Aggregation-prone proteins have been suggested to overwhelm and impair the ubiquitin/proteasome system (UPS) in polyglutamine (polyQ) disorders, such as Huntington's disease (HD). Overexpression of an N-terminal fragment of mutant huntingtin (NmutHtt), an aggregation-prone polyQ protein responsible for HD, obstructs the UPS in cellular models. Furthermore, based on the accumulation of polyubiquitin conjugates in brains of R6/2 mice, which express human N-mutHtt and are one of the most severe polyQ disorder models, it has been proposed that UPS dysfunction is a consistent feature of this pathology, occurring in both in vitro and in vivo models. Here, we have exploited transgenic mice that ubiquitously express a ubiquitin fusion degradation proteasome substrate to directly assess the functionality of the UPS in R6/2 mice or the slower onset R6/1 mice. Although expression of N-mutHtt caused a general inhibition of the UPS in PC12 cells, we did not observe an increase in the levels of proteasome reporter substrate in the brains of R6/2 and R6/1 mice. We show that the increase in ubiquitin conjugates in R6/2 mice can be primarily attributed to an accumulation of large ubiquitin conjugates that are different from the conjugates observed upon UPS inhibition. Together our data show that polyubiquitylated proteins accumulate in R6/2 brain despite a largely operative UPS, and suggest that neurons are able to avoid or compensate for the inhibitory effects of N-mutHtt.Huntington ͉ neurodegeneration ͉ protein degradation T he primary proteolytic machinery responsible for the turnover of proteins in the cytosol and nuclei of cells, including the destruction of misfolded or otherwise abnormal proteins, is the ubiquitin/proteasome system (UPS) (1). The UPS is in essence a two-step process: the targeting of proteins through the covalent linkage of polyubiquitin chains (2), and the destruction of ubiquitylated proteins by the proteasome (3). A number of studies have implicated UPS dysfunction in a range of polyglutamine (polyQ) neurodegenerative diseases (4). The aggregation-prone polyQ proteins are postulated to impair the UPS in these diseases, either by overloading the capacity of the cell's UPS machinery (5), by sequestration of essential components of the UPS into inclusions (6), or by obstruction of the proteasome (7). If polyQ proteins themselves inhibit the system crucial to their own degradation, this could elicit a self-perpetuating pathogenic cascade of events, both accelerating the accumulation of the toxic protein, and impairing essential regulatory functions of the UPS (4). With the help of specifically designed reporter substrates, it has been shown that polyQ proteins can cause UPS impairment in cell lines (5,8,9). However, since these experiments rely on acute overexpression of the polyQ protein in cells with limited physiological relevance, it is difficult to extrapolate these findings to the status of the UPS during the progression of the disease in patients.In contrast to the observation with in vitro models, ...