The Bacterial Proteasome at the Core of Diverse Degradation Pathways

Abstract

Proteasomal protein degradation exists in mycobacteria and other actinobacteria, and expands their repertoire of compartmentalizing protein degradation pathways beyond the usual bacterial types. A product of horizontal gene transfer, bacterial proteasomes have evolved to support the organism's survival under challenging environmental conditions like nutrient starvation and physical or chemical stresses. Like the eukaryotic 20S proteasome, the bacterial core particle is gated and must associate with a regulator complex to form a fully active protease capable of recruiting and internalizing substrate proteins. By association with diverse regulator complexes that employ different recruitment strategies, the bacterial 20S core particle is able to act in different cellular degradation pathways. In association with the mycobacterial proteasomal ATPase Mpa, the proteasome degrades substrates post-translationally modified with prokaryotic, ubiquitin-like protein Pup in a process called pupylation. Upon interaction with the ATP-independent bacterial proteasome activator Bpa, poorly structured substrates are recruited for proteasomal degradation. A potential third degradation route might employ a Cdc48-like protein of actinobacteria (Cpa), for which interaction with the 20S core was recently demonstrated but no degradation substrates have been identified yet. The alternative interaction partners and wide range of substrate proteins suggest that the bacterial proteasome is a modular, functionally flexible and conditionally regulated degradation machine in bacteria that encounter rapidly changing and challenging conditions.

Keywords: Cdc48-like protein of actinobacteria Cpa; bacterial proteasome; bacterial proteasome activator Bpa; degradation; mycobacterial proteasomal ATPase Mpa; pupylation.

Figure 1

Cellular pathways involving the bacterial proteasome in Mycobacterium tuberculosis. The proteasome core particle (beige) can interact with different regulator complexes: Mpa (mycobacterial proteasome activator, orange), Bpa (bacterial proteasome activator, purple) or Cpa (Cdc48-like protein of actinobacteria, blue). By formation of different activator-proteasome complexes the cell can tune the degradation activity according to its needs under different conditions. The Mpa-proteasome degrades otherwise stable, folded proteins that have been tagged with Pup (prokaryotic ubiquitin-like protein, red). The Pup-ligase PafA, depupylase Dop, Pup, Mpa, and the proteasome subunits are all encoded in close proximity to one another in a region of the genome referred to as Pup-proteasome system (PPS) gene locus. Pupylation-mediated degradation was shown to be important under various conditions, such as recovery from DNA damage, nitrogen starvation, and persistence in the host macrophage. Bpa forms a dodecameric ring with a large pore, and, upon interaction with the proteasome core, it opens the proteasomal gate to allow substrate entry into the proteolytic chamber. Unlike Mpa and Cpa, Bpa has no ATPase activity and thus only allows unstructured or partially unfolded proteins to enter. Due to its recent discovery, the Cpa-proteasome complex is less well-studied and no substrates or recruitment mechanisms are known so far. However, Cpa was shown to play a role under carbon starvation conditions.