Characterization of bafilomycin biosynthesis in Kitasatospora setae KM-6054 and comparative analysis of gene clusters in Actinomycetales microorganisms

Abstract

(setamycin) produced by Kitasatospora setae KM-6054 belong to the plecomacrolide family, which exhibit antibacterial, antifungal, antineoplastic and immunosuppressive activities. An analysis of gene clusters from K. setae KM-6054 governing the biosynthesis of bafilomycins revealed that it contains five large open reading frames (ORFs) encoding the multifunctional polypeptides of bafilomycin polyketide synthases (PKSs). These clustered PKS genes, which are responsible for bafilomycin biosynthesis, together encode 11 homologous sets of enzyme activities, each catalyzing a specific round of polyketide chain elongation. The region contains an additional 13 ORFs spanning a distance of 73 287 bp, some of which encode polypeptides governing other key steps in bafilomycin biosynthesis. Five ORFs, BfmB, BfmC, BfmD, BfmE and BfmF, were involved in the formation of methoxymalonyl-acyl carrier protein (ACP). Two possible regulatory genes, bfmR and bfmH, were found downstream of the above genes. A gene-knockout analysis revealed that BfmR was only a transcriptional regulator for the transcription of bafilomycin biosynthetic genes. Two genes, bfmI and bfmJ, were found downstream of bfmH. An analysis of these gene-disruption mutants in addition to an enzymatic analysis of BfmI and BfmJ revealed that BfmJ activated fumarate and BfmI functioned as a catalyst to form a fumaryl ester at the C21 hydroxyl residue of bafilomycin A 1 . A comparative analysis of bafilomycin gene clusters in K. setae KM-6054, Streptomyces lohii JCM 14114 and Streptomyces griseus DSM 2608 revealed that each ORF of both gene clusters in two Streptomyces strains were quite similar to each other. However, each ORF of gene cluster in K. setae KM-6054 was of lower similarity to that of corresponding ORF in the two Streptomyces species.

Comparative Genomics of Marine Sponge-Derived Streptomyces spp. Isolates SM17 and SM18 With Their Closest Terrestrial Relatives Provides Novel Insights Into Environmental Niche Adaptations and Secondary Metabolite Biosynthesis Potential

“…SM17 also contains clusters that may potentially encode for the production of surugamides (Figure 4) and the glycopeptide antibiotic mannopeptimycin (Supplementary Table S1), with the former possessing gene similarity with the surugamide A/D sequence from Streptomyces albus in the database (Ninomiya et al, 2016), and the latter sharing similarity to the mannopeptimycin sequence from Streptomyces hygroscopicus in the database, with the main biosynthetic genes being present in the predicted smBGC (Singh et al, 2003; Magarvey et al, 2006). SM18 appears to possess a cluster encoding the anti-bacterial compound bafilomycin (Figure 4 and Supplementary Table S2), with similarity to the bafilomycin sequence from Streptomyces lohii (Bowman et al, 1988; Zhang et al, 2013; Nara et al, 2017); as well other clusters with similarity to known smBGCs that encode anti-fungal and anti-bacterial compounds such as SGR PTMs, curamycin, and caboxamycin (Figure 4), from Streptomyces griseus (Luo et al, 2013), Streptomyces curacoi (Galmarini and Deulofeu, 1961), and Streptomyces sp. NTK 937 (Hohmann et al, 2009; Losada et al, 2017), respectively.…”

Bioprospecting Through Cloning of Whole Natural Product Biosynthetic Gene Clusters

“…The approach does, however, require highly efficient screening assays as the library will have a very low fraction of positives. Many groups have successfully used sequence-independent library cloning based on different library construction strategies [e.g., cosmids, fosmids, bacterial artificial chromosomes (BACs), phage artificial chromosomes (PACs)] for natural product discovery (Table 1) (Deng et al, 2017;Nara et al, 2017).…”

Complete elucidation of the late steps of bafilomycin biosynthesis in Streptomyces lohii

“…Note added in proof-During the review process, another paper was published relating to the topics in this article (52).…”