Survival of mycobacteria depends on proteasome‐mediated amino acid recycling under nutrient limitation

Abstract

Intracellular protein degradation is an essential process in all life domains. While in all eukaryotes regulated protein degradation involves ubiquitin tagging and the 26S-proteasome, bacterial prokaryotic ubiquitin-like protein (Pup) tagging and proteasomes are conserved only in species belonging to the phyla Actinobacteria and Nitrospira. In Mycobacterium tuberculosis, the Pup-proteasome system (PPS) is important for virulence, yet its physiological role in non-pathogenic species has remained an enigma. We now report, using Mycobacterium smegmatis as a model organism, that the PPS is essential for survival under starvation. Upon nitrogen limitation, PPS activity is induced, leading to accelerated tagging and degradation of many cytoplasmic proteins. We suggest a model in which the PPS functions to recycle amino acids under nitrogen starvation, thereby enabling the cell to maintain basal metabolic activities. We also find that the PPS auto-regulates its own activity via pupylation and degradation of its components in a manner that promotes the oscillatory expression of PPS components. As such, the destructive activity of the PPS is carefully balanced to maintain cellular functions during starvation.

Posttranslational regulation of coordinated enzyme activities in the Pup-proteasome system

“…PafA is the sole enzyme catalyzing Pup conjugation to target substrates, coupling ATP hydrolysis to the formation of an isopeptide bond between the side chains of Pup C-terminal glutamate and a substrate lysine (6,14). PafA presents a remarkable broad specificity, recognizing a variety and apparently unrelated protein targets via a mechanism that remains poorly understood (5,9,(15)(16)(17). The broad specificity of PafA correlated well with the proposed role of the PPS as an amino acid recycling factory under starvation conditions (5).…”

“…PafA presents a remarkable broad specificity, recognizing a variety and apparently unrelated protein targets via a mechanism that remains poorly understood (5,9,(15)(16)(17). The broad specificity of PafA correlated well with the proposed role of the PPS as an amino acid recycling factory under starvation conditions (5).…”

“…At the time of its discovery, the PPS was deemed as being important for Mycobacterium tuberculosis virulence (3). Later, the PPS was found to be essential in both M. tuberculosis and the nonpathogenic model mycobacterial species Mycobacterium smegmatis under starvation conditions (4,5). In response to nitrogen limitation, the PPS activity is induced, leading to accelerated tagging and degradation of cellular proteins, presumably to meet nutritional needs (5).…”

“…Later, the PPS was found to be essential in both M. tuberculosis and the nonpathogenic model mycobacterial species Mycobacterium smegmatis under starvation conditions (4,5). In response to nitrogen limitation, the PPS activity is induced, leading to accelerated tagging and degradation of cellular proteins, presumably to meet nutritional needs (5). The tagging molecule, Pup (prokaryotic ubiquitin-like protein), is a small protein comprising 64 amino acids in M. tuberculosis and M. smegmatis (6).…”

Genome reduction in an abundant and ubiquitous soil bacterium ‘Candidatus Udaeobacter copiosus’

“…U. copiosus also encodes for all components of the bacterial proteasome. Proteasomal degradation is critical for amino acid recycling under starvation conditions in mycobacteria 39 . The enrichment of peptide transport and degradation systems in the Ca.…”