Omar Reine El, Abdellaoui Naoill, Coulibaly Safiatou T, Fontenille Laura, Lanza François, Gachet Christian, Freund Jean-Noel, Negroni Matteo, Kissa Karima, Tavian Manuela
Macrophage depletion overcomes human hematopoietic cell engraftment failure in zebrafish embryo Journal Article
In: Cell Death Dis, vol. 15, no. 5, pp. 305, 2024, ISSN: 2041-4889.
Abstract | Links | BibTeX | Tags: NEGRONI, Unité ARN
@article{pmid38693109,
title = {Macrophage depletion overcomes human hematopoietic cell engraftment failure in zebrafish embryo},
author = {Reine El Omar and Naoill Abdellaoui and Safiatou T Coulibaly and Laura Fontenille and François Lanza and Christian Gachet and Jean-Noel Freund and Matteo Negroni and Karima Kissa and Manuela Tavian},
doi = {10.1038/s41419-024-06682-x},
issn = {2041-4889},
year = {2024},
date = {2024-05-01},
urldate = {2024-05-01},
journal = {Cell Death Dis},
volume = {15},
number = {5},
pages = {305},
abstract = {Zebrafish is widely adopted as a grafting model for studying human development and diseases. Current zebrafish xenotransplantations are performed using embryo recipients, as the adaptive immune system, responsible for host versus graft rejection, only reaches maturity at juvenile stage. However, transplanted primary human hematopoietic stem/progenitor cells (HSC) rapidly disappear even in zebrafish embryos, suggesting that another barrier to transplantation exists before the onset of adaptive immunity. Here, using a labelled macrophage zebrafish line, we demonstrated that engraftment of human HSC induces a massive recruitment of macrophages which rapidly phagocyte transplanted cells. Macrophages depletion, by chemical or pharmacological treatments, significantly improved the uptake and survival of transplanted cells, demonstrating the crucial implication of these innate immune cells for the successful engraftment of human cells in zebrafish. Beyond identifying the reasons for human hematopoietic cell engraftment failure, this work images the fate of human cells in real time over several days in macrophage-depleted zebrafish embryos.},
keywords = {NEGRONI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
A. Niedner-Boblenz, T. Monecke, J. Hennig, M. Klostermann, M. Hofweber, A.P. Gerber, I. Anosova, W. Mayer, M. Müller, R. Heym, R. Janowski, C. Paillart J., D. Dormann, K. Zarnack, M. Sattler
Intrinsically disordered RNA-binding motifs cooperate to catalyze RNA folding and drive phase separation Journal Article
In: bioRxiv, 2024.
Abstract | Links | BibTeX | Tags: MARQUET, PAILLART, Unité ARN
@article{A.2024,
title = {Intrinsically disordered RNA-binding motifs cooperate to catalyze RNA folding and drive phase separation},
author = {Niedner-Boblenz A. and Monecke T. and Hennig J. and Klostermann M. and Hofweber M. and Gerber A.P. and Anosova I. and Mayer W. and Müller M. and Heym R. and Janowski R. and Paillart J. C. and Dormann D. and Zarnack K. and Sattler M.},
url = {https://www.biorxiv.org/content/10.1101/2024.03.27.586925v2},
doi = {10.1101/2024.03.27.586925},
year = {2024},
date = {2024-03-29},
urldate = {2024-03-29},
journal = {bioRxiv},
abstract = {RNA-binding proteins are essential for gene regulation and the spatial organization of cells. Here, we report that the yeast ribosome biogenesis factor Loc1p is an intrinsically disordered RNA-binding protein with eight repeating positively charged, unstructured nucleic acid binding (PUN) motifs. While a single of these previously undefined motifs stabilizes folded RNAs, multiple copies strongly cooperate to catalyze RNA folding. In the presence of RNA, these multivalent PUN motifs drive phase separation. Proteome-wide searches in pro-and eukaryotes for proteins with similar arrays of PUN motifs reveal a strong enrichment in RNA-mediated processes and DNA remodeling. Thus, PUN motifs are potentially involved in a large variety of RNA-and DNA-related processes by concentrating them in membrane-less organelles. The general function and wide distribution of PUN motifs across species suggests that in an ancient “RNA world” PUN-like motifs may have supported the correct folding of early ribozymes.},
keywords = {MARQUET, PAILLART, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Pellequer Jean-Luc, Westhof Eric
Marc van Regenmortel, personal recollections on a forward-thinking editor Journal Article
In: J Mol Recognit, pp. e3080, 2024, ISSN: 1099-1352.
Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF
@article{pmid38439188,
title = {Marc van Regenmortel, personal recollections on a forward-thinking editor},
author = {Jean-Luc Pellequer and Eric Westhof},
doi = {10.1002/jmr.3080},
issn = {1099-1352},
year = {2024},
date = {2024-03-01},
urldate = {2024-03-01},
journal = {J Mol Recognit},
pages = {e3080},
abstract = {Marc van Regenmortel was the Editor-in-Chief of the Journal of Molecular Recognition for the last 25 years. Without attempting to summarize Marc's exceptional career and achievements, we would like to tell the story of the tortuous and contingent path to the unravelling of a key molecular recognition process in antigenicity. Life is indeed full of contingencies and scientific life, full of meetings and random encounters, is prone to contingencies, a key element in discovery and innovation.},
keywords = {Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Messmer Mélanie, Pierson Louison, Pasquier Charline, Djordjevic Nikola, Chicher Johana, Hammann Philippe, Pfeffer Sébastien, Girardi Erika
DEAD box RNA helicase 5 is a new pro-viral host factor for Sindbis virus infection Journal Article
In: Virol J, vol. 21, no. 1, pp. 76, 2024, ISSN: 1743-422X.
Abstract | Links | BibTeX | Tags: PFEFFER, PPSE, Unité ARN
@article{pmid38553727,
title = {DEAD box RNA helicase 5 is a new pro-viral host factor for Sindbis virus infection},
author = {Mélanie Messmer and Louison Pierson and Charline Pasquier and Nikola Djordjevic and Johana Chicher and Philippe Hammann and Sébastien Pfeffer and Erika Girardi},
doi = {10.1186/s12985-024-02349-3},
issn = {1743-422X},
year = {2024},
date = {2024-03-01},
urldate = {2024-03-01},
journal = {Virol J},
volume = {21},
number = {1},
pages = {76},
abstract = {BACKGROUND: RNA helicases are emerging as key factors regulating host-virus interactions. The DEAD-box ATP-dependent RNA helicase DDX5, which plays an important role in many aspects of cellular RNA biology, was also found to either promote or inhibit viral replication upon infection with several RNA viruses. Here, our aim is to examine the impact of DDX5 on Sindbis virus (SINV) infection.nnMETHODS: We analysed the interaction between DDX5 and the viral RNA using imaging and RNA-immunoprecipitation approaches. The interactome of DDX5 in mock- and SINV-infected cells was determined by mass spectrometry. We validated the interaction between DDX17 and the viral capsid by co- immunoprecipitation in the presence or absence of an RNase treatment. We determined the subcellular localization of DDX5, its cofactor DDX17 and the viral capsid protein by co-immunofluorescence. Finally, we investigated the impact of DDX5 depletion and overexpression on SINV infection at the viral protein, RNA and infectious particle accumulation level. The contribution of DDX17 was also tested by knockdown experiments.nnRESULTS: In this study we demonstrate that DDX5 interacts with the SINV RNA during infection. Furthermore, the proteomic analysis of the DDX5 interactome in mock and SINV-infected HCT116 cells identified new cellular and viral partners and confirmed the interaction between DDX5 and DDX17. Both DDX5 and DDX17 re-localize from the nucleus to the cytoplasm upon SINV infection and interact with the viral capsid protein. We also show that DDX5 depletion negatively impacts the viral replication cycle, while its overexpression has a pro-viral effect. Finally, we observed that DDX17 depletion reduces SINV infection, an effect which is even more pronounced in a DDX5-depleted background, suggesting a synergistic pro-viral effect of the DDX5 and DDX17 proteins on SINV.nnCONCLUSIONS: These results not only shed light on DDX5 as a novel and important host factor to the SINV life cycle, but also expand our understanding of the roles played by DDX5 and DDX17 as regulators of viral infections.},
keywords = {PFEFFER, PPSE, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
D'Agostino Mattia, Simonetti Angelita, Motta Stefano, Wolff Philippe, Romagnoli Alice, Piccinini Astra, Spinozzi Francesco, Marino Daniele Di, Teana Anna La, Ennifar Eric
Crystal structure of archaeal IF5A-DHS complex reveals insights into the hypusination mechanism Journal Article
In: Structure, 2024, ISSN: 1878-4186.
Abstract | Links | BibTeX | Tags: ARN-MS, ENNIFAR, Unité ARN
@article{pmid38582076,
title = {Crystal structure of archaeal IF5A-DHS complex reveals insights into the hypusination mechanism},
author = {Mattia D'Agostino and Angelita Simonetti and Stefano Motta and Philippe Wolff and Alice Romagnoli and Astra Piccinini and Francesco Spinozzi and Daniele Di Marino and Anna La Teana and Eric Ennifar},
doi = {10.1016/j.str.2024.03.008},
issn = {1878-4186},
year = {2024},
date = {2024-03-01},
urldate = {2024-03-01},
journal = {Structure},
abstract = {The translation factor IF5A is highly conserved in Eukarya and Archaea and undergoes a unique post-translational hypusine modification by the deoxyhypusine synthase (DHS) enzyme. DHS transfers the butylamine moiety from spermidine to IF5A using NAD as a cofactor, forming a deoxyhypusine intermediate. IF5A is a key player in protein synthesis, preventing ribosome stalling in proline-rich sequences during translation elongation and facilitating translation elongation and termination. Additionally, human eIF5A participates in various essential cellular processes and contributes to cancer metastasis, with inhibiting hypusination showing anti-proliferative effects. The hypusination pathway of IF5A is therefore an attractive new therapeutic target. We elucidated the 2.0 Å X-ray crystal structure of the archaeal DHS-IF5A complex, revealing hetero-octameric architecture and providing a detailed view of the complex active site including the hypusination loop. This structure, along with biophysical data and molecular dynamics simulations, provides new insights into the catalytic mechanism of the hypusination reaction.},
keywords = {ARN-MS, ENNIFAR, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Zhang Jian-Hui, Eriani Gilbert, Zhou Xiao-Long
Pathophysiology of human mitochondrial tRNA metabolism Journal Article
In: Trends Endocrinol Metab, 2024, ISSN: 1879-3061.
Abstract | Links | BibTeX | Tags: ERIANI, Unité ARN
@article{pmid38307811,
title = {Pathophysiology of human mitochondrial tRNA metabolism},
author = {Jian-Hui Zhang and Gilbert Eriani and Xiao-Long Zhou},
doi = {10.1016/j.tem.2024.01.002},
issn = {1879-3061},
year = {2024},
date = {2024-02-01},
urldate = {2024-02-01},
journal = {Trends Endocrinol Metab},
abstract = {Mitochondria play multiple critical roles in cellular activity. In particular, mitochondrial translation is pivotal in the regulation of mitochondrial and cellular homeostasis. In this forum article, we discuss human mitochondrial tRNA metabolism and highlight its tight connection with various mitochondrial diseases caused by mutations in aminoacyl-tRNA synthetases, tRNAs, and tRNA-modifying enzymes.},
keywords = {ERIANI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Brillet Karl, Janczuk-Richter Marta, Poon Amanda, Laukart-Bradley Joanne, Ennifar Eric, Lebars Isabelle
Characterization of SLA RNA promoter from dengue virus and its interaction with the viral non-structural NS5 protein Journal Article
In: Biochimie, vol. 222, pp. 87–100, 2024, ISSN: 1638-6183.
Abstract | Links | BibTeX | Tags: ENNIFAR, Unité ARN
@article{pmid38408720,
title = {Characterization of SLA RNA promoter from dengue virus and its interaction with the viral non-structural NS5 protein},
author = {Karl Brillet and Marta Janczuk-Richter and Amanda Poon and Joanne Laukart-Bradley and Eric Ennifar and Isabelle Lebars},
doi = {10.1016/j.biochi.2024.02.005},
issn = {1638-6183},
year = {2024},
date = {2024-02-01},
urldate = {2024-02-01},
journal = {Biochimie},
volume = {222},
pages = {87--100},
abstract = {The Dengue virus (DENV) is the most significant arthropod-borne viral pathogen in humans with 400 million infections annually. DENV comprises four distinct serotypes (DENV-1 to -4) which complicates vaccine development. Any of the four serotypes can cause clinical illness but with distinctive infection dynamics. Variations in sequences identified within the four genomes induce structural differences in crucial RNA motifs that were suggested to be correlated to the degree of pathogenicity among DENV-1 to -4. In particular, the RNA Stem-loop A (SLA) at the 5'-end of the genome, acts as a key regulator of the viral replication cycle by interacting with the viral NS5 polymerase to initiate the minus-strand viral RNA synthesis and later to methylate and cap the synthesized RNA. The molecular details of this interaction remain not fully described. Here, we report the solution secondary structures of SLA from DENV-1 to -4. Our results highlight that the four SLA exhibit structural and dynamic differences. Secondly, to determine whether SLA RNA contains serotype-specific determinants for the recognition by the viral NS5 protein, we investigated interactions between SLA from DENV -1 to -4 and DENV2 NS5 using combined biophysical approaches. Our results show that NS5 from DENV2 is able to bind SLA from other serotypes, but that other viral or host factors may be necessary to stabilize the complex and promote the catalytically active state of the NS5. By contrast, we show that a serotype-specific binding is driven by specific interactions involving conformational changes within the SLA RNA.},
keywords = {ENNIFAR, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Soufi G El, Jorio L Di, Gerber Z, Cluzel N, Assche J Van, Delafoy D, Olaso R, Daviaud C, Loustau T, Schwartz C, Trebouet D, Hernalsteens O, Marechal V, Raffestin S, Rousset D, Lint C Van, Deleuze J F, Boni M, and O Rohr, Villain-Gambier M, Wallet C
In: Water Res, vol. 249, pp. 120959, 2024, ISSN: 1879-2448.
Abstract | Links | BibTeX | Tags: ROHR, Unité ARN
@article{pmid38070350,
title = {Highly efficient and sensitive membrane-based concentration process allows quantification, surveillance, and sequencing of viruses in large volumes of wastewater},
author = {G El Soufi and L Di Jorio and Z Gerber and N Cluzel and J Van Assche and D Delafoy and R Olaso and C Daviaud and T Loustau and C Schwartz and D Trebouet and O Hernalsteens and V Marechal and S Raffestin and D Rousset and C Van Lint and J F Deleuze and M Boni and and O Rohr and M Villain-Gambier and C Wallet},
doi = {10.1016/j.watres.2023.120959},
issn = {1879-2448},
year = {2024},
date = {2024-02-01},
urldate = {2024-02-01},
journal = {Water Res},
volume = {249},
pages = {120959},
abstract = {Wastewater-based epidemiology is experiencing exponential development. Despite undeniable advantages compared to patient-centered approaches (cost, anonymity, survey of large populations without bias, detection of asymptomatic infected peoples…), major technical limitations persist. Among them is the low sensitivity of the current methods used for quantifying and sequencing viral genomes from wastewater. In situations of low viral circulation, during initial stages of viral emergences, or in areas experiencing heavy rains, the extremely low concentrations of viruses in wastewater may fall below the limit of detection of the current methods. The availability during crisis and the cost of the commercial kits, as well as the requirement of expensive materials such as high-speed centrifuge, can also present major blocks to the development of wastewater-based epidemiological survey, specifically in low-income countries. Thereby, highly sensitive, low cost and standardized methods are still needed, to increase the predictability of the viral emergences, to survey low-circulating viruses and to make the results from different labs comparable. Here, we outline and characterize new protocols for concentrating and quantifying SARS-CoV-2 from large volumes (500 mL-1 L) of untreated wastewater. In addition, we report that the methods are applicable for monitoring and sequencing. Our nucleic acid extraction technique (the routine C: 5 mL method) does not require sophisticated equipment such as automatons and is not reliant on commercial kits, making it readily available to a broader range of laboratories for routine epidemiological survey. Furthermore, we demonstrate the efficiency, the repeatability, and the high sensitivity of a new membrane-based concentration method (MBC: 500 mL method) for enveloped (SARS-CoV-2) and non-enveloped (F-specific RNA phages of genogroup II / FRNAPH GGII) viruses. We show that the MBC method allows the quantification and the monitoring of viruses in wastewater with a significantly improved sensitivity compared to the routine C method. In contexts of low viral circulation, we report quantifications of SARS-CoV-2 in wastewater at concentrations as low as 40 genome copies per liter. In highly diluted samples collected in wastewater treatment plants of French Guiana, we confirmed the accuracy of the MBC method compared to the estimations done with the routine C method. Finally, we demonstrate that both the routine C method processing 5 mL and the MBC method processing 500 mL of untreated wastewater are both compatible with SARS-CoV-2 sequencing. We show that the quality of the sequence is correlated with the concentration of the extracted viral genome. Of note, the quality of the sequences obtained with some MBC processed wastewater was improved by dilutions or enzyme substitutions suggesting the presence of specific enzyme inhibitors in some wastewater. To the best of our knowledge, our MBC method is one of the first efficient, sensitive, and repeatable method characterized for SARS-CoV-2 quantification and sequencing from large volumes of wastewater.},
keywords = {ROHR, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Compain Guillaume, Monsarrat Clément, Blagojevic Julie, Brillet Karl, Dumas Philippe, Hammann Philippe, Kuhn Lauriane, Martiel Isabelle, Engilberge Sylvain, Oliéric Vincent, Wolff Philippe, Burnouf Dominique Y, Wagner Jérôme, Guichard Gilles
Peptide-Based Covalent Inhibitors Bearing Mild Electrophiles to Target a Conserved His Residue of the Bacterial Sliding Clamp Journal Article
In: JACS Au, vol. 4, no. 2, pp. 432–440, 2024, ISSN: 2691-3704.
Abstract | Links | BibTeX | Tags: ARN-MS, ENNIFAR, PPSE, Unité ARN
@article{pmid38425897,
title = {Peptide-Based Covalent Inhibitors Bearing Mild Electrophiles to Target a Conserved His Residue of the Bacterial Sliding Clamp},
author = {Guillaume Compain and Clément Monsarrat and Julie Blagojevic and Karl Brillet and Philippe Dumas and Philippe Hammann and Lauriane Kuhn and Isabelle Martiel and Sylvain Engilberge and Vincent Oliéric and Philippe Wolff and Dominique Y Burnouf and Jérôme Wagner and Gilles Guichard},
doi = {10.1021/jacsau.3c00572},
issn = {2691-3704},
year = {2024},
date = {2024-02-01},
urldate = {2024-02-01},
journal = {JACS Au},
volume = {4},
number = {2},
pages = {432--440},
abstract = {Peptide-based covalent inhibitors targeted to nucleophilic protein residues have recently emerged as new modalities to target protein-protein interactions (PPIs) as they may provide some benefits over more classic competitive inhibitors. Covalent inhibitors are generally targeted to cysteine, the most intrinsically reactive amino acid residue, and to lysine, which is more abundant at the surface of proteins but much less frequently to histidine. Herein, we report the structure-guided design of targeted covalent inhibitors (TCIs) able to bind covalently and selectively to the bacterial sliding clamp (SC), by reacting with a well-conserved histidine residue located on the edge of the peptide-binding pocket. SC is an essential component of the bacterial DNA replication machinery, identified as a promising target for the development of new antibacterial compounds. Thermodynamic and kinetic analyses of ligands bearing different mild electrophilic warheads confirmed the higher efficiency of the chloroacetamide compared to Michael acceptors. Two high-resolution X-ray structures of covalent inhibitor-SC adducts were obtained, revealing the canonical orientation of the ligand and details of covalent bond formation with histidine. Proteomic studies were consistent with a selective SC engagement by the chloroacetamide-based TCI. Finally, the TCI of SC was substantially more active than the parent noncovalent inhibitor in an in vitro SC-dependent DNA synthesis assay, validating the potential of the approach to design covalent inhibitors of protein-protein interactions targeted to histidine.},
keywords = {ARN-MS, ENNIFAR, PPSE, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Lechner Antony, Wolff Philippe
In-Gel Cyanoethylation for Pseudouridines Mass Spectrometry Detection of Bacterial Regulatory RNA Journal Article
In: Methods Mol Biol, vol. 2741, pp. 273–287, 2024, ISSN: 1940-6029.
Abstract | Links | BibTeX | Tags: ARN-MS, Unité ARN
@article{pmid38217659,
title = {In-Gel Cyanoethylation for Pseudouridines Mass Spectrometry Detection of Bacterial Regulatory RNA},
author = {Antony Lechner and Philippe Wolff},
doi = {10.1007/978-1-0716-3565-0_15},
issn = {1940-6029},
year = {2024},
date = {2024-01-01},
urldate = {2024-01-01},
journal = {Methods Mol Biol},
volume = {2741},
pages = {273--287},
abstract = {Regulatory RNAs, as well as many RNA families, contain chemically modified nucleotides, including pseudouridines (ψ). To map nucleotide modifications, approaches based on enzymatic digestion of RNA followed by nano liquid chromatography-tandem mass spectrometry (nanoLC-MS/MS) analysis were implemented several years ago. However, detection of ψ by mass spectrometry (MS) is challenging as ψ exhibits the same mass as uridine. Thus, a chemical labeling strategy using acrylonitrile was developed to detect this mass-silent modification. Acrylonitrile reacts specifically to ψ to form 1-cyanoethylpseudouridine (Ceψ), resulting in a mass shift of ψ detectable by MS. Here, a protocol detailing the steps from the purification of RNA by polyacrylamide gel electrophoresis, including in-gel labeling of ψ, to MS data interpretation to map ψ and other modifications is proposed. To demonstrate its efficiency, the protocol was applied to bacterial regulatory RNAs from E. coli: 6S RNA and transfer-messenger RNA (tmRNA, also known as 10Sa RNA). Moreover, ribonuclease P (RNase P) was also mapped using this approach. This method enabled the detection of several ψ at single nucleotide resolution.},
keywords = {ARN-MS, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Kohl Maximilian P, Chane-Woon-Ming Béatrice, Bahena-Ceron Roberto, Jaramillo-Ponce Jose, Antoine Laura, Herrgott Lucas, Romby Pascale, Marzi Stefano
Ribosome Profiling Methods Adapted to the Study of RNA-Dependent Translation Regulation in Staphylococcus aureus Journal Article
In: Methods Mol Biol, vol. 2741, pp. 73–100, 2024, ISSN: 1940-6029.
Abstract | Links | BibTeX | Tags: MARZI, ROMBY, Unité ARN
@article{pmid38217649,
title = {Ribosome Profiling Methods Adapted to the Study of RNA-Dependent Translation Regulation in Staphylococcus aureus},
author = {Maximilian P Kohl and Béatrice Chane-Woon-Ming and Roberto Bahena-Ceron and Jose Jaramillo-Ponce and Laura Antoine and Lucas Herrgott and Pascale Romby and Stefano Marzi},
doi = {10.1007/978-1-0716-3565-0_5},
issn = {1940-6029},
year = {2024},
date = {2024-01-01},
urldate = {2024-01-01},
journal = {Methods Mol Biol},
volume = {2741},
pages = {73--100},
abstract = {Noncoding RNAs, including regulatory RNAs (sRNAs), are instrumental in regulating gene expression in pathogenic bacteria, allowing them to adapt to various stresses encountered in their host environments. Staphylococcus aureus is a well-studied model for RNA-mediated regulation of virulence and pathogenicity, with sRNAs playing significant roles in shaping S. aureus interactions with human and animal hosts. By modulating the translation and/or stability of target mRNAs, sRNAs regulate the synthesis of virulence factors and regulatory proteins required for pathogenesis. Moreover, perturbation of the levels of RNA modifications in two other classes of noncoding RNAs, rRNAs, and tRNAs, has been proposed to contribute to stress adaptation. However, the study of how these various factors affect translation regulation has often been restricted to specific genes, using in vivo reporters and/or in vitro translation systems. Genome-wide sequencing approaches offer novel perspectives for studying RNA-dependent regulation. In particular, ribosome profiling methods provide a powerful resource for characterizing the overall landscape of translational regulation, contributing to a better understanding of S. aureus physiopathology. Here, we describe protocols that we have adapted to perform ribosome profiling in S. aureus.},
keywords = {MARZI, ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Baldaccini Morgane, Gaucherand Léa, Chane-Woon-Ming Béatrice, Messmer Mélanie, Gucciardi Floriane, Pfeffer Sébastien
The helicase domain of human Dicer prevents RNAi-independent activation of antiviral and inflammatory pathways Journal Article
In: EMBO J, 2024, ISSN: 1460-2075.
Abstract | Links | BibTeX | Tags: PFEFFER, Unité ARN
@article{pmid38287188,
title = {The helicase domain of human Dicer prevents RNAi-independent activation of antiviral and inflammatory pathways},
author = {Morgane Baldaccini and Léa Gaucherand and Béatrice Chane-Woon-Ming and Mélanie Messmer and Floriane Gucciardi and Sébastien Pfeffer},
doi = {10.1038/s44318-024-00035-2},
issn = {1460-2075},
year = {2024},
date = {2024-01-01},
urldate = {2024-01-01},
journal = {EMBO J},
abstract = {In mammalian somatic cells, the relative contribution of RNAi and the type I interferon response during viral infection is unclear. The apparent inefficiency of antiviral RNAi might be due to self-limiting properties and mitigating co-factors of the key enzyme Dicer. In particular, the helicase domain of human Dicer appears to be an important restriction factor of its activity. Here, we study the involvement of several helicase-truncated mutants of human Dicer in the antiviral response. All deletion mutants display a PKR-dependent antiviral phenotype against certain viruses, and one of them, Dicer N1, acts in a completely RNAi-independent manner. Transcriptomic analyses show that many genes from the interferon and inflammatory response pathways are upregulated in Dicer N1 expressing cells. We show that some of these genes are controlled by NF-kB and that blocking this pathway abrogates the antiviral phenotype of Dicer N1. Our findings highlight the crosstalk between Dicer, PKR, and the NF-kB pathway, and suggest that human Dicer may have repurposed its helicase domain to prevent basal activation of antiviral and inflammatory pathways.},
keywords = {PFEFFER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Nerantzaki Maria, Husser Claire, Ryckelynck Michael, Lutz Jean-François
Exchanging and Releasing Information in Synthetic Digital Polymers Using a Strand-Displacement Strategy Journal Article
In: J Am Chem Soc, 2024, ISSN: 1520-5126.
Abstract | Links | BibTeX | Tags: RYCKELYNCK, Unité ARN
@article{pmid38286022,
title = {Exchanging and Releasing Information in Synthetic Digital Polymers Using a Strand-Displacement Strategy},
author = {Maria Nerantzaki and Claire Husser and Michael Ryckelynck and Jean-François Lutz},
doi = {10.1021/jacs.3c13953},
issn = {1520-5126},
year = {2024},
date = {2024-01-01},
urldate = {2024-01-01},
journal = {J Am Chem Soc},
abstract = {Toehold-mediated strand displacement (TMSD) was tested as a tool to edit information in synthetic digital polymers. Uniform DNA-polymer biohybrid macromolecules were first synthesized by automated phosphoramidite chemistry and characterized by HPLC, mass spectrometry, and polyacrylamide gel electrophoresis (PAGE). These precursors were diblock structures containing a synthetic poly(phosphodiester) (PPDE) segment covalently attached to a single-stranded DNA sequence. Three types of biohybrids were prepared herein: a substrate containing an accessible toehold as well as input and output macromolecules. The substrate and the input macromolecules contained noncoded PPDE homopolymers, whereas the output macromolecule contained a digitally encoded segment. After hybridization of the substrate with the output, incubation in the presence of the input led to efficient TMSD and the release of the digital segment. TMSD can therefore be used to erase or rewrite information in self-assembled biohybrid superstructures. Furthermore, it was found in this work that the conjugation of DNA single strands to synthetic segments of chosen lengths greatly facilitates the characterization and PAGE visualization of the TMSD process.},
keywords = {RYCKELYNCK, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Quignon E., Ferhadian D., Hache A., Vivet-Boudou V., Isel C., Printz-Schweigert A., Donchet A., Crépin T., Marquet R.
Structural Impact of the Interaction of the Influenza A Virus Nucleoprotein with Genomic RNA Segments Journal Article
In: Viruses, vol. 16, no. 3, pp. 421, 2024, ISBN: 10.3390/v16030421.
Abstract | Links | BibTeX | Tags: MARQUET, MARQUET influenza A virus NP nucleoprotein vRNA RNA structure RNA chaperon chemical probing, Unité ARN
@article{nokey,
title = {Structural Impact of the Interaction of the Influenza A Virus Nucleoprotein with Genomic RNA Segments},
author = {E. Quignon and D. Ferhadian and A. Hache and V. Vivet-Boudou and C. Isel and A. Printz-Schweigert and A. Donchet and T. Crépin and R. Marquet},
url = {https://www.mdpi.com/1999-4915/16/3/421},
isbn = {10.3390/v16030421},
year = {2024},
date = {2024-01-01},
urldate = {2024-01-01},
journal = {Viruses},
volume = {16},
number = {3},
pages = {421},
abstract = {Influenza A viruses (IAVs) possess a segmented genome consisting of eight viral RNAs (vRNAs) associated with multiple copies of viral nucleoprotein (NP) and a viral polymerase complex. Despite the crucial role of RNA structure in IAV replication, the impact of NP binding on vRNA structure is not well understood. In this study, we employed SHAPE chemical probing to compare the structure of NS and M vRNAs of WSN IAV in various states: before the addition of NP, in complex with NP, and after the removal of NP. Comparison of the RNA structures before the addition of NP and after its removal reveals that NP, while introducing limited changes, remodels local structures in both vRNAs and long-range interactions in the NS vRNA, suggesting a potentially biologically relevant RNA chaperone activity. In contrast, NP significantly alters the structure of vRNAs in vRNA/NP complexes, though incorporating experimental data into RNA secondary structure prediction proved challenging. Finally, our results suggest that NP not only binds single-stranded RNA but also helices with interruptions, such as bulges or small internal loops, with a preference for G-poor and C/U-rich regions.},
keywords = {MARQUET, MARQUET influenza A virus NP nucleoprotein vRNA RNA structure RNA chaperon chemical probing, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Hayek Hassan, Gross Lauriane, Alghoul Fatima, Martin Franck, Eriani Gilbert, Allmang Christine
Immunoprecipitation Methods to Isolate Messenger Ribonucleoprotein Complexes (mRNP) Journal Article
In: Adv Exp Med Biol, vol. 3234, pp. 1–15, 2024, ISSN: 0065-2598.
Abstract | Links | BibTeX | Tags: ERIANI, MARTIN, PPSE, Unité ARN
@article{pmid38507196,
title = {Immunoprecipitation Methods to Isolate Messenger Ribonucleoprotein Complexes (mRNP)},
author = {Hassan Hayek and Lauriane Gross and Fatima Alghoul and Franck Martin and Gilbert Eriani and Christine Allmang},
doi = {10.1007/978-3-031-52193-5_1},
issn = {0065-2598},
year = {2024},
date = {2024-01-01},
urldate = {2024-01-01},
journal = {Adv Exp Med Biol},
volume = {3234},
pages = {1--15},
abstract = {Throughout their life cycle, messenger RNAs (mRNAs) associate with proteins to form ribonucleoproteins (mRNPs). Each mRNA is part of multiple successive mRNP complexes that participate in their biogenesis, cellular localization, translation and decay. The dynamic composition of mRNP complexes and their structural remodelling play crucial roles in the control of gene expression. Studying the endogenous composition of different mRNP complexes is a major challenge. In this chapter, we describe the variety of protein-centric immunoprecipitation methods available for the identification of mRNP complexes and the requirements for their experimental settings.},
keywords = {ERIANI, MARTIN, PPSE, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Janvier Aurélie, Hayek Hassan, Alghoul Fatima, Gross Lauriane, Allmang Christine, Martin Franck, Eriani Gilbert
Purification of In Vivo or In Vitro-Assembled RNA-Protein Complexes by RNA Centric Methods Journal Article
In: Adv Exp Med Biol, vol. 3234, pp. 17–29, 2024, ISSN: 0065-2598.
Abstract | Links | BibTeX | Tags: ERIANI, MARTIN, Unité ARN
@article{pmid38507197,
title = {Purification of In Vivo or In Vitro-Assembled RNA-Protein Complexes by RNA Centric Methods},
author = {Aurélie Janvier and Hassan Hayek and Fatima Alghoul and Lauriane Gross and Christine Allmang and Franck Martin and Gilbert Eriani},
doi = {10.1007/978-3-031-52193-5_2},
issn = {0065-2598},
year = {2024},
date = {2024-01-01},
urldate = {2024-01-01},
journal = {Adv Exp Med Biol},
volume = {3234},
pages = {17--29},
abstract = {Throughout their entire life cycle, RNAs are associated with RNA-binding proteins (RBPs), forming ribonucleoprotein (RNP) complexes with highly dynamic compositions and very diverse functions in RNA metabolism, including splicing, translational regulation, ribosome assembly. Many RNPs remain poorly characterized due to the challenges inherent in their purification and subsequent biochemical characterization. Therefore, developing methods to isolate specific RNA-protein complexes is an important initial step toward understanding their function. Many elegant methodologies have been developed to isolate RNPs. This chapter describes different approaches and methods devised for RNA-specific purification of a target RNP. We focused on general methods for selecting RNPs that target a given RNA under conditions favourable for the copurification of associated factors including RNAs and protein components of the RNP.},
keywords = {ERIANI, MARTIN, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Khodr Radi, Husser Claire, Ryckelynck Michael
Direct fluoride monitoring using a fluorogenic RNA-based biosensor Journal Article
In: Methods Enzymol, vol. 696, pp. 85–107, 2024, ISSN: 1557-7988.
Abstract | Links | BibTeX | Tags: RYCKELYNCK, Unité ARN
@article{pmid38658090,
title = {Direct fluoride monitoring using a fluorogenic RNA-based biosensor},
author = {Radi Khodr and Claire Husser and Michael Ryckelynck},
doi = {10.1016/bs.mie.2023.12.019},
issn = {1557-7988},
year = {2024},
date = {2024-01-01},
urldate = {2024-01-01},
journal = {Methods Enzymol},
volume = {696},
pages = {85--107},
abstract = {Fluorinated compounds, whether naturally occurring or from anthropogenic origin, have been extensively exploited in the last century. Degradation of these compounds by physical or biochemical processes is expected to result in the release of fluoride. Several fluoride detection mechanisms have been previously described. However, most of these methods are not compatible with high- and ultrahigh-throughput screening technologies, lack the ability to real-time monitor the increase of fluoride concentration in solution, or rely on costly reagents (such as cell-free expression systems). Our group recently developed "FluorMango" as the first completely RNA-based and direct fluoride-specific fluorogenic biosensor. To do so, we merged and engineered the Mango-III light-up RNA aptamer and the fluoride-specific aptamer derived from a riboswitch, crcB. In this chapter, we explain how this RNA-based biosensor can be produced in large scale before providing examples of how it can be used to quantitatively detect (end-point measurement) or monitor in real-time fluoride release in complex biological systems by translating it into measurable fluorescent signal.},
keywords = {RYCKELYNCK, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Skerniskyte Jurate, Mulet Céline, André Antonin C, Anderson Mark C, Injarabian Louise, Buck Achim, Prade Verena M, Sansonetti Philippe J, Reibel-Foisset Sophie, Walch Axel K, Lebel Michel, Lykkesfeldt Jens, Marteyn Benoit S
Ascorbate deficiency increases progression of shigellosis in guinea pigs and mice infection models Journal Article
In: Gut Microbes, vol. 15, no. 2, pp. 2271597, 2023, ISSN: 1949-0984.
Abstract | Links | BibTeX | Tags: MARTEYN, Unité ARN
@article{pmid37876025,
title = {Ascorbate deficiency increases progression of shigellosis in guinea pigs and mice infection models},
author = {Jurate Skerniskyte and Céline Mulet and Antonin C André and Mark C Anderson and Louise Injarabian and Achim Buck and Verena M Prade and Philippe J Sansonetti and Sophie Reibel-Foisset and Axel K Walch and Michel Lebel and Jens Lykkesfeldt and Benoit S Marteyn},
doi = {10.1080/19490976.2023.2271597},
issn = {1949-0984},
year = {2023},
date = {2023-12-01},
urldate = {2023-12-01},
journal = {Gut Microbes},
volume = {15},
number = {2},
pages = {2271597},
abstract = { spp. are the causative agents of bacterial dysentery and shigellosis, mainly in children living in developing countries. The study of entire life cycle and the evaluation of vaccine candidates' protective efficacy have been hampered by the lack of a suitable animal model of infection. None of the studies evaluated so far (rabbit, guinea pig, mouse) allowed the recapitulation of full shigellosis symptoms upon oral challenge. Historical reports have suggested that dysentery and scurvy are both metabolic diseases associated with ascorbate deficiency. Mammals, which are susceptible to infection (humans, non-human primates and guinea pigs) are among the few species unable to synthesize ascorbate. We optimized a low-ascorbate diet to induce moderate ascorbate deficiency, but not scurvy, in guinea pigs to investigate whether poor vitamin C status increases the progression of shigellosis. Moderate ascorbate deficiency increased shigellosis symptom severity during an extended period of time (up to 48 h) in all strains tested (, 5a, and 2a). At late time points, an important influx of neutrophils was observed both within the disrupted colonic mucosa and in the luminal compartment, although was able to disseminate deep into the organ to reach the sub-mucosal layer and the bloodstream. Moreover, we found that ascorbate deficiency also increased penetration into the colon epithelium layer in a Gulo mouse infection model. The use of these new rodent models of shigellosis opens new doors for the study of both infection strategies and immune responses to infection.},
keywords = {MARTEYN, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Kompatscher Maria, Bartosik Karolina, Erharter Kevin, Plangger Raphael, Juen Fabian Sebastian, Kreutz Christoph, Micura Ronald, Westhof Eric, Erlacher Matthias D
Contribution of tRNA sequence and modifications to the decoding preferences of E. coli and M. mycoides tRNAGlyUCC for synonymous glycine codons Journal Article
In: Nucleic Acids Res, 2023, ISSN: 1362-4962.
Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF
@article{pmid38050960,
title = {Contribution of tRNA sequence and modifications to the decoding preferences of E. coli and M. mycoides tRNAGlyUCC for synonymous glycine codons},
author = {Maria Kompatscher and Karolina Bartosik and Kevin Erharter and Raphael Plangger and Fabian Sebastian Juen and Christoph Kreutz and Ronald Micura and Eric Westhof and Matthias D Erlacher},
doi = {10.1093/nar/gkad1136},
issn = {1362-4962},
year = {2023},
date = {2023-12-01},
urldate = {2023-12-01},
journal = {Nucleic Acids Res},
abstract = {tRNA superwobbling, used by certain bacteria and organelles, is an intriguing decoding concept in which a single tRNA isoacceptor is used to decode all synonymous codons of a four-fold degenerate codon box. While Escherichia coli relies on three tRNAGly isoacceptors to decode the four glycine codons (GGN), Mycoplasma mycoides requires only a single tRNAGly. Both organisms express tRNAGly with the anticodon UCC, which are remarkably similar in sequence but different in their decoding ability. By systematically introducing mutations and altering the number and type of tRNA modifications using chemically synthesized tRNAs, we elucidated the contribution of individual nucleotides and chemical groups to decoding by the E. coli and M. mycoides tRNAGly. The tRNA sequence was identified as the key factor for superwobbling, revealing the T-arm sequence as a novel pivotal element. In addition, the presence of tRNA modifications, although not essential for providing superwobbling, was shown to delicately fine-tune and balance the decoding of synonymous codons. This emphasizes that the tRNA sequence and its modifications together form an intricate system of high complexity that is indispensable for accurate and efficient decoding.},
keywords = {Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Bahena-Ceron Roberto, Teixeira Chloe, Ponce Jose R Jaramillo, Wolff Philippe, Couzon Florence, François Pauline, Klaholz Bruno, Vandenesch François, Romby Pascale, Moreau Karen, Marzi Stefano
RlmQ: A Newly Discovered rRNA Modification Enzyme Bridging RNA Modification and Virulence Traits in Journal Article
In: RNA, vol. 30, no. 3, pp. 200-212, 2023, ISSN: 1469-9001.
Abstract | Links | BibTeX | Tags: ARN-MS, ROMBY, Unité ARN
@article{pmid38164596,
title = {RlmQ: A Newly Discovered rRNA Modification Enzyme Bridging RNA Modification and Virulence Traits in },
author = {Roberto Bahena-Ceron and Chloe Teixeira and Jose R Jaramillo Ponce and Philippe Wolff and Florence Couzon and Pauline François and Bruno Klaholz and François Vandenesch and Pascale Romby and Karen Moreau and Stefano Marzi},
doi = {10.1261/rna.079850.123},
issn = {1469-9001},
year = {2023},
date = {2023-12-01},
urldate = {2023-12-01},
journal = {RNA},
volume = {30},
number = {3},
pages = {200-212},
abstract = {rRNA modifications play crucial roles in fine-tuning the delicate balance between translation speed and accuracy, yet the underlying mechanisms remain elusive. Comparative analyses of the ribosomal RNA modifications in taxonomically distant bacteria could help define their general, as well as species-specific, roles. In this study, we identified a new methyltransferase, RlmQ, in responsible for the Gram-positive specific mG2601, which is not modified in (G2574). We also demonstrate the absence of methylation on C1989, equivalent to C1962, which is methylated at position 5 by the Gram-negative specific RlmI methyltransferase, a paralogue of RlmQ. Both modifications ( mG2601 and mC1962) are situated within the same tRNA accommodation corridor, hinting at a potential shared function in translation. Inactivation of Q causes the loss of methylation at G2601 and significantly impacts growth, cytotoxicity, and biofilm formation. These findings unravel the intricate connections between rRNA modifications, translation, and virulence in pathogenic Gram-positive bacteria.},
keywords = {ARN-MS, ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Ponce José R Jaramillo, Frugier Magali
Plasmodium, the Apicomplexa Outlier When It Comes to Protein Synthesis Journal Article
In: Biomolecules, vol. 14, no. 1, pp. 46, 2023, ISSN: 2218-273X.
Abstract | Links | BibTeX | Tags: FRUGIER, Unité ARN
@article{pmid38254646,
title = {Plasmodium, the Apicomplexa Outlier When It Comes to Protein Synthesis},
author = {José R Jaramillo Ponce and Magali Frugier},
doi = {10.3390/biom14010046},
issn = {2218-273X},
year = {2023},
date = {2023-12-01},
urldate = {2023-12-01},
journal = {Biomolecules},
volume = {14},
number = {1},
pages = {46},
abstract = {Plasmodium is an obligate intracellular parasite that has numerous interactions with different hosts during its elaborate life cycle. This is also the case for the other parasites belonging to the same phylum Apicomplexa. In this study, we bioinformatically identified the components of the multi-synthetase complexes (MSCs) of several Apicomplexa parasites and modelled their assembly using AlphaFold2. It appears that none of these MSCs resemble the two MSCs that we have identified and characterized in Plasmodium. Indeed, tRip, the central protein involved in the association of the two Plasmodium MSCs is different from its homologues, suggesting also that the tRip-dependent import of exogenous tRNAs is not conserved in other apicomplexan parasites. Based on this observation, we searched for obvious differences that could explain the singularity of Plasmodium protein synthesis by comparing tRNA genes and amino acid usage in the different genomes. We noted a contradiction between the large number of asparagine residues used in Plasmodium proteomes and the single gene encoding the tRNA that inserts them into proteins. This observation remains true for all the Plasmodia strains studied, even those that do not contain long asparagine homorepeats. },
keywords = {FRUGIER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Lu Kunpeng, Pan Yifei, Shen Jianghong, Yang Lin, Zhan Chengyu, Liang Shubo, Tai Shuaishuai, Wan Linrong, Li Tian, Cheng Tingcai, Ma Bi, Pan Guoqing, He Ningjia, Lu Cheng, Westhof Eric, Xiang Zhonghuai, Han Min-Jin, Tong Xiaoling, Dai Fangyin
SilkMeta: a comprehensive platform for sharing and exploiting pan-genomic and multi-omic silkworm data Journal Article
In: Nucleic Acids Res, vol. 52, iss. D1, pp. D1024-D1032, 2023, ISSN: 1362-4962.
Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF
@article{pmid37941143,
title = {SilkMeta: a comprehensive platform for sharing and exploiting pan-genomic and multi-omic silkworm data},
author = {Kunpeng Lu and Yifei Pan and Jianghong Shen and Lin Yang and Chengyu Zhan and Shubo Liang and Shuaishuai Tai and Linrong Wan and Tian Li and Tingcai Cheng and Bi Ma and Guoqing Pan and Ningjia He and Cheng Lu and Eric Westhof and Zhonghuai Xiang and Min-Jin Han and Xiaoling Tong and Fangyin Dai},
doi = {10.1093/nar/gkad956},
issn = {1362-4962},
year = {2023},
date = {2023-11-01},
urldate = {2023-11-01},
journal = {Nucleic Acids Res},
volume = {52},
issue = {D1},
pages = {D1024-D1032},
abstract = {The silkworm Bombyx mori is a domesticated insect that serves as an animal model for research and agriculture. The silkworm super-pan-genome dataset, which we published last year, is a unique resource for the study of global genomic diversity and phenotype-genotype association. Here we present SilkMeta (http://silkmeta.org.cn), a comprehensive database covering the available silkworm pan-genome and multi-omics data. The database contains 1082 short-read genomes, 546 long-read assembled genomes, 1168 transcriptomes, 294 phenotype characterizations (phenome), tens of millions of variations (variome), 7253 long non-coding RNAs (lncRNAs), 18 717 full length transcripts and a set of population statistics. We have compiled publications on functional genomics research and genetic stock deciphering (mutant map). A range of bioinformatics tools is also provided for data visualization and retrieval. The large batch of omics data and tools were integrated in twelve functional modules that provide useful strategies and data for comparative and functional genomics research. The interactive bioinformatics platform SilkMeta will benefit not only the silkworm but also the insect biology communities.},
keywords = {Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Arrivé Mathilde, Bruggeman Mathieu, Skaltsogiannis Vasileios, Coudray Léna, Quan Yi-Fat, Schelcher Cédric, Cognat Valérie, Hammann Philippe, Chicher Johana, Wolff Philippe, Gobert Anthony, Giegé Philippe
A tRNA-modifying enzyme facilitates RNase P activity in Arabidopsis nuclei Journal Article
In: Nat Plants, vol. 9, iss. 12, pp. 2031-2041, 2023, ISSN: 2055-0278.
Abstract | Links | BibTeX | Tags: ARN-MS, PPSE, Unité ARN
@article{pmid37945696,
title = {A tRNA-modifying enzyme facilitates RNase P activity in Arabidopsis nuclei},
author = {Mathilde Arrivé and Mathieu Bruggeman and Vasileios Skaltsogiannis and Léna Coudray and Yi-Fat Quan and Cédric Schelcher and Valérie Cognat and Philippe Hammann and Johana Chicher and Philippe Wolff and Anthony Gobert and Philippe Giegé},
doi = {10.1038/s41477-023-01564-0},
issn = {2055-0278},
year = {2023},
date = {2023-11-01},
urldate = {2023-11-01},
journal = {Nat Plants},
volume = {9},
issue = {12},
pages = {2031-2041},
abstract = {RNase P is the essential activity that performs the 5' maturation of transfer RNA (tRNA) precursors. Beyond the ancestral form of RNase P containing a ribozyme, protein-only RNase P enzymes termed PRORP were identified in eukaryotes. In human mitochondria, PRORP forms a complex with two protein partners to become functional. In plants, although PRORP enzymes are active alone, we investigate their interaction network to identify potential tRNA maturation complexes. Here we investigate functional interactions involving the Arabidopsis nuclear RNase P PRORP2. We show, using an immuno-affinity strategy, that PRORP2 occurs in a complex with the tRNA methyl transferases TRM1A and TRM1B in vivo. Beyond RNase P, these enzymes can also interact with RNase Z. We show that TRM1A/TRM1B localize in the nucleus and find that their double knockout mutation results in a severe macroscopic phenotype. Using a combination of immuno-detections, mass spectrometry and a transcriptome-wide tRNA sequencing approach, we observe that TRM1A/TRM1B are responsible for the mG26 modification of 70% of cytosolic tRNAs in vivo. We use the transcriptome wide tRNAseq approach as well as RNA blot hybridizations to show that RNase P activity is impaired in TRM1A/TRM1B mutants for specific tRNAs, in particular, tRNAs containing a mG modification at position 26 that are strongly downregulated in TRM1A/TRM1B mutants. Altogether, results indicate that the mG-adding enzymes TRM1A/TRM1B functionally cooperate with nuclear RNase P in vivo for the early steps of cytosolic tRNA biogenesis.},
keywords = {ARN-MS, PPSE, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Silva P Malaka De, Bennett Rebecca J, Kuhn Lauriane, Ngondo Patryk, Debande Lorine, Njamkepo Elisabeth, Ho Brian, Weill François-Xavier, Marteyn Benoît S, Jenkins Claire, Baker Kate S
Escherichia coli killing by epidemiologically successful sublineages of Shigella sonnei is mediated by colicins Journal Article
In: EBioMedicine, vol. 97, pp. 104822, 2023, ISSN: 2352-3964.
Abstract | Links | BibTeX | Tags: MARTEYN, PPSE, Unité ARN
@article{pmid37806286,
title = {Escherichia coli killing by epidemiologically successful sublineages of Shigella sonnei is mediated by colicins},
author = {P Malaka De Silva and Rebecca J Bennett and Lauriane Kuhn and Patryk Ngondo and Lorine Debande and Elisabeth Njamkepo and Brian Ho and François-Xavier Weill and Benoît S Marteyn and Claire Jenkins and Kate S Baker},
doi = {10.1016/j.ebiom.2023.104822},
issn = {2352-3964},
year = {2023},
date = {2023-10-01},
urldate = {2023-10-01},
journal = {EBioMedicine},
volume = {97},
pages = {104822},
abstract = {BACKGROUND: Shigella sp. are enteric pathogens which causes >125 million cases of shigellosis annually. S. sonnei accounts for about a quarter of those cases and is increasingly prevalent in industrialising nations. Being an enteric pathogen, S. sonnei benefits from outcompeting gut commensals such as Escherichia coli to establish itself and cause disease. There are numerous mechanisms that bacterial pathogens use to outcompete its rivals including molecules called colicins. A Type 6 Secretion System (T6SS) was recently described as contributing to E. coli killing in S. sonnei.nnMETHODS: We used Bulk Phenotyping of Epidemiological Replicates (BPER) which combined bacterial Genome Wide Association Studies (bGWAS) and high throughput phenotyping on a collection of S. sonnei surveillance isolates to identify the genetic features associated with E. coli killing and explore their relationship with epidemiological behaviour. We further explored the presence of colicins and T6SS components in the isolates using genomics, laboratory experimentation, and proteomics.nnFINDINGS: Our bGWAS analysis returned known and novel colicin and colicin related genes as significantly associated with E. coli killing. In silico analyses identified key colicin clusters responsible for the killing phenotype associated with epidemiologically successful sub-lineages. The killing phenotype was not associated with the presence of a T6SS. Laboratory analyses confirmed the presence of the key colicin clusters and that killing was contact-independent.nnINTERPRETATION: Colicins are responsible for E. coli killing by S. sonnei, not a T6SS. This phenotype contributes to shaping the observed epidemiology of S. sonnei and may contribute to its increasing prevalence globally. BPER is an epidemiologically relevant approach to phenotypic testing that enables the rapid identification of genetic drivers of phenotypic changes, and assessment of their relevance to epidemiology in natural settings.nnFUNDING: Biotechnology and Biological Sciences Research Council, Biotechnology and Biological Sciences Research Council Doctoral Training Partnership studentship, Wellcome Trust, Medical Research Council (UK), French National Research Agency.},
keywords = {MARTEYN, PPSE, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Das Rhiju, Kretsch Rachael C, Simpkin Adam J, Mulvaney Thomas, Pham Phillip, Rangan Ramya, Bu Fan, Keegan Ronan M, Topf Maya, Rigden Daniel J, Miao Zhichao, Westhof Eric
Assessment of three-dimensional RNA structure prediction in CASP15 Journal Article
In: Proteins, vol. 91, iss. 12, pp. 1747-1770, 2023, ISSN: 1097-0134.
Abstract | Links | BibTeX | Tags: Unité ARN, WESTHOF
@article{pmid37876231,
title = {Assessment of three-dimensional RNA structure prediction in CASP15},
author = {Rhiju Das and Rachael C Kretsch and Adam J Simpkin and Thomas Mulvaney and Phillip Pham and Ramya Rangan and Fan Bu and Ronan M Keegan and Maya Topf and Daniel J Rigden and Zhichao Miao and Eric Westhof},
doi = {10.1002/prot.26602},
issn = {1097-0134},
year = {2023},
date = {2023-10-01},
urldate = {2023-10-01},
journal = {Proteins},
volume = {91},
issue = {12},
pages = {1747-1770},
abstract = {The prediction of RNA three-dimensional structures remains an unsolved problem. Here, we report assessments of RNA structure predictions in CASP15, the first CASP exercise that involved RNA structure modeling. Forty-two predictor groups submitted models for at least one of twelve RNA-containing targets. These models were evaluated by the RNA-Puzzles organizers and, separately, by a CASP-recruited team using metrics (GDT, lDDT) and approaches (Z-score rankings) initially developed for assessment of proteins and generalized here for RNA assessment. The two assessments independently ranked the same predictor groups as first (AIchemy_RNA2), second (Chen), and third (RNAPolis and GeneSilico, tied); predictions from deep learning approaches were significantly worse than these top ranked groups, which did not use deep learning. Further analyses based on direct comparison of predicted models to cryogenic electron microscopy (cryo-EM) maps and x-ray diffraction data support these rankings. With the exception of two RNA-protein complexes, models submitted by CASP15 groups correctly predicted the global fold of the RNA targets. Comparisons of CASP15 submissions to designed RNA nanostructures as well as molecular replacement trials highlight the potential utility of current RNA modeling approaches for RNA nanotechnology and structural biology, respectively. Nevertheless, challenges remain in modeling fine details such as noncanonical pairs, in ranking among submitted models, and in prediction of multiple structures resolved by cryo-EM or crystallography.},
keywords = {Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
LABARONNE E., DECIMO D., BERTRAND L., GUIGUETTAZ L., SOHIER T. J. M., CLUET D., VIVET-BOUDOU V., DAHOUI C., FRANçOIS P., HATIN I., LAMBOTTE O., SAMRI A., AUTRAN B., ETIENNE L., GOUJON C., PAILLART J. -C., NAMY O., RAMIREZ B. C., OHLMANN T., MORRIS A., RICCI E. P.
In: (bioRxiv & medRxiv), 2023.
Links | BibTeX | Tags: PAILLART, Unité ARN
@article{nokey,
title = {Extensive uORF translation from HIV-1 transcripts elicits specific T cell immune responses in infected individuals and conditions DDX3 dependency for expression of main ORFs},
author = {LABARONNE , E. and DECIMO , D. and BERTRAND , L. and GUIGUETTAZ , L. and SOHIER , T.J.M. and CLUET , D. and VIVET-BOUDOU , V. and DAHOUI , C. and FRANçOIS , P. and HATIN , I. and LAMBOTTE , O. and SAMRI , A. and AUTRAN , B. and ETIENNE , L. and GOUJON , C. and PAILLART , J.-C. and NAMY , O. and RAMIREZ , B.C. and OHLMANN , T. and MORRIS , A. and RICCI, E.P.},
doi = {10.1101/2022.04.29.489990},
year = {2023},
date = {2023-09-20},
urldate = {2023-09-20},
journal = {(bioRxiv & medRxiv)},
keywords = {PAILLART, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Zheng Wen-Qiang, Zhang Jian-Hui, Li Zi-Han, Liu Xiuxiu, Zhang Yong, Huang Shuo, Li Jinsong, Zhou Bin, Eriani Gilbert, Wang En-Duo, Zhou Xiao-Long
Mammalian mitochondrial translation infidelity leads to oxidative stress-induced cell cycle arrest and cardiomyopathy Journal Article
In: Proc Natl Acad Sci U S A, vol. 120, no. 37, pp. e2309714120, 2023, ISSN: 1091-6490.
Abstract | Links | BibTeX | Tags: ERIANI, Unité ARN
@article{pmid37669377,
title = {Mammalian mitochondrial translation infidelity leads to oxidative stress-induced cell cycle arrest and cardiomyopathy},
author = {Wen-Qiang Zheng and Jian-Hui Zhang and Zi-Han Li and Xiuxiu Liu and Yong Zhang and Shuo Huang and Jinsong Li and Bin Zhou and Gilbert Eriani and En-Duo Wang and Xiao-Long Zhou},
doi = {10.1073/pnas.2309714120},
issn = {1091-6490},
year = {2023},
date = {2023-09-01},
urldate = {2023-09-01},
journal = {Proc Natl Acad Sci U S A},
volume = {120},
number = {37},
pages = {e2309714120},
abstract = {Proofreading (editing) of mischarged tRNAs by cytoplasmic aminoacyl-tRNA synthetases (aaRSs), whose impairment causes neurodegeneration and cardiac diseases, is of high significance for protein homeostasis. However, whether mitochondrial translation needs fidelity and the significance of editing by mitochondrial aaRSs have been unclear. Here, we show that mammalian cells critically depended on the editing of mitochondrial threonyl-tRNA synthetase (mtThrRS, encoded by ), disruption of which accumulated Ser-tRNA and generated a large abundance of Thr-to-Ser misincorporated peptides in vivo. Such infidelity impaired mitochondrial translation and oxidative phosphorylation, causing oxidative stress and cell cycle arrest in the G0/G1 phase. Notably, reactive oxygen species (ROS) scavenging by N-acetylcysteine attenuated this abnormal cell proliferation. A mouse model of heart-specific defective mtThrRS editing was established. Increased ROS levels, blocked cardiomyocyte proliferation, contractile dysfunction, dilated cardiomyopathy, and cardiac fibrosis were observed. Our results elucidate that mitochondria critically require a high level of translational accuracy at Thr codons and highlight the cellular dysfunctions and imbalance in tissue homeostasis caused by mitochondrial mistranslation.},
keywords = {ERIANI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Dufossez Robin, Krafft Marie-Pierre, Ursuegui Sylvain, Mosser Michel, Mouftakhir Safae, Pernod Ketty, Chaubet Guilhem, Ryckelynck Michael, Wagner Alain
Microfluidic Droplet Stabilization via SPAAC Promoted Antibody Conjugation at the Water/Oil Interface Journal Article
In: ACS Appl Mater Interfaces, vol. 15, iss. 38, pp. 45498-45505, 2023, ISSN: 1944-8252.
Abstract | Links | BibTeX | Tags: RYCKELYNCK, Unité ARN
@article{pmid37704020,
title = {Microfluidic Droplet Stabilization via SPAAC Promoted Antibody Conjugation at the Water/Oil Interface},
author = {Robin Dufossez and Marie-Pierre Krafft and Sylvain Ursuegui and Michel Mosser and Safae Mouftakhir and Ketty Pernod and Guilhem Chaubet and Michael Ryckelynck and Alain Wagner},
doi = {10.1021/acsami.3c10655},
issn = {1944-8252},
year = {2023},
date = {2023-09-01},
urldate = {2023-09-01},
journal = {ACS Appl Mater Interfaces},
volume = {15},
issue = {38},
pages = {45498-45505},
abstract = {Droplet-based microfluidics is leading the development of miniaturized, rapid, and sensitive version of enzyme-linked immunosorbent assays (ELISAs), a central method for protein detection. These assays involve the use of a functionalized surface able to selectively capture the desired analyte. Using the droplet's oil water interface as a capture surface requires designing custom-perfluorinated fluorosurfactants bearing azide-containing polar groups, which spontaneously react when forming the droplet with strain-alkyne-functionalized antibodies solubilized in the aqueous phase. In this article, we present our research on the influence of the structure of surfactant's hydrophilic heads on the efficiency of SPAAC functionalization and on the effect of this antibody grafting process on droplet stability. We have shown that while short linkers lead to high grafting efficiency, long linkers lead to high stability, and that an intermediate size is required to balance both parameters. In the described family of surfactants, the optimal structure proved to be a PEG linker connecting a polar di-azide head and a per-fluoropolyether tail (Krytox). We also found that grafting an increasing amount of antibody, thus increasing interface coverage, increases droplet stability. It thus appears that such a bi-partite system with a reactive fluoro-surfactant in the oil phase and reactive antibody counterpart in the aqueous phase gives access in situ to novel surfactant construct providing unexplored interface structures and droplet functionality.},
keywords = {RYCKELYNCK, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Tidu Antonin, Martin Franck
The interplay between cis- and trans-acting factors drives selective mRNA translation initiation in eukaryotes Journal Article
In: Biochimie, vol. 217, pp. 20-30, 2023, ISSN: 1638-6183.
Abstract | Links | BibTeX | Tags: MARTIN, Unité ARN
@article{pmid37741547,
title = {The interplay between cis- and trans-acting factors drives selective mRNA translation initiation in eukaryotes},
author = {Antonin Tidu and Franck Martin},
doi = {10.1016/j.biochi.2023.09.017},
issn = {1638-6183},
year = {2023},
date = {2023-09-01},
urldate = {2023-09-01},
journal = {Biochimie},
volume = {217},
pages = {20-30},
abstract = {Translation initiation consists in the assembly of the small and large ribosomal subunits on the start codon. This important step directly modulates the general proteome in living cells. Recently, genome wide studies revealed unexpected translation initiation events from unsuspected novel open reading frames resulting in the synthesis of a so-called 'dark proteome'. Indeed, the identification of the start codon by the translation machinery is a critical step that defines the translational landscape of the cell. Therefore, translation initiation is a highly regulated process in all organisms. In this review, we focus on the various cis- and trans-acting factors that rule the regulation of translation initiation in eukaryotes. Recent discoveries have shown that the guidance of the translation machinery for the choice of the start codon require sophisticated molecular mechanisms. In particular, the 5'UTR and the coding sequences contain cis-acting elements that trigger the use of AUG codons but also non-AUG codons to initiate protein synthesis. The use of these alternative start codons is also largely influenced by numerous trans-acting elements that drive selective mRNA translation in response to environmental changes.},
keywords = {MARTIN, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Saeb Sepideh, Wallet Clémentine, Rohr Olivier, Schwartz Christian, Loustau Thomas
Targeting and eradicating latent CNS reservoirs of HIV-1: Original strategies and new models Journal Article
In: Biochem Pharmacol, vol. 214, pp. 115679, 2023, ISSN: 1873-2968.
Abstract | Links | BibTeX | Tags: ROHR, Unité ARN
@article{pmid37399950,
title = {Targeting and eradicating latent CNS reservoirs of HIV-1: Original strategies and new models},
author = {Sepideh Saeb and Clémentine Wallet and Olivier Rohr and Christian Schwartz and Thomas Loustau},
doi = {10.1016/j.bcp.2023.115679},
issn = {1873-2968},
year = {2023},
date = {2023-08-01},
urldate = {2023-08-01},
journal = {Biochem Pharmacol},
volume = {214},
pages = {115679},
abstract = {Nowadays, combination antiretroviral therapy (cART) is the standard treatment for all people with human immunodeficiency virus (HIV-1). Although cART is effective in treating productive infection, it does not eliminate latent reservoirs of the virus. This leads to lifelong treatment associated with the occurrence of side effects and the development of drug-resistant HIV-1. Suppression of viral latency is therefore the major hurdle to HIV-1 eradication. Multiple mechanisms exist to regulate viral gene expression and drive the transcriptional and post-transcriptional establishment of latency. Epigenetic processes are amongst the most studied mechanisms influencing both productive and latent infection states. The central nervous system (CNS) represents a key anatomical sanctuary for HIV and is the focal point of considerable research efforts. However, limited and difficult access to CNS compartments makes understanding the HIV-1 infection state in latent brain cells such as microglial cells, astrocytes, and perivascular macrophages challenging. This review examines the latest advances on epigenetic transformations involved in CNS viral latency and targeting of brain reservoirs. Evidence from clinical studies as well as in vivo and in vitro models of HIV-1 persistence in the CNS will be discussed, with a special focus on recent 3D in vitro models such as human brain organoids. Finally, the review will address therapeutic considerations for targeting latent CNS reservoirs.},
keywords = {ROHR, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Wright Duncan E, Krol Alain
FEBS fellowships: supporting excellent science for over four decades Miscellaneous
2023, ISSN: 2211-5463.
Abstract | Links | BibTeX | Tags: KROL, Unité ARN
@misc{pmid37394995,
title = {FEBS fellowships: supporting excellent science for over four decades},
author = {Duncan E Wright and Alain Krol},
doi = {10.1002/2211-5463.13659},
issn = {2211-5463},
year = {2023},
date = {2023-07-01},
urldate = {2023-07-01},
journal = {FEBS Open Bio},
volume = {13},
number = {7},
pages = {1138--1139},
abstract = {The Federation of European Biochemical Societies (FEBS) awarded FEBS Long-Term Fellowships from 1979 until 2020, at which time the scheme was replaced with the FEBS Excellence Award. Over four decades, FEBS awarded a huge number of Long-Term Fellowships, helping to support and promote the careers of excellent young researchers across Europe. To celebrate the exciting work performed by the FEBS Long-Term Fellows, we present here a special 'In the Limelight' issue of FEBS Open Bio, containing four Mini-reviews and four Research Protocols authored by the fellows themselves. The four Review articles provide timely updates on the respective research fields, while the Research Protocols describe how to perform challenging experimental methods in detail. We hope this issue will be a valuable resource for the community, and a celebration of the high-quality work done by young scientists.},
keywords = {KROL, Unité ARN},
pubstate = {published},
tppubtype = {misc}
}
Pitolli Martina, Cela Marta, Paulus Caroline, Rudinger-Thirion Joëlle, Frugier Magali
RNA aptamers developed against tRip: A preliminary approach targeting tRNA entry in Plasmodium Journal Article
In: Biochimie, vol. 217, pp. 106-115, 2023, ISSN: 1638-6183.
Abstract | Links | BibTeX | Tags: FRUGIER, Unité ARN
@article{pmid37414209,
title = {RNA aptamers developed against tRip: A preliminary approach targeting tRNA entry in Plasmodium},
author = {Martina Pitolli and Marta Cela and Caroline Paulus and Joëlle Rudinger-Thirion and Magali Frugier},
doi = {10.1016/j.biochi.2023.06.011},
issn = {1638-6183},
year = {2023},
date = {2023-07-01},
urldate = {2023-07-01},
journal = {Biochimie},
volume = {217},
pages = {106-115},
abstract = {Malaria is caused by Plasmodium parasites that multiply inside host cells and can be lethal when P. falciparum is involved. We identified tRip as a membrane protein that facilitates the import of exogenous transfer RNA (tRNA) into the parasite. tRip encompasses a tRNA binding domain exposed on the parasite surface. We used the SELEX approach to isolate high-affinity and specific tRip-binding RNA motifs from a library of random 25 nucleotide-long sequences. In five rounds of combined negative and positive selections, an enriched pool of aptamers was obtained; sequencing revealed that they were all different in their primary sequence; only by comparing their structure predictions did most of the selected aptamers reveal a conserved 5-nucleotide motif sequence. We showed that the integral motif is essential for tRip-binding while the rest of the molecule can be significantly reduced or mutated as long as the motif is presented in a single-stranded region. Such RNA aptamers bind in place of the original tRNA substrate and act as an efficient competitor, suggesting that they can block tRip function and slow parasite development.},
keywords = {FRUGIER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Tardivat Yann, Sosnowski Piotr, Tidu Antonin, Westhof Eric, Eriani Gilbert, Martin Franck
SARS-CoV-2 NSP1 induces mRNA cleavages on the ribosome Journal Article
In: Nucleic Acids Res, vol. 51, iss. 16, pp. 8677-8690, 2023, ISSN: 1362-4962.
Abstract | Links | BibTeX | Tags: ERIANI, MARTIN, Unité ARN
@article{pmid37503833b,
title = {SARS-CoV-2 NSP1 induces mRNA cleavages on the ribosome},
author = {Yann Tardivat and Piotr Sosnowski and Antonin Tidu and Eric Westhof and Gilbert Eriani and Franck Martin},
doi = {10.1093/nar/gkad627},
issn = {1362-4962},
year = {2023},
date = {2023-07-01},
urldate = {2023-07-01},
journal = {Nucleic Acids Res},
volume = {51},
issue = {16},
pages = {8677-8690},
abstract = {In severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the non-structural protein NSP1 inhibits translation of host mRNAs by binding to the mRNA entry channel of the ribosome and, together with the 5'-untranslated region (UTR) of the viral mRNAs, allows the evasion of that inhibition. Here, we show that NSP1 mediates endonucleolytic cleavages of both host and viral mRNAs in the 5'UTR, but with different cleavage patterns. The first pattern is observed in host mRNAs with cleavages interspersed regularly and close to the 5' cap (6-11 nt downstream of the cap). Those cleavage positions depend more on the position relative to the 5' cap than on the sequence itself. The second cleavage pattern occurs at high NSP1 concentrations and only in SARS-CoV-2 RNAs, with the cleavages clustered at positions 45, 46 and 49. Both patterns of cleavage occur with the mRNA and NSP1 bound to the ribosome, with the SL1 hairpin at the 5' end sufficient to protect from NSP1-mediated degradation at low NSP1 concentrations. We show further that the N-terminal domain of NSP1 is necessary and sufficient for efficient cleavage. We suggest that in the ribosome-bound NSP1 protein the catalytic residues of the N-terminal domain are unmasked by the remodelling of the α1- and α2-helices of the C-terminal domain.},
keywords = {ERIANI, MARTIN, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Gaucherand Lea, Iyer Amrita, Gilabert Isabel, Rycroft Chris H, Gaglia Marta M
Cut site preference allows influenza A virus PA-X to discriminate between host and viral mRNAs Journal Article
In: Nat Microbiol, 2023, ISSN: 2058-5276.
Abstract | Links | BibTeX | Tags: PFEFFER, Unité ARN
@article{pmid37349586,
title = {Cut site preference allows influenza A virus PA-X to discriminate between host and viral mRNAs},
author = {Lea Gaucherand and Amrita Iyer and Isabel Gilabert and Chris H Rycroft and Marta M Gaglia},
doi = {10.1038/s41564-023-01409-8},
issn = {2058-5276},
year = {2023},
date = {2023-06-01},
urldate = {2023-06-01},
journal = {Nat Microbiol},
abstract = {Many viruses block host gene expression to take over the infected cell. This process, termed host shutoff, is thought to promote viral replication by preventing antiviral responses and redirecting cellular resources to viral processes. Several viruses from divergent families accomplish host shutoff through RNA degradation by endoribonucleases. However, viruses also need to ensure expression of their own genes. The influenza A virus endoribonuclease PA-X solves this problem by sparing viral mRNAs and some host RNAs necessary for viral replication. To understand how PA-X distinguishes between RNAs, we characterized PA-X cut sites transcriptome-wide using 5' rapid amplification of complementary DNA ends coupled to high-throughput sequencing. This analysis, along with RNA structure predictions and validation experiments using reporters, shows that PA-Xs from multiple influenza strains preferentially cleave RNAs at GCUG tetramers in hairpin loops. Importantly, GCUG tetramers are enriched in the human but not the influenza transcriptome. Moreover, optimal PA-X cut sites inserted in the influenza A virus genome are quickly selected against during viral replication in cells. This finding suggests that PA-X evolved these cleavage characteristics to preferentially target host over viral mRNAs in a manner reminiscent of cellular self versus non-self discrimination.},
keywords = {PFEFFER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Pivard Mariane, Caldelari Isabelle, Brun Virginie, Croisier Delphine, Jaquinod Michel, Anzala Nelson, Gilquin Benoît, Teixeira Chloé, Benito Yvonne, Couzon Florence, Romby Pascale, Moreau Karen, Vandenesch François
Complex Regulation of Gamma-Hemolysin Expression Impacts Staphylococcus aureus Virulence Journal Article
In: Microbiol Spectr, pp. e0107323, 2023, ISSN: 2165-0497.
Abstract | Links | BibTeX | Tags: ROMBY, Unité ARN
@article{pmid37347186,
title = {Complex Regulation of Gamma-Hemolysin Expression Impacts Staphylococcus aureus Virulence},
author = {Mariane Pivard and Isabelle Caldelari and Virginie Brun and Delphine Croisier and Michel Jaquinod and Nelson Anzala and Benoît Gilquin and Chloé Teixeira and Yvonne Benito and Florence Couzon and Pascale Romby and Karen Moreau and François Vandenesch},
doi = {10.1128/spectrum.01073-23},
issn = {2165-0497},
year = {2023},
date = {2023-06-01},
urldate = {2023-06-01},
journal = {Microbiol Spectr},
pages = {e0107323},
abstract = {Staphylococcus aureus gamma-hemolysin CB (HlgCB) is a core-genome-encoded pore-forming toxin that targets the C5a receptor, similar to the phage-encoded Panton-Valentine leucocidin (PVL). Absolute quantification by mass spectrometry of HlgCB in 39 community-acquired pneumonia (CAP) isolates showed considerable variations in the HlgC and HlgB yields between isolates. Moreover, although HlgC and HlgB are encoded on a single operon, their levels were dissociated in 10% of the clinical strains studied. To decipher the molecular basis for the variation in expression and protein production among strains, different regulation levels were analyzed in representative clinical isolates and reference strains. Both the HlgCB level and the HlgC/HlgB ratio were found to depend on promoter activity and mRNA processing and translation. Strikingly, only one single nucleotide polymorphism (SNP) in the 5' untranslated region (UTR) of mRNA strongly impaired translation in the USA300 strain, leading to a strong decrease in the level of HlgC but not in HlgB. Finally, we found that high levels of HlgCB synthesis led to mortality in a rabbit model of pneumonia, correlated with the implication of the role of HlgCB in severe S. aureus CAP. Taken together, this work illustrates the complexity of virulence factor expression in clinical strains and demonstrates a butterfly effect where subtle genomic variations have a major impact on phenotype and virulence. S. aureus virulence in pneumonia results in its ability to produce several virulence factors, including the leucocidin PVL. Here, we demonstrate that HlgCB, another leucocidin, which targets the same receptors as PVL, highly contributes to S. aureus virulence in -negative strains. In addition, considerable variations in HlgCB quantities are observed among clinical isolates from patients with CAP. Biomolecular analyses have revealed that a few SNPs in the promoter sequences and only one SNP in the 5' UTR of mRNA induce the differential expression of , drastically impacting mRNA translation. This work illustrates the subtlety of regulatory mechanisms in bacteria, especially the sometimes major effects on phenotypes of single nucleotide variation in noncoding regions.},
keywords = {ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Jakob Celia, Lovate Gabriel L, Desirò Daniel, Gießler Lara, Smyth Redmond P, Marquet Roland, Lamkiewicz Kevin, Marz Manja, Schwemmle Martin, Bolte Hardin
Sequential disruption of SPLASH-identified vRNA-vRNA interactions challenges their role in influenza A virus genome packaging Journal Article
In: Nucleic Acids Res, vol. 51, iss. 12, pp. 6479-6494, 2023, ISSN: 1362-4962.
Abstract | Links | BibTeX | Tags: MARQUET, Unité ARN
@article{pmid37224537,
title = {Sequential disruption of SPLASH-identified vRNA-vRNA interactions challenges their role in influenza A virus genome packaging},
author = {Celia Jakob and Gabriel L Lovate and Daniel Desirò and Lara Gießler and Redmond P Smyth and Roland Marquet and Kevin Lamkiewicz and Manja Marz and Martin Schwemmle and Hardin Bolte},
doi = {10.1093/nar/gkad442},
issn = {1362-4962},
year = {2023},
date = {2023-05-01},
urldate = {2023-05-01},
journal = {Nucleic Acids Res},
volume = {51},
issue = {12},
pages = {6479-6494},
abstract = {A fundamental step in the influenza A virus (IAV) replication cycle is the coordinated packaging of eight distinct genomic RNA segments (i.e. vRNAs) into a viral particle. Although this process is thought to be controlled by specific vRNA-vRNA interactions between the genome segments, few functional interactions have been validated. Recently, a large number of potentially functional vRNA-vRNA interactions have been detected in purified virions using the RNA interactome capture method SPLASH. However, their functional significance in coordinated genome packaging remains largely unclear. Here, we show by systematic mutational analysis that mutant A/SC35M (H7N7) viruses lacking several prominent SPLASH-identified vRNA-vRNA interactions involving the HA segment package the eight genome segments as efficiently as the wild-type virus. We therefore propose that the vRNA-vRNA interactions identified by SPLASH in IAV particles are not necessarily critical for the genome packaging process, leaving the underlying molecular mechanism elusive.},
keywords = {MARQUET, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Lavie Julie, Lalou Claude, Mahfouf Walid, Dupuy Jean-William, Lacaule Aurélie, Cywinska Agata Ars, Lacombe Didier, Duchêne Anne-Marie, Raymond Anne-Aurélie, Rezvani Hamid Reza, Ngondo Richard Patryk, Bénard Giovanni
The E3 ubiquitin ligase FBXL6 controls the quality of newly synthesized mitochondrial ribosomal proteins Journal Article
In: Cell Rep, vol. 42, no. 6, pp. 112579, 2023, ISSN: 2211-1247.
Abstract | Links | BibTeX | Tags: MARTEYN, Unité ARN
@article{pmid37267103,
title = {The E3 ubiquitin ligase FBXL6 controls the quality of newly synthesized mitochondrial ribosomal proteins},
author = {Julie Lavie and Claude Lalou and Walid Mahfouf and Jean-William Dupuy and Aurélie Lacaule and Agata Ars Cywinska and Didier Lacombe and Anne-Marie Duchêne and Anne-Aurélie Raymond and Hamid Reza Rezvani and Richard Patryk Ngondo and Giovanni Bénard},
doi = {10.1016/j.celrep.2023.112579},
issn = {2211-1247},
year = {2023},
date = {2023-05-01},
urldate = {2023-05-01},
journal = {Cell Rep},
volume = {42},
number = {6},
pages = {112579},
abstract = {In mammals, about 99% of mitochondrial proteins are synthesized in the cytosol as precursors that are subsequently imported into the organelle. The mitochondrial health and functions rely on an accurate quality control of these imported proteins. Here, we show that the E3 ubiquitin ligase F box/leucine-rich-repeat protein 6 (FBXL6) regulates the quality of cytosolically translated mitochondrial proteins. Indeed, we found that FBXL6 substrates are newly synthesized mitochondrial ribosomal proteins. This E3 binds to chaperones involved in the folding and trafficking of newly synthesized peptide and to ribosomal-associated quality control proteins. Deletion of these interacting partners is sufficient to hamper interactions between FBXL6 and its substrate. Furthermore, we show that cells lacking FBXL6 fail to degrade specifically mistranslated mitochondrial ribosomal proteins. Finally, showing the role of FBXL6-dependent mechanism, FBXL6-knockout (KO) cells display mitochondrial ribosomal protein aggregations, altered mitochondrial metabolism, and inhibited cell cycle in oxidative conditions.},
keywords = {MARTEYN, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Vindry Caroline, Guillin Olivia, Wolff Philippe, Marie Paul, Mortreux Franck, Mangeot Philippe E, Ohlmann Théophile, Chavatte Laurent
A homozygous mutation in the human selenocysteine tRNA gene impairs UGA recoding activity and selenoproteome regulation by selenium Journal Article
In: Nucleic Acids Res, vol. 51, iss. 14, pp. 7580-7601, 2023, ISSN: 1362-4962.
Abstract | Links | BibTeX | Tags: ARN-MS, Unité ARN
@article{pmid37254812,
title = {A homozygous mutation in the human selenocysteine tRNA gene impairs UGA recoding activity and selenoproteome regulation by selenium},
author = {Caroline Vindry and Olivia Guillin and Philippe Wolff and Paul Marie and Franck Mortreux and Philippe E Mangeot and Théophile Ohlmann and Laurent Chavatte},
doi = {10.1093/nar/gkad482},
issn = {1362-4962},
year = {2023},
date = {2023-05-01},
urldate = {2023-05-01},
journal = {Nucleic Acids Res},
volume = {51},
issue = {14},
pages = {7580-7601},
abstract = {The selenocysteine (Sec) tRNA (tRNA[Ser]Sec) governs Sec insertion into selenoproteins by the recoding of a UGA codon, typically used as a stop codon. A homozygous point mutation (C65G) in the human tRNA[Ser]Sec acceptor arm has been reported by two independent groups and was associated with symptoms such as thyroid dysfunction and low blood selenium levels; however, the extent of altered selenoprotein synthesis resulting from this mutation has yet to be comprehensively investigated. In this study, we used CRISPR/Cas9 technology to engineer homozygous and heterozygous mutant human cells, which we then compared with the parental cell lines. This C65G mutation affected many aspects of tRNA[Ser]Sec integrity and activity. Firstly, the expression level of tRNA[Ser]Sec was significantly reduced due to an altered recruitment of RNA polymerase III at the promoter. Secondly, selenoprotein expression was strongly altered, but, more surprisingly, it was no longer sensitive to selenium supplementation. Mass spectrometry analyses revealed a tRNA isoform with unmodified wobble nucleotide U34 in mutant cells that correlated with reduced UGA recoding activities. Overall, this study demonstrates the pleiotropic effect of a single C65G mutation on both tRNA phenotype and selenoproteome expression.},
keywords = {ARN-MS, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Lista María José, Jousset Anne-Caroline, Cheng Mingpan, Saint-André Violaine, Perrot Elouan, Rodrigues Melissa, Primo Carmelo Di, Gadelle Danielle, Toccafondi Elenia, Segeral Emmanuel, Berlioz-Torrent Clarisse, Emiliani Stéphane, Mergny Jean-Louis, Lavigne Marc
DNA topoisomerase 1 represses HIV-1 promoter activity through its interaction with a guanine quadruplex present in the LTR sequence Journal Article
In: Retrovirology, vol. 20, no. 1, pp. 10, 2023, ISSN: 1742-4690.
Abstract | Links | BibTeX | Tags: MARQUET, NEGRONI, PAILLART, Unité ARN
@article{pmid37254203,
title = {DNA topoisomerase 1 represses HIV-1 promoter activity through its interaction with a guanine quadruplex present in the LTR sequence},
author = {María José Lista and Anne-Caroline Jousset and Mingpan Cheng and Violaine Saint-André and Elouan Perrot and Melissa Rodrigues and Carmelo Di Primo and Danielle Gadelle and Elenia Toccafondi and Emmanuel Segeral and Clarisse Berlioz-Torrent and Stéphane Emiliani and Jean-Louis Mergny and Marc Lavigne},
doi = {10.1186/s12977-023-00627-6},
issn = {1742-4690},
year = {2023},
date = {2023-05-01},
urldate = {2023-05-01},
journal = {Retrovirology},
volume = {20},
number = {1},
pages = {10},
abstract = {BACKGROUND: Once integrated in the genome of infected cells, HIV-1 provirus is transcribed by the cellular transcription machinery. This process is regulated by both viral and cellular factors, which are necessary for an efficient viral replication as well as for the setting up of viral latency, leading to a repressed transcription of the integrated provirus.nnRESULTS: In this study, we examined the role of two parameters in HIV-1 LTR promoter activity. We identified DNA topoisomerase1 (TOP1) to be a potent repressor of this promoter and linked this repression to its catalytic domain. Additionally, we confirmed the folding of a Guanine quadruplex (G4) structure in the HIV-1 promoter and its repressive effect. We demonstrated a direct interaction between TOP1 and this G4 structure, providing evidence of a functional relationship between the two repressive elements. Mutations abolishing G4 folding affected TOP1/G4 interaction and hindered G4-dependent inhibition of TOP1 catalytic activity in vitro. As a result, HIV-1 promoter activity was reactivated in a native chromatin environment. Lastly, we noticed an enrichment of predicted G4 sequences in the promoter of TOP1-repressed cellular genes.nnCONCLUSIONS: Our results demonstrate the formation of a TOP1/G4 complex on the HIV-1 LTR promoter and its repressive effect on the promoter activity. They reveal the existence of a new mechanism of TOP1/G4-dependent transcriptional repression conserved between viral and human genes. This mechanism contrasts with the known property of TOP1 as global transcriptional activator and offers new perspectives for anti-cancer and anti-viral strategies.},
keywords = {MARQUET, NEGRONI, PAILLART, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Husser Claire, Vuilleumier Stéphane, Ryckelynck Michael
FluorMango, an RNA-Based Fluorogenic Biosensor for the Direct and Specific Detection of Fluoride Journal Article
In: Small, vol. 19, iss. 13, pp. e2205232, 2023, ISSN: 1613-6829.
Abstract | Links | BibTeX | Tags: RYCKELYNCK, Unité ARN
@article{pmid36436882,
title = {FluorMango, an RNA-Based Fluorogenic Biosensor for the Direct and Specific Detection of Fluoride},
author = {Claire Husser and Stéphane Vuilleumier and Michael Ryckelynck},
doi = {10.1002/smll.202205232},
issn = {1613-6829},
year = {2023},
date = {2023-03-29},
urldate = {2023-03-01},
journal = {Small},
volume = {19},
issue = {13},
pages = {e2205232},
abstract = {Nucleic acids are not only essential actors of cell life but also extremely appealing molecular objects in the development of synthetic molecules for biotechnological application, such as biosensors to report on the presence and concentration of a target ligand by emission of a measurable signal. In this work, FluorMango, a fluorogenic ribonucleic acid (RNA)-based biosensor specific for fluoride is introduced. The molecule consists of two RNA aptamer modules, a fluoride-specific sensor derived from the crcB riboswitch which changes its structure upon interaction with the target ion, and the light-up RNA Mango-III that emits fluorescence when complexed with a fluorogen. The two modules are connected by an optimized communication module identified by ultrahigh-throughput screening, which results in extremely high fluorescence of FluorMango in the presence of fluoride, and background fluorescence in its absence. The value and efficiency of this biosensor by direct monitoring of defluorinase activity in living bacterial cells is illustrated, and the use of this new tool in future screening campaigns aiming at discovering new defluorinase activities is discussed.},
keywords = {RYCKELYNCK, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Toccafondi Elenia, Kanja Marine, Winter Flore, Lener Daniela, Negroni Matteo
A snapshot on HIV-1 evolution through the identification of phylogenetic-specific properties of HIV-1 integrases M/O Journal Article
In: PLoS Pathog, vol. 19, no. 3, pp. e1011207, 2023, ISSN: 1553-7374.
Abstract | Links | BibTeX | Tags: NEGRONI, Unité ARN
@article{pmid36996029,
title = {A snapshot on HIV-1 evolution through the identification of phylogenetic-specific properties of HIV-1 integrases M/O},
author = {Elenia Toccafondi and Marine Kanja and Flore Winter and Daniela Lener and Matteo Negroni},
doi = {10.1371/journal.ppat.1011207},
issn = {1553-7374},
year = {2023},
date = {2023-03-01},
urldate = {2023-03-01},
journal = {PLoS Pathog},
volume = {19},
number = {3},
pages = {e1011207},
abstract = {Transmissions of simian viruses to humans has originated the different groups of HIV-1. We recently identified a functional motif (CLA), in the C-terminal domain of the integrase, essential for integration in HIV-1 group M. Here, we found that the motif is instead dispensable in group O isolates, because of the presence, in the N-terminal domain of HIV-1 O of a specific sequence, Q7G27P41H44, that we define as the NOG motif. Alterations of reverse transcription and of 3' processing observed by mutating the CLA motif of IN M are fully rescued to wt levels by inserting the sequence of the NOG motif in the N-ter of the protein. These results indicate that the two motifs (CLA and NOG) functionally complement each other and a working model accounting for these observations is proposed. The establishment of these two alternative motifs seems to be due to the different phylogenetic origin and history of these two groups. Indeed, the NOG motif is already present in the ancestor of group O (SIVgor) while it is absent from SIVcpzPtt, the ancestor of group M. The CLA motif, instead, seems to have emerged after SIVcpzPtt has been transferred to humans, since no conservation is found at the same positions in these simian viruses. These results show the existence of two-group specific motifs in HIV-1 M and O integrases. In each group, only one of the motifs is functional, potentially leading the other motif to diverge from its original function and, in an evolutionary perspective, assist other functions of the protein, further increasing HIV genetic diversity.},
keywords = {NEGRONI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Girardi Erika, Messmer Mélanie, Lopez Paula, Fender Aurélie, Chicher Johana, Chane-Woon-Ming Béatrice, Hammann Philippe, Pfeffer Sébastien
Proteomics-based determination of double-stranded RNA interactome reveals known and new factors involved in Sindbis virus infection Journal Article
In: RNA, vol. 29, no. 3, pp. 361–375, 2023, ISSN: 1469-9001.
Abstract | Links | BibTeX | Tags: PFEFFER, PPSE, Unité ARN
@article{pmid36617674b,
title = {Proteomics-based determination of double-stranded RNA interactome reveals known and new factors involved in Sindbis virus infection},
author = {Erika Girardi and Mélanie Messmer and Paula Lopez and Aurélie Fender and Johana Chicher and Béatrice Chane-Woon-Ming and Philippe Hammann and Sébastien Pfeffer},
doi = {10.1261/rna.079270.122},
issn = {1469-9001},
year = {2023},
date = {2023-03-01},
urldate = {2023-03-01},
journal = {RNA},
volume = {29},
number = {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}
}
Dufossez Robin, Ursuegui Sylvain, Baudrey Stephanie, Pernod Ketty, Mouftakhir Safae, Oulad-Abdelghani Mustapha, Mosser Michel, Chaubet Guilhem, Ryckelynck Michael, Wagner Alain
Droplet Surface Immunoassay by Relocation (D-SIRe) for High-Throughput Analysis of Cytosolic Proteins at the Single-Cell Level Journal Article
In: Anal Chem, vol. 95, iss. 9, pp. 4470-4478, 2023, ISSN: 1520-6882.
Abstract | Links | BibTeX | Tags: RYCKELYNCK, Unité ARN
@article{pmid36821722,
title = {Droplet Surface Immunoassay by Relocation (D-SIRe) for High-Throughput Analysis of Cytosolic Proteins at the Single-Cell Level},
author = {Robin Dufossez and Sylvain Ursuegui and Stephanie Baudrey and Ketty Pernod and Safae Mouftakhir and Mustapha Oulad-Abdelghani and Michel Mosser and Guilhem Chaubet and Michael Ryckelynck and Alain Wagner},
doi = {10.1021/acs.analchem.2c05168},
issn = {1520-6882},
year = {2023},
date = {2023-02-01},
urldate = {2023-02-01},
journal = {Anal Chem},
volume = {95},
issue = {9},
pages = {4470-4478},
abstract = {Enzyme-linked immunosorbent assay (ELISA) is a central analytic method in biological science for the detection of proteins. Introduction of droplet-based microfluidics allowed the development of miniaturized, less-consuming, and more sensitive ELISA assays by coencapsulating the biological sample and antibody-functionalized particles. We report herein an alternative in-droplet immunoassay format, which avoids the use of particles. It exploits the oil/aqueous-phase interface as a protein capture and detection surface. This is achieved using tailored perfluorinated surfactants bearing azide-functionalized PEG-based polar headgroups, which spontaneously react when meeting at the droplet formation site, with strained alkyne-functionalized antibodies solubilized in the water phase. The resulting antibody-functionalized inner surface can then be used to capture a target protein. This surface capture process leads to concomitant relocation at the surface of a labeled detection antibody and in turn to a drastic change in the shape of the fluorescence signal from a convex shape (not captured) to a characteristic concave shape (captured). This novel droplet surface immunoassay by fluorescence relocation (D-SIRe) proved to be fast and sensitive at 2.3 attomoles of analyte per droplet. It was further demonstrated to allow detection of cytosolic proteins at the single bacteria level.},
keywords = {RYCKELYNCK, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Lee Seungjae, Jee David, Srivastava Sid, Yang Acong, Ramidi Abhinav, Shang Renfu, Bortolamiol-Becet Diane, Pfeffer Sébastien, Gu Shuo, Wen Jiayu, Lai Eric C
Promiscuous splicing-derived hairpins are dominant substrates of tailing-mediated defense of miRNA biogenesis in mammals Journal Article
In: Cell Rep, vol. 42, no. 2, pp. 112111, 2023, ISSN: 2211-1247.
Abstract | Links | BibTeX | Tags: PFEFFER, Unité ARN
@article{pmid36800291,
title = {Promiscuous splicing-derived hairpins are dominant substrates of tailing-mediated defense of miRNA biogenesis in mammals},
author = {Seungjae Lee and David Jee and Sid Srivastava and Acong Yang and Abhinav Ramidi and Renfu Shang and Diane Bortolamiol-Becet and Sébastien Pfeffer and Shuo Gu and Jiayu Wen and Eric C Lai},
doi = {10.1016/j.celrep.2023.112111},
issn = {2211-1247},
year = {2023},
date = {2023-02-01},
urldate = {2023-02-01},
journal = {Cell Rep},
volume = {42},
number = {2},
pages = {112111},
abstract = {Canonical microRNA (miRNA) hairpins are processed by the RNase III enzymes Drosha and Dicer into ∼22 nt RNAs loaded into an Argonaute (Ago) effector. In addition, splicing generates numerous intronic hairpins that bypass Drosha (mirtrons) to yield mature miRNAs. Here, we identify hundreds of previously unannotated, splicing-derived hairpins in intermediate-length (∼50-100 nt) but not small (20-30 nt) RNA data. Since we originally defined mirtrons from small RNA duplexes, we term this larger set as structured splicing-derived RNAs (ssdRNAs). These associate with Dicer and/or Ago complexes, but generally accumulate modestly and are poorly conserved. We propose they contaminate the canonical miRNA pathway, which consequently requires defense against the siege of splicing-derived substrates. Accordingly, ssdRNAs/mirtrons comprise dominant hairpin substrates for 3' tailing by multiple terminal nucleotidyltransferases, notably TUT4/7 and TENT2. Overall, the rampant proliferation of young mammalian mirtrons/ssdRNAs, coupled with an inhibitory molecular defense, comprises a Red Queen's race of intragenomic conflict.},
keywords = {PFEFFER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Giegé Richard, Eriani Gilbert
The tRNA identity landscape for aminoacylation and beyond Journal Article
In: Nucleic Acids Res, vol. 51, no. 4, pp. 1528–1570, 2023, ISSN: 1362-4962.
Abstract | Links | BibTeX | Tags: ERIANI, GIEGE, Unité ARN
@article{pmid36744444,
title = {The tRNA identity landscape for aminoacylation and beyond},
author = {Richard Giegé and Gilbert Eriani},
doi = {10.1093/nar/gkad007},
issn = {1362-4962},
year = {2023},
date = {2023-02-01},
urldate = {2023-02-01},
journal = {Nucleic Acids Res},
volume = {51},
number = {4},
pages = {1528--1570},
abstract = {tRNAs are key partners in ribosome-dependent protein synthesis. This process is highly dependent on the fidelity of tRNA aminoacylation by aminoacyl-tRNA synthetases and relies primarily on sets of identities within tRNA molecules composed of determinants and antideterminants preventing mischarging by non-cognate synthetases. Such identity sets were discovered in the tRNAs of a few model organisms, and their properties were generalized as universal identity rules. Since then, the panel of identity elements governing the accuracy of tRNA aminoacylation has expanded considerably, but the increasing number of reported functional idiosyncrasies has led to some confusion. In parallel, the description of other processes involving tRNAs, often well beyond aminoacylation, has progressed considerably, greatly expanding their interactome and uncovering multiple novel identities on the same tRNA molecule. This review highlights key findings on the mechanistics and evolution of tRNA and tRNA-like identities. In addition, new methods and their results for searching sets of multiple identities on a single tRNA are discussed. Taken together, this knowledge shows that a comprehensive understanding of the functional role of individual and collective nucleotide identity sets in tRNA molecules is needed for medical, biotechnological and other applications.},
keywords = {ERIANI, GIEGE, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Husser Claire, Baudrey Stéphanie, Ryckelynck Michael
High-Throughput Development and Optimization of RNA-Based Fluorogenic Biosensors of Small Molecules Using Droplet-Based Microfluidics Journal Article
In: Methods Mol Biol, vol. 2570, pp. 243–269, 2023, ISSN: 1940-6029.
Abstract | Links | BibTeX | Tags: RYCKELYNCK, Unité ARN
@article{pmid36156788,
title = {High-Throughput Development and Optimization of RNA-Based Fluorogenic Biosensors of Small Molecules Using Droplet-Based Microfluidics},
author = {Claire Husser and Stéphanie Baudrey and Michael Ryckelynck},
doi = {10.1007/978-1-0716-2695-5_19},
issn = {1940-6029},
year = {2023},
date = {2023-01-01},
urldate = {2023-01-01},
journal = {Methods Mol Biol},
volume = {2570},
pages = {243--269},
abstract = {Small-molecule sensing is a major issue as they can serve both in fundamental science and as makers of various diseases, contaminations, or even environment pollution. RNA aptamers are single-stranded nucleic acids that can adopt different conformations and specifically recognize a wide range of ligands, making them good candidates to develop biosensors of small molecules. Recently, light-up RNA aptamers have been introduced and used as starting building blocks of RNA-based fluorogenic biosensors. They are typically made of three domains: a reporter domain (a light-up aptamer), connected to a sensor domain (another aptamer) via a communication module. The latter is instrumental as being in charge of information transmission between the sensor and the reporting domains. Here we present an ultrahigh-throughput screening procedure to develop RNA-based fluorogenic biosensors by selecting optimized communication modules through an exhaustive functional exploration of every possible sequence permutation using droplet-based microfluidics and next-generation sequencing.},
keywords = {RYCKELYNCK, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Gosset-Erard Clarisse, Didierjean Mévie, Pansanel Jérome, Lechner Antony, Wolff Philippe, Kuhn Lauriane, Aubriet Frédéric, Leize-Wagner Emmanuelle, Chaimbault Patrick, François Yannis-Nicolas
In: Anal Chem, vol. 95, iss. 2, pp. 1608-1617, 2023, ISSN: 1520-6882.
Abstract | Links | BibTeX | Tags: ARN-MS, PPSE, Unité ARN
@article{pmid36598775,
title = {Nucleos'ID: A New Search Engine Enabling the Untargeted Identification of RNA Post-transcriptional Modifications from Tandem Mass Spectrometry Analyses of Nucleosides},
author = {Clarisse Gosset-Erard and Mévie Didierjean and Jérome Pansanel and Antony Lechner and Philippe Wolff and Lauriane Kuhn and Frédéric Aubriet and Emmanuelle Leize-Wagner and Patrick Chaimbault and Yannis-Nicolas François},
doi = {10.1021/acs.analchem.2c04722},
issn = {1520-6882},
year = {2023},
date = {2023-01-01},
urldate = {2023-01-01},
journal = {Anal Chem},
volume = {95},
issue = {2},
pages = {1608-1617},
abstract = {As RNA post-transcriptional modifications are of growing interest, several methods were developed for their characterization. One of them established for their identification, at the nucleosidic level, is the hyphenation of separation methods, such as liquid chromatography or capillary electrophoresis, to tandem mass spectrometry. However, to our knowledge, no software is yet available for the untargeted identification of RNA post-transcriptional modifications from MS/MS data-dependent acquisitions. Thus, very long and tedious manual data interpretations are required. To meet the need of easier and faster data interpretation, a new user-friendly search engine, called Nucleos'ID, was developed for CE-MS/MS and LC-MS/MS users. Performances of this new software were evaluated on CE-MS/MS data from nucleoside analyses of already well-described transfer RNA and total tRNA extract. All samples showed great true positive, true negative, and false discovery rates considering the database size containing all modified and unmodified nucleosides referenced in the literature. The true positive and true negative rates obtained were above 0.94, while the false discovery rates were between 0.09 and 0.17. To increase the level of sample complexity, untargeted identification of several RNA modifications from 70S ribosome was achieved by the Nucleos'ID search following CE-MS/MS analysis.},
keywords = {ARN-MS, PPSE, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Ponce José R Jaramillo, Théobald-Dietrich Anne, Bénas Philippe, Paulus Caroline, Sauter Claude, Frugier Magali
Solution x-ray scattering highlights discrepancies in Plasmodium multi-aminoacyl-tRNA synthetase complexes Journal Article
In: Protein Sci, pp. e4564, 2023, ISSN: 1469-896X.
Abstract | Links | BibTeX | Tags: FRUGIER, SAUTER, Unité ARN
@article{pmid36606712,
title = {Solution x-ray scattering highlights discrepancies in Plasmodium multi-aminoacyl-tRNA synthetase complexes},
author = {José R Jaramillo Ponce and Anne Théobald-Dietrich and Philippe Bénas and Caroline Paulus and Claude Sauter and Magali Frugier},
doi = {10.1002/pro.4564},
issn = {1469-896X},
year = {2023},
date = {2023-01-01},
urldate = {2023-01-01},
journal = {Protein Sci},
pages = {e4564},
abstract = {tRip is a tRNA import protein specific to Plasmodium, the causative agent of malaria. In addition to its membrane localization and tRNA trafficking properties, tRip has the capacity to associate with three aminoacyl-tRNA synthetases (aaRS), the glutamyl- (ERS), glutaminyl- (QRS), and methionyl- (MRS) tRNA synthetases. In eukaryotes, such multi-aaRSs complexes (MSC) regulate the moonlighting activities of aaRSs. In Plasmodium, tRip and the three aaRSs all contain an N-terminal GST-like domain involved in the assembly of two independent complexes: the Q-complex (tRip:ERS:QRS) and the M-complex (tRip:ERS:MRS) with a 2:2:2 stoichiometry and in which the association of the GST-like domains of tRip and ERS (tRip-N:ERS-N) is central. In this study, the crystal structure of the N-terminal GST-like domain of ERS was solved and made possible further investigation of the solution architecture of the Q- and M-complexes by small-angle X-ray scattering (SAXS). This strategy relied on the engineering of a tRip-N-ERS-N chimeric protein to study the structural scaffold of both Plasmodium MSCs and confirm the unique homodimerization pattern of tRip in solution. The biological impact of these structural arrangements is discussed. This article is protected by copyright. All rights reserved.},
keywords = {FRUGIER, SAUTER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
L. Urzhumtseva, V. Lunin, A. Urzhumtsev
Algorithms and programs for the shell decomposition of oscillating functions in space Journal Article
In: J Appl Cryst, vol. 56, no. 1, pp. 302-311, 2023.
Abstract | Links | BibTeX | Tags: Unité ARN, Urzhumtseva
@article{nokey,
title = {Algorithms and programs for the shell decomposition of oscillating functions in space},
author = {Urzhumtseva L. and Lunin V. and Urzhumtsev A.},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1107/S160057672201144X},
doi = {10.1107/S160057672201144X},
year = {2023},
date = {2023-01-01},
urldate = {2023-01-01},
journal = {J Appl Cryst},
volume = {56},
number = {1},
pages = {302-311},
abstract = {Real-space refinement of atomic models in macromolecular crystallography and cryo-electron microscopy fits a model to a map obtained with experimental data. To do so, the atomic model is converted into a map of limited resolution and then this map is compared quantitatively with the experimental one. For an appropriate comparison, the atomic contributions comprising the model map should reflect the resolution of the experimental map and the atomic displacement parameter (ADP) values. Such contributions are spherically symmetric oscillating functions, different for chemically different kinds of atoms, different ADPs and different resolution values, and their derivatives with respect to atomic parameters rule the model refinement. For given parameter values, every contribution may be calculated numerically using two Fourier transforms, which is highly time consuming and makes calculation of the respective derivatives problematic. Alternatively, for an atom of each required type its contribution can be expressed in an analytical form as a sum of specially designed terms. Each term is different from zero essentially inside a spherical shell, and changing the ADP value does not change its form but rather changes the value of one of its arguments. In general, these terms become a convenient tool for the decomposition of oscillating spherically symmetric functions. This work describes the algorithms and respective software, named dec3D, to carry out such a shell decomposition for density contributions of different kinds of atoms and ions.},
keywords = {Unité ARN, Urzhumtseva},
pubstate = {published},
tppubtype = {article}
}
Giuliodori Anna Maria, Belardinelli Riccardo, Duval Melodie, Garofalo Raffaella, Schenckbecher Emma, Hauryliuk Vasili, Ennifar Eric, Marzi Stefano
CspA stimulates translation in the cold of its own mRNA by promoting ribosome progression Journal Article
In: Front Microbiol, vol. 14, pp. 1118329, 2023, ISSN: 1664-302X.
Abstract | Links | BibTeX | Tags: ENNIFAR, ROMBY, Unité ARN
@article{pmid36846801b,
title = { CspA stimulates translation in the cold of its own mRNA by promoting ribosome progression},
author = {Anna Maria Giuliodori and Riccardo Belardinelli and Melodie Duval and Raffaella Garofalo and Emma Schenckbecher and Vasili Hauryliuk and Eric Ennifar and Stefano Marzi},
doi = {10.3389/fmicb.2023.1118329},
issn = {1664-302X},
year = {2023},
date = {2023-01-01},
urldate = {2023-01-01},
journal = {Front Microbiol},
volume = {14},
pages = {1118329},
abstract = { CspA is an RNA binding protein that accumulates during cold-shock and stimulates translation of several mRNAs-including its own. Translation in the cold of mRNA involves a cis-acting thermosensor element, which enhances ribosome binding, and the trans-acting action of CspA. Using reconstituted translation systems and probing experiments we show that, at low temperature, CspA specifically promotes the translation of the mRNA folded in the conformation less accessible to the ribosome, which is formed at 37°C but is retained upon cold shock. CspA interacts with its mRNA without inducing large structural rearrangements, but allowing the progression of the ribosomes during the transition from translation initiation to translation elongation. A similar structure-dependent mechanism may be responsible for the CspA-dependent translation stimulation observed with other probed mRNAs, for which the transition to the elongation phase is progressively facilitated during cold acclimation with the accumulation of CspA.},
keywords = {ENNIFAR, ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}