Cloning and characterization of the ravidomycin and chrysomycin biosynthetic gene clusters

Abstract

The gene clusters responsible for the biosynthesis of two antitumor antibiotics, ravidomycin and chrysomycin, have been cloned from Streptomyces ravidus and Streptomyces albaduncus, respectively. Sequencing of the 33.28 kb DNA region of the cosmid cosRav32 and the 34.65 kb DNA region of cosChry1-1 and cosChryF2 revealed 36 and 35 open reading frames (ORFs), respectively, harboring tandem sets of type II polyketide synthase (PKS) genes, D-ravidosamine and D-virenose biosynthetic genes, post-PKS tailoring genes, regulatory genes, and genes of unknown function. The isolated ravidomycin gene cluster was confirmed to be involved in ravidomycin biosynthesis through the production of a new analogue of ravidomycin along with anticipated pathway intermediates and biosynthetic shunt products upon heterologous expression of the cosmid, cosRav32, in Streptomyces lividans TK24. The identity of the cluster was further verified through cross complementation of gilvocarcin V (GV) mutants. Similarly, the chrysomycin gene cluster was demonstrated to be indirectly involved in chrysomycin biosynthesis through cross-complementation of gilvocarcin mutants deficient in the oxygenases GilOII, GilOIII, and GilOIV with the respective chrysomycin monooxygenase homologues. The ravidomycin glycosyltransferase (RavGT) appears to be able to transfer both amino- and neutral sugars, exemplified through the structurally distinct 6-membered D-ravidosamine and 5-membered D-fucofuranose, to the coumarin-based polyketide derived backbone. These results expand the library of biosynthetic genes involved in the biosyntheses of gilvocarcin class compounds that can be used to generate novel analogues through combinatorial biosynthesis.

Scheme 1

Ravidomycins, chrysomycins and related natural products.

Figure 1

Gene clusters for A) ravidomycin and B) chrysomycin biosyntheses. The black filled arrows indicate biosynthetic genes, gray arrows represent regulatory genes, and blank arrows represent the genes with unknown functions.

Scheme 2

Proposed pathways for the biosyntheses of ravidomycin V and chrysomycin V. For the NDP sugar structures 37, 40 and 43, see Scheme 3.

Scheme 3

Proposed pathways for the biosyntheses of 4′-O-acetyl-NDP-d-ravidosamine and NDP-d-virenose.

Figure 2

A) HPLC analysis of the metabolites of S. lividans TK24 (cosRav32); B) Standard deacetylravidomycin E (31)