The progression of peroxisomal degradation through autophagy requires peroxisomal division

Mao, Kai; Liu, Xu; Feng, Yuchen; Klionsky, Daniel J.

doi:10.4161/auto.27852

Cited by 65 publications

(80 citation statements)

References 31 publications

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“…Similarly, pexophagy can be stimulated by culturing S. cerevisiae cells in oleate medium (YTO: 0.67% yeast nitrogen base without amino acids, 0.1% Tween-40, 0.1% oleic acid, pH 5.5; or YPO: 0.25% yeast extract, 0.5% peptone, 1% oleate, 5% Tween-40, 5 mM phosphate buffer, pH 5.5), and shifting to SD-N for at least 2 h [6, 58, 59] (see the accompanying review by Guimaraes et al for a detailed protocol to measure pexophagy). Growth in medium containing oleic acid (or methanol in the case of methylotrophic fungi such as P. pastoris and H. polymorpha ) as the sole carbon source causes peroxisome proliferation (in both size and number); the subsequent shift to glucose (or ethanol) medium with or without nitrogen starvation induces pexophagy to degrade the superfluous peroxisomes [6, 59–62].…”

Section: Induction and Nucleation Of The Phagophorementioning

confidence: 99%

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The yeast Saccharomyces cerevisiae: An overview of methods to study autophagy progression

Delorme-Axford

Guimarães²,

Reggiori³

et al. 2015

Methods

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Macroautophagy (hereafter autophagy) is a highly evolutionarily conserved process essential for sustaining cellular integrity, homeostasis, and survival. Most eukaryotic cells constitutively undergo autophagy at a low basal level. However, various stimuli, including starvation, organelle deterioration, stress, and pathogen infection, potently upregulate autophagy. The hallmark morphological feature of autophagy is the formation of the double-membrane vesicle known as the autophagosome. In yeast, flux through the pathway culminates in autophagosome-vacuole fusion, and the subsequent degradation of the resulting autophagic bodies and cargo by vacuolar hydrolases, followed by efflux of the breakdown products. Importantly, aberrant autophagy is associated with diverse human pathologies. Thus, there is a need for ongoing work in this area to further understand the cellular factors regulating this process. The field of autophagy research has grown exponentially in recent years, and although numerous model organisms are being used to investigate autophagy, the baker’s yeast Saccharomyces cerevisiae remains highly relevant, as there are significant and unique benefits to working with this organism. In this review, we will focus on the current methods available to evaluate and monitor autophagy in S. cerevisiae, which in several cases have also been subsequently exploited in higher eukaryotes.

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Section: Induction and Nucleation Of The Phagophorementioning

confidence: 99%

“…In yeast, autophagosomes typically range from ∼300–900 nm in diameter [3, 4]. Nonetheless, efficient degradation of organelles such as peroxisomes and mitochondria involves their fission by the dynamin-related GTPase Dnm1 complex prior to, or during, engulfment by phagophores [5, 6]. …”

Section: Introductionmentioning

confidence: 99%

The yeast Saccharomyces cerevisiae: An overview of methods to study autophagy progression

Delorme-Axford

Guimarães²,

Reggiori³

et al. 2015

Methods

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“…Briefly, in the BiFC assay, the Venus yellow fluorescent protein (vYFP) is split into 2 fragments, VN (corresponding to the N terminus of vYFP) and VC (the C terminus of vYFP). 48,49 We fused VN to Atg9 and VC to either Atg23 or Atg27 on the genome. Fluorescence from these 2 chimeras can only be detected when the 2 proteins interact and bring the 2 fragments of vYFP proximal to each other.…”

Section: Phosphorylation Of S122 Regulates Atg9 Through Its Interactimentioning

confidence: 99%

“…21,49,57,58 Antibodies against Atg9, Ape1 and Pgk1 (a generous gift from Dr. Jeremy Thorner, University of California, Berkeley), and a commercial antibody that reacts with protein A (no longer available) were used as described previously. 15,35 Anti-Dpm1 was from Molecular Probes/Invitrogen (A-6429).…”

Section: Additional Assaysmentioning

confidence: 99%

Phosphorylation of Atg9 regulates movement to the phagophore assembly site and the rate of autophagosome formation

Feng¹,

Backues²,

Baba³

et al. 2016

Autophagy

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Macroautophagy is primarily a degradative process that cells use to break down their own components to recycle macromolecules and provide energy under stress conditions, and defects in macroautophagy lead to a wide range of diseases. Atg9, conserved from yeast to mammals, is the only identified transmembrane protein in the yeast core macroautophagy machinery required for formation of the sequestering compartment termed the autophagosome. This protein undergoes dynamic movement between the phagophore assembly site (PAS), where the autophagosome precursor is nucleated, and peripheral sites that may provide donor membrane for expansion of the phagophore. Atg9 is a phosphoprotein that is regulated by the Atg1 kinase. We used stable isotope labeling by amino acids in cell culture (SILAC) to identify phosphorylation sites on this protein and identified an Atg1-independent phosphorylation site at serine 122. A nonphosphorylatable Atg9 mutant showed decreased autophagy activity, whereas the phosphomimetic mutant enhanced activity. Electron microscopy analysis suggests that the different levels of autophagy activity reflect differences in autophagosome formation, correlating with the delivery of Atg9 to the PAS. Finally, this phosphorylation regulates Atg9 interaction with Atg23 and Atg27.

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“…In budding yeast, efficient organelle autophagy requires the participation of organelle fission machinery, suggesting that it is important to match the size of the organelle cargo with the size of the autophagosome (Mao et al, 2013(Mao et al, , 2014. We found in this study that an organelle autophagy defect and a reduction of autophagosome size are two correlated phenotypes of mutants that lack Atg20-and Atg24-family proteins.…”

Section: Discussionmentioning

confidence: 58%

Atg20- and Atg24-family proteins promote organelle autophagy in fission yeast

Zhao

Liu

et al. 2016

Journal of Cell Science

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Autophagy cargos include not only soluble cytosolic materials but also bulky organelles, such as ER and mitochondria. In budding yeast, two proteins that contain the PX domain and the BAR domain, Atg20 and Atg24 (also known as Snx42 and Snx4, respectively) are required for organelle autophagy and contribute to general autophagy in a way that can be masked by compensatory mechanisms. It remains unclear why these proteins are important for organelle autophagy. Here, we show that in a distantly related fungal organism, the fission yeast Schizosaccharomyces pombe, autophagy of ER and mitochondria is induced by nitrogen starvation and is promoted by three Atg20-and Atg24-family proteins -Atg20, Atg24 and SPBC1711.11 (named here as Atg24b). These proteins localize at the pre-autophagosomal structure, or phagophore assembly site (PAS), during starvation. S. pombe Atg24 forms a homo-oligomer and acts redundantly with Atg20 and Atg24b, and the latter two proteins can form a hetero-oligomer. The organelle autophagy defect caused by the loss of these proteins is associated with a reduction of autophagosome size and a decrease in Atg8 accumulation at the PAS. These results provide new insights into the autophagic function of Atg20-and Atg24-family proteins.

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The progression of peroxisomal degradation through autophagy requires peroxisomal division

Cited by 65 publications

References 31 publications

The yeast Saccharomyces cerevisiae: An overview of methods to study autophagy progression

The yeast Saccharomyces cerevisiae: An overview of methods to study autophagy progression

Phosphorylation of Atg9 regulates movement to the phagophore assembly site and the rate of autophagosome formation

Atg20- and Atg24-family proteins promote organelle autophagy in fission yeast

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