The metazoan history of the COE transcription factors. Selection of a variant HLH motif by mandatory inclusion of a duplicated exon in vertebrates

<p>Abstract</p> <p>Background</p> <p>The increasing number of available genomic sequences makes it now possible to study the evolutionary history of specific genes or gene families. Transcription factors (TFs) involved in regulation of gene-specific expression are key players in the evolution of metazoan development. The low complexity COE (Collier/Olfactory-1/Early B-Cell Factor) family of transcription factors constitutes a well-suited paradigm for studying evolution of TF structure and function, including the specific question of protein modularity. Here, we compare the structure of <it>coe </it>genes within the metazoan kingdom and report on the mechanism behind a vertebrate-specific exon duplication.</p> <p>Results</p> <p>COE proteins display a modular organisation, with three highly conserved domains : a COE-specific DNA-binding domain (DBD), an Immunoglobulin/Plexin/transcription (IPT) domain and an atypical Helix-Loop-Helix (HLH) motif. Comparison of the splice structure of <it>coe </it>genes between cnidariae and bilateriae shows that the ancestral COE DBD was built from 7 separate exons, with no evidence for exon shuffling with other metazoan gene families. It also confirms the presence of an ancestral H1LH2 motif present in all COE proteins which partly overlaps the repeated H2d-H2a motif first identified in rodent EBF. Electrophoretic Mobility Shift Assays show that formation of COE dimers is mediated by this ancestral motif. The H2d-H2a α-helical repetition appears to be a vertebrate characteristic that originated from a tandem exon duplication having taken place prior to the splitting between gnathostomes and cyclostomes. We put-forward a two-step model for the inclusion of this exon in the vertebrate transcripts.</p> <p>Conclusion</p> <p>Three main features in the history of the <it>coe </it>gene family can be inferred from these analyses: (i) each conserved domain of the ancestral <it>coe </it>gene was built from multiple exons and the same scattered structure has been maintained throughout metazoan evolution. (ii) There exists a single <it>coe </it>gene copy per metazoan genome except in vertebrates. The H2a-H2d duplication that is specific to vertebrate proteins provides an example of a novel vertebrate characteristic, which may have been fixed early in the gnathostome lineage. (iii) This duplication provides an interesting example of counter-selection of alternative splicing.</p

Non-redundant Functions of ATM and DNA-PKcs in Response to DNA Double-Strand Breaks

DNA double-strand breaks (DSBs) elicit the so-called DNA damage response (DDR), largely relying on ataxia telangiectasia mutated (ATM) and DNA-dependent protein kinase (DNA-PKcs), two members of the PI3K-like kinase family, whose respective functions during the sequential steps of the DDR remains controversial. Using the DIvA system (DSB inducible via AsiSI) combined with high-resolution mapping and advanced microscopy, we uncovered that both ATM and DNA-PKcs spread in cis on a confined region surrounding DSBs, independently of the pathway used for repair. However, once recruited, these kinases exhibit non-overlapping functions on end joining and γH2AX domain establishment. More specifically, we found that ATM is required to ensure the association of multiple DSBs within “repair foci.” Our results suggest that ATM acts not only on chromatin marks but also on higher-order chromatin organization to ensure repair accuracy and survival.Spanish Government SAF2010-21017Spanish Government BES-2011-0473

A Short Receptor Downregulates JAK/STAT Signalling to Control the Drosophila Cellular Immune Response

Regulation of JAK/STAT signalling by a short, nonsignalling receptor in Drosophila modulates response to specific immune challenges such as parasitoid infestations

Réactivité différentielle du Chaperome de Drosophila en réponse au stress froid et chaud

International audienc

Thermal stress causes DNA damage and mortality in a tropical insect

International audienceCold tolerance is considered an important factor determining the geographic distribution of insects. We have previously shown that despite its tropical origin, the cockroach is capable of surviving exposures to cold. However, the freezing tolerance of this species had not yet been examined. Low temperature is known to alter membrane integrity in insects, but whether chilling or freezing compromises DNA integrity remains a matter of speculation. In the present study, we subjected the adults to freezing to determine their supercooling point (SCP) and evaluated whether the cockroaches were capable of surviving partial and complete freezing. Next, we conducted single cell gel electrophoresis (SCGE) assays to determine whether heat, cold and freezing altered hemocyte DNA integrity. The SCP of this species was high and around -4.76°C, which is within the typical range of freezing-tolerant species. Most cockroaches survived to 1 day after partial ice formation (20% mortality), but died progressively in the next few days after cold stress (70% mortality after 4 days). One day after complete freezing, most insects died (70% mortality), and after 4 days, 90% of them had succumbed. The SCGE assays showed substantial levels of DNA damage in hemocytes. When cockroaches were heat-stressed, the level of DNA damage was similar to that observed in the freezing treatment, though all heat-stressed insects survived. The present study shows that can be considered as moderately freeze-tolerant, and that extreme low temperature stress can affect DNA integrity, suggesting that this cockroach may possess an efficient DNA repair system

Élaboration d’un milieu de culture pour Pseudomonas veronii

Rapport de stage de L3 en microbiologi

Analysis of Small Non-coding RNAs as Signaling Intermediates of Environmentally Integrated Responses to Abiotic Stress

International audienceResearch to date on abiotic stress responses in plants has been largely focused on the plant itself, but current knowledge indicates that microorganisms can interact with and help plants during periods of abiotic stress. In our research, we aim to investigate the interkingdom communication between the plant root and the rhizo-microbiota. Our investigation showed that miRNA plays a pivotal role in this interkingdom communication. Here, we describe a protocol for the analysis of miRNA secreted by the plant root, which includes all of the steps from the isolation of the miRNA to the bioinformatics analysis. Because of their short nucleotide length, Next Generation Sequencing (NGS) library preparation from miRNAs can be challenging due to the presence of dimer adapter contaminants. Therefore, we highlight some strategies we adopt to inhibit the generation of dimer adapters during library preparation. Current screens of miRNA targets mostly focus on the identification of targets present in the same organism expressing the miRNA. Our bioinformatics analysis challenges the barrier of evolutionary divergent organisms to identify candidate sequences of the microbiota targeted by the miRNA of plant roots. This protocol should be of interest to researchers investigating interkingdom RNA-based communication between plants and their associated microorganisms, particularly in the context of holobiont responses to abiotic stresses

Shaping of soil microbial communities by plants does not translate into specific legacy effects on organic carbon mineralization

International audiencePlants shape soil microbial communities through their root architecture, their rhizodeposits and return of dead plant material to the soil. These interactions can have a strong influence on the soil organic carbon dynamics. However, it is unclear whether the plant species effects on the soil microbial community could influence the organic carbon mineralization through plant legacy effects. Therefore, we examined how and to what extent a short-term plant growing phase affected the total and active soil microorganisms and through a possible plant legacy, also the mineralization of soil organic carbon, a central ecosystem function. Using a controlled pot experiment, we first showed that the two phylogenetically distinct plants, Arabidopsis thaliana and Triticum aestivum, differently shaped the soil microbial communities when recruiting from the same soil community. Although both plants recruited plant-growth promoting bacteria in the vicinity of their roots, A. thaliana had a stronger effect than T. aestivum and also recruited saprophytic fungi, while inhibiting fungal pathogens. Due to plant legacy effects on the soil microbial communities, different microbial successions occurred in the two previously planted soils when subjected to plant litter. By contrast, plant legacy effects on soil basal respiration were not plant-specific, with basal respiration increasing similarly in both cases and moreover did not translate to changes in litter carbon mineralization in the short-term of 49 days. Our results suggest that the soil nutrient dynamics rather than changes in soil microbial community composition drive the organic carbon mineralization of added litter. The present study brings new insights in how the relationships between plants, microorganisms and soil nutrient dynamics affect litter carbon cycling

Caractérisation des bioaérosols émis par les sols anthropisés: quantification et composition des communautés fongiques et bactériennes.

International audienceSoils are a major interface for the exchange of matter and gases with the atmosphere. They are also immense reservoirs of microbial biodiversity, including human pathogens. This raises the question of whether anthropized soils are sources of biological aerosols that have been underestimated and insufficiently taken into account in models for predicting outdoor air quality. It has recently been shown that human activity increases aerosol emissions through soil disturbance, particularly in agricultural areas. External forces such as wind and the impact of raindrops on the soil, as well as soil texture and moisture, appear to play an important role in the emission of bioaerosols of soil origin. The microorganisms associated with emitted particles of size < 3.5 µm represent a risk to human health, as these fractions are easily airborne and can penetrate the respiratory tract to the alveoli, generating cases of asthma, rhinitis and chronic bronchitis. To study the distribution of microorganisms in the different size fractions of bioaerosols in agricultural areas, atmospheric samples were collected close to the ground with a cascade impactor (Model 120 MOUDI II), in winter 2020-2021 at the SOERE - EFELE observatory (INRAE, Allenvi). Fungal and bacterial communities were quantified by real-time PCR and their composition analyzed by high-throughput sequencing. The results show a wide biodiversity and that microorganisms are distributed differently across bioaerosol size classes. In order to gain a better understanding of the factors and mechanisms involved in the emission of bioaerosols from land-based sources, an aerosolization tunnel was built.Les sols constituent une interface majeure d’échanges de matières et de gaz avec l’atmosphère. Ils sont aussi d’immenses réservoirs de biodiversité microbienne incluant des pathogènes pour l’homme. Alors se pose la question de savoir si les sols anthropisés sont des sources d’aérosols biologiques jusqu’alors sous-estimées et insuffisamment prises en compte dans les modèles de prédiction de la qualité de l’air extérieur. Or il a été montré récemment que l’activité humaine augmente les émissions d’aérosols par perturbation des sols, notamment en zones agricoles. Des forces externes telles que le vent et l’impact des gouttes de pluie sur le sol, la texture et l’humidité du sol semblent jouer un rôle important dans les processus d’émission de bioaérosols d’origine tellurique. Les microorganismes associés aux particules émises de taille < 3,5 µm représentent un risque pour la santé humaine car ces fractions sont facilement aéroportées et peuvent pénétrer dans les voies respiratoires jusqu’aux alvéoles et générer des cas d’asthme, de rhinites et bronchites chroniques. Afin d’étudier la répartition des micro-organismes dans les différentes fractions de tailles des bioaérosols en zone agricole, des échantillons atmosphériques ont été collectés proches du sol avec un impacteur en cascade (Model 120 MOUDI II), en hiver 2020-2021 sur l'observatoire SOERE - EFELE (INRAE, Allenvi). Les communautés fongiques et bactériennes ont été quantifiées par PCR en temps réel et leur composition analysée par séquençage haut-débit. Les résultats montrent une large biodiversité et que les microorganismes se répartissent différemment sur les classes de taille des bioaérosols. Afin de mieux comprendre les facteurs et mécanismes d’émission des bioaérosols d’origine tellurique, un tunnel d’aérosolisation a été construit

Responses of active soil microorganisms facing to a soil biostimulant input compared to plant legacy effects

International audienceAgriculture is changing to rely on agroecological practices that take into account biodiversity, and the ecological processes occurring in soils. The use of agricultural biostimulants has emerged as a valid alternative to chemicals to indirectly sustain plant growth and productivity. Certain BS have been shown to select and stimulate plant beneficial soil microorganisms. However, there is a lack of knowledge on the effects and way of action of the biostimulants operating on soil functioning as well as on the extent and dynamic of these effects. In this study we aimed to decipher the way of action of a seaweed and amino-acids based biostimulant intended to be applied on soil crop residues to increase their microbial mineralization and the further release of nutrients. By setting-up a two-phase experiment (soil plant-growing and soil incubation), our objectives were to (1) determine the effects of the soil biostimulant over time on the active soil bacteria and fungi and the consequences on the organic carbon mineralization in bare soils, and (2) assess the biostimulant effects on soil microorganisms relatively to plant legacy effects in planted soils. We demonstrated that the soil biostimulant had a delayed effect on the active soil microorganisms and activated both plant growth promoting bacteria and saprophytes microorganisms at the medium-term of 49 days. However, the changes in the abundances of active microbial decomposers were not associated to a higher mineralization rate of organic carbon derived from soil and/or litter. The present study assessed the biostimulant beneficial effect on active soil microbial communities as similar as or even higher than the legacy effects of either A. thaliana or T. aestivum plants. We specifically showed that the biostimulant increased the active fungal richness to a higher extent than observed in soils that previously grew the two plants tested