A transcriptional-switch model for Slr1738-controlled gene expression in the cyanobacterium Synechocystis

<p>Abstract</p> <p>Background</p> <p>Protein-DNA interactions play a crucial role in the life of biological organisms in controlling transcription, regulation, as well as DNA recombination and repair. The deep understanding of these processes, which requires the atomic description of the interactions occurring between the proteins and their DNA partners is often limited by the absence of a 3D structure of such complexes.</p> <p>Results</p> <p>In this study, using a method combining sequence homology, structural analogy modeling and biochemical data, we first build the 3D structure of the complex between the poorly-characterized PerR-like regulator Slr1738 and its target DNA, which controls the defences against metal and oxidative stresses in <it>Synechocystis</it>. In a second step, we propose an expanded version of the Slr1738-DNA structure, which accommodates the DNA binding of Slr1738 multimers, a feature likely operating in the complex Slr1738-mediated regulation of stress responses. Finally, in agreement with experimental data we present a 3D-structure of the Slr1738-DNA complex resulting from the binding of multimers of the FUR-like regulator onto its target DNA that possesses internal repeats.</p> <p>Conclusion</p> <p>Using a combination of different types of data, we build and validate a relevant model of the tridimensional structure of a biologically important protein-DNA complex. Then, based on published observations, we propose more elaborated multimeric models that may be biologically important to understand molecular mechanisms.</p

Lesion-induced DNA weak structural changes detected by pulsed EPR spectroscopy combined with site-directed spin labelling

Double electron-electron resonance (DEER) was applied to determine nanometre spin–spin distances on DNA duplexes that contain selected structural alterations. The present approach to evaluate the structural features of DNA damages is thus related to the interspin distance changes, as well as to the flexibility of the overall structure deduced from the distance distribution. A set of site-directed nitroxide-labelled double-stranded DNA fragments containing defined lesions, namely an 8-oxoguanine, an abasic site or abasic site analogues, a nick, a gap and a bulge structure were prepared and then analysed by the DEER spectroscopic technique. New insights into the application of 4-pulse DEER sequence are also provided, in particular with respect to the spin probes’ positions and the rigidity of selected systems. The lesion-induced conformational changes observed, which were supported by molecular dynamics studies, confirm the results obtained by other, more conventional, spectroscopic techniques. Thus, the experimental approaches described herein provide an efficient method for probing lesion-induced structural changes of nucleic acids

Specificity of LTR DNA recognition by a peptide mimicking the HIV-1 integrase α4 helix

HIV-1 integrase integrates retroviral DNA through 3′-processing and strand transfer reactions in the presence of a divalent cation (Mg2+ or Mn2+). The α4 helix exposed at the catalytic core surface is essential to the specific recognition of viral DNA. To define group determinants of recognition, we used a model composed of a peptide analogue of the α4 helix, oligonucleotides mimicking processed and unprocessed U5 LTR end and 5 mM Mg2+. Circular dichroism, fluorescence and NMR experiments confirmed the implication of the α4 helix polar/charged face in specific and non-specific bindings to LTR ends. The specific binding requires unprocessed LTR ends—i.e. an unaltered 3′-processing site CA↓GT3′—and is reinforced by Mg2+ (Kd decreases from 2 to 0.8 nM). The latter likely interacts with the ApG and GpT3′ steps of the 3′-processing site. With deletion of GT3′, only persists non-specific binding (Kd of 100 μM). Proton chemical shift deviations showed that specific binding need conserved amino acids in the α4 helix and conserved nucleotide bases and backbone groups at LTR ends. We suggest a conserved recognition mechanism based on both direct and indirect readout and which is subject to evolutionary pressure

Cycle biologique du sporozoaire Klossiella mabokensis (Adeleidea) parasite de Murid\ue9s africains

Volume: 135Start Page: 721End Page: 74

\uc9tude morphologique des Coccidies (Adeleidea) Klossiella killicki n. sp. Chez des Microchiropt\ue8res africains et Klossiella tejerai Scorza, 1957, chez un Marsupial sud-am\ue9ricain

Volume: 284Start Page: 83End Page: 8

Ultrastructure des gamétocytes de cinq espèces d&#039;&lt;i&gt;Haemoproteus&lt;/i&gt;, hémosporidie de gecko et d&#039;agames

L’ultrastructure des gamétocytes de cinq espèces d’Haemoproteus de Reptiles est comparée. Ces espèces sont : H. edomensis parasite d’Agama stellio, capturé à l’Est de Jérusalem ; H. mackerrasi chez Heteronotia binoei et H. oedurae chez Oedura castelnaui, ces deux hôtes venant du Nord-Est de l’Australie ; H. ptyodactyli chez Ptyodactylus hasselquistii de la vallée du Jourdain et H. tarentolae chez Tarentola mauritanica du Sud-Ouest de la France. Par leurs organites cytoplasmiques et la présence d’une enveloppe tri-membranaire, tous les gamétocytes présentent une organisation proche de celle déjà décrite chez les Haemoproteus et plusieurs Plasmodium de Reptiles et d’Oiseaux. En même temps, chaque espèce présente des structures caractéristiques : un corps trapézoïde chez H. edomensis ; un espace central transparent aux électrons chez H. tarentolae et, à la différence des espèces déjà décrites, de nombreux corps osmiophiles : petits et allongés chez H. oedurae, très petits et ronds chez H. ptyodactyli, grands et ronds chez H. tarentolae. Chez ces trois dernières espèces, un noyau lobé est présent dans les présumés microgamétocytes.The fine structure of gametocytes of five species of Haemoproteus from reptilian hosts was compared. The species were: H. edomensis from Agama stellio, collected East of Jerusalem; H. mackerrasi from Heteronotia binoei and H. oedurae from Oedura castelnaui, both from Northeast Australia; H. ptyodactyli from Ptyodactylus hasselquistii from the Jordan valley, and H. tarentolae from Tarentola mauritanica of Southwest France. All gametocytes showed close conformity with the previously studied reptilian and avian species of Haemoproteus as well as with the several known species of Plasmodium of reptiles and birds, in their being bound by a three-layered limiting membrane system, and in their cytoplasmic organization. At the same time, each species showed distinguishable characteristic configurations: a trapezoid organelle in H. edomensis, a large electron-lucent central space in H. tarentolae and, unlike the previous studied species, osmiophilic bodies were found: small and elongated in H. oedurae, very small and round in H. ptyodactyli, large and round in H. tarentolae. The presumed microgametocytes of these last three species exhibited also a lobated nucleus.</p

Fine structure of gametocytes in five species of Haemoproteus (Haemosporidia) from geckos and agamid lizards

Paperna, Ilan, Boulard, Yves (2000): Fine structure of gametocytes in five species of Haemoproteus (Haemosporidia) from geckos and agamid lizards. Zoosystema 22 (3): 443-457, DOI: http://doi.org/10.5281/zenodo.540053

Pertinence du dosage de la C réactive protéine dans un service d'urgences adultes

PARIS6-Bibl.Pitié-Salpêtrie (751132101) / SudocPARIS-BIUM (751062103) / SudocSudocFranceF

The hepatitis C virus RNA-dependent RNA polymerase directs incoming nucleotides to its active site through magnesium-dependent dynamics within its F motif

International audienceRNA viruses synthesize new genomes in the infected host thanks to dedicated, virally-encoded RNA-dependent RNA polymerases (RdRps). As such, these enzymes are prime targets for antiviral therapy, as has recently been demonstrated for hepatitis C virus (HCV). However, peculiarities in the architecture and dynamics of RdRps raise fundamental questions about access to their active site during RNA polymerization. Here, we used molecular modelling and molecular dynamics simulations, starting from the available crystal structures of HCV NS5B in ternary complex with template-primer duplexes and nucleotides, to address the question of ribonucleotide entry into the active site of viral RdRp. Tracing the possible passage of incoming UTP or GTP through the RdRp-specific entry tunnel, we found two successive checkpoints that regulate nucleotide traffic to the active site. We observed that a magnesium-bound nucleotide first binds next to the tunnel entry, and interactions with the triphosphate moiety orient it such that its base moiety enters first. Dynamics of the RdRp motifs F1 + F3 then allow the nucleotide to interrogate the RNA template base prior to nucleotide insertion into the active site. These dynamics are finely regulated by a second magnesium dication, thus coordinating the entry of a magnesium-bound nucleotide with shuttling of the second magnesium necessary for the two-metal ion catalysis. The findings of our work suggest that some at least of these features are general to viral RdRps and provide further details on the original nucleotide selection mechanism operating in RdRps of RNA viruses