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 byStreptomyces hawaiiensis. Most sequenced genomes ofStreptomyceshave fiveclpPgenes, organized as two distinct bicistronic operons,clpP1clpP2andclpP3clpP4, and a singleclpP5gene. 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-typeStreptomyces lividans,clpP3clpP4expression is constitutively repressed and the reason for the maintenance of this operon inStreptomyceshas been elusive. ClpP activity is indispensable for survival of actinomycetes; we therefore tested whether theclpP3clpP4operon, encoding an ADEP-insensitive Clp protease, contributes to a mechanism of ADEP resistance by target substitution. We report that inS. 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 theStreptomyces coelicolormultidrug resistance pump SCO4959–SCO4960) is also able to confer ADEP resistance, and analysis of strains withsclABdeletions indicates that there are also other mechanisms of ADEP resistance.