Biosynthetic Gene Cluster of Simocyclinone, a Natural Multihybrid Antibiotic

Abstract

The entire simocyclinone biosynthetic cluster (sim gene cluster) from the producer Streptomyces antibioticus Tü6040 was identified on six overlapping cosmids (1N1, 5J10, 2L16, 2P6, 4G22, and 1K3). In total, 80.7 kb of DNA from these cosmids was sequenced, and the analysis revealed 49 complete open reading frames (ORFs). These ORFs include genes responsible for the formation and attachment of four different moieties originating from at least three different pools of primary metabolites. Also in the sim gene cluster, four ORFs were detected that resemble putative regulatory and export functions. Based on the putative function of the gene products, a model for simocyclinone D8 biosynthesis was proposed. Biosynthetic mutants were generated by insertional gene inactivation experiments, and culture extracts of these mutants were analyzed by high-performance liquid chromatography. Production of simocyclinone D8 was clearly detectable in the wild-type strain but was not detectable in the mutant strains. This indicated that indeed the sim gene cluster had been cloned.Simocyclinone D8 (Fig. 1) is produced by Streptomyces antibioticus Tü6040. It is active against gram-positive bacteria and also shows distinct cytostatic activities against human tumor cell lines (39,40,46). Simocyclinone D8 consists of four different moieties, an angucyclic polyketide core, a deoxyhexose (D-olivose), a tetraene side chain, and a halogenated aminocoumarin. The aromatic polyketide moiety is characterized by a large number of unusually placed hydroxyl groups and an oxiran bridge at positions C-12a and C-6a. It contains a Cglycosidically linked D-olivose at position C-9. Attached to the 4-OH group of D-olivose is an acetyl group, and attached to the 3-OH group is a tetraene side chain. Both are linked to the deoxysugar by ester bonds. The final amino-coumarin moiety is linked to the tetraene chain by an amide bond, resulting in an unusual polyene-amide structure. Features that distinguish simocyclinone from other angucycline antibiotics are the enormous size of the molecule and the fact that it originates from at least three different pools of primary metabolites. S. antibioticus Tü6040 also produces other simocyclinones, which can be seen as intermediates of simocyclinone D8. These compounds include simocyclinones of the A-series, the B-series, and the C-series, consisting either of the polyketide moiety (series A), the polyketide moiety plus D-olivose (series B), and the polyketide moiety plus D-olivose plus the tetraene side chain (series C) (40). Genetic engineering and combinatorial biosynthesis in bacteria provide an important new tool for drug discovery and drug design (16,19,24). Knowledge of the sequence and function of genes involved in the biosynthesis of natural products is prerequisite for this new approach. In the present study we describe the isolation of the simocyclinone biosynthetic gene cluster. Sequencing of the entire gene cluster revealed the presence of 49 open reading frames (ORFs) probably involved in simocyclinone bios...

Molecular cloning and sequence analysis of the clorobiocin biosynthetic gene cluster: new insights into the biosynthesis of aminocoumarin antibiotics The GenBank accession number for the sequence of cosmid K1F2 is AF329398.

“…An important finding of our study is that no novC homologue was detected in or near the clorobiocin gene cluster. Likewise, no novC homologue was detected in the simocyclinone cluster (Galm et al, 2002 ;Trefzer et al, 2002). We therefore suggest that novC is not related to aminocoumarin biosynthesis.…”

“…cloJ and cloK, the genes immediately downstream of cloH and cloI, are homologous to novJK and couJK of the novobiocin and coumermycin clusters, respectively. The detection of cloJ and cloK in the clorobiocin cluster, and the homologous simJ1 and simK genes in the biosynthetic gene cluster of the aminocoumarin antibiotic simocyclinone (Galm et al, 2002 ;Trefzer et al, 2002), now strongly supports the hypothesis that these genes are indeed related to aminocoumarin biosynthesis. cloJ shows homology to 3-oxo-acyl-[ACP] reductases and may likely be involved in the oxidation of a β-hydroxy-tyrosyl to a β-keto-tyrosyl intermediate (Fig.…”

DNA-binding activity of LndI protein and temporal expression of the gene that upregulates landomycin E production in Streptomyces globisporus 1912

“…Genes encoding putative transcriptional activators were identified within these clusters (Fedorenko et al, 2000;Trefzer et al, 2002;Westrich et al, 1999;Yang et al, 2001). They are distinct from other members of the SARP family in that they contain a winged helix-turn-helix DNA-binding domain in their C-terminal region (Wietzorreck & Bibb, 1997).…”

The TetR Family of Regulators

“…SimR is located in the biosynthesis cluster for simocyclinone D8 in Streptomyces antibioticus Tü 6040 (85,86). Simocyclinone D8 is a structurally complex inhibitor of DNA gyrase (87,88).…”