Identification of an antibiotic biosynthetic gene cluster in pantoea agglomerans B025670

Abstract

The rise of multi-drug resistant isolates of several pathogens, including Gram-negative members of the Enterobacteriaceae, requires the identification of new antimicrobials that can target them. Members of the genus Pantoea, a Gram-negative bacterial group, produce natural products with antimicrobial properties. A survey of a Pantoea collection against clinically relevant pathogens, including VRE, Enterobacter, Klebsiella, Citrobacter and Kosakonia, revealed 25 strains that produce at least one antibiotic against one or more of these pathogens. Of these strains, Pantoea agglomerans B025670 produces at least one antibiotic (denoted PNP-4) that has activity against strains of Enterobacter and Kosakonia. The conventional genetic approach was used to identify the antibiotic-producing biosynthetic gene cluster. This involved transposon mutagenesis of wild type B025670 (B025670-WT) followed by genetic screens on the mutants to identify candidates that no longer produced the antibiotic. The antibiotic production in B025670-WT was disrupted by mutations in several amino acid biosynthetic pathways, including mutations in histidine, leucine, arginine, isoleucine, cysteine and tryptophan operons. However, this was reversed upon supplementation with the corresponding amino acids in the growth medium. Furthermore, none of the candidate mutants appeared to have disruptions in the cluster responsible for PNP-4 production. Comparative genomics was then used to identify the mystery cluster. A comparison of B025670-WT draft genome with closely related non-producers of the antibiotic revealed two clusters that are unique to B025670-WT. Mutations in one of these clusters, potentially involved in fatty acid biosynthesis, results in a disruption of antibiotic production. Furthermore,the distribution of this cluster across Pantoea strains is limited.