Computational prediction of the Crc regulon identifies genus-wide and species-specific targets of catabolite repression control in Pseudomonas bacteria

<p>Abstract</p> <p>Background</p> <p>Catabolite repression control (CRC) is an important global control system in <it>Pseudomonas </it>that fine tunes metabolism in order optimise growth and metabolism in a range of different environments. The mechanism of CRC in <it>Pseudomonas </it>spp. centres on the binding of a protein, Crc, to an A-rich motif on the 5' end of an mRNA resulting in translational down-regulation of target genes. Despite the identification of several Crc targets in <it>Pseudomonas </it>spp. the Crc regulon has remained largely unexplored.</p> <p>Results</p> <p>In order to predict direct targets of Crc, we used a bioinformatics approach based on detection of A-rich motifs near the initiation of translation of all protein-encoding genes in twelve fully sequenced <it>Pseudomonas </it>genomes. As expected, our data predict that genes related to the utilisation of less preferred nutrients, such as some carbohydrates, nitrogen sources and aromatic carbon compounds are targets of Crc. A general trend in this analysis is that the regulation of transporters is conserved across species whereas regulation of specific enzymatic steps or transcriptional activators are often conserved only within a species. Interestingly, some nucleoid associated proteins (NAPs) such as HU and IHF are predicted to be regulated by Crc. This finding indicates a possible role of Crc in indirect control over a subset of genes that depend on the DNA bending properties of NAPs for expression or repression. Finally, some virulence traits such as alginate and rhamnolipid production also appear to be regulated by Crc, which links nutritional status cues with the regulation of virulence traits.</p> <p>Conclusions</p> <p>Catabolite repression control regulates a broad spectrum of genes in <it>Pseudomonas</it>. Some targets are genus-wide and are typically related to central metabolism, whereas other targets are species-specific, or even unique to particular strains. Further study of these novel targets will enhance our understanding of how <it>Pseudomonas </it>bacteria integrate nutritional status cues with the regulation of traits that are of ecological, industrial and clinical importance.</p

Maternal effects shape the seed mycobiome in Quercus petraea

The tree seed mycobiome has received little attention despite its potential role in forest regeneration and health. The aim of the present study was to analyze the processes shaping the composition of seed fungal communities in natural forests as seeds transition from the mother plant to the ground for establishment. We used metabarcoding approaches and confocal microscopy to analyze the fungal communities of seeds collected in the canopy and on the ground in four natural populations of sessile oak (Quercus petraea). Ecological processes shaping the seed mycobiome were inferred using joint species distribution models. Fungi were present in seed internal tissues, including the embryo. The seed mycobiome differed among oak populations and trees within the same population. Its composition was largely influenced by the mother, with weak significant environmental influences. The models also revealed several probable interactions among fungal pathogens and mycoparasites. Our results demonstrate that maternal effects, environmental filtering and biotic interactions all shape the seed mycobiome of sessile oak. They provide a starting point for future research aimed at understanding how maternal genes and environments interact to control the vertical transmission of fungal species that could then influence seed dispersal and germination, and seedling recruitment.Peer reviewe

Defining composition and function of the rhizosphere microbiota of barley genotypes exposed to growth-limiting nitrogen supplies

The microbiota populating the rhizosphere, the interface between roots and soil, can modulate plant growth, development, and health. These microbial communities are not stochastically assembled from the surrounding soil, but their composition and putative function are controlled, at least partially, by the host plant. Here, we use the staple cereal barley as a model to gain novel insights into the impact of differential applications of nitrogen, a rate-limiting step for global crop production, on the host genetic control of the rhizosphere microbiota. Using a high-throughput amplicon sequencing survey, we determined that nitrogen availability for plant uptake is a factor promoting the selective enrichment of individual taxa in the rhizosphere of wild and domesticated barley genotypes. Shotgun sequencing and metagenome-assembled genomes revealed that this taxonomic diversification is mirrored by a functional specialization, manifested by the differential enrichment of multiple Gene Ontology terms, of the microbiota of plants exposed to nitrogen conditions limiting barley growth. Finally, a plant soil feedback experiment revealed that host control of the barley microbiota underpins the assembly of a phylogenetically diverse group of bacteria putatively required to sustain plant performance under nitrogen-limiting supplies. Taken together, our observations indicate that under nitrogen conditions limiting plant growth, host-microbe and microbe-microbe interactions fine-tune the host genetic selection of the barley microbiota at both taxonomic and functional levels. The disruption of these recruitment cues negatively impacts plant growth

Promoting the use of the PRECISE score for prostate MRI during active surveillance: results from the ESOR Nicholas Gourtsoyiannis teaching fellowship

OBJECTIVES: The PRECISE criteria for serial multiparametric magnetic resonance imaging (MRI) of the prostate during active surveillance recommend the use of a dedicated scoring system (PRECISE score) to assess the likelihood of clinically significant radiological change. This pilot study assesses the effect of an interactive teaching course on prostate MRI during active surveillance in assessing radiological change in serial imaging. METHODS: Eleven radiology fellows and registrars with different experience in prostate MRI reading participated in a dedicated teaching course where they initially evaluated radiological change (based on their previous training in prostate MRI reading) independently in fifteen patients on active surveillance (baseline and follow-up scan), and then attended a lecture on the PRECISE score. The initial scans were reviewed for teaching purposes and afterwards the participants re-assessed the degree of radiological change in a new set of images (from fifteen different patients) applying the PRECISE score. Receiver operating characteristic analysis was performed. Confirmatory biopsies and PRECISE scores given in consensus by two radiologists (involved in the original draft of the PRECISE score) were the reference standard. RESULTS: There was a significant improvement in the average area under the curve (AUC) for the assessment of radiological change from baseline (AUC: 0.60 [Confidence Intervals: 0.51-0.69] to post-teaching (AUC: 0.77 [0.70-0.84]). This was an improvement of 0.17 [0.016-0.28] (p = 0.004). CONCLUSIONS: A dedicated teaching course on the use of the PRECISE score improves the accuracy in the assessment of radiological change in serial MRI of the prostate

Analyse différentielle du transcriptome de la rhizobactérie Pseudomonas fluorescens Pf29Arp lors d'intercations avec le champignon pathogène du blé Gaeumannomyces graminis var. tritici

Diplôme : Dr. d'UniversitéCertaines bactéries contribuent à réduire les maladies racinaires des plantes causées par des champignons pathogènes. La compétence rhizosphérique de ces bactéries antagonistes est un pré-requis à leur efficacité. Cependant, l’influence du champignon pathogène sur le déterminisme génétique de cette compétence n’est pas connue. L’influence d’une part du champignon seul, ou effet hyphosphère et d’autre part de la plante et du champignon, ou effet pathorhizosphère sur la régulation des déterminants génétiques bactérien a été évaluée dans ce travail. Pour cela, des confrontations entre la rhizobactérie antagoniste, /Pseudomonas/ /fluorescens/ Pf29Arp, et le champignon responsable du piétin-échaudage du blé, /Gaeumannomyces/ /graminis/ var. /tritici,/ ont été conduites /in vitro/ en absence ou présence de racine. La construction d’une puce génomique de Pf29Arp a permis de mener une approche transcriptomique comparative dans ces dispositifs expérimentaux. Les types d’interaction entre Pf29Arp et /Ggt /varient au cours du cycle infectieux et couvrent des relations commensale, amensale et neutre. L’effet hyphosphère seul se manifeste avant contact entre les deux micro-organismes par l’induction de gènes impliqués dans la colonisation des eucaryotes et après contact par une induction de gènes codant des protéines de réponse au stress et une « patatin-like » protéine. Cependant, les modifications transcriptomiques majeures sont observées dans la pathorhizosphère sur les racines colonisées par /Ggt/ avec un effet augmenté par les racines nécrosées. Ainsi, des gènes codant des protéines impliquées dans le métabolisme carboné et la réponse au stress sont induits en présence de /Ggt/, et un effecteur du système de sécrétion de type VI est spécifique des racines nécrosées. Ces effets hyphosphère et pathorhizosphère modifient donc les traits bactériens impliqués dans les étapes de reconnaissance et de persistance dans ces environnement

Analyse différentielle du transcriptome de la rhizobactérie Pseudomonas fluorescens Pf29Arp lors d interactions avec le champignon pathogène du blé Gaeumannomyces graminis var. tritici

Certaines bactéries contribuent à réduire les maladies racinaires de plantes causées par des champignons pathogènes. La compétence rhizosphérique de ces bactéries antagonistes est un pré-requis à leur efficacité. Cependant, l influence du champignon pathogène sur le déterminisme génétique de cette compétence n est pas connue. L influence d une part du champignon seul, ou effet hyphosphère et d autre part de la plante et du champignon, ou effet pathorhizosphère sur la régulation des déterminants génétiques bactérien a été évaluée dans ce travail. Pour cela, des confrontations entre la rhizobactérie antagoniste, Pseudomonas fluorescens Pf29Arp, et le champignon responsable du piétin-échaudage du blé, Gaeumannomyces graminis var. tritici, ont été conduites in vitro en absence ou présence de racine. La constructin d une puce génomique de Pf29Arp a permis de mener une approche transcriptomique comparative dans ces dispositifs expérimentaux.Some bacteria reduce root diseases caused by phytopathogenic fungi. Rhizosphere competence is an important prerequisite for the efficacy of biocontrol. However, whether fungal presence alters genetic rhizosphere competence traits remains unknown. Influence of fungus alone, so-called hyposphere effect, and combined fungal-root influence, so-called pathorhizosphere effect, on regulation of bacterial determinants was assessed in this work. In vitro confronations between the antagonistic rhizobacteria Pseudomonas fluorescens PF29Arp and the take-all fungus Gaeumannomyces graminis var. tritici were conducted in absence or in presence of root. The related bacterial transcriptome were compared thanks to the build-up of a Pf29Arp shotgun DNA icroarray.RENNES-Agrocampus-CRD (352382323) / SudocSudocFranceF

Table Ronde "Phytobiome"

Table Ronde "Phytobiome". 2017 Scientific MEM days: Journées scientifiques MEM (Métaomiques et écosystèmes microbiens