Pup, a ubiquitin analog, tags proteins for degradation by the bacterial proteasome. As an intracellular proteolytic system, the Pup-proteasome system (PPS) must be carefully regulated to prevent excessive protein degradation. Currently, those factors underlying PPS regulation remain poorly understood. Here, experimental analysis combined with theoretical modeling of in vivo protein pupylation revealed how the basic PPS design allows stable and controlled protein pupylation. Specifically, the recycling of Pup when targets are degraded allows the PPS to maintain steady-state levels of protein pupylation and degradation at a rate limited by proteasome function, and at a pupylome level limited by Pup concentrations. This design allows the Pup-ligase, a highly promiscuous enzyme, to act in a controlled manner without causing damage, and the PPS to be effectively tuned to control protein degradation. This study thus provides understanding of how the inherent design of an intracellular proteolytic system serves crucial regulatory purposes.
Despite being a destructive process, regulated protein degradation is fundamental for proper cell function. While regulated proteolysis in eukaryotes largely involves the ubiquitin-proteasome system (UPS), most bacterial species rely on multiple ATPdependent proteases, such as the Clp proteases. Mycobacteria and related actinobacterial species also possess a degradation system analogous in its function to the UPS. In this system, a prokaryotic ubiquitin-like protein (Pup) is conjugated to proteins, thereby marking them for proteasomal degradation. A single ligase, PafA, is responsible for Pup conjugation to many protein targets, thus playing a central role in the Pup-proteasome system (PPS). In Mycobacterium smegmatis, a model mycobacterial organism where the PPS is essential under starvation conditions, cellular PafA levels change in response to nutrient availability. Indeed, increased PafA levels are observed upon nutrient limitation. We found that a multi-layered network involving transcriptional, translational and post-translational regulation determines cellular PafA levels. Induced expression is observed at stationary phase, whereas PafA degradation by the proteasome and ClpCP occurs in exponentially growing cells, as opposed to starved cells. In both growth stages, translation attenuation maintains low PafA expression levels. Altogether, these mechanisms establish the dynamics in PafA levels during bacterial growth.
The prokaryotic ubiquitin-like protein presents poor cleavage sites for proteasomal degradation Graphical abstract Highlights d Pup, the bacterial ubiquitin analog, lacks favorable proteasome cleavage sites d Pup can escape the proteasome conjugated to a targetderived degradation fragment d Dop, a depupylase, efficiently removes the degradation fragment from Pup d Dop activity facilitates Pup recycling and re-conjugation to a new target
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