Encyclopedia of Signaling Molecules

2018 Edition
| Editors: Sangdun Choi


Reference work entry
DOI: https://doi.org/10.1007/978-3-319-67199-4_65


Historical Background

Regulatory particle triple-A (Rpt) subunits are associated with the ubiquitin-proteasome system, a central mechanism of protein breakdown with a rich historical background. Aaron Ciechanover, Avram Hershko, and Irwin Rose were awarded the 2004 Nobel Prize in Chemistry for their “discovery of ubiquitin-mediated protein degradation” by proteasomes and have outlined some of this history in reviews (e.g., Ciechanover 2010). The term “proteasome” was first coined by Arrigo et al. (1988) for a “large alkaline multifunctional protease” known to mediate energy-dependent intracellular protein breakdown, once it was clear that this protease was related to the ring-shaped “prosomes” of unknown function commonly found in eukaryotic cells. The Rpt nomenclature was later proposed by Finley et al. (1998) to designate the subunits of the yeast 26S proteasome that cluster to the ATPases associated with various cellular activities (AAA) family of the AAA+ superfamily (Wollenberg and Swaffield 2001). AAA+ proteins are required for the degradation of folded proteins by self-compartmentalized proteases such as proteasomes.

Proteasomes and Rpt Subunits

Protein degradation by proteasomes is a major regulatory mechanism in eukarya, archaea, and actinobacteria. Proteasomes can degrade short-lived proteins that control cell division, apoptosis, DNA repair, information processing (transcription and translation), and other cellular processes (Navon and Ciechanover 2009). Proteasomes are also important in maintaining protein quality by destroying improperly synthesized, foreign, and damaged proteins (Schrader et al. 2009).

All proteasomes are composed of a 20S core particle (CP) lined on its interior with proteolytic active sites that are sequestered away from the cytosol (Stadtmueller and Hill 2011) (Fig. 1). CPs are barrel-like and formed from four-stacked heptameric rings of α- and β-type subunits. The α-type subunits form the outermost rings, while the β-type subunits form the inner two rings. The N-terminal tails of α-type subunits can gate the pores on each end of CPs and limit substrate access to the proteolytic active sites formed by β-type subunits.
RPT, Fig. 1

20S proteasomes. The central proteolytic component of all proteasomes is a cylindrical 20S core particle (CP) formed from four-stacked heptameric rings. The outer rings are of α-type subunits and inner rings are of β-type subunits. The N-terminal tails of α-type subunits gate substrate access to the central channel that connects three chambers (two antechambers and one catalytic chamber). The proteolytic active sites are sequestered from the cytosol and formed by the N-terminal threonine residues of β-type subunits that are exposed by autocatalytic processing of the β-type proteins during complex assembly (Modified with permission from Stadtmueller and Hill (2011))

CPs associate with various regulators (Stadtmueller and Hill 2011). In eukarya, CPs bind 19S regulatory particles (RPs) to form an energy-dependent protease known as the 26S proteasome (Fig. 2). Substrates of 26S proteasomes include proteins covalently conjugated to chains of ubiquitin (Ub) through a process termed ubiquitylation (Ravid and Hochstrasser 2008). The primary roles of 19S RPs are to recognize, unfold, and translocate substrate proteins to the catalytic central chamber of CPs for protein degradation. In yeast, the 19S RP can be separated into base and lid subcomplexes by deletion of the gene encoding the regulatory particle non-ATPase Rpn10 subunit (Tomko and Hochstrasser 2011). The base subcomplex is composed of three Rpn subunits (Rpn1, Rpn2, and Rpn13) and six proteins termed regulatory particle triple-A subunits (Rpt1-6) that cluster to the AAA family of the AAA+ superfamily. Rpt1-6 form a heterohexameric ring that directly interacts with 20S CPs and are arranged in Rpt1-Rpt2-Rpt6-Rpt3-Rpt4-Rpt5 order in 26S proteasomes (Tomko and Hochstrasser 2011). The lid subcomplex is composed of nine other Rpn subunits and harbors the deubiquitylating enzyme Rpn11 that removes polyubiquitin chains from substrate proteins.
RPT, Fig. 2

ATP-dependent proteasomes. Proteasomal CPs can associate on each end with heptameric rings of AAA+ proteins including eukaryal Rpt1-6, archaeal PAN, and actinobacterial ARC (or Mpa). In eukaryotes, Rpt1-6 are the ATPase subunits of the 19S regulatory particles (RPs) that together with CPs form 26S proteasomes. In yeast, the 19S RP can be dissociated into lid and base subcomplexes by deletion of the RPN10 gene

Archaea and actinobacteria synthesize proteasomes that are relatively simple in subunit complexity, yet these proteases share many basic structural and functional features with eukaryal 26S proteasomes (Bar-Nun and Glickman 2011). Like eukarya, the CPs and proteasomal AAA+ proteins of archaea and actinobacteria can associate together in vitro and catalyze the energy-dependent degradation of folded proteins (Fig. 2). The prokaryotic AAA+ proteins are often hexameric rings formed from a single protein including the archaeal proteasome-associated nucleotidase (PAN) and actinobacterial AAA ATPase forming ring-shaped complexes (ARC) or mycobacterium proteasome ATPase (Mpa). The archaeal PAN is closely related to the eukaryal Rpt subunits, while the actinobacterial ARC/Mpa proteins are divergent members of the AAA family. It has been proposed that the six different types of eukaryal Rpt proteins (Rpt1-6) evolved from a single archaeal PAN ancestor, which over time was duplicated and diversified (Wollenberg and Swaffield 2001).

Rpt and Related AAA+ Proteins in Proteolysis

While the hydrolysis of peptide bonds is exergonic, ATP binding and hydrolysis by AAA+ proteins (or domains) is needed to fuel the regulated degradation of folded proteins by self-compartmentalized proteases such as 26S proteasomes. The AAA+ rings can bind substrate proteins, open the gates of the protease chamber (closed-gates limit substrate access to the proteolytic active sites), unfold substrate proteins, and facilitate the translocation of protein substrates into the proteolytic center of the protease.

Subdomain X-ray crystal and cryo-electron microscopy structures of proteasomal AAA+ proteins are now available and provide valuable insight into how this group of ATPases might function at the atomic level (Bar-Nun and Glickman 2011). Details on the related bacterial AAA+ proteases such as ClpXP and HslUV have also guided proteasomal models (Sauer and Baker 2011). In general, proteasomal ATPases have a central channel that is coaxial to the 20S CP channel (Fig. 3). On the distal face of the proteasomal ATPase ring are six protruding and paired N-terminal coiled-coil (CC) domains that are required for substrate binding. Moving down the ATPase channel, one finds a conserved interdomain region with an oligonucleotide-binding (OB)-fold domain that is important for AAA+ ring formation. The OB-fold domain also appears to serve as a rigid entryway for substrates that traverse the ATPase channel. The archaeal PAN and eukaryal Rpt1-6 proteins have a single OB-fold (as depicted in Fig. 3), while the actinobacterial ARC/Mpa has a double OB-fold that forms two separate ring-like structures within the ATPase channel. The C-terminal AAA+ domain mediates cycles of ATP hydrolysis and harbors a highly conserved aromatic-hydrophobic (Ar-phi) loop within its channel. The Ar-phi loop is common to energy-dependent AAA+ proteases and is thought to grab onto hydrophobic tails of substrates that may extend into the ATPase channel. Once bound, cycles of ATP hydrolysis around the ATPase ring are thought to mediate conformational changes in the Ar-phi loop that result in the tugging and unfolding of the substrate protein. The rigid OB-fold pore is believed to serve as a platform for this unfolding process. Thus, the protein substrate is thought to be unfolded and translocated through the ATPase and into the CP for destruction.
RPT, Fig. 3

Model of proteasome-mediated degradation of folded proteins. Model is based on archaeal PAN, a close relative of the Rpt1-6 subunits of eukaryal 26S proteasomes. Substrate proteins are thought to be unfolded on the distal face of the proteasomal ATPase, translocated through the central ATPase channel, and ultimately reach the central chamber of CPs for destruction. The N-terminal coiled-coil (CC) domain, oligonucleotide-binding (OB)-fold domain, and aromatic-hydrophobic (Ar-phi) loop discussed in text are indicated (Modified with permission from Zhang et al. (2009))

Many of the proteasomal ATPases (e.g., archaeal PAN and eukaryal Rpt2, 3 and 5) have C-terminal hydrophobic-tyrosine-any residue (HbYX) motifs that bind to pockets between the α-type subunits of CPs and induce CP gate opening. The proteasome-associated regulator Blm10 and α-ring assembly factor Pba1-Pba2 also have penultimate tyrosine (or phenylalanine) residues that appear important for binding within the α/α-intersubunit interface (Stadtmueller and Hill 2011; Kusmierczyk et al. 2011).

Substrate Recognition by Proteasomes

Protein degradation is a highly regulated process. In order to ensure that only the desired proteins are degraded, eukaryotes and prokaryotes have evolved various strategies for identifying proteins for degradation. Specific degradation signals or “degrons” within the protein often initiate the process of proteolysis. Degrons range from the phosphorylation or glycosylation status of a protein to the exposure of destabilizing N- or C-termini (Ravid and Hochstrasser 2008). In eukaryotic cells, the ubiquitylation system often recognizes these degrons and results in the covalent attachment of polyubiquitin (Ub) chains. While all seven lysine residues of Ub can form chains, Ub chains linked through Lys48 commonly target proteins for destruction by 26S proteasomes (Xu et al. 2009). These ubiquitylated proteins are thought to first bind the Rpn10 and Rpn13 subunits of 26S proteasomes by a mechanism stimulated by ATP binding to the Rpt subunits (Peth et al. 2010) (Fig. 4). Next, Rpt-mediated ATP hydrolysis is thought to unfold and expose unstructured portions of the substrate protein for tighter binding to 26S proteasomes. Ultimately, this is thought to ready the substrate for the editing or removal of polyUb chains by deubiquitylases. The Rpt subunits would unfold and translocate the protein while opening the CP gates for protein degradation.
RPT, Fig. 4

26S proteasome-mediated degradation of ubiquitylated proteins. Initially, the 26S proteasomal subunits Rpn10 and 13 (Ub receptors) bind the Ub chain of ubiquitylated substrate proteins by a mechanism that is stimulated by ATP binding. In the next phase, ATP is hydrolyzed by the Rpt subunits and an unfolded domain of the substrate protein is exposed, resulting in tighter binding to 26S proteasomes. After these binding events, deubiquitylation, Ub-chain editing, substrate unfolding, CP gate opening, translocation, and proteolysis can occur (Modified with permission from Peth et al. 2010)

In actinobacteria and archaea, the covalent attachment of small protein modifiers to substrate proteins appears to be linked to proteasome-mediated proteolysis– much like the process of ubiquitylation in eukaryotic cells. It has recently been shown in Mycobacterium tuberculosis that a small protein termed Pup can covalently modify proteins at lysine residues (Burns and Darwin 2010). While the mechanism of pupylation differs from ubiquitylation and the disordered structure of Pup is not like the highly ordered beta-grasp fold of Ub, Pup can target proteins for proteasome-mediated degradation (Burns and Darwin 2010). Interestingly, the mycobacterial proteasomal AAA+ Mpa (required for cellular resistance to reactive nitrogen intermediates) binds and induces formation of an alpha helix within Pup and is required for degradation of pupylated substrates by proteasomes (Burns and Darwin 2010). The haloarchaeon Haloferax volcanii can also attach small archaeal protein modifiers or SAMPs to substrate proteins (Humbard et al. 2010). However, unlike Pup, the archaeal SAMPs have a predicted beta-grasp fold structure similar to Ub and require the presence of an E1 Ub activating homolog (UbaA) for attachment (Miranda et al. 2011). Other enzyme (E2 Ub conjugating and E3 Ub ligase) homologs for the attachment of SAMPs to protein targets have yet to be identified. Sampylation has not been directly linked to targeting proteins for proteasome-mediated degradation. However, the sampylome accumulates in strains deficient in the synthesis of the proteasomal Rpt-like PAN-A and CP α1 subunits, suggesting sampylation may trigger proteins for degradation by proteasomes. However, green fluorescent protein (GFP) derivatives with hydrophobic C-terminal tails that are not modified by sampylation or other types of posttranslational modification are degraded in vitro by proteasomal CPs in the presence of archaeal PAN and hydrolyzable ATP (Navon and Goldberg 2001). Therefore, by an ATP-dependent mechanism, Rpt-like proteins can bind and unfold non-sampylated protein substrates with exposed hydrophobic regions. Interestingly, in eukaryotic cells, the chaperonin-like activities of the proteasomal Rpt proteins appear to also serve non-proteolytic roles (Kodadek 2010).


Proteins of the AAA+ superfamily that include eukaryal Rpt, archaeal PAN, and actinobacterial Mpa/ARC are structurally related and important in protein degradation. These proteasomal ATPases can unfold proteins, open CP gates, and translocate proteins for ultimate destruction within the self-compartmentalized 20S CP structure that protects cells from uncontrolled proteolysis. In eukarya, Rpt1-6 associate with non-ATPase subunits in complexes such as the 19S RP to form 26S proteasomes but also appear to serve non-proteolytic roles. Whether the archaeal PAN and actinobacterial Mpa/ARC are similar to eukaryal Rpt in their association with proteasomal CPs and other non-ATPase factors in vivo remains an exciting area of research.



This work was funded in part by grants from the National Institutes of Health (GM57498) and the Department of Energy Office of Basic Energy Sciences (DE-FG02-05ER15650).


  1. Arrigo AP, Tanaka K, Goldberg AL, Welch WJ. Identity of the 19S ‘prosome’ particle with the large multifunctional protease complex of mammalian cells (the proteasome). Nature. 1988;331(6152):192–4. doi:10.1038/331192a0.PubMedCrossRefGoogle Scholar
  2. Bar-Nun S, Glickman MH. Proteasomal AAA-ATPases: structure and function. Biochim Biophys Acta. 2011. doi:10.1016/j.bbamcr.2011.07.009.Google Scholar
  3. Burns KE, Darwin KH. Pupylation versus ubiquitylation: tagging for proteasome-dependent degradation. Cell Microbiol. 2010;12:424–31.PubMedPubMedCentralCrossRefGoogle Scholar
  4. Ciechanover A. The ubiquitin system: historical perspective. Proc Am Thorac Soc. 2010;7:11–2. doi:10.1513/pats.200908-095JS.PubMedCrossRefGoogle Scholar
  5. Finley D, Tanaka K, Mann C, Feldmann H, Hochstrasser M, Vierstra R, Johnston S, Hampton R, Haber J, Mccusker J, Silver P, Frontali L, Thorsness P, Varshavsky A, Byers B, Madura K, Reed SI, Wolf D, Jentsch S, Sommer T, Baumeister W, Goldberg A, Fried V, Rubin DM, Toh-e A, et al. Unified nomenclature for subunits of the Saccharomyces cerevisiae proteasome regulatory particle. Trends Biochem Sci. 1998;23:244–5. doi:10.1016/S0968-0004(98)01222-5.PubMedCrossRefGoogle Scholar
  6. Humbard MA, Miranda HV, Lim JM, Krause DJ, Pritz JR, Zhou G, Chen S, Wells L, Maupin-Furlow JA. Ubiquitin-like small archaeal modifier proteins (SAMPs) in Haloferax volcanii. Nature. 2010;463:54–60.PubMedPubMedCentralCrossRefGoogle Scholar
  7. Kodadek T. No Splicing, no dicing: non-proteolytic roles of the ubiquitin-proteasome system in transcription. J Biol Chem. 2010;285:2221–6.PubMedCrossRefGoogle Scholar
  8. Kusmierczyk AR, Kunjappu MJ, Kim RY, Hochstrasser M. A conserved 20S proteasome assembly factor requires a C-terminal HbYX motif for proteasomal precursor binding. Nat Struct Mol Biol. 2011;18:622–9. doi:10.1038/nsmb.2027.PubMedPubMedCentralCrossRefGoogle Scholar
  9. Miranda HV, Nembhard N, Su D, Hepowit N, Krause DJ, Pritz JR, Phillips C, Söll D, Maupin-Furlow JA. E1- and ubiquitin-like proteins provide a direct link between protein conjugation and sulfur transfer in archaea. Proc Natl Acad Sci USA. 2011;108:4417–22.PubMedPubMedCentralCrossRefGoogle Scholar
  10. Navon A, Ciechanover A. The 26S proteasome: from basic mechanisms to drug targeting. J Biol Chem. 2009;284:33713–8. doi:10.1074/jbc.R109.018481.PubMedPubMedCentralCrossRefGoogle Scholar
  11. Navon A, Goldberg AL. Proteins are unfolded on the surface of the ATPase ring before transport into the proteasome. Mol Cell. 2001;8:1339–49. doi:10.1016/S1097-2765(01)00407-5.PubMedCrossRefGoogle Scholar
  12. Peth A, Uchiki T, Goldberg AL. ATP-dependent steps in the binding of ubiquitin conjugates to the 26S proteasome that commit to degradation. Mol Cell. 2010;40(4):671–81. doi:10.1016/j.molcel.2010.11.002.PubMedPubMedCentralCrossRefGoogle Scholar
  13. Ravid T, Hochstrasser M. Diversity of degradation signals in the ubiquitin-proteasome system. Nat Rev Mol Cell Biol. 2008;9:679–90.PubMedPubMedCentralCrossRefGoogle Scholar
  14. Sauer RT, Baker TA. AAA+ proteases: ATP-fueled machines of protein destruction. Annu Rev Biochem. 2011;80:587–612.PubMedCrossRefGoogle Scholar
  15. Schrader EK, Harstad KG, Matouschek A. Targeting proteins for degradation. Nat Chem Biol. 2009;5:815–22. doi:10.1038/nchembio.250.PubMedPubMedCentralCrossRefGoogle Scholar
  16. Stadtmueller BM, Hill CP. Proteasome activators. Mol Cell. 2011;41:8–19. doi:10.1016/j.molcel.2010.12.020.PubMedPubMedCentralCrossRefGoogle Scholar
  17. Tomko Jr RJ, Hochstrasser M. Order of the proteasomal ATPases and eukaryotic proteasome assembly. Cell Biochem Biophys. 2011;60:13–20.CrossRefGoogle Scholar
  18. Wollenberg K, Swaffield JC. Evolution of proteasomal ATPases. Mol Biol Evol. 2001;18:962–74.PubMedCrossRefGoogle Scholar
  19. Xu P, Duong DM, Seyfried NT, Cheng D, Xie Y, Robert J, Rush J, Hochstrasser M, Finley D, Peng J. Quantitative proteomics reveals the function of unconventional ubiquitin chains in proteasomal degradation. Cell. 2009;137:133–45.PubMedPubMedCentralCrossRefGoogle Scholar
  20. Zhang F, Wu Z, Zhang P, Tian G, Finley D, Shi Y. Mechanism of substrate unfolding and translocation by the regulatory particle of the proteasome from Methanocaldococcus jannaschii. Mol Cell. 2009;34:485–96. doi:10.1016/j.molcel.2009.04.022.PubMedPubMedCentralCrossRefGoogle Scholar

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© Springer International Publishing AG 2018

Authors and Affiliations

  1. 1.Department of Microbiology and Cell ScienceUniversity of FloridaGainesvilleUSA