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Updated: Jun 5, 2026

In-vitro Reconstitution of Bacterial Ubiquitination and VCP/p97-mediated Elimination
Published on: January 2, 2026
Pupylation : A Signal for Proteasomal Degradation in Mycobacterium tuberculosis
Kristin E Burns1, K Heran Darwin
1Department of Microbiology, New York University School of Medicine, 550 First Avenue, MSB 236, New York, New York, 10016, USA.
Abstract:
This chapter describes the identification of the first prokaryotic ubiquitin-like protein modifier, Pup, which covalently attaches to proteins to target them for destruction by a bacterial proteasome in a manner akin to ubiquitin in eukaryotes. Despite using a proteasome as the end point for proteolysis, Pup and ubiquitin differ in sequence, structure and method of activation and conjugation to protein substrates. Pup is so far the only known posttranslational protein modifier in prokaryotes and its discovery opens the door to the possibility that others are present not only for proteolysis, but also to regulate protein function or localization. Here, we discuss the putative mechanism of activation and conjugation of Pup (termed "pupylation") to target proteins. In addition, because it is unclear whether or not Pup, like ubiquitin, is recycled or degraded during substrate targeting to the proteasome, we propose methods that may identify Pup deconjugation enzymes ("depupylases"). Finally, we outline future directions for Pup research and anti-tuberculosis drug discovery.
Insights
Researchers discovered Pup, a bacterial protein modifier similar to eukaryotic ubiquitin. Pup targets proteins for destruction by the bacterial proteasome, offering new avenues for anti-tuberculosis drug discovery.
Area of Science:
- Biochemistry
- Molecular Biology
- Microbiology
Background:
- Eukaryotes utilize ubiquitin for protein degradation via proteasomes.
- Prokaryotes were thought to lack similar posttranslational protein modification systems.
Purpose of the Study:
- To identify and characterize the first prokaryotic ubiquitin-like protein modifier, Pup.
- To explore the mechanism of Pup conjugation and its potential roles in prokaryotes.
- To propose methods for identifying Pup deconjugation enzymes and discuss future research directions.
Main Methods:
- Identification of Pup as a novel protein modifier in prokaryotes.
- Analysis of Pup's sequence, structure, and conjugation mechanism.
- Proposal of experimental strategies to investigate Pup deconjugation.
Main Results:
- Pup is the first identified prokaryotic posttranslational protein modifier.
- Pup covalently attaches to proteins, targeting them for bacterial proteasome degradation.
- Pup differs significantly from ubiquitin in its activation and conjugation pathways.
Conclusions:
- Pup represents a novel mechanism for protein regulation and degradation in prokaryotes.
- The discovery of Pup suggests the existence of other prokaryotic posttranslational modifiers.
- Further research into Pupylation and depupylases could lead to new anti-tuberculosis drug targets.
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