Membrane Trafficking in Autophagy

Søreng, Kristiane; Neufeld, Thomas P.; Simonsen, Anne

doi:10.1016/bs.ircmb.2017.07.001

Cited by 91 publications

(69 citation statements)

References 387 publications

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“…The assays of the first three phases of our pipeline are focused on assessing the chemicals' effect on autophagy activity, and the fourth phase puts the activity into a broader context. Due to the overwhelming complexity of the network, it is frequently overlooked that autophagy is an integral part of the endomembrane trafficking system (Ponpuak et al, 2015;Pečenková et al, 2017;Søreng et al, 2017). The assays in the fourth phase identify treatment conditions under which candidate compounds significantly influence autophagy activity without causing detectable aberrations in other components of the trafficking machinery.…”

Section: Discussionmentioning

confidence: 99%

Chemical Screening Pipeline for Identification of Specific Plant Autophagy Modulators

et al. 2019

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Autophagy is a major catabolic process in eukaryotes with a key role in homeostasis, programmed cell death, and aging. In plants, autophagy is also known to regulate agronomically important traits such as stress resistance, longevity, vegetative biomass, and seed yield. Despite its significance, there is still a shortage of reliable tools modulating plant autophagy. Here, we describe the first robust pipeline for identification of specific plant autophagy-modulating compounds. Our screening protocol comprises four phases: (1) high-throughput screening of chemical compounds in cell cultures of tobacco (Nicotiana tabacum); (2) confirmation of the identified hits in planta using Arabidopsis (Arabidopsis thaliana); (3) further characterization of the effect using conventional molecular biology methods; and (4) verification of chemical specificity on autophagy in planta. The methods detailed here streamline the identification of specific plant autophagy modulators and aid in unraveling the molecular mechanisms of plant autophagy.

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Section: Discussionmentioning

confidence: 99%

Chemical Screening Pipeline for Identification of Specific Plant Autophagy Modulators

et al. 2019

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“…The expression of genes involved in membrane trafficking, autophagy, and mitophagy was also activated in glucoserelieved conidia. Membrane trafficking is involved in endocytosis, exocytosis (Zheng et al, 2015), autophagy (Soreng et al, 2018), and vesicle formation and fusion (Jurgens, 2004), and is, therefore, vital for fungal growth and differentiation. In this study, conidial germination rates of autophagy pathway mutants ATG1 and ATG5 decreased significantly in soil suspension.…”

Section: Discussionmentioning

confidence: 99%

Comparative Transcriptomics Reveals Features and Possible Mechanisms of Glucose-Mediated Soil Fungistasis Relief in Arthrobotrys oligospora

et al. 2020

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Soil-borne pest diseases result in large annual agricultural losses globally. Fungal biocontrol agents are an alternative means of controlling pest diseases; however, soil fungistasis limits the effect of fungal agents. Nutrients can relieve soil fungistasis, but the mechanisms behind this process remain poorly understood. In this study, we determined and quantified the transcriptomes of Arthrobotrys oligospora, a nematodetrapping fungus, derived from samples of fresh conidia, germinated conidia, soil fungistatic conidia, and glucose-relieved conidia. The transcriptomes of fungistatic and glucose-relieved conidia were significantly different from those of the other two conidia samples. KEGG pathway analyses showed that those genes upregulated in fungistatic and glucose-relieved conidia were mainly involved in translation and substance metabolism, and the downregulated genes were mainly involved in MAPK pathway, autophagy, mitophagy, and endocytosis. As being different from the transcriptome of fungistatic conidia, upregulated genes in the transcriptome of glucose-relieved conidia are also related to replication and repair, spliceosome, oxidative phosphorylation, autophagy, and degradation pathway (lysosome, proteasome, and RNA degradation). And the upregulated genes resulted from comparison of glucose-relieved conidia and fungistatic conidia were enriched in metabolic pathways, cycle, DNA replication, and repair. The differentially splicing events in the transcriptome of glucose-relieved conidia are far more than that of other two transcriptomes, and genes regulated by differentially splicing were analyzed through KEGG pathway analysis. Furthermore, autophagy genes were proved to play important role in resisting soil fungistasis and glucose-mediated soil fungistasis relief. These data indicate that, in addition to being a carbon and energy source for conidia germination, glucose may also help to relieve soil fungistasis by activating many cellular processes, including autophagy, DNA replication and repair, RNA alternative splicing, and degradation pathways.

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“…While assays of the first three phases are focused on assessing the drug effect on autophagy activity, the fourth phase puts the drug activity into a broader context. Due to overwhelming complexity of the network, it is frequently overlooked that autophagy is an integral part of the endomembrane trafficking system 26, 29, 30 . The assays in the fourth phase help to identify treatment conditions under which the candidate drugs significantly influence autophagy activity while not causing detectable aberrations in other components of the trafficking machinery.…”

Section: Discussionmentioning

confidence: 99%

Chemical screening pipeline for identification of specific plant autophagy modulators

Dauphinee

Cardoso

Dalman

et al. 2019

Preprint

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16Autophagy is a major catabolic process in eukaryotes and is implicated in responses to biotic 17 and abiotic stresses, programs of aging and cell death. Autophagy is known to regulate 18 agriculturally important traits such as plant fitness, longevity, biomass and seed yield. 19 However, despite its obvious significance, there is still a shortage of reliable tools modulating 20 plant autophagy. Here we describe the first robust pipeline for identification of specific plant 21 autophagy-modulating compounds. Our novel screening protocol comprises four phases: (i) 22 high-throughput screening of chemical compounds in cell cultures of Nicotiana tabacum; (ii) 23 confirmation of the identified hits in planta using Arabidopsis thaliana; (iii) further 24 characterization of the effect using conventional molecular biology methods; (iv) verification 25 of specificity of the effect to autophagy in planta. The methods detailed here streamline 26 identification of specific plant autophagy modulators and greatly aid in unravelling the 27 molecular mechanisms of plant autophagy. 28 Main 29Autophagy is a key regulator of eukaryotic cellular homeostasis and plays an essential role in 30 abiotic and biotic stress responses, fecundity, aging and cell death 1-5 . The autophagy pathway 31 comprises selective or bulk sequestration of cytosolic contents into double-membraned vesicles 32 known as autophagosomes and their delivery to the lytic compartment, where autophagy 33 activity (or autophagic flux) completes with the degradation of the delivered cargo 6 . Autophagy 34 in eukaryotes is coordinated by evolutionary conserved autophagy-related (ATG) proteins that 35 orchestrate sequestration of the cargo, formation and trafficking of the autophagosomes and 36 cargo degradation. Among these proteins, ATG8 is remarkable in the sense that it is 37 incorporated into the membranes of forming autophagosomes, trafficked to the lytic 38 compartment and degraded together with the cargo, making it an ideal tool for autophagy 39 activity read-out 7 . 40 The importance of autophagy for plant stress tolerance in general and crop performance in 41 particular is of critical interest in plant biology, requiring continuous development of 42 increasingly sophisticated tools for its investigation 1,8 . The forward and reverse genetic 43 approaches such as knockouts, knockdowns and overexpression of ATG genes, although being 44 effective tools, have certain limitations 1,7 . The chemical modulation of autophagy presents an 45 alternative option and has also been instrumental for our current understanding of the 46 3 underlying mechanisms controlling autophagy 7 . However, an increasing number of studies 47 describe significant off-target effects of commonly used autophagy-modulating drugs. For 48 example, 3-methyladenine (3-MA) that is typically used as an inhibitor of autophagy 7 , can also 49 increase autophagic flux after prolonged treatments due to its transient suppression of class III 50 phosphoinositide 3-kinases (PI3Ks) 9 . Another ...

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Membrane Trafficking in Autophagy

Cited by 91 publications

References 387 publications

Chemical Screening Pipeline for Identification of Specific Plant Autophagy Modulators

Chemical Screening Pipeline for Identification of Specific Plant Autophagy Modulators

Comparative Transcriptomics Reveals Features and Possible Mechanisms of Glucose-Mediated Soil Fungistasis Relief in Arthrobotrys oligospora

Chemical screening pipeline for identification of specific plant autophagy modulators

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