Critical analysis of polycyclic tetramate macrolactam biosynthetic cluster phylogeny and functional diversity

Abstract

Polycyclic tetramate macrolactams (PTMs) are bioactive natural products commonly associated with certain actinobacterial and proteobacterial lineages. These molecules have been the subject of numerous structure-activity investigations since the 1970s. New members continue to be pursued in wild and engineered bacterial strains, and advances in PTM biosynthesis suggests their outwardly simplistic biosynthetic gene clusters (BGCs) belie unexpected product complexity. Towards addressing the origins of this complexity and understanding its influence on PTM discovery, we engaged in a combination of bioinformatics to systematically classify PTM BGCs, and PTM- targeted metabolomics to compare the products of select BGC types. By comparing groups of producers and BGC mutants, we exposed knowledge gaps that complicate bioinformatics-driven product predictions. In sum, we provide new insights into the evolution of PTM BGCs while systematically accounting for the PTMs discovered thus far. The combined computational and metabologenomic findings presented here should prove useful for guiding future discovery.

Piperazate-Guided Isolation of Caveamides A and B, Cyclohexenylalanine-Containing Nonribosomal Peptides from a Cave Actinomycete

“…strain BE230 was collected from New Rankin Cave in Eureka, MO as described elsewhere. 9 The strain was identified as a potential Piz producer via an established PCR screen (using degenerate oligonucleotides LMPzbB FN2 and LMPzbB RN1) 10 that targets Piz synthases. Revealing BE230 as a candidate producer, this triggered genome-sequencing of the strain (described elsewhere 9 ) plus LC/MS 2 scanning for Piz-associated mass features in growth extracts (essentially as described 11 ).…”

“…Streptomyces sp. strain BE230 was collected from New Rankin Cave in Eureka, MO as described elsewhere . The strain was identified as a potential Piz producer via an established PCR screen (using degenerate oligonucleotides LMPzbB FN2 and LMPzbB RN1) that targets Piz synthases.…”

“…The strain was identified as a potential Piz producer via an established PCR screen (using degenerate oligonucleotides LMPzbB FN2 and LMPzbB RN1) that targets Piz synthases. Revealing BE230 as a candidate producer, this triggered genome-sequencing of the strain (described elsewhere) plus LC/MS 2 scanning for Piz-associated mass features in growth extracts (essentially as described). The production of Piz compounds by BE230 was finally confirmed by the detection of Piz-characteristic 15 N-NMR resonances upon cultivation with 15 N 2 - l -ornithine ( l -Orn).…”