Publications

@article{pmid39248656,

title = {Beyond RNAi: How the Dicer protein modulates the antiviral innate immune response in mammalian cells: Mammalian Dicer could regulate the innate immune response in an RNAi-independent manner as a result of losing long dsRNA processive activity},

author = {Léa Gaucherand and Morgane Baldaccini and Sébastien Pfeffer},

doi = {10.1002/bies.202400173},

issn = {1521-1878},

year  = {2024},

date = {2024-09-01},

journal = {Bioessays},

pages = {e2400173},

abstract = {While Dicer plays an important antiviral role through the RNAi pathway in plants and invertebrates, its contribution to antiviral immunity in vertebrates and more specifically mammals is more controversial. The apparent limited RNAi activity in mammalian cells has been attributed to the reduced long dsRNA processive activity of mammalian Dicer, as well as a functional incompatibility between the RNAi and IFN pathways. Why Dicer has lost this antiviral activity in the profit of the IFN pathway is still unclear. We propose that the primary direct antiviral activity of Dicer has been functionally replaced by other sensors in the IFN pathway, leading to its specialization toward microRNA maturation. As a result, Dicer can regulate the innate immune response and prevent basal activation of the IFN pathway in mammals. Here, we discuss this hypothesis, highlighting how the adaptation of the helicase domain of mammalian Dicer may be key to this process.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38761168,

title = {In planta imaging of pyridine nucleotides using second-generation fluorescent protein biosensors},

author = {Shey-Li Lim and Jinhong Liu and Gilles Dupouy and Gaurav Singh and Stéphanie Baudrey and Lang Yang and Jia Yi Zhong and Marie-Edith Chabouté and Boon Leong Lim},

doi = {10.1111/tpj.16796},

issn = {1365-313X},

year  = {2024},

date = {2024-08-01},

journal = {Plant J},

volume = {119},

number = {3},

pages = {1643--1658},

abstract = {Redox changes of pyridine nucleotides in cellular compartments are highly dynamic and their equilibria are under the influence of various reducing and oxidizing reactions. To obtain spatiotemporal data on pyridine nucleotides in living plant cells, typical biochemical approaches require cell destruction. To date, genetically encoded fluorescent biosensors are considered to be the best option to bridge the existing technology gap, as they provide a fast, accurate, and real-time readout. However, the existing pyridine nucleotides genetically encoded fluorescent biosensors are either sensitive to pH change or slow in dissociation rate. Herein, we employed the biosensors which generate readouts that are pH stable for in planta measurement of NADH/NAD ratio and NADPH level. We generated transgenic Arabidopsis lines that express these biosensors in plastid stroma and cytosol of whole plants and pollen tubes under the control of CaMV 35S and LAT52 promoters, respectively. These transgenic biosensor lines allow us to monitor real-time dynamic changes in NADH/NAD ratio and NADPH level in the plastids and cytosol of various plant tissues, including pollen tubes, root hairs, and mesophyll cells, using a variety of fluorescent instruments. We anticipate that these valuable transgenic lines may allow improvements in plant redox biology studies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid39194605,

title = {Fluorogenic RNA-Based Biosensors of Small Molecules: Current Developments, Uses, and Perspectives},

author = {Janine Kehrli and Claire Husser and Michael Ryckelynck},

doi = {10.3390/bios14080376},

issn = {2079-6374},

year  = {2024},

date = {2024-08-01},

journal = {Biosensors (Basel)},

volume = {14},

number = {8},

abstract = {Small molecules are highly relevant targets for detection and quantification. They are also used to diagnose and monitor the progression of disease and infectious processes and track the presence of contaminants. Fluorogenic RNA-based biosensors (FRBs) represent an appealing solution to the problem of detecting these targets. They combine the portability of molecular systems with the sensitivity and multiplexing capacity of fluorescence, as well as the exquisite ligand selectivity of RNA aptamers. In this review, we first present the different sensing and reporting aptamer modules currently available to design an FRB, together with the main methodologies used to discover modules with new specificities. We next introduce and discuss how both modules can be functionally connected prior to exploring the main applications for which FRB have been used. Finally, we conclude by discussing how using alternative nucleotide chemistries may improve FRB properties and further widen their application scope.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid39005296,

title = {The  small non-coding RNA IsrR regulates TCA cycle activity and virulence},

author = {Gustavo Rios-Delgado and Aubrey K G McReynolds and Emma A Pagella and Javiera Norambuena and Paul Briaud and Vincent Zheng and Matthew J Munneke and Jisun Kim and Hugo Racine and Ronan Carroll and Ehud Zelzion and Eric Skaar and Jeffrey L Bose and Dane Parker and David Lalaouna and Jeffrey M Boyd},

doi = {10.1101/2024.07.03.601953},

issn = {2692-8205},

year  = {2024},

date = {2024-07-01},

journal = {bioRxiv},

abstract = { has evolved mechanisms to cope with low iron (Fe) availability in host tissues.  uses the ferric uptake transcriptional regulator (Fur) to sense titers of cytosolic Fe. Upon Fe depletion, apo-Fur relieves transcriptional repression of genes utilized for Fe uptake. We demonstrate that an  Δ mutant has decreased expression of , which codes for the Fe-dependent enzyme aconitase. Decreased  expression prevented the Δ mutant from growing with amino acids as sole carbon and energy sources. Suppressor analysis determined that a mutation in , which produces a regulatory RNA, permitted growth by decreasing  transcription. The decreased AcnA activity of the Δ mutant was partially relieved by an Δ mutation. Directed mutation of bases predicted to facilitate the interaction between the  transcript and IsrR, decreased the ability of IsrR to control  expression  and IsrR bound to the  transcript . IsrR also bound to the transcripts coding the alternate TCA cycle proteins , , , and . Whole cell metal analyses suggest that IsrR promotes Fe uptake and increases intracellular Fe not ligated by macromolecules. Lastly, we determined that Fur and IsrR promote infection using murine skin and acute pneumonia models.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid39011971,

title = {Direct Zeptomole Detection of RNA Biomarkers by Ultrabright Fluorescent Nanoparticles on Magnetic Beads},

author = {Elisabete Cruz Da Silva and Paraskevi Gaki and Fabien Flieg and Melanie Messmer and Floriane Gucciardi and Yevheniia Markovska and Andreas Reisch and Samira Fafi-Kremer and Sébastien Pfeffer and Andrey S Klymchenko},

doi = {10.1002/smll.202404167},

issn = {1613-6829},

year  = {2024},

date = {2024-07-01},

journal = {Small},

pages = {e2404167},

abstract = {Nucleic acids are important biomarkers in cancer and viral diseases. However, their ultralow concentration in biological/clinical samples makes direct target detection challenging, because it leads to slow hybridization kinetics with the probe and its insufficient signal-to-noise ratio. Therefore, RNA target detection is done by molecular (target) amplification, notably by RT-PCR, which is a tedious multistep method that includes nucleic acid extraction and reverse transcription. Here, a direct method based on ultrabright dye-loaded polymeric nanoparticles in a sandwich-like hybridization assay with magnetic beads is reported. The ultrabright DNA-functionalized nanoparticle, equivalent to ≈10 000 strongly emissive rhodamine dyes, is hybridized with the magnetic bead to the RNA target, providing the signal amplification for the detection. This concept (magneto-fluorescent sandwich) enables high-throughput detection of DNA and RNA sequences of varied lengths from 48 to 1362 nt with the limit of detection down to 0.3 fm using a plate reader (15 zeptomoles), among the best reported for optical sandwich assays. Moreover, it allows semi-quantitative detection of SARS-CoV-2 viral RNA directly in clinical samples without a dedicated RNA extraction step. The developed technology, combining ultrabright nanoparticles with magnetic beads, addresses fundamental challenges in RNA detection; it is expected to accelerate molecular diagnostics of diseases.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38963319,

title = {Comparative proteomics uncovers low asparagine content in Plasmodium tRip-KO proteins},

author = {Martina Pitolli and Marta Cela and Delphine Kapps and Johana Chicher and Laurence Despons and Magali Frugier},

doi = {10.1002/iub.2891},

issn = {1521-6551},

year  = {2024},

date = {2024-07-01},

journal = {IUBMB Life},

abstract = {tRNAs are not only essential for decoding the genetic code, but their abundance also has a strong impact on the rate of protein production, folding, and on the stability of the translated messenger RNAs. Plasmodium expresses a unique surface protein called tRip, involved in the import of exogenous tRNAs into the parasite. Comparative proteomic analysis of the blood stage of wild-type and tRip-KO variant of P. berghei parasites revealed that downregulated proteins in the mutant parasite are distinguished by a bias in their asparagine content. Furthermore, the demonstration of the possibility of charging host tRNAs with Plasmodium aminoacyl-tRNA synthetases led us to propose that imported host tRNAs participate in parasite protein synthesis. These results also suggest a novel mechanism of translational control in which import of host tRNAs emerge as regulators of gene expression in the Plasmodium developmental cycle and pathogenesis, by enabling the synthesis of asparagine-rich regulatory proteins that efficiently and selectively control the parasite infectivity.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid39065030,

title = {Molecular Mechanisms of Bacterial Resistance to Antimicrobial Peptides in the Modern Era: An Updated Review},

author = {Layla Tajer and Jean-Christophe Paillart and Hanna Dib and Jean-Marc Sabatier and Ziad Fajloun and Ziad Abi Khattar},

doi = {10.3390/microorganisms12071259},

issn = {2076-2607},

year  = {2024},

date = {2024-06-01},

journal = {Microorganisms},

volume = {12},

number = {7},

abstract = {Antimicrobial resistance (AMR) poses a serious global health concern, resulting in a significant number of deaths annually due to infections that are resistant to treatment. Amidst this crisis, antimicrobial peptides (AMPs) have emerged as promising alternatives to conventional antibiotics (ATBs). These cationic peptides, naturally produced by all kingdoms of life, play a crucial role in the innate immune system of multicellular organisms and in bacterial interspecies competition by exhibiting broad-spectrum activity against bacteria, fungi, viruses, and parasites. AMPs target bacterial pathogens through multiple mechanisms, most importantly by disrupting their membranes, leading to cell lysis. However, bacterial resistance to host AMPs has emerged due to a slow co-evolutionary process between microorganisms and their hosts. Alarmingly, the development of resistance to last-resort AMPs in the treatment of MDR infections, such as colistin, is attributed to the misuse of this peptide and the high rate of horizontal genetic transfer of the corresponding resistance genes. AMP-resistant bacteria employ diverse mechanisms, including but not limited to proteolytic degradation, extracellular trapping and inactivation, active efflux, as well as complex modifications in bacterial cell wall and membrane structures. This review comprehensively examines all constitutive and inducible molecular resistance mechanisms to AMPs supported by experimental evidence described to date in bacterial pathogens. We also explore the specificity of these mechanisms toward structurally diverse AMPs to broaden and enhance their potential in developing and applying them as therapeutics for MDR bacteria. Additionally, we provide insights into the significance of AMP resistance within the context of host-pathogen interactions.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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},

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 = {},

pubstate = {published},

tppubtype = {article}

}

@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 = {Labex, MARQUET  influenza A virus  NP  nucleoprotein  vRNA  RNA structure  RNA chaperon  chemical probing},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38071475,

title = {The  gene encodes RlmQ, the 23S rRNA methyltransferase forming mG2574 in the A-site of the peptidyl transferase center},

author = {Philippe Wolff and Geoffray Labar and Antony Lechner and Dany Van Elder and Romuald Soin and Cyril Gueydan and Véronique Kruys and Louis Droogmans and Martine Roovers},

doi = {10.1261/rna.079853.123},

issn = {1469-9001},

year  = {2024},

date = {2024-01-01},

urldate = {2024-01-01},

journal = {RNA},

volume = {30},

number = {2},

pages = {105--112},

abstract = {Ribosomal RNA contains many posttranscriptionally modified nucleosides, particularly in the functional parts of the ribosome. The distribution of these modifications varies from one organism to another. In , the model organism for Gram-positive bacteria, mass spectrometry experiments revealed the presence of 7-methylguanosine (mG) at position 2574 of the 23S rRNA, which lies in the A-site of the peptidyl transferase center of the large ribosomal subunit. Testing several mG methyltransferase candidates allowed us to identify the RlmQ enzyme, encoded by the  open reading frame, as the MTase responsible for this modification. The enzyme methylates free RNA and not ribosomal 50S or 70S particles, suggesting that modification occurs in the early steps of ribosome biogenesis.},

keywords = {Labex},

pubstate = {published},

tppubtype = {article}

}

@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 = {Labex},

pubstate = {published},

tppubtype = {article}

}

@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 = {Labex},

pubstate = {published},

tppubtype = {article}

}

@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 = {Labex},

pubstate = {published},

tppubtype = {article}

}

@article{pmid37914398,

title = {Identification of a putative Gag binding site critical for feline immunodeficiency virus genomic RNA packaging},

author = {Anjana Krishnan and Lizna M Ali and Suresha G Prabhu and Vineeta N Pillai and Akhil Chameettachal and Valérie Vivet-Boudou and Serena Bernacchi and Farah Mustafa and Roland Marquet and Tahir A Rizvi},

doi = {10.1261/rna.079840.123},

issn = {1469-9001},

year  = {2023},

date = {2023-12-01},

journal = {RNA},

volume = {30},

number = {1},

pages = {68--88},

abstract = {The retroviral Gag precursor plays a central role in the selection and packaging of viral genomic RNA (gRNA) by binding to virus-specific packaging signal(s) (psi or ψ). Previously, we mapped the feline immunodeficiency virus (FIV) ψ to two discontinuous regions within the 5' end of the gRNA that assumes a higher order structure harboring several structural motifs. To better define the region and structural elements important for gRNA packaging, we methodically investigated these FIV ψ sequences using genetic, biochemical, and structure-function relationship approaches. Our mutational analysis revealed that the unpaired UCUG stretch within FIV ψ is crucial for gRNA encapsidation into nascent virions. High-throughput selective 2' hydroxyl acylation analyzed by primer extension (hSHAPE) performed on wild type (WT) and mutant FIV ψ sequences, with substitutions in the UCUG stretch, revealed that these mutations had limited structural impact and maintained nucleotides 80-92 unpaired, as in the WT structure. Since these mutations dramatically affected packaging, our data suggest that the single-stranded UCUG sequence is important during FIV RNA packaging. Filter-binding assays performed using purified FIV Pr50 on WT and mutant UCUG ψ RNAs led to reduced levels of Pr50 binding to mutant UCUG ψ RNAs, indicating that the UCUG stretch is crucial for ψ RNA-Pr50 interactions. Delineating sequences important for FIV gRNA encapsidation should enhance our understanding of both gRNA packaging and virion assembly, making them potential targets for novel retroviral therapeutic interventions, as well as the development of FIV-based vectors for human gene therapy.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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 = {2023-12-01},

journal = {Nat Plants},

volume = {9},

number = {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 = {},

pubstate = {published},

tppubtype = {article}

}

@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 = {Labex},

pubstate = {published},

tppubtype = {article}

}

@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},

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 = {Labex},

pubstate = {published},

tppubtype = {article}

}

@article{pmid37659413,

title = {The virus-induced cyclic dinucleotide 2'3'-c-di-GMP mediates STING-dependent antiviral immunity in Drosophila},

author = {Hua Cai and Lihua Li and Kailey M Slavik and Jingxian Huang and Ting Yin and Xianlong Ai and Léna Hédelin and Gabrielle Haas and Zhangmin Xiang and Yunyun Yang and Xiaoyan Li and Yuqiang Chen and Ziming Wei and Huimin Deng and Di Chen and Renjie Jiao and Nelson Martins and Carine Meignin and Philip J Kranzusch and Jean-Luc Imler},

doi = {10.1016/j.immuni.2023.08.006},

issn = {1097-4180},

year  = {2023},

date = {2023-09-01},

urldate = {2023-09-01},

journal = {Immunity},

volume = {56},

number = {9},

pages = {1991--2005.e9},

abstract = {In mammals, the enzyme cGAS senses the presence of cytosolic DNA and synthesizes the cyclic dinucleotide (CDN) 2'3'-cGAMP, which triggers STING-dependent immunity. In Drosophila melanogaster, two cGAS-like receptors (cGLRs) produce 3'2'-cGAMP and 2'3'-cGAMP to activate STING. We explored CDN-mediated immunity in 14 Drosophila species covering 50 million years of evolution and found that 2'3'-cGAMP and 3'2'-cGAMP failed to control infection by Drosophila C virus in D. serrata and two other species. We discovered diverse CDNs produced in a cGLR-dependent manner in response to viral infection in D. melanogaster, including 2'3'-c-di-GMP. This CDN was a more potent STING agonist than cGAMP in D. melanogaster and it also activated a strong antiviral transcriptional response in D. serrata. Our results shed light on the evolution of cGLRs in flies and provide a basis for understanding the function and regulation of this emerging family of pattern recognition receptors in animal innate immunity.},

keywords = {Labex},

pubstate = {published},

tppubtype = {article}

}

@article{pmid37715842,

title = {Extensive natural Agrobacterium-induced transformation in the genus Camellia},

author = {Ke Chen and Hai Liu and Todd Blevins and Jie Hao and Léon Otten},

doi = {10.1007/s00425-023-04234-9},

issn = {1432-2048},

year  = {2023},

date = {2023-09-01},

urldate = {2023-09-01},

journal = {Planta},

volume = {258},

number = {4},

pages = {81},

abstract = {The genus Camellia underwent extensive natural transformation by Agrobacterium. Over a period of 15 million years, at least 12 different inserts accumulated in 72 investigated Camellia species. Like a wide variety of other wild and cultivated plants, Camellia species carry cellular T-DNA sequences (cT-DNAs) in their nuclear genomes, resulting from natural Agrobacterium-mediated transformation. Short and long DNA sequencing reads of 435 accessions belonging to 72 Camellia species (representing 12 out of 14 sections) were investigated for the occurrence of cT-DNA insertions. In all, 12 different cT-DNAs were recovered, either completely or partially, called CaTA to CaTL. Divergence analysis of internal cT-DNA repeats revealed that the insertion events span a period from 0.075 to 15 Mio years ago, and yielded an average transformation frequency of one event per 1.25 Mio years. The two oldest inserts, CaTA and CaTD, have been modified by spontaneous deletions and inversions, and by insertion of various plant sequences. In those cases where enough accessions were available (C. japonica, C. oleifera, C. chekiangoleosa, C. sasanqua and C. pitardii), the younger cT-DNA inserts showed a patchy distribution among different accessions of each species, indicating that they are not genetically fixed. It could be shown that Camellia breeding has led to intersectional transfer of cT-DNAs. Altogether, the cT-DNAs cover 374 kb, and carry 47 open reading frames (ORFs). Two Camellia cT-DNA genes, CaTH-orf358 and CaTK-orf8, represent new types of T-DNA genes. With its large number of cT-DNA sequences, the genus Camellia constitutes an interesting model for the study of natural Agrobacterium transformants.},

keywords = {Labex},

pubstate = {published},

tppubtype = {article}

}

@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},

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 = {Labex},

pubstate = {published},

tppubtype = {article}

}

@article{pmid37177985,

title = {An extensive survey of phytoviral RNA 3' uridylation identifies extreme variations and virus-specific patterns},

author = {Anne Caroline Joly and Shahinez Garcia and Jean-Michel Hily and Sandrine Koechler and Gérard Demangeat and Damien Garcia and Emmanuelle Vigne and Olivier Lemaire and Hélène Zuber and Dominique Gagliardi},

doi = {10.1093/plphys/kiad278},

issn = {1532-2548},

year  = {2023},

date = {2023-08-01},

urldate = {2023-08-01},

journal = {Plant Physiol},

volume = {193},

number = {1},

pages = {271--290},

abstract = {Viral RNAs can be uridylated in eukaryotic hosts. However, our knowledge of uridylation patterns and roles remains rudimentary for phytoviruses. Here, we report global 3' terminal RNA uridylation profiles for representatives of the main families of positive single-stranded RNA phytoviruses. We detected uridylation in all 47 viral RNAs investigated here, revealing its prevalence. Yet, uridylation levels of viral RNAs varied from 0.2% to 90%. Unexpectedly, most poly(A) tails of grapevine fanleaf virus (GFLV) RNAs, including encapsidated tails, were strictly monouridylated, which corresponds to an unidentified type of viral genomic RNA extremity. This monouridylation appears beneficial for GFLV because it became dominant when plants were infected with nonuridylated GFLV transcripts. We found that GFLV RNA monouridylation is independent of the known terminal uridylyltransferases (TUTases) HEN1 SUPPRESSOR 1 (HESO1) and UTP:RNA URIDYLYLTRANSFERASE 1 (URT1) in Arabidopsis (Arabidopsis thaliana). By contrast, both TUTases can uridylate other viral RNAs like turnip crinkle virus (TCV) and turnip mosaic virus (TuMV) RNAs. Interestingly, TCV and TuMV degradation intermediates were differentially uridylated by HESO1 and URT1. Although the lack of both TUTases did not prevent viral infection, we detected degradation intermediates of TCV RNA at higher levels in an Arabidopsis heso1 urt1 mutant, suggesting that uridylation participates in clearing viral RNA. Collectively, our work unveils an extreme diversity of uridylation patterns across phytoviruses and constitutes a valuable resource to further decipher pro- and antiviral roles of uridylation.},

keywords = {Labex},

pubstate = {published},

tppubtype = {article}

}

@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 = {2023-07-01},

urldate = {2023-07-01},

journal = {Nat Microbiol},

volume = {8},

number = {7},

pages = {1304--1317},

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 = {Labex},

pubstate = {published},

tppubtype = {article}

}

@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},

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 = {Labex},

pubstate = {published},

tppubtype = {article}

}

@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 = {Labex},

pubstate = {published},

tppubtype = {article}

}

@article{pmid36759127,

title = {Identification of U47 in three thermophilic archaea, one mesophilic archaeon, and one hyperthermophilic bacterium},

author = {Philippe Wolff and Antony Lechner and Louis Droogmans and Henri Grosjean and Eric Westhof},

doi = {10.1261/rna.079546.122},

issn = {1469-9001},

year  = {2023},

date = {2023-05-01},

urldate = {2023-05-01},

journal = {RNA},

volume = {29},

number = {5},

pages = {551--556},

abstract = {Analysis of the profile of the tRNA modifications in several  allowed us to observe a novel modified uridine in the V-loop of several tRNAs from two species:  and  Recently, Ohira and colleagues characterized 2'-phosphouridine (U) at position 47 in tRNAs of thermophilic , as well as in several other archaea and thermophilic bacteria. From the presence of the gene  corresponding to the RNA kinase responsible for U47 formation, they also concluded that U47 should be present in tRNAs of other thermophilic  Reanalysis of our earlier data confirms that the unidentified residue in tRNAs of both  and  is indeed 2'-phosphouridine followed by mC48. Moreover, we find this modification in several tRNAs of other  and of the hyperthermophilic bacterium .},

keywords = {Labex},

pubstate = {published},

tppubtype = {article}

}

@article{pmid36436882,

title = {FluorMango, an RNA-Based Fluorogenic Biosensor for the Direct and Specific Detection of Fluoride},

author = {C. Husser and S. Vuilleumier and M. 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 = {Labex},

pubstate = {published},

tppubtype = {article}

}

@article{pmid36882445,

title = {Distinct roles of Arabidopsis ORC1 proteins in DNA replication and heterochromatic H3K27me1 deposition},

author = {Zaida Vergara and María S Gomez and Bénédicte Desvoyes and Joana Sequeira-Mendes and Kinda Masoud and Celina Costas and Sandra Noir and Elena Caro and Victoria Mora-Gil and Pascal Genschik and Crisanto Gutierrez},

doi = {10.1038/s41467-023-37024-8},

issn = {2041-1723},

year  = {2023},

date = {2023-03-01},

urldate = {2023-03-01},

journal = {Nat Commun},

volume = {14},

number = {1},

pages = {1270},

abstract = {Most cellular proteins involved in genome replication are conserved in all eukaryotic lineages including yeast, plants and animals. However, the mechanisms controlling their availability during the cell cycle are less well defined. Here we show that the Arabidopsis genome encodes for two ORC1 proteins highly similar in amino acid sequence and that have partially overlapping expression domains but with distinct functions. The ancestral ORC1b gene, present before the partial duplication of the Arabidopsis genome, has retained the canonical function in DNA replication. ORC1b is expressed in both proliferating and endoreplicating cells, accumulates during G1 and is rapidly degraded upon S-phase entry through the ubiquitin-proteasome pathway. In contrast, the duplicated ORC1a gene has acquired a specialized function in heterochromatin biology. ORC1a is required for efficient deposition of the heterochromatic H3K27me1 mark by the ATXR5/6 histone methyltransferases. The distinct roles of the two ORC1 proteins may be a feature common to other organisms with duplicated ORC1 genes and a major difference with animal cells.},

keywords = {Labex},

pubstate = {published},

tppubtype = {article}

}

@article{pmid36853733,

title = {Protocol for the analysis of double-stranded RNAs in virus-infected insect cells using anti-dsRNA antibodies},

author = {Isaque J S de Faria and Jean-Luc Imler and João T Marques},

doi = {10.1016/j.xpro.2022.102033},

issn = {2666-1667},

year  = {2023},

date = {2023-03-01},

urldate = {2023-03-01},

journal = {STAR Protoc},

volume = {4},

number = {1},

pages = {102033},

abstract = {Characterization of double-stranded (ds)RNAs is relevant to the understanding of viral replication and immune sensing. Here, we provide a protocol describing the use of anti-dsRNA antibodies for immunofluorescence and immunoblotting in virus-infected insect cells, which can also be applied to tissues and other organisms. We describe the procedures to prepare insect cells for viral infection, followed by RNA extraction and in vitro production of synthetic dsRNA controls. We then detail the steps for dsRNA detection by immunoblotting and immunofluorescence. For complete details on the use and execution of this protocol, please refer to de Faria et al. (2022)..},

keywords = {Labex},

pubstate = {published},

tppubtype = {article}

}

@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 = {Labex},

pubstate = {published},

tppubtype = {article}

}

@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 = {2023-02-01},

urldate = {2023-02-01},

journal = {Protein Sci},

volume = {32},

number = {2},

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.},

keywords = {Labex},

pubstate = {published},

tppubtype = {article}

}

@article{pmid36740835,

title = {No-go decay as a novel route to restrict viral infection in plants},

author = {Aude Pouclet and Dominique Gagliardi and Damien Garcia},

doi = {10.1016/j.molp.2023.02.001},

issn = {1752-9867},

year  = {2023},

date = {2023-02-01},

journal = {Mol Plant},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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 = {Labex},

pubstate = {published},

tppubtype = {article}

}

@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},

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 = {Labex},

pubstate = {published},

tppubtype = {article}

}

@article{pmid36308692,

title = {Exploring Protein Interactome Data with IPinquiry: Statistical Analysis and Data Visualization by Spectral Counts},

author = {Lauriane Kuhn and Timothée Vincent and Philippe Hammann and Hélène Zuber},

doi = {10.1007/978-1-0716-1967-4_11},

issn = {1940-6029},

year  = {2023},

date = {2023-01-01},

urldate = {2023-01-01},

journal = {Methods Mol Biol},

volume = {2426},

pages = {243--265},

abstract = {Immunoprecipitation mass spectrometry (IP-MS) is a popular method for the identification of protein-protein interactions. This approach is particularly powerful when information is collected without a priori knowledge and has been successively used as a first key step for the elucidation of many complex protein networks. IP-MS consists in the affinity purification of a protein of interest and of its interacting proteins followed by protein identification and quantification by mass spectrometry analysis. We developed an R package, named IPinquiry, dedicated to IP-MS analysis and based on the spectral count quantification method. The main purpose of this package is to provide a simple R pipeline with a limited number of processing steps to facilitate data exploration for biologists. This package allows to perform differential analysis of protein accumulation between two groups of IP experiments, to retrieve protein annotations, to export results, and to create different types of graphics. Here we describe the step-by-step procedure for an interactome analysis using IPinquiry from data loading to result export and plot production.},

keywords = {Labex},

pubstate = {published},

tppubtype = {article}

}

@article{pmid36604511,

title = {Mosquito vector competence for dengue is modulated by insect-specific viruses},

author = {Roenick P Olmo and Yaovi M H Todjro and Eric R G R Aguiar and João Paulo P de Almeida and Flávia V Ferreira and Juliana N Armache and Isaque J S de Faria and Alvaro G A Ferreira and Siad C G Amadou and Ana Teresa S Silva and Kátia P R de Souza and Ana Paula P Vilela and Antinea Babarit and Cheong H Tan and Mawlouth Diallo and Alioune Gaye and Christophe Paupy and Judicaël Obame-Nkoghe and Tessa M Visser and Constantianus J M Koenraadt and Merril A Wongsokarijo and Ana Luiza C Cruz and Mariliza T Prieto and Maisa C P Parra and Maurício L Nogueira and Vivian Avelino-Silva and Renato N Mota and Magno A Z Borges and Betânia P Drumond and Erna G Kroon and Mario Recker and Luigi Sedda and Eric Marois and Jean-Luc Imler and João T Marques},

doi = {10.1038/s41564-022-01289-4},

issn = {2058-5276},

year  = {2023},

date = {2023-01-01},

urldate = {2023-01-01},

journal = {Nat Microbiol},

volume = {8},

number = {1},

pages = {135--149},

abstract = {Aedes aegypti and A. albopictus mosquitoes are the main vectors for dengue virus (DENV) and other arboviruses, including Zika virus (ZIKV). Understanding the factors that affect transmission of arboviruses from mosquitoes to humans is a priority because it could inform public health and targeted interventions. Reasoning that interactions among viruses in the vector insect might affect transmission, we analysed the viromes of 815 urban Aedes mosquitoes collected from 12 countries worldwide. Two mosquito-specific viruses, Phasi Charoen-like virus (PCLV) and Humaita Tubiacanga virus (HTV), were the most abundant in A. aegypti worldwide. Spatiotemporal analyses of virus circulation in an endemic urban area revealed a 200% increase in chances of having DENV in wild A. aegypti mosquitoes when both HTV and PCLV were present. Using a mouse model in the laboratory, we showed that the presence of HTV and PCLV increased the ability of mosquitoes to transmit DENV and ZIKV to a vertebrate host. By transcriptomic analysis, we found that in DENV-infected mosquitoes, HTV and PCLV block the downregulation of histone H4, which we identify as an important proviral host factor in vivo.},

keywords = {Labex},

pubstate = {published},

tppubtype = {article}

}

@article{pmid36846801,

title = { Escherichia coli 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 = {Labex},

pubstate = {published},

tppubtype = {article}

}

@article{pmid36156788,

title = {High-Throughput Development and Optimization of RNA-Based Fluorogenic Biosensors of Small Molecules Using Droplet-Based Microfluidics},

author = {C. Husser and S. Baudrey and M. 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 = {Labex},

pubstate = {published},

tppubtype = {article}

}

@article{pmid36617674,

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

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

doi = {10.1261/rna.079270.122},

issn = {1469-9001},

year  = {2022},

date = {2022-12-01},

urldate = {2022-12-01},

journal = {RNA},

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 = {Labex},

pubstate = {published},

tppubtype = {article}

}

@article{pmid36450801,

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

author = {A-S Neyroud and J. Rudinger-Thirion and M. Frugier and L. G Riley and M. Bidet and L. Akloul and A. Simpson and D. Gilot and J. Christodoulou and C. Ravel and A. H Sinclair and M-A Belaud-Rotureau and E. J Tucker and S. Jaillard},

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

issn = {1476-5438},

year  = {2022},

date = {2022-12-01},

urldate = {2022-12-01},

journal = {Eur J Hum Genet},

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

keywords = {Labex},

pubstate = {published},

tppubtype = {article}

}

@article{pmid36269824,

title = {Proteasome-associated ubiquitin ligase relays target plant hormone-specific transcriptional activators},

author = {Zhishuo Wang and Beatriz Orosa-Puente and Mika Nomoto and Heather Grey and Thomas Potuschak and Takakazu Matsuura and Izumi C Mori and Yasuomi Tada and Pascal Genschik and Steven H Spoel},

doi = {10.1126/sciadv.abn4466},

issn = {2375-2548},

year  = {2022},

date = {2022-10-01},

urldate = {2022-10-01},

journal = {Sci Adv},

volume = {8},

number = {42},

pages = {eabn4466},

abstract = {The ubiquitin-proteasome system is vital to hormone-mediated developmental and stress responses in plants. Ubiquitin ligases target hormone-specific transcriptional activators (TAs) for degradation, but how TAs are processed by proteasomes remains unknown. We report that in , the salicylic acid- and ethylene-responsive TAs, NPR1 and EIN3, are relayed from pathway-specific ubiquitin ligases to proteasome-associated HECT-type UPL3/4 ligases. Activity and stability of NPR1 were regulated by sequential action of three ubiquitin ligases, including UPL3/4, while proteasome processing of EIN3 required physical handover between ethylene-responsive SCF and UPL3/4 ligases. Consequently, UPL3/4 controlled extensive hormone-induced developmental and stress-responsive transcriptional programs. Thus, our findings identify unknown ubiquitin ligase relays that terminate with proteasome-associated HECT-type ligases, which may be a universal mechanism for processive degradation of proteasome-targeted TAs and other substrates.},

keywords = {Labex},

pubstate = {published},

tppubtype = {article}

}

@article{pmid36353712,

title = {30S Ribosomal Subunit Purification and Its Biochemical and Cryo-EM Analysis},

author = {M Belinite and I Khusainov and S Marzi},

doi = {10.21769/BioProtoc.4532},

issn = {2331-8325},

year  = {2022},

date = {2022-10-01},

urldate = {2022-10-01},

journal = {Bio Protoc},

volume = {12},

number = {20},

abstract = {The ribosome is a complex cellular machinery whose solved structure allowed for an incredible leap in structural biology research. Different ions bind to the ribosome, stabilizing inter-subunit interfaces and structurally linking rRNAs, proteins, and ligands. Besides cations such as K and Mg , polyamines are known to stabilize the folding of RNA and overall structure. The bacterial ribosome is composed of a small (30S) subunit containing the decoding center and a large (50S) subunit devoted to peptide bond formation. We have previously shown that the small ribosomal subunit of is sensitive to changes in ionic conditions and polyamines concentration. In particular, its decoding center, where mRNA codons and tRNA anticodons interact, is prone to structural deformations in the absence of spermidine. Here, we report a detailed protocol for the purification of the intact and functional 30S, achieved through specific ionic conditions and the addition of spermidine. Using this protocol, we obtained the cryo-electron microscopy (cryo-EM) structure of the 30S-mRNA complex from at 3.6 Å resolution. The 30S-mRNA complex formation was verified by a toeprinting assay. In this article, we also include a description of toeprinting and cryo-EM protocols. The described protocols can be further used to study the process of translation regulation. Graphical abstract.},

keywords = {Labex},

pubstate = {published},

tppubtype = {article}

}

@article{pmid36140409,

title = {Dynamic Regulation of NF-κB Response in Innate Immunity: The Case of the IMD Pathway in Drosophila},

author = {Alexandre Cammarata-Mouchtouris and Adrian Acker and Akira Goto and Di Chen and Nicolas Matt and Vincent Leclerc},

doi = {10.3390/biomedicines10092304},

issn = {2227-9059},

year  = {2022},

date = {2022-09-01},

urldate = {2022-09-01},

journal = {Biomedicines},

volume = {10},

number = {9},

abstract = {Metazoans have developed strategies to protect themselves from pathogenic attack. These preserved mechanisms constitute the immune system, composed of innate and adaptive responses. Among the two kinds, the innate immune system involves the activation of a fast response. NF-κB signaling pathways are activated during infections and lead to the expression of timely-controlled immune response genes. However, activation of NF-κB pathways can be deleterious when uncontrolled. Their regulation is necessary to prevent the development of inflammatory diseases or cancers. The similarity of the NF-κB pathways mediating immune mechanisms in insects and mammals makes  a suitable model for studying the innate immune response and learning general mechanisms that are also relevant for humans. In this review, we summarize what is known about the dynamic regulation of the central NF-κB-pathways and go into detail on the molecular level of the IMD pathway. We report on the role of the nuclear protein Akirin in the regulation of the NF-κB Relish immune response. The use of the  model allows the understanding of the fine-tuned regulation of this central NF-κB pathway.},

keywords = {Labex},

pubstate = {published},

tppubtype = {article}

}

@article{pmid36108089,

title = {A tRNA-derived fragment present in E. coli OMVs regulates host cell gene expression and proliferation},

author = {I. Diallo and J. Ho and M. Lambert and A. Benmoussa and Z. Husseini and D. Lalaouna and E. Massé and P. Provost},

doi = {10.1371/journal.ppat.1010827},

issn = {1553-7374},

year  = {2022},

date = {2022-09-01},

urldate = {2022-09-01},

journal = {PLoS Pathog},

volume = {18},

number = {9},

pages = {e1010827},

abstract = {RNA-sequencing has led to a spectacular increase in the repertoire of bacterial sRNAs and improved our understanding of their biological functions. Bacterial sRNAs have also been found in outer membrane vesicles (OMVs), raising questions about their potential involvement in bacteria-host relationship, but few studies have documented this issue. Recent RNA-Sequencing analyses of bacterial RNA unveiled the existence of abundant very small RNAs (vsRNAs) shorter than 16 nt. These especially include tRNA fragments (tRFs) that are selectively loaded in OMVs and are predicted to target host mRNAs. Here, in Escherichia coli (E. coli), we report the existence of an abundant vsRNA, Ile-tRF-5X, which is selectively modulated by environmental stress, while remaining unaffected by inhibition of transcription or translation. Ile-tRF-5X is released through OMVs and can be transferred to human HCT116 cells, where it promoted MAP3K4 expression. Our findings provide a novel perspective and paradigm on the existing symbiosis between bacteria and human cells.},

keywords = {Labex},

pubstate = {published},

tppubtype = {article}

}

@article{pmid35732126,

title = {Invading viral DNA triggers dsRNA synthesis by RNA polymerase II to activate antiviral RNA interference in Drosophila},

author = {Isaque J S de Faria and Eric R G R Aguiar and Roenick P Olmo and Juliana Alves da Silva and Laurent Daeffler and Richard W Carthew and Jean-Luc Imler and João T Marques},

doi = {10.1016/j.celrep.2022.110976},

issn = {2211-1247},

year  = {2022},

date = {2022-06-01},

urldate = {2022-06-01},

journal = {Cell Rep},

volume = {39},

number = {12},

pages = {110976},

abstract = {dsRNA sensing triggers antiviral responses against RNA and DNA viruses in diverse eukaryotes. In Drosophila, Invertebrate iridescent virus 6 (IIV-6), a large DNA virus, triggers production of small interfering RNAs (siRNAs) by the dsRNA sensor Dicer-2. Here, we show that host RNA polymerase II (RNAPII) bidirectionally transcribes specific AT-rich regions of the IIV-6 DNA genome to generate dsRNA. Both replicative and naked IIV-6 genomes trigger production of dsRNA in Drosophila cells, implying direct sensing of invading DNA. Loquacious-PD, a Dicer-2 co-factor essential for the biogenesis of endogenous siRNAs, is dispensable for processing of IIV-6-derived dsRNAs, which suggests that they are distinct. Consistent with this finding, inhibition of the RNAPII co-factor P-TEFb affects the synthesis of endogenous, but not virus-derived, dsRNA. Altogether, our results suggest that a non-canonical RNAPII complex recognizes invading viral DNA to synthesize virus-derived dsRNA, which activates the antiviral siRNA pathway in Drosophila.},

keywords = {Labex},

pubstate = {published},

tppubtype = {article}

}

@article{pmid35487244,

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

author = {José R Jaramillo Ponce and Delphine Kapps and Caroline Paulus and Johana Chicher and Magali Frugier},

doi = {10.1016/j.jbc.2022.101987},

issn = {1083-351X},

year  = {2022},

date = {2022-06-01},

urldate = {2022-06-01},

journal = {J Biol Chem},

volume = {298},

number = {6},

pages = {101987},

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

keywords = {Labex},

pubstate = {published},

tppubtype = {article}

}