Imaging

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@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}

}

@article{,

title = {Comparative study on tertiary contacts and folding of RNase P RNAs from a psychrophilic, a mesophilic/radiation-resistant and a thermophilic bacterium},

author = {M Marszalkowski and A Werner and R Feltens and D Helmecke and M Gossringer and E Westhof and R K Hartmann},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=34266994},

doi = {10.1261/rna.078735.121},

isbn = {34266994},

year  = {2021},

date = {2021-01-01},

journal = {Rna},

abstract = {In most bacterial type A RNase P RNAs (P RNAs), two major loop-helix tertiary contacts (L8-P4 and L18-P8) help to orient the two independently folding S- and C-domains for concerted recognition of precursor tRNA substrates. Here, we analyze the effects of mutations in these tertiary contacts in P RNAs from three different species: (i) the psychrophilic bacterium Pseudoalteromonas translucida (Ptr), (ii) the mesophilic radiation-resistant bacterium Deinococcus radiodurans (Dra), and (iii) the thermophilic bacterium Thermus thermophilus (Tth). We show by UV melting experiments that simultaneous disruption of these two interdomain contacts has a stabilizing effect on all three P RNAs. This can be inferred from reduced RNA unfolding at lower temperatures and a more concerted unfolding at higher temperatures. Thus, when the two domains tightly interact via the tertiary contacts, one domain facilitates structural transitions in the other. P RNA mutants with disrupted interdomain contacts showed severe kinetic defects that were most pronounced upon simultaneous disruption of the L8-P4 and L18-P8 contacts. At 37 degrees C, the mildest effects were observed for the thermostable Tth RNA. A third interdomain contact, L9-P1, makes only a minor contribution to P RNA tertiary folding. Furthermore, D. radiodurans RNase P RNA forms an additional pseudoknot structure between the P9 and P12 of its S-domain. This interaction was found to be particularly crucial for RNase P holoenzyme activity at near-physiological Mg2+ concentrations (2 mM). We further analyzed an exceptionally stable folding trap of the G,C-rich Tth P RNA.},

note = {1469-9001 (Electronic) 

1355-8382 (Linking) 

Journal Article},

keywords = {Unité ARN, WESTHOF},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Assembling the Current Pieces: The Puzzle of RNA-Mediated Regulation in Staphylococcus aureus},

author = {L Barrientos and N Mercier and D Lalaouna and I Caldelari},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=34367109},

doi = {10.3389/fmicb.2021.706690},

isbn = {34367109},

year  = {2021},

date = {2021-01-01},

journal = {Front Microbiol},

volume = {12},

pages = {706690},

abstract = {The success of the major opportunistic human Staphylococcus aureus relies on the production of numerous virulence factors, which allow rapid colonization and dissemination in any tissues. Indeed, regulation of its virulence is multifactorial, and based on the production of transcriptional factors, two-component systems (TCS) and small regulatory RNAs (sRNAs). Advances in high-throughput sequencing technologies have unveiled the existence of hundreds of potential RNAs with regulatory functions, but only a fraction of which have been validated in vivo. These discoveries have modified our thinking and understanding of bacterial physiology and virulence fitness by placing sRNAs, alongside transcriptional regulators, at the center of complex and intertwined regulatory networks that allow S. aureus to rapidly adapt to the environmental cues present at infection sites. In this review, we describe the recently acquired knowledge of characterized regulatory RNAs in S. aureus that are associated with metal starvation, nutrient availability, stress responses and virulence. These findings highlight the importance of sRNAs for the comprehension of S. aureus infection processes while raising questions about the interplay between these key regulators and the pathways they control.},

note = {1664-302X (Print) 

1664-302X (Linking) 

Journal Article 

Review},

keywords = {ROMBY, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Burning the Candle at Both Ends: Have Exoribonucleases Driven Divergence of Regulatory RNA Mechanisms in Bacteria?},

author = {D G Mediati and D Lalaouna and J J Tree},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=34372700},

doi = {10.1128/mBio.01041-21},

isbn = {34372700},

year  = {2021},

date = {2021-01-01},

journal = {mBio},

pages = {e0104121},

abstract = {Regulatory RNAs have emerged as ubiquitous gene regulators in all bacterial species studied to date. The combination of sequence-specific RNA interactions and malleable RNA structure has allowed regulatory RNA to adopt different mechanisms of gene regulation in a diversity of genetic backgrounds. In the model Gammaproteobacteria Escherichia coli and Salmonella, the regulatory RNA chaperone Hfq appears to play a global role in gene regulation, directly controlling approximately 20 to 25% of the entire transcriptome. While the model Firmicutes Bacillus subtilis and Staphylococcus aureus encode a Hfq homologue, its role has been significantly depreciated. These bacteria also have marked differences in RNA turnover. E. coli and Salmonella degrade RNA through internal endonucleolytic and 3'-->5' exonucleolytic cleavage that appears to allow transient accumulation of mRNA 3' UTR cleavage fragments that contain stabilizing 3' structures. In contrast, B. subtilis and S. aureus are able to exonucleolytically attack internally cleaved RNA from both the 5' and 3' ends, efficiently degrading mRNA 3' UTR fragments. Here, we propose that the lack of 5'-->3' exoribonuclease activity in Gammaproteobacteria has allowed the accumulation of mRNA 3' UTR ends as the "default" setting. This in turn may have provided a larger pool of unconstrained RNA sequences that has fueled the expansion of Hfq function and small RNA (sRNA) regulation in E. coli and Salmonella. Conversely, the exoribonuclease RNase J may be a significant barrier to the evolution of 3' UTR sRNAs in B. subtilis and S. aureus that has limited the pool of RNA ligands available to Hfq and other sRNA chaperones, depreciating their function in these model Firmicutes.},

note = {2150-7511 (Electronic) 

Journal Article},

keywords = {ROMBY, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Safe and easy in vitro evaluation of tmRNA-SmpB-mediated trans-translation from ESKAPE pathogenic bacteria},

author = {M Thepaut and R Campos-Silva and E Renard and F Barloy-Hubler and E Ennifar and D Boujard and R Gillet},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=34353925},

doi = {10.1261/rna.078773.121},

isbn = {34353925},

year  = {2021},

date = {2021-01-01},

journal = {Rna},

abstract = {In bacteria, trans-translation is the major quality control system for rescuing stalled ribosomes. It is mediated by tmRNA, a hybrid RNA with properties of both a tRNA and a mRNA, and the small protein SmpB. Because trans-translation is absent in eukaryotes but necessary for bacterial fitness or survival, it is a promising target for the development of novel antibiotics. To facilitate screening of chemical libraries, various reliable in vitro and in vivo systems have been created for assessing trans-translational activity. However, the aim of the current work was to permit the safe and easy in vitro evaluation of trans-translation from pathogenic bacteria, which are obviously the ones we should be targeting. Based on green fluorescent protein (GFP) reassembly during active trans-translation, we have created a cell-free assay adapted to the rapid evaluation of trans-translation in ESKAPE bacteria, with 24 different possible combinations. It can be used for easy high-throughput screening of chemical compounds as well as for exploring the mechanism of trans-translation in these pathogens.},

note = {1469-9001 (Electronic) 

1355-8382 (Linking) 

Journal Article},

keywords = {ENNIFAR, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Bacterial translation machinery for deliberate mistranslation of the genetic code},

author = {O Vargas-Rodriguez and A H Badran and K S Hoffman and M Chen and A Crnkovic and Y Ding and J R Krieger and E Westhof and D Soll and S Melnikov},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=34413202},

doi = {10.1073/pnas.2110797118},

isbn = {34413202},

year  = {2021},

date = {2021-01-01},

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

volume = {118},

number = {35},

abstract = {Inaccurate expression of the genetic code, also known as mistranslation, is an emerging paradigm in microbial studies. Growing evidence suggests that many microbial pathogens can deliberately mistranslate their genetic code to help invade a host or evade host immune responses. However, discovering different capacities for deliberate mistranslation remains a challenge because each group of pathogens typically employs a unique mistranslation mechanism. In this study, we address this problem by studying duplicated genes of aminoacyl-transfer RNA (tRNA) synthetases. Using bacterial prolyl-tRNA synthetase (ProRS) genes as an example, we identify an anomalous ProRS isoform, ProRSx, and a corresponding tRNA, tRNA(ProA), that are predominately found in plant pathogens from Streptomyces species. We then show that tRNA(ProA) has an unusual hybrid structure that allows this tRNA to mistranslate alanine codons as proline. Finally, we provide biochemical, genetic, and mass spectrometric evidence that cells which express ProRSx and tRNA(ProA) can translate GCU alanine codons as both alanine and proline. This dual use of alanine codons creates a hidden proteome diversity due to stochastic Ala-->Pro mutations in protein sequences. Thus, we show that important plant pathogens are equipped with a tool to alter the identity of their sense codons. This finding reveals the initial example of a natural tRNA synthetase/tRNA pair for dedicated mistranslation of sense codons.},

note = {1091-6490 (Electronic) 

0027-8424 (Linking) 

Journal Article},

keywords = {Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{Vilimova2021,

title = {Cis regulation within a cluster of viral microRNAs},

author = {M Vilimova and M Contrant and R Randrianjafy and P Dumas and E Elbasani and P M Ojala and S Pfeffer and A Fender},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=34417603},

doi = {10.1093/nar/gkab806},

isbn = {34417603},

year  = {2021},

date = {2021-01-01},

journal = {Nucleic Acids Res},

abstract = {MicroRNAs (miRNAs) are small regulatory RNAs involved in virtually all biological processes. Although many of them are co-expressed from clusters, little is known regarding the impact of this organization on the regulation of their accumulation. In this study, we set to decipher a regulatory mechanism controlling the expression of the ten clustered pre-miRNAs from Kaposi's sarcoma associated herpesvirus (KSHV). We measured in vitro the efficiency of cleavage of each individual pre-miRNA by the Microprocessor and found that pre-miR-K1 and -K3 were the most efficiently cleaved pre-miRNAs. A mutational analysis showed that, in addition to producing mature miRNAs, they are also important for the optimal expression of the whole set of miRNAs. We showed that this feature depends on the presence of a canonical pre-miRNA at this location since we could functionally replace pre-miR-K1 by a heterologous pre-miRNA. Further in vitro processing analysis suggests that the two stem-loops act in cis and that the cluster is cleaved in a sequential manner. Finally, we exploited this characteristic of the cluster to inhibit the expression of the whole set of miRNAs by targeting the pre-miR-K1 with LNA-based antisense oligonucleotides in cells either expressing a synthetic construct or latently infected with KSHV.},

note = {1362-4962 (Electronic) 

0305-1048 (Linking) 

Journal Article},

keywords = {PFEFFER, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {RNA Modifications in Pathogenic Bacteria: Impact on Host Adaptation and Virulence},

author = {L Antoine and R Bahena-Ceron and H Devi Bunwaree and M Gobry and V Loegler and P Romby and S Marzi},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=34440299},

doi = {10.3390/genes12081125},

isbn = {34440299},

year  = {2021},

date = {2021-01-01},

journal = {Genes (Basel)},

volume = {12},

number = {8},

abstract = {RNA modifications are involved in numerous biological processes and are present in all RNA classes. These modifications can be constitutive or modulated in response to adaptive processes. RNA modifications play multiple functions since they can impact RNA base-pairings, recognition by proteins, decoding, as well as RNA structure and stability. However, their roles in stress, environmental adaptation and during infections caused by pathogenic bacteria have just started to be appreciated. With the development of modern technologies in mass spectrometry and deep sequencing, recent examples of modifications regulating host-pathogen interactions have been demonstrated. They show how RNA modifications can regulate immune responses, antibiotic resistance, expression of virulence genes, and bacterial persistence. Here, we illustrate some of these findings, and highlight the strategies used to characterize RNA modifications, and their potential for new therapeutic applications.},

note = {2073-4425 (Electronic) 

2073-4425 (Linking) 

Journal Article 

Review},

keywords = {ROMBY, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{Welker2021,

title = {Importance of Viral Late Domains in Budding and Release of Enveloped RNA Viruses},

author = {L Welker and J C Paillart and S Bernacchi},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=34452424},

doi = {10.3390/v13081559},

isbn = {34452424},

year  = {2021},

date = {2021-01-01},

urldate = {2021-01-01},

journal = {Viruses},

volume = {13},

number = {8},

pages = {1559},

abstract = {Late assembly (L) domains are conserved sequences that are necessary for the late steps of viral replication, acting like cellular adaptors to engage the ESCRT membrane fission machinery that promote virion release. These short sequences, whose mutation or deletion produce the accumulation of immature virions at the plasma membrane, were firstly identified within retroviral Gag precursors, and in a further step, also in structural proteins of many other enveloped RNA viruses including arenaviruses, filoviruses, rhabdoviruses, reoviruses, and paramyxoviruses. Three classes of L domains have been identified thus far (PT/SAP, YPXnL/LXXLF, and PPxY), even if it has recently been suggested that other motifs could act as L domains. Here, we summarize the current state of knowledge of the different types of L domains and their cellular partners in the budding events of RNA viruses, with a particular focus on retroviruses.},

note = {1999-4915 (Electronic) 

1999-4915 (Linking) 

Journal Article 

Review},

keywords = {PAILLART, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Antibacterial activity of a dual peptide targeting the Escherichia coli sliding clamp and the ribosome},

author = {C Andre and F Veillard and P Wolff and A M Lobstein and G Compain and C Monsarrat and J M Reichhart and D Y Burnouf and G Guichard and J E Wagner},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=34459830},

doi = {10.1039/d1cb90020j},

isbn = {34459830},

year  = {2021},

date = {2021-01-01},

journal = {RSC Chem Biol},

volume = {2},

number = {4},

pages = {1296},

abstract = {[This corrects the article DOI: 10.1039/D0CB00060D.].},

note = {2633-0679 (Electronic) 

2633-0679 (Linking) 

Published Erratum},

keywords = {ARN-MS, ENNIFAR, reichhart, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Identification of host tRNAs preferentially recognized by the Plasmodium surface protein tRip},

author = {M Cela and A Theobald-Dietrich and J Rudinger-Thirion and P Wolff and R Geslain and M Frugier},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=34530443},

doi = {10.1093/nar/gkab769},

isbn = {34530443},

year  = {2021},

date = {2021-01-01},

journal = {Nucleic Acids Res},

abstract = {Malaria is a life-threatening and devastating parasitic disease. Our previous work showed that parasite development requires the import of exogenous transfer RNAs (tRNAs), which represents a novel and unique form of host-pathogen interaction, as well as a potentially druggable target. This import is mediated by tRip (tRNA import protein), a membrane protein located on the parasite surface. tRip displays an extracellular domain homologous to the well-characterized OB-fold tRNA-binding domain, a structural motif known to indiscriminately interact with tRNAs. We used MIST (Microarray Identification of Shifted tRNAs), a previously established in vitro approach, to systematically assess the specificity of complexes between native Homo sapiens tRNAs and recombinant Plasmodium falciparum tRip. We demonstrate that tRip unexpectedly binds to host tRNAs with a wide range of affinities, suggesting that only a small subset of human tRNAs is preferentially imported into the parasite. In particular, we show with in vitro transcribed constructs that tRip does not bind specific tRNAs solely based on their primary sequence, hinting that post-transcriptional modifications modulate the formation of our host/parasite molecular complex. Finally, we discuss the potential utilization of the most efficient tRip ligands for the translation of the parasite's genetic information.},

note = {1362-4962 (Electronic) 

0305-1048 (Linking) 

Journal Article},

keywords = {ARN-MS, FRUGIER, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Chemical and Enzymatic Probing of Viral RNAs: From Infancy to Maturity and Beyond},

author = {O Gilmer and E Quignon and A C Jousset and J C Paillart and R Marquet and V Vivet-Boudou},

url = {https://www.mdpi.com/1999-4915/13/10/1894},

doi = {v13101894},

year  = {2021},

date = {2021-01-01},

urldate = {2021-01-01},

journal = {Viruses},

volume = {13},

number = {10},

pages = {1894},

abstract = {RNA molecules are key players in a variety of biological events, and this is particularly true for viral RNAs. To better understand the replication of those pathogens and try to block them, special attention has been paid to the structure of their RNAs. Methods to probe RNA structures have been developed since the 1960s; even if they have evolved over the years, they are still in use today and provide useful information on the folding of RNA molecules, including viral RNAs. The aim of this review is to offer a historical perspective on the structural probing methods used to decipher RNA structures before the development of the selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) methodology and to show how they have influenced the current probing techniques. Actually, these technological breakthroughs, which involved advanced detection methods, were made possible thanks to the development of next-generation sequencing (NGS) but also to the previous works accumulated in the field of structural RNA biology. Finally, we will also discuss how high-throughput SHAPE (hSHAPE) paved the way for the development of sophisticated RNA structural techniques.},

keywords = {Capillary electrophoresis, chemical probe, enzymatic probe, high-throughput sequencing, MARQUET, mutational profiling, PAILLART, RNA, SHAPE, structure, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Binding of the RNA Chaperone Hfq on Target mRNAs Promotes the Small RNA RyhB-Induced Degradation in Escherichia coli},

author = {D. Lalaouna and K. Prévost and S. Park and T. Chénard and M - P. Bouchard and M - P. Caron and C. K. Vanderpool and J. Fei and E. Massé},

url = {https://www.mdpi.com/2311-553X/7/4/64},

doi = {10.3390/ncrna7040064},

year  = {2021},

date = {2021-01-01},

journal = {Non-Coding RNA},

volume = {7},

number = {4},

pages = {64},

abstract = {Many RNA-RNA interactions depend on molecular chaperones to form and remain stable in living cells. A prime example is the RNA chaperone Hfq, which is a critical effector involved in regulatory interactions between small RNAs (sRNAs) and cognate target mRNAs in Enterobacteriaceae. While there is a great deal of in vitro biochemical evidence supporting the model that Hfq enhances rates or affinities of sRNA:mRNA interactions, there is little corroborating in vivo evidence. Here we used in vivo tools including reporter genes, co-purification assays, and super-resolution microscopy to analyze the role of Hfq in RyhB-mediated regulation, and we found that Hfq is often unnecessary for efficient RyhB:mRNA complex formation in vivo. Remarkably, our data suggest that a primary function of Hfq is to promote RyhB-induced cleavage of mRNA targets by RNase E. Moreover, our work indicates that Hfq plays a more limited role in dictating regulatory outcomes following sRNAs RybB and DsrA complex formation with specific target mRNAs. Our investigation helps evaluate the roles played by Hfq in some RNA-mediated regulation.},

keywords = {ROMBY, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Real-time tracking of root hair nucleus morphodynamics using a microfluidic approach},

author = {G. Singh and D. Pereira and S. Baudrey and E. Hoffmann and M. Ryckelynck and A. Asnacios and M. E. Chaboute},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=34562320},

doi = {10.1111/tpj.15511},

isbn = {34562320},

year  = {2021},

date = {2021-01-01},

urldate = {2021-01-01},

journal = {Plant J},

volume = {108},

issue = {2},

pages = {303-313},

abstract = {Root hairs (RHs) are tubular extensions of root epidermal cells that favour nutrient uptake and microbe interactions. RH shows a fast apical growth, constituting a unique single cell model system to analyse cellular morphodynamics. In this context, live cell imaging using microfluidics recently developed to analyze root development is appealing, but high-resolution imaging is still lacking to study accurate spatiotemporal morphodynamics of organelles. Here, we provide a powerful coverslip based microfluidic device (CMD) which enables us to capture high resolution confocal imaging of Arabidopsis RH development with real-time monitoring of nuclear movement and shape changes. To validate the setup, we confirmed the typical RH growth rates and the mean nuclear positioning previously reported with classical methods. Moreover, in order to illustrate the possibilities offered by the CMD, we have compared the real-time variations in the circularity, area, and aspect ratio of nuclei moving in growing and mature RH. Interestingly, we observed higher aspect ratios in the nuclei of mature RH, correlating with higher speeds of nuclear migration. This observation opens the way for further investigations of the effect of mechanical constraints on nuclear shape changes during RH growth and nuclear migration and its role in RH and plant development.},

note = {1365-313X (Electronic) 

0960-7412 (Linking) 

Journal Article},

keywords = {RYCKELYNCK, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {CCA-addition in the cold: Structural characterization of the psychrophilic CCA-adding enzyme from the permafrost bacterium Planococcus halocryophilus},

author = {R. De Wijn and K. Rollet and F. G.M.Ernst and K. Wellner and H. Betat and M. Mörl and M. Sauter},

url = {https://www.sciencedirect.com/science/article/pii/S2001037021004402?via%3Dihub},

doi = {10.1016/j.csbj.2021.10.018},

isbn = {ISBN/2001-0370},

year  = {2021},

date = {2021-01-01},

journal = {Computational and Structural Biotechnology Journal},

volume = {19},

pages = {5845-5855},

abstract = {CCA-adding enzymes are highly specific RNA polymerases that add and maintain the sequence C-C-A at tRNA 3ﾑ-ends. Recently, we could reveal that cold adaptation of such a polymerase is not only achieved at the expense of enzyme stability, but also at the cost of polymerization fidelity. Enzymes from psychrophilic organisms usually show an increased structural flexibility to enable catalysis at low temperatures. Here, polymerases face a dilemma, as there is a discrepancy between the need for a tightly controlled flexibility during polymerization and an increased flexibility as strategy for cold adaptation. Based on structural and biochemical analyses, we contribute to clarify the cold adaptation strategy of the psychrophilic CCA-adding enzyme from Planococcus halocryophilus, a gram-positive bacterium thriving in the arctic permafrost at low temperatures down to −15 °C. A comparison with the closely related enzyme from the thermophilic bacterium Geobacillus stearothermophilus reveals several features of cold adaptation - a significantly reduced amount of alpha-helical elements in the C-terminal tRNA-binding region and a structural adaptation in one of the highly conserved catalytic core motifs located in the N-terminal catalytic core of the enzyme},

keywords = {CCA-adding enzyme, Cold adaptation, FRUGIER, Psychrophilic protein, Psychrophilic RNA polymerase, SAXS, tRNA, Unité ARN, X-ray crystallography},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Short-Range Imbalances in the AMBER Lennard-Jones Potential for (Deoxy)Ribose.Nucleobase Lone-Pair.pi Contacts in Nucleic Acids},

author = {K. Mrazikova and J. Sponer and V. Mlynsky and P. Auffinger and H. Kruse},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=34738826},

doi = {10.1021/acs.jcim.1c01047},

isbn = {34738826},

year  = {2021},

date = {2021-01-01},

urldate = {2021-01-01},

journal = {J Chem Inf Model},

volume = {61},

number = {11},

pages = {5644-5657},

abstract = {The lone-pair.pi (lp.pi) (deoxy)ribose.nucleobase stacking is a recurring interaction in Z-DNA and RNAs that is characterized by sub-van der Waals lp.pi contacts (<3.0 A). It is a part of the structural signature of CpG Z-step motifs in Z-DNA and r(UNCG) tetraloops that are known to behave poorly in molecular dynamics (MD) simulations. Although the exact origin of the MD simulation issues remains unclear, a significant part of the problem might be due to an imbalanced description of nonbonded interactions, including the characteristic lp.pi stacking. To gain insights into the links between lp.pi stacking and MD, we present an in-depth comparison between accurate large-basis-set double-hybrid Kohn-Sham density functional theory calculations DSD-BLYP-D3/ma-def2-QZVPP (DHDF-D3) and data obtained with the nonbonded potential of the AMBER force field (AFF) for NpN Z-steps (N = G, A, C, and U). Among other differences, we found that the AFF overestimates the DHDF-D3 lp.pi distances by approximately 0.1-0.2 A, while the deviation between the DHDF-D3 and AFF descriptions sharply increases in the short-range region of the interaction. Based on atom-in-molecule polarizabilities and symmetry-adapted perturbation theory analysis, we inferred that the DHDF-D3 versus AFF differences partly originate in identical nucleobase carbon atom Lennard-Jones (LJ) parameters despite the presence/absence of connected electron-withdrawing groups that lead to different effective volumes or vdW radii. Thus, to precisely model the very short CpG lp.pi contact distances, we recommend revision of the nucleobase atom LJ parameters. Additionally, we suggest that the large discrepancy between DHDF-D3 and AFF short-range repulsive part of the interaction energy potential may significantly contribute to the poor performances of MD simulations of nucleic acid systems containing Z-steps. Understanding where, and if possible why, the point-charge-type effective potentials reach their limits is vital for developing next-generation FFs and for addressing specific issues in contemporary MD simulations.},

note = {1549-960X (Electronic) 

1549-9596 (Linking) 

Journal Article},

keywords = {ENNIFAR, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@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  = {2021},

date = {2021-01-01},

journal = {Brain Dev},

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}

}

@article{nokey,

title = {Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions},

author = {F. Carrascoza and M. Antczak and Z. Miao and E. Westhof and M. Szachniuk},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=34819324},

doi = {10.1261/rna.078685.121},

isbn = {34819324},

year  = {2021},

date = {2021-01-01},

journal = {Rna},

abstract = {In silico prediction is a well-established approach to derive a general shape of an RNA molecule based on its sequence or secondary structure. This paper reports an analysis of the stereochemical quality of the RNA three-dimensional models predicted using dedicated computer programs. The stereochemistry of 1,052 RNA 3D structures, including 1,030 models predicted by fully automated and human-guided approaches within 22 RNA-Puzzles challenges and reference structures, is analysed. The evaluation is based on standards of RNA stereochemistry that the Protein Data Bank requires from deposited experimental structures. Deviations from standard bond lengths and angles, planarity or chirality are quantified. A reduction in the number of such deviations should help in the improvement of RNA 3D structure modelling approaches.},

note = {1469-9001 (Electronic) 

1355-8382 (Linking) 

Journal Article},

keywords = {Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Iterative Structure-Based Optimization of Short Peptides Targeting the Bacterial Sliding Clamp},

author = {C. Monsarrat and G. Compain and C. Andre and S. Engilberge and I. Martiel and V. Olieric and P. Wolff and K. Brillet and M. Landolfo and C. Silva da Veiga and J. Wagner and G. Guichard and D. Y. Burnouf},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=34806883},

doi = {10.1021/acs.jmedchem.1c00918},

isbn = {34806883},

year  = {2021},

date = {2021-01-01},

journal = {J Med Chem},

abstract = {The bacterial DNA sliding clamp (SC), or replication processivity factor, is a promising target for the development of novel antibiotics. We report a structure-activity relationship study of a new series of peptides interacting within the Escherichia coli SC ((Ec)SC) binding pocket. Various modifications were explored including N-alkylation of the peptide bonds, extension of the N-terminal moiety, and introduction of hydrophobic and constrained residues at the C-terminus. In each category, single modifications were identified that increased affinity to (Ec)SC. A combination of such modifications yielded in several cases to a substantially increased affinity compared to the parent peptides with Kd in the range of 30-80 nM. X-ray structure analysis of 11 peptide/(Ec)SC co-crystals revealed new interactions at the peptide-protein interface (i.e., stacking interactions, hydrogen bonds, and hydrophobic contacts) that can account for the improved binding. Several compounds among the best binders were also found to be more effective in inhibiting SC-dependent DNA synthesis.},

note = {1520-4804 (Electronic) 

0022-2623 (Linking) 

Journal Article},

keywords = {ARN-MS, ENNIFAR, Unité ARN},

pubstate = {published},

tppubtype = {article}

}