The ADEP Biosynthetic Gene Cluster inStreptomyces hawaiiensisNRRL 15010 Reveals an AccessoryclpPGene as a Novel Antibiotic Resistance Factor Academic Article uri icon

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  • ABSTRACTThe increasing threat posed by multiresistant bacterial pathogens necessitates the discovery of novel antibacterials with unprecedented modes of action. ADEP1, a natural compound produced byStreptomyces hawaiiensisNRRL 15010, is the prototype for a new class of acyldepsipeptide (ADEP) antibiotics. ADEP antibiotics deregulate the proteolytic core ClpP of the bacterial caseinolytic protease, thereby exhibiting potent antibacterial activity against Gram-positive bacteria, including multiresistant pathogens. ADEP1 and derivatives, here collectively called ADEP, have been previously investigated for their antibiotic potency against different species, structure-activity relationship, and mechanism of action; however, knowledge on the biosynthesis of the natural compound and producer self-resistance have remained elusive. In this study, we identified and analyzed the ADEP biosynthetic gene cluster inS. hawaiiensisNRRL 15010, which comprises two NRPSs, genes necessary for the biosynthesis of (4S,2R)-4-methylproline, and a type II polyketide synthase (PKS) for the assembly of highly reduced polyenes. While no resistance factor could be identified within the gene cluster itself, we discovered an additionalclpPhomologous gene (namedclpPADEP) located further downstream of the biosynthetic genes, separated from the biosynthetic gene cluster by several transposable elements. Heterologous expression of ClpPADEPin three ADEP-sensitiveStreptomycesspecies proved its role in conferring ADEP resistance, thereby revealing a novel type of antibiotic resistance determinant.IMPORTANCEAntibiotic acyldepsipeptides (ADEPs) represent a promising new class of potent antibiotics and, at the same time, are valuable tools to study the molecular functioning of their target, ClpP, the proteolytic core of the bacterial caseinolytic protease. Here, we present a straightforward purification procedure for ADEP1 that yields substantial amounts of the pure compound in a time- and cost-efficient manner, which is a prerequisite to conveniently study the antimicrobial effects of ADEP and the operating mode of bacterial ClpP machineries in diverse bacteria. Identification and characterization of the ADEP biosynthetic gene cluster inStreptomyces hawaiiensisNRRL 15010 enables future bioinformatics screenings for similar gene clusters and/or subclusters to find novel natural compounds with specific substructures. Most strikingly, we identified a cluster-associatedclpPhomolog (namedclpPADEP) as an ADEP resistance gene. ClpPADEPconstitutes a novel bacterial resistance factor that alone is necessary and sufficient to confer high-level ADEP resistance toStreptomycesacross species.


  • Thomy, Dhana
  • Culp, Elizabeth
  • Adamek, Martina
  • Cheng, Eric Y
  • Ziemert, Nadine
  • Wright, Gerard
  • Sass, Peter
  • Brötz-Oesterhelt, Heike

publication date

  • August 9, 2019