Enzyme-catalyzed proximity labeling (PL) has proven to be a valuable resource for proteomic mapping of subcellular compartments and protein networks in living cells. We have used engineered ascorbate peroxidase (APEX2) to develop a PL approach for budding yeast. It is based on semipermeabilized cells to overcome poor cellular permeability of the APEX2 substrate biotin-phenol and difficulties in its delivery into the cell. The use of semipermeabilized cells has several advantages, in particular the avoidance of generating fragile spheroplasts and the opportunity of employing cells from a glucose-containing medium for APEX2 tagging. In this protocol we describe how to perform a ratiometric three-state stable isotope labeling by amino acids in cell culture (SILAC) approach that allows to map an open cellular compartment like the yeast nucleus. In particular, we focus on the proteomic sample preparation and provide instructions to achieve high-resolution mapping of a subcellular yeast proteome.

Enzyme-catalyzed proximity labeling (PL) with the engineered ascorbate peroxidase APEX2 is a novel approach to map organelle compartmentalization and protein networks in living cells. Current procedures developed for mammalian cells do not allow delivery of the cosubstrate, biotin-phenol, into living yeast cells. Here, we present a new method based on semipermeabilized yeast cells. Combined with stable isotope labeling by amino acids in cell culture (SILAC), we demonstrate proteomic mapping of a membrane-enclosed and a semiopen compartment, the mitochondrial matrix and the nucleus. APEX2 PL revealed nuclear proteins that were previously not identified by conventional techniques. One of these, the Yer156C protein, is highly conserved but of unknown function. Its human ortholog, melanocyte proliferating gene 1, is linked to developmental processes and dermatological diseases. A first characterization of the Yer156C neighborhood reveals an array of proteins linked to proteostasis and RNA binding. Thus, our approach establishes APEX2 PL as another powerful tool that complements the methods palette for the model system yeast.

mRNA localization and localized translation is a common mechanism that contributes to cell polarity and cellular asymmetry. In metazoan, mRNA transport participates in embryonic axis determination and neuronal plasticity. Since the mRNA localization process and its molecular machinery are rather complex in higher eukaryotes, the unicellular yeast Saccharomyces cerevisiae has become an attractive model to study mRNA localization. Although the focus has so far been on the mechanism of ASH1 mRNA transport, it has become evident that mRNA localization also assists in protein sorting to organelles, as well as in polarity establishment and maintenance. A diversity of different pathways has been identified that targets mRNA to their destination site, ranging from motor protein-dependent trafficking of translationally silenced mRNAs to co-translational targeting, in which mRNAs hitch-hike to organelles on ribosomes during nascent polypeptide chain elongation. The presence of these diverse pathways in yeast allows a systemic analysis of the contribution of mRNA localization to the physiology of a cell.

mRNA localization and localized translation is a common mechanism that contributes to cell polarity and cellular asymmetry. In metazoan, mRNA transport participates in embryonic axis determination and neuronal plasticity. Since the mRNA localization process and its molecular machinery are rather complex in higher eukaryotes, the unicellular yeast Saccharomyces cerevisiae has become an attractive model to study mRNA localization. Although the focus has so far been on the mechanism of ASH1 mRNA transport, it has become evident that mRNA localization also assists in protein sorting to organelles, as well as in polarity establishment and maintenance. A diversity of different pathways has been identified that targets mRNA to their destination site, ranging from motor protein-dependent trafficking of translationally silenced mRNAs to co-translational targeting, in which mRNAs hitch-hike to organelles on ribosomes during nascent polypeptide chain elongation. The presence of these diverse pathways in yeast allows a systemic analysis of the contribution of mRNA localization to the physiology of a cell.

Yeast Dop1p is an essential protein that is highly conserved in evolution and whose function is largely unknown. Here, we provide evidence that Dop1p localizes to endosomes and exists in a complex with two other conserved proteins: Neo1p, a P-4-ATPase and putative flippase, and the scaffolding protein Ysl2p/Mon2p. The latter operates during membrane budding at the tubular endosomal network/trans-Golgi network (TEN/TGN) in a process that includes clathrin recruitment via adaptor proteins. Consistent with a role for Dop1p during this process, temperature-sensitive dop1-3 cells accumulate multivesicular, elongated tubular and ring-like structures similar to those displayed by neo1 and ysl2 mutants. In further agreement with the concept of Dop1p-Neo1p-Ysl2p complex formation and co-operation, we show that dop1-3 cells exhibit reduced levels of Neo1p and Ysl2p at steady state. Conversely, mutations or deletions in NEO1 and YSL2 lead to a decrease in Dop1p levels. In addition to binding to Neo1p and Ysl2p, Dop1p can form dimers or multimers. A critical region for dimerization resides in the C-terminus with leucine zipper-like domains. Dop1p's membrane association is largely mediated by its internal region, but Ysl2p might not be crucial for membrane recruitment.

The Gga proteins represent a family of ubiquitously expressed clathrin adaptors engaged in vesicle budding at the tubular endosomal network/trans Golgi network. Their membrane recruitment is commonly thought to involve interactions with Arf and signals in cargo through the so-called VHS domain. For yeast Gga proteins, however, partners binding to its VHS domain have remained elusive and Gga localization does not absolutely depend on Arf. Here, we demonstrate that yeast Gga recruitment relies on a network of interactions between the scaffold Ysl2p/Mon2p, the small GTPase Arl1p, and the flippase Neo1p. Deletion of either YSL2 or ARL1 causes mislocalization of Gga2p, whereas a neo1-69 mutant accumulates Gga2p on aberrant structures. Remarkably, Ysl2p directly interacts with human and yeast Ggas through the VHS domain, and binding to Gga proteins is also found for the human Ysl2p orthologue hMon2. Thus, Ysl2p represents an essential, evolutionarily conserved member of a network controlling direct binding and membrane docking of Ggas. Because activated Arl1p is part of the network that binds Gga2p, Arf and Arf-like GTPases may interact in a regulatory cascade.

Sjl2p is one of three yeast phosphoinositide 5′‐phosphatases that belong to the conserved family of synaptojanins. Here, we show that Sjl2p is specifically associated with cortical actin patches which aggregate upon loss of the actin‐regulating kinases Ark1p and Prk1p. The Sjl2p‐containing clumps overlap with clathrin and early endocytic structures generated independently of NSF/Sec18p, but not with endosome‐ and trans Golgi network‐derived membranes. Consistent with the finding that Sjl2p can bind to clathrin heavy chain in vitro, our results suggest that Sjl2p localizes to smooth endocytic vesicles that may be derived from clathrin‐coated structures.

Neo1p is an essential yeast member of the highly conserved Drs2 family of P-type ATPases with proposed aminophospholipid translocase activity. Here we present evidence that Neo1p localizes to endosomes and Golgi elements. In agreement with that finding, the temperature-sensitive neo1-37 and neo1-69 mutants exhibit defects in receptor-mediated endocytosis, vacuole biogenesis, and vacuolar protein sorting. Furthermore, neo1 mutants accumulate aberrantly shaped membranous structures most likely derived from vacuoles and the endosomal/Golgi system. At permissive temperatures, HA-Neo1-69p, like wild-type Neo1p, is stable and associates with endosomes. In contrast, HA-Neo1-37p is rapidly degraded and is predominantly retained within the endoplasmic reticulum (ER). Thus, the two neo1 alleles affect the stability and localization of the mutant polypeptides in different ways. A C-terminally truncated and a C-terminally epitope-tagged version of Neo1p are nonfunctional and also mislocalize to the ER. In agreement with a role within the endomembrane system, Neo1p exhibits genetic and physical interactions with Ysl2p, a potential guanine nucleotide exchange factor for Arl1p. Interestingly, deletion of ARL1 rescues the temperature sensitivity of neo1-37 and neo1-69. We demonstrate that Arl1p in its myristoylated and GTP-bound form is responsible for the inhibitory effect. Thus, Neo1p, Ysl2p, and Arl1p represent three proteins that collaborate in membrane trafficking within the endosomal/Golgi system.

In this study we identified a novel protein, Bsp1p, that interacts directly with two yeast synaptojanins, Sjl2p and Sjl3p, but not with Sjl1p. The interaction takes place via the Sac1/polyphosphoinositide phosphatase domain, whose conserved C-terminal region is important for binding. Subcellular localization and genetic interactions revealed a function of Bsp1p in the cortical actin cytoskeleton. A fraction of Bsp1p was found to be membrane-associated. Studies with mutants of phosphatidylinositol 4-kinase, PIK1, suggested that the interaction with membranes is facilitated by phosphoinositides. We propose that Bsp1p is an adapter that links Sjl2p and Sjl3p to the cortical actin cytoskeleton.

We previously described the isolation of ysl2-1 due to its genetic interaction with Deltaypt51/vps21, a mutant with a deletion of the coding sequence for the yeast Rab5 homolog, which regulates endocytic traffic between early and late endosomes. Here we report that Ys12p is a novel 186.8-kDa peripheral membrane protein homologous to members of the Sec7 family. We provide multiple genetic and biochemical evidence for an interaction between Ys112p and the Arf-like protein Ar11p, consistent with a potential function as an Arf guanine nucleotide exchange factor (GEF). The temperature-sensitive alleles ysl2-307 and ysl2-316 are specifically defective in ligand-induced degradation of Ste2p and alpha-factor and exhibit vacuole fragmentation directly upon a shift to 37degreesC. In living cells, green fluorescent protein (GFP)-Ysl2p colocalizes with endocytic elements that accumulate FM4-64. The GFP-Ysl2p staining is sensitive to a mutation in VPS27 resulting in the formation of an aberrant class E compartment, but it is not affected by a sec7 mutation. Consistent with the idea that Ysl2p and Ar11p have closely related functions, Deltaarl1 cells are defective in endocytic transport and in vacuolar protein sorting.

S. cerevisiae exists in two haploid cell types, a and α, which mate with each other to form the diploid a/α cell. Essential to the mating process is the reciprocal action of two peptide mating factors called a- and α-factor. The factors induce changes in the pattern of mRNA and protein synthesis, an arrest in the G1 phase of the cell cycle and a morphological change called the “shmoo”. This oriented projection is the site where the two haploid cells fuse (see Cross et al 1988 for a review). The a- and α-factor receptors have been identified as the products of the STE3 and STE2 genes respectively (Jenness et al 1983; Nakayama et al 1985; Hagen et al 1986). These two receptors are polytopic membrane proteins that share a common basic structure with the β- adrenergic receptor (Dixon et al 1986). Like this receptor, the STE2 and STE3 gene products are coupled to a G protein (Dietzel and Kurjan 1987; Miyajima et al 1987; Whiteway et al 1989). The enzyme controlled by the G-protein has not been identified although several other genes acting downstream in the signal transduction pathway are known (Nakayama et al 1988; Blinder et al 1989).

This chapter describes the yeast endocytosis assays. Lucifer Yellow carbohydrazide (LY) is asmall fluorescent molecule that can be used as a marker of fluid-phase endocytosis in mammalian systems. Internalized LY accumulates in the yeast vacuole and can easily be visualized by fluorescence microscopy. Results obtained with LY are best interpreted when combined with the results from α-factor uptake and degradation assays. The only specific marker of endocytosis by yeast cells described to date is the pheromone α-factor, α-Factor binds to the α-factor receptor on a cells. Using α-factor one can distinguish three distinct events: binding to cell surface receptors, internalization of the pheromone, and degradation of internalized α-factor. Recently, researchers have detected a vesicular intermediate in the transport of α-factor to the vacuole. The α-factor carded in this vesicle is protected from protease digestion by the membrane and floats in density gradients. The identification of this vesicular intermediate provides evidence for the delivery of α-factor to the vacuole via an endocytic mechanism. α-factor internalization is to date the most reliable way to quantitatively assess the earlier stages of endocytosis in yeast. An inability to degrade internalized α-factor could reflect, depending on the circumstances, the absence of vacuolar hydrolase activity or a defect in transport of α-factor to the vacuole.