Biosynthetic Gene Cluster for the Cladoniamides, Bis-Indoles with a Rearranged Scaffold

Katherine S Ryan,Jörg D Hoheisel

doi:10.1371/journal.pone.0023694

Abstract

The cladoniamides are bis-indole alkaloids isolated from Streptomyces uncialis, a lichen-associated actinomycete strain. The cladoniamides have an unusual, indenotryptoline structure rarely observed among bis-indole alkaloids. I report here the isolation, sequencing, and annotation of the cladoniamide biosynthetic gene cluster and compare it to the recently published gene cluster for BE-54017, a closely related indenotryptoline natural product. The cladoniamide gene cluster differs from the BE-54017 gene cluster in gene organization and in the absence of one N-methyltransferase gene but otherwise contains close homologs to all genes in the BE-54017 cluster. Both gene clusters encode enzymes needed for the construction of an indolocarbazole core, as well as flavin-dependent enzymes putatively involved in generating the indenotryptoline scaffold from an indolocarbazole. These two bis-indolic gene clusters exemplify the diversity of biosynthetic routes that begin from the oxidative dimerization of two molecules of l-tryptophan, highlight enzymes for further study, and provide new opportunities for combinatorial engineering.

Highlights

Streptomyces uncialis is an actinomycete bacterial strain isolated with the lichen Cladonia uncialis near the Pitt River in British Columbia
The cladoniamides are unusual among bis-indole natural products: most bis-indoles have an indolocarbazole structure [4], whereas the cladoniamides have a rarely observed indenotryptoline structure (Figure 1)
Identification of the cladoniamide gene cluster The cladoniamide producer Streptomyces uncialis [1,3] was cultivated in YEME media and genomic DNA was isolated

Summary

Introduction

Streptomyces uncialis is an actinomycete bacterial strain isolated with the lichen Cladonia uncialis near the Pitt River in British Columbia. This bacterial strain is the source of the enediyne uncialamycin [1,2], and the cladoniamides, a series of bis-indole alkaloids [3]. The commonly observed indolocarbazole structure is found in a number of important molecules, including rebeccamycin, analogs of which are DNA-topoisomerase I inhibitors [5,6], and staurosporine, a kinase inhibitor [7,8]. The indolocarbazole core in rebeccamycin, staurosporine, and related natural product molecules derives biosynthetically from the face-to-face dimerization of two molecules of L-tryptophan [4,9,10,11,12]. Williams et al have postulated that the cladoniamides are biosynthetically generated from the enzymatic degradation and rearrangement of an indolocarbazole intermediate [3]

Methods

Results

Conclusion