Dalibor Mijaljica

Different fates of mitochondria: alternative ways for degradation?

Cellular degradative processes including proteasomal and vacuolar / lysosomal (autophagic) degradation, as well as the activity of proteases (both cytosolic and mitochondrial), provide for a continuous turnover of damaged and obsolete macromolecules and organelles. Mitochondria are organelles essential for respiration and oxidative energy production in aerobic cells; they are also required for multiple biosynthetic pathways. As such, mitochondrial homeostasis is very important for cell survival. We review the evidence regarding the possible mechanisms for mitochondrial degradation. Increasingly, the evidence suggests autophagy plays a central role in the degradation of mitochondria. How mitochondria might be specifically selected for autophagy (mitophagy) remains an open question, although some evidence suggests that, under certain circumstances, in mammalian cells the Mitochondrial Permeability Transition (MPT) plays a role in initiation of the process. As more is learned about the functioning of autophagy as a degradation process, the greater the appreciation we are developing concerning its role in the control of mitochondrial degradation.

Rosella: a fluorescent pH-biosensor for reporting vacuolar turnover of cytosol and organelles in yeast.

We have developed a method for monitoring autophagy using Rosella, a biosensor comprised of a fast-maturing pH-stable red fluorescent protein fused to a pH-sensitive green fluorescent protein variant. Its mode of action relies upon differences in pH between different cellular compartments and the vacuole. Here we demonstrate its utility in yeast (Saccharomyces cerevisiae) by expression in the cytosol, and targeting to mitochondria or to the nucleus. When cells were cultured in nitrogen depleted medium, uptake of the compartment labelled with the biosensor (i.e. cytosol, mitochondria, or nucleus) into the vacuole was observed. We showed that this vacuolar uptake was, for cytosol and mitochondria, an ATG8-dependent process while the uptake of the nucleus was significantly reduced in the absence of Atg8p and can be said to be partially ATG8-dependent. We further demonstrated the value of the biosensor as a reporter of autophagy by employing fluorescence-activated cell sorting of discrete populations of cells undergoing autophagy.

Endoplasmic Reticulum and Golgi Complex: Contributions to, and Turnover by, Autophagy

The degradation of cytoplasmic contents, especially organelles [mitochondria, peroxisomes, endoplasmic reticulum (ER), Golgi complex (GC)], cannot be accomplished solely by the cytosolic degradation machinery, of which the most prominent component is the proteasome. However, it is possible that such organelles (or portions thereof) can be degraded by the cell’s autophagic machinery. In this manner, organelles can be either specifically or non‐specifically targeted to the vacuole/lysosome for degradation. These processes can be triggered in response to different environmental cues. Here, we focus on two particular organelles, the ER and the GC, and their relationship with the autophagic process. Firstly, we briefly consider how these two organelles contribute to the synthesis and delivery of hydrolytic enzymes involved in autophagy as well as how they may potentially contribute to their own degradation by addressing the origin of the autophagic membrane. Secondly, we summarize the evidence for the turnover of these two organelles by autophagic processes in different organisms.

Nucleophagy at a glance.

Summary Under certain circumstances, the removal of damaged or non-essential parts of the nucleus, or even an entire nucleus, is crucial in order to promote cell longevity and enable proper function. A selective form of autophagy, known as nucleophagy, can be used to accomplish the degradation of nucleus-derived material. In this Cell Science at a Glance article and the accompanying poster, we summarize the similarities and differences between the divergent modes of nucleophagy that have been described to date, emphasizing, where possible, the molecular mechanism, the membrane interactions and rearrangements, and the nature of the nucleus-derived material that is degraded. In turn, we will consider nucleophagy processes in the lower eukaryotes, the budding yeast Saccharomyces cerevisiae, filamentous fungi Aspergillus and Magnaporthe oryzae and the ciliated protozoan Tetrahymena thermophila, and finally in mammalian cells. We will also briefly discuss the emerging links between nucleophagy and human disease.

Receptor protein complexes are in control of autophagy

In autophagic processes a variety of cargos is delivered to the degradative compartment of cells. Recent progress in autophagy research has provided support for the notion that when autophagic processes are operating in selective mode, a receptor protein complex will process the cargo. Here we present a concept of receptor protein complexes as comprising a functional tetrad of components: a ligand, a receptor, a scaffold and an Atg8 family protein. Our current understanding of each of the four components and their interaction in the context of cargo selection are considered in turn.

Autophagy and Vacuole Homeostasis: A Case for Self-Degradation?

The vacuole of yeast plays an important role in pH- and ion-homeostasis. Another important function of the vacuole, especially during nutrient deprivation, is the degradation of proteins, other macromolecules and organelles. To deliver these components into the vacuolar lumen, specific and sophisticated transport pathways such as autophagy have evolved. This review will first look at autophagy and its relationship to vacuole homeostasis, then move to the topic of vacuole self-degradation and possible reasons for its existence, and close by pointing very briefly to some areas for further research in these topics.

V-ATPase engagement in autophagic processes

The proton pumping activity of V-ATPase is responsible for acidification of the lysosome/vacuole. The low lumenal pH of this organelle stimulates the activity of a battery of resident hydrolases responsible for the degradation of various nonselective and selective cargos delivered by autophagic processes. However, the role of V-ATPase in membrane dynamics required for the uptake of autophagic cargo is far from fully understood. Consideration of the available data leads us to speculate that autophagic processes involving direct membrane-to-membrane contacts between the selected cargo and the vacuolar membrane require functional V-ATPase.

Determination of Adenosine A1 Receptor Agonist and Antagonist Pharmacology Using Saccharomyces cerevisiae: Implications for Ligand Screening and Functional Selectivity

The budding yeast, Saccharomyces cerevisiae, is a convenient system for coupling heterologous G protein-coupled receptors (GPCRs) to the pheromone response pathway to facilitate empirical ligand screening and/or GPCR mutagenesis studies. However, few studies have applied this system to define GPCR-G protein-coupling preferences and furnish information on ligand affinities, efficacies, and functional selectivity. We thus used different S. cerevisiae strains, each expressing a specific human Gα/yeast Gpa1 protein chimera, and determined the pharmacology of various ligands of the coexpressed human adenosine A1 receptor. These assays, in conjunction with the application of quantitative models of agonism and antagonism, revealed that (−)-N6-(2-phenylisopropyl)adenosine was a high-efficacy agonist that selectively coupled to Gpa/1Gαo, Gpa1/Gαi1/2, and Gpa1/Gαi3, whereas the novel compound, 5′-deoxy-N6-(endo-norborn-2-yl)-5′-(2-fluorophenylthio)adenosine (VCP-189), was a lower-efficacy agonist that selectively coupled to Gpa1/Gαi proteins; the latter finding suggested that VCP-189 might be functionally selective. The affinity of the antagonist, 8-cyclopentyl-1,3-dipropylxanthine, was also determined at the various strains. Subsequent experiments performed in mammalian Chinese hamster ovary cells monitoring cAMP formation/inhibition, intracellular calcium mobilization, phosphorylation of extracellular signal-regulated kinase 1 and 2 or 35S-labeled guanosine 5′-(γ-thio)triphosphate binding, were in general agreement with the yeast data regarding agonist efficacy estimation and antagonist affinity estimation, but revealed that the apparent functional selectivity of VCP-189 could be explained by differences in stimulus-response coupling between yeast and mammalian cells. Our results suggest that this yeast system is a useful tool for quantifying ligand affinity and relative efficacy, but it may lack the sensitivity required to detect functional selectivity of low-efficacy agonists.

A late form of nucleophagy in Saccharomyces cerevisiae.

Autophagy encompasses several processes by which cytosol and organelles can be delivered to the vacuole/lysosome for breakdown and recycling. We sought to investigate autophagy of the nucleus (nucleophagy) in the yeast Saccharomyces cerevisiae by employing genetically encoded fluorescent reporters. The use of such a nuclear reporter, n-Rosella, proved the basis of robust assays based on either following its accumulation (by confocal microscopy), or degradation (by immunoblotting), within the vacuole. We observed the delivery of n-Rosella to the vacuole only after prolonged periods of nitrogen starvation. Dual labeling of cells with Nvj1p-EYFP, a nuclear membrane reporter of piecemeal micronucleophagy of the nucleus (PMN), and the nucleoplasm-targeted NAB35-DsRed.T3 allowed us to detect PMN soon after the commencement of nitrogen starvation whilst delivery to the vacuole of the nucleoplasm reporter was observed only after prolonged periods of nitrogen starvation. This later delivery of nuclear components to the vacuole has been designated LN (late nucleophagy). Only a very few cells showed simultaneous accumulation of both reporters (Nvj1p-EYFP and NAB35-DsRed.T3) in the vacuole. We determined, therefore, that delivery of the two respective nuclear reporters to the vacuole is temporally and spatially separated. Furthermore, our data suggest that LN is mechanistically distinct from PMN because it can occur in nvj1Δ and vac8Δ cells, and does not require ATG11. Nevertheless, a subset of the components of the core macroautophagic machinery is required for LN as it is efficiently inhibited in null mutants of several autophagy-related genes (ATG) specifying such components. Moreover, the inhibition of LN in some mutants is accompanied by alterations in nuclear morphology.

The intriguing life of autophagosomes.

Autophagosomes are double-membrane vesicles characteristic of macroautophagy, a degradative pathway for cytoplasmic material and organelles terminating in the lysosomal or vacuole compartment for mammals and yeast, respectively. This highly dynamic, multi-step process requires significant membrane reorganization events at different stages of the macroautophagic process. Such events include exchange and flow of lipids and proteins between membranes and vesicles (e.g., during initiation and growth of the phagophore), vesicular positioning and trafficking within the cell (e.g., autophagosome location and movement) and fusion of autophagosomes with the boundary membranes of the degradative compartment. Here, we review current knowledge on the contribution of different organelles to the formation of autophagosomes, their trafficking and fate within the cell. We will consider some of the unresolved questions related to the molecular mechanisms that regulate the “life and death” of the autophagosome.