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The E3 ubiquitin-protein ligases play an important role in controlling substrate specificity of the ubiquitin proteolysis system. A biochemical approach was taken to identify substrates of Rsp5, an essentialhect (homologous to E6-AP carboxyl terminus) E3 ofSaccharomyces cerevisiae . We show here that Rsp5 binds and ubiquitinates the largest subunit of RNA polymerase II (Rpb1)in vitro . Stable complex formation between Rsp5 and Rpb1 was also detected in yeast cell extracts, and repression ofRSP5 expressionin vivo led to an elevated steady-state level of Rpb1. The amino-terminal domain of Rsp5 mediates binding to Rpb1, while the carboxyl-terminal domain of Rpb1, containing the heptapeptide repeats characteristic of polymerase II, is necessary and sufficient for binding to Rsp5. Fusion of the Rpb1 carboxyl-terminal domain to another protein also causes that protein to be ubiquitinated by Rsp5. These findings indicate that Rsp5 targets at least a subset of cellular Rpb1 molecules for ubiquitin-dependent degradation and may therefore play a role in regulating polymerase II activities. In addition, the results support a model forhect E3 function in which the amino-terminal domain mediates substrate binding, while the carboxyl-terminalhect domain catalyzes ubiquitination of bound substrates.

The large subunit of RNA polymerase II is a substrate of the Rsp5 ubiquitin-protein ligase