Chemical Biology Strategies to Study Autophagy

Growing amount of evidence in the last two decades highlight that macroautophagy (generally referred to as autophagy) is not only indispensable for survival in yeast but also equally important to maintain cellular quality control in higher eukaryotes as well. Importantly, dysfunctional autophagy has been explicitly shown to be involved in various physiological and pathological conditions such as cell death, cancer, neurodegenerative, and other diseases. Therefore, modulation and regulation of the autophagy pathway has emerged as an alternative strategy for the treatment of various disease conditions in the recent years. Several studies have shown genetic or pharmacological modulation of autophagy to be effective in treating cancer, clearing intracellular aggregates and pathogens. Understanding and controlling the autophagic flux, either through a genetic or pharmacological approach is therefore a highly promising approach and of great scientific interest as spatiotemporal and cell-tissue-organ level autophagy regulation is not clearly understood. Indeed, chemical biology approaches that identify small molecule effectors of autophagy have thus a dual benefit: the modulators act as tools to study and understand the process of autophagy, and may also have therapeutic potential. In this review, we discuss different strategies that have appeared to screen and identify potent small molecule modulators of autophagy

A yeast MAPK cascade regulates pexophagy but not other autophagy pathways

The S. cerevisiae Slt2p MAPK cascade picks out peroxisomes for autophagy-mediated degradation (pexophagy) but is not involved in turnover of other cellular components

Fluorescence microscopy: A tool to study autophagy

Autophagy is a cellular recycling process through which a cell degrades old and damaged cellular components such as organelles and proteins and the degradation products are reused to provide energy and building blocks. Dysfunctional autophagy is reported in several pathological situations. Hence, autophagy plays an important role in both cellular homeostasis and diseased conditions. Autophagy can be studied through various techniques including fluorescence based microscopy. With the advancements of newer technologies in fluorescence microscopy, several novel processes of autophagy have been discovered which makes it an essential tool for autophagy research. Moreover, ability to tag fluorescent proteins with sub cellular targets has enabled us to evaluate autophagy processes in real time under fluorescent microscope. In this article, we demonstrate different aspects of autophagy in two different model organisms i.e. yeast and mammalian cells, with the help of fluorescence microscopy

A small molecule autophagy inducer exerts cytoprotection against alpha-synuclein toxicity

alpha-synucleopathies are protein-misfolding disorders occur primarily due to aggregation and toxicity of alpha-synuclein. This study characterized the small molecule AGK2 as a modifier of alpha-synuclein mediated toxicity in an autophagy dependent manner in both yeast and mammalian cell line models. In yeast system, AGK2 enhances autophagy to clear toxic alpha-synuclein aggregates in an autophagy dependent manner. Autophagy flux analyses revealed that AGK2 induces autophagy especially autolysosomes. Importantly, AGK2 induces autophagy in an mTOR independent manner. These features enable AGK2 to exert cytoprotective potential against a-synuclein mediated toxicity in different model systems

The 3' Untranslated Region of Bovine Follicle-Stimulating Hormone β\beta Messenger RNA Downregulates Reporter Expression: Involvement of AU-Rich Elements and Transfactors

FSH$\beta$ mRNA has a unique 3' untranslated region (3'UTR) that is highly conserved across the species. Sequence analyses of the mouse, rat, human, bovine, and ovine 3'UTRs revealed the presence of elements implicated in mRNA instability and translational control such as AU-Rich Element (ARE) and lipoxygenase differentiation control elements. Bovine FSH$\beta$ 3'UTR down-regulated reporter expression in aT3-1 and NIH3T3 cells, but not in HEK 293 cells, suggesting the involvement of a cellspecific factor or mechanism. The presence of a 3'UTR did not influence reporter mRNA stability, but it did decrease its association with polysomes, indicating that the downregulatory effect may be exerted at the translational level. The segment spanning 601–800 bases (U4) of the bovine FSH$\beta$ 3'UTR was found to be the most effective downregulating segment, its effect being equal to that of the full-length 3'UTR. RNA electrophoretic mobility shift assay with U4 showed the presence of specific transfactors in the cytosolic preparations of bovine pituitary and the cell lines. U4 contained an ARE that appeared to be functional, because the mutated U4 ARE was ineffective in downregulating the reporter expression and inhibiting [32P]-labeled U4-transfactor complex formation. Downregulation of reporter activity by the full-length 3'UTR and U4 could be overcome by overexpression of HuR, a protein known to stabilize ARE-containing mRNAs in NIH3T3 cells, but not in the aT3-1 cells, once again indicating that factors other than HuR may also be involved in the regulation of FSH$\beta$ in the pituitary

The 3' untranslated region of bovine follicle-stimulating hormone β messenger RNA downregulates reporter expression: involvement of AU-rich elements and transfactors

FSHβ mRNA has a unique 3' untranslated region (3'UTR) that is highly conserved across the species. Sequence analyses of the mouse, rat, human, bovine, and ovine 3'UTRs revealed the presence of elements implicated in mRNA instability and translational control such as AU-Rich Element (ARE) and lipoxygenase differentiation control elements. Bovine FSHβ 3'UTR down-regulated reporter expression in aT3-1 and NIH3T3 cells, but not in HEK 293 cells, suggesting the involvement of a cell-specific factor or mechanism. The presence of a 3'UTR did not influence reporter mRNA stability, but it did decrease its association with polysomes, indicating that the downregulatory effect may be exerted at the translational level. The segment spanning 601-800 bases (U4) of the bovine FSHβ 3'UTR was found to be the most effective downregulating segment, its effect being equal to that of the full-length 3'UTR. RNA electrophoretic mobility shift assay with U4 showed the presence of specific transfactors in the cytosolic preparations of bovine pituitary and the cell lines. U4 contained an ARE that appeared to be functional, because the mutated U4 ARE was ineffective in downregulating the reporter expression and inhibiting [32P]-labeled U4-transfactor complex formation. Downregulation of reporter activity by the full-length 3'UTR and U4 could be overcome by overexpression of HuR, a protein known to stabilize ARE-containing mRNAs in NIH3T3 cells, but not in the αT3-1 cells, once again indicating that factors other than HuR may also be involved in the regulation of FSHβ in the pituitary

Role of diacylglycerol kinase in autophagy, ER biogenesis, and triterpene metabolism

Saccharomyces cerevisiae is widely used for producing various triterpenes by exploiting its native mevalonate/ergosterol pathway. Yeasts that accumulate phospholipids can produce more triterpenes. Our recent study demonstrated that a high phospholipid-accumulating yeast phenotype, as in spt10Δ yeast, results in increased endoplasmic reticulum (ER) biogenesis, resulting in ER expansion. However, the spt10Δ strain also exhibits high reticulophagy. Dgk1 (diacylglycerol kinase) is an important enzyme in lipid metabolism, which synthesizes phosphatidic acid (PA) by phosphorylating diacylglycerol (DG). We demonstrate that spt10Δ yeast with increased Dgk1 activity offer two desired results, (i) a highly expanded ER, due to redirection of the lipid pathway away from triglycerides towards phospholipid synthesis, increasing ER biogenesis; and (ii) decreased reticulophagy, by increasing the PA pool that activates TOR complex-mediated autophagy suppression. It was speculated that more ER-bound pathway enzymes can fit in the expanded ER, and the mevalonate-ergosterol pathway, being ER bound, might have higher activity. This was demonstrated by the co-expression of Dgk1 and plant triterpene synthase in spt10Δ yeast, which shows a high accumulation of plant triterpene