Dapdiamides, Tripeptide Antibiotics Formed by Unconventional Amide Ligases

Abstract

Construction of a genomic DNA library from Pantoea agglomerans strain CU0119 and screening against the plant pathogen Erwinia amylovora yielded a new family of antibiotics, dapdiamides A−E (1−5). The structures were established through 2D-NMR experiments and mass spectrometry, as well as the synthesis of dapdiamide A (1). Transposon mutagenesis of the active cosmid allowed identification of the biosynthetic gene cluster. The dapdiamide family’s promiscuous biosynthetic pathway contains two unconventional amide ligases that are predicted to couple its constituent monomers.

Characterization of the Biosynthetic Operon for the Antibacterial Peptide Herbicolin in Pantoea vagans Biocontrol Strain C9-1 and Incidence in Pantoea Species

“…1) (35). We previously proposed (37) that this compound would be identical to dapdiamide E, but now we are referring to the compound as herbicolin I to be consistent with earlier publications (7,18) and because the stereochemistry for both compounds has not been determined.…”

“…The biosynthesis of the dapdiamide antibiotics comprises the linkage of L-2,3-diaminopropionic acid (DAP) to two variable units (e.g., amino acids, fumaramic acid and derivates) via amide bond formation (7,15). Culture supernatants of E. coli expressing the dapdiamide biosynthetic cluster from P. agglomerans CU0119 contained dapdiamide A as well as the less-abundant variants dapdiamide B and C, having an isoleucine or leucine moiety instead of valine.…”

“…Dapdiamide D and dapdiamide E also were present. These differ in linkage of DAP to fumaramic acid and an epoxide instead of the fumaramic acid double bond, respectively (7,15). It is possible that P. vagans C9-1 produces other dapdiamides that were not detected or isolated by the protocols used for isolation of N ß -epoxysuccinamoyl-DAPvaline.…”

“…Note that the gene cluster of P. vagans C9-1 differs in the number of genes due to the naturally separated genes ddaF1 and ddaF2, which together constitute the biochemical function of ddaF in P. agglomerans CU0119. pressed in E. coli and shown to produce a mixture of dapdiamides (7). Since the sequence of P. agglomerans CU0119 (7) comprises only the dapdiamide biosynthesis cluster, no evidence for horizontal transfer to P. agglomerans CU0119 is available.…”

“…This study confirms the chemical structure of herbicolin I, while the gene cluster was identified using plasposon mutants. The analysis of the biosynthetic genes revealed a similar gene cluster in P. agglomerans CU0119, which produces a family of dapdiamide antibiotics (dapdiamide A to E) (7,16). Additionally, we evaluated the incidence of homologous biosynthetic genes across a wide range of Pantoea spp., including plant, environmental, and clinical isolates.…”