Analysis of the mitochondria-associated degradation pathway (MAD) in yeast cells.

Mitochondria are critical for cellular function in health, disease and aging. Mitochondria-associated degradation (MAD), a pathway for quality control of the organelle, recognizes and ubiquitinates unfolded mitochondrial proteins, removes them from the organelle using a conserved segregase complex, which contains an AAA-ATPase Cdc48 and its cofactors, and degrades them using the ubiquitin-proteasome system (UPS). Here, we describe an approach to (1) study the turnover and ubiquitination of candidate MAD substrates, (2) assay retrotranslocation and export of MAD substrates from the mitochondrial matrix in vitro, and (3) study interactions between MAD substrates and Cdc48 using the budding yeast, Saccharomyces cerevisiae, as a model organism.

Isolation of yeast mitochondria by affinity purification using magnetic beads.

Isolated mitochondria have been widely utilized in various model organisms to investigate the diverse functions of the organelle. Techniques such as differential centrifugation, density gradient ultracentrifugation and antibody-coated magnetic beads are employed for isolation of the organelle from whole cells. However, mitochondria isolated using differential centrifugation are often contaminated with other organelles; isolation using density gradient ultracentrifugation can reduce contamination but is time-intensive and requires large amounts of starting materials; and mitochondria isolated using antibody-coated magnetic beads are irreversibly bound to the beads.

Optical Control of G-Actin with a Photoswitchable Latrunculin.

Actin is one of the most abundant proteins in eukaryotic cells and is a key component of the cytoskeleton. A range of small molecules has emerged that interfere with actin dynamics by either binding to polymeric F-actin or monomeric G-actin to stabilize or destabilize filaments or prevent their formation and growth, respectively. Among these, the latrunculins, which bind to G-actin and affect polymerization, are widely used as tools to investigate actin-dependent cellular processes.

Optical Control of G-Actin with a Photoswitchable Latrunculin.

Actin is one of the most abundant proteins in eukaryotic cells and a key component of the cytoskeleton. A range of small molecules have emerged that interfere with actin dynamics by either binding to polymeric F-actin or monomeric G-actin to stabilize or destabilize filaments or prevent their formation and growth, respectively. Amongst these, the latrunculins, which bind to G-actin and affect polymerization, are widely used as tools to investigate actin-dependent cellular processes.

Enrichment of aging yeast cells and budding polarity assay in .

Replicative lifespan, a measure of the number of times that a yeast cell can divide before senescence, is one model for aging. Here, we provide a protocol for enrichment of yeast as a function of replicative age using a miniature chemostat aging device (mCAD). This protocol allows for isolation of quantities of cells that are sufficient for biochemical or genomic analysis.

Identification of a modulator of the actin cytoskeleton, mitochondria, nutrient metabolism and lifespan in yeast.

In yeast, actin cables are F-actin bundles that are essential for cell division through their function as tracks for cargo movement from mother to daughter cell. Actin cables also affect yeast lifespan by promoting transport and inheritance of higher-functioning mitochondria to daughter cells. Here, we report that actin cable stability declines with age.

A role for cell polarity in lifespan and mitochondrial quality control in the budding yeast .

Babies are born young, largely independent of the age of their mothers. Mother-daughter age asymmetry in yeast is achieved, in part, by inheritance of higher-functioning mitochondria by buds and retention of some high-functioning mitochondria in mother cells. The mitochondrial F box protein, Mfb1p, tethers mitochondria at both poles in a cell cycle-regulated manner: it localizes to and anchors mitochondria at the mother cell tip throughout the cell cycle and at the bud tip before cytokinesis.

Touch and Go: Membrane Contact Sites Between Lipid Droplets and Other Organelles.

Lipid droplets (LDs) have emerged not just as storage sites for lipids but as central regulators of metabolism and organelle quality control. These critical functions are achieved, in part, at membrane contact sites (MCS) between LDs and other organelles. MCS are sites of transfer of cellular constituents to or from LDs for energy mobilization in response to nutrient limitations, as well as LD biogenesis, expansion and autophagy.

Lipid droplets in stress protection: distinct mechanisms of lipid droplet microautophagy.

Lipid droplets (LDs) are organelles that function as sites for lipid storage. LDs have also been implicated in the cellular response to proteotoxic or lipotoxic stress as sites for sequestering dysfunctional or excess proteins or lipids, and targeting those cargos for degradation by LD microautophagy (microlipophagy, μLP). Here, we describe two mechanisms for μLP in yeast, which are triggered by different stressors.

Roles for L microdomains and ESCRT in ER stress-induced lipid droplet microautophagy in budding yeast.

Microlipophagy (µLP), degradation of lipid droplets (LDs) by microautophagy, occurs by autophagosome-independent direct uptake of LDs at lysosomes/vacuoles in response to nutrient limitations and ER stressors in . In nutrient-limited yeast, liquid-ordered (L) microdomains, sterol-rich raftlike regions in vacuolar membranes, are sites of membrane invagination during LD uptake. The endosome sorting complex required for transport (ESCRT) is required for sterol transport during L formation under these conditions.

Imaging the Actin Cytoskeleton in Fixed Budding Yeast Cells.

Budding yeast, Saccharomyces cerevisiae, is an appealing model organism to study the organization and function of the actin cytoskeleton. With the advent of techniques to perform high-resolution, multidimensional analysis of the yeast cell, imaging of yeast has emerged as an important tool for research on the cytoskeleton. This chapter describes techniques and approaches for visualizing the actin cytoskeleton in fixed yeast cells with wide-field and super-resolution fluorescence microscopy.

Imaging the Actin Cytoskeleton in Live Budding Yeast Cells.

Although budding yeast, Saccharomyces cerevisiae, is widely used as a model organism in biological research, studying cell biology in yeast was hindered due to its small size, rounded morphology, and cell wall. However, with improved techniques, researchers can acquire high-resolution images and carry out rapid multidimensional analysis of a yeast cell. As a result, imaging in yeast has emerged as an important tool to study cytoskeletal organization, function, and dynamics.

Live-Cell Imaging of Mitochondrial Redox State in Yeast Cells.

The redox state of mitochondria is one indicator of the functional state of the organelles. Mitochondria are also the primary endogenous source of reactive oxygen species (ROS). Therefore, the redox state of the organelles also reflects their function in ROS production.

Membrane dynamics and protein targets of lipid droplet microautophagy during ER stress-induced proteostasis in the budding yeast, .

Our previous studies reveal a mechanism for lipid droplet (LD)-mediated proteostasis in the endoplasmic reticulum (ER) whereby unfolded proteins that accumulate in the ER in response to lipid imbalance-induced ER stress are removed by LDs and degraded by microlipophagy (µLP), autophagosome-independent LD uptake into the vacuole (the yeast lysosome). Here, we show that dithiothreitol- or tunicamycin-induced ER stress also induces µLP and identify an unexpected role for vacuolar membrane dynamics in this process. All stressors studied induce vacuolar fragmentation prior to µLP.

Mitochondria-Associated Degradation Pathway (MAD) Function beyond the Outer Membrane.

The mitochondria-associated degradation pathway (MAD) mediates ubiquitination and degradation of mitochondrial outer membrane (MOM) proteins by the proteasome. We find that the MAD, but not other quality-control pathways including macroautophagy, mitophagy, or mitochondrial chaperones and proteases, is critical for yeast cellular fitness under conditions of paraquat (PQ)-induced oxidative stress in mitochondria. Specifically, inhibition of the MAD increases PQ-induced defects in growth and mitochondrial quality and decreases chronological lifespan.

Lysosomal recycling of amino acids affects ER quality control.

Recent work has highlighted the fact that lysosomes are a critical signaling hub of metabolic processes, providing fundamental building blocks crucial for anabolic functions. How lysosomal functions affect other cellular compartments is not fully understood. Here, we find that lysosomal recycling of the amino acids lysine and arginine is essential for proper ER quality control through the UPR.

Live-cell imaging of mitochondrial motility and interactions in Drosophila neurons and yeast.

Mitochondria are highly dynamic organelles that undergo directed movement and anchorage, which in turn are critical for calcium buffering and energy mobilization at specific regions within cells or at sites of contact with other organelles. Physical and functional interactions between mitochondria and other organelles also impact processes, including phospholipid biogenesis and calcium homeostasis. Indeed, mitochondrial motility, localization, and interaction with other organelles are compromised in many neurodegenerative diseases.

Isolation of mitochondria from cells and tissues.

Isolated mitochondria are useful to study fundamental processes including mitochondrial respiration, metabolic activity, protein import, membrane fusion, protein complex assembly, as well as interactions of mitochondria with the cytoskeleton, nuclear encoded mRNAs, and other organelles. In addition, studies of the mitochondrial proteome, phosphoproteome, and lipidome are dependent on preparation of highly purified mitochondria (Boldogh, Vojtov, Karmon, & Pon, 1998; Cui, Conte, Fox, Zara, & Winge, 2014; Marc et al., 2002; Meeusen, McCaffery, & Nunnari, 2004; Reinders et al.

Live cell imaging of mitochondrial redox state in mammalian cells and yeast.

The redox state of mitochondria is determined by the levels of reducing and oxidizing species in the organelle, which reflects mitochondrial metabolic activity and overall fitness. Mitochondria are also the primary endogenous source of reactive oxygen species (ROS). This chapter describes methods to measure the mitochondrial superoxide levels and the redox state of the organelle in mammalian cells and yeast.

Reciprocal interactions between mtDNA and lifespan control in budding yeast.

Loss of mitochondrial DNA (mtDNA) results in loss of mitochondrial respiratory activity, checkpoint-regulated inhibition of cell cycle progression, defects in growth, and nuclear genome instability. However, after several generations, yeast cells can adapt to the loss of mtDNA. During this adaptation, rho cells, which have no mtDNA, exhibit increased growth rates and nuclear genome stabilization.

Isolation of mitochondria from Saccharomyces cerevisiae using magnetic bead affinity purification.

Isolated mitochondria are widely used to study the function of the organelle. Typically, mitochondria are prepared using differential centrifugation alone or in conjunction with density gradient ultracentrifugation. However, mitochondria isolated using differential centrifugation contain membrane or organelle contaminants, and further purification of crude mitochondria by density gradient ultracentrifugation requires large amounts of starting material, and is time-consuming.

Mitochondrial Tethers and Their Impact on Lifespan in Budding Yeast.

Tethers that link mitochondria to other organelles are critical for lipid and calcium transport as well as mitochondrial genome replication and fission of the organelle. Here, we review recent advances in the characterization of interorganellar mitochondrial tethers in the budding yeast, . We specifically focus on evidence for a role for mitochondrial tethers that anchor mitochondria to specific regions within yeast cells.

Lipid droplet autophagy during energy mobilization, lipid homeostasis and protein quality control.

Lipid droplets (LDs) have well-established functions as sites for lipid storage and energy mobilization to meet the metabolic demands of cells. However, recent studies have expanded the roles of LDs to protein quality control. Lipophagy, or LD degradation by autophagy, plays a vital role not only in the mobilization of free fatty acids (FFAs) and lipid homeostasis at LDs, but also in the adaptation of cells to certain forms of stress including lipid imbalance.

ER-mitochondria tethering by PDZD8 regulates Ca dynamics in mammalian neurons.

Interfaces between organelles are emerging as critical platforms for many biological responses in eukaryotic cells. In yeast, the ERMES complex is an endoplasmic reticulum (ER)-mitochondria tether composed of four proteins, three of which contain a SMP (synaptotagmin-like mitochondrial-lipid binding protein) domain. No functional ortholog for any ERMES protein has been identified in metazoans.