Yeast Autophagy-Related Genes field, and make it quite intimidating for researchers in other fields, or even for autophagy researchers in nonyeast systems, to keep track of the various gene prod-Perhaps the most striking advantage of working with ucts. Accordingly, following discussions at the first Gorcertain yeast systems is the ability to use genetic don Research Conference on “Autophagy in Stress, screens that allow a relatively rapid identification of Development, and Disease,” the different labs working genes involved in various biological processes. Because on these genes have recently decided to adopt a unified of its smaller size, the Saccharomyces cerevisiae genome gene and protein nomenclature (Table 1). The new gene was the first eukaryotic genome to be sequenced. Subse- and protein names will be ATG and Atg, respectively, quent sequencing of genomes from higher eukaryotes which stand for “autophagy-related.” For simplicity, has revealed what had already been implicated from genes in S. cerevisiae are typically not denoted with a biochemical and molecular genetic studies performed genus and species prefix. When referring to other over many years: homologs of yeast genes exist in other yeasts, it is appropriate to use a capital followed by a eukaryotes, and in many cases the corresponding gene lower case letter to designate the genus and species, products are orthologs that carry out similar functions respectively (eg, PpATG1 for the Pichia pastoris homo-(Reggiori and Klionsky, 2002). Accordingly, the analysis log of the S. cerevisiae ATG1 gene, or PpAtg1 for the of genes and proteins in fungal cells has direct relevance corresponding protein). For clarity, when comparing diffor studies in other organisms. ferent organisms, however, it may be appropriate to use Along these lines, fungal systems have proven to be the “Sc” designation to denote S. cerevisiae. extremely useful in the analysis of autophagy and au- For convenience, additional genes involved in autophtophagy-related processes (reviewed in Klionsky, 2003). agy-related processes are included in Table 2. These Autophagy is a process in which portions of cytoplasm genes have been previously identified and the standard are sequestered by membrane (s), delivered to the lyso- names as indicated in the Saccharomyces Genome Dasome-like vacuole, degraded, and recycled under stress tabase will be used. conditions such as starvation. The sequestration pro- We consider it a notable feat to agree on a nomenclacess can occur either away from the vacuole (ie, in the ture that spans at least three genera and four species. cytosol), in which case it is termed macroautophagy, or There are putative homologs of autophagy genes in all at the vacuole surface, termed microautophagy. eukaryotic organisms where genomic sequence infor-The identification of molecular components involved mation is available. In only a few cases, however, have in macroautophagy has been carried out primarily in S. analyses been carried out to demonstrate that the corre-cerevisiae. In this organism, macroautophagy overlaps sponding gene products are involved in autophagy (Tawith a biosynthetic process termed the cytoplasm-toble 3). For simplicity, we hope that researchers using vacuole targeting (Cvt) pathway. The Cvt pathway is an higher eukaryotic systems will adopt the nomenclature example of a specific type of autophagy; proteins that presented in this paper. To avoid confusion in the yeast are destined to become resident vacuolar hydrolases field, we urge authors of papers describing new autophare specifically packaged into cytosolic vesicles and agy-related genes to contact …