Identification of trans‐AT polyketide clusters in two marine bacteria reveals cryptic similarities between distinct symbiosis factors

Abstract

Summary Glutarimide‐containing polyketides are known as potent antitumoral and antimetastatic agents. The associated gene clusters have only been identified in a few Streptomyces producers and Burkholderia gladioli symbiont. The new glutarimide‐family polyketides, denominated sesbanimides D, E and F along with the previously known sesbanimide A and C, were isolated from two marine alphaproteobacteria Stappia indica PHM037 and Labrenzia aggregata PHM038. Structures of the isolated compounds were elucidated based on 1D and 2D homo and heteronuclear NMR analyses and ESI‐MS spectrometry. All compounds exhibited strong antitumor activity in lung, breast and colorectal cancer cell lines. Subsequent whole genome sequencing and genome mining revealed the presence of the trans‐AT PKS gene cluster responsible for the sesbanimide biosynthesis, described as sbn cluster. Strikingly, the modular architecture of downstream mixed type PKS/NRPS, SbnQ, revealed high similarity to PedH in pederin and Lab13 in labrenzin gene clusters, although those clusters are responsible for the production of structurally completely different molecules. The unexpected presence of SbnQ homologues in unrelated polyketide gene clusters across phylogenetically distant bacteria, raises intriguing questions about the evolutionary relationship between glutarimide‐like and pederin‐like pathways, as well as the functionality of their synthetic products.

Sesbanimide R, a Novel Cytotoxic Polyketide Produced by Magnetotactic Bacteria

“…Taken together, our devised biosynthesis scheme for sesbanimide R is very similar to the pathway suggested in parallel by Ka car et al for the biosynthesis of sesbanimide F from Stappia indica PHM037 (28,60). The main differences between the two BGC lie in the distribution of DH and KR domains in SbnQ, the presence of three additional transport-associated genes in the M. gryphiswaldense cluster, and a phosphopantetheinyl transferase in the Stappia indica cluster which is absent in the M. gryphiswaldense BGC.…”

“…The two double bonds are conjugated based on COSY correlations of the four dienone double bond protons and their deshielded carbon chemical shifts at d structure. This structure is highly similar to the structure of sesbanimide F, which became available at a late stage of our work in a study by Ka car et al (28,60). However, our compound contains an additional terminal arginine (R) moiety.…”

“…The main differences between the two BGC lie in the distribution of DH and KR domains in SbnQ, the presence of three additional transport-associated genes in the M. gryphiswaldense cluster, and a phosphopantetheinyl transferase in the Stappia indica cluster which is absent in the M. gryphiswaldense BGC. Notably, the final products from the strains under investigation by Ka car et al do not contain the terminal arginine moiety observed in sesbanimide R, even though the corresponding biosynthetic gene cluster contains the L-arginine-incorporating NRPS module (28,60). We speculate that the BGC from M. gryphiswaldense responsible for sesbanimide R formation is an evolutionary intermediate in a developmental line leading to the sesbanimide gene cluster from PHM037 and PHM038 or that these clusters may carry a nonfunctional NRPS module.…”

“…We set out to unambiguously assign the corresponding secondary metabolite from M. gryphiswaldense by markerless deletion of the gene cluster, to isolate the polyketide product and to elucidate its structure. Furthermore, we devised a model for sesbanimide biosynthesis that complements the one suggested by Ka car et al (28,60) and revealed the new sesbanimide R as a missing link between the sesbanimide biosynthesis pathways when compared across several taxa (29). In addition, we demonstrate cytotoxic activity of the novel sesbanimide congener.…”

“…In this study, we focused on the role of a trans-acyltransferase PKS (trans-AT PKS) BGC in M. gryphiswaldense, which we identified as a homologue of the sesbanimide gene cluster described by Ka car et al in parallel to our studies (28,60). We set out to unambiguously assign the corresponding secondary metabolite from M. gryphiswaldense by markerless deletion of the gene cluster, to isolate the polyketide product and to elucidate its structure.…”