Stereostructure of Rimocidin

Transposon-based identification of genes involved in the rimocidin biosynthesis in Streptomyces rimosus M527

The transposon mutagenesis strategy has been employed to generate random insertion mutants and analyze the correlation between genes and secondary metabolites in the genus Streptomyces. In this study, our primary objective was to identify an unknown gene involved in rimocidin biosynthesis and elucidate its role in rimocidin production in Streptomyces rimosus M527. To achieve this, we established a random mutant library of S. rimosus M527 using a Tn5 transposon-mediated random mutagenesis strategy. Among the 137 isolated mutants, M527-G10 and M527-W5 exhibited the most significant variations in antagonistic activity against the plant pathogenic fungus Fusarium oxysporum f. sp. cucumerinum. Specifically, M527-G10 displayed a 72.93% reduction, while M527-W5 showed a 49.8% increase in rimocidin production compared to the wild-type (WT) strain S. rimosus M527. Subsequently, we employed a plasmid rescue strategy to identify the insertion loci of the transposon in the genomes of mutants M527-G10 and M527-W5, revealing a response regulator transcription factor (rrt) and a hypothetical protein (hyp), respectively. The roles of rrt and hyp in rimocidin biosynthesis were determined through gene deletion, overexpression in the WT strain, and complemented expression in the transposon mutants. Notably, the gene-deletion mutants M527-ΔRRT and M527-ΔHYP exhibited similar behavior in rimocidin production compared to the corresponding transposon mutants M527-G10 and M527-W5, suggesting that transposon insertions in genes rrt and hyp led to alterations in rimocidin production. Furthermore, both gene deletion and overexpression of rrt and hyp had no discernible effects on cell growth. These results reveal that genes rrt and hyp have positive and negative impacts on rimocidin production in S. rimosus M527, respectively.

Improvement of rimocidin production in Streptomyces rimosus M527 by reporter-guided mutation selection

In this study, we employed a reporter-guided mutation selection (RGMS) strategy to improve the rimocidin production of Streptomyces rimosus M527, which is based on a single-reporter plasmid pAN and atmospheric and room temperature plasma (ARTP). In plasmid pAN, PrimA, a native promoter of the loading module of rimocidin biosynthesis (RimA) was chosen as a target, and the kanamycin resistance gene (neo) under the control of PrimA was chosen as the reporter gene. The integrative plasmid pAN was introduced into the chromosome of S. rimosus M527 by conjugation to yield the initial strain S. rimosus M527-pAN. Subsequently, mutants of M527-pAN were generated by ARTP. 79 mutants were obtained in total, of which 67 mutants showed a higher level of kanamycin resistance (Kanr) than that of the initial strain M527-pAN. The majority of mutants exhibited a slight increase in rimocidin production compared with M527-pAN. Notably, 3 mutants, M527-pAN-S34, S38, and S52, which exhibited highest kanamycin resistance among all Kanr mutants, showed 34%, 52%, and 45% increase in rimocidin production compared with M527-pAN, respectively. Quantitative RT-PCR analysis revealed that the transcriptional levels of neo and rim genes were increased in mutants M527-pAN-S34, S38, and S52 compared with M527-pAN. These results confirmed that the RGMS approach was successful in improving the rimocidin production in S. rimosus M527.

Improvement of Rimocidin Biosynthesis by Increasing Supply of Precursor Malonyl-CoA via Over-expression of Acetyl-CoA Carboxylase in Streptomyces rimosus M527

Precursor engineering is an effective strategy for the overproduction of secondary metabolites. The polyene macrolide rimocidin, which is produced by Streptomyces rimosus M527, exhibits a potent activity against a broad range of phytopathogenic fungi. It has been predicted that malonyl-CoA is used as extender units for rimocidin biosynthesis. Based on a systematic analysis of three sets of time-series transcriptome microarray data of S. rimosus M527 fermented in different conditions, the differentially expressed acc_sr gene that encodes acetyl-CoA carboxylase (ACC) was found. To understand how the formation of rimocidin is being influenced by the expression of the acc_sr gene and by the concentration of malonyl-CoA, the acc_sr gene was cloned and over-expressed in the wild-type strain S. rimosus M527 in this study. The recombinant strain S. rimosus M527-ACC harboring the over-expressed acc_sr gene exhibited better performances based on the enzymatic activity of ACC, intracellular malonyl-CoA concentrations, and rimocidin production compared to S. rimosus M527 throughout the fermentation process. The enzymatic activity of ACC and intracellular concentration of malonyl-CoA of S. rimosus M527-ACC were 1.0- and 1.5-fold higher than those of S. rimosus M527, respectively. Finally, the yield of rimocidin produced by S. rimosus M527-ACC reached 320.7 mg/L, which was 34.0% higher than that of S. rimosus M527. These results confirmed that malonyl-CoA is an important precursor for rimocidin biosynthesis and suggested that an adequate supply of malonyl-CoA caused by acc_sr gene over-expression led to the improvement in rimocidin production.

Iso-Partricin, an Aromatic Analogue of Amphotericin B: How Shining Light on Old Drugs Might Help Create New Ones

Partricin is a heptaene macrolide antibiotic complex that exhibits exceptional antifungal activity, yet poor selective toxicity, in the pathogen/host system. It consists of two compounds, namely partricin A and B, and both of these molecules incorporate two cis-type bonds within their heptaenic chromophores: 28Z and 30Z. In this contribution, we have proven that partricins are susceptible to a chromophore-straightening photoisomerization process. The occurring 28Z→28E and 30Z→30E switches are irreversible in given conditions, and they are the only structural changes observed during the experiment. The obtained all-trans partricin's derivatives, namely iso-partricins A and B, exhibit very promising features, potentially resulting in the improvement of their selective toxicity.

Ipertrofan Revisited-The Proposal of the Complete Stereochemistry of Mepartricin A and B

Being a methyl ester of partricin, the mepartricin complex is the active substance of a drug called Ipertrofan (Tricandil), which was proven to be useful in treatment of benign prostatic hyperplasia and chronic nonbacterial prostatitis/chronic pelvic pain syndrome. Nevertheless, no direct structural evidence on the stereochemistry of its components has been presented to date. In this contribution, we have conducted detailed, NMR-driven stereochemical studies on mepartricins A and B, aided by molecular dynamics simulations. The absolute configuration of all the stereogenic centers of mepartricin A and B was defined as 3R, 7R, 9R, 11S, 13S, 15R, 17S, 18R, 19S, 21R, 36S, 37R, and 38S, and proposed as 41R. The geometry of the heptaenic chromophore of both compounds has been established as 22E, 24E, 26E, 28Z, 30Z, 32E, and 34E. Our studies on mepartricin ultimately proved that partricins A and B are structurally identical to the previously described main components of the aureofacin complex: gedamycin and vacidin, respectively. The knowledge of the stereochemistry of this drug is a fundamental matter not only in terms of studies on its molecular mode of action, but also for potential derivatization, aiming at improvement of its pharmacological properties.

Identification of a gene from Streptomyces rimosus M527 negatively affecting rimocidin biosynthesis and morphological differentiation

The polyene macrolide rimocidin, produced by Streptomyces rimosus M527, was found to be highly effective against a broad range of fungal plant pathogens. Current understanding of the regulatory mechanism of rimocidin biosynthesis and morphological differentiation in S. rimosus M527 is limited. NsdA is considered a negative regulator involved in morphological differentiation and biosynthesis of secondary metabolites in some Streptomyces species. In this study, nsdA_sr was cloned from S. rimosus M527. The role of nsdA_sr in rimocidin biosynthesis and morphological differentiation was investigated by gene deletion, complementation, and over-expression. A ΔnsdA_sr mutant was obtained using CRISPR/Cas9. The mutant produced more rimocidin (46%) and accelerated morphological differentiation than the wild-type strain. Over-expression of nsdA_sr led to a decrease in rimocidin production and impairment of morphological differentiation. Quantitative RT-PCR analysis revealed that transcription of rim genes responsible for rimocidin biosynthesis was upregulated in the ΔnsdA_sr mutant but downregulated in the nsdA_sr over-expression strain. Similar effects have been described for Streptomyces coelicolor M145 and the industrial toyocamycin-producing strain Streptomyces diastatochromogenes 1628. KEY POINTS: • A negative regulator for sporulation and rimocidin production was identified. • The CRISPR/Cas9 system was used for gene deletion in S. rimosus M527.

Evolution of Anion Relay Chemistry: Construction of Architecturally Complex Natural Products

Multicomponent union tactics in which three or more fragments are rapidly connected are highly prized in the construction of architecturally complex natural products. Anion Relay Chemistry (ARC), a multicomponent union tactic, has just such potential to elaborate structurally diverse scaffolds in a single operation with excellent stereochemical control. Conceptually, the ARC tactic can be divided into two main classes: "Through-Bond," by the relay of negative charge through the bonding system of a molecule; and "Through-Space," by the migration of negative charge across space by a transfer agent. "Through-Space" Anion Relay Chemistry, the focus of this Account, can be further subdivided into two types: Type I ARC, originated from the Tietze-Schaumann-Smith coupling reaction, which for the first time permits controllable Brook rearrangements to construct unsymmetrical adducts, and as such has been successfully employed in the total syntheses of diverse natural products, including the mycoticins, bryostatin 1, spongistatins, rimocidin, indolizidine alkaloids, and enigmazole A; and Type II ARC, central to which is the design of novel bifunctional linchpins that enable rapid assembly of linear and cyclic fragments with diverse architectural features, ranging from polyols, spiroketals, and polyenes to polypropionate scaffolds. Recently, the Type II ARC tactic has been exploited as the key construction tactic in the total syntheses of the spirastrellolides, the cryptocarya acetates, secu'amamine A, mandelalide A, and nahuoic acid C_i (B_ii). This Account will present the evolution of both the Type I and Type II Anion Relay tactics, in conjunction with some prominent applications.

Effects of addition of elicitors on rimocidin biosynthesis in Streptomyces rimosus M527

The polyene macrolide rimocidin, produced by Streptomyces rimosus M527, is highly effective against a broad range of fungal plant pathogens, but at low yields. Elicitation is an effective method of stimulating the yield of bioactive secondary metabolites. In this study, the biomass and filtrate of a culture broth of Escherichia coli JM109, Bacillus subtilis WB600, Saccharomyces cerevisiae, and Fusarium oxysporum f. sp. cucumerinum were employed as elicitors to promote rimocidin production in S. rimosus M527. Adding culture broth and biomass of S. cerevisiae (A3) and F. oxysporum f. sp. cucumerinum (B4) resulted in an increase of rimocidin production by 51.2% and 68.3% respectively compared with the production under normal conditions in 5-l fermentor. In addition, quantitative RT-PCR analysis revealed that the transcriptions of ten genes (rimA to rimK) located in the gene cluster involved in rimocidin biosynthesis in A3 or B4 elicitation experimental group were all higher than those of a control group. Using a β-glucuronidase (GUS) reporter system, GUS enzyme activity assay, and Western blot analysis, we discovered that elicitation of A3 or B4 increased protein synthesis in S. rimosus M527. These results demonstrate that the addition of elicitors is a useful approach to improve rimocidin production.Key Points • An effective strategy for enhancing rimocidin production in S. rimosus M527 is demonstrated. • Overproduction of rimocidin is a result of higher expressed structural genes followed by an increase in protein synthesis.

Monosaccharides as Potential Chiral Probes for the Determination of the Absolute Configuration of Secondary Alcohols

Herein, a new method for the elucidation of the absolute configuration of chiral secondary alcohols is proposed. This method is an alternative for a widely used approach reported by Mosher and Dale and similar methods that are based on the ¹H NMR shift (δ) changes of protons that are attached to the substituents of the oxymethine carbon atom. The presented method is not based on tracking the chemical shift changes and utilizes stereochemically defined monosaccharides as chiral probes. A secondary alcohol is glycosylated, and the resulting glycoside is subjected to NMR studies. The observation of dipolar couplings between the protons of the monosaccharide moiety and the protons of the secondary alcohol moiety via the NOESY/ROESY spectra enables the determination of the absolute configuration of the oxymethine carbon atom.

Antifungal activity of rimocidin and a new rimocidin derivative BU16 produced by Streptomyces mauvecolor BU16 and their effects on pepper anthracnose

AIMS

The objective of this study was to explore antifungal metabolites targeting fungal cell envelope and to evaluate the control efficacy against anthracnose development in pepper plants.

METHODS AND RESULTS

A natural product library comprising 3000 microbial culture extracts was screened via an adenylate kinase (AK)-based cell lysis assay to detect antifungal metabolites targeting the cell envelope of plant-pathogenic fungi. The culture extract of Streptomyces mauvecolor strain BU16 displayed potent AK-releasing activity. Rimocidin and a new rimocidin derivative, BU16, were identified from the extract as active constituents. BU16 is a tetraene macrolide containing a six-membered hemiketal ring with an ethyl group side chain instead of the propyl group in rimocidin. Rimocidin and BU16 showed broad-spectrum antifungal activity against various plant-pathogenic fungi and demonstrated potent control efficacy against anthracnose development in pepper plants.

CONCLUSIONS

Antifungal metabolites produced by S. mauvecolor strain BU16 were identified to be rimocidin and BU16. The compounds displayed potent control efficacy against pepper anthracnose.

SIGNIFICANCE AND IMPACT OF THE STUDY

Rimocidin and BU16 would be active ingredients of disease control agents disrupting cell envelope of plant-pathogenic fungi. The structure and antifungal activity of rimocidin derivative BU16 is first described in this study.

Stereostructure of mycoheptin A(2)

The absolute configurations of all the stereogenic centers of the antibiotic mycoheptin A(2) were established upon previously elaborated general procedure, consisting of DQF-COSY, NOESY, ROESY, HSQC and HMBC experiments as major tools. The structure of mycoheptin A(2) without stereochemistry of its aglycone has been reported before.

(+)-Rimocidin synthetic studies: construction of the C(1-27) aglycone skeleton

Assembly of the C(1-27) macrocyclic skeleton of rimocidinolide, the aglycone of (+)-rimocidin (1), has been achieved in convergent fashion. Key features of the synthetic strategy entail application of multicomponent Type I Anion Relay Chemistry (ARC), in conjunction with the S(N)2/S(N)2' reaction manifolds of vinyl epoxides, both employing 2-substituted 1,3-dithianes to construct the C(1-19) carbon backbone. Yamaguchi union of a C(20-27) vinyl borate ester, possessing the all-trans triene, with an advanced C(1-19) vinyl iodide followed by macrocyclization via Suzuki-Miyaura cross-coupling completed construction of the C(1-27) rimocidinolide skeleton.

Genetics of Streptomyces rimosus, the oxytetracycline producer

From a genetic standpoint, Streptomyces rimosus is arguably the best-characterized industrial streptomycete as the producer of oxytetracycline and other tetracycline antibiotics. Although resistance to these antibiotics has reduced their clinical use in recent years, tetracyclines have an increasing role in the treatment of emerging infections and noninfective diseases. Procedures for in vivo and in vitro genetic manipulations in S. rimosus have been developed since the 1950s and applied to study the genetic instability of S. rimosus strains and for the molecular cloning and characterization of genes involved in oxytetracycline biosynthesis. Recent advances in the methodology of genome sequencing bring the realistic prospect of obtaining the genome sequence of S. rimosus in the near term.

Monosaccharides as internal probes for the determination of the absolute configuration of 2-butanol

D-Glucose, D-mannose and L-rhamnose were reacted with a racemic mixture of 2-butanol, and the resulting alpha-glycosides were analyzed by 1H NMR with COSY and NOESY experiments. Conformational analysis of alpha-glycosidic bonds performed with molecular modeling and appropriate heteronuclear long-range coupling measurements and combined with analysis of dipolar couplings observed in NOESY spectra allowed the assignment of absolute configuration in the aglycones of elucidated alpha-glycosides.

Two polyene amides produced by genetically modified Streptomyces diastaticus var. 108

Streptomyces diastaticus var. 108, a newly isolated strain, was recently characterized as a producer of two polyene macrolide antibiotics (rimocidin and CE-108), and the biosynthetic gene cluster was partially characterized. When the producer strain was genetically modified by transformation with some engineered SCP2*-derived vectors carrying the ermE gene, two previously uncharacterized macrolides were detected in the fermentation broth of the recombinant strain and chemically characterized as the amides of the parental polyene carboxylic acids. The biological activity and some in vitro toxicity assays showed that this chemical modification resulted in pharmaceuticals with improved biological properties compared with the parental products.

Starter unit choice determines the production of two tetraene macrolides, rimocidin and CE-108, in Streptomyces diastaticus var. 108

Streptomyces diastaticus var. 108, a newly isolated strain, produces two closely related tetraene macrolides (rimocidin and CE-108) as well as oxytetracycline. A region of 19,065 base pairs of DNA from the S. diastaticus var. 108 genome was isolated, sequenced, and characterized. Ten complete genes and one truncated ORF were located. Disruption of these genes proved that this genomic region is part of the biosynthetic cluster for the two tetraenes. The choice of starter units by the loading module and the in vivo availability of the starter metabolites are crucial for the final ratio of the two macrolides. A second type I PKS, unrelated to tetraene biosynthesis, was also identified; disruption of these genes suggests that they would code for enzymes involved in the biosynthesis of a polyketide that might compete metabolically with rimocidin production.

A unified approach to polyene macrolides: synthesis of candidin and nystatin polyols

Polyene macrolide antibiotics are naturally occurring antifungal agents. Members of this class include amphotericin B, which has been used widely to treat systemic fungal infections. A general synthetic strategy has been devised to prepare polyol chains associated with the polyene macrolides. Cyanohydrin acetonide alkylations were used to assemble the carbon skeleton, and a simple modification of the strategy allowed an advanced intermediate to be converted to either the candidin polyol or the nystatin polyol. The candidin polyol was further elaborated to a protected candidin aglycone. This strategy will be applicable to other members of the polyene macrolide natural products.

Evolution of dithiane-based strategies for the construction of architecturally complex natural products

Umpolung-based strategies play a significant role in organic synthesis. Particularly important are 1,3-dithiane linchpins, which serve as convenient acyl anion equivalents. The general synthetic accessibility and impressive reactivity of 1,3-dithianes have thus led to widespread application. Since the late 1970s, dithianes have featured prominently in our program directed toward the synthesis of complex natural and unnatural products, both for effective union of advanced fragments and for multicomponent linchpin couplings. In this Account, we present the evolution of dithiane chemistry in our laboratory.

(+)-Rimocidin synthetic studies. Construction of an advanced C(1-18) polyol fragment

[structure: see text] The synthesis of an appropriately functionalized advanced C(1-18) polyol fragment of the mycosamine-glycosylated polyene macrolide, (+)-rimocidin (1), has been achieved in a highly efficient manner. Highlights of the strategy include the S(N)2/S(N)2' addition of dithiane anions to vinyl epoxides and the multicomponent linchpin union of 2-TBS-1,3-dithiane with two advanced epoxides.

Solution NMR structure of five representative glycosylated polyene macrolide antibiotics with a sterol-dependent antifungal activity

Glycosylated polyene macrolide antibiotics, as nystatins and amphotericins, are amphiphilic structures known to exert antifungal activity by disrupting the fungal cell membrane, leading to leakage of cellular materials, and cell death. This membrane disruption is strongly influenced by the presence and the exact nature of the membrane sterols. The solution structures of five representative glycosylated members, three tetraenes (pimaricin, nystatin A1 and rimocidin) and two heptaenes (candidin and vacidin A) have been calculated using geometric restraints derived from 1H-NMR data and random searches of their conformational space. Despite a different apparent structural order, the NMR solutions structure indicate that the hydroxyl groups all clustered on one side of the rod-shaped structures, and the glycosyl moieties are structurally conserved both in their conformation and their apparent order. The molecular structures afford an understanding of their selective interaction with the membrane sterols and the design of new polyene macrolides with improved activities.

Solution NMR structures of the polyene macrolide antibiotic filipin III

The solution structure of filipin III, an antifungal polyene macrolide biosynthesized by Streptomyces filipinensis and widely used for the detection and the quantitation of cholesterol in biomembranes, has been calculated with a set of geometrical restraints derived from 1H NMR in DMSO-d(6) at 25 degrees C. Filipin III appears as a rod-shaped molecule of 18 A length. Its amphiphilic structure is made of an all-syn 1,3-polyol motif, stabilized by intramolecular hydrogen bonds on one side, and a conjugated pentaene moiety on the other side of the molecule. The overall shape is comparable to cholesterol, and the molecular structure of filipin III affords a first molecular basis to the comprehensive understanding of the interactions possible in the filipin III-cholesterol complex which is still unknown at the atomic resolution.