Acyl depsipeptide (ADEP) resistance in Streptomyces

Abstract

ADEP, a molecule of the acyl depsipeptide family, has an antibiotic activity with a unique mode of action. ADEP binding to the ubiquitous protease ClpP alters the structure of the enzyme. Access of protein to the ClpP proteolytic chamber is therefore facilitated and its cohort regulatory ATPases (ClpA, ClpC, ClpX) are not required. The consequent uncontrolled protein degradation in the cell appears to kill the ADEP-treated bacteria. ADEP is produced by Streptomyces hawaiiensis. Most sequenced genomes of Streptomyces have five clpP genes, organized as two distinct bicistronic operons, clpP1clpP2 and clpP3clpP4, and a single clpP5 gene. We investigated whether the different Clp proteases are all sensitive to ADEP. We report that ClpP1 is a target of ADEP whereas ClpP3 is largely insensitive. In wild-type Streptomyces lividans, clpP3clpP4 expression is constitutively repressed and the reason for the maintenance of this operon in Streptomyces has been elusive. ClpP activity is indispensable for survival of actinomycetes; we therefore tested whether the clpP3clpP4 operon, encoding an ADEPinsensitive Clp protease, contributes to a mechanism of ADEP resistance by target substitution. We report that in S. lividans, inactivation of ClpP1ClpP2 production or protease activity is indeed a mode of resistance to ADEP although it is neither the only nor the most frequent mode of resistance. The ABC transporter SclAB (orthologous to the Streptomyces coelicolor multidrug resistance pump SCO4959-SCO4960) is also able to confer ADEP resistance, and analysis of strains with sclAB deletions indicates that there are also other mechanisms of ADEP resistance.

Enzymatic resistance to the lipopeptide surfactin as identified through imaging mass spectrometry of bacterial competition

“…Surfactin belongs to the lipodepsipeptide class of natural products, which includes antibiotics such as daptomycin and ADEPs (46,47). Although the surfactin hydrolase had activity against the lipopeptide plipastatin in addition to surfactin, other compounds tested were not substrates for the enzyme.…”

Bacterial proteolytic complexes as therapeutic targets

“…Sequencing of resistant mutants revealed that the potential target was Clp protease, but as Clp protease is not required for normal growth in these organisms it was surprising that ADEPs exhibited their bactericidal effect through an interaction with a dispensable protease 90 . An in vitro peptidase assay using ClpP protease from Bacillus subtilis revealed that ADEPs activated proteolysis.…”

“…The natural product cyclomarin is difficult to synthesize or modify, and exhibited high clearance (due to hepatic clearance) and a short half-life when tested in mice (V. Dartois, personal communication). Although ADEPs are attractive as they are able to kill organisms even though their target is often not essential for survival, loss of ClpP activity renders these compounds inactive, resulting in high rates of resistance in vitro 90 . However, as there is strong selection to retain protease activity during infection, loss of ClpP activity as a resistance mechanism seems to be unlikely to occur during treatment, but this has yet to be confirmed.…”

Bacterial proteases, untapped antimicrobial drug targets

“…[34][35][36] In contrast to most bacteria, two or more copies of clpP are found in actinobacteria and cyanobacteria and at least one functional copy is essential for viability. 37,38 In Mycobacterium tuberculosis, clpP1 and clpP2 form an operon and both genes are essential. These isoforms work together to create a functional protease by stacking ClpP1 and ClpP2 homoheptamers into a heterotetradecamer.…”