Plant Molecular Biology Reporter 12 (2) 1994 pages $77-$78 CPGN Supplement

WOrldng Group on UBiquitins: Viers~a@macc,wisc.edu

Genes Encoding Ubiquitin and Related Proteins

Richard Vierstra

Horticulture Department, University of Wisconsin, Madison, WI 53706, USA

T his group includes a variety of genes encoding ubiquitin and essential enzymes in the ubiquitin-dependent proteolytic path way. For each of the categories, we list the gene product, the

proposed mnemonic designation, and some comments on the rationale for the classification and the choice of designations.

ubiquitins Ubql The ubiquitin family includes polyubiquitin, polyubiquitin-like pro- teins, and ubiquitins fused to the two ribosomal proteins (previously referred to as Ube or Ucep). We propose a single class of genes because recent isolations show mixtures of the three classes of proteins rather than three distinct classes.

ubiquitin-activating enzymes Ubal The Enzyme Commission lists ubiquitin-activating enzymes and ubiquitin-conjugating enzymes (below) as EC 6.3.2.19. Product also represented as Els. Designation is consistent with all eukaryotic genes isolated to date.

ubiquitin-conjugating enzymes Ubcl Product also represented as E2s. They were previously called ubiquitin- carrier proteins but still used the Ubc designation for the genes. Designa- tion is consistent among all eukaryotic genes isolated to date.

ubiquitin-protein ligases Ubrl Product also represented as E3s. They are ubiquitin-pathway enzymes involved in substrate recognition, hence the letter "R". While originally called ligases, it is unclear whether all E3s actually participate in ubiquitin

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ligation directly or just facilitate the interactions of E2s with appropriate substrates for ubiquitination. Designation is going to change in the next few years to show their actual function is in recognition, not ligation. No genes have been cloned from plants yet, but a single gene, UBR1, has been cloned from yeast.

ubiquitin carboxy-terminal hydrolase Uchl Proteins that cleave ubiquitin monomers from the initial (x-linked trans- lation products of Ubq genes and cleave ubiquitin monomers linked via a peptide bond to ~-amino-linked target proteins. Ubiquitin-specific protease (Ubp) is also used in yeast for this class of enzymes. However, this designation as a protease, while correct, generates potential confu- sion with genes encoding the 26S proteasome, which are more directly involved in ubiquitin conjugate degradation (see below).

20 S and 26 S proteasome subunits Prsl Proteasome is required for the degradation of ubiquitin-protein conju- gates. No ubiquitin prefix is used because proteasome may operate in a ubiquitin-independent manner. In animal systems, this family is espe- cially confusing with names like RING, UBP, LMP, and PRE in use.