Higher-Level Structural Organization of Pseudomonas Cyclic Lipopeptides through Exploration of Their Bioactive Conformation

Cyclic lipodepsipeptides (CLiPs) produced by the ubiquitous bacterial genus of Pseudomonas comprise a large pool of secondary metabolites with a wide range of associated ecological roles and antimicrobial activities. In the past decades abundant efforts have been made to unravel the chemical constitution and configuration of CLiPs towards establishing structure–function correlations and harness their potential in biocontrol and/or clinical settings. Knowledge on the conformation of these compounds, however, remains generally scattered or wanting. In this work we elucidate the conformation of 8 plant-beneficial Pseudomonas CLiPs from different CLiP families as well as a synthetic CLiP variant in membrane-mimicking micellar DPC solution using a uniform protocol based on NMR spectroscopy and all-atom molecular dynamics simulations. We find that only left-handed alfa-helical conformations occur which can be grouped into two conformational superfamilies based on the particular motif type defined by the macrocycle residue number. Using the obtained CLiP conformations as templates and exploiting sequence homology the conformational landscape of CLiPs produced by Pseudomonas is presented which is further supported by newfound correlations between the CLiP conformation and the organization of the producing biosynthetic gene cluster.