Investigation of the biosynthesis of the pipecolate moiety of neuroprotective polyketide meridamycin.

Biogenesis of the pipecolate moiety of neuroprotective agent meridamycin in Streptomyces sp. NRRL30748 was investigated in feeding studies using lysine specifically labeled with (15)N at the α-amino or the ε-amino nitrogen position. Fourier transform mass spectrometry analysis with ultra-high mass resolving power and accurate mass measurement capability was employed to resolve the (15)N peak of labeled meridamycin from the (13)C peak of unlabeled meridamycin, allowing the precise calculation of labeling contents under each condition. The relative enrichment of (15)N-labeled meridamycin was ~43% with L-[α-(15)N]-lysine feeding and ~14% with L-[α-(15)N]-lysine feeding, suggesting two distinguishable pathways, with concomitant loss of either the ε-amino group or the α-amino group of lysine, were involved in the generation of the pipecolate moiety of meridamycin in this bacterium. PCR cloning using degenerate primers identified a proC gene encoding a putative pyrroline-5-carboxylate reductase, which was expected to catalyze the conversion of piperideine-6-carboxylate to pipecolate. However, inactivation of this locus did not significantly affect the incorporation of α-(15)N- or ε-(15)N-labeled lysine into meridamycin, indicating the existence of an alternative route for the last step of the lysine ε-transamination pathway. This work revealed the diversity and complexity of the biosynthetic pathways for pipecolate synthesis in the meridamycin producing bacterium Streptomyces sp. NRRL30748.

Rapid cloning and heterologous expression of the meridamycin biosynthetic gene cluster using a versatile Escherichia coli-streptomyces artificial chromosome vector, pSBAC.

Expression of biosynthetic pathways in heterologous hosts is an emerging approach to expedite production improvement and biosynthetic modification of natural products derived from microbial secondary metabolites. Herein we describe the development of a versatile Escherichia coli-Streptomyces shuttle Bacterial Artificial Chromosomal (BAC) conjugation vector, pSBAC, to facilitate the cloning, genetic manipulation, and heterologous expression of actinomycetes secondary metabolite biosynthetic gene clusters. The utility of pSBAC was demonstrated through the rapid cloning and heterologous expression of one of the largest polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) biosynthetic pathways: the meridamycin biosynthesis gene cluster (mer). The entire mer gene cluster ( approximately 90 kb) was captured in a single pSBAC clone through a straightforward restriction enzyme digestion and cloning approach and transferred into Streptomyces lividans. The production of meridamycin (1) in the heterologous host was achieved after replacement of the original promoter with an ermE* promoter and was enhanced by feeding with a biosynthetic precursor. The success of heterologous expression of such a giant gene cluster demonstrates the versatility of BAC cloning technology and paves the road for future exploration of expression of the meridamycin biosynthetic pathway in various hosts, including strains that have been optimized for polyketide production.

Septocylindrins A and B: peptaibols produced by the terrestrial fungus Septocylindrium sp. LL-Z1518.

Two new peptaibols, septocylindrin A (1) and septocylindrin B (2), related to the well-studied membrane-channel-forming peptaibol alamethicin, were obtained from a terrestrial isolate of the fungus Septocylindrium sp. Both 1 and 2 are linear 19-amino acid peptides with a modified phenylalanine C-terminus. Analysis of the HRMS data indicated that they differ only in the 18th residue, where 1 contains Glu and 2 contains Gln. The structures of these two peptaibols were determined by extensive NMR and HRMS analysis. The absolute configurations of amino acids present in 1 were determined using Marfey's methodology. Both compounds were isolated through bioassay-guided fractionation and exhibited significant antibacterial and antifungal activity.

Isolation and characterization of meridamycin biosynthetic gene cluster from Streptomyces sp. NRRL 30748.

Meridamycin is a non-immunosuppressive, FKBP12-binding natural macrolide with potential therapeutic applications in a variety of medical conditions. To set the stage for structural modification of meridamycin by genetic engineering, we have cloned and completely sequenced approximately 117 kb of DNA encompassing the meridamycin biosynthetic gene cluster from the producing strain, Streptomyces sp. NRRL 30748. Clustered in the center of the cloned DNA stretch are six genes responsible for the construction of the core structure of meridamycin, including merP encoding a non-ribosomal peptide synthase for pipecolate-incorporation, four PKS genes (merA-D) together encoding 1 loading module and 14 extension modules, and merE encoding a cytochrome P450 monooxygenase. A number of genes with potential pathway-specific regulatory or resistance functions have also been identified. The absence of the gene encoding lysine cyclodeaminase in the sequenced gene cluster and the rest of the genome of NRRL 30748 indicated the synthesis of pipecolate in this strain is not through the common lysine cyclodeamination route previously described for rapamycin and FK506/FK520 biosynthesis. An efficient conjugation method has been developed for Streptomyces sp. NRRL 30748 to facilitate the genetic manipulation of meridamycin biosynthetic gene cluster. Disruption of merP resulted in the complete abolition of meridamycin production, proving the identity of the gene cluster. A novel meridamycin analogue, C36-keto-meridamycin, has been successfully generated through deletion of a DNA fragment encoding KR1 domain of MerA from the chromosomal DNA.

3-normeridamycin: a potent non-immunosuppressive immunophilin ligand is neuroprotective in dopaminergic neurons.

3-Normeridamycin (1), isolated from fermentation extracts of the soil actinomycete Streptomyces sp. LL-C31037, demonstrated potent neuroprotective activity. When challenged with the neurotoxin 1-methyl-4-phenylpyridinium (MPP+), known to induce parkinsonism, 1 restored functional dopamine uptake in a concentration-dependent manner, with an EC50 of 110 nM in dopaminergic neurons. The structure of 1 was determined via spectroscopic methods, and the immunosuppressive and immunophilin binding properties of the compound were also measured.

Production of novel rapamycin analogs by precursor-directed biosynthesis.

The natural product rapamycin, produced during fermentation by Streptomyces hygroscopicus, is known for its potent antifungal, immunosuppressive, and anticancer activities. During rapamycin biosynthesis, the amino acid l-pipecolate is incorporated into the rapamycin molecule. We investigated the use of precursor-directed biosynthesis to create new rapamycin analogs by substitution of unusual l-pipecolate analogs in place of the normal amino acid. Our results suggest that the l-pipecolate analog (+/-)-nipecotic acid inhibits the biosynthesis of l-pipecolate, thereby limiting the availability of this molecule for rapamycin biosynthesis. We used (+/-)-nipecotic acid in our precursor-directed biosynthesis studies to reduce l-pipecolate availability and thereby enhance the incorporation of other pipecolate analogs into the rapamycin molecule. We describe here the use of this method for production of two new sulfur-containing rapamycin analogs, 20-thiarapamycin and 15-deoxo-19-sulfoxylrapamycin, and report measurement of their binding to FKBP12.

Novel sulfur-containing rapamycin analogs prepared by precursor-directed biosynthesis.

[reaction: see text] Two novel sulfur-containing analogs of the immunosuppressive natural product rapamycin (1) were obtained by feeding cultures of Streptomyces hygroscopicus with l-nipecotic acid (4) and either (S)-1,3-thiazane-4-carboxylic acid (5) or (S)-1,4-thiazane-3-carboxylic acid (6). The structures of the two new compounds, 20-thiarapamycin (2) and 15-deoxo-19-sulfoxylrapamycin (3), were determined by spectroscopic methods.

New approaches to augment fungal biotransformation.

The possibility of using solid supports and intermittent substrate feeding to manipulate biotransformation by fungi was examined, with amoxapine as a model compound. Cunninghamella elegans ATCC 8688a grown as free cells in six-well plates showed 7-hydroxyamoxapine as the major metabolite of amoxapine biotransformation. However, when cells were grown in the presence of activated carbon, N-formyl-7-hydroxyamoxapine was formed as the major metabolite. Intermittent feeding of amoxapine also favored the formation of N-formyl-7-hydroxyamoxapine.