Phenylpyrroles: 30 years, two molecules and (nearly) no resistance

Phenypyrroles are chemical analogs of the natural antifungal compound pyrrolnitrine. Fenpiclonil, but mainly fludioxonil are registered against multiple fungal crop diseases since over 25 years for seed or foliar treatment. They have severe physiological impacts on the pathogen, including membrane hyperpolarization, changes in carbon metabolism and the accumulation of metabolites leading to hyphal swelling and burst. The selection and characterization of mutants resistant to phenylpyrroles have revealed that these fungicides activate the fungal osmotic signal transduction pathway through their perception by a typical fungal hybrid histidine kinase (HHK). The HHK is prone to point mutations that confer fungicide resistance and affect its sensor domain, composed of tandem repeats of HAMP motifs. Fludioxonil resistant mutants have been selected in many fungal species under laboratory conditions. Generally they present severe impacts on fitness parameters. Since only few cases of field resistance specific to phenylpyrroles have been reported one may suspect that the fitness penalty of phenylpyrrole resistance is the reason for the lack of field resistance

Deciphering stress signal transduction cascades in Botrytis cinerea by phosphoproteomics and functional genetics

La perception et l’adaptation à l’environnement sont des processus indispensables pour la survie des organismes vivants. Le champignon phytopathogène Botrytis cinerea peut ainsi percevoir différents types de signaux qu’ils soient chimiques ou physiques. La voie de signalisation de la MAPK Sak1 est impliquée dans l’adaptation au stress osmotique, oxydatif et pariétal, mais aussi dans la sporulation et le pouvoir pathogène en régulant la pénétration de la plante et le développement des nécroses. Afin d’approfondir les connaissances existantes sur la voie de Sak1, nous avons réalisé des études globales basées sur des techniques de protéomique et phosphoprotéomique. L’analyse de protéomique comparative entre la souche sauvage et les mutants de signalisation ∆bos1 et ∆sak1 a notamment mis en évidence que la MAPK Sak1 régule l’abondance de protéines impliquées dans la voie des protéines G et la voie calcique. Cette connexion avec les protéines G a été confirmée par une baisse de la concentration en AMPc chez le mutant ∆sak1. L’utilisation du fludioxonil comme signal de l’activation de la MAPK Sak1 pour l’analyse par phosphoprotéomique a mis en évidence des modifications de l’état de phosphorylation de protéines. Parmi ces protéines différentiellement phosphorylées, la présence de PKAR (sous-unité régulatrice de la protéine kinase A) et du facteur de transcription CRZ1, indiquent respectivement une action sur la voie via protéines G et la voie calcique, validant les résultats obtenus par protéomique. Le phosphoprotéome a révélé une « phosducin-like protein », PhnA. Sa caractérisation fonctionnelle montre son rôle dans l’adaptation aux stress, la sporulation et la germination, ainsi que dans le pouvoir pathogène mettant ainsi en évidence un nouveau facteur de pathogénicité chez B. cinerea. Notre étude a permis de révéler des interactions entre Sak1 et d’autres voies de signalisation non suspectées, agissant aussi bien sur la production de certains composants (régulations transcriptionnelles et traductionnelles) que sur la phosphorylation (modifications post-traductionnelles). Nos résultats constitueront la base de nouvelles recherches pour compléter nos connaissances sur ces interactions impliquant l’adaptation au stress et la pathogénie de B. cinerea.Perception and adaptation to the environment are essential processes for the survival of living organisms. The phytopathogenic fungus Botrytis cinerea can thus perceive different types of signals, whether they are chemical or physical. The signalling pathway of the Sak1 MAPK is involved in the adaptation to osmotic, oxidative and cell wall stress, but also in sporulation and pathogenicity by regulating plant penetration and necrosis development. In order to deepen existing knowledge of the Sak1 pathway, we have carried out global studies based on proteomics and phosphoproteomics techniques. A comparative proteomics analysis between the wild type and the signalling mutants ∆bos1 and ∆sak1 showed, among others, that Sak1 regulates the abundance of proteins involved in the G-protein pathway and calcium pathway. This connection with G-proteins was confirmed by a decrease in cAMP concentration in the ∆sak1 mutant. Using fludioxonil as signal for the activation of Sak1 for a phosphoproteomic analysis revealed changes in the state of protein phosphorylation. Among these differentially phosphorylated proteins, the presence of PKAR (regulatory subunit of protein kinase A) and the transcription factor CRZ1, indicates an action on the G-protein and calcium pathway respectively, validating the results obtained by proteomics. Phosphoproteomics revealed a phosducin-like protein, PhnA. Its functional characterization reveals its role in stress adaptation, sporulation and germination, as well as in pathogenicity, thus demonstrating a new pathogenicity factor in B. cinerea. Our study revealed interactions between Sak1 and other unsuspected signalling pathways, affecting both the production of certain components (transcriptional and translational regulations) and phosphorylation (post-translational modifications). Our results will create the basis for new research questions to complement our understanding of these interactions involving adaptation to stress and pathogenesis of B. cinerea

Décryptage des cascades de signalisation liées au stress par phosphoprotéomique et génétique fonctionnelle chez Botrytis cinerea

Perception and adaptation to the environment are essential processes for the survival of living organisms. The phytopathogenic fungus Botrytis cinerea can thus perceive different types of signals, whether they are chemical or physical. The signalling pathway of the Sak1 MAPK is involved in the adaptation to osmotic, oxidative and cell wall stress, but also in sporulation and pathogenicity by regulating plant penetration and necrosis development. In order to deepen existing knowledge of the Sak1 pathway, we have carried out global studies based on proteomics and phosphoproteomics techniques. A comparative proteomics analysis between the wild type and the signalling mutants ∆bos1 and ∆sak1 showed, among others, that Sak1 regulates the abundance of proteins involved in the G-protein pathway and calcium pathway. This connection with G-proteins was confirmed by a decrease in cAMP concentration in the ∆sak1 mutant. Using fludioxonil as signal for the activation of Sak1 for a phosphoproteomic analysis revealed changes in the state of protein phosphorylation. Among these differentially phosphorylated proteins, the presence of PKAR (regulatory subunit of protein kinase A) and the transcription factor CRZ1, indicates an action on the G-protein and calcium pathway respectively, validating the results obtained by proteomics. Phosphoproteomics revealed a phosducin-like protein, PhnA. Its functional characterization reveals its role in stress adaptation, sporulation and germination, as well as in pathogenicity, thus demonstrating a new pathogenicity factor in B. cinerea. Our study revealed interactions between Sak1 and other unsuspected signalling pathways, affecting both the production of certain components (transcriptional and translational regulations) and phosphorylation (post-translational modifications). Our results will create the basis for new research questions to complement our understanding of these interactions involving adaptation to stress and pathogenesis of B. cinerea.La perception et l’adaptation à l’environnement sont des processus indispensables pour la survie des organismes vivants. Le champignon phytopathogène Botrytis cinerea peut ainsi percevoir différents types de signaux qu’ils soient chimiques ou physiques. La voie de signalisation de la MAPK Sak1 est impliquée dans l’adaptation au stress osmotique, oxydatif et pariétal, mais aussi dans la sporulation et le pouvoir pathogène en régulant la pénétration de la plante et le développement des nécroses. Afin d’approfondir les connaissances existantes sur la voie de Sak1, nous avons réalisé des études globales basées sur des techniques de protéomique et phosphoprotéomique. L’analyse de protéomique comparative entre la souche sauvage et les mutants de signalisation ∆bos1 et ∆sak1 a notamment mis en évidence que la MAPK Sak1 régule l’abondance de protéines impliquées dans la voie des protéines G et la voie calcique. Cette connexion avec les protéines G a été confirmée par une baisse de la concentration en AMPc chez le mutant ∆sak1. L’utilisation du fludioxonil comme signal de l’activation de la MAPK Sak1 pour l’analyse par phosphoprotéomique a mis en évidence des modifications de l’état de phosphorylation de protéines. Parmi ces protéines différentiellement phosphorylées, la présence de PKAR (sous-unité régulatrice de la protéine kinase A) et du facteur de transcription CRZ1, indiquent respectivement une action sur la voie via protéines G et la voie calcique, validant les résultats obtenus par protéomique. Le phosphoprotéome a révélé une « phosducin-like protein », PhnA. Sa caractérisation fonctionnelle montre son rôle dans l’adaptation aux stress, la sporulation et la germination, ainsi que dans le pouvoir pathogène mettant ainsi en évidence un nouveau facteur de pathogénicité chez B. cinerea. Notre étude a permis de révéler des interactions entre Sak1 et d’autres voies de signalisation non suspectées, agissant aussi bien sur la production de certains composants (régulations transcriptionnelles et traductionnelles) que sur la phosphorylation (modifications post-traductionnelles). Nos résultats constitueront la base de nouvelles recherches pour compléter nos connaissances sur ces interactions impliquant l’adaptation au stress et la pathogénie de B. cinerea

Quantitative comparative phosphoproteomics to decipher signal transduction

Adaptation to changing environmental conditions takes place rapidly in all living organisms: cells must respond to a wide variety of signals. Through successive protein phosphorylation and de-phosphorylation steps, signal transduction cascades mediate between the perception of the extracellular conditions and the adaptation of intracellular processes. The first event after the perception of the external signal is the auto-phosphorylation of a receptor kinase, which, on its turn, phosphorylates down-stream targets, mainly kinase cascades. The downstream effectors, mitogen-activated protein kinases (MAPKs) and other kinases, regulate the activity of transcription factors, metabolic enzymes and other factors, thereby initiating the fungal adaptive response. Understanding these adaptive responses requires deciphering early phosphorylation events. While global proteomic analyses have been improved over decades, the global study of protein (de)phosphorylation events in living organisms only became possible recently. Significant advances in mass spectrometry based phosphoproteomics have taken place, including phosphopeptide enrichment, detection and quantification, and phosphorylation site localization. Reports of fungal phosphoproteomic studies are increasing, but those dealing with filamentous ascomycetes are still rare. The first phosphoproteomic study of kinase dependent phosphorylation events has been reported for the model fungus Neurospora crassa. In Botrytis cinerea, phosphoproteomics have been used to study the global phosphoprotein content in axenic culture and the differential phosphorylation profiles between mycelia grown on glucose or tomato-cell wall as carbon-source. We have undertaken a comparative proteomics and phosphoproteomics study of the B. cinerea osmosensing pathway challenged by the fungicide fludioxonil. We compared mutants of the sensor histidine-kinase Bos1 and of the MAPK Sak1 to the parental wild-type. Strains were exposed (or not) to fludioxonil for 15 min. during exponential in vitro growth. Shotgun proteomics revealed considerable differences in protein content among the strains, but no treatment effect. These results indicate a strong transcriptional and/or translational regulation under Bos1 and Sak1 control, respectively, under standard conditions. Quantitative phosphoproteomics revealed a clear response to the fludioxonil treatment as well as (de)phosphorylation events controlled by Bos1, Sak1, or both

Comparative proteomics and phosphoproteomics to decipher signal transduction in Botrytis cinerea.

Adaptation to changing environmental conditions takes place rapidly in all living organisms: cells must respond to a wide variety of signals. Through successive protein phosphorylation and de-phosphorylation steps, signal transduction cascades mediate between the perception of the extracellular conditions and the adaptation of intracellular processes. Botrytis cinerea is a necrotrophic, polyphageous plant pathogen, that causes gray mold disease and can infect over 1000 plant species including several agronomically important crops (grapevine, strawberry, tomatoes …). Fungicides remain the most effective means to combat this disease. However B. cinerea rapidly adapts to fungicides. Presently, the phenylpyrrole fludioxonil is one of the most efficient fungicides against B. cinerea. Therefore deciphering the response to fludioxonil in B. cinerea is crucial. In Botrytis cinerea, the fungicide fludioxonil activates the Sak1 (Hog1-like) and Bmp3 (Slt2-like) MAPKs, which are respectively involved in osmoregulation, cell wall integrity, development and pathogenicity. In order to trace the transduction of fludioxonil to the MAPK pathways, we have undertaken a comparative proteomics and phosphoproteomics study of the B. cinerea osmosensing pathway challenged by the fungicide fludioxonil. We compared mutants of the sensor histidine-kinase Bos1 and of the MAPK Sak1 to the parental wild-type. Strains were exposed (or not) to fludioxonil for 15 min during exponential in vitro growth. Shotgun proteomics revealed considerable differences in protein content among the strains, but no treatment effect. These results indicate a strong transcriptional and/or translational regulation under Bos1 and Sak1 control, respectively, under standard conditions. One of the most relevant result is the abundance of 263 proteins controlled by Bos1 and Sak1 independently. Proteins of the oxidative stress response are under negative control of Bos1, while some proteases are positively regulated. In addition, proteins involved in translation are specifically regulated by Bos1. It appears that Bos1 is important in different biological processes. Sak1, on its turn, controls the abundance of proteins involved in oxidative stress response, early secretome, protein folding, primary metabolism and secondary metabolism. Quantitative phosphoproteomics is ongoing and it will permit to verify a clear response to the fludioxonil treatment as well as (de)phosphorylation events controlled independently by Bos1 or Sak1, or by both kinase

Comparative quantitative proteomics of osmotic signal transduction mutants in Botrytis cinerea explain mutant phenotypes and highlight interaction with cAMP and Ca2+ signalling pathways

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Light-induced gene expression in Botrytis cinerea involves GATA-transcription factors and the stress-activated MAP kinase module.

Botrytis cinerea is a plant pathogen that exhibits prominent light responses including the formation of the reproduction structures (photomorphogenesis), secondary metabolites/ pigments, and antioxidant enzymes. A complex regulatory network of photoreceptors, transcription factors (TFs) and chromatin modifiers is supposed to initiate, transmit, and fine-tune the responses to different wavelengths of light on the transcriptional level that finally leads to the observable phenotypes. As the formation of the reproduction structures is strictly regulated by light in this fungus - conidia are formed in the light, sclerotia in the dark - the output can be easily monitored. The GATA-type TFs BcWCL1 (as part of the White Collar complex (WCC)) and BcLTF1 are important regulators as their deletions result in light-independent conidiation (“always conidia”) due to the deregulation of BcLTF2 (Schumacher et al. 2014; Canessa et al. 2013; Cohrs et al. 2016). Study of light-induced gene (LIG) expression in both deletion mutants highlighted the role of the TFs in activating EARLY and in repressing LATE LIG expression, including bcltf2 encoding the master regulator of conidiation and further LTFs that may function downstream or in parallel with BcLTF2 in regulating the conidiation process. As the group of LIGs also contained genes that are induced by various stresses in a BcSAK1-dependent manner, the phosphorylation status of the stress-activated MAPK BcSAK1 was studied and shown to increase after exposure to light. Deletion of bcsak1 impairs LIG expression suggesting that BcSAK1 functions as a co-activator of the WCC in inducing EARLY genes, and as a component releasing the LATE promoters (e.g. bcltf2) from repression by BcLTF1 and the WCC resulting in the expression of the conidiation genes. This preliminary model is in agreement with the observations that the deletion of BcSAK1 results in a “never conidia” phenotype (Segmüller et al. 2007), and that the exposure of the wild type to heat and osmotic stress bypasses the requirement of light for conidiation

Cytokinin Sensing in Bacteria

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Remodeling of perturbed chromatin can initiate de novo transcriptional and post-transcriptional silencing

Posted June 27, 2024 on bioRxiv.International audienceIn eukaryotes, repetitive DNA can become silenced de novo, either transcriptionally or post-transcriptionally, by processes independent of strong sequence-specific cues. The mechanistic nature of such processes remains poorly understood. We found that in the fungus Neurospora crassa, de novo initiation of both transcriptional and post-transcriptional silencing was linked to perturbed chromatin, which was produced experimentally by the aberrant activity of transcription factors at the tetO operator array. Transcriptional silencing was mediated by canonical constitutive heterochromatin. On the other hand, post-transcriptional silencing resembled repeat-induced quelling but occurred normally when homologous recombination was inactivated. All silencing of the tetO array was dependent on SAD-6 (a fungal ortholog of the SWI/SNF chromatin remodeler ATRX), which was required to maintain nucleosome occupancy at the perturbed locus. In addition, we found that two other types of sequences (the lacO array and native AT-rich DNA) could also undergo recombination-independent quelling associated with perturbed chromatin. These results suggested a model in which the de novo initiation of transcriptional and post-transcriptional silencing is coupled to the remodeling of perturbed chromatin