Biol. Chem. 2020; 401(1): 183–199 Review Parijat Majumder and Wolfgang Baumeister* Proteasomes: unfoldase-assisted protein degradation machines https://doi.org/10.1515/hsz-2019-0344 housekeeping functions such as cell cycle control, signal Received August 13, 2019; accepted October 2, 2019; previously transduction, transcription, DNA repair and translation published online October 29, 2019 (Alves dos Santos et al., 2001; Goldberg, 2007; Bader and Steller, 2009; Koepp, 2014). Consequently, any disrup- Abstract: Proteasomes are the principal molecular tion of selective protein degradation pathways leads to a machines for the regulated degradation of intracellular broad array of pathological states, including cancer, neu- proteins. These self-compartmentalized macromolecu- rodegeneration, immune-related disorders, cardiomyo- lar assemblies selectively degrade misfolded, mistrans- pathies, liver and gastrointestinal disorders, and ageing lated, damaged or otherwise unwanted proteins, and (Dahlmann, 2007; Motegi et al., 2009; Dantuma and Bott, play a pivotal role in the maintenance of cellular proteo- 2014; Schmidt and Finley, 2014). stasis, in stress response, and numerous other processes In eukaryotes, two major pathways have been identi- of vital importance. Whereas the molecular architecture fied for the selective removal of unwanted proteins – the of the proteasome core particle (CP) is universally con- ubiquitin-proteasome-system (UPS), and the autophagy- served, the unfoldase modules vary in overall structure, lysosome pathway (Ciechanover, 2005; Dikic, 2017). UPS subunit complexity, and regulatory principles. Proteas- constitutes the principal degradation route for intracel- omal unfoldases are AAA+ ATPases (ATPases associated lular proteins, whereas cellular organelles, cell-surface with a variety of cellular activities) that unfold protein proteins, and invading pathogens are mostly degraded substrates, and translocate them into the CP for degra- via autophagy. The two pathways significantly differ dation. In this review, we summarize the current state with respect to their substrates, and the machinery of knowledge about proteasome – unfoldase systems in involved. However, the elements of control are carefully bacteria, archaea, and eukaryotes, the three domains of orchestrated, and jointly they ensure cellular protein life. homeostasis (Korolchuk et al., 2010). Keywords: 19S RP; 20S proteasome; MPA; PAN; proteasome The unifying element that links both UPS and selec- activators; VAT. tive autophagy is a small protein, ubiquitin, which marks substrates for destruction. Via an enzymatic cascade, ubiquitin is covalently bound to substrate proteins by an Introduction isopeptide bond between the carboxyl group of its C-ter- minal glycine residue, and the ε-NH2 group of substrate Selective protein degradation plays a crucial role in lysines. Iterations of the same reaction generate a ‘ubiq- almost every aspect of cellular physiology. The degrada- uitin code’ of signals with different topologies and lengths tion of mistranslated, misfolded, damaged or otherwise (Ravid and Hochstrasser, 2008; Komander and Rape, 2012). malfunctioning proteins is an essential element of protein Depending on the type of ubiquitin modification, a protein quality control (Chen et al., 2011). Likewise, the timely substrate is degraded either by the UPS or by autophagy removal of regulatory proteins is of vital importance in (Kim et al., 2008; Korolchuk et al., 2010). Hence, ubiqui- tin labeling imparts specificity to a degradation process that is executed by an essentially non- specific molecular *Corresponding author: Wolfgang Baumeister, Department of machine. Molecular Structural Biology, Max Planck Institute of Biochemistry, In bacteria and archaea, the existence of UPS or Am Klopferspitz 18, D-82152 Martinsried, Germany, autophagy-lysosome pathways have not been reported. e-mail: [email protected] Parijat Majumder: Department of Molecular Structural Biology, However, the occurrence of proteasomes, and ubiquitin- Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 like small modifier proteins (SAMP and Pup) has been Martinsried, Germany confirmed for all three domains of life. 184 P. Majumder and W. Baumeister: Proteasomes and associated unfoldases Occurrence of proteasomes proteasomes, the core particle (CP) (also known as the 20S proteasome) exhibits a high level of architectural conser- The first description of proteasomes dates back to the vation (Figure 1). The CP is a barrel-shaped, self-compart- late nineteen sixties, when a ‘cylinder shaped’ particle of mentalized, protein complex, composed of four stacked unknown function was observed on electron micrographs seven-membered rings (Baumeister et al., 1998). The outer of erythrocyte ghosts (Harris, 1968). More than a decade rings comprise α-type subunits, whereas β-type subunits later, a cation-sensitive high-molecular-mass endopepti- form the inner rings. The co-axial stacking of four rings dase was discovered in bovine pituitaries, and designated (α7β7β7α7) creates three internal cavities, bound by four the ‘multicatalytic protease complex’ (Wilk and Orlowski, narrow constrictions, as originally observed in three- 1980). Thereafter, the particle was rediscovered several dimensional (3D) reconstructions from electron micro- times, and shown to exist ubiquitously in all eukaryotic graphs (Hegerl et al., 1991). The central cavity, formed at cells. However, a lack of consensus over its biochemi- the junction of two β-rings, is the catalytic chamber, where cal nature, and physiological role, resulted in a plethora protein degradation takes place. The two outer cavities, of names for the same protein complex. Eventually, the formed at α-β junctions serve as antechambers, where name ‘proteasome’ was coined (Arrigo et al., 1988), to substrate proteins can be stored in an unfolded state prior highlight its character as a complex molecular machine to degradation (Sharon et al., 2006; Ruschak et al., 2010). with proteolytic function. For a review of the early history In archaea and actinobacteria, only one or two types of the field, see Coux et al., 1996; Baumeister et al., 1997. of α and β-subunits exist, while in eukaryotes, at least 14 The first non-eukaryotic proteasomes were discovered unique subunits (α1-7 and β1-7) build the constitutive CP. in Thermoplasma acidophilum (Dahlmann et al., 1989), In addition, higher eukaryotes express specialized protea- paving the way for a detailed analysis of proteasome struc- somes such as the immunoproteasomes and thymopro- ture and function in the other domains of life. Eventually, teasomes, where β subunit variants (β1i, β2i, β5i, and β5t) homologous protein complexes were isolated from Pyro- substitute the house-keeping ones (Murata et al., 2018). coccus furiosus (Bauer et al., 1997), Methanosarcina ther- The α- and β-type subunits are structurally related, dif- mophila (Maupin-Furlow et al., 1998), and several other fering only in their N-terminal regions. The N-terminal archaea. Similarly in bacteria, the discovery of proteas- tails of α-subunits form a CP gate, which prevents access omes in Rhodococcus erythropolis (Tamura et al., 1995) lead of folded proteins into the CP-axial channel (Wenzel and to its purification from Mycobacterium smegmatis (Knipfer Baumeister 1995). Whereas the N-terminal regions of β and Shrader, 1997) and other related actinobacteria. So far, subunits serve as pro-peptides that are autocatalytically proteasomes have been characterized from at least 75 dif- cleaved off during proteasome maturation to expose the ferent genera, spanning all three domains of life (Figure 1). proteolytic active sites (Seemuller et al., 1996; Groll et al., In eukaryotes, proteasomes are the only known 1999; Huber et al., 2016). soluble ATP-dependent proteases present in the cyto- plasm and nucleus. In bacteria however, a more diverse set of ATP-dependent proteases (ClpXP, ClpAP, ClpCP, HslUV, Lon and FtsH systems) are known to exist, whose Proteasome active sites are molecular architecture are analogous to the proteasome sequestered within the CP (Gur et al., 2011). Among these proteases, Lon is wide- spread, while an analogue of ClpP shows an infrequent Active sites of the proteasome are located on the inner presence in archaea (Maupin-Furlow, 2018). In eukary- walls of the CP catalytic chamber, and comprise a triad of otes, homologues of Lon, ClpP, and FtsH are only found in residues Thr1, Lys33, and Asp/Glu17 (Huber et al., 2016) the cellular organelles of bacterial descent, such as mito- (Figure 2). These residues are conserved among all pro- chondria, and chloroplasts (Adam et al., 2001). teolytically active β-type subunits in eukaryotic, bacte- rial and archaeal proteasomes, and hence the mechanism of peptide bond cleavage follows a universal principle among all CPs (Figure 2). The substrate cleavage prefer- Structure of the proteasome core is ence is however distinct for every subunit, and depends universally conserved on the chemical nature of the substrate-binding channel, especially the active site’s S1 specificity pocket (Groll and Across the domains of life, proteasomes vary in subunit Huber, 2003). Thus, the CP in archaea and actinobacteria composition. However, the central component of all comprise 14 identical catalytic sites (Seemuller et al., 1995; P. Majumder and W. Baumeister: Proteasomes and associated unfoldases 185 Figure 1: Dendrogram showing the distribution and relatedness of CP across domains of