Proteasomal degradation of RPN4 via two distinct mechanisms, ubiquitin-dependent and -independent

Substrates of the ubiquitin system are degraded by the 26 S proteasome, a complex protease consisting of at least 32 different subunits. Recent studies showed that RPN4 (also named SON1 and UFD5) is a transcriptional activator required for normal expression of the Saccharomyces cerevisiae proteasome genes. Interestingly, RPN4 is extremely short-lived and degraded by the 26 S proteasome, establishing a feedback circuit that controls the homeostatic abundance of the 26 S proteasome. The mechanism underlying the degradation of RPN4, however, remains unclear. Here we demonstrate that the proteasomal degradation of RPN4 is mediated by two independent degradation signals (degron). One degron leads to ubiquitylation on internal lysine(s), whereas the other is independent of ubiquitylation. Stabilization of RPN4 requires inhibition of internal ubiquitylation and inactivation of the ubiquitin-independent degron. RPN4 represents the first proteasomal substrate in S. cerevisiae that can be degraded through ubiquitylation or without prior ubiquitylation. This finding makes it possible to use both yeast genetics and biochemical analysis to investigate the mechanism of ubiquitin-independent proteolysis.