Ume6 transcription factor is part of a signaling cascade that regulates autophagy

Abstract

Autophagy has been implicated in a number of physiological processes important for human heath and disease. Autophagy involves the formation of a double-membrane cytosolic vesicle, an autophagosome. Central to the formation of the autophagosome is the ubiquitin-like protein autophagy-related (Atg)8 (microtubuleassociated protein 1 light chain 3/LC3 in mammalian cells). Following autophagy induction, Atg8 shows the greatest change in expression of any of the proteins required for autophagy. The magnitude of autophagy is, in part, controlled by the amount of Atg8; thus, controlling Atg8 protein levels is one potential mechanism for modulating autophagy activity. We have identified a negative regulator of ATG8 transcription, Ume6, which acts along with a histone deacetylase complex including Sin3 and Rpd3 to regulate Atg8 levels; deletion of any of these components leads to an increase in Atg8 and a concomitant increase in autophagic activity. A similar regulatory mechanism is present in mammalian cells, indicating that this process is highly conserved.lysosome | membrane biogenesis | phagophore | stress | vacuole M acroautophagy, hereafter referred to as autophagy, is an evolutionarily conserved process used by eukaryotic cells for the bulk degradation of intracellular proteins and organelles (1). Autophagy is not only vital for cell survival in nutrient-poor conditions (2) but is also linked to various physiological processes, including immune defense, tumor suppression, and prevention of neurodegeneration (3). Whereas autophagy plays a primarily protective role, it can also contribute to cell death; thus, the magnitude of autophagy must be carefully regulated.Central to autophagy is the formation of autophagosomes (4), double-membrane-bound structures that engulf and deliver cytoplasmic materials to the vacuole/lysosome for degradation. During autophagosome formation, the autophagy-related ubiquitin-like protein Atg8/microtubule-associated protein 1 light chain 3 (LC3) covalently modifies phosphatidylethanolamine (PE). Almost one-fourth of the characterized autophagy-related (Atg) proteins in yeast are involved in the formation or stability of Atg8-PE, which plays a critical role in controlling expansion of the phagophore (the initial sequestering membrane), and in determining autophagosome size, thereby regulating autophagy activity (5, 6). Upon starvation, the level of ATG8 mRNA sharply increases, leading to a subsequent induction of the Atg8 protein level (7,8). The increase in the amount of Atg8 during autophagy is critical for supplying a sufficient amount of this protein to maintain normal levels of autophagy; yeast strains deficient in Atg8 induction generate abnormally small autophagosomes (5). Thus, characterization of how Atg8 protein levels are modulated is of tremendous importance both in understanding the regulation of autophagy and for the elucidation of potential therapeutic targets. However, little is known about the mechanisms regulating ATG8 transcription. ResultsUme6-Sin3-Rpd3 Complex Represse...

A large-scale analysis of autophagy-related gene expression identifies new regulators of autophagy

“…S1). 24,18 The results for all 139 strains in the different conditions are listed in Tables S1 to S3.…”

“…Such a phenotype is seen, for example, in the ume6D strain, where higher basal Atg8 levels result in a more rapid increase in autophagy activity in starvation conditions. 24 To extend our analysis we used the GFP-Atg8 processing assay. During autophagy, Atg8 is lipidated by conjugation with PE and recruited to the phagophore, the precursor to the autophagosome.…”

“…[22][23] In yeast, recent studies characterized Ume6 and Pho23 as transcriptional repressors of ATG genes and negative regulators of autophagy. 24,17 Nevertheless, very few transcription factors involved in the regulation of the expression of ATG genes in either yeast or mammals are known. To identify such regulators we conducted a screen in which DNA-binding protein deletion strains were tested for the expression of ATG genes.…”

Autophagic Processes in Yeast: Mechanism, Machinery and Regulation

“…The Ume6 transcription factor is part of a large complex that includes the Sin3 corepressor and the Rpd3 histone deacetylase. Deletion of any of the corresponding genes results in a dramatic increase in the amount of Atg8 prior to macroautophagy induction (Bartholomew et al 2012). The ATG8 promoter contains a consensus DNA binding sequence for Ume6.…”

Impacts of autophagy on nitrogen use efficiency in plants

“…The ubiquitin-like protein Atg8 has a central role in autophagosome formation. Atg8 levels determine the size of autophagosomes in yeast (Xie et al 2008;Bartholomew et al 2012). The functions of many of the core Atgs are related to the production of Atg8-PE.…”