Bacterial Proteasomes

Abstract

Interest in bacterial proteasomes was sparked by the discovery that proteasomal degradation is required for the pathogenesis of Mycobacterium tuberculosis, one of the world's deadliest pathogens. Although bacterial proteasomes are structurally similar to their eukaryotic and archaeal homologs, there are key differences in their mechanisms of assembly, activation, and substrate targeting for degradation. In this article, we compare and contrast bacterial proteasomes with their archaeal and eukaryotic counterparts, and we discuss recent advances in our understanding of how bacterial proteasomes function to influence microbial physiology.

Keywords: Mycobacterium; Pup; proteasome; pupylation; regulated proteolysis.

Figure 1

Structure of a proteasome 20S CP and schematic of the Ub-proteasome system. (a) Crystal structure of the 20S CP from Mycobacterium tuberculosis [Protein Data Bank (PDB) ID: 3MI0] (32). (b) Eukaryotic Ub-proteasome system. An E1 enzyme activates Ub by adenylating the C-terminal G of Ub and then forming a thioester bond. Ub is then transferred to an E2 Ub-conjugating enzyme, which then transfers Ub to an E3 ligase that conjugates Ub to a lysine on a target substrate. Additional rounds of ubiquitylation on Ub are generally required for receptors on the 26S proteasome to recognize the doomed protein for degradation. Abbreviations: CP, core particle; G, glycine; Sub, substrate; Ub, ubiquitin.

Figure 2

The Pup-proteasome system (PPS). (a) Genomic organization of bacterial proteasome operons in Mycobacterium tuberculosis and Rhodococcus erythropolis. (b) Proteasome gate structures differ among domains of life. Top-view comparison of the 20S CP α ring from Saccharomyces cerevisiae [Protein Data Bank (PDB) ID: 2F16] (27), Thermoplasma acidophilum (PDB: 1PMA) (65), and Mycobacterium tuberculosis (inset view is rotated and magnified) (32). Subunits that assume equivalent structures are colored similarly. (c) Mpa/ARC is a bacterial proteasomal ATPase. (Bottom) X-ray crystal structure of the coiled coil (CC)- and oligosaccharide/oligonucleotide-binding (OB) domains of Mycobacterium tuberculosis Mpa (PDB: 3M9B) (adapted from 80). (d) PafA and Dop have highly similar structures. X-ray crystal structure of PafA from Corynebacterium glutamicum (left) and Dop from Acidophilus cellulolyticus (right) (adapted from 53). (e) Schematic representation of the PPS.

Figure 3

Biological roles of bacterial proteasomes. (a) Accumulation of Log sensitizes PPS-deficient Mycobacterium tuberculosis to nitric oxide. (b) The RicR regulon mediates copper resistance of Mycobacterium tuberculosis. (c) The PPS is required to survive nitrogen starvation in Mycobacterium smegmatis. (d) PafE-dependent proteasomal degradation of HspR contributes to the heat shock response of Mycobacterium tuberculosis. (e) Mpa, Dop, and the 20S CP contribute differently to the degradation of pupylated substrates in Mycobacterium smegmatis. Ectopically produced FLAG-FabD-His₆ detected in Mycobacterium smegmatis strains mc² 155 and in isogenic mpa∷kan and ΔprcBA strains, as well as in SMR5 and isogenic Δdop∷kan strains. Panel e is reproduced with permission. Abbreviations: AA, amino acid; CP, core particle; HspR, heat shock protein repressor; IB, immunoblot; PPS, Pup-proteasome system; Sub, substrate; WT, wild-type.