NMR structure of the Aquifex aeolicus tmRNA pseudoknot PK1: new insights into the recoding event of the ribosomal trans-translation

The transfer-messenger RNA (tmRNA) pseudoknot PK1 is essential for bacterial trans-translation, a ribosomal rescue mechanism. We report the solution structure of PK1 from Aquifex aeolicus, which despite an unprecedented small number of nucleotides and thus an unprecented compact size, displays a very high thermal stability. Several unusual structural features account for these properties and indicate that PK1 belongs to the class of ribosomal frameshift pseudoknots. This suggests a similarity between the mechanism of programmed ribosomal frameshifting and trans-translation

Terminal Base Pairs of Oligodeoxynucleotides: Imino Proton Exchange and Fraying

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The tRNA-like domains of E coli and A.aeolicus transfer-messenger RNA: structural and functional studies.

International audienceTransfer-messenger RNA (tmRNA, 10Sa RNA or ssrA) acts to rescue stalled bacterial ribosomes while encoding a peptide tag added trans-translationally to the nascent peptide, targeting it for proteolysis. The understanding at molecular level of this ubiquitous quality control system in eubacteria requires structural information. Here, we describe the purification and structural analysis of a functional fragment of both Aquifex aeolicus and Escherichia coli tmRNA, recapitulating their tRNA-like domain, which were expressed in vivo from synthetic genes. Both recombinant RNA are correctly processed at both 5' and 3' ends and are produced in quantities suitable for structural analysis by NMR and/or X-ray crystallography. The sequence and solution structure of the tRNA-like domains were analysed by various methods including structural mapping with chemical and enzymatic probes and 2D NMR spectroscopy. The minimalist RNAs contain two post-transcriptional base modifications, 5-methyluridine and pseudouridine, as the full-length tmRNA. Both RNAs fold into three stems, a D-analogue, a T-loop and a GAAA tetra-loop. 2D NMR analysis of the imino proton resonances of both RNAs allowed the assignment of the three stems and of a number of tertiary interactions. It shows the existence of interactions between the TPsiC-loop and the D-analogue, exhibiting a number of similarities and also differences with the canonical tRNA fold, indicating that RNA tertiary interactions can be modulated according to the sequence and secondary structure contexts. Furthermore, the E.coli minimalist RNA is aminoacylatable with alanine with a catalytic efficiency an order of magnitude higher than that for full-length tmRNA

Capsicumicine, a new bioinspired peptide from red peppers prevents staphylococcal biofilm in vitro and in vivo via a matrix anti-assembly mechanism of action

Staphylococci are pathogenic biofilm-forming bacteria and a source of multidrug resistance and/or tolerance causing a broad spectrum of infections. These bacteria are enclosed in a matrix that allows them to colonize medical devices, such as catheters and tissues, and that protects against antibiotics and immune systems. Advances in antibiofilm strategies for targeting this matrix are therefore extremely relevant. Here, we describe the development of the Capsicum pepper bioinspired peptide “capsicumicine.” By using microbiological, microscopic, and nuclear magnetic resonance (NMR) approaches, we demonstrate that capsicumicine strongly prevents methicillin-resistant Staphylococcus epidermidis biofilm via an extracellular “matrix anti-assembly” mechanism of action. The results were confirmed in vivo in a translational preclinical model that mimics medical device-related infection. Since capsicumicine is not cytotoxic, it is a promising candidate for complementary treatment of infectious diseases

Human centromeric satellite III cytosine-rich repeats (CCATT)n fold into the i-motif in vitro ; Solution structure of the d(mCCATTCCAUTCCUTTCC) monomer

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Human centromeric satellite III cytosine-rich repeats (CCATT)n fold into the i-motif in vitro ; Solution structure of the d(mCCATTCCAUTCCUTTCC) monomer

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La médiation par les élèves. Enjeux et perspectives pour la vie scolaire

International audienceLa prévention de la violence et la gestion des conflits sont actuellement au centre des préoccupations ministérielles comme des usagers du système éducatif.La médiation par les élèves : enjeux et perspectives pour la vie scolaire fait le point sur la médiation par les pairs, démarche placée sous le signe de la pacification des relations et qui fait intervenir les élèves pour la prévention des « petits conflits ».Elle porte une dimension éducative ambitieuse. Son enjeu est non seulement politique, éducatif et pédagogique, mais aussi professionnel pour les enseignants, les conseillers principaux d’éducation et, d’une façon générale, pour l’ensemble des acteurs des écoles et des établissements.Les auteures ont cherché à articuler des savoirs théoriques prenant en compte l’évolution du fonctionnement des établissements scolaires, en France et à l’étranger, et des fiches-outils, dans une démarche de formation des lecteurs. L’ambition est de conduire les élèves sur la voie de la responsabilisation et de l’autonomie et d’amener les personnels (dans leur dimension éducative) à envisager autrement la relation adulte-jeune.Le projet de la médiation ne vise donc pas seulement la pacification scolaire. Il se donne pour objectif de promouvoir la participation active de tous dans un double but de défense et de promotion des valeurs démocratiques qui demandent sans cesse à être confortées ou réaffirmées

Structure and Conversion Kinetics of a Bi-stable DNA i-motif: Broken Symmetry in the [d(5mCCTCC)]4 Tetramer

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Imino proton exchange and base-pair kinetics in the AMP-RNA aptamer complex 1 1Edited by I. Tinoco

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Self-organisation of an oligodeoxynucleotide containing the G- and C-rich stretches of the direct repeats of the human mitochondrial DNA.

Stretches of cytosines and guanosines have been shown in vitro to adopt non-canonical structures known as i-motifs and G-quartets, respectively. When combined, such sequences are expected to either retain their structure or form duplexes or triple helices. All these structures may occur in vivo whenever the sequence criteria are met. Such stretches are present in the circular genome of human mitochondria, as two 10 nucleotide-long perfect tandem direct repeats (DR1 and DR2). The DR1 and DR2 repeats are G-rich on the heavy strand and C-rich on the light strand. Previous results suggested that during replication, transient formation of a parallel GGC triple helix between the neo-synthesised G-rich DR1 and the double-stranded homologous DR2 could be involved in a rearrangement process leading to genome instability. In order to get structural insights into the interaction between the two repeats, we have studied by nuclear magnetic resonance (NMR) the assembly properties of a 24-mer oligodeoxyribonucleotide in which the C- and G-rich segments of the DRs are covalently tethered by a TTTT linker. We show here that this 24-mer self-associates into a triplex-containing symmetrical tetramer. The core of the structure is composed of anti-parallel Watson-Crick (WC) base pairs. Two additional strands are hydrogen-bonded to the Hoogsteen side of the Gs, thus forming CGC(+) triple helices, with G-rich ends folding into G-quartets. These results suggest that such structures could occur when the two DRs are put to close proximity in a biological context