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

Kilani, Jaafar; Davanture, Marlène; Simon, Adeline; Zivy, Michel; Fillinger, Sabine

doi:10.1016/j.jprot.2019.103580

Cited by 6 publications

(2 citation statements)

References 79 publications

(119 reference statements)

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“…To detect TaFRQ LUC oscillations at protein levels, TaFRQ LUC reporter strains were subjected to a time-course experiment in GYEC+ peas culture media, for which samples were taken every 4 hr for 52 hr, following a time-course protocol similar to the ones in Neurospora ( Larrondo et al, 2015 ), except that T. atroviride cultures were kept in DD, and reset by a strong LP to mimic an LL to DD transition. Proteins were extracted as described by Kilani et al, 2020 . Protein concentration was determined by the Bradford method, using the Bio-Rad Protein Assay (Bio-Rad Laboratories, Inc, CA).…”

Section: Methodsmentioning

confidence: 99%

Circadian oscillations in Trichoderma atroviride and the role of core clock components in secondary metabolism, development, and mycoparasitism against the phytopathogen Botrytis cinerea

Henríquez-Urrutia

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et al. 2022

eLife

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Circadian clocks are important for an individual’s fitness, and recent studies have underlined their role in the outcome of biological interactions. However, the relevance of circadian clocks in fungal-fungal interactions remains largely unexplored. We sought to characterize a functional clock in the biocontrol agent Trichoderma atroviride to assess its importance in the mycoparasitic interaction against the phytopathogen Botrytis cinerea. By utilizing luciferase reporters to monitor the T. atroviride core-clock, we confirmed the existence of circadian oscillations of ~26h that are temperature-compensated and modulated by environmental cues such as light and temperature. Notably, the presence of such rhythms appears to be highly dependent on the nutritional composition of the media. Heterologous expression of the T. atroviride negative clock component (tafrq) in a clock null (Δfrq) strain of Neurospora crassa restored core clock function in the latter fungus, with the same period observed in T. atroviride, confirming the role of tafrq as a bona fide core-clock component. Confrontation assays between wild-type and clock mutant strains of T. atroviride and B. cinerea, in constant light or darkness, revealed an inhibitory effect of light on T. atroviride's mycoparasitic capabilities. Interestingly, when confrontation assays were performed under light/dark cycles, T. atroviride's overgrowth capacity was enhanced when inoculations were at dawn compared to dusk. Deleting the core-clock negative element FRQ in B. cinerea, but not in T. atroviride, was vital for the daily differential phenotype, suggesting that the B. cinerea clock has a more significant influence on the result of this interaction. Additionally, we observed that T. atroviride clock components modulate development and secondary metabolism in this fungus, affecting the production of several molecules, including volatile compounds, such as 6-pentyl-α-pyrone (6-PP). Notably, we detected the rhythmic production of distinct T. atroviride volatile organic compounds (VOCs), which depended on its circadian clock. Thus, this study provides evidence on how clock components impact diverse aspects of T. atroviride lifestyle and how daily changes modulate fungal interactions and dynamics.

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Section: Methodsmentioning

confidence: 99%

Circadian oscillations in Trichoderma atroviride and the role of core clock components in secondary metabolism, development, and mycoparasitism against the phytopathogen Botrytis cinerea

Henríquez-Urrutia

Spanner

Olivares-Yañez

et al. 2022

eLife

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“…UPS2 contains a mixture of 48 human proteins at six different molar concentrations, where there are eight proteins of different molecular masses present at each concentration level. Multiple studies have found strong positive correlations between the expected and observed relative abundances of UPS2 proteins [ 7 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 ]. However, in all cases, there was a need for massive amounts of UPS2 to carry out quantification (e.g., up to 3–10 µg per mass spectrometry run), which is a constraint if the goal is to analyze large cohorts.…”

Section: Introductionmentioning

confidence: 99%

Comparison of Different Label-Free Techniques for the Semi-Absolute Quantification of Protein Abundance

et al. 2022

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In proteomics, it is essential to quantify proteins in absolute terms if we wish to compare results among studies and integrate high-throughput biological data into genome-scale metabolic models. While labeling target peptides with stable isotopes allow protein abundance to be accurately quantified, the utility of this technique is constrained by the low number of quantifiable proteins that it yields. Recently, label-free shotgun proteomics has become the “gold standard” for carrying out global assessments of biological samples containing thousands of proteins. However, this tool must be further improved if we wish to accurately quantify absolute levels of proteins. Here, we used different label-free quantification techniques to estimate absolute protein abundance in the model yeast Saccharomyces cerevisiae. More specifically, we evaluated the performance of seven different quantification methods, based either on spectral counting (SC) or extracted-ion chromatogram (XIC), which were applied to samples from five different proteome backgrounds. We also compared the accuracy and reproducibility of two strategies for transforming relative abundance into absolute abundance: a UPS2-based strategy and the total protein approach (TPA). This study mentions technical challenges related to UPS2 use and proposes ways of addressing them, including utilizing a smaller, more highly optimized amount of UPS2. Overall, three SC-based methods (PAI, SAF, and NSAF) yielded the best results because they struck a good balance between experimental performance and protein quantification.

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Phenanthrene Degradation by Sphingobium sp. PM1B in Soil Containing Polyethylene Microplastics: Effects and Mechanisms

Liu,

Huang,

2023

Water Air Soil Pollut

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

Cited by 6 publications

References 79 publications

Circadian oscillations in Trichoderma atroviride and the role of core clock components in secondary metabolism, development, and mycoparasitism against the phytopathogen Botrytis cinerea

Circadian oscillations in Trichoderma atroviride and the role of core clock components in secondary metabolism, development, and mycoparasitism against the phytopathogen Botrytis cinerea

Comparison of Different Label-Free Techniques for the Semi-Absolute Quantification of Protein Abundance

Phenanthrene Degradation by Sphingobium sp. PM1B in Soil Containing Polyethylene Microplastics: Effects and Mechanisms

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