Simocyclinones: diversity of metabolites is dependent on fermentation conditions 3

Schimana, Judith; Walker, Martina; Zeeck, Axel; Hp, Fiedler

doi:10.1038/sj.jim.7000024

Cited by 29 publications

(31 citation statements)

References 4 publications

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“…The presence of various simocyclinone intermediates in S. antibioticus, such as simocyclinone B (anguclinone moiety linked to the D-olivose sugar) and simocyclinone C (D-olivose linked to the decatetraenoic acid and angucyclinone moieties) (8), suggests that the ligation of the aminocoumarin ring to form simocyclinone D may be the final biosynthetic step. The reconstitution of SimL has provided the first opportunity to test in vitro enzymatic substrate specificity.…”

Section: +mentioning

confidence: 99%

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Characterization of the Aminocoumarin Ligase SimL from the Simocyclinone Pathway and Tandem Incubation with NovM,P,N from the Novobiocin Pathway

et al. 2005

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Simocyclinone D 8 consists of an anguicycline C-glycoside tethered by a tetraene diester linker to an aminocoumarin. Unlike the antibiotics novobiocin, clorobiocin, and coumermycin A 1 , the phenolic hydroxyl group of the aminocoumarin in simocyclinone is not glycosylated with a decorated noviosyl moiety that is the pharmacophore for targeting bacterial DNA gyrase. We have expressed the Streptomyces antibioticus simocyclinone ligase SimL, purified it from Escherichia coli, and established its ATP-dependent amide bond forming activity with a variety of polyenoic acids including retinoic acid and fumagillin. We have then used the last three enzymes from the novobiocin pathway, NovM, NovP, and NovN, to convert a SimL product to a novel novobiocin analogue, in which the 3-prenyl-4-hydroxybenzoate of novobiocin is replaced with a tetraenoate moiety, to evaluate antibacterial activity.The aminocoumarin antibiotics novobiocin 1, clorobiocin 2, and coumermycin A 1 3, produced by various Streptomyces species (Figure 1), contain a bicyclic 3-amino-4,7-dihydroxycoumarin ring system, which serves as an essential scaffold for targeting them to the bacterial type II topoisomerases DNA gyrase and topoisomerase IV (1-5). Coumermycin A 1 is a pseudosymmetric dimer, containing elements of novobiocin (the 8-methylaminocoumarin) and clorobiocin (the 3′-O-methylpyrrolyl acyl group). Cocrystals of the N-terminal 24 kDa subfragment of the DNA gyrase B subunit (GyrB) 1 with 1 and 2 (1, 2) reveal that this family of antibiotics uses the aminocoumarin as a planar scaffold to present the decorated 4′-O-methyl-3′-O-acyl noviosyl moiety as the pharmacophore for inhibiting ATP hydrolysis in GyrB. These decorations of the L-deoxy sugar noviose include 4′-Omethylation and 3′-O-acylation with either a carbamoyl or methylpyrrolyl group. This 3′-O-acyl substituent is in intimate contact with GyrB active site residues and/or bound water molecules.Recently, another antibiotic containing the conserved aminocoumarin moiety, simocyclinone D 4 from Streptomyces antibioticus, has been discovered (6, 7). Simocyclinone D is a structurally unique antibiotic containing an aromatic anguicycline polyketide nucleus, the deoxy sugar D-olivose, and either the 8-chloro or 8-desmethyl version of the 3-amino-4,7-dihydroxycoumarin (8). The anguicycline Cglycoside and the aminocoumarin elements are linked by a tetraene dicarboxylic acid moiety. Simocyclinone possesses antimicrobial activity against Gram-positive bacteria, as well as exhibiting cytostatic effects against human tumor cell lines (6). However, its lack of a decorated noviosyl moiety at the 7-hydroxy position of the aminocoumarin scaffold suggests a molecular mechanism of action different than that of 1 and 2 given the X-ray information on GyrB complexes noted above for 1 and 2 (1, 2). Indeed, recent studies reveal that simocyclinone D8 is a potent inhibitor of gyrase, albeit through a novel mode of action by preventing the initial binding of gyrase to DNA (Anthony Maxwell, personal communicatio...

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confidence: 99%

“…Simocyclinone D is a structurally unique antibiotic containing an aromatic anguicycline polyketide nucleus, the deoxy sugar D-olivose, and either the 8-chloro or 8-desmethyl version of the 3-amino-4,7-dihydroxycoumarin (8). The anguicycline Cglycoside and the aminocoumarin elements are linked by a tetraene dicarboxylic acid moiety.…”

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confidence: 99%

Characterization of the Aminocoumarin Ligase SimL from the Simocyclinone Pathway and Tandem Incubation with NovM,P,N from the Novobiocin Pathway

et al. 2005

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“…For maintenance of mutants, erythromycin was added to a final concentration of 50 g/ml. For simocyclinone production, liquid medium (20 ml in a single-baffled 100-ml Erlenmeyer flask) was used (39,40,46). DNA manipulation was carried out in Escherichia coli XL-1 Blue MRFЈ (Stratagene).…”

Section: Methodsmentioning

confidence: 99%

“…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.…”

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confidence: 99%

“…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).…”

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Biosynthetic Gene Cluster of Simocyclinone, a Natural Multihybrid Antibiotic

Trefzer

Pelzer

Schimana

et al. 2002

Antimicrob Agents Chemother

110

116

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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...

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Chemistry and Biod iversity of the Biologically Active Natural Glycosides

Dembitsky¹

2004

Chemistry & Biodiversity

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Simocyclinones: diversity of metabolites is dependent on fermentation conditions 3

Cited by 29 publications

References 4 publications

Characterization of the Aminocoumarin Ligase SimL from the Simocyclinone Pathway and Tandem Incubation with NovM,P,N from the Novobiocin Pathway

Characterization of the Aminocoumarin Ligase SimL from the Simocyclinone Pathway and Tandem Incubation with NovM,P,N from the Novobiocin Pathway

Biosynthetic Gene Cluster of Simocyclinone, a Natural Multihybrid Antibiotic

Chemistry and Biod iversity of the Biologically Active Natural Glycosides

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