Libre C, Seissler T, Guerrero S, Batisse J, Verriez C, Stupfler B, Gilmer O, Cabrera-Rodriguez R, Weber M, Valenzuela-Fernandez A, Cimarelli A, Etienne L, Marquet R, Paillart J C
A Conserved uORF Regulates APOBEC3G Translation and Is Targeted by HIV-1 Vif Protein to Repress the Antiviral Factor Article de journal
Dans: Biomedicines, vol. 10, no. 1, p. 13, 2022.
Résumé | Liens | BibTeX | Étiquettes: MARQUET, PAILLART, Unité ARN
@article{Libre2022,
title = {A Conserved uORF Regulates APOBEC3G Translation and Is Targeted by HIV-1 Vif Protein to Repress the Antiviral Factor},
author = {C Libre and T Seissler and S Guerrero and J Batisse and C Verriez and B Stupfler and O Gilmer and R Cabrera-Rodriguez and M Weber and A Valenzuela-Fernandez and A Cimarelli and L Etienne and R Marquet and J C Paillart},
url = {https://www.mdpi.com/2227-9059/10/1/13},
doi = {10.1101/2021.01.13.426487},
year = {2022},
date = {2022-01-01},
urldate = {2022-01-01},
journal = {Biomedicines},
volume = {10},
number = {1},
pages = {13},
abstract = {The HIV-1 Vif protein is essential for viral fitness and pathogenicity. Vif decreases expression of cellular cytosine deaminases APOBEC3G (A3G), A3F, A3D and A3H, which inhibit HIV-1 replication by inducing hypermutations during reverse transcription. Vif counteracts A3G by several non-redundant mechanisms (transcription, translation and protein degradation) that concur in reducing the levels of A3G in cell and in preventing its incorporation into viral particles. How Vif affects A3G translation remains unclear. Here, we uncovered the importance of a short conserved uORF (upstream ORF) located within two critical stem-loop structures of the 5-untranslated region (5-UTR) of A3G mRNA. Extensive mutagenesis of A3G 5-UTR, combined with an analysis of their translational effect in transfected cells, indicated that the uORF represses A3G translation and that A3G mRNA is translated through a dual leaky-scanning and re-initiation mechanism. Interestingly, the uORF is also mandatory for the Vif-mediated repression of A3G translation. Furthermore, we showed that the redirection of A3G mRNA into stress granules was dependent not only on Vif, but also on the uORF. Overall, we discovered that A3G translation is regulated by a small uORF conserved in the human population and that Vif uses this specific motif to repress its translation.},
keywords = {MARQUET, PAILLART, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Desgranges E., Barrientos L., Herrgott L., Marzi S., Toledo-Arana A., Moreau K., Vandenesch F., Romby P., Caldelari I.
The 3'UTR-derived sRNA RsaG coordinates redox homeostasis and metabolism adaptation in response to glucose-6-phosphate uptake in Staphylococcus aureus Article de journal
Dans: Mol Microbiol, 2022, ISBN: 34783400, (1365-2958 (Electronic) 0950-382X (Linking) Journal Article).
Résumé | Liens | BibTeX | Étiquettes: ROMBY, Unité ARN
@article{nokey,
title = {The 3'UTR-derived sRNA RsaG coordinates redox homeostasis and metabolism adaptation in response to glucose-6-phosphate uptake in Staphylococcus aureus},
author = {E. Desgranges and L. Barrientos and L. Herrgott and S. Marzi and A. Toledo-Arana and K. Moreau and F. Vandenesch and P. Romby and I. Caldelari},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=34783400},
doi = {10.1111/mmi.14845},
isbn = {34783400},
year = {2022},
date = {2022-01-01},
urldate = {2021-01-01},
journal = {Mol Microbiol},
abstract = {Staphylococcus aureus RsaG is a 3' untranslated region (3'UTR) derived sRNA from the conserved uhpT gene encoding a glucose-6-phosphate (G6P) transporter expressed in response to extracellular G6P. The transcript uhpT-RsaG undergoes degradation from 5' to 3' end by the action of the exoribonucleases J1/J2, which are blocked by a stable hairpin structure at the 5' end of RsaG, leading to its accumulation. RsaG together with uhpT are induced when bacteria are internalized into host cells or in presence of mucus-secreting cells. Using MS2 affinity purification coupled with RNA sequencing, several RNAs were identified as targets including mRNAs encoding the transcriptional factors Rex, CcpA, SarA and the sRNA RsaI. Our data suggested that RsaG contributes to the control of redox homeostasis and adjusts metabolism to changing environmental conditions. RsaG uses different molecular mechanisms to stabilize, to degrade, or to repress translation of its mRNA targets. While RsaG is conserved only in closely related species, the uhpT 3'UTR of the ape pathogen S. simiae harbors a sRNA, whose sequence is highly different, and which does not respond to G6P levels. Our results hypothesized that the 3'UTRs from UhpT transporter encoding mRNAs could have rapidly evolved to enable adaptation to host niches.},
note = {1365-2958 (Electronic)
0950-382X (Linking)
Journal Article},
keywords = {ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Camara A., Lavanant A. C., Abe J., Desforges H. L., Alexandre Y. O., Girardi E., Igamberdieva Z., Asano K., Tanaka M., Hehlgans T., Pfeffer K., Pfeffer S., Mueller S. N., Stein J. V., Mueller C. G.
CD169(+) macrophages in lymph node and spleen critically depend on dual RANK and LTbetaR signaling Article de journal
Dans: Proc Natl Acad Sci U S A, vol. 119, no. 3, p. e2108540119, 2022, ISBN: 35031565, (1091-6490 (Electronic) 0027-8424 (Linking) Journal Article).
Résumé | Liens | BibTeX | Étiquettes: PFEFFER, Unité ARN
@article{nokey,
title = {CD169(+) macrophages in lymph node and spleen critically depend on dual RANK and LTbetaR signaling},
author = {A. Camara and A. C. Lavanant and J. Abe and H. L. Desforges and Y. O. Alexandre and E. Girardi and Z. Igamberdieva and K. Asano and M. Tanaka and T. Hehlgans and K. Pfeffer and S. Pfeffer and S. N. Mueller and J. V. Stein and C. G. Mueller},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=35031565},
isbn = {35031565},
year = {2022},
date = {2022-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {119},
number = {3},
pages = {e2108540119},
abstract = {CD169(+) macrophages reside in lymph node (LN) and spleen and play an important role in the immune defense against pathogens. As resident macrophages, they are responsive to environmental cues to shape their tissue-specific identity. We have previously shown that LN CD169(+) macrophages require RANKL for formation of their niche and their differentiation. Here, we demonstrate that they are also dependent on direct lymphotoxin beta (LTbeta) receptor (R) signaling. In the absence or the reduced expression of either RANK or LTbetaR, their differentiation is perturbed, generating myeloid cells expressing SIGN-R1 in LNs. Conditions of combined haploinsufficiencies of RANK and LTbetaR revealed that both receptors contribute equally to LN CD169(+) macrophage differentiation. In the spleen, the Cd169-directed ablation of either receptor results in a selective loss of marginal metallophilic macrophages (MMMs). Using a RANKL reporter mouse, we identify splenic marginal zone stromal cells as a source of RANKL and demonstrate that it participates in MMM differentiation. The loss of MMMs had no effect on the splenic B cell compartments but compromised viral capture and the expansion of virus-specific CD8(+) T cells. Taken together, the data provide evidence that CD169(+) macrophage differentiation in LN and spleen requires dual signals from LTbetaR and RANK with implications for the immune response.},
note = {1091-6490 (Electronic)
0027-8424 (Linking)
Journal Article},
keywords = {PFEFFER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Costa P. J. Da, Hamdane M., Buee L., Martin F.
Tau mRNA Metabolism in Neurodegenerative Diseases: A Tangle Journey Article de journal
Dans: Biomedicines, vol. 10, no. 2, p. 241, 2022.
Résumé | Liens | BibTeX | Étiquettes: ERIANI, mRNA metabolism, Neurodegenerative Diseases, tau protein, Translation, Unité ARN
@article{nokey,
title = {Tau mRNA Metabolism in Neurodegenerative Diseases: A Tangle Journey},
author = {P. J. Da Costa and M. Hamdane and L. Buee and F. Martin},
url = {https://www.mdpi.com/2227-9059/10/2/241/htm},
doi = {10.3390/biomedicines10020241},
year = {2022},
date = {2022-01-01},
journal = {Biomedicines},
volume = {10},
number = {2},
pages = {241},
abstract = {Tau proteins are known to be mainly involved in regulation of microtubule dynamics. Besides this function, which is critical for axonal transport and signal transduction, tau proteins also have other roles in neurons. Moreover, tau proteins are turned into aggregates and consequently trigger many neurodegenerative diseases termed tauopathies, of which Alzheimerメs disease (AD) is the figurehead. Such pathological aggregation processes are critical for the onset of these diseases. Among the various causes of tau protein pathogenicity, abnormal tau mRNA metabolism, expression and dysregulation of tau post-translational modifications are critical steps. Moreover, the relevance of tau function to general mRNA metabolism has been highlighted recently in tauopathies. In this review, we mainly focus on how mRNA metabolism impacts the onset and development of tauopathies. Thus, we intend to portray how mRNA metabolism of, or mediated by, tau is associated with neurodegenerative diseases.},
keywords = {ERIANI, mRNA metabolism, Neurodegenerative Diseases, tau protein, Translation, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Gilmer O., Mailler E., Paillart J. C., Mouhand A., Tisne C., Mak J., Smyth R. P., Marquet R., Vivet-Boudou V.
Structural maturation of the HIV-1 RNA 5' untranslated region by Pr55(Gag) and its maturation products Article de journal
Dans: RNA Biol, vol. 19, no. 1, p. 191-205, 2022, ISBN: 35067194, (1555-8584 (Electronic) 1547-6286 (Linking) Journal Article).
Résumé | Liens | BibTeX | Étiquettes: MARQUET, PAILLART, Unité ARN
@article{nokey,
title = {Structural maturation of the HIV-1 RNA 5' untranslated region by Pr55(Gag) and its maturation products},
author = {O. Gilmer and E. Mailler and J. C. Paillart and A. Mouhand and C. Tisne and J. Mak and R. P. Smyth and R. Marquet and V. Vivet-Boudou},
url = {https://www.tandfonline.com/doi/full/10.1080/15476286.2021.2021677},
isbn = {35067194},
year = {2022},
date = {2022-01-01},
journal = {RNA Biol},
volume = {19},
number = {1},
pages = {191-205},
abstract = {Maturation of the HIV-1 viral particles shortly after budding is required for infectivity. During this process, the Pr55(Gag) precursor undergoes a cascade of proteolytic cleavages, and whilst the structural rearrangements of the viral proteins are well understood, the concomitant maturation of the genomic RNA (gRNA) structure is unexplored, despite evidence that it is required for infectivity. To get insight into this process, we systematically analysed the interactions between Pr55(Gag) or its maturation products (NCp15, NCp9 and NCp7) and the 5' gRNA region and their structural consequences, in vitro. We show that Pr55(Gag) and its maturation products mostly bind at different RNA sites and with different contributions of their two zinc knuckle domains. Importantly, these proteins have different transient and permanent effects on the RNA structure, the late NCp9 and NCp7 inducing dramatic structural rearrangements. Altogether, our results reveal the distinct contributions of the different Pr55(Gag) maturation products on the gRNA structural maturation.},
note = {1555-8584 (Electronic)
1547-6286 (Linking)
Journal Article},
keywords = {MARQUET, PAILLART, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Chan D. L., Rudinger-Thirion J., Frugier M., Riley L. G., Ho G., Kothur K., Mohammad S. S.
A case of QARS1 associated epileptic encephalopathy and review of epilepsy in aminoacyl-tRNA synthetase disorders Article de journal
Dans: Brain Dev, vol. 44, no. 2, p. 142-147, 2022, ISBN: 34774383, (1872-7131 (Electronic) 0387-7604 (Linking) Case Reports).
Résumé | Liens | BibTeX | Étiquettes: FRUGIER, Unité ARN
@article{nokey,
title = {A case of QARS1 associated epileptic encephalopathy and review of epilepsy in aminoacyl-tRNA synthetase disorders},
author = {D. L. Chan and J. Rudinger-Thirion and M. Frugier and L. G. Riley and G. Ho and K. Kothur and S. S. Mohammad},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=34774383},
doi = {10.1016/j.braindev.2021.10.009},
isbn = {34774383},
year = {2022},
date = {2022-01-01},
journal = {Brain Dev},
volume = {44},
number = {2},
pages = {142-147},
abstract = {INTRODUCTION: Mutations in QARS1, which encodes human glutaminyl-tRNA synthetase, have been associated with epilepsy, developmental regression, progressive microcephaly and cerebral atrophy. Epilepsy caused by variants in QARS1 is usually drug-resistant and intractable. Childhood onset epilepsy is also reported in various aminoacyl-tRNA synthetase disorders. We describe a case with a milder neurological phenotype than previously reported with QARS1 variants and review the seizure associations with aminoacyl-tRNA synthetase disorders. CASE REPORT: The patient is a 4-year-old girl presenting at 6 weeks of age with orofacial dyskinesia and hand stereotypies. She developed focal seizures at 7 months of age. Serial electroencephalograms showed shifting focality. Her seizures were controlled after introduction of carbamazepine. Progress MRI showed very mild cortical volume loss without myelination abnormalities or cerebellar atrophy. She was found to have novel compound heterozygous variants in QARS1 (NM_005051.2): c.[1132C > T];[1574G > A], p.[(Arg378Cys)];[(Arg525Gln)] originally classified as "variants of uncertain significance" and later upgraded to "likely pathogenic" based on functional testing and updated variant database review. Functional testing showed reduced solubility of the corresponding QARS1 mutants in vitro, but only mild two-fold loss in catalytic efficiency with the c.1132C > T variant and no noted change in tRNA(Gln) aminoacylation with the c.1574G > A variant. CONCLUSION: We describe two QARS1 variants associated with overall conserved tRNA aminoacylation activity but characterized by significantly reduced QARS protein solubility, resulting in a milder clinical phenotype. 86% of previous patients reported with QARS1 had epilepsy and 79% were pharmaco-resistant. We also summarise literature regarding epilepsy in aminoacyl-tRNA synthetase disorders, which is also often early onset, severe and drug-refractory.},
note = {1872-7131 (Electronic)
0387-7604 (Linking)
Case Reports},
keywords = {FRUGIER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Andre A. C., Laborde M., Marteyn B. S.
The battle for oxygen during bacterial and fungal infections Article de journal
Dans: Trends Microbiol, vol. S0966-842X, iss. 22, no. 00002-6, p. in press, 2022, ISBN: 35131160, (1878-4380 (Electronic) 0966-842X (Linking) Journal Article Review).
Résumé | Liens | BibTeX | Étiquettes: MARTEYN, Unité ARN
@article{nokey,
title = {The battle for oxygen during bacterial and fungal infections},
author = {A. C. Andre and M. Laborde and B. S. Marteyn},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=35131160},
doi = {10.1016/j.tim.2022.01.002},
isbn = {35131160},
year = {2022},
date = {2022-01-01},
urldate = {2022-01-01},
journal = {Trends Microbiol},
volume = {S0966-842X},
number = {00002-6},
issue = {22},
pages = {in press},
abstract = {Bacterial and fungal pathogens face various microenvironmental conditions during infection. In addition to acidosis, nutrient consumption, and hypercapnia, pathogen infections are associated with hypoxia, which is induced by bacterial and fungal respiration during the formation of foci of infection or biofilms. Consequently, the in vivo interaction between host immune cells and pathogens is anticipated to occur mainly under low-oxygen conditions. Various infectious disease models have reported that pathogens benefit from hypoxia, which dampens the oxygen-dependent antimicrobial activities of macrophages and neutrophils, such as the production of reactive oxygen species (ROS). Due to their dual respiration capacity (aerobic and anaerobic) or phenotypical adaptation (e.g., dormancy), pathogens have the capacity to survive and disseminate in the absence of oxygen. In addition, hypoxia modulates various mechanisms of pathogen virulence, promoting the dissemination of pathogens. Further investigations are still required to evaluate the relative importance of oxygen on the capacity of pathogens to invade and colonize host organs and to better understand alternative strategies developed by immune cells to circumvent pathogen dissemination in the absence of oxygen. Addressing this important and fundamental question in various models of infection may direct the development of innovative therapeutic strategies.},
note = {1878-4380 (Electronic)
0966-842X (Linking)
Journal Article
Review},
keywords = {MARTEYN, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Bernacchi S.
Visualization of Retroviral Gag-Genomic RNA Cellular Interactions Leading to Genome Encapsidation and Viral Assembly: An Overview Article de journal
Dans: Viruses, vol. 14, no. 2, 2022, ISBN: 35215917, (1999-4915 (Electronic) 1999-4915 (Linking) Journal Article Review Research Support, Non-U.S. Gov't).
Résumé | Liens | BibTeX | Étiquettes: MARQUET, PAILLART, Unité ARN
@article{nokey,
title = {Visualization of Retroviral Gag-Genomic RNA Cellular Interactions Leading to Genome Encapsidation and Viral Assembly: An Overview},
author = {S. Bernacchi},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=35215917},
doi = {10.3390/v14020324},
isbn = {35215917},
year = {2022},
date = {2022-01-01},
journal = {Viruses},
volume = {14},
number = {2},
abstract = {Retroviruses must selectively recognize their unspliced RNA genome (gRNA) among abundant cellular and spliced viral RNAs to assemble into newly formed viral particles. Retroviral gRNA packaging is governed by Gag precursors that also orchestrate all the aspects of viral assembly. Retroviral life cycles, and especially the HIV-1 one, have been previously extensively analyzed by several methods, most of them based on molecular biology and biochemistry approaches. Despite these efforts, the spatio-temporal mechanisms leading to gRNA packaging and viral assembly are only partially understood. Nevertheless, in these last decades, progress in novel bioimaging microscopic approaches (as FFS, FRAP, TIRF, and wide-field microscopy) have allowed for the tracking of retroviral Gag and gRNA in living cells, thus providing important insights at high spatial and temporal resolution of the events regulating the late phases of the retroviral life cycle. Here, the implementation of these recent bioimaging tools based on highly performing strategies to label fluorescent macromolecules is described. This report also summarizes recent gains in the current understanding of the mechanisms employed by retroviral Gag polyproteins to regulate molecular mechanisms enabling gRNA packaging and the formation of retroviral particles, highlighting variations and similarities among the different retroviruses.},
note = {1999-4915 (Electronic)
1999-4915 (Linking)
Journal Article
Review
Research Support, Non-U.S. Gov't},
keywords = {MARQUET, PAILLART, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Sosnowski P., Tidu A., Eriani G., Westhof E., Martin F.
Correlated sequence signatures are present within the genomic 5'UTR RNA and NSP1 protein in coronaviruses Article de journal
Dans: Rna, vol. 28, iss. 5, p. 729-741, 2022, ISBN: 35236777, (1469-9001 (Electronic) 1355-8382 (Linking) Journal Article).
Résumé | Liens | BibTeX | Étiquettes: ERIANI, MARTIN, Unité ARN, WESTHOF
@article{nokey,
title = {Correlated sequence signatures are present within the genomic 5'UTR RNA and NSP1 protein in coronaviruses},
author = {P. Sosnowski and A. Tidu and G. Eriani and E. Westhof and F. Martin},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=35236777},
doi = {10.1261/rna.078972.121},
isbn = {35236777},
year = {2022},
date = {2022-01-01},
urldate = {2022-01-01},
journal = {Rna},
volume = {28},
issue = {5},
pages = {729-741},
abstract = {The 5'UTR part of coronavirus genomes plays key roles in the viral replication cycle and the translation of the viral mRNAs. The first 75-80 nucleotides, also called the leader sequence, are identical for the genomic mRNA and for the subgenomic mRNAs. Recently, it was shown that cooperative actions of a 5'UTR segment and the non-structural protein NSP1 are essential for both the inhibition of host mRNAs and for specific translation of viral mRNAs. Here, sequence analyses of both the 5'UTR RNA segment and the NSP1 protein have been done for several coronaviruses with special attention to the betacoronaviruses. The conclusions are (i) precise specific molecular signatures can be found in both the RNA and the NSP1 protein; (ii) both types of signatures strongly correlate between each other. Indeed, definite sequence motifs in the RNA correlate with sequence motifs in the protein indicating a co-evolution of 5'UTR with NSP1 in betacoronaviruses. Experimental mutational data on 5'UTR and NSP1 from SARS-CoV-2 using cell-free translation extracts support those conclusions and show that the N-terminal half of the NSP1 protein contains conserved key residues that are essential for evasion to the inhibitory effect of NSP1 on translation.},
note = {1469-9001 (Electronic)
1355-8382 (Linking)
Journal Article},
keywords = {ERIANI, MARTIN, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Brugier A., Hafirrassou M. L., Pourcelot M., Baldaccini M., Kril V., Couture L., Kummerer B. M., Gallois-Montbrun S., Bonnet-Madin L., Vidalain P. O., Delaugerre C., Pfeffer S., Meertens L., Amara A.
RACK1 Associates with RNA-Binding Proteins Vigilin and SERBP1 to Facilitate Dengue Virus Replication Article de journal
Dans: J Virol, p. e0196221, 2022, ISBN: 35266803, (1098-5514 (Electronic) 0022-538X (Linking) Journal Article).
Résumé | Liens | BibTeX | Étiquettes: PFEFFER, Unité ARN
@article{nokey,
title = {RACK1 Associates with RNA-Binding Proteins Vigilin and SERBP1 to Facilitate Dengue Virus Replication},
author = {A. Brugier and M. L. Hafirrassou and M. Pourcelot and M. Baldaccini and V. Kril and L. Couture and B. M. Kummerer and S. Gallois-Montbrun and L. Bonnet-Madin and P. O. Vidalain and C. Delaugerre and S. Pfeffer and L. Meertens and A. Amara},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=35266803},
doi = {10.1128/jvi.01962-21},
isbn = {35266803},
year = {2022},
date = {2022-01-01},
journal = {J Virol},
pages = {e0196221},
abstract = {Dengue virus (DENV) is a mosquito-borne flavivirus responsible for dengue disease, a major human health concern for which no effective treatment is available. DENV relies heavily on the host cellular machinery for productive infection. Here, we show that the scaffold protein RACK1, which is part of the DENV replication complex, mediates infection by binding to the 40S ribosomal subunit. Mass spectrometry analysis of RACK1 partners coupled to an RNA interference screen-identified Vigilin and SERBP1 as DENV host-dependency factors. Both are RNA-binding proteins that interact with the DENV genome. Genetic ablation of Vigilin or SERBP1 rendered cells poorly susceptible to DENV, as well as related flaviviruses, by hampering the translation and replication steps. Finally, we established that a Vigilin or SERBP1 mutant lacking RACK1 binding but still interacting with the viral RNA is unable to mediate DENV infection. We propose that RACK1 recruits Vigilin and SERBP1, linking the DENV genome to the translation machinery for efficient infection. IMPORTANCE We recently identified the scaffolding RACK1 protein as an important host-dependency factor for dengue virus (DENV), a positive-stranded RNA virus responsible for the most prevalent mosquito-borne viral disease worldwide. Here, we have performed the first RACK1 interactome in human cells and identified Vigilin and SERBP1 as DENV host-dependency factors. Both are RNA-binding proteins that interact with the DENV RNA to regulate viral replication. Importantly, Vigilin and SERBP1 interact with RACK1 and the DENV viral RNA (vRNA) to mediate viral replication. Overall, our results suggest that RACK1 acts as a binding platform at the surface of the 40S ribosomal subunit to recruit Vigilin and SERBP1, which may therefore function as linkers between the viral RNA and the translation machinery to facilitate infection.},
note = {1098-5514 (Electronic)
0022-538X (Linking)
Journal Article},
keywords = {PFEFFER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Westhof E., Thornlow B., Chan P. P., Lowe T. M.
Eukaryotic tRNA sequences present conserved and amino acid-specific structural signatures Article de journal
Dans: Nucleic Acids Res, vol. 50, iss. 5, p. 4100-4112, 2022, ISBN: 35380696, (1362-4962 (Electronic) 0305-1048 (Linking) Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Unité ARN, WESTHOF
@article{nokey,
title = {Eukaryotic tRNA sequences present conserved and amino acid-specific structural signatures},
author = {E. Westhof and B. Thornlow and P. P. Chan and T. M. Lowe},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=35380696},
doi = {10.1093/nar/gkac222},
isbn = {35380696},
year = {2022},
date = {2022-01-01},
urldate = {2022-01-01},
journal = {Nucleic Acids Res},
volume = {50},
issue = {5},
pages = {4100-4112},
abstract = {Metazoan organisms have many tRNA genes responsible for decoding amino acids. The set of all tRNA genes can be grouped in sets of common amino acids and isoacceptor tRNAs that are aminoacylated by corresponding aminoacyl-tRNA synthetases. Analysis of tRNA alignments shows that, despite the high number of tRNA genes, specific tRNA sequence motifs are highly conserved across multicellular eukaryotes. The conservation often extends throughout the isoacceptors and isodecoders with, in some cases, two sets of conserved isodecoders. This study is focused on non-Watson-Crick base pairs in the helical stems, especially GoU pairs. Each of the four helical stems may contain one or more conserved GoU pairs. Some are amino acid specific and could represent identity elements for the cognate aminoacyl tRNA synthetases. Other GoU pairs are found in more than a single amino acid and could be critical for native folding of the tRNAs. Interestingly, some GoU pairs are anticodon-specific, and others are found in phylogenetically-specific clades. Although the distribution of conservation likely reflects a balance between accommodating isotype-specific functions as well as those shared by all tRNAs essential for ribosomal translation, such conservations may indicate the existence of specialized tRNAs for specific translation targets, cellular conditions, or alternative functions.},
note = {1362-4962 (Electronic)
0305-1048 (Linking)
Journal Article},
keywords = {Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Eriani G., Martin F.
Viral and cellular translation during SARS-CoV-2 infection Article de journal
Dans: FEBS Open Bio, 2022, ISBN: 35429230, (2211-5463 (Electronic) 2211-5463 (Linking) Journal Article Review).
Résumé | Liens | BibTeX | Étiquettes: ERIANI, Unité ARN
@article{nokey,
title = {Viral and cellular translation during SARS-CoV-2 infection},
author = {G. Eriani and F. Martin},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=35429230},
doi = {10.1002/2211-5463.13413},
isbn = {35429230},
year = {2022},
date = {2022-01-01},
journal = {FEBS Open Bio},
abstract = {SARS-CoV-2 is a betacoronavirus that emerged in China in December 2019 and which is the causative agent of the Covid-19 pandemic. This enveloped virus contains a large positive-sense single-stranded RNA genome. In this review, we summarize the current knowledge on the molecular mechanisms for the translation of both viral transcripts and cellular messenger RNAs. Non-structural proteins are encoded by the genomic RNA and are produced in the early steps of infection. In contrast, the structural proteins are produced from subgenomic RNAs that are translated in the late phase of the infectious program. Non-structural protein 1 (NSP1) is a key molecule that regulates both viral and cellular translation. In addition, NSP1 interferes with multiple steps of the interferon I pathway and thereby blocks host antiviral responses. Therefore, NSP1 is a drug target of choice for the development of antiviral therapies.},
note = {2211-5463 (Electronic)
2211-5463 (Linking)
Journal Article
Review},
keywords = {ERIANI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Geraci I., Autour A., Pietruschka G., Shiian A., Borisova M., Mayer C., Ryckelynck M., Mayer G.
Fluorogenic RNA-Based Biosensor to Sense the Glycolytic Flux in Mammalian Cells Article de journal
Dans: ACS Chem Biol, 2022, ISBN: 35427113, (1554-8937 (Electronic) 1554-8929 (Linking) Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Labex, RYCKELYNCK, Unité ARN
@article{nokey,
title = {Fluorogenic RNA-Based Biosensor to Sense the Glycolytic Flux in Mammalian Cells},
author = {I. Geraci and A. Autour and G. Pietruschka and A. Shiian and M. Borisova and C. Mayer and M. Ryckelynck and G. Mayer},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=35427113},
doi = {10.1021/acschembio.2c00100},
isbn = {35427113},
year = {2022},
date = {2022-01-01},
urldate = {2022-01-01},
journal = {ACS Chem Biol},
abstract = {The visualization of metabolic flux in real time requires sensor molecules that transduce variations of metabolite concentrations into an appropriate output signal. In this regard, fluorogenic RNA-based biosensors are promising molecular tools as they fluoresce only upon binding to another molecule. However, to date no such sensor is available that enables the direct observation of key metabolites in mammalian cells. Toward this direction, we selected and characterized an RNA light-up sensor designed to respond to fructose 1,6-bisphosphate and applied it to probe glycolytic flux variation in mammal cells.},
note = {1554-8937 (Electronic)
1554-8929 (Linking)
Journal Article},
keywords = {Labex, RYCKELYNCK, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Fam K. T., Pelletier R., Bouhedda F., Ryckelynck M., Collot M., Klymchenko A. S.
Rational Design of Self-Quenched Rhodamine Dimers as Fluorogenic Aptamer Probes for Live-Cell RNA Imaging Article de journal
Dans: Anal Chem, p. in press, 2022, ISBN: 35486532, (1520-6882 (Electronic) 0003-2700 (Linking) Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Labex, RYCKELYNCK, Unité ARN
@article{nokey,
title = {Rational Design of Self-Quenched Rhodamine Dimers as Fluorogenic Aptamer Probes for Live-Cell RNA Imaging},
author = {K. T. Fam and R. Pelletier and F. Bouhedda and M. Ryckelynck and M. Collot and A. S. Klymchenko},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=35486532},
doi = {10.1021/acs.analchem.1c04556},
isbn = {35486532},
year = {2022},
date = {2022-01-01},
journal = {Anal Chem},
pages = {in press},
abstract = {With the growing interest in the understanding of the importance of RNAs in health and disease, detection of RNAs in living cells is of high importance. Fluorogenic dyes that light up specifically selected RNA aptamers constitute an attractive direction in the design of RNA imaging probes. In this work, based on our recently proposed concept of a fluorogenic dimer, we aim to develop a robust molecular tool for intracellular RNA imaging. We rationally designed a fluorogenic self-quenched dimer (orange Gemini, o-Gemini) based on rhodamine and evaluated its capacity to light up its cognate aptamer o-Coral in solution and live cells. We found that the removal of biotin from the dimer slightly improved the fluorogenic response without losing the affinity to the cognate aptamer (o-Coral). On the other hand, replacing sulforhodamine with a carboxyrhodamine produced drastic improvement of the affinity and the turn-on response to o-Coral and, thus, a better limit of detection. In live cells expressing o-Coral-tagged RNAs, the carboxyrhodamine analogue of o-Gemini without a biotin unit displayed a higher signal as well as faster internalization into the cells. We suppose that less hydrophilic carboxyrhodamine compared to sulforhodamine can more readily penetrate through the cell plasma membrane and, together with its higher affinity to o-Coral, provide the observed improvement in the imaging experiments. The promiscuity of the o-Coral RNA aptamer to the fluorogenic dimer allowed us to tune a fluorogen chemical structure and thus drastically improve the fluorescence response of the probe to o-Coral-tagged RNAs.},
note = {1520-6882 (Electronic)
0003-2700 (Linking)
Journal Article},
keywords = {Labex, RYCKELYNCK, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Geersens E., Vuilleumier S., Ryckelynck M.
Growth-Associated Droplet Shrinkage for Bacterial Quantification, Growth Monitoring, and Separation by Ultrahigh-Throughput Microfluidics Article de journal
Dans: ACS Omega, vol. 7, no. 14, p. 12039-12047, 2022, ISBN: 35449964, (2470-1343 (Electronic) 2470-1343 (Linking) Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Labex, RYCKELYNCK, Unité ARN
@article{nokey,
title = {Growth-Associated Droplet Shrinkage for Bacterial Quantification, Growth Monitoring, and Separation by Ultrahigh-Throughput Microfluidics},
author = {E. Geersens and S. Vuilleumier and M. Ryckelynck},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=35449964},
doi = {10.1021/acsomega.2c00248},
isbn = {35449964},
year = {2022},
date = {2022-01-01},
journal = {ACS Omega},
volume = {7},
number = {14},
pages = {12039-12047},
abstract = {Microbiology still relies on en masse cultivation for selection, isolation, and characterization of microorganisms of interest. This constrains the diversity of microbial types and metabolisms that can be investigated in the laboratory also because of intercellular competition during cultivation. Cell individualization by droplet-based microfluidics prior to experimental analysis provides an attractive alternative to access a larger fraction of the microbial biosphere, miniaturizing the required equipment and minimizing reagent use for increased and more efficient analytical throughput. Here, we show that cultivation of a model two-strain bacterial community in droplets significantly reduces representation bias in the grown culture compared to batch cultivation. Further, and based on the droplet shrinkage observed upon cell proliferation, we provide proof-of-concept for a simple strategy that allows absolute quantification of microbial cells in a sample as well as selective recovery of microorganisms of interest for subsequent experimental characterization.},
note = {2470-1343 (Electronic)
2470-1343 (Linking)
Journal Article},
keywords = {Labex, RYCKELYNCK, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Ponce J. R. Jaramillo, Kapps D., Paulus C., Chicher J., Frugier M.
Discovery of two distinct aminoacyl-tRNA synthetase complexes anchored to the Plasmodium surface tRNA import protein Article de journal
Dans: J Biol Chem, p. 101987, 2022, ISBN: 35487244, (1083-351X (Electronic) 0021-9258 (Linking) Journal Article).
Résumé | Liens | BibTeX | Étiquettes: FRUGIER, Labex, PPSE, Unité ARN
@article{nokey,
title = {Discovery of two distinct aminoacyl-tRNA synthetase complexes anchored to the Plasmodium surface tRNA import protein},
author = {J. R. Jaramillo Ponce and D. Kapps and C. Paulus and J. Chicher and M. Frugier},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=35487244},
doi = {0.1016/j.jbc.2022.101987},
isbn = {35487244},
year = {2022},
date = {2022-01-01},
urldate = {2022-01-01},
journal = {J Biol Chem},
pages = {101987},
abstract = {Aminoacyl-tRNA synthetases (aaRSs) attach amino acids to their cognate transfer RNAs. In eukaryotes, a subset of cytosolic aaRSs is organized into a multi-synthetase complex (MSC), along with specialized scaffolding proteins referred to as aaRS-interacting multifunctional proteins (AIMPs). In Plasmodium, the causative agent of malaria, the tRNA import protein (tRip), is a membrane protein that has been shown to participate in tRNA trafficking; here, we show that tRip also functions as an AIMP. We identified three aaRSs, namely the glutamyl- (ERS), glutaminyl- (QRS), and methionyl- (MRS) tRNA synthetases, which were specifically co-immunoprecipitated with tRip in P. berghei blood stage parasites. All four proteins contain an N-terminal GST-like domain that was demonstrated to be involved in MSC assembly. In contrast to previous studies, further dissection of GST-like interactions identified two exclusive heterotrimeric complexes: the Q-complex (tRip:ERS:QRS) and the M-complex (tRip:ERS:MRS). Gel filtration and light scattering suggest a 2:2:2 stoichiometry for both complexes but with distinct biophysical properties, and mutational analysis further revealed that the GST-like domains of QRS and MRS use different strategies to bind ERS. Taken together our results demonstrate that neither the singular homodimerization of tRip, nor its localization in the parasite plasma membrane prevents the formation of MSCs in Plasmodium. Besides, the extracellular localization of the tRNA-binding module of tRip is compensated by the presence of additional tRNA-binding modules fused to MRS and QRS, providing each MSC with two spatially distinct functions: aminoacylation of intraparasitic tRNAs and binding of extracellular tRNAs. This unique host-pathogen interaction is discussed.},
note = {1083-351X (Electronic)
0021-9258 (Linking)
Journal Article},
keywords = {FRUGIER, Labex, PPSE, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Vicens Q, Bochler A, Jobe A, Frank J, Hashem Y
Interaction Networks of Ribosomal Expansion Segments in Kinetoplastids Chapitre d'ouvrage
Dans: vol. 96, p. 433-450, Subcellular Biochemistry, 2021.
Résumé | Liens | BibTeX | Étiquettes: Eukaryotic translation, Expansion segment, Kinetoplastid parasite, Ribosomal RNA, Ribosome structure, Unité ARN
@inbook{Vicens2021,
title = {Interaction Networks of Ribosomal Expansion Segments in Kinetoplastids },
author = {Q Vicens and A Bochler and A Jobe and J Frank and Y Hashem },
url = {https://pubmed.ncbi.nlm.nih.gov/33252739/},
doi = {10.1007/978-3-030-58971-4_13 },
year = {2021},
date = {2021-01-01},
volume = {96},
pages = {433-450},
publisher = {Subcellular Biochemistry},
abstract = {Expansion segments (ES) are insertions of a few to hundreds of nucleotides at discrete locations on eukaryotic ribosomal RNA (rRNA) chains. Some cluster around ‘hot spots’ involved in translation regulation and some may participate in biogenesis. Whether ES play the same roles in different organisms is currently unclear, especially since their size may vary dramatically from one species to another and very little is known about their functions. Most likely, ES variation is linked to adaptation to a particular environment. In this chapter, we compare the interaction networks of ES from four kinetoplastid parasites, which have evolved in diverse insect vectors and mammalian hosts: Trypanosoma cruzi, Trypanosoma brucei, Leishmania donovani and Leishmania major. Here, we comparatively analyze ribosome structures from these representative kinetoplastids and ascertain meaningful structural differences from mammalian ribosomes. We base our analysis on sequence alignments and three-dimensional structures of 80S ribosomes solved by cryo-electron microscopy (cryo-EM). Striking differences in size are observed between ribosomes of different parasites, indicating that not all ES are expanded equally. Larger ES are not always matched by large surrounding ES or proteins extensions in their vicinity, a particularity that may lead to clues about their biological function. ES display different species-specific patterns of conservation, which underscore the density of their interaction network at the surface of the ribosome. Making sense of the conservation patterns of ES is part of a global effort to lay the basis for functional studies aimed at discovering unique kinetoplastid-specific sites suitable for therapeutic applications against these human and often animal pathogens.},
keywords = {Eukaryotic translation, Expansion segment, Kinetoplastid parasite, Ribosomal RNA, Ribosome structure, Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
Bec G, Ennifar E
switchSENSE Technology for Analysis of DNA Polymerase Kinetics Chapitre d'ouvrage
Dans: Rederstorff, M (Ed.): vol. 2247, p. 145-153, Springer Protocols, Humana Press, New York, NY, Small Non-Coding RNAs, 2021.
Résumé | BibTeX | Étiquettes: Biosensor, DNA polymerase, ENNIFAR, HIV reverse transcriptase, Kinetics, switchSENSE technology, Unité ARN
@inbook{Bec2021,
title = {switchSENSE Technology for Analysis of DNA Polymerase Kinetics },
author = {G Bec and E Ennifar
},
editor = {M Rederstorff},
year = {2021},
date = {2021-01-01},
journal = {Methods in Molecular Biology },
volume = {2247},
pages = {145-153},
publisher = {Springer Protocols, Humana Press},
address = {New York, NY},
edition = {Small Non-Coding RNAs},
series = {Methods in Molecular Biology},
abstract = {The switchSENSE technology is a recent approach based on surface sensor chips for the analysis of interactions of macromolecules. The technology relies on electro-switchable DNA nanolevers tethered at one end on a gold surface via a sulfur linker and labeled with a Cy3 dye on the other end. The switchSENSE approach is effective in the determination of a large panel of biophysical parameters such as binding kinetics, dissociation constant, hydrodynamic radius, or melting temperature. In addition, it can also give access to some enzymatic data such as nuclease or polymerase activity. Here we describe a DNA polymerase assay that allows retrieving, in a single experimental set, association and dissociation rates, as well as the catalytic rate of the enzyme. },
keywords = {Biosensor, DNA polymerase, ENNIFAR, HIV reverse transcriptase, Kinetics, switchSENSE technology, Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
Lalaouna D, Fochesato S, Harir M, Ortet P, Schmitt-Kopplin P, Heulin T, Achouak W
Amplifying and Fine-Tuning Rsm sRNAs Expression and Stability to Optimize the Survival of Pseudomonas brassicacerum in Nutrient-Poor Environments Article de journal
Dans: Microorganisms, vol. 9, no. 2, p. 250, 2021.
Résumé | Liens | BibTeX | Étiquettes: GacA-dependent, nutritional stress, Pseudomonas brassicacearum, ROMBY, Rsm sRNAs, sRNAs stability, Unité ARN
@article{,
title = {Amplifying and Fine-Tuning Rsm sRNAs Expression and Stability to Optimize the Survival of Pseudomonas brassicacerum in Nutrient-Poor Environments},
author = {D Lalaouna and S Fochesato and M Harir and P Ortet and P Schmitt-Kopplin and T Heulin and W Achouak},
url = {https://www.mdpi.com/2076-2607/9/2/250},
doi = {10.3390/microorganisms9020250},
year = {2021},
date = {2021-01-01},
journal = {Microorganisms},
volume = {9},
number = {2},
pages = {250},
abstract = {In the beneficial plant root-associated Pseudomonas brassicacearum strain NFM421, the GacS/GacA two-component system positively controls biofilm formation and the production of secondary metabolites through the synthesis of rsmX, rsmY and rsmZ. Here, we evidenced the genetic amplification of Rsm sRNAs by the discovery of a novel 110-nt long sRNA encoding gene, rsmX-2, generated by the duplication of rsmX-1 (formerly rsmX). Like the others rsm genes, its overexpression overrides the gacA mutation. We explored the expression and the stability of rsmX-1, rsmX-2, rsmY and rsmZ encoding genes under rich or nutrient-poor conditions, and showed that their amount is fine-tuned at the transcriptional and more interestingly at the post-transcriptional level. Unlike rsmY and rsmZ, we noticed that the expression of rsmX-1 and rsmX-2 genes was exclusively GacA-dependent. The highest expression level and longest half-life for each sRNA were correlated with the highest ppGpp and cyclic-di-GMP levels and were recorded under nutrient-poor conditions. Together, these data support the view that the Rsm system in P. brassicacearum is likely linked to the stringent response, and seems to be required for bacterial adaptation to nutritional stress.},
keywords = {GacA-dependent, nutritional stress, Pseudomonas brassicacearum, ROMBY, Rsm sRNAs, sRNAs stability, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Li G, Eriani G, Wang E D, Zhou X L
Distinct pathogenic mechanisms of various RARS1 mutations in Pelizaeus-Merzbacher-like disease Article de journal
Dans: Sci China Life Sci, vol. 64, no. 10, p. 1645-1660, 2021, ISBN: 33515434, (1869-1889 (Electronic) 1674-7305 (Linking) Journal Article).
Résumé | Liens | BibTeX | Étiquettes: aminoacyl-tRNA synthetase (aaRS), central nervous system (CNS), ERIANI, Protein Biosynthesis, translation initiation, tRNA, Unité ARN
@article{,
title = {Distinct pathogenic mechanisms of various RARS1 mutations in Pelizaeus-Merzbacher-like disease},
author = {G Li and G Eriani and E D Wang and X L Zhou},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=33515434},
doi = {10.1007/s11427-020-1838-2},
isbn = {33515434},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Sci China Life Sci},
volume = {64},
number = {10},
pages = {1645-1660},
abstract = {Mutations of the genes encoding aminoacyl-tRNA synthetases are highly associated with various central nervous system disorders. Recurrent mutations, including c.5A>G, p.D2G; c.1367C>T, p.S456L; c.1535G>A, p.R512Q and c.1846_1847del, p. Y616Lfs*6 of RARS1 gene, which encodes two forms of human cytoplasmic arginyl-tRNA synthetase (hArgRS), are linked to Pelizaeus-Merzbacher-like disease (PMLD) with unclear pathogenesis. Among these mutations, c.5A>G is the most extensively reported mutation, leading to a p.D2G mutation in the N-terminal extension of the long-form hArgRS. Here, we showed the detrimental effects of R512Q substitution and DeltaC mutations on the structure and function of hArgRS, while the most frequent mutation c.5A>G, p.D2G acted in a different manner without impairing hArgRS activity. The nucleotide substitution c.5A>G reduced translation of hArgRS mRNA, and an upstream open reading frame contributed to the suppressed translation of the downstream main ORF. Taken together, our results elucidated distinct pathogenic mechanisms of various RARS1 mutations in PMLD.},
note = {1869-1889 (Electronic)
1674-7305 (Linking)
Journal Article},
keywords = {aminoacyl-tRNA synthetase (aaRS), central nervous system (CNS), ERIANI, Protein Biosynthesis, translation initiation, tRNA, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Mercier N, Prévost K, Massé E, Romby P, Caldelari I, Lalaouna D
MS2-Affinity Purification Coupled with RNA Sequencing in Gram-Positive Bacteria Article de journal
Dans: J Vis Exp, p. e61731, 2021.
Résumé | Liens | BibTeX | Étiquettes: ROMBY, Unité ARN
@article{Mercier2021,
title = {MS2-Affinity Purification Coupled with RNA Sequencing in Gram-Positive Bacteria},
author = {N Mercier and K Prévost and E Massé and P Romby and I Caldelari and D Lalaouna},
url = {https://www.jove.com/t/61731/ms2-affinity-purification-coupled-with-rna-sequencing-gram-positive},
doi = {10.3791/61731},
year = {2021},
date = {2021-01-01},
journal = {J Vis Exp},
pages = {e61731},
abstract = {Although small regulatory RNAs (sRNAs) are widespread among the bacterial domain of life, the functions of many of them remain poorly characterized notably due to the difficulty of identifying their mRNA targets. Here, we described a modified protocol of the MS2-Affinity Purification coupled with RNA Sequencing (MAPS) technology, aiming to reveal all RNA partners of a specific sRNA in vivo. Broadly, the MS2 aptamer is fused to the 5’ extremity of the sRNA of interest. This construct is then expressed in vivo, allowing the MS2-sRNA to interact with its cellular partners. After bacterial harvesting, cells are mechanically lysed. The crude extract is loaded into an amylose-based chromatography column previously coated with the MS2 protein fused to the maltose binding protein. This enables the specific capture of MS2-sRNA and interacting RNAs. After elution, co-purified RNAs are identified by high-throughput RNA sequencing and subsequent bioinformatic analysis. The following protocol has been implemented in the Gram-positive human pathogen Staphylococcus aureus and is, in principle, transposable to any Gram-positive bacteria. To sum up, MAPS technology constitutes an efficient method to deeply explore the regulatory network of a particular sRNA, offering a snapshot of its whole targetome. However, it is important to keep in mind that putative targets identified by MAPS still need to be validated by complementary experimental approaches.},
keywords = {ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Catalan-Moreno A, Cela M, Menendez-Gil P, Irurzun N, Caballero C J, Caldelari I, Toledo-Arana A
RNA thermoswitches modulate Staphylococcus aureus adaptation to ambient temperatures Article de journal
Dans: Nucleic Acids Res, p. on press, 2021, ISBN: 33660769, (1362-4962 (Electronic) 0305-1048 (Linking) Journal Article).
Résumé | Liens | BibTeX | Étiquettes: ROMBY, Unité ARN
@article{Catalan-Moreno2021,
title = {RNA thermoswitches modulate Staphylococcus aureus adaptation to ambient temperatures},
author = {A Catalan-Moreno and M Cela and P Menendez-Gil and N Irurzun and C J Caballero and I Caldelari and A Toledo-Arana},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=33660769},
doi = {0.1093/nar/gkab117},
isbn = {33660769},
year = {2021},
date = {2021-01-01},
journal = {Nucleic Acids Res},
pages = {on press},
abstract = {Thermoregulation of virulence genes in bacterial pathogens is essential for environment-to-host transition. However, the mechanisms governing cold adaptation when outside the host remain poorly understood. Here, we found that the production of cold shock proteins CspB and CspC from Staphylococcus aureus is controlled by two paralogous RNA thermoswitches. Through in silico prediction, enzymatic probing and site-directed mutagenesis, we demonstrated that cspB and cspC 5'UTRs adopt alternative RNA structures that shift from one another upon temperature shifts. The open (O) conformation that facilitates mRNA translation is favoured at ambient temperatures (22 degrees C). Conversely, the alternative locked (L) conformation, where the ribosome binding site (RBS) is sequestered in a double-stranded RNA structure, is folded at host-related temperatures (37 degrees C). These structural rearrangements depend on a long RNA hairpin found in the O conformation that sequesters the anti-RBS sequence. Notably, the remaining S. aureus CSP, CspA, may interact with a UUUGUUU motif located in the loop of this long hairpin and favour the folding of the L conformation. This folding represses CspB and CspC production at 37 degrees C. Simultaneous deletion of the cspB/cspC genes or their RNA thermoswitches significantly decreases S. aureus growth rate at ambient temperatures, highlighting the importance of CspB/CspC thermoregulation when S. aureus transitions from the host to the environment.},
note = {1362-4962 (Electronic)
0305-1048 (Linking)
Journal Article},
keywords = {ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Pitchai F, Chameettachal A, Vivet-Boudou V, Ali L M, Pillai V N, Krishnan A, Bernacchi S, Mustafa F, R Marquet, Rizvi T A
Identification of Pr78Gag binding sites on the Mason-Pfizer monkey virus genomic RNA packaging determinants Article de journal
Dans: J Mol Biol, vol. 433, no. 10, p. 166923, 2021.
Résumé | Liens | BibTeX | Étiquettes: MARQUET, Retroviruses Gag-RNA interactions Purines Footprinting hSHAPE, Unité ARN
@article{F2021,
title = {Identification of Pr78Gag binding sites on the Mason-Pfizer monkey virus genomic RNA packaging determinants},
author = {F Pitchai and A Chameettachal and V Vivet-Boudou and L M Ali and V N Pillai and A Krishnan and S Bernacchi and F Mustafa and Marquet R and T A Rizvi},
url = {https://www.sciencedirect.com/science/article/pii/S0022283621001224?via%3Dihub},
doi = {10.1016/j.jmb.2021.166923},
year = {2021},
date = {2021-01-01},
journal = {J Mol Biol},
volume = {433},
number = {10},
pages = {166923},
abstract = {How retroviral Gag proteins recognize the packaging signals (Psi) on their genomic RNA (gRNA) is a key question that we addressed here using Mason-Pfizer monkey virus (MPMV) as a model system by combining band-shift assays and footprinting experiments. Our data show that Pr78Gag selects gRNA against spliced viral RNA by simultaneously binding to two single stranded loops on the MPMV Psi RNA: (1) a large purine loop (ssPurines), and (2) a loop which partially overlaps with a mostly base-paired purine repeat (bpPurines) and extends into a GU-rich binding motif. Importantly, this second Gag binding site is located immediately downstream of the major splice donor (mSD) and is thus absent from the spliced viral RNAs. Identifying elements crucial for MPMV gRNA packaging should help in understanding not only the mechanism of virion assembly by retroviruses, but also facilitate construction of safer retroviral vectors for human gene therapy.},
keywords = {MARQUET, Retroviruses Gag-RNA interactions Purines Footprinting hSHAPE, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Busienne C, Marquet R, Paillart J C, Bernacchi S
Post-Translational Modifications of Retroviral HIV-1 Gag Precursors: An Overview of Their Biological Role Article de journal
Dans: Int. J. Mol. Sci., vol. 22, no. 6, p. 2871, 2021.
Résumé | Liens | BibTeX | Étiquettes: HIV-1, MARQUET, PAILLART, post-translational modifications, Pr55Gag precursor, retroviral Gag precursors, retroviral life cycle, Unité ARN
@article{C2021b,
title = {Post-Translational Modifications of Retroviral HIV-1 Gag Precursors: An Overview of Their Biological Role},
author = {C Busienne and R Marquet and J C Paillart and S Bernacchi},
url = {https://www.mdpi.com/1422-0067/22/6/2871},
doi = {10.3390/ijms22062871},
year = {2021},
date = {2021-01-01},
journal = {Int. J. Mol. Sci.},
volume = {22},
number = {6},
pages = {2871},
abstract = {Protein post-translational modifications (PTMs) play key roles in eukaryotes since they finely regulate numerous mechanisms used to diversify the protein functions and to modulate their signaling networks. Besides, these chemical modifications also take part in the viral hijacking of the host, and also contribute to the cellular response to viral infections. All domains of the human immunodeficiency virus type 1 (HIV-1) Gag precursor of 55-kDa (Pr55Gag), which is the central actor for viral RNA specific recruitment and genome packaging, are post-translationally modified. In this review, we summarize the current knowledge about HIV-1 Pr55Gag PTMs such as myristoylation, phosphorylation, ubiquitination, sumoylation, methylation, and ISGylation in order to figure out how these modifications affect the precursor functions and viral replication. Indeed, in HIV-1, PTMs regulate the precursor trafficking between cell compartments and its anchoring at the plasma membrane, where viral assembly occurs. Interestingly, PTMs also allow Pr55Gag to hijack the cell machinery to achieve viral budding as they drive recognition between viral proteins or cellular components such as the ESCRT machinery. Finally, we will describe and compare PTMs of several other retroviral Gag proteins to give a global overview of their role in the retroviral life cycle.},
keywords = {HIV-1, MARQUET, PAILLART, post-translational modifications, Pr55Gag precursor, retroviral Gag precursors, retroviral life cycle, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Chameettachal A, Vivet-Boudou V, Pitchai F N, N Pillai V, Ali L M, Krishnan A, Bernacchi S, Mustafa F, Marquet R, Rizvi T A
A purine loop and the primer binding site are critical for the selective encapsidation of mouse mammary tumor virus genomic RNA by Pr77Gag Article de journal
Dans: Nucleic Acids Res, vol. 49, no. 8, p. 4668-4688, 2021.
BibTeX | Étiquettes: MARQUET, PAILLART, Unité ARN
@article{Chameettachal2021,
title = {A purine loop and the primer binding site are critical for the selective encapsidation of mouse mammary tumor virus genomic RNA by Pr77Gag},
author = {A Chameettachal and V Vivet-Boudou and F N Pitchai and Pillai V N and L M Ali and A Krishnan and S Bernacchi and F Mustafa and R Marquet and T A Rizvi},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Nucleic Acids Res},
volume = {49},
number = {8},
pages = {4668-4688},
keywords = {MARQUET, PAILLART, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Westhof E, Leontis N B
An RNA-centric historical narrative around the Protein Data Bank Article de journal
Dans: J Biol Chem, vol. 296, p. 100555, 2021, ISBN: 33744291, (1083-351X (Electronic) 0021-9258 (Linking) Journal Article Review).
Résumé | Liens | BibTeX | Étiquettes: Computational Biology, Databases, modelling, Protein Data Bank, RNA, Structural biology, Unité ARN, WESTHOF
@article{Westhof2021,
title = {An RNA-centric historical narrative around the Protein Data Bank},
author = {E Westhof and N B Leontis},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=33744291},
doi = {10.1016/j.jbc.2021.100555},
isbn = {33744291},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {J Biol Chem},
volume = {296},
pages = {100555},
abstract = {Some of the amazing contributions brought to the scientific community by the PDB are described. The focus is on nucleic acid structures with a bias towards RNA. The evolution and key roles in science of the PDB and other structural databases for nucleic acids illustrate how small initial ideas can become huge and indispensable resources with the unflinching willingness of scientists to cooperate globally. The progress in the understanding of the molecular interactions driving RNA architectures followed the rapid increase in RNA structures in the PDB. That increase was consecutive to improvements in chemical synthesis and purification of RNA molecules, as well as in biophysical methods for structure determination and computer technology. The RNA modeling efforts from the early beginnings are also described together with their links to the state of structural knowledge and technological development. Structures of RNA and of its assemblies are physical objects which, together with genomic data, allow us to integrate present-day biological functions and the historical evolution in all living species on earth.},
note = {1083-351X (Electronic)
0021-9258 (Linking)
Journal Article
Review},
keywords = {Computational Biology, Databases, modelling, Protein Data Bank, RNA, Structural biology, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Husser C, Dentz N, Ryckelynck M
Structure-Switching RNAs: From Gene Expression Regulation to Small Molecule Detection Article de journal
Dans: Small Structures, vol. 2, no. 4, p. 2000132, 2021.
Résumé | Liens | BibTeX | Étiquettes: biosensing, Gene Expression Regulation, riboswitches, RNA aptamers, RYCKELYNCK, Synthetic Biology, Unité ARN
@article{C2021c,
title = {Structure-Switching RNAs: From Gene Expression Regulation to Small Molecule Detection},
author = {C Husser and N Dentz and M Ryckelynck},
url = {https://doi.org/10.1002/sstr.202000132},
doi = {10.1002/sstr.202000132},
year = {2021},
date = {2021-01-01},
journal = {Small Structures},
volume = {2},
number = {4},
pages = {2000132},
abstract = {RNA is instrumental to cell life in many aspects, especially gene expression regulation. Among the various known regulatory RNAs, riboswitches are particularly interesting cis‐acting molecules as they do not need cellular factor to achieve their function and are therefore highly portable from one organism to the other. These molecules usually found in the 5′ untranslated region of bacterial messenger RNAs are able to specifically sense a target ligand via an aptamer domain prior to transmitting this recognition event to an expression platform that turns on, or off, the expression of downstream genes. In addition to their obvious scientific interest, these modular molecules can also serve for the development of synthetic RNA devices with applications ranging from the control of transgene expression in gene therapy to the specific biosensing of small molecules. The engineering of such nanomachines is greatly facilitated by the proper understanding of their structure as well as the introduction of new technologies. Herein, a general overview of the current knowledge on natural riboswitches prior to explaining the main strategies used to develop new synthetic structure‐switching molecules (riboswitches or biosensors) controlled by small molecules is given.},
keywords = {biosensing, Gene Expression Regulation, riboswitches, RNA aptamers, RYCKELYNCK, Synthetic Biology, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Stupfler B, Verriez C, Gallois-Montbrun S, Marquet R, Paillart J C
Degradation-independent inhibition of APOBEC3G by HIV-1 Vif protein Article de journal
Dans: Viruses, vol. 13, no. 4, p. 617, 2021.
Résumé | Liens | BibTeX | Étiquettes: APOBEC3G, deamination, encapsidation, HIV, MARQUET, PAILLART, proteasome, RNP granules, Translation, ubiquitin, Unité ARN, vif
@article{Stupfler2021,
title = {Degradation-independent inhibition of APOBEC3G by HIV-1 Vif protein},
author = {B Stupfler and C Verriez and S Gallois-Montbrun and R Marquet and J C Paillart},
url = {https://www.mdpi.com/1999-4915/13/4/617},
doi = {10.3390/v13040617},
year = {2021},
date = {2021-01-01},
journal = {Viruses},
volume = {13},
number = {4},
pages = {617},
abstract = {The ubiquitinproteasome system plays an important role in the cell under normal physiological conditions but also during viral infections. Indeed, many auxiliary proteins from the (HIV-1) divert this system to its own advantage, notably to induce the degradation of cellular restriction factors. For instance, the HIV-1 viral infectivity factor (Vif) has been shown to specifically counteract several cellular deaminases belonging to the apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC3 or A3) family (A3A to A3H) by recruiting an E3-ubiquitin ligase complex and inducing their polyubiquitination and degradation through the proteasome. Although this pathway has been extensively characterized so far, Vif has also been shown to impede A3s through degradation-independent processes, but research on this matter remains limited. In this review, we describe our current knowledge regarding the degradation-independent inhibition of A3s, and A3G in particular, by the HIV-1 Vif protein, the molecular mechanisms involved, and highlight important properties of this small viral protein.},
keywords = {APOBEC3G, deamination, encapsidation, HIV, MARQUET, PAILLART, proteasome, RNP granules, Translation, ubiquitin, Unité ARN, vif},
pubstate = {published},
tppubtype = {article}
}
Chagot M E, Quinternet M, Manival X, Lebars I
Application of NMR Spectroscopy to Determine the 3D Structure of Small Non-Coding RNAs Article de journal
Dans: Methods Mol Biol, vol. 2300, p. 251-266, 2021, ISBN: 33792884, (1940-6029 (Electronic) 1064-3745 (Linking) Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 3D structure, dynamics, ENNIFAR, NMR, RNA, Unité ARN
@article{Chagot2021,
title = {Application of NMR Spectroscopy to Determine the 3D Structure of Small Non-Coding RNAs},
author = {M E Chagot and M Quinternet and X Manival and I Lebars},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=33792884},
doi = {10.1007/978-1-0716-1386-3_19},
isbn = {33792884},
year = {2021},
date = {2021-01-01},
journal = {Methods Mol Biol},
volume = {2300},
pages = {251-266},
abstract = {Many RNA architectures were discovered to be involved in a wide range of essential biological processes in all organisms from carrying genetic information to gene expression regulation. The remarkable ability of RNAs to adopt various architectures depending on their environment enables the achievement of their myriads of biological functions. Nuclear Magnetic Resonance (NMR) is a powerful technique to investigate both their structure and dynamics. NMR is also a key tool for studying interactions between RNAs and their numerous partners such as small molecules, ions, proteins, or other nucleic acids.In this chapter, to illustrate the use of NMR for 3D structure determination of small noncoding RNA, we describe detailed methods that we used for the yeast C/D box small nucleolar RNA U14 from sample preparation to 3D structure calculation.},
note = {1940-6029 (Electronic)
1064-3745 (Linking)
Journal Article},
keywords = {3D structure, dynamics, ENNIFAR, NMR, RNA, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Andre A C, Debande L, Marteyn B S
The selective advantage of facultative anaerobes relies on their unique ability to cope with changing oxygen levels during infection Article de journal
Dans: Cell Microbiol, vol. 23, no. 8, p. e13338, 2021, ISBN: 33813807, (1462-5822 (Electronic) 1462-5814 (Linking) Journal Article Review).
Résumé | Liens | BibTeX | Étiquettes: MARTEYN, Unité ARN
@article{Andre2021,
title = {The selective advantage of facultative anaerobes relies on their unique ability to cope with changing oxygen levels during infection},
author = {A C Andre and L Debande and B S Marteyn},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=33813807},
doi = {10.1111/cmi.13338},
isbn = {33813807},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Cell Microbiol},
volume = {23},
number = {8},
pages = {e13338},
abstract = {Bacteria, including those that are pathogenic, have been generally classified according to their ability to survive and grow in the presence or absence of oxygen: aerobic and anaerobic bacteria, respectively. Strict aerobes require oxygen to grow (e.g. Neisseria), and strict anaerobes grow exclusively without, and do not survive oxygen exposure (e.g. Clostridia); aerotolerant bacteria (e.g. Lactobacilli) are insensitive to oxygen exposure. Facultative anaerobes (e.g. E. coli) have the unique ability to grow in the presence or in the absence of oxygen. and are thus well-adapted to these changing conditions which may constitute an underestimated selective advantage for infection. In the WHO antibiotic-resistant "priority pathogens" list, facultative anaerobes are overrepresented (8 among 12 listed pathogens), consistent with clinical studies performed in populations particularly susceptible to infectious diseases. Bacteria aerobic respiratory chain plays a central role in oxygen consumption, leading to the formation of hypoxic infectious sites (infectious hypoxia). Facultative anaerobes have developed a wide diversity of aerotolerance and anaerotolerance strategies in vivo. However, at a single cell level, the modulation of the intracellular oxygen level in host infected cells remains elusive and will be discussed in this review. In conclusion, the ability of facultative bacteria to evolve in the presence or the absence of oxygen is essential for their virulence strategy and constitute a selective advantage. This article is protected by copyright. All rights reserved.},
note = {1462-5822 (Electronic)
1462-5814 (Linking)
Journal Article
Review},
keywords = {MARTEYN, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
de Wijn R, Rollet K, Olieric V, Hennig O, Thome N, Nous C, Paulus C, Lorber B, Betat H, Morl M, Sauter C
Crystallization and Structural Determination of an Enzyme:Substrate Complex by Serial Crystallography in a Versatile Microfluidic Chip Article de journal
Dans: J Vis Exp, no. 169, 2021, ISBN: 33818565, (1940-087X (Electronic) 1940-087X (Linking) Journal Article Video-Audio Media).
Résumé | Liens | BibTeX | Étiquettes: FRUGIER, Unité ARN
@article{deWijn2021,
title = {Crystallization and Structural Determination of an Enzyme:Substrate Complex by Serial Crystallography in a Versatile Microfluidic Chip},
author = {R de Wijn and K Rollet and V Olieric and O Hennig and N Thome and C Nous and C Paulus and B Lorber and H Betat and M Morl and C Sauter},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=33818565},
doi = {10.3791/61972},
isbn = {33818565},
year = {2021},
date = {2021-01-01},
journal = {J Vis Exp},
number = {169},
abstract = {The preparation of well diffracting crystals and their handling before their X-ray analysis are two critical steps of biocrystallographic studies. We describe a versatile microfluidic chip that enables the production of crystals by the efficient method of counter-diffusion. The convection-free environment provided by the microfluidic channels is ideal for crystal growth and useful to diffuse a substrate into the active site of the crystalline enzyme. Here we applied this approach to the CCA-adding enzyme of the psychrophilic bacterium Planococcus halocryophilus in the presented example. After crystallization and substrate diffusion/soaking, the crystal structure of the enzyme:substrate complex was determined at room temperature by serial crystallography and the analysis of multiple crystals directly inside the chip. The whole procedure preserves the genuine diffraction properties of the samples because it requires no crystal handling.},
note = {1940-087X (Electronic)
1940-087X (Linking)
Journal Article
Video-Audio Media},
keywords = {FRUGIER, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Injarabian L, Skerniskyte J, Gianetto Q G, Witko-Sarsat V, Marteyn B S
Reducing neutrophil exposure to oxygen allows their basal state maintenance Article de journal
Dans: Immunol Cell Biol, vol. 99, no. 7, p. 782-789, 2021, ISBN: 33811670, (1440-1711 (Electronic) 0818-9641 (Linking) Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Activation, anoxia, hyperoxia, MARTEYN, neutrophils, Unité ARN, viability
@article{Injarabian2021,
title = {Reducing neutrophil exposure to oxygen allows their basal state maintenance},
author = {L Injarabian and J Skerniskyte and Q G Gianetto and V Witko-Sarsat and B S Marteyn},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=33811670},
doi = {10.1111/imcb.12458},
isbn = {33811670},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Immunol Cell Biol},
volume = {99},
number = {7},
pages = {782-789},
abstract = {Neutrophils are the most abundant circulating white blood cells and are the central players of the innate immune response. During their lifecycle, neutrophils mainly evolve under low oxygen conditions (0.1-4% O2), to which they are well adapted. Neutrophils are atypical cells since they are highly glycolytic, and susceptible to oxygen exposure, which induces their activation and death, through mechanisms, which remain currently elusive. Nevertheless, nearly all studies conducted on neutrophils are carried out under atmospheric oxygen (21%), corresponding to hyperoxia. Here, we investigated the impact of hyperoxia during neutrophil purification and culture on neutrophil viability, activation and cytosolic protein content. We demonstrate that neutrophil hyper-activation (CD62L shedding) is induced during culture under hyperoxic conditions (24 h), compared to neutrophils cultured under anoxic conditions. Spontaneous neutrophil extracellular trap (NET) formation is observed when neutrophils face hyperoxia during purification or culture. In addition, we show that maintaining neutrophils in autologous plasma is the preferred strategy to maintain their basal state. Our results show that manipulating neutrophils under hyperoxic conditions leads to the loss of 57 cytosolic proteins during purification, while it does not lead to an immediate impact on neutrophil activation (CD11b(high), CD54(high), CD62L(neg)) or viability (DAPI(+)). We identified two clusters of proteins belonging to the cholesterol metabolism and to the complement and coagulation cascade pathways, which are highly susceptible to neutrophil oxygen exposure during neutrophil purification. In conclusion, protecting neutrophil from oxygen during their purification and culture is recommended to avoid activation and prevent the alteration cytosolic protein composition.},
note = {1440-1711 (Electronic)
0818-9641 (Linking)
Journal Article},
keywords = {Activation, anoxia, hyperoxia, MARTEYN, neutrophils, Unité ARN, viability},
pubstate = {published},
tppubtype = {article}
}
Velours C, Aumont-Nicaise M, Uebel S, England P, Velazquez-Campoy A, Stroebel D, Bec G, Soule P, Quetard C, Ebel C, Roussel A, Charbonnier J B, Varela P F
Macromolecular interactions in vitro, comparing classical and novel approaches Article de journal
Dans: Eur Biophys J, vol. 50, no. 3-4, p. 313-330, 2021, ISBN: 33792745, (1432-1017 (Electronic) 0175-7571 (Linking) Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Artificial binders, Double-stranded DNA breaks repair factors, ENNIFAR, Macromolecular interactions, Molecular scale biophysics, Unité ARN
@article{,
title = {Macromolecular interactions in vitro, comparing classical and novel approaches},
author = {C Velours and M Aumont-Nicaise and S Uebel and P England and A Velazquez-Campoy and D Stroebel and G Bec and P Soule and C Quetard and C Ebel and A Roussel and J B Charbonnier and P F Varela},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=33792745},
doi = {10.1007/s00249-021-01517-5},
isbn = {33792745},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Eur Biophys J},
volume = {50},
number = {3-4},
pages = {313-330},
abstract = {Biophysical quantification of protein interactions is central to unveil the molecular mechanisms of cellular processes. Researchers can choose from a wide panel of biophysical methods that quantify molecular interactions in different ways, including both classical and more novel techniques. We report the outcome of an ARBRE-MOBIEU training school held in June 2019 in Gif-sur-Yvette, France (https://mosbio.sciencesconf.org/). Twenty European students benefited from a week's training with theoretical and practical sessions in six complementary approaches: (1) analytical ultracentrifugation with or without a fluorescence detector system (AUC-FDS), (2) isothermal titration calorimetry (ITC), (3) size exclusion chromatography coupled to multi-angle light scattering (SEC-MALS), (4) bio-layer interferometry (BLI), (5) microscale thermophoresis (MST) and, (6) switchSENSE. They implemented all these methods on two examples of macromolecular interactions with nanomolar affinity: first, a protein-protein interaction between an artificial alphaRep binder, and its target protein, also an alphaRep; second, a protein-DNA interaction between a DNA repair complex, Ku70/Ku80 (hereafter called Ku), and its cognate DNA ligand. We report the approaches used to analyze the two systems under study and thereby showcase application of each of the six techniques. The workshop provided students with improved understanding of the advantages and limitations of different methods, enabling future choices concerning approaches that are most relevant or informative for specific kinds of sample and interaction.},
note = {1432-1017 (Electronic)
0175-7571 (Linking)
Journal Article},
keywords = {Artificial binders, Double-stranded DNA breaks repair factors, ENNIFAR, Macromolecular interactions, Molecular scale biophysics, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Alghoul F, Eriani G, Martin F
RNA Secondary Structure Study by Chemical Probing Methods Using DMS and CMCT Chapitre d'ouvrage
Dans: Rederstorff, M (Ed.): Methods Mol Biol, vol. 2300, p. 241-250, Springer Protocols, Humana Press, New York, NY, 2021, ISBN: 978-1-0716-1385-6/ISSN, (1940-6029 (Electronic) 1064-3745 (Linking) Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Capillary electrophoresis, chemical probing, CMCT, DMS, ERIANI, Primer extension, QuSHAPE, RNA secondary structure, Unité ARN
@inbook{Alghoul2021,
title = {RNA Secondary Structure Study by Chemical Probing Methods Using DMS and CMCT},
author = {F Alghoul and G Eriani and F Martin},
editor = {M Rederstorff},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=33792883},
doi = {10.1007/978-1-0716-1386-3_18},
isbn = {978-1-0716-1385-6/ISSN},
year = {2021},
date = {2021-01-01},
booktitle = {Methods Mol Biol},
volume = {2300},
pages = {241-250},
publisher = {Springer Protocols, Humana Press},
address = {New York, NY},
series = {Methods in Molecular Biology},
abstract = {RNA folds into secondary structures that can serve in understanding various RNA functions (Weeks KM. Curr Opin Struct Biol 20(3):295-304, 2010). Chemical probing is a method that enables the characterization of RNA secondary structures using chemical reagents that specifically modify RNA nucleotides that are located in single-stranded areas. In our protocol, we used Dimethyl Sulfate (DMS) and Cyclohexyl-3-(2-Morpholinoethyl) Carbodiimide metho-p-Toluene sulfonate (CMCT) that are both base-specific modifying reagents (Behm-Ansmant I, et al. J Nucleic Acids 2011:408053, 2011). These modifications are mapped by primer extension arrests using 5' fluorescently labeled primers. In this protocol, we show a comprehensive method to identify RNA secondary structures in vitro using fluorescently labeled oligos. To demonstrate the efficiency of the method, we give an example of a structure we have designed which corresponds to a part of the 5'-UTR regulatory element called Translation Inhibitory Element (TIE) from Hox a3 mRNA (Xue S, et al. Nature 517(7532):33-38, 2015).},
note = {1940-6029 (Electronic)
1064-3745 (Linking)
Journal Article},
keywords = {Capillary electrophoresis, chemical probing, CMCT, DMS, ERIANI, Primer extension, QuSHAPE, RNA secondary structure, Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
Bouhedda F, Cubi R, Baudrey S, Ryckelynck M
microIVC-Seq: A Method for Ultrahigh-Throughput Development and Functional Characterization of Small RNAs Chapitre d'ouvrage
Dans: Rederstorff, M (Ed.): Small Non-Coding RNAs, vol. 2300, p. 203-237, Springer Protocols, Humana Press, New York, NY, Small Non-Coding RNAs, 2021, ISBN: 978-1-0716-1385-6/ISSN, (1940-6029 (Electronic) 1064-3745 (Linking) Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Artificial RNAs, directed evolution, Droplet microfluidics, Functional screening, In vitro selection, RNA, RYCKELYNCK, RYCKELYNCK Artificial RNAs, Unité ARN
@inbook{Bouhedda2021,
title = {microIVC-Seq: A Method for Ultrahigh-Throughput Development and Functional Characterization of Small RNAs},
author = {F Bouhedda and R Cubi and S Baudrey and M Ryckelynck},
editor = {M Rederstorff},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=33792882},
doi = {10.1007/978-1-0716-1386-3_17},
isbn = {978-1-0716-1385-6/ISSN},
year = {2021},
date = {2021-01-01},
booktitle = {Small Non-Coding RNAs},
volume = {2300},
pages = {203-237},
publisher = {Springer Protocols, Humana Press},
address = {New York, NY},
edition = {Small Non-Coding RNAs},
series = {Methods in Molecular Biology},
abstract = {For a long time, artificial RNAs have been developed by in vitro selection methodologies like Systematic Evolution of Ligands by EXponential enrichment (SELEX). Yet, even though this technology is extremely powerful to isolate specific and high-affinity binders, it is less suited for the isolation of RNAs optimized for more complex functions such as fluorescence emission or multiple-turnover catalysis. Whereas such RNAs should ideally be developed by screening approaches, conventional microtiter plate assays become rapidly cost-prohibitive. However, the advent of droplet-based microfluidics recently enabled us to devise microfluidic-assisted In Vitro Compartmentalization (muIVC), a strongly miniaturized and highly parallelized screening technology allowing to functionally screen millions of mutants in a single day while using a very low amount of reagent. Used in combination with high-throughput sequencing, the resulting muIVC-seq pipeline described in this chapter now allows rapid and semiautomated screening to be performed at low cost and in an ultrahigh-throughput regime.},
note = {1940-6029 (Electronic)
1064-3745 (Linking)
Journal Article},
keywords = {Artificial RNAs, directed evolution, Droplet microfluidics, Functional screening, In vitro selection, RNA, RYCKELYNCK, RYCKELYNCK Artificial RNAs, Unité ARN},
pubstate = {published},
tppubtype = {inbook}
}
Skerniskyte J, Karazijaite E, Luciunaite A, Suziedeliene E
OmpA Protein-Deficient Acinetobacter baumannii Outer Membrane Vesicles Trigger Reduced Inflammatory Response Article de journal
Dans: Pathogens, vol. 10, no. 4, p. 407, 2021, ISBN: 33807410, (2076-0817 (Print) 2076-0817 (Linking) Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Acinetobacter baumannii, inflammasome, inflammation, Macrophages, MARTEYN, outer membrane vesicles, Unité ARN
@article{Skerniskyte2021,
title = {OmpA Protein-Deficient Acinetobacter baumannii Outer Membrane Vesicles Trigger Reduced Inflammatory Response},
author = {J Skerniskyte and E Karazijaite and A Luciunaite and E Suziedeliene},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=33807410},
doi = {10.3390/pathogens10040407},
isbn = {33807410},
year = {2021},
date = {2021-01-01},
journal = {Pathogens},
volume = {10},
number = {4},
pages = {407},
abstract = {Multidrug resistant Acinetobacter baumannii shows a growing number of nosocomial infections worldwide during the last decade. The outer membrane vesicles (OMVs) produced by this bacterium draw increasing attention as a possible treatment target. OMVs have been implicated in the reduction of antibiotic level in the surrounding environment, transfer of virulence factors into the host cells, and induction of inflammatory response. Although the evidence on the involvement of OMVs in A. baumannii pathogenesis is currently growing, their role during inflammation is insufficiently explored. It is likely that bacteria, by secreting OMVs, can expand the area of their exposure and prepare surrounding matrix for infection. Here, we investigated the impact of A. baumannii OMVs on activation of macrophages in vitro. We show that OmpA protein present in A. baumannii OMVs substantially contributes to the proinflammatory response in J774 murine macrophages and to the cell death in both lung epithelium cells and macrophages. The loss of OmpA protein in OMVs, obtained from A. baumannii ompA mutant, resulted in the altered expression of genes coding for IL-6, NLRP3 and IL-1beta proinflammatory molecules in macrophages in vitro. These results imply that OmpA protein in bacterial OMVs could trigger a more intense proinflammatory response.},
note = {2076-0817 (Print)
2076-0817 (Linking)
Journal Article},
keywords = {Acinetobacter baumannii, inflammasome, inflammation, Macrophages, MARTEYN, outer membrane vesicles, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Bereiter R, Himmelstoss M, Renard E, Mairhofer E, Egger M, Breuker K, Kreutz C, Ennifar E, Micura R
Impact of 3-deazapurine nucleobases on RNA properties Article de journal
Dans: Nucleic Acids Res, vol. 49, no. 8, p. 4281-4293, 2021, ISBN: 33856457, (1362-4962 (Electronic) 0305-1048 (Linking) Journal Article).
Résumé | Liens | BibTeX | Étiquettes: ENNIFAR, Unité ARN
@article{,
title = {Impact of 3-deazapurine nucleobases on RNA properties},
author = {R Bereiter and M Himmelstoss and E Renard and E Mairhofer and M Egger and K Breuker and C Kreutz and E Ennifar and R Micura},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=33856457},
isbn = {33856457},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Nucleic Acids Res},
volume = {49},
number = {8},
pages = {4281-4293},
abstract = {Deazapurine nucleosides such as 3-deazaadenosine (c3A) are crucial for atomic mutagenesis studies of functional RNAs. They were the key for our current mechanistic understanding of ribosomal peptide bond formation and of phosphodiester cleavage in recently discovered small ribozymes, such as twister and pistol RNAs. Here, we present a comprehensive study on the impact of c3A and the thus far underinvestigated 3-deazaguanosine (c3G) on RNA properties. We found that these nucleosides can decrease thermodynamic stability of base pairing to a significant extent. The effects are much more pronounced for 3-deazapurine nucleosides compared to their constitutional isomers of 7-deazapurine nucleosides (c7G, c7A). We furthermore investigated base pair opening dynamics by solution NMR spectroscopy and revealed significantly enhanced imino proton exchange rates. Additionally, we solved the X-ray structure of a c3A-modified RNA and visualized the hydration pattern of the minor groove. Importantly, the characteristic water molecule that is hydrogen-bonded to the purine N3 atom and always observed in a natural double helix is lacking in the 3-deazapurine-modified counterpart. Both, the findings by NMR and X-ray crystallographic methods hence provide a rationale for the reduced pairing strength. Taken together, our comparative study is a first major step towards a comprehensive understanding of this important class of nucleoside modifications.},
note = {1362-4962 (Electronic)
0305-1048 (Linking)
Journal Article},
keywords = {ENNIFAR, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Omar R El, Julien E, Biasch K, Guffroy B, Lioure B, Vallat L, Gross I, Domon-Dell C, Lanza F, Gachet C, Negroni M, Freund J N, Tavian M
CDX2 regulates ACE expression in blood development and leukemia cells Article de journal
Dans: Blood Adv, vol. 5, no. 7, p. 2012-2016, 2021, ISBN: 33843985, (2473-9537 (Electronic) 2473-9529 (Linking) Journal Article).
Liens | BibTeX | Étiquettes: NEGRONI, Unité ARN
@article{,
title = {CDX2 regulates ACE expression in blood development and leukemia cells},
author = {R El Omar and E Julien and K Biasch and B Guffroy and B Lioure and L Vallat and I Gross and C Domon-Dell and F Lanza and C Gachet and M Negroni and J N Freund and M Tavian},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=33843985},
doi = {10.1182/bloodadvances.2020003563},
isbn = {33843985},
year = {2021},
date = {2021-01-01},
journal = {Blood Adv},
volume = {5},
number = {7},
pages = {2012-2016},
note = {2473-9537 (Electronic)
2473-9529 (Linking)
Journal Article},
keywords = {NEGRONI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Schenckbecher E, Bec G, Sakamoto T, Meyer B, Ennifar E
Biophysical Studies of the Binding of Viral RNA with the 80S Ribosome Using switchSENSE Article de journal
Dans: Methods Mol Biol, vol. 2263, p. 341-350, 2021, ISBN: 33877606, (1940-6029 (Electronic) 1064-3745 (Linking) Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Biophysics, ENNIFAR, Kinetics, Ribosome, RNA, switchSENSE, Unité ARN
@article{,
title = {Biophysical Studies of the Binding of Viral RNA with the 80S Ribosome Using switchSENSE},
author = {E Schenckbecher and G Bec and T Sakamoto and B Meyer and E Ennifar},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=33877606},
doi = {10.1007/978-1-0716-1197-5_15},
isbn = {33877606},
year = {2021},
date = {2021-01-01},
journal = {Methods Mol Biol},
volume = {2263},
pages = {341-350},
abstract = {Translation initiation, in both eukaryotes and bacteria, requires essential elements such as mRNA, ribosome, initiator tRNA, and a set of initiation factors. For each domain of life, canonical mechanisms and signals are observed to initiate protein synthesis. However, other initiation mechanism can be used, especially in viral mRNAs. Some viruses hijack cellular machinery to translate some of their mRNAs through a noncanonical initiation pathway using internal ribosome entry site (IRES), a highly structured RNAs which can directly recruit the ribosome with a restricted set of initiation factors, and in some cases even without cap and initiator tRNA. In this chapter, we describe the use of biosensors relying on electro-switchable nanolevers using the switchSENSE((R)) technology, to investigate kinetics of the intergenic (IGR) IRES of the cricket paralysis virus (CrPV) binding to 80S yeast ribosome. This study provides a proof of concept for the application of this method on large complexes.},
note = {1940-6029 (Electronic)
1064-3745 (Linking)
Journal Article},
keywords = {Biophysics, ENNIFAR, Kinetics, Ribosome, RNA, switchSENSE, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Toccafondi E, Lener D, Negroni M
HIV-1 Capsid Core: A Bullet to the Heart of the Target Cell Article de journal
Dans: Front Microbiol, vol. 12, p. 652486, 2021, ISBN: 33868211, (1664-302X (Print) 1664-302X (Linking) Journal Article Review).
Résumé | Liens | BibTeX | Étiquettes: NEGRONI, Unité ARN
@article{,
title = {HIV-1 Capsid Core: A Bullet to the Heart of the Target Cell},
author = {E Toccafondi and D Lener and M Negroni},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=33868211},
doi = {10.3389/fmicb.2021.652486},
isbn = {33868211},
year = {2021},
date = {2021-01-01},
journal = {Front Microbiol},
volume = {12},
pages = {652486},
abstract = {The first step of the intracellular phase of retroviral infection is the release of the viral capsid core in the cytoplasm. This structure contains the viral genetic material that will be reverse transcribed and integrated into the genome of infected cells. Up to recent times, the role of the capsid core was considered essentially to protect this genetic material during the earlier phases of this process. However, increasing evidence demonstrates that the permanence inside the cell of the capsid as an intact, or almost intact, structure is longer than thought. This suggests its involvement in more aspects of the infectious cycle than previously foreseen, particularly in the steps of viral genomic material translocation into the nucleus and in the phases preceding integration. During the trip across the infected cell, many host factors are brought to interact with the capsid, some possessing antiviral properties, others, serving as viral cofactors. All these interactions rely on the properties of the unique component of the capsid core, the capsid protein CA. Likely, the drawback of ensuring these multiple functions is the extreme genetic fragility that has been shown to characterize this protein. Here, we recapitulate the busy agenda of an HIV-1 capsid in the infectious process, in particular in the light of the most recent findings.},
note = {1664-302X (Print)
1664-302X (Linking)
Journal Article
Review},
keywords = {NEGRONI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Velazquez-Campoy A, Claro B, Abian O, Horing J, Bourlon L, Claveria-Gimeno R, Ennifar E, England P, Chaires J B, Wu D, Piszczek G, Brautigam C, Tso S C, Zhao H, Schuck P, Keller S, Bastos M
A multi-laboratory benchmark study of isothermal titration calorimetry (ITC) using Ca(2+) and Mg(2+) binding to EDTA Article de journal
Dans: Eur Biophys J, vol. 50, no. 3-4, p. 429-451, 2021, ISBN: 33864101, (1432-1017 (Electronic) 0175-7571 (Linking) Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Benchmark study, Data treatment, ENNIFAR, Isothermal Titration Calorimetry (ITC), Ligand-binding, Sample preparation, Standard reaction, Unité ARN
@article{,
title = {A multi-laboratory benchmark study of isothermal titration calorimetry (ITC) using Ca(2+) and Mg(2+) binding to EDTA},
author = {A Velazquez-Campoy and B Claro and O Abian and J Horing and L Bourlon and R Claveria-Gimeno and E Ennifar and P England and J B Chaires and D Wu and G Piszczek and C Brautigam and S C Tso and H Zhao and P Schuck and S Keller and M Bastos},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=33864101},
doi = {10.1007/s00249-021-01523-7},
isbn = {33864101},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Eur Biophys J},
volume = {50},
number = {3-4},
pages = {429-451},
abstract = {A small-scale ITC benchmarking study was performed involving 9 biophysics laboratories/facilities, to evaluate inter-laboratory and intra-laboratory basal levels of uncertainty. Our prime goal was to assess a number of important factors that can influence both the data gathered by this technique and the thermodynamic parameter values derived therefrom. In its first part, the study involved 5 laboratories and 13 different instruments, working with centrally prepared samples and the same experimental protocol. The second part involved 4 additional laboratories and 6 more instruments, where the users prepared their own samples according to provided instructions and did the experiments following the same protocol as in the first part. The study design comprised: (1) selecting a minimal set of laboratories; (2) providing very stable samples; (3) providing samples not requiring preparation or manipulation; and (4) providing a well-defined and detailed experimental protocol. Thus, we were able to assess: (i) the variability due to instrument and data analysis performed by each user on centrally prepared samples; (ii) the comparability of data retrieved when using 4 different software packages to analyze the same data, besides the data analysis carried out by the different users on their own experimental results; and (iii) the variability due to local sample preparation (second part of the study). Individual values, as well as averages and standard deviations for the binding parameters for EDTA-cation interaction, were used as metrics for comparing the equilibrium association constant (logK), enthalpy of interaction (DeltaH), and the so-called "stoichiometry" (n), a concentration-correction factor.},
note = {1432-1017 (Electronic)
0175-7571 (Linking)
Journal Article},
keywords = {Benchmark study, Data treatment, ENNIFAR, Isothermal Titration Calorimetry (ITC), Ligand-binding, Sample preparation, Standard reaction, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Goettsch W, Beerenwinkel N, Deng L, Dolken L, Dutilh B E, Erhard F, Kaderali L, von Kleist M, Marquet R, Matthijnssens J, McCallin S, McMahon D, Rattei T, Rij R P Van, Robertson D L, Schwemmle M, Stern-Ginossar N, Marz M
ITN-VIROINF: Understanding (Harmful) Virus-Host Interactions by Linking Virology and Bioinformatics Article de journal
Dans: Viruses, vol. 13, no. 5, 2021, ISBN: 33925452, (1999-4915 (Electronic) 1999-4915 (Linking) Journal Article).
Résumé | Liens | BibTeX | Étiquettes: MARQUET, Unité ARN
@article{Goettsch2021,
title = {ITN-VIROINF: Understanding (Harmful) Virus-Host Interactions by Linking Virology and Bioinformatics},
author = {W Goettsch and N Beerenwinkel and L Deng and L Dolken and B E Dutilh and F Erhard and L Kaderali and M von Kleist and R Marquet and J Matthijnssens and S McCallin and D McMahon and T Rattei and R P Van Rij and D L Robertson and M Schwemmle and N Stern-Ginossar and M Marz},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=33925452},
doi = {10.3390/v13050766},
isbn = {33925452},
year = {2021},
date = {2021-01-01},
journal = {Viruses},
volume = {13},
number = {5},
abstract = {Many recent studies highlight the fundamental importance of viruses. Besides their important role as human and animal pathogens, their beneficial, commensal or harmful functions are poorly understood. By developing and applying tailored bioinformatical tools in important virological models, the Marie Sklodowska-Curie Initiative International Training Network VIROINF will provide a better understanding of viruses and the interaction with their hosts. This will open the door to validate methods of improving viral growth, morphogenesis and development, as well as to control strategies against unwanted microorganisms. The key feature of VIROINF is its interdisciplinary nature, which brings together virologists and bioinformaticians to achieve common goals.},
note = {1999-4915 (Electronic)
1999-4915 (Linking)
Journal Article},
keywords = {MARQUET, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Cubi R, Bouhedda F, Collot M, Klymchenko A S, Ryckelynck M
Dans: Rna, vol. 27, no. 7, p. 841-853, 2021, ISBN: 33952671, (1469-9001 (Electronic) 1355-8382 (Linking) Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Bioinformatics, droplet-based microfluidics, high-throughput screening, light-up RNA aptamer, RNA engineering, RYCKELYNCK, Unité ARN
@article{,
title = {microIVC-Useq: a microfluidic-assisted high-throughput functionnal screening in tandem with next generation sequencing and artificial neural network to rapidly characterize RNA molecules},
author = {R Cubi and F Bouhedda and M Collot and A S Klymchenko and M Ryckelynck},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=33952671},
doi = {10.1261/rna.077586.120},
isbn = {33952671},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Rna},
volume = {27},
number = {7},
pages = {841-853},
abstract = {The function of an RNA is intimately linked to its three-dimensional structure. X-ray crystallography or NMR allow the fine structural characterization of small RNA (e.g., aptamers) with a precision down to atomic resolution. Yet, these technics are time consuming, laborious and do not inform on mutational robustness and the extent to which a sequence can be modified without altering RNA function, an important set of information to assist RNA engineering. On another hand, thought powerful, in silico predictions still lack the required accuracy. These limitations can be overcome by using high-throughput microfluidic-assisted functional screening technologies, as they allow exploring large mutant libraries in a rapid and cost-effective manner. Among them, we recently introduced the microfluidic-assisted In Vitro Compartmentalization (microIVC), an efficient screening strategy in which reactions are performed in picoliter droplets at rates of several thousand per second. We later improved microIVC efficiency by using in tandem with high throughput sequencing, thought a laborious bioinformatic step was still required at the end of the process. In the present work, we strongly increased the automation level of the pipeline by implementing an artificial neural network enabling unsupervised bioinformatic analysis. We demonstrate the efficiency of this "microIVC-Useq" technology by rapidly identifying a set of sequences readily accepted by a key domain of the light-up RNA aptamer SRB-2. This work not only shed some new light on the way this aptamer can be engineered, but it also allowed us to easily identify new variants with an up-to 10-fold improved performance.},
note = {1469-9001 (Electronic)
1355-8382 (Linking)
Journal Article},
keywords = {Bioinformatics, droplet-based microfluidics, high-throughput screening, light-up RNA aptamer, RNA engineering, RYCKELYNCK, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Montavon T C, Baldaccini M, Lefevre M, Girardi E, Chane-Woon-Ming B, Messmer M, Hammann P, Chicher J, Pfeffer S
Human DICER helicase domain recruits PKR and modulates its antiviral activity Article de journal
Dans: PLoS Pathog, vol. 17, no. 5, p. e1009549, 2021, ISBN: 33984068, (1553-7374 (Electronic) 1553-7366 (Linking) Journal Article).
Résumé | Liens | BibTeX | Étiquettes: PFEFFER, PPSE, Unité ARN
@article{Montavon2021,
title = {Human DICER helicase domain recruits PKR and modulates its antiviral activity},
author = {T C Montavon and M Baldaccini and M Lefevre and E Girardi and B Chane-Woon-Ming and M Messmer and P Hammann and J Chicher and S Pfeffer},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=33984068},
doi = {0.1371/journal.ppat.1009549},
isbn = {33984068},
year = {2021},
date = {2021-01-01},
journal = {PLoS Pathog},
volume = {17},
number = {5},
pages = {e1009549},
abstract = {The antiviral innate immune response mainly involves type I interferon (IFN) in mammalian cells. The contribution of the RNA silencing machinery remains to be established, but several recent studies indicate that the ribonuclease DICER can generate viral siRNAs in specific conditions. It has also been proposed that type I IFN and RNA silencing could be mutually exclusive antiviral responses. In order to decipher the implication of DICER during infection of human cells with alphaviruses such as the Sindbis virus and Semliki forest virus, we determined its interactome by proteomics analysis. We show that DICER specifically interacts with several double-stranded RNA binding proteins and RNA helicases during viral infection. In particular, proteins such as DHX9, ADAR-1 and the protein kinase RNA-activated (PKR) are enriched with DICER in virus-infected cells. We demonstrate that the helicase domain of DICER is essential for this interaction and that its deletion confers antiviral properties to this protein in an RNAi-independent, PKR-dependent, manner.},
note = {1553-7374 (Electronic)
1553-7366 (Linking)
Journal Article},
keywords = {PFEFFER, PPSE, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Alghoul F, Laure S, Eriani G, Martin F
Translation inhibitory elements from Hoxa3 and Hoxa11 mRNAs use uORFs for translation inhibition Article de journal
Dans: Elife, vol. 10, 2021, ISBN: 34076576, (2050-084X (Electronic) 2050-084X (Linking) Journal Article).
Résumé | Liens | BibTeX | Étiquettes: ERIANI, Unité ARN
@article{Alghoul2021b,
title = {Translation inhibitory elements from Hoxa3 and Hoxa11 mRNAs use uORFs for translation inhibition},
author = {F Alghoul and S Laure and G Eriani and F Martin},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=34076576},
doi = {10.7554/eLife.66369},
isbn = {34076576},
year = {2021},
date = {2021-01-01},
journal = {Elife},
volume = {10},
abstract = {During embryogenesis, Hox mRNA translation is tightly regulated by a sophisticated molecular mechanism that combines two RNA regulons located in their 5'UTR. First, an internal ribosome entry site (IRES) enables cap-independent translation. The second regulon is a translation inhibitory element or TIE, which ensures concomitant cap-dependent translation inhibition. In this study, we deciphered the molecular mechanisms of mouse Hoxa3 and Hoxa11 TIEs. Both TIEs possess an upstream open reading frame (uORF) that is critical to inhibit cap-dependent translation. However, the molecular mechanisms used are different. In Hoxa3 TIE, we identify an uORF which inhibits cap-dependent translation and we show the requirement of the non-canonical initiation factor eIF2D for this process. The mode of action of Hoxa11 TIE is different, it also contains an uORF but it is a minimal uORF formed by an uAUG followed immediately by a stop codon, namely a 'start-stop'. The 'start-stop' sequence is species-specific and in mice, is located upstream of a highly stable stem loop structure which stalls the 80S ribosome and thereby inhibits cap-dependent translation of Hoxa11 main ORF.},
note = {2050-084X (Electronic)
2050-084X (Linking)
Journal Article},
keywords = {ERIANI, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Ramos-Morales E, Bayam E, Del-Pozo-Rodriguez J, Salinas-Giege T, Marek M, Tilly P, Wolff P, Troesch E, Ennifar E, Drouard L, Godin J D, Romier C
The structure of the mouse ADAT2/ADAT3 complex reveals the molecular basis for mammalian tRNA wobble adenosine-to-inosine deamination Article de journal
Dans: Nucleic Acids Res, vol. 49, no. 11, p. 6529-6548, 2021, ISBN: 34057470, (1362-4962 (Electronic) 0305-1048 (Linking) Journal Article).
Résumé | Liens | BibTeX | Étiquettes: ARN-MS, ENNIFAR, Unité ARN
@article{,
title = {The structure of the mouse ADAT2/ADAT3 complex reveals the molecular basis for mammalian tRNA wobble adenosine-to-inosine deamination},
author = {E Ramos-Morales and E Bayam and J Del-Pozo-Rodriguez and T Salinas-Giege and M Marek and P Tilly and P Wolff and E Troesch and E Ennifar and L Drouard and J D Godin and C Romier},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=34057470},
doi = {10.1093/nar/gkab436},
isbn = {34057470},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Nucleic Acids Res},
volume = {49},
number = {11},
pages = {6529-6548},
abstract = {Post-transcriptional modification of tRNA wobble adenosine into inosine is crucial for decoding multiple mRNA codons by a single tRNA. The eukaryotic wobble adenosine-to-inosine modification is catalysed by the ADAT (ADAT2/ADAT3) complex that modifies up to eight tRNAs, requiring a full tRNA for activity. Yet, ADAT catalytic mechanism and its implication in neurodevelopmental disorders remain poorly understood. Here, we have characterized mouse ADAT and provide the molecular basis for tRNAs deamination by ADAT2 as well as ADAT3 inactivation by loss of catalytic and tRNA-binding determinants. We show that tRNA binding and deamination can vary depending on the cognate tRNA but absolutely rely on the eukaryote-specific ADAT3 N-terminal domain. This domain can rotate with respect to the ADAT catalytic domain to present and position the tRNA anticodon-stem-loop correctly in ADAT2 active site. A founder mutation in the ADAT3 N-terminal domain, which causes intellectual disability, does not affect tRNA binding despite the structural changes it induces but most likely hinders optimal presentation of the tRNA anticodon-stem-loop to ADAT2.},
note = {1362-4962 (Electronic)
0305-1048 (Linking)
Journal Article},
keywords = {ARN-MS, ENNIFAR, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Ortet P, Fochesato S, Bitbol A F, Whitworth D E, Lalaouna D, Santaella C, Heulin T, Achouak W, Barakat M
Evolutionary history expands the range of signaling interactions in hybrid multikinase networks Article de journal
Dans: Sci Rep, vol. 11, no. 1, p. 11763, 2021, ISBN: 34083699.
Résumé | Liens | BibTeX | Étiquettes: ROMBY, Unité ARN
@article{,
title = {Evolutionary history expands the range of signaling interactions in hybrid multikinase networks},
author = {P Ortet and S Fochesato and A F Bitbol and D E Whitworth and D Lalaouna and C Santaella and T Heulin and W Achouak and M Barakat},
url = {https://pubmed.ncbi.nlm.nih.gov/34083699/},
doi = {10.1038/s41598-021-91260-w},
isbn = {34083699},
year = {2021},
date = {2021-01-01},
journal = {Sci Rep},
volume = {11},
number = {1},
pages = {11763},
abstract = {Two-component systems (TCSs) are ubiquitous signaling pathways, typically comprising a sensory histidine kinase (HK) and a response regulator, which communicate via intermolecular kinase-to-receiver domain phosphotransfer. Hybrid HKs constitute non-canonical TCS signaling pathways, with transmitter and receiver domains within a single protein communicating via intramolecular phosphotransfer. Here, we report how evolutionary relationships between hybrid HKs can be used as predictors of potential intermolecular and intramolecular interactions ('phylogenetic promiscuity'). We used domain-swap genes chimeras to investigate the specificity of phosphotransfer within hybrid HKs of the GacS-GacA multikinase network of Pseudomonas brassicacearum. The receiver domain of GacS was replaced with those from nine donor hybrid HKs. Three chimeras with receivers from other hybrid HKs demonstrated correct functioning through complementation of a gacS mutant, which was dependent on strains having a functional gacA. Formation of functional chimeras was predictable on the basis of evolutionary heritage, and raises the possibility that HKs sharing a common ancestor with GacS might remain components of the contemporary GacS network. The results also demonstrate that understanding the evolutionary heritage of signaling domains in sophisticated networks allows their rational rewiring by simple domain transplantation, with implications for the creation of designer networks and inference of functional interactions.},
keywords = {ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Himmelstoss M, Erharter K, Renard E, Ennifar E, Kreutz C, Micura R
2'-O-Trifluoromethylated RNA - a powerful modification for RNA chemistry and NMR spectroscopy Article de journal
Dans: Chem Sci, vol. 11, no. 41, p. 11322-11330, 2021, ISBN: 34094374, (2041-6520 (Print) 2041-6520 (Linking) Journal Article).
Résumé | Liens | BibTeX | Étiquettes: ENNIFAR, Unité ARN
@article{,
title = {2'-O-Trifluoromethylated RNA - a powerful modification for RNA chemistry and NMR spectroscopy},
author = {M Himmelstoss and K Erharter and E Renard and E Ennifar and C Kreutz and R Micura},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=34094374},
doi = {10.1039/d0sc04520a},
isbn = {34094374},
year = {2021},
date = {2021-01-01},
journal = {Chem Sci},
volume = {11},
number = {41},
pages = {11322-11330},
abstract = {New RNA modifications are needed to advance our toolbox for targeted manipulation of RNA. In particular, the development of high-performance reporter groups facilitating spectroscopic analysis of RNA structure and dynamics, and of RNA-ligand interactions has attracted considerable interest. To this end, fluorine labeling in conjunction with (19)F-NMR spectroscopy has emerged as a powerful strategy. Appropriate probes for RNA previously focused on single fluorine atoms attached to the 5-position of pyrimidine nucleobases or at the ribose 2'-position. To increase NMR sensitivity, trifluoromethyl labeling approaches have been developed, with the ribose 2'-SCF3 modification being the most prominent one. A major drawback of the 2'-SCF3 group, however, is its strong impact on RNA base pairing stability. Interestingly, RNA containing the structurally related 2'-OCF3 modification has not yet been reported. Therefore, we set out to overcome the synthetic challenges toward 2'-OCF3 labeled RNA and to investigate the impact of this modification. We present the syntheses of 2'-OCF3 adenosine and cytidine phosphoramidites and their incorporation into oligoribonucleotides by solid-phase synthesis. Importantly, it turns out that the 2'-OCF3 group has only a slight destabilizing effect when located in double helical regions which is consistent with the preferential C3'-endo conformation of the 2'-OCF3 ribose as reflected in the (3) J (H1'-H2') coupling constants. Furthermore, we demonstrate the exceptionally high sensitivity of the new label in (19)F-NMR analysis of RNA structure equilibria and of RNA-small molecule interactions. The study is complemented by a crystal structure at 0.9 A resolution of a 27 nt hairpin RNA containing a single 2'-OCF3 group that well integrates into the minor groove. The new label carries high potential to outcompete currently applied fluorine labels for nucleic acid NMR spectroscopy because of its significantly advanced performance.},
note = {2041-6520 (Print)
2041-6520 (Linking)
Journal Article},
keywords = {ENNIFAR, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Moya-Alvarez V, Koyembi J J, Kaye L M, Mbecko J R, Sanke-Waigana H, Djorie S G, Nyasenu Y T, Mad-Bondo D, Kongoma J B, Nakib S, Madec Y, Ulmann G, Neveux N, Sansonetti P J, Vray M, Marteyn B
Vitamin C levels in a Central-African mother-infant cohort: Does hypovitaminosis C increase the risk of enteric infections? Article de journal
Dans: Matern Child Nutr, p. e13215, 2021, ISBN: 34137176, (1740-8709 (Electronic) 1740-8695 (Linking) Journal Article).
Résumé | Liens | BibTeX | Étiquettes: MARTEYN, Unité ARN
@article{,
title = {Vitamin C levels in a Central-African mother-infant cohort: Does hypovitaminosis C increase the risk of enteric infections?},
author = {V Moya-Alvarez and J J Koyembi and L M Kaye and J R Mbecko and H Sanke-Waigana and S G Djorie and Y T Nyasenu and D Mad-Bondo and J B Kongoma and S Nakib and Y Madec and G Ulmann and N Neveux and P J Sansonetti and M Vray and B Marteyn},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=34137176},
doi = {10.1111/mcn.13215},
isbn = {34137176},
year = {2021},
date = {2021-01-01},
journal = {Matern Child Nutr},
pages = {e13215},
abstract = {In the MITICA (Mother-to-Infant TransmIssion of microbiota in Central-Africa) study, 48 mothers and their 50 infants were followed from delivery to 6 months between December 2017 and June 2019 in Bangui (Central-African Republic). Blood tests and stool analyses were performed in mothers at delivery, and their offspring at birth, 11 weeks and 25 weeks. Stool cultures were performed in specific growth media for Salmonella, Shigella, E. coli, Campylobacter, Enerobacter, Vibrio cholerae, Citrobacter and Klebsiella, as well as rotavirus, yeasts and parasitological exams. The median vitamin C levels in mothers at delivery were 15.3 mumol/L (inter-quartile-range [IQR] 6.2-27.8 mumol/L). In infants, the median vitamin C levels at birth were 35.2 mumol/L (IQR 16.5-63.9 mumol/L). At 11 and 25 weeks, the median vitamin C levels were 41.5 mumol/L (IQR 18.7-71.6 mumol/L) and 18.2 mumol/L (IQR 2.3-46.6 mumol/L), respectively. Hypovitaminosis C was defined as seric vitamin C levels <28 mumol/L and vitamin C deficiency was defined as vitamin C levels <11 mumol/L according to the WHO definition. In mothers, the prevalence of hypovitaminosis-C and vitamin C deficiency at delivery was 34/45 (75.6%) and 19/45 (42.2%), respectively. In infants, the prevalence of hypovitaminosis-C and vitamin C deficiency at 6 months was 18/33 (54.6%) and 11/33 (33.3%), respectively. Vitamin C levels in mothers and infants were correlated at birth (Spearman's rho = 0.5; P value = 0.002), and infants had significantly higher levels of vitamin C (median = 35.2 mumol/L; IQR 16.5-63.9 mumol/L), compared to mothers (median = 15.3 mumol/L; IQR 6.2-27.8 mumol/L; P value <0.001). The offspring of vitamin C-deficient mothers had significantly lower vitamin C levels at delivery (median = 18.7 mumol/L; IQR 13.3-30.7 mumol/L), compared to the offspring of non-deficient mothers (median = 62.2 mumol/L; IQR 34.6-89.2 mumol/L; P value <0.001). Infants with hypovitaminosis-C were at significantly higher risk of having a positive stool culture during the first 6 months of life (adjusted OR = 5.3, 95% CI 1.1; 26.1; P value = 0.038).},
note = {1740-8709 (Electronic)
1740-8695 (Linking)
Journal Article},
keywords = {MARTEYN, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Giuliodori A M, Marzi S
Editorial: Interview With the Translational Apparatus: Stories of Intriguing Circuits and Mechanisms to Regulate Translation in Bacteria Article de journal
Dans: Front Microbiol, vol. 12, p. 707354, 2021, ISBN: 34220790, (1664-302X (Print) 1664-302X (Linking) Editorial).
Liens | BibTeX | Étiquettes: ROMBY, Unité ARN
@article{,
title = {Editorial: Interview With the Translational Apparatus: Stories of Intriguing Circuits and Mechanisms to Regulate Translation in Bacteria},
author = {A M Giuliodori and S Marzi},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=34220790},
doi = {10.3389/fmicb.2021.707354},
isbn = {34220790},
year = {2021},
date = {2021-01-01},
journal = {Front Microbiol},
volume = {12},
pages = {707354},
note = {1664-302X (Print)
1664-302X (Linking)
Editorial},
keywords = {ROMBY, Unité ARN},
pubstate = {published},
tppubtype = {article}
}