Applications of Bacterial Degrons and Degraders — Toward Targeted Protein Degradation in Bacteria

Abstract

A repertoire of proteolysis-targeting signals known as degrons is a necessary component of protein homeostasis in every living cell. In bacteria, degrons can be used in place of chemical genetics approaches to interrogate and control protein function. Here, we provide a comprehensive review of synthetic applications of degrons in targeted proteolysis in bacteria. We describe recent advances ranging from large screens employing tunable degradation systems and orthogonal degrons, to sophisticated tools and sensors for imaging. Based on the success of proteolysis-targeting chimeras as an emerging paradigm in cancer drug discovery, we discuss perspectives on using bacterial degraders for studying protein function and as novel antimicrobials.

Directed evolution of the rRNA methylating enzyme Cfr reveals molecular basis of antibiotic resistance

“…Based on previous biochemical work, it is unlikely that CfrWT and CfrN2K/I would have different N-terminal processing, since fMN… and fMK/I… are likely to be efficiently de-formylated ( Ragusa et al, 1999 ) and resistant to methionine excision ( Hirel et al, 1989 ; Frottin et al, 2006 ; Xiao et al, 2010 ). Although the precise mechanism by which N2K/I improves Cfr stability remains elusive, these mutations may alter recognition by other enzymes important for degradation, such as endopeptidases or L/F-tRNA-protein transferase ( Izert et al, 2021 ; Ottofuelling et al, 2021 ).…”

A Novel Phage Infecting the Marine Photoheterotrophic Bacterium Citromicrobium bathyomarinum

“…The g89 encodes a bacterial proteasome homolog (BPH) that mediates protein degradation and enables rapid cellular responses to different environmental conditions. The refolding and degradation of proteins are powered by ATP hydrolysis conducted by ATPases associated with diverse cellular activities (RXM Gp57) [ 35 ].…”

Targeted Protein Degradation: The New Frontier of Antimicrobial Discovery?

“…Some general concepts pertaining to the adaptation of TPD to bacterial systems were recently described by Gopal and Dick and Izert and co-workers . Toward this endgame, consideration must be given to ensure the TPD approach is appropriately aligned with the location of the bacterial threat.…”

“…In its inactive conformer, N-terminal segments of each monomer cluster together at the head of the chamber, forming a flexible gate blocking substrate access. , ATPase unfoldase chaperones (ClpA, ClpC, and ClpX) allosterically bind within inter-subunit hydrophobic grooves of the complex to expand the degradation chamber, facilitate ATP-assisted opening of the gate, and align the Ser-His-Asp active sites. ,, The ATPase partners also partially unfold substrates to facilitate passage through the open pore into the degradation chamber . This family is predominantly responsible for cytoplasmic protein quality control in prokaryotes, and is characterized by its potent proteolytic activity and propensity to recognize substrates through a wide array of degradation pathways, including the N-end rule, SsrA, and pArg pathways …”

“…The idea of a universal antibacterial degrader that engages the bacterial proteasome, akin to the engagement of E3 ligases driving eukaryotic TPD via polyubiquitination, is limited both by its prevalence only in the bacterial orders Actinomycetales and Nitrospirales and its nonessentiality. In any event, one could conceivably engage the PafA Pup-ligase to pupylate recruited POIs for targeting to the proteasome, which might have utility in the creation of new antibiotics against M.tb …”