Genomic analysis of the regulatory elements and links with intrinsic DNA structural properties in the shrunken genome of Buchnera

International audienceBackground Buchnera aphidicola is an obligate symbiotic bacterium, associated with most of the aphididae, whose genome has drastically shrunk during intracellular evolution. Gene regulation in Buchnera has been a matter of controversy in recent years as the combination of genomic information with the experimental results has been contradictory, refuting or arguing in favour of a functional and responsive transcription regulation in Buchnera.The goal of this study was to describe the gene transcription regulation capabilities of Buchnera based on the inventory of cis- and trans-regulators encoded in the genomes of five strains from different aphids (Acyrthosiphon pisum, Schizaphis graminum, Baizongia pistacea, Cinara cedri and Cinara tujafilina), as well as on the characterisation of some intrinsic structural properties of the DNA molecule in these bacteria.ResultsInteraction graph analysis shows that gene neighbourhoods are conserved between E. coli and Buchnera in structures called transcriptons, interactons and metabolons, indicating that selective pressures have acted on the evolution of transcriptional, protein-protein interaction and metabolic networks in Buchnera. The transcriptional regulatory network in Buchnera is composed of a few general DNA-topological regulators (Nucleoid Associated Proteins and topoisomerases), with the quasi-absence of any specific ones (except for multifunctional enzymes with a known gene expression regulatory role in Escherichia coli, such as AlaS, PepA and BolA, and the uncharacterized hypothetical regulators YchA and YrbA). The relative positioning of regulatory genes along the chromosome of Buchnera seems to have conserved its ancestral state, despite the genome erosion. Sigma-70 promoters with canonical thermodynamic sequence profiles were detected upstream of about 94% of the CDS of Buchnera in the different aphids. Based on Stress-Induced Duplex Destabilization (SIDD) measurements, unstable σ70 promoters were found specifically associated with the regulator and transporter genes.ConclusionsThis genomic analysis provides supporting evidence of a selection of functional regulatory structures and it has enabled us to propose hypotheses concerning possible links between these regulatory elements and the DNA-topology (i.e., supercoiling, curvature, flexibility and base-pair stability) in the regulation of gene expression in the shrunken genome of Buchnera

Negative Regulation of NKG2D Expression by IL-4 in Memory CD8 T Cells

International audienceIL-4 is one of the main cytokines produced during Th2-inducing pathologies. This cytokine has been shown to affect a number of immune processes such as Th differentiation and innate immune responses. However, the impact of IL-4 on CD8 T cell responses remains unclear. In this study, we analyzed the effects of IL-4 on global gene expression profiles of Ag-induced memory CD8 T cells in the mouse. Gene ontology analysis of this signature revealed that IL-4 regulated most importantly genes associated with immune responses. Moreover, this IL-4 signature overlapped with the set of genes preferentially expressed by memory CD8 T cells over naive CD8 T cells. In particular, IL-4 downregulated in vitro and in vivo in a STAT6-dependent manner the memory-specific expression of NKG2D, thereby increasing the activation threshold of memory CD8 T cells. Furthermore, IL-4 impaired activation of memory cells as well as their differentiation into effector cells. This phenomenon could have an important clinical relevance as patients affected by Th2 pathologies such as parasitic infections or atopic dermatitis often suffer from viral-induced complications possibly linked to inefficient CD8 T cell responses

Structure and dynamics of the operon map of Buchnera aphidicola sp. strain APS

<p>Abstract</p> <p>Background</p> <p>Gene expression regulation is still poorly documented in bacteria with highly reduced genomes. Understanding the evolution and mechanisms underlying the regulation of gene transcription in <it>Buchnera aphidicola</it>, the primary endosymbiont of aphids, is expected both to enhance our understanding of this nutritionally based association and to provide an intriguing case-study of the evolution of gene expression regulation in a reduced bacterial genome.</p> <p>Results</p> <p>A Bayesian predictor was defined to infer the <it>B. aphidicola </it>transcription units, which were further validated using transcriptomic data and RT-PCR experiments. The characteristics of <it>B. aphidicola </it>predicted transcription units (TUs) were analyzed in order to evaluate the impact of operon map organization on the regulation of gene transcription.</p> <p>On average, <it>B. aphidicola </it>TUs contain more genes than those of <it>E. coli</it>. The global layout of <it>B. aphidicola </it>operon map was mainly shaped by the big reduction and the rearrangements events, which occurred at the early stage of the symbiosis. Our analysis suggests that this operon map may evolve further only by small reorganizations around the frontiers of <it>B. aphidicola </it>TUs, through promoter and/or terminator sequence modifications and/or by pseudogenization events. We also found that the need for specific transcription regulation exerts some pressure on gene conservation, but not on gene assembling in the operon map in <it>Buchnera</it>. Our analysis of the TUs spacing pointed out that a selection pressure is maintained on the length of the intergenic regions between divergent adjacent gene pairs.</p> <p>Conclusions</p> <p><it>B. aphidicola </it>can seemingly only evolve towards a more polycistronic operon map. This implies that gene transcription regulation is probably subject to weak selection pressure in <it>Buchnera </it>conserving operons composed of genes with unrelated functions.</p

Exploration et inférence du réseau de régulation de la transcription de la bactérie symbiotique intracellulaire à génome réduit Buchnera aphidicola

This thesis is a systemic study of the gene transcription regulation in Buchnera aphidicola, the intracellular obligatory symbiont of the peaaphid, Acyrthosiphon pisum. Several previous experimental studies showed that the bacterium provides to aphid the complementary nutrients absent from its diet, and that Buchnera adapts the supplying to the host demand. Nevertheless, the mechanisms underlying this regulation remain unknown. Our study is composed of four parts. The first one draws up an inventory of the transcription machinery of Buchnera. In the second part, we analyse the Buchnera dynamic genomic architecture, i.e. the organization and the evolution of its operon map. ln this context, we developed a Bayesian operon predictor (Dis Ter), adapted to the Buchnera model, which allowed us to propose a new Buchnera operon map. In the third part, we analysed the sequence-dependent structural properties of the bacterium genome. The results of theses three analyses, which fall within a bottom-up approach, allowed us to build a first mode! of Buchnera aphidicola transcription regulatory network. Finally, the last part followed a top-down modelling approach. We developed a new method for the inference of gene networks named IGOIM and using gene expression data as input data. IGOIM was tested and validated on simulated gene expression data.Cette thèse est une étude systémique de la régulation de la transcription des gènes de la bactérie Buchnera aphidicola vivant en symbiose intracellulaire obligatoire avec le puceron du pois, Acyrthosiphon pisum. Plusieurs études expérimentales antérieures sur ce modèle de symbiose attestent d'une part que la bactérie fournit à son hôte le complément nutritionnel qu'il ne trouve pas dans son alimentation, et d'autre part, que la bactérie adapte cette fourniture aux variations de la demande de son hôte, les mécanismes impliqués dans cette régulation demeurant relativement obscurs. Nous avons structuré notre analyse de la régulation de la transcription chez Buchnera en quatre parties. La première dresse l'inventaire de la machinerie transcriptionnelle de Buchnera. La deuxième partie analyse l'architecture génomique de Buchnera, i.e. l'organisation et l'évolution de sa carte opéronique. Pour cette étude, nous avons été amenés à développer une méthode bayésienne de prédiction d'opérons adaptée à Buchnera, ce qui nous a permis de proposer une nouvelle carte opéronique de la bactérie. La troisième partie porte sur les propriétés structurelles séquence-dépendantes du chromosome de Buchnera. Les résultats obtenus à l'Issue de cette approche ascendante, nous ont amené à construire un premier modèle de réseau de la régulation transcriptionnelle chez Buchnera. Enfin, la quatrième partie est un travail de modélisation suivant une approche descendante. Il s'agit du développement d'une méthode d'inférence de réseau de régulation à partir de données d'expression que nous avons appelée IGOIM. Cette méthode a été validée sur des jeux de données simulées et de la littérature

Exploring the regulatory network of Buchnera aphidicola: a case-study of genome evolution in a symbiotic context

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WATER STATUS AND STRESS-MEMORY FORMATION IN PHASEOLUS PLANTS WITH DIFFERENT DROUGHT RESISTANCE POTENTIAL.

The results of the investigations about the impact of repeated stress on the plant water status have been analysed by taking the literature information about some mechanisms, associated with the stress-memory formation and resistance of plants to drought. The concept of stress-memory existence as an ability of quick and adequate plant response to recurring stress exposure (it is stated that reaction of plants affected by repeated stress differs from the reaction of plants, exposed to stress factors for the first time) was experimentally demonstrated. It was established that beans plants of the species Phaseolus lunatus, L., variety ?Fetanisa?, Phaseolus acutifolius, Gray, variety ?Acutifolius 5? and Phaseolus vulgaris L., variety ?Nina?, which have been undergone a mild drought condition at phase \"first trifoliate leaf\" more easily supports repeated stress to the stage of \"flowering- pods formation\" as a result of the formation of stress memory - the ability to react appropriately to the unfavorable factor. The dependence of stress-memory formation on homeostatic water capacity in tissues and on the constitutive resistance of the genotype have been demonstrated. The self-regulation of water status by increasing water retention capacity and preserving turgescence are nonspecific mechanisms important for stress-memory formation and plant adaptation to fluctuating humidity conditions and water stress recurring over time