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

Abstract

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.

Hygromycin B hypersensitive (hhy) mutants implicate an intact trans-Golgi and late endosome interface in efficient Tor1 vacuolar localization and TORC1 function

“…They also include the conserved master regulatory signaling complex involved in regulation of cell proliferation and growth, Tor Complex 1 (TORC1) (reviewed in Loewith and Hall 2011). TORC1 positively regulates several anabolic processes including ribosome biogenesis, protein synthesis and nutrient uptake; it also negatively regulates catabolic processes such as autophagy and ubiquitin-mediated proteolysis (Hall 2008; Cybulski and Hall 2009; reviewed in (Reggiori et al 2013; Delorme-Axford et al 2015)). mTOR complex 1 (mTORC1) is known to activate stress-responsive transcription factors (reviewed in Aramburu et al 2014; Ho and Gasch, 2015).…”

Autophagy in Plant Pathogenic Fungi

“…Limited numbers of studies examining autophagy in filamentous fungi have extended the knowledge gleaned from S. cerevisiae, the model organism for the study of autophagy [23]. Generally, autophagy consists of four sequential steps: (1) induction of autophagy; (2) recruitment of ATG proteins by phagophore assembly site proteins, the rapid formation of two-layer autophagosomal membrane structures, and isolation of the cytoplasm and organelles; (3) fusion of autophagosomes with lysosomes/vacuoles, in which the inner membrane of the autophagosome and the cytoplasm-derived materials are contained in the autophagosome; and (4) degradation of autophagic bodies in the vacuole into macromolecules that will be recycled.…”

“…Fungi can also be induced by treatment with rapamycin, often with concentrations between 200 and 500 ng/ml in fungal culture [23,24,28,29].…”

Assessing the progression of autophagy pathways in different organisms and tissues

“…The general conceptual views behind the available techniques are described in a article focused on yeast Saccharomyces cerevisiae, which has been the leading model organism to investigate autophagy for numerous years (Article 1, Elisabeth DelormeAxford and co-workers, ''The yeast Saccharomyces cerevisiae: An overview of methods to study autophagy progression'') [13].…”