Cdc48: a power machine in protein degradation Alexandra Stolz 1 , Wolfgang Hilt 1 , Alexander Buchberger 2 and Dieter H. Wolf 1 1 Institute for Biochemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany 2 Department of Biochemistry, Biocenter, University of Wu ¨ rzburg, Am Hubland, 97074 Wu ¨ rzburg, Germany Cdc48 is an essential, highly prominent ATP driven ma- chine in eukaryotic cells. Physiological function of Cdc48 has been found in a multitude of cellular processes, for instance cell cycle progression, homotypic membrane fusion, chromatin remodeling, transcriptional and met- abolic regulation, and many others. The molecular function of Cdc48 is arguably best understood in endo- plasmic reticulum-associated protein degradation by the ubiquitin proteasome system. In this review, we sum- marize the general characteristics of Cdc48/p97 and the most recent results on the molecular function of Cdc48 in some of the above processes, which were found to finally end in proteolysis-connected pathways, either involving the proteasome or autophagocytosis-mediat- ed lysosomal degradation. Cdc48 function Even though peptide bond hydrolysis in proteins is a chemically exergonic reaction, which does not require en- ergy, intracellular protein degradation is highly energy dependent. This is mainly due to the requirement for selectivity and precise regulation of the degradation pro- cess as well as for protein transport and unfolding. A major player in eukaryotic protein degradation is the essential, highly conserved ATPase Cdc48 (p97/VCP in mammals, TER94 in the fly and CDC-48 in nematodes). Cdc48 (cell division cycle), which belongs to the family of ATPases associated with various cellular activities (AAA), forms a homohexameric, ring-shaped complex. With approximate- ly 1% of the cytosolic protein [1], Cdc48 is highly abundant in mammalian cells. The CDC48 gene was first identified in a yeast screen for conditional mutations affecting the cell cycle [2]. In 1991, the gene was sequenced and the encoded protein of 92 kDa was identified [3]. Studies in the years thereafter unraveled a central function of Cdc48 in ubiquitin-dependent proteolysis, and in 2007 it was dubbed a ‘molecular gearbox in the ubiquitin pathway’ [4]. Until recently, little was known about Cdc48 functions at the molecular level outside the ubiquitin proteasome system (UPS). In addition to its well-known molecular function in protein quality control in the process of endo- plasmic reticulum associated protein degradation (ERAD) [5,6], the participation of Cdc48 in a variety of other cellular processes has been revealed only recently. These include transcriptional and metabolic regulation, DNA damage response, chromatin remodeling, selective autop- hagy, cell cycle progression and cell death [7–12]. In many cases it has still to be elucidated if the reported function of Cdc48 is directly linked to protein degradation processes. Also, in its long-known involvement in membrane fusion no molecular mechanism of Cdc48 has been unraveled [9]. Concerning new molecular functions, it has been found that Cdc48 specifically controls transcription through the turnover of RNA Pol II upon UV irradiation or high protein accumulation [12,13] and is required for metabolic regula- tion in glucose controlled catabolite degradation [7]. Under stress conditions, damaged proteins are not instantly de- graded but stored in aggresomes. This enables the cell to focus on essential tasks. Aggresomes are resolubilized and eliminated when conditions allow. Both processes, aggre- some formation and aggresome elimination, are Cdc48- dependent [14–16]. In general, protein degradation is executed by the UPS or by autophagy, which finally results in lysosomal (vacuolar) degradation. Impairment in basic protein degradation pro- cesses is the reason for many human diseases such as Parkinson’s disease, Alzheimer’s disease and Huntington’s disease, and many others [13]. Although Cdc48 function is well established in the UPS [4–6], recent reports unraveled a function of Cdc48 in several selective autophagy pathways, with and without involvement of ubiquitin [17,18]. When degradation is the task, obviously Cdc48 guides proteins either into the UPS or into autophagy [14]. This decision enables the cell to dispose of an unwanted or dysfunctional protein by at least one of the two degradation pathways. This review describes the basic characteristics of Cdc48 and summarizes recent findings of Cdc48 functions as well as the identification of new cofactors involved in protein degradation. Cited studies in this review were done in a variety of organisms, regardless we will use the term ‘Cdc48’ for this AAA ATPase throughout. The Cdc48 machinery In the following sections we will describe the structure of the Cdc48 complex and its modifications, substrate han- dling by the complex as well as the cofactors with their Cdc48 interaction motifs. Cdc48 structure Cdc48 is a homohexameric complex composed of six proto- mers arranged in a ring around a central pore (Figure 1). Each protomer contains four domains: a mobile N-terminal domain, two conserved AAA domains called D1 and D2, and Review Corresponding author: Wolf, D.H. (dieter.wolf@ibc.uni-stuttgart.de). 0968-0004/$ – see front matter ß 2011 Elsevier Ltd. All rights reserved. doi:10.1016/j.tibs.2011.06.001 Trends in Biochemical Sciences, October 2011, Vol. 36, No. 10 515