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Review
. 2013:66:297-327.
doi: 10.1007/978-94-007-5940-4_11.

Archaeal proteasomes and sampylation

Julie A Maupin-Furlow  1
Affiliations
Review

Archaeal proteasomes and sampylation

Julie A Maupin-Furlow. Subcell Biochem. 2013.

Abstract

Archaea contain, both a functional proteasome and an ubiquitin-like protein conjugation system (termed sampylation) that is related to the ubiquitin proteasome system (UPS) of eukaryotes. Archaeal proteasomes have served as excellent models for understanding how proteins are degraded by the central energy-dependent proteolytic machine of eukaryotes, the 26S proteasome. While sampylation has only recently been discovered, it is thought to be linked to proteasome-mediated degradation in archaea. Unlike eukaryotes, sampylation only requires an E1 enzyme homolog of the E1-E2-E3 ubiquitylation cascade to mediate protein conjugation. Furthermore, recent evidence suggests that archaeal and eurkaryotic E1 enzyme homologs can serve dual roles in mediating protein conjugation and activating sulfur for incorporation into biomolecules. The focus of this book chapter is the energy-dependent proteasome and sampylation systems of Archaea.

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Figures

Fig. 11.1
Fig. 11.1. 20S proteasome core particles (CPs)
CPs are composed of four stacked heptameric rings of α- and β-type subunits (indicated by α7 and β7, respectively) that form a cylindrical structure. The central channel of the CP is accessed by gated pores on each end of the cylinder and connects three interior chambers. Proteolytic active sites formed by β-type subunits (indicated in red) line the central chamber that is flanked by two antechambers. CPs of (a) the eukaryote Saccharomyces cerevisiae and (b) the archaeon Thermoplasma acidophilum are presented as examples. (Figure modified from [22, 23] with permission)
Fig. 11.2
Fig. 11.2. Mechanism of proteasomes and other related Ntn-hydrolyases in the hydrolysis of an amide bond
Substrate, shaded in blue; Ntn active site residue, shaded in red; oxyanion hole, shaded in green; charged state, indicated by + or − in red font; Y, oxygen or sulfur; X, nitrogen or oxygen; R-R', substrate bond cleaved (comparable to the P1–P1' peptide bond cleaved by proteases as depicted in the inset) (Figure modified from [26] with permission)
Fig. 11.3
Fig. 11.3. ATP-dependent proteasomes of eukaryotes compared to archaea
Proteasomal CPs can associate on each end of their cylindrical structure with heptameric rings of AAA + proteins including eukaryotic Rpt1-6 and archaeal PAN. Rpt1-6 are AAA + subunits of the 19S regulatory particle (RP) that associates with CPs to form 26S proteasomes. In yeast, the 19S RP can be dissociated into lid and base subcomplexes by deletion of the RPN10 gene. PAN is an AAA ATPase that forms a hexameric ring and associates with CPs in vitro. PAN is common to many but not all archaea
Fig. 11.4
Fig. 11.4. Eukaryal proteasomal CPs are gated
In X-ray crystal structures of eukaryotic (e.g., yeast and bovine) CPs, the central channel used for protein substrate entry is gated by the N-terminal tails of α-type subunits (Figure modified from [67] with permission)
Fig. 11.5
Fig. 11.5. Archaeal proteasomal CPs are gated
Cryo-electron microscopy reveals: (a) sites within the intersubunit pockets of α subunits in the TaCP that are bound by peptides mimicking the C-terminal tail of MjPAN and (b) structures of the TaCP gate in the closed and open forms induced by these peptides (Figure modified from [85] with permission)
Fig. 11.6
Fig. 11.6. Archaeal PAN subdomain structures provide a foundation for modelling the overall structure of an energy-dependent proteasome
(a) and (b) Subcomplex I and II generated by limited proteolysis of MjPAN are indicated with the N-terminal coiled-coil (CC), OB fold and AAA domains highlighted. (c) Evidence supports the docking of MjPAN C-terminal tails with pockets formed at the α-α intersubunit interface of TaCPs. The N-terminal CC-domains are assumed to be distal to the CP and act as tentacles that grab protein substrates, thus, enabling the Ar-Φ loop within subcomplex II to grip regions of the substrate that extend through the pore formed by the OB fold domain. The Ar-Φ loop is also thought to undergo ATP-fuelled conformational changes resulting in pulling and tugging at the protein substrate while the OB fold domain provides a passive force that blocks the movement of folded protein structure through the pore. As the protein is unfolded by this mechanism, it is translocated through the ATPase into the central channel of the CP for degradation (Figure modified from [84] with permission)
Fig. 11.7
Fig. 11.7. Ubiquitylation and sampylation
(a) Eukaryotes use an elaborate E1-E2-E3 mediated mechanism for the attachment of ubiquitin to protein substrates. (b) Similarly to eukaryotes, small archaeal ubiquitin-like modifier proteins (termed SAMPs) can form protein conjugates in the archaeon H. volcanii by a pathway that is dependent upon the synthesis of an E1 homolog (termed UbaA). Based on genome sequence, E2 and E3 homologs are not predicted for this pathway. UbaA and SAMP proteins appear to also be linked to sulfur incorporation pathways (such as the biosynthesis of MoCo and thiolated tRNA) that require an E1-type adenylation reaction for the formation of a thiocarboxylated sulfur carrier protein with a ubiquitin-type β-grasp fold
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