The proteolytic landscape of the yeast vacuole

Abstract

The vacuole in the yeast Saccharomyces cerevisiae plays a number of essential roles, and to provide some of these required functions the vacuole harbors at least seven distinct proteases. These proteases exhibit a range of activities and different classifications, and they follow unique paths to arrive at their ultimate, common destination in the cell. This review will first summarize the major functions of the yeast vacuole and delineate how proteins are targeted to this organelle. We will then describe the specific trafficking itineraries and activities of the characterized vacuolar proteases, and outline select features of a new member of this protease ensemble. Finally, we will entertain the question of why so many proteases evolved and reside in the vacuole, and what future research challenges exist in the field.

Keywords: CPY; Pff1; S. cerevisiae; Vps10; autophagy; endocytosis; hydrolysis; metalloprotease; protease; secretory pathway.

Figure 1. Protein trafficking and vacuolar sorting pathways. Cellular compartments are labeled in black and secretory pathways discussed in this review are highlighted and color-coded. Of particular note are the vacuolar sorting pathways: the CPY pathway, shown in light blue; the ALP pathway, shown in green; and the Cvt pathway, shown in brown (see text for details). This image was adapted from Bowers et al. 2005.

Figure 2. (A) Sequence alignment of Ape3 (MEROPS accession: MER001288) and Pff1 (MEROPS accession: MER001911), two vacuole-resident yeast metalloproteases. A global sequence alignment was performed using ClustalW default parameters. Only the M28 domains of Ape3 and Ybr074 are shown according to the MEROPS defined protease domain boundaries. (B) Active site of the M28 metalloprotease, AM-1 Aminopeptidase, from Aneurinibacillus sp. strain AM-1 (MEROPS accession: MER100667; protease domain: Gly173-Arg436). Of the M28 metalloproteases whose crystal structures have been solved, the protease domain amino acid sequence of AM-1 Aminopeptidase is most similar to that of the yeast Pff1 (MEROPS accession: MER001911; protease domain: Asn96-Ala341). The MEROPS defined protease domain boundaries of AM-1 and Pff1 show 19.2% identity when compared by global sequence alignment using ClustalW default parameters. Catalytic residues are labeled in blue and metal coordinating residues are labeled in red in both this panel and in part (A). Zinc ions are depicted as red spheres. This image was captured from PDB ID: 2EK9 using 3D Molecule Viewer of Vector NTI Advance, Version 11.5.2 (Life Technologies).