J. V., Mueller C. G.

CD169(+) macrophages in lymph node and spleen critically depend on dual RANK and LTbetaR signaling Article de journal

Dans: Proc Natl Acad Sci U S A, vol. 119, no. 3, p. e2108540119, 2022, ISBN: 35031565, (1091-6490 (Electronic) 0027-8424 (Linking) Journal Article).

Résumé | Liens | BibTeX | Étiquettes: PFEFFER, Team-Mueller, Unité ARN

@article{nokey,

title = {CD169(+) macrophages in lymph node and spleen critically depend on dual RANK and LTbetaR signaling},

author = {A. Camara and A. C. Lavanant and J. Abe and H. L. Desforges and Y. O. Alexandre and E. Girardi and Z. Igamberdieva and K. Asano and M. Tanaka and T. Hehlgans and K. Pfeffer and S. Pfeffer and S. N. Mueller and J. V. Stein and C. G. Mueller},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=35031565},

isbn = {35031565},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {Proc Natl Acad Sci U S A},

volume = {119},

number = {3},

pages = {e2108540119},

abstract = {CD169(+) macrophages reside in lymph node (LN) and spleen and play an important role in the immune defense against pathogens. As resident macrophages, they are responsive to environmental cues to shape their tissue-specific identity. We have previously shown that LN CD169(+) macrophages require RANKL for formation of their niche and their differentiation. Here, we demonstrate that they are also dependent on direct lymphotoxin beta (LTbeta) receptor (R) signaling. In the absence or the reduced expression of either RANK or LTbetaR, their differentiation is perturbed, generating myeloid cells expressing SIGN-R1 in LNs. Conditions of combined haploinsufficiencies of RANK and LTbetaR revealed that both receptors contribute equally to LN CD169(+) macrophage differentiation. In the spleen, the Cd169-directed ablation of either receptor results in a selective loss of marginal metallophilic macrophages (MMMs). Using a RANKL reporter mouse, we identify splenic marginal zone stromal cells as a source of RANKL and demonstrate that it participates in MMM differentiation. The loss of MMMs had no effect on the splenic B cell compartments but compromised viral capture and the expansion of virus-specific CD8(+) T cells. Taken together, the data provide evidence that CD169(+) macrophage differentiation in LN and spleen requires dual signals from LTbetaR and RANK with implications for the immune response.},

note = {1091-6490 (Electronic) 

0027-8424 (Linking) 

Journal Article},

keywords = {PFEFFER, Team-Mueller, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

Fermer

Costa P. J. Da, Hamdane M., Buee L., Martin F.

Tau mRNA Metabolism in Neurodegenerative Diseases: A Tangle Journey Article de journal

Dans: Biomedicines, vol. 10, no. 2, p. 241, 2022.

Résumé | Liens | BibTeX | Étiquettes: ERIANI, mRNA metabolism, Neurodegenerative Diseases, tau protein, Translation, Unité ARN

Gilmer O., Mailler E., Paillart J. C., Mouhand A., Tisne C., Mak J., Smyth R. P., Marquet R., Vivet-Boudou V.

Structural maturation of the HIV-1 RNA 5' untranslated region by Pr55(Gag) and its maturation products Article de journal

Dans: RNA Biol, vol. 19, no. 1, p. 191-205, 2022, ISBN: 35067194, (1555-8584 (Electronic) 1547-6286 (Linking) Journal Article).

Résumé | Liens | BibTeX | Étiquettes: MARQUET, PAILLART, Unité ARN

Chan D. L., Rudinger-Thirion J., Frugier M., Riley L. G., Ho G., Kothur K., Mohammad S. S.

A case of QARS1 associated epileptic encephalopathy and review of epilepsy in aminoacyl-tRNA synthetase disorders Article de journal

Dans: Brain Dev, vol. 44, no. 2, p. 142-147, 2022, ISBN: 34774383, (1872-7131 (Electronic) 0387-7604 (Linking) Case Reports).

Résumé | Liens | BibTeX | Étiquettes: FRUGIER, Unité ARN

@article{nokey,

title = {A case of QARS1 associated epileptic encephalopathy and review of epilepsy in aminoacyl-tRNA synthetase disorders},

author = {D. L. Chan and J. Rudinger-Thirion and M. Frugier and L. G. Riley and G. Ho and K. Kothur and S. S. Mohammad},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=34774383},

doi = {10.1016/j.braindev.2021.10.009},

isbn = {34774383},

year  = {2022},

date = {2022-01-01},

journal = {Brain Dev},

volume = {44},

number = {2},

pages = {142-147},

abstract = {INTRODUCTION: Mutations in QARS1, which encodes human glutaminyl-tRNA synthetase, have been associated with epilepsy, developmental regression, progressive microcephaly and cerebral atrophy. Epilepsy caused by variants in QARS1 is usually drug-resistant and intractable. Childhood onset epilepsy is also reported in various aminoacyl-tRNA synthetase disorders. We describe a case with a milder neurological phenotype than previously reported with QARS1 variants and review the seizure associations with aminoacyl-tRNA synthetase disorders. CASE REPORT: The patient is a 4-year-old girl presenting at 6 weeks of age with orofacial dyskinesia and hand stereotypies. She developed focal seizures at 7 months of age. Serial electroencephalograms showed shifting focality. Her seizures were controlled after introduction of carbamazepine. Progress MRI showed very mild cortical volume loss without myelination abnormalities or cerebellar atrophy. She was found to have novel compound heterozygous variants in QARS1 (NM_005051.2): c.[1132C > T];[1574G > A], p.[(Arg378Cys)];[(Arg525Gln)] originally classified as "variants of uncertain significance" and later upgraded to "likely pathogenic" based on functional testing and updated variant database review. Functional testing showed reduced solubility of the corresponding QARS1 mutants in vitro, but only mild two-fold loss in catalytic efficiency with the c.1132C > T variant and no noted change in tRNA(Gln) aminoacylation with the c.1574G > A variant. CONCLUSION: We describe two QARS1 variants associated with overall conserved tRNA aminoacylation activity but characterized by significantly reduced QARS protein solubility, resulting in a milder clinical phenotype. 86% of previous patients reported with QARS1 had epilepsy and 79% were pharmaco-resistant. We also summarise literature regarding epilepsy in aminoacyl-tRNA synthetase disorders, which is also often early onset, severe and drug-refractory.},

note = {1872-7131 (Electronic) 

0387-7604 (Linking) 

Case Reports},

keywords = {FRUGIER, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

Fermer

Andre A. C., Laborde M., Marteyn B. S.

The battle for oxygen during bacterial and fungal infections Article de journal

Dans: Trends Microbiol, vol. 30, iss. 7, p. 643-653, 2022, ISBN: 35131160, (1878-4380 (Electronic) 0966-842X (Linking) Journal Article Review).

Résumé | Liens | BibTeX | Étiquettes: MARTEYN, Unité ARN

@article{nokey,

title = {The battle for oxygen during bacterial and fungal infections},

author = {A. C. Andre and M. Laborde and B. S. Marteyn},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=35131160},

doi = {10.1016/j.tim.2022.01.002},

isbn = {35131160},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {Trends Microbiol},

volume = {30},

issue = {7},

pages = {643-653},

abstract = {Bacterial and fungal pathogens face various microenvironmental conditions during infection. In addition to acidosis, nutrient consumption, and hypercapnia, pathogen infections are associated with hypoxia, which is induced by bacterial and fungal respiration during the formation of foci of infection or biofilms. Consequently, the in vivo interaction between host immune cells and pathogens is anticipated to occur mainly under low-oxygen conditions. Various infectious disease models have reported that pathogens benefit from hypoxia, which dampens the oxygen-dependent antimicrobial activities of macrophages and neutrophils, such as the production of reactive oxygen species (ROS). Due to their dual respiration capacity (aerobic and anaerobic) or phenotypical adaptation (e.g., dormancy), pathogens have the capacity to survive and disseminate in the absence of oxygen. In addition, hypoxia modulates various mechanisms of pathogen virulence, promoting the dissemination of pathogens. Further investigations are still required to evaluate the relative importance of oxygen on the capacity of pathogens to invade and colonize host organs and to better understand alternative strategies developed by immune cells to circumvent pathogen dissemination in the absence of oxygen. Addressing this important and fundamental question in various models of infection may direct the development of innovative therapeutic strategies.},

note = {1878-4380 (Electronic) 

0966-842X (Linking) 

Journal Article 

Review},

keywords = {MARTEYN, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

Fermer

Bernacchi S.

Visualization of Retroviral Gag-Genomic RNA Cellular Interactions Leading to Genome Encapsidation and Viral Assembly: An Overview Article de journal

Dans: Viruses, vol. 14, no. 2, 2022, ISBN: 35215917, (1999-4915 (Electronic) 1999-4915 (Linking) Journal Article Review Research Support, Non-U.S. Gov't).

Résumé | Liens | BibTeX | Étiquettes: MARQUET, PAILLART, Unité ARN

@article{nokey,

title = {Visualization of Retroviral Gag-Genomic RNA Cellular Interactions Leading to Genome Encapsidation and Viral Assembly: An Overview},

author = {S. Bernacchi},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=35215917},

doi = {10.3390/v14020324},

isbn = {35215917},

year  = {2022},

date = {2022-01-01},

journal = {Viruses},

volume = {14},

number = {2},

abstract = {Retroviruses must selectively recognize their unspliced RNA genome (gRNA) among abundant cellular and spliced viral RNAs to assemble into newly formed viral particles. Retroviral gRNA packaging is governed by Gag precursors that also orchestrate all the aspects of viral assembly. Retroviral life cycles, and especially the HIV-1 one, have been previously extensively analyzed by several methods, most of them based on molecular biology and biochemistry approaches. Despite these efforts, the spatio-temporal mechanisms leading to gRNA packaging and viral assembly are only partially understood. Nevertheless, in these last decades, progress in novel bioimaging microscopic approaches (as FFS, FRAP, TIRF, and wide-field microscopy) have allowed for the tracking of retroviral Gag and gRNA in living cells, thus providing important insights at high spatial and temporal resolution of the events regulating the late phases of the retroviral life cycle. Here, the implementation of these recent bioimaging tools based on highly performing strategies to label fluorescent macromolecules is described. This report also summarizes recent gains in the current understanding of the mechanisms employed by retroviral Gag polyproteins to regulate molecular mechanisms enabling gRNA packaging and the formation of retroviral particles, highlighting variations and similarities among the different retroviruses.},

note = {1999-4915 (Electronic) 

1999-4915 (Linking) 

Journal Article 

Review 

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

keywords = {MARQUET, PAILLART, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

Fermer

Sosnowski P, Tidu A, Eriani G, Westhof E, Martin F

Dans: Rna, vol. 28, iss. 5, p. 729-741, 2022, ISBN: 35236777, (1469-9001 (Electronic) 1355-8382 (Linking) Journal Article).

Résumé | Liens | BibTeX | Étiquettes: ERIANI, MARTIN, Unité ARN, WESTHOF

Brugier A., Hafirrassou M. L., Pourcelot M., Baldaccini M., Kril V., Couture L., Kummerer B. M., Gallois-Montbrun S., Bonnet-Madin L., Vidalain P. O., Delaugerre C., Pfeffer S., Meertens L., Amara A.

RACK1 Associates with RNA-Binding Proteins Vigilin and SERBP1 to Facilitate Dengue Virus Replication Article de journal

Dans: J Virol, vol. 96, iss. 7, p. e0196221, 2022, ISBN: 35266803, (1098-5514 (Electronic) 0022-538X (Linking) Journal Article).

Résumé | Liens | BibTeX | Étiquettes: PFEFFER, Unité ARN

@article{nokey,

title = {RACK1 Associates with RNA-Binding Proteins Vigilin and SERBP1 to Facilitate Dengue Virus Replication},

author = {A. Brugier and M. L. Hafirrassou and M. Pourcelot and M. Baldaccini and V. Kril and L. Couture and B. M. Kummerer and S. Gallois-Montbrun and L. Bonnet-Madin and P. O. Vidalain and C. Delaugerre and S. Pfeffer and L. Meertens and A. Amara},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=35266803},

doi = {10.1128/jvi.01962-21},

isbn = {35266803},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {J Virol},

volume = {96},

issue = {7},

pages = {e0196221},

abstract = {Dengue virus (DENV) is a mosquito-borne flavivirus responsible for dengue disease, a major human health concern for which no effective treatment is available. DENV relies heavily on the host cellular machinery for productive infection. Here, we show that the scaffold protein RACK1, which is part of the DENV replication complex, mediates infection by binding to the 40S ribosomal subunit. Mass spectrometry analysis of RACK1 partners coupled to an RNA interference screen-identified Vigilin and SERBP1 as DENV host-dependency factors. Both are RNA-binding proteins that interact with the DENV genome. Genetic ablation of Vigilin or SERBP1 rendered cells poorly susceptible to DENV, as well as related flaviviruses, by hampering the translation and replication steps. Finally, we established that a Vigilin or SERBP1 mutant lacking RACK1 binding but still interacting with the viral RNA is unable to mediate DENV infection. We propose that RACK1 recruits Vigilin and SERBP1, linking the DENV genome to the translation machinery for efficient infection. IMPORTANCE We recently identified the scaffolding RACK1 protein as an important host-dependency factor for dengue virus (DENV), a positive-stranded RNA virus responsible for the most prevalent mosquito-borne viral disease worldwide. Here, we have performed the first RACK1 interactome in human cells and identified Vigilin and SERBP1 as DENV host-dependency factors. Both are RNA-binding proteins that interact with the DENV RNA to regulate viral replication. Importantly, Vigilin and SERBP1 interact with RACK1 and the DENV viral RNA (vRNA) to mediate viral replication. Overall, our results suggest that RACK1 acts as a binding platform at the surface of the 40S ribosomal subunit to recruit Vigilin and SERBP1, which may therefore function as linkers between the viral RNA and the translation machinery to facilitate infection.},

note = {1098-5514 (Electronic) 

0022-538X (Linking) 

Journal Article},

keywords = {PFEFFER, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

Fermer

Westhof E, Thornlow B, Chan P P, Lowe T M

Eukaryotic tRNA sequences present conserved and amino acid-specific structural signatures Article de journal

Dans: Nucleic Acids Res, vol. 50, iss. 7, p. 4100-4112, 2022, ISBN: 35380696, (1362-4962 (Electronic) 0305-1048 (Linking) Journal Article).

Résumé | Liens | BibTeX | Étiquettes: Unité ARN, WESTHOF

@article{nokey,

title = {Eukaryotic tRNA sequences present conserved and amino acid-specific structural signatures},

author = {E Westhof and B Thornlow and P P Chan and T M Lowe},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=35380696},

doi = {10.1093/nar/gkac222},

isbn = {35380696},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {Nucleic Acids Res},

volume = {50},

issue = {7},

pages = {4100-4112},

abstract = {Metazoan organisms have many tRNA genes responsible for decoding amino acids. The set of all tRNA genes can be grouped in sets of common amino acids and isoacceptor tRNAs that are aminoacylated by corresponding aminoacyl-tRNA synthetases. Analysis of tRNA alignments shows that, despite the high number of tRNA genes, specific tRNA sequence motifs are highly conserved across multicellular eukaryotes. The conservation often extends throughout the isoacceptors and isodecoders with, in some cases, two sets of conserved isodecoders. This study is focused on non-Watson-Crick base pairs in the helical stems, especially GoU pairs. Each of the four helical stems may contain one or more conserved GoU pairs. Some are amino acid specific and could represent identity elements for the cognate aminoacyl tRNA synthetases. Other GoU pairs are found in more than a single amino acid and could be critical for native folding of the tRNAs. Interestingly, some GoU pairs are anticodon-specific, and others are found in phylogenetically-specific clades. Although the distribution of conservation likely reflects a balance between accommodating isotype-specific functions as well as those shared by all tRNAs essential for ribosomal translation, such conservations may indicate the existence of specialized tRNAs for specific translation targets, cellular conditions, or alternative functions.},

note = {1362-4962 (Electronic) 

0305-1048 (Linking) 

Journal Article},

keywords = {Unité ARN, WESTHOF},

pubstate = {published},

tppubtype = {article}

}

Fermer

Eriani G., Martin F.

Viral and cellular translation during SARS-CoV-2 infection Article de journal

Dans: FEBS Open Bio, vol. 12, iss. 9, p. 1584-1601, 2022, ISBN: 35429230, (2211-5463 (Electronic) 2211-5463 (Linking) Journal Article Review).

Résumé | Liens | BibTeX | Étiquettes: ERIANI, Unité ARN

Geraci I., Autour A., Pietruschka G., Shiian A., Borisova M., Mayer C., Ryckelynck M., Mayer G.

Fluorogenic RNA-Based Biosensor to Sense the Glycolytic Flux in Mammalian Cells Article de journal

Dans: ACS Chem Biol, vol. 17, iss. 5, p. 1164-1173, 2022, ISBN: 35427113, (1554-8937 (Electronic) 1554-8929 (Linking) Journal Article).

Résumé | Liens | BibTeX | Étiquettes: Labex, RYCKELYNCK, Unité ARN

Fam K. T., Pelletier R., Bouhedda F., Ryckelynck M., Collot M., Klymchenko A. S.

Rational Design of Self-Quenched Rhodamine Dimers as Fluorogenic Aptamer Probes for Live-Cell RNA Imaging Article de journal

Dans: Anal Chem, vol. 94, iss. 18, p. 6657-6664, 2022, ISBN: 35486532, (1520-6882 (Electronic) 0003-2700 (Linking) Journal Article).

Résumé | Liens | BibTeX | Étiquettes: Labex, RYCKELYNCK, Unité ARN

@article{nokey,

title = {Rational Design of Self-Quenched Rhodamine Dimers as Fluorogenic Aptamer Probes for Live-Cell RNA Imaging},

author = {K. T. Fam and R. Pelletier and F. Bouhedda and M. Ryckelynck and M. Collot and A. S. Klymchenko},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=35486532},

doi = {10.1021/acs.analchem.1c04556},

isbn = {35486532},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {Anal Chem},

volume = {94},

issue = {18},

pages = {6657-6664},

abstract = {With the growing interest in the understanding of the importance of RNAs in health and disease, detection of RNAs in living cells is of high importance. Fluorogenic dyes that light up specifically selected RNA aptamers constitute an attractive direction in the design of RNA imaging probes. In this work, based on our recently proposed concept of a fluorogenic dimer, we aim to develop a robust molecular tool for intracellular RNA imaging. We rationally designed a fluorogenic self-quenched dimer (orange Gemini, o-Gemini) based on rhodamine and evaluated its capacity to light up its cognate aptamer o-Coral in solution and live cells. We found that the removal of biotin from the dimer slightly improved the fluorogenic response without losing the affinity to the cognate aptamer (o-Coral). On the other hand, replacing sulforhodamine with a carboxyrhodamine produced drastic improvement of the affinity and the turn-on response to o-Coral and, thus, a better limit of detection. In live cells expressing o-Coral-tagged RNAs, the carboxyrhodamine analogue of o-Gemini without a biotin unit displayed a higher signal as well as faster internalization into the cells. We suppose that less hydrophilic carboxyrhodamine compared to sulforhodamine can more readily penetrate through the cell plasma membrane and, together with its higher affinity to o-Coral, provide the observed improvement in the imaging experiments. The promiscuity of the o-Coral RNA aptamer to the fluorogenic dimer allowed us to tune a fluorogen chemical structure and thus drastically improve the fluorescence response of the probe to o-Coral-tagged RNAs.},

note = {1520-6882 (Electronic) 

0003-2700 (Linking) 

Journal Article},

keywords = {Labex, RYCKELYNCK, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

Fermer

Geersens E., Vuilleumier S., Ryckelynck M.

Growth-Associated Droplet Shrinkage for Bacterial Quantification, Growth Monitoring, and Separation by Ultrahigh-Throughput Microfluidics Article de journal

Dans: ACS Omega, vol. 7, no. 14, p. 12039-12047, 2022, ISBN: 35449964, (2470-1343 (Electronic) 2470-1343 (Linking) Journal Article).

Résumé | Liens | BibTeX | Étiquettes: Labex, RYCKELYNCK, Unité ARN

Ponce J. R. Jaramillo, Kapps D., Paulus C., Chicher J., Frugier M.

Discovery of two distinct aminoacyl-tRNA synthetase complexes anchored to the Plasmodium surface tRNA import protein Article de journal

Dans: J Biol Chem, vol. 298, iss. 6, p. 101987, 2022, ISBN: 35487244, (1083-351X (Electronic) 0021-9258 (Linking) Journal Article).

Résumé | Liens | BibTeX | Étiquettes: FRUGIER, Labex, PPSE, Unité ARN

@article{nokey,

title = {Discovery of two distinct aminoacyl-tRNA synthetase complexes anchored to the Plasmodium surface tRNA import protein},

author = {J. R. Jaramillo Ponce and D. Kapps and C. Paulus and J. Chicher and M. Frugier},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=35487244},

doi = {0.1016/j.jbc.2022.101987},

isbn = {35487244},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {J Biol Chem},

volume = {298},

issue = {6},

pages = {101987},

abstract = {Aminoacyl-tRNA synthetases (aaRSs) attach amino acids to their cognate transfer RNAs. In eukaryotes, a subset of cytosolic aaRSs is organized into a multi-synthetase complex (MSC), along with specialized scaffolding proteins referred to as aaRS-interacting multifunctional proteins (AIMPs). In Plasmodium, the causative agent of malaria, the tRNA import protein (tRip), is a membrane protein that has been shown to participate in tRNA trafficking; here, we show that tRip also functions as an AIMP. We identified three aaRSs, namely the glutamyl- (ERS), glutaminyl- (QRS), and methionyl- (MRS) tRNA synthetases, which were specifically co-immunoprecipitated with tRip in P. berghei blood stage parasites. All four proteins contain an N-terminal GST-like domain that was demonstrated to be involved in MSC assembly. In contrast to previous studies, further dissection of GST-like interactions identified two exclusive heterotrimeric complexes: the Q-complex (tRip:ERS:QRS) and the M-complex (tRip:ERS:MRS). Gel filtration and light scattering suggest a 2:2:2 stoichiometry for both complexes but with distinct biophysical properties, and mutational analysis further revealed that the GST-like domains of QRS and MRS use different strategies to bind ERS. Taken together our results demonstrate that neither the singular homodimerization of tRip, nor its localization in the parasite plasma membrane prevents the formation of MSCs in Plasmodium. Besides, the extracellular localization of the tRNA-binding module of tRip is compensated by the presence of additional tRNA-binding modules fused to MRS and QRS, providing each MSC with two spatially distinct functions: aminoacylation of intraparasitic tRNAs and binding of extracellular tRNAs. This unique host-pathogen interaction is discussed.},

note = {1083-351X (Electronic) 

0021-9258 (Linking) 

Journal Article},

keywords = {FRUGIER, Labex, PPSE, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

Fermer

Laveilhe A., Fochesato S., Lalaouna D., Heulin T., Achouak W.

Phytobeneficial traits of rhizobacteria under the control of multiple molecular dialogues Article de journal

Dans: Microb Biotechnol, vol. 15, iss. 7, p. 2083-2096, 2022, ISBN: 35502577, (1751-7915 (Electronic) 1751-7915 (Linking) Journal Article).

Résumé | Liens | BibTeX | Étiquettes: ROMBY, Unité ARN

@article{nokey,

title = {Phytobeneficial traits of rhizobacteria under the control of multiple molecular dialogues},

author = {A. Laveilhe and S. Fochesato and D. Lalaouna and T. Heulin and W. Achouak},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=35502577},

doi = {10.1111/1751-7915.14023},

isbn = {35502577},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {Microb Biotechnol},

volume = {15},

issue = {7},

pages = {2083-2096},

abstract = {Pseudomonads play crucial roles in plant growth promotion and control of plant diseases. However, under natural conditions, other microorganisms competing for the same nutrient resources in the rhizosphere may exert negative control over their phytobeneficial characteristics. We assessed the expression of phytobeneficial genes involved in biocontrol, biostimulation and iron regulation such as, phlD, hcnA, acdS, and iron-small regulatory RNAs prrF1 and prrF2 in Pseudomonas brassicacearum co-cultivated with three phytopathogenic fungi, and two rhizobacteria in the presence or absence of Brassica napus, and in relation to iron availability. We found that the antifungal activity of P. brassicacearum depends mostly on the production of DAPG and not on HCN whose production is suppressed by fungi. We have also shown that the two-competing bacterial strains modulate the plant growth promotion activity of P. brassicacearum by modifying the expression of phlD, hcnA and acdS according to iron availability. Overall, it allows us to better understand the complexity of the multiple molecular dialogues that take place underground between microorganisms and between plants and its rhizosphere microbiota and to show that synergy in favour of phytobeneficial gene expression may exist between different bacterial species.},

note = {1751-7915 (Electronic) 

1751-7915 (Linking) 

Journal Article},

keywords = {ROMBY, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

Fermer

Bereiter R., Renard E., Breuker K., Kreutz C., Ennifar E., Micura R.

1-Deazaguanosine-Modified RNA: The Missing Piece for Functional RNA Atomic Mutagenesis Article de journal

Dans: J Am Chem Soc, vol. 144, iss. 23, p. 10344-10352, 2022, ISBN: 35666572, (1520-5126 (Electronic) 0002-7863 (Linking) Journal Article).

Résumé | Liens | BibTeX | Étiquettes: ENNIFAR, Unité ARN

Baudrey Stéphanie, Cubi Roger, Ryckelynck Michael

Droplet-Based Microfluidic Chip Design, Fabrication, and Use for Ultrahigh-Throughput DNA Analysis and Quantification Article de journal

Dans: Adv Exp Med Biol, vol. 1379, p. 445–460, 2022, ISSN: 0065-2598.

Résumé | Liens | BibTeX | Étiquettes: RYCKELYNCK, Unité ARN

@article{pmid35761003,

title = {Droplet-Based Microfluidic Chip Design, Fabrication, and Use for Ultrahigh-Throughput DNA Analysis and Quantification},

author = {Stéphanie Baudrey and Roger Cubi and Michael Ryckelynck},

doi = {10.1007/978-3-031-04039-9_18},

issn = {0065-2598},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {Adv Exp Med Biol},

volume = {1379},

pages = {445--460},

abstract = {DNA is widely used as a biomarker of contamination, infection, or disease, which has stimulated the development of a wide palette of detection and quantification methods. Even though several analytical approaches based on isothermal amplification have been proposed, DNA is still mainly detected and quantified by quantitative PCR (qPCR). However, for some analyses (e.g., in cancer research) qPCR may suffer from limitations arising from competitions between highly similar template DNAs, the presence of inhibitors, or suboptimal primer design. Nevertheless, digitalizing the analysis (i.e., individualizing DNA molecules into compartments prior to amplifying them in situ) allows to address most of these issues. By its capacity to generate and manipulate millions of highly similar picoliter volume water-in-oil droplets, microfluidics offers both the required miniaturization and parallelization capacity, and led to the introduction of digital droplet PCR (ddPCR). This chapter aims at introducing the reader to the basic principles behind ddPCR while also providing the key guidelines to fabricate, set up, and use his/her own ddPCR platform. We further provide procedures to detect and quantify DNA either purified in solution or directly from individualized cells. This approach not only gives access to DNA absolute concentration with unrivaled sensitivity, but it may also be the starting point of more complex in vitro analytical pipelines discussed at the end of the chapter.},

keywords = {RYCKELYNCK, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

Fermer

Charbonnier Mathilde, González-Espinoza Gabriela, Kehl-Fie Thomas E, Lalaouna David

Battle for Metals: Regulatory RNAs at the Front Line Article de journal

Dans: Front Cell Infect Microbiol, vol. 12, p. 952948, 2022, ISSN: 2235-2988.

Résumé | Liens | BibTeX | Étiquettes: ROMBY, Unité ARN

@article{pmid35865816,

title = {Battle for Metals: Regulatory RNAs at the Front Line},

author = {Mathilde Charbonnier and Gabriela González-Espinoza and Thomas E Kehl-Fie and David Lalaouna},

doi = {10.3389/fcimb.2022.952948},

issn = {2235-2988},

year  = {2022},

date = {2022-01-01},

urldate = {2022-01-01},

journal = {Front Cell Infect Microbiol},

volume = {12},

pages = {952948},

abstract = {Metal such as iron, zinc, manganese, and nickel are essential elements for bacteria. These nutrients are required in crucial structural and catalytic roles in biological processes, including precursor biosynthesis, DNA replication, transcription, respiration, and oxidative stress responses. While essential, in excess these nutrients can also be toxic. The immune system leverages both of these facets, to limit bacterial proliferation and combat invaders. Metal binding immune proteins reduce the bioavailability of metals at the infection sites starving intruders, while immune cells intoxicate pathogens by providing metals in excess leading to enzyme mismetallation and/or reactive oxygen species generation. In this dynamic metal environment, maintaining metal homeostasis is a critical process that must be precisely coordinated. To achieve this, bacteria utilize diverse metal uptake and efflux systems controlled by metalloregulatory proteins. Recently, small regulatory RNAs (sRNAs) have been revealed to be critical post-transcriptional regulators, working in conjunction with transcription factors to promote rapid adaptation and to fine-tune bacterial adaptation to metal abundance. In this mini review, we discuss the expanding role for sRNAs in iron homeostasis, but also in orchestrating adaptation to the availability of other metals like manganese and nickel. Furthermore, we describe the sRNA-mediated interdependency between metal homeostasis and oxidative stress responses, and how regulatory networks controlled by sRNAs contribute to survival and virulence.},

keywords = {ROMBY, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

Fermer

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Résumé | Liens | BibTeX | Étiquettes: Drug discovery RNA structure & dynamics RNA targeting SARS-CoV2, Unité ARN, WESTHOF

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Liens | BibTeX | Étiquettes: PFEFFER, Unité ARN

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