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}
}
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}
}
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
@article{pmid36322050,
title = {The Toll pathway mediates Drosophila resilience to Aspergillus mycotoxins through specific Bomanins},
author = {Rui Xu and Yanyan Lou and Antonin Tidu and Philippe Bulet and Thorsten Heinekamp and Franck Martin and Axel Brakhage and Zi Li and Samuel Liégeois and Dominique Ferrandon},
url = {https://pubmed.ncbi.nlm.nih.gov/36322050/},
doi = {10.15252/embr.202256036},
issn = {1469-3178},
year = {2022},
date = {2022-11-01},
urldate = {2022-11-01},
journal = {EMBO Rep},
pages = {e56036},
abstract = {Host defense against infections encompasses both resistance, which targets microorganisms for neutralization or elimination, and resilience/disease tolerance, which allows the host to withstand/tolerate pathogens and repair damages. In Drosophila, the Toll signaling pathway is thought to mediate resistance against fungal infections by regulating the secretion of antimicrobial peptides, potentially including Bomanins. We find that Aspergillus fumigatus kills Drosophila Toll pathway mutants without invasion because its dissemination is blocked by melanization, suggesting a role for Toll in host defense distinct from resistance. We report that mutants affecting the Toll pathway or the 55C Bomanin locus are susceptible to the injection of two Aspergillus mycotoxins, restrictocin and verruculogen. The vulnerability of 55C deletion mutants to these mycotoxins is rescued by the overexpression of Bomanins specific to each challenge. Mechanistically, flies in which BomS6 is expressed in the nervous system exhibit an enhanced recovery from the tremors induced by injected verruculogen and display improved survival. Thus, innate immunity also protects the host against the action of microbial toxins through secreted peptides and thereby increases its resilience to infection.},
keywords = {ERIANI, ferrandon, M3i, MARTIN, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
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
@article{pmid36353712b,
title = { 30S Ribosomal Subunit Purification and Its Biochemical and Cryo-EM Analysis},
author = {Margarita Belinite and Iskander Khusainov and Stefano Marzi},
doi = {10.21769/BioProtoc.4532},
issn = {2331-8325},
year = {2022},
date = {2022-10-01},
urldate = {2022-10-01},
journal = {Bio Protoc},
volume = {12},
number = {20},
abstract = {The ribosome is a complex cellular machinery whose solved structure allowed for an incredible leap in structural biology research. Different ions bind to the ribosome, stabilizing inter-subunit interfaces and structurally linking rRNAs, proteins, and ligands. Besides cations such as K and Mg , polyamines are known to stabilize the folding of RNA and overall structure. The bacterial ribosome is composed of a small (30S) subunit containing the decoding center and a large (50S) subunit devoted to peptide bond formation. We have previously shown that the small ribosomal subunit of is sensitive to changes in ionic conditions and polyamines concentration. In particular, its decoding center, where mRNA codons and tRNA anticodons interact, is prone to structural deformations in the absence of spermidine. Here, we report a detailed protocol for the purification of the intact and functional 30S, achieved through specific ionic conditions and the addition of spermidine. Using this protocol, we obtained the cryo-electron microscopy (cryo-EM) structure of the 30S-mRNA complex from at 3.6 Å resolution. The 30S-mRNA complex formation was verified by a toeprinting assay. In this article, we also include a description of toeprinting and cryo-EM protocols. The described protocols can be further used to study the process of translation regulation. Graphical abstract.},
keywords = {ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Bonaventure Boris, Rebendenne Antoine, Valadão Ana Luiza Chaves, Arnaud-Arnould Mary, Gracias Ségolène, de Gracia Francisco Garcia, McKellar Joe, Labaronne Emmanuel, Tauziet Marine, Vivet-Boudou Valérie, Bernard Eric, Briant Laurence, Gros Nathalie, Djilli Wassila, Courgnaud Valérie, Parrinello Hugues, Rialle Stéphanie, Blaise Mickaël, Lacroix Laurent, Lavigne Marc, Paillart Jean-Christophe, Ricci Emiliano P, Schulz Reiner, Jouvenet Nolwenn, Moncorgé Olivier, Goujon Caroline
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 = {Boris Bonaventure and Antoine Rebendenne and Ana Luiza Chaves Valadão and Mary Arnaud-Arnould and Ségolène Gracias and Francisco Garcia de Gracia and Joe McKellar and Emmanuel Labaronne and Marine Tauziet and Valérie Vivet-Boudou and Eric Bernard and Laurence Briant and Nathalie Gros and Wassila Djilli and Valérie Courgnaud and Hugues Parrinello and Stéphanie Rialle and Mickaël Blaise and Laurent Lacroix and Marc Lavigne and Jean-Christophe Paillart and Emiliano P Ricci and Reiner Schulz and Nolwenn Jouvenet and Olivier Moncorgé and Caroline 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}
}
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}
}
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
@article{pmid36139107,
title = {eIF3 Interacts with Selenoprotein mRNAs},
author = {Hassan Hayek and Gilbert Eriani and Christine Allmang},
doi = {10.3390/biom12091268},
issn = {2218-273X},
year = {2022},
date = {2022-09-01},
urldate = {2022-09-01},
journal = {Biomolecules},
volume = {12},
number = {9},
abstract = {The synthesis of selenoproteins requires the co-translational recoding of an in-frame UGASec codon. Interactions between the Selenocysteine Insertion Sequence (SECIS) and the SECIS binding protein 2 (SBP2) in the 3'untranslated region (3'UTR) of selenoprotein mRNAs enable the recruitment of the selenocysteine insertion machinery. Several selenoprotein mRNAs undergo unusual cap hypermethylation and are not recognized by the translation initiation factor 4E (eIF4E) but nevertheless translated. The human eukaryotic translation initiation factor 3 (eIF3), composed of 13 subunits (a-m), can selectively recruit several cellular mRNAs and plays roles in specialized translation initiation. Here, we analyzed the ability of eIF3 to interact with selenoprotein mRNAs. By combining ribonucleoprotein immunoprecipitation (RNP IP) in vivo and in vitro with cross-linking experiments, we found interactions between eIF3 and a subgroup of selenoprotein mRNAs. We showed that eIF3 preferentially interacts with hypermethylated capped selenoprotein mRNAs rather than mG-capped mRNAs. We identified direct contacts between GPx1 mRNA and eIF3 c, d, and e subunits and showed the existence of common interaction patterns for all hypermethylated capped selenoprotein mRNAs. Differential interactions of eIF3 with selenoprotein mRNAs may trigger specific translation pathways independent of eIF4E. eIF3 could represent a new player in the translation regulation and hierarchy of selenoprotein expression.},
keywords = {ERIANI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
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
@article{pmid36108089,
title = {A tRNA-derived fragment present in E. coli OMVs regulates host cell gene expression and proliferation},
author = {Idrissa Diallo and Jeffrey Ho and Marine Lambert and Abderrahim Benmoussa and Zeinab Husseini and David Lalaouna and Eric Massé and Patrick Provost},
doi = {10.1371/journal.ppat.1010827},
issn = {1553-7374},
year = {2022},
date = {2022-09-01},
urldate = {2022-09-01},
journal = {PLoS Pathog},
volume = {18},
number = {9},
pages = {e1010827},
abstract = {RNA-sequencing has led to a spectacular increase in the repertoire of bacterial sRNAs and improved our understanding of their biological functions. Bacterial sRNAs have also been found in outer membrane vesicles (OMVs), raising questions about their potential involvement in bacteria-host relationship, but few studies have documented this issue. Recent RNA-Sequencing analyses of bacterial RNA unveiled the existence of abundant very small RNAs (vsRNAs) shorter than 16 nt. These especially include tRNA fragments (tRFs) that are selectively loaded in OMVs and are predicted to target host mRNAs. Here, in Escherichia coli (E. coli), we report the existence of an abundant vsRNA, Ile-tRF-5X, which is selectively modulated by environmental stress, while remaining unaffected by inhibition of transcription or translation. Ile-tRF-5X is released through OMVs and can be transferred to human HCT116 cells, where it promoted MAP3K4 expression. Our findings provide a novel perspective and paradigm on the existing symbiosis between bacteria and human cells.},
keywords = {ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
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}
}
Jakob Celia, Paul-Stansilaus Rithu, Schwemmle Martin, Marquet Roland, Bolte Hardin
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 = {Celia Jakob and Rithu Paul-Stansilaus and Martin Schwemmle and Roland Marquet and Hardin 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}
}
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}
}
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}
}
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
@article{pmid35732654,
title = {RNase III CLASH in MRSA uncovers sRNA regulatory networks coupling metabolism to toxin expression},
author = {Stuart W McKellar and Ivayla Ivanova and Pedro Arede and Rachel L Zapf and Noémie Mercier and Liang-Cui Chu and Daniel G Mediati and Amy C Pickering and Paul Briaud and Robert G Foster and Grzegorz Kudla and J Ross Fitzgerald and Isabelle Caldelari and Ronan K Carroll and Jai J Tree and Sander Granneman},
doi = {10.1038/s41467-022-31173-y},
issn = {2041-1723},
year = {2022},
date = {2022-06-01},
urldate = {2022-06-01},
journal = {Nat Commun},
volume = {13},
number = {1},
pages = {3560},
abstract = {Methicillin-resistant Staphylococcus aureus (MRSA) is a bacterial pathogen responsible for significant human morbidity and mortality. Post-transcriptional regulation by small RNAs (sRNAs) has emerged as an important mechanism for controlling virulence. However, the functionality of the majority of sRNAs during infection is unknown. To address this, we performed UV cross-linking, ligation, and sequencing of hybrids (CLASH) in MRSA to identify sRNA-RNA interactions under conditions that mimic the host environment. Using a double-stranded endoribonuclease III as bait, we uncovered hundreds of novel sRNA-RNA pairs. Strikingly, our results suggest that the production of small membrane-permeabilizing toxins is under extensive sRNA-mediated regulation and that their expression is intimately connected to metabolism. Additionally, we also uncover an sRNA sponging interaction between RsaE and RsaI. Taken together, we present a comprehensive analysis of sRNA-target interactions in MRSA and provide details on how these contribute to the control of virulence in response to changes in metabolism.},
keywords = {ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
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
@article{pmid35710145b,
title = {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},
author = {Martine L Roovers and Geoffray Labar and Philippe Wolff and Andre Feller and Dany Van Elder and Romuald Soin and Cyril Gueydan and Veronique Kruys and Louis Droogmans},
doi = {10.1261/rna.079131.122},
issn = {1469-9001},
year = {2022},
date = {2022-06-01},
urldate = {2022-06-01},
journal = {RNA},
volume = {28},
issue = {9},
pages = {1185-1196},
abstract = {A previous bioinformatic analysis predicted that the ysgA open reading frame of Bacillus subtilis encodes an RNA methyltransferase of the SPOUT superfamily. Here we show that YsgA is the 2'-O-methyltransferase that targets position G2553 (Escherichia coli numbering) of the A-loop of 23S rRNA. This was shown by a combination of biochemical and mass spectrometry approaches using both rRNA extracted from B. subtilis wild-type or ΔysgA cells and in vitro synthesized rRNA. When the target G2553 is mutated, YsgA is able to methylate the ribose of adenosine. However it cannot methylate cytidine nor uridine. The enzyme modifies free 23S rRNA but not the fully assembled ribosome nor the 50S subunit, suggesting that the modification occurs early during ribosome biogenesis. Nevertheless ribosome subunits assembly is unaffected in a B. subtilis ΔysgA mutant strain. The crystal structure of the recombinant YsgA protein, combined with mutagenesis data, outlined in this article highlights a typical SPOUT fold preceded by an L7Ae/L30 (eL8/eL30 in a new nomenclature) N-terminal domain.},
keywords = {ARN-MS, ENNIFAR, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
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}
}
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}
}
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}
}
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}
}
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
@article{nokey,
title = {Tau mRNA Metabolism in Neurodegenerative Diseases: A Tangle Journey},
author = {P. J. Da Costa and M. Hamdane and L. Buee and F. Martin},
url = {https://www.mdpi.com/2227-9059/10/2/241/htm},
doi = {10.3390/biomedicines10020241},
year = {2022},
date = {2022-01-01},
journal = {Biomedicines},
volume = {10},
number = {2},
pages = {241},
abstract = {Tau proteins are known to be mainly involved in regulation of microtubule dynamics. Besides this function, which is critical for axonal transport and signal transduction, tau proteins also have other roles in neurons. Moreover, tau proteins are turned into aggregates and consequently trigger many neurodegenerative diseases termed tauopathies, of which Alzheimerメs disease (AD) is the figurehead. Such pathological aggregation processes are critical for the onset of these diseases. Among the various causes of tau protein pathogenicity, abnormal tau mRNA metabolism, expression and dysregulation of tau post-translational modifications are critical steps. Moreover, the relevance of tau function to general mRNA metabolism has been highlighted recently in tauopathies. In this review, we mainly focus on how mRNA metabolism impacts the onset and development of tauopathies. Thus, we intend to portray how mRNA metabolism of, or mediated by, tau is associated with neurodegenerative diseases.},
keywords = {ERIANI, mRNA metabolism, Neurodegenerative Diseases, tau protein, Translation, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
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
@article{nokey,
title = {Structural maturation of the HIV-1 RNA 5' untranslated region by Pr55(Gag) and its maturation products},
author = {O. Gilmer and E. Mailler and J. C. Paillart and A. Mouhand and C. Tisne and J. Mak and R. P. Smyth and R. Marquet and V. Vivet-Boudou},
url = {https://www.tandfonline.com/doi/full/10.1080/15476286.2021.2021677},
isbn = {35067194},
year = {2022},
date = {2022-01-01},
journal = {RNA Biol},
volume = {19},
number = {1},
pages = {191-205},
abstract = {Maturation of the HIV-1 viral particles shortly after budding is required for infectivity. During this process, the Pr55(Gag) precursor undergoes a cascade of proteolytic cleavages, and whilst the structural rearrangements of the viral proteins are well understood, the concomitant maturation of the genomic RNA (gRNA) structure is unexplored, despite evidence that it is required for infectivity. To get insight into this process, we systematically analysed the interactions between Pr55(Gag) or its maturation products (NCp15, NCp9 and NCp7) and the 5' gRNA region and their structural consequences, in vitro. We show that Pr55(Gag) and its maturation products mostly bind at different RNA sites and with different contributions of their two zinc knuckle domains. Importantly, these proteins have different transient and permanent effects on the RNA structure, the late NCp9 and NCp7 inducing dramatic structural rearrangements. Altogether, our results reveal the distinct contributions of the different Pr55(Gag) maturation products on the gRNA structural maturation.},
note = {1555-8584 (Electronic)
1547-6286 (Linking)
Journal Article},
keywords = {MARQUET, PAILLART, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
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}
}
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}
}
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}
}
Sosnowski P, Tidu A, Eriani G, Westhof E, Martin F
Correlated sequence signatures are present within the genomic 5'UTR RNA and NSP1 protein in coronaviruses Article de journal
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
@article{nokey,
title = {Correlated sequence signatures are present within the genomic 5'UTR RNA and NSP1 protein in coronaviruses},
author = {P Sosnowski and A Tidu and G Eriani and E Westhof and F Martin},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=35236777},
doi = {10.1261/rna.078972.121},
isbn = {35236777},
year = {2022},
date = {2022-01-01},
urldate = {2022-01-01},
journal = {Rna},
volume = {28},
issue = {5},
pages = {729-741},
abstract = {The 5'UTR part of coronavirus genomes plays key roles in the viral replication cycle and the translation of the viral mRNAs. The first 75-80 nucleotides, also called the leader sequence, are identical for the genomic mRNA and for the subgenomic mRNAs. Recently, it was shown that cooperative actions of a 5'UTR segment and the non-structural protein NSP1 are essential for both the inhibition of host mRNAs and for specific translation of viral mRNAs. Here, sequence analyses of both the 5'UTR RNA segment and the NSP1 protein have been done for several coronaviruses with special attention to the betacoronaviruses. The conclusions are (i) precise specific molecular signatures can be found in both the RNA and the NSP1 protein; (ii) both types of signatures strongly correlate between each other. Indeed, definite sequence motifs in the RNA correlate with sequence motifs in the protein indicating a co-evolution of 5'UTR with NSP1 in betacoronaviruses. Experimental mutational data on 5'UTR and NSP1 from SARS-CoV-2 using cell-free translation extracts support those conclusions and show that the N-terminal half of the NSP1 protein contains conserved key residues that are essential for evasion to the inhibitory effect of NSP1 on translation.},
note = {1469-9001 (Electronic)
1355-8382 (Linking)
Journal Article},
keywords = {ERIANI, MARTIN, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
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}
}
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}
}
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
@article{nokey,
title = {Viral and cellular translation during SARS-CoV-2 infection},
author = {G. Eriani and F. Martin},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=35429230},
doi = {10.1002/2211-5463.13413},
isbn = {35429230},
year = {2022},
date = {2022-01-01},
urldate = {2022-01-01},
journal = {FEBS Open Bio},
volume = {12},
issue = {9},
pages = {1584-1601},
abstract = {SARS-CoV-2 is a betacoronavirus that emerged in China in December 2019 and which is the causative agent of the Covid-19 pandemic. This enveloped virus contains a large positive-sense single-stranded RNA genome. In this review, we summarize the current knowledge on the molecular mechanisms for the translation of both viral transcripts and cellular messenger RNAs. Non-structural proteins are encoded by the genomic RNA and are produced in the early steps of infection. In contrast, the structural proteins are produced from subgenomic RNAs that are translated in the late phase of the infectious program. Non-structural protein 1 (NSP1) is a key molecule that regulates both viral and cellular translation. In addition, NSP1 interferes with multiple steps of the interferon I pathway and thereby blocks host antiviral responses. Therefore, NSP1 is a drug target of choice for the development of antiviral therapies.},
note = {2211-5463 (Electronic)
2211-5463 (Linking)
Journal Article
Review},
keywords = {ERIANI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
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
@article{nokey,
title = {Fluorogenic RNA-Based Biosensor to Sense the Glycolytic Flux in Mammalian Cells},
author = {I. Geraci and A. Autour and G. Pietruschka and A. Shiian and M. Borisova and C. Mayer and M. Ryckelynck and G. Mayer},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=35427113},
doi = {10.1021/acschembio.2c00100},
isbn = {35427113},
year = {2022},
date = {2022-01-01},
urldate = {2022-01-01},
journal = {ACS Chem Biol},
volume = {17},
issue = {5},
pages = {1164-1173},
abstract = {The visualization of metabolic flux in real time requires sensor molecules that transduce variations of metabolite concentrations into an appropriate output signal. In this regard, fluorogenic RNA-based biosensors are promising molecular tools as they fluoresce only upon binding to another molecule. However, to date no such sensor is available that enables the direct observation of key metabolites in mammalian cells. Toward this direction, we selected and characterized an RNA light-up sensor designed to respond to fructose 1,6-bisphosphate and applied it to probe glycolytic flux variation in mammal cells.},
note = {1554-8937 (Electronic)
1554-8929 (Linking)
Journal Article},
keywords = {Labex, RYCKELYNCK, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
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}
}
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
@article{nokey,
title = {Growth-Associated Droplet Shrinkage for Bacterial Quantification, Growth Monitoring, and Separation by Ultrahigh-Throughput Microfluidics},
author = {E. Geersens and S. Vuilleumier and M. Ryckelynck},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=35449964},
doi = {10.1021/acsomega.2c00248},
isbn = {35449964},
year = {2022},
date = {2022-01-01},
journal = {ACS Omega},
volume = {7},
number = {14},
pages = {12039-12047},
abstract = {Microbiology still relies on en masse cultivation for selection, isolation, and characterization of microorganisms of interest. This constrains the diversity of microbial types and metabolisms that can be investigated in the laboratory also because of intercellular competition during cultivation. Cell individualization by droplet-based microfluidics prior to experimental analysis provides an attractive alternative to access a larger fraction of the microbial biosphere, miniaturizing the required equipment and minimizing reagent use for increased and more efficient analytical throughput. Here, we show that cultivation of a model two-strain bacterial community in droplets significantly reduces representation bias in the grown culture compared to batch cultivation. Further, and based on the droplet shrinkage observed upon cell proliferation, we provide proof-of-concept for a simple strategy that allows absolute quantification of microbial cells in a sample as well as selective recovery of microorganisms of interest for subsequent experimental characterization.},
note = {2470-1343 (Electronic)
2470-1343 (Linking)
Journal Article},
keywords = {Labex, RYCKELYNCK, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
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}
}
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}
}
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
@article{nokey,
title = {1-Deazaguanosine-Modified RNA: The Missing Piece for Functional RNA Atomic Mutagenesis},
author = {R. Bereiter and E. Renard and K. Breuker and C. Kreutz and E. Ennifar and R. Micura},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=35666572},
doi = {10.1021/jacs.2c01877},
isbn = {35666572},
year = {2022},
date = {2022-01-01},
urldate = {2022-01-01},
journal = {J Am Chem Soc},
volume = {144},
issue = {23},
pages = {10344-10352},
abstract = {Atomic mutagenesis is the key to advance our understanding of RNA recognition and RNA catalysis. To this end, deazanucleosides are utilized to evaluate the participation of specific atoms in these processes. One of the remaining challenges is access to RNA-containing 1-deazaguanosine (c(1)G). Here, we present the synthesis of this nucleoside and its phosphoramidite, allowing first time access to c(1)G-modified RNA. Thermodynamic analyses revealed the base pairing parameters for c(1)G-modified RNA. Furthermore, by NMR spectroscopy, a c(1)G-triggered switch of Watson-Crick into Hoogsteen pairing in HIV-2 TAR RNA was identified. Additionally, using X-ray structure analysis, a guanine-phosphate backbone interaction affecting RNA fold stability was characterized, and finally, the critical impact of an active-site guanine in twister ribozyme on the phosphodiester cleavage was revealed. Taken together, our study lays the synthetic basis for c(1)G-modified RNA and demonstrates the power of the completed deazanucleoside toolbox for RNA atomic mutagenesis needed to achieve in-depth understanding of RNA recognition and catalysis.},
note = {1520-5126 (Electronic)
0002-7863 (Linking)
Journal Article},
keywords = {ENNIFAR, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
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}
}
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}
}
Vincens Q, Westhof E
Brief considerations on targeting RNA with small molecules Article de journal
Dans: Faculty Reviews, vol. 11, no. 39, 2022.
Résumé | Liens | BibTeX | Étiquettes: Drug discovery RNA structure & dynamics RNA targeting SARS-CoV2, Unité ARN, WESTHOF
@article{nokey,
title = {Brief considerations on targeting RNA with small molecules},
author = {Q Vincens and E Westhof},
url = {https://facultyopinions.com/prime/reports/b/11/39/},
doi = {10.12703/r/11-39},
year = {2022},
date = {2022-01-01},
urldate = {2022-01-01},
journal = {Faculty Reviews},
volume = {11},
number = {39},
abstract = {For more than three decades, RNA has been known to be a relevant and attractive macromolecule to target but figuring out which RNA should be targeted and how remains challenging. Recent years have seen the confluence of approaches for screening, drug optimization, and target validation that have led to the approval of a few RNA-targeting therapeutics for clinical applications. This focused perspective aims to highlight but not exhaustively review key factors accounting for these successes while pointing at crucial aspects worth considering for further breakthroughs.},
keywords = {Drug discovery RNA structure & dynamics RNA targeting SARS-CoV2, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Vilimova Monika, Contrant Maud, Randrianjafy Ramy, Dumas Philippe, Elbasani Endrit, Ojala Päivi M, Pfeffer Sébastien, Fender Aurélie
Correction to 'Cis regulation within a cluster of viral microRNAs' Divers
2021, ISSN: 1362-4962.
Liens | BibTeX | Étiquettes: PFEFFER, Unité ARN
@misc{pmid34520556,
title = {Correction to 'Cis regulation within a cluster of viral microRNAs'},
author = {Monika Vilimova and Maud Contrant and Ramy Randrianjafy and Philippe Dumas and Endrit Elbasani and Päivi M Ojala and Sébastien Pfeffer and Aurélie Fender},
doi = {10.1093/nar/gkab806},
issn = {1362-4962},
year = {2021},
date = {2021-10-01},
urldate = {2021-10-01},
journal = {Nucleic Acids Res},
volume = {49},
number = {18},
pages = {10804--10805},
keywords = {PFEFFER, Unité ARN},
pubstate = {published},
tppubtype = {misc}
}
Saeb Sepideh, Ravanshad Mehrdad, Pourkarim Mahmoud Reza, Daouad Fadoua, Baesi Kazem, Rohr Olivier, Wallet Clémentine, Schwartz Christian
Brain HIV-1 latently-infected reservoirs targeted by the suicide gene strategy Article de journal
Dans: Virol J, vol. 18, no. 1, p. 107, 2021, ISSN: 1743-422X.
Résumé | Liens | BibTeX | Étiquettes: ROHR, Unité ARN
@article{pmid34059075,
title = {Brain HIV-1 latently-infected reservoirs targeted by the suicide gene strategy},
author = {Sepideh Saeb and Mehrdad Ravanshad and Mahmoud Reza Pourkarim and Fadoua Daouad and Kazem Baesi and Olivier Rohr and Clémentine Wallet and Christian Schwartz},
doi = {10.1186/s12985-021-01584-2},
issn = {1743-422X},
year = {2021},
date = {2021-05-01},
urldate = {2021-05-01},
journal = {Virol J},
volume = {18},
number = {1},
pages = {107},
abstract = {Reducing the pool of HIV-1 reservoirs in patients is a must to achieve functional cure. The most prominent HIV-1 cell reservoirs are resting CD4 + T cells and brain derived microglial cells. Infected microglial cells are believed to be the source of peripheral tissues reseedings and the emergence of drug resistance. Clearing infected cells from the brain is therefore crucial. However, many characteristics of microglial cells and the central nervous system make extremely difficult their eradication from brain reservoirs. Current methods, such as the "shock and kill", the "block and lock" and gene editing strategies cannot override these difficulties. Therefore, new strategies have to be designed when considering the elimination of brain reservoirs. We set up an original gene suicide strategy using latently infected microglial cells as model cells. In this paper we provide proof of concept of this strategy.},
keywords = {ROHR, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Vicens Q, Bochler A, Jobe A, Frank J, Hashem Y
Interaction Networks of Ribosomal Expansion Segments in Kinetoplastids Chapitre d'ouvrage
Dans: vol. 96, p. 433-450, Subcellular Biochemistry, 2021.
Résumé | Liens | BibTeX | Étiquettes: Eukaryotic translation, Expansion segment, Kinetoplastid parasite, Ribosomal RNA, Ribosome structure, Unité ARN
@inbook{Vicens2021,
title = {Interaction Networks of Ribosomal Expansion Segments in Kinetoplastids },
author = {Q Vicens and A Bochler and A Jobe and J Frank and Y Hashem },
url = {https://pubmed.ncbi.nlm.nih.gov/33252739/},
doi = {10.1007/978-3-030-58971-4_13 },
year = {2021},
date = {2021-01-01},
volume = {96},
pages = {433-450},
publisher = {Subcellular Biochemistry},
abstract = {Expansion segments (ES) are insertions of a few to hundreds of nucleotides at discrete locations on eukaryotic ribosomal RNA (rRNA) chains. Some cluster around ‘hot spots’ involved in translation regulation and some may participate in biogenesis. Whether ES play the same roles in different organisms is currently unclear, especially since their size may vary dramatically from one species to another and very little is known about their functions. Most likely, ES variation is linked to adaptation to a particular environment. In this chapter, we compare the interaction networks of ES from four kinetoplastid parasites, which have evolved in diverse insect vectors and mammalian hosts: Trypanosoma cruzi, Trypanosoma brucei, Leishmania donovani and Leishmania major. Here, we comparatively analyze ribosome structures from these representative kinetoplastids and ascertain meaningful structural differences from mammalian ribosomes. We base our analysis on sequence alignments and three-dimensional structures of 80S ribosomes solved by cryo-electron microscopy (cryo-EM). Striking differences in size are observed between ribosomes of different parasites, indicating that not all ES are expanded equally. Larger ES are not always matched by large surrounding ES or proteins extensions in their vicinity, a particularity that may lead to clues about their biological function. ES display different species-specific patterns of conservation, which underscore the density of their interaction network at the surface of the ribosome. Making sense of the conservation patterns of ES is part of a global effort to lay the basis for functional studies aimed at discovering unique kinetoplastid-specific sites suitable for therapeutic applications against these human and often animal pathogens.},
keywords = {Eukaryotic translation, Expansion segment, Kinetoplastid parasite, Ribosomal RNA, Ribosome structure, Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
Bec G, Ennifar E
switchSENSE Technology for Analysis of DNA Polymerase Kinetics Chapitre d'ouvrage
Dans: Rederstorff, M (Ed.): vol. 2247, p. 145-153, Springer Protocols, Humana Press, New York, NY, Small Non-Coding RNAs, 2021.
Résumé | BibTeX | Étiquettes: Biosensor, DNA polymerase, ENNIFAR, HIV reverse transcriptase, Kinetics, switchSENSE technology, Unité ARN
@inbook{Bec2021,
title = {switchSENSE Technology for Analysis of DNA Polymerase Kinetics },
author = {G Bec and E Ennifar
},
editor = {M Rederstorff},
year = {2021},
date = {2021-01-01},
journal = {Methods in Molecular Biology },
volume = {2247},
pages = {145-153},
publisher = {Springer Protocols, Humana Press},
address = {New York, NY},
edition = {Small Non-Coding RNAs},
series = {Methods in Molecular Biology},
abstract = {The switchSENSE technology is a recent approach based on surface sensor chips for the analysis of interactions of macromolecules. The technology relies on electro-switchable DNA nanolevers tethered at one end on a gold surface via a sulfur linker and labeled with a Cy3 dye on the other end. The switchSENSE approach is effective in the determination of a large panel of biophysical parameters such as binding kinetics, dissociation constant, hydrodynamic radius, or melting temperature. In addition, it can also give access to some enzymatic data such as nuclease or polymerase activity. Here we describe a DNA polymerase assay that allows retrieving, in a single experimental set, association and dissociation rates, as well as the catalytic rate of the enzyme. },
keywords = {Biosensor, DNA polymerase, ENNIFAR, HIV reverse transcriptase, Kinetics, switchSENSE technology, Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
Lalaouna D, Fochesato S, Harir M, Ortet P, Schmitt-Kopplin P, Heulin T, Achouak W
Amplifying and Fine-Tuning Rsm sRNAs Expression and Stability to Optimize the Survival of Pseudomonas brassicacerum in Nutrient-Poor Environments Article de journal
Dans: Microorganisms, vol. 9, no. 2, p. 250, 2021.
Résumé | Liens | BibTeX | Étiquettes: GacA-dependent, nutritional stress, Pseudomonas brassicacearum, ROMBY, Rsm sRNAs, sRNAs stability, Unité ARN
@article{,
title = {Amplifying and Fine-Tuning Rsm sRNAs Expression and Stability to Optimize the Survival of Pseudomonas brassicacerum in Nutrient-Poor Environments},
author = {D Lalaouna and S Fochesato and M Harir and P Ortet and P Schmitt-Kopplin and T Heulin and W Achouak},
url = {https://www.mdpi.com/2076-2607/9/2/250},
doi = {10.3390/microorganisms9020250},
year = {2021},
date = {2021-01-01},
journal = {Microorganisms},
volume = {9},
number = {2},
pages = {250},
abstract = {In the beneficial plant root-associated Pseudomonas brassicacearum strain NFM421, the GacS/GacA two-component system positively controls biofilm formation and the production of secondary metabolites through the synthesis of rsmX, rsmY and rsmZ. Here, we evidenced the genetic amplification of Rsm sRNAs by the discovery of a novel 110-nt long sRNA encoding gene, rsmX-2, generated by the duplication of rsmX-1 (formerly rsmX). Like the others rsm genes, its overexpression overrides the gacA mutation. We explored the expression and the stability of rsmX-1, rsmX-2, rsmY and rsmZ encoding genes under rich or nutrient-poor conditions, and showed that their amount is fine-tuned at the transcriptional and more interestingly at the post-transcriptional level. Unlike rsmY and rsmZ, we noticed that the expression of rsmX-1 and rsmX-2 genes was exclusively GacA-dependent. The highest expression level and longest half-life for each sRNA were correlated with the highest ppGpp and cyclic-di-GMP levels and were recorded under nutrient-poor conditions. Together, these data support the view that the Rsm system in P. brassicacearum is likely linked to the stringent response, and seems to be required for bacterial adaptation to nutritional stress.},
keywords = {GacA-dependent, nutritional stress, Pseudomonas brassicacearum, ROMBY, Rsm sRNAs, sRNAs stability, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Li G, Eriani G, Wang E D, Zhou X L
Distinct pathogenic mechanisms of various RARS1 mutations in Pelizaeus-Merzbacher-like disease Article de journal
Dans: Sci China Life Sci, vol. 64, no. 10, p. 1645-1660, 2021, ISBN: 33515434, (1869-1889 (Electronic) 1674-7305 (Linking) Journal Article).
Résumé | Liens | BibTeX | Étiquettes: aminoacyl-tRNA synthetase (aaRS), central nervous system (CNS), ERIANI, Protein Biosynthesis, translation initiation, tRNA, Unité ARN
@article{,
title = {Distinct pathogenic mechanisms of various RARS1 mutations in Pelizaeus-Merzbacher-like disease},
author = {G Li and G Eriani and E D Wang and X L Zhou},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=33515434},
doi = {10.1007/s11427-020-1838-2},
isbn = {33515434},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Sci China Life Sci},
volume = {64},
number = {10},
pages = {1645-1660},
abstract = {Mutations of the genes encoding aminoacyl-tRNA synthetases are highly associated with various central nervous system disorders. Recurrent mutations, including c.5A>G, p.D2G; c.1367C>T, p.S456L; c.1535G>A, p.R512Q and c.1846_1847del, p. Y616Lfs*6 of RARS1 gene, which encodes two forms of human cytoplasmic arginyl-tRNA synthetase (hArgRS), are linked to Pelizaeus-Merzbacher-like disease (PMLD) with unclear pathogenesis. Among these mutations, c.5A>G is the most extensively reported mutation, leading to a p.D2G mutation in the N-terminal extension of the long-form hArgRS. Here, we showed the detrimental effects of R512Q substitution and DeltaC mutations on the structure and function of hArgRS, while the most frequent mutation c.5A>G, p.D2G acted in a different manner without impairing hArgRS activity. The nucleotide substitution c.5A>G reduced translation of hArgRS mRNA, and an upstream open reading frame contributed to the suppressed translation of the downstream main ORF. Taken together, our results elucidated distinct pathogenic mechanisms of various RARS1 mutations in PMLD.},
note = {1869-1889 (Electronic)
1674-7305 (Linking)
Journal Article},
keywords = {aminoacyl-tRNA synthetase (aaRS), central nervous system (CNS), ERIANI, Protein Biosynthesis, translation initiation, tRNA, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Mercier N, Prévost K, Massé E, Romby P, Caldelari I, Lalaouna D
MS2-Affinity Purification Coupled with RNA Sequencing in Gram-Positive Bacteria Article de journal
Dans: J Vis Exp, p. e61731, 2021.
Résumé | Liens | BibTeX | Étiquettes: ROMBY, Unité ARN
@article{Mercier2021,
title = {MS2-Affinity Purification Coupled with RNA Sequencing in Gram-Positive Bacteria},
author = {N Mercier and K Prévost and E Massé and P Romby and I Caldelari and D Lalaouna},
url = {https://www.jove.com/t/61731/ms2-affinity-purification-coupled-with-rna-sequencing-gram-positive},
doi = {10.3791/61731},
year = {2021},
date = {2021-01-01},
journal = {J Vis Exp},
pages = {e61731},
abstract = {Although small regulatory RNAs (sRNAs) are widespread among the bacterial domain of life, the functions of many of them remain poorly characterized notably due to the difficulty of identifying their mRNA targets. Here, we described a modified protocol of the MS2-Affinity Purification coupled with RNA Sequencing (MAPS) technology, aiming to reveal all RNA partners of a specific sRNA in vivo. Broadly, the MS2 aptamer is fused to the 5’ extremity of the sRNA of interest. This construct is then expressed in vivo, allowing the MS2-sRNA to interact with its cellular partners. After bacterial harvesting, cells are mechanically lysed. The crude extract is loaded into an amylose-based chromatography column previously coated with the MS2 protein fused to the maltose binding protein. This enables the specific capture of MS2-sRNA and interacting RNAs. After elution, co-purified RNAs are identified by high-throughput RNA sequencing and subsequent bioinformatic analysis. The following protocol has been implemented in the Gram-positive human pathogen Staphylococcus aureus and is, in principle, transposable to any Gram-positive bacteria. To sum up, MAPS technology constitutes an efficient method to deeply explore the regulatory network of a particular sRNA, offering a snapshot of its whole targetome. However, it is important to keep in mind that putative targets identified by MAPS still need to be validated by complementary experimental approaches.},
keywords = {ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Catalan-Moreno A, Cela M, Menendez-Gil P, Irurzun N, Caballero C J, Caldelari I, Toledo-Arana A
RNA thermoswitches modulate Staphylococcus aureus adaptation to ambient temperatures Article de journal
Dans: Nucleic Acids Res, p. on press, 2021, ISBN: 33660769, (1362-4962 (Electronic) 0305-1048 (Linking) Journal Article).
Résumé | Liens | BibTeX | Étiquettes: ROMBY, Unité ARN
@article{Catalan-Moreno2021,
title = {RNA thermoswitches modulate Staphylococcus aureus adaptation to ambient temperatures},
author = {A Catalan-Moreno and M Cela and P Menendez-Gil and N Irurzun and C J Caballero and I Caldelari and A Toledo-Arana},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=33660769},
doi = {0.1093/nar/gkab117},
isbn = {33660769},
year = {2021},
date = {2021-01-01},
journal = {Nucleic Acids Res},
pages = {on press},
abstract = {Thermoregulation of virulence genes in bacterial pathogens is essential for environment-to-host transition. However, the mechanisms governing cold adaptation when outside the host remain poorly understood. Here, we found that the production of cold shock proteins CspB and CspC from Staphylococcus aureus is controlled by two paralogous RNA thermoswitches. Through in silico prediction, enzymatic probing and site-directed mutagenesis, we demonstrated that cspB and cspC 5'UTRs adopt alternative RNA structures that shift from one another upon temperature shifts. The open (O) conformation that facilitates mRNA translation is favoured at ambient temperatures (22 degrees C). Conversely, the alternative locked (L) conformation, where the ribosome binding site (RBS) is sequestered in a double-stranded RNA structure, is folded at host-related temperatures (37 degrees C). These structural rearrangements depend on a long RNA hairpin found in the O conformation that sequesters the anti-RBS sequence. Notably, the remaining S. aureus CSP, CspA, may interact with a UUUGUUU motif located in the loop of this long hairpin and favour the folding of the L conformation. This folding represses CspB and CspC production at 37 degrees C. Simultaneous deletion of the cspB/cspC genes or their RNA thermoswitches significantly decreases S. aureus growth rate at ambient temperatures, highlighting the importance of CspB/CspC thermoregulation when S. aureus transitions from the host to the environment.},
note = {1362-4962 (Electronic)
0305-1048 (Linking)
Journal Article},
keywords = {ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Pitchai F, Chameettachal A, Vivet-Boudou V, Ali L M, Pillai V N, Krishnan A, Bernacchi S, Mustafa F, R Marquet, Rizvi T A
Identification of Pr78Gag binding sites on the Mason-Pfizer monkey virus genomic RNA packaging determinants Article de journal
Dans: J Mol Biol, vol. 433, no. 10, p. 166923, 2021.
Résumé | Liens | BibTeX | Étiquettes: MARQUET, Retroviruses Gag-RNA interactions Purines Footprinting hSHAPE, Unité ARN
@article{F2021,
title = {Identification of Pr78Gag binding sites on the Mason-Pfizer monkey virus genomic RNA packaging determinants},
author = {F Pitchai and A Chameettachal and V Vivet-Boudou and L M Ali and V N Pillai and A Krishnan and S Bernacchi and F Mustafa and Marquet R and T A Rizvi},
url = {https://www.sciencedirect.com/science/article/pii/S0022283621001224?via%3Dihub},
doi = {10.1016/j.jmb.2021.166923},
year = {2021},
date = {2021-01-01},
journal = {J Mol Biol},
volume = {433},
number = {10},
pages = {166923},
abstract = {How retroviral Gag proteins recognize the packaging signals (Psi) on their genomic RNA (gRNA) is a key question that we addressed here using Mason-Pfizer monkey virus (MPMV) as a model system by combining band-shift assays and footprinting experiments. Our data show that Pr78Gag selects gRNA against spliced viral RNA by simultaneously binding to two single stranded loops on the MPMV Psi RNA: (1) a large purine loop (ssPurines), and (2) a loop which partially overlaps with a mostly base-paired purine repeat (bpPurines) and extends into a GU-rich binding motif. Importantly, this second Gag binding site is located immediately downstream of the major splice donor (mSD) and is thus absent from the spliced viral RNAs. Identifying elements crucial for MPMV gRNA packaging should help in understanding not only the mechanism of virion assembly by retroviruses, but also facilitate construction of safer retroviral vectors for human gene therapy.},
keywords = {MARQUET, Retroviruses Gag-RNA interactions Purines Footprinting hSHAPE, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Busienne C, Marquet R, Paillart J C, Bernacchi S
Post-Translational Modifications of Retroviral HIV-1 Gag Precursors: An Overview of Their Biological Role Article de journal
Dans: Int. J. Mol. Sci., vol. 22, no. 6, p. 2871, 2021.
Résumé | Liens | BibTeX | Étiquettes: HIV-1, MARQUET, PAILLART, post-translational modifications, Pr55Gag precursor, retroviral Gag precursors, retroviral life cycle, Unité ARN
@article{C2021b,
title = {Post-Translational Modifications of Retroviral HIV-1 Gag Precursors: An Overview of Their Biological Role},
author = {C Busienne and R Marquet and J C Paillart and S Bernacchi},
url = {https://www.mdpi.com/1422-0067/22/6/2871},
doi = {10.3390/ijms22062871},
year = {2021},
date = {2021-01-01},
journal = {Int. J. Mol. Sci.},
volume = {22},
number = {6},
pages = {2871},
abstract = {Protein post-translational modifications (PTMs) play key roles in eukaryotes since they finely regulate numerous mechanisms used to diversify the protein functions and to modulate their signaling networks. Besides, these chemical modifications also take part in the viral hijacking of the host, and also contribute to the cellular response to viral infections. All domains of the human immunodeficiency virus type 1 (HIV-1) Gag precursor of 55-kDa (Pr55Gag), which is the central actor for viral RNA specific recruitment and genome packaging, are post-translationally modified. In this review, we summarize the current knowledge about HIV-1 Pr55Gag PTMs such as myristoylation, phosphorylation, ubiquitination, sumoylation, methylation, and ISGylation in order to figure out how these modifications affect the precursor functions and viral replication. Indeed, in HIV-1, PTMs regulate the precursor trafficking between cell compartments and its anchoring at the plasma membrane, where viral assembly occurs. Interestingly, PTMs also allow Pr55Gag to hijack the cell machinery to achieve viral budding as they drive recognition between viral proteins or cellular components such as the ESCRT machinery. Finally, we will describe and compare PTMs of several other retroviral Gag proteins to give a global overview of their role in the retroviral life cycle.},
keywords = {HIV-1, MARQUET, PAILLART, post-translational modifications, Pr55Gag precursor, retroviral Gag precursors, retroviral life cycle, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Chameettachal A, Vivet-Boudou V, Pitchai F N, N Pillai V, Ali L M, Krishnan A, Bernacchi S, Mustafa F, Marquet R, Rizvi T A
A purine loop and the primer binding site are critical for the selective encapsidation of mouse mammary tumor virus genomic RNA by Pr77Gag Article de journal
Dans: Nucleic Acids Res, vol. 49, no. 8, p. 4668-4688, 2021.
BibTeX | Étiquettes: MARQUET, PAILLART, Unité ARN
@article{Chameettachal2021,
title = {A purine loop and the primer binding site are critical for the selective encapsidation of mouse mammary tumor virus genomic RNA by Pr77Gag},
author = {A Chameettachal and V Vivet-Boudou and F N Pitchai and Pillai V N and L M Ali and A Krishnan and S Bernacchi and F Mustafa and R Marquet and T A Rizvi},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Nucleic Acids Res},
volume = {49},
number = {8},
pages = {4668-4688},
keywords = {MARQUET, PAILLART, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Westhof E, Leontis N B
An RNA-centric historical narrative around the Protein Data Bank Article de journal
Dans: J Biol Chem, vol. 296, p. 100555, 2021, ISBN: 33744291, (1083-351X (Electronic) 0021-9258 (Linking) Journal Article Review).
Résumé | Liens | BibTeX | Étiquettes: Computational Biology, Databases, modelling, Protein Data Bank, RNA, Structural biology, Unité ARN, WESTHOF
@article{Westhof2021,
title = {An RNA-centric historical narrative around the Protein Data Bank},
author = {E Westhof and N B Leontis},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=33744291},
doi = {10.1016/j.jbc.2021.100555},
isbn = {33744291},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {J Biol Chem},
volume = {296},
pages = {100555},
abstract = {Some of the amazing contributions brought to the scientific community by the PDB are described. The focus is on nucleic acid structures with a bias towards RNA. The evolution and key roles in science of the PDB and other structural databases for nucleic acids illustrate how small initial ideas can become huge and indispensable resources with the unflinching willingness of scientists to cooperate globally. The progress in the understanding of the molecular interactions driving RNA architectures followed the rapid increase in RNA structures in the PDB. That increase was consecutive to improvements in chemical synthesis and purification of RNA molecules, as well as in biophysical methods for structure determination and computer technology. The RNA modeling efforts from the early beginnings are also described together with their links to the state of structural knowledge and technological development. Structures of RNA and of its assemblies are physical objects which, together with genomic data, allow us to integrate present-day biological functions and the historical evolution in all living species on earth.},
note = {1083-351X (Electronic)
0021-9258 (Linking)
Journal Article
Review},
keywords = {Computational Biology, Databases, modelling, Protein Data Bank, RNA, Structural biology, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Husser C, Dentz N, Ryckelynck M
Structure-Switching RNAs: From Gene Expression Regulation to Small Molecule Detection Article de journal
Dans: Small Structures, vol. 2, no. 4, p. 2000132, 2021.
Résumé | Liens | BibTeX | Étiquettes: biosensing, Gene Expression Regulation, riboswitches, RNA aptamers, RYCKELYNCK, Synthetic Biology, Unité ARN
@article{C2021c,
title = {Structure-Switching RNAs: From Gene Expression Regulation to Small Molecule Detection},
author = {C Husser and N Dentz and M Ryckelynck},
url = {https://doi.org/10.1002/sstr.202000132},
doi = {10.1002/sstr.202000132},
year = {2021},
date = {2021-01-01},
journal = {Small Structures},
volume = {2},
number = {4},
pages = {2000132},
abstract = {RNA is instrumental to cell life in many aspects, especially gene expression regulation. Among the various known regulatory RNAs, riboswitches are particularly interesting cis‐acting molecules as they do not need cellular factor to achieve their function and are therefore highly portable from one organism to the other. These molecules usually found in the 5′ untranslated region of bacterial messenger RNAs are able to specifically sense a target ligand via an aptamer domain prior to transmitting this recognition event to an expression platform that turns on, or off, the expression of downstream genes. In addition to their obvious scientific interest, these modular molecules can also serve for the development of synthetic RNA devices with applications ranging from the control of transgene expression in gene therapy to the specific biosensing of small molecules. The engineering of such nanomachines is greatly facilitated by the proper understanding of their structure as well as the introduction of new technologies. Herein, a general overview of the current knowledge on natural riboswitches prior to explaining the main strategies used to develop new synthetic structure‐switching molecules (riboswitches or biosensors) controlled by small molecules is given.},
keywords = {biosensing, Gene Expression Regulation, riboswitches, RNA aptamers, RYCKELYNCK, Synthetic Biology, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Stupfler B, Verriez C, Gallois-Montbrun S, Marquet R, Paillart J C
Degradation-independent inhibition of APOBEC3G by HIV-1 Vif protein Article de journal
Dans: Viruses, vol. 13, no. 4, p. 617, 2021.
Résumé | Liens | BibTeX | Étiquettes: APOBEC3G, deamination, encapsidation, HIV, MARQUET, PAILLART, proteasome, RNP granules, Translation, ubiquitin, Unité ARN, vif
@article{Stupfler2021,
title = {Degradation-independent inhibition of APOBEC3G by HIV-1 Vif protein},
author = {B Stupfler and C Verriez and S Gallois-Montbrun and R Marquet and J C Paillart},
url = {https://www.mdpi.com/1999-4915/13/4/617},
doi = {10.3390/v13040617},
year = {2021},
date = {2021-01-01},
journal = {Viruses},
volume = {13},
number = {4},
pages = {617},
abstract = {The ubiquitinproteasome system plays an important role in the cell under normal physiological conditions but also during viral infections. Indeed, many auxiliary proteins from the (HIV-1) divert this system to its own advantage, notably to induce the degradation of cellular restriction factors. For instance, the HIV-1 viral infectivity factor (Vif) has been shown to specifically counteract several cellular deaminases belonging to the apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC3 or A3) family (A3A to A3H) by recruiting an E3-ubiquitin ligase complex and inducing their polyubiquitination and degradation through the proteasome. Although this pathway has been extensively characterized so far, Vif has also been shown to impede A3s through degradation-independent processes, but research on this matter remains limited. In this review, we describe our current knowledge regarding the degradation-independent inhibition of A3s, and A3G in particular, by the HIV-1 Vif protein, the molecular mechanisms involved, and highlight important properties of this small viral protein.},
keywords = {APOBEC3G, deamination, encapsidation, HIV, MARQUET, PAILLART, proteasome, RNP granules, Translation, ubiquitin, Unité ARN, vif},
pubstate = {published},
tppubtype = {article}
}