Clorobiocin biosynthesis in Streptomyces: identification of the halogenase and generation of structural analogs

Clorobiocin (clo) and novobiocin (nov) are potent inhibitors of bacterial DNA gyrase. The two substances differ in the substitution pattern at C-8' of the aminocoumarin ring, carrying a chlorine atom or a methyl group, respectively. By gene inactivation, clo-hal was identified as the gene of the halogenase responsible for the introduction of the chlorine atom of clorobiocin. Inactivation of cloZ did not affect clorobiocin formation, showing that this ORF is not essential for clorobiocin biosynthesis. Expression of the methyltransferase gene novO in the clo-hal(-) mutant led to the very efficient formation of a hybrid antibiotic containing a methyl group instead of a chlorine atom at C-8'. Comparison of the antibacterial activity of clorobiocin analogs with -Cl, -H, or -CH(3) at C-8' showed that chlorine leads to 8-fold higher activity than hydrogen and to 2-fold higher activity than a methyl group.     

Exploration of single molecule events in a haloperoxidase and its biomimic: localization of halogenation activity

In situ observation of single oxidation/halogenation events by catalytically generated hypobromite species using single molecule fluorescence microscopy allows monitoring of the diffusion behavior of these halonium species from the catalyst into the bulk solution. The fluororgenic probe specifically reacts with hypohalites, yielding fluorescein that can be detected with single molecule sensitivity. It was found for two investigated catalysts (Curvularia verruculosa enzymes and tungstate-exchanged LDH crystals) that in steady-state conditions hypobromite is able to diffuse over 800 nm in the bulk solution before it oxidizes organic substrates.     

Structure and biosynthesis of amychelin, an unusual mixed-ligand siderophore from Amycolatopsis sp. AA4

Actinobacteria generate a large number of structurally diverse small molecules with potential therapeutic value. Genomic analyses of this productive group of bacteria show that their genetic potential to manufacture small molecules exceeds their observed ability by roughly an order of magnitude, and this revelation has prompted a number of studies to identify members of the unknown majority. As a potential window into this cryptic secondary metabolome, pairwise assays for developmental interactions within a set of 20 sequenced actinomycetes were carried out. These assays revealed that Amycolatopsis sp. AA4, a so-called "rare" actinomycete, produces a novel siderophore, amychelin, which alters the developmental processes of several neighboring streptomycetes. Using this phenotype as an assay, we isolated amychelin and solved its structure by NMR and MS methods coupled with an X-ray crystallographic analysis of its Fe-complex. The iron binding affinity of amychelin was determined using EDTA competition assays, and a biosynthetic cluster was identified and annotated to provide a tentative biosynthetic scheme for amychelin.     

Glycopeptide biosynthesis: Dbv21/Orf2 from dbv/tcp gene clusters are N-Ac-Glm teicoplanin pseudoaglycone deacetylases and Orf15 from cep gene cluster is a Glc-1-P thymidyltransferase

The unique pharmacokinetic/pharmacodynamic activities of glycopeptide antibiotics are conferred from the tailoring steps occurring on the aglycone. It was hypothesized that the sugar moiety attached to the aglycone is derived from an unusual UDP-glucosamine and is followed by an acylation reaction in the biosynthesis of teicoplanin/A40926. Here we report that three homologous (>65% identical) proteins Dbv21, Orf2*, and Orf15, previously assigned as hypothetical proteins in the biosynthesis of A40926, teicoplanin, and chloroeremomycin, respectively, are novel deacetylases (Dbv21 and Orf2*) and thymidyltransferase (Orf15). Dbv21 and Orf2* catalyze the deacetylation reaction of N-acetylglucosaminyl-teicoplanin pseudoaglycone, while Orf15 catalyzes the formation of dTDP-glucose that is required for the epi-vancosamine/vancosamine decoration of chloroeremomycin/vancomycin.     

Rapamycin biosynthesis: Elucidation of gene product function

The function of gene products involved in the biosynthesis of the clinically important polyketide rapamycin were elucidated by biotransformation and gene complementation.     

Structure of rifamycin W : A novel ansamycin from a mutant of Nocardia mediterranei

On the basis of spectroscopic studies (UV, IR, MS, ¹H and ¹³C NMR) on rifamycin W and its tetrahydro- and dimethyl-derivatives, in comparison with the model compound rifamycin S (2), structure 1 is assigned to rifamycin W, a novel ansamycin isolated from a mutant strain of Nocardia mediterranei. The structural similarity of rifamycin W with other rifamycins and with streptovaricins is discussed from the biosynthetic point of view.     

Lasso peptides: structure, function, biosynthesis, and engineering

Covering: up to May 2012Lasso peptides are a class of ribosomally-synthesized and posttranslationally-modified natural products with diverse bioactivities. This review describes the structure and function of all known lasso peptides (as of mid-2012) and covers our current knowledge about the biosynthesis of those molecules. The isolation and characterization of lasso peptides are also covered as are bioinformatics strategies for the discovery of new lasso peptides from genomic sequence data. Several studies on the engineering of new or improved function into lasso peptides are highlighted, and unanswered questions in the field are also described.     

Insights into polyether biosynthesis from analysis of the nigericin biosynthetic gene cluster in Streptomyces sp. DSM4137

Nigericin was among the first polyether ionophores to be discovered, but its biosynthesis remains obscure. The biosynthetic gene cluster for nigericin has been serendipitously cloned from Streptomyces sp. DSM4137, and deletion of this gene cluster abolished the production of both nigericin and the closely related metabolite abierixin. Detailed comparison of the nigericin biosynthetic genes with their counterparts in the biosynthetic clusters for other polyketides has prompted a significant revision of the proposed common pathway for polyether biosynthesis. In particular, we present evidence that in nigericin, nanchangmycin, and monensin, an unusual ketosynthase-like protein, KSX, transfers the initially formed linear polyketide chain to a discrete acyl carrier protein, ACPX, for oxidative cyclization. Consistent with this, deletion of either monACPX or monKSX from the monensin gene cluster effectively abolished monensin A biosynthesis.     

Secondary Metabolites of the Genus Amycolatopsis: Structures,Bioactivities and Biosynthesis

Actinomycetes are regarded as important sources for the generation of various bioactive secondary metabolites with rich chemical and bioactive diversities. Amycolatopsis falls under the rare actinomycete genus with the potential to produce antibiotics. In this review, all literatures were searched in the Web of Science, Google Scholar and PubMed up to March 2021. The keywords used in the search strategy were “Amycolatopsis”, “secondary metabolite”, “new or novel compound”, “bioactivity”, “biosynthetic pathway” and “derivatives”. The objective in this review is to summarize the chemical structures and biological activities of secondary metabolites from the genus Amycolatopsis. A total of 159 compounds derived from 8 known and 18 unidentified species are summarized in this paper. These secondary metabolites are mainly categorized into polyphenols, linear polyketides, macrolides, macrolactams, thiazolyl peptides, cyclic peptides, glycopeptides, amide and amino derivatives, glycoside derivatives, enediyne derivatives and sesquiterpenes. Meanwhile, they mainly showed unique antimicrobial, anti-cancer, antioxidant, anti-hyperglycemic, and enzyme inhibition activities. In addition, the biosynthetic pathways of several potent bioactive compounds and derivatives are included and the prospect of the chemical substances obtained from Amycolatopsis is also discussed to provide ideas for their implementation in the field of therapeutics and drug discovery.     

Enzymatic generation of the antimetabolite gamma,gamma-dichloroaminobutyrate by NRPS and mononuclear iron halogenase action in a streptomycete

Four adjacent open reading frames, cytC1-C4, were cloned from a cytotrienin-producing strain of a Streptomyces sp. by using primers derived from the conserved region of a gene encoding a nonheme iron halogenase, CmaB, in coronamic acid biosynthesis. CytC1-3 were active after expression in Escherichia coli, and CytC4 was active after expression in Pseudomonas putida. CytC1, a relatively promiscuous adenylation enzyme, installs the aminoacyl moieties on the phosphopantetheinyl arm of the holo carrier protein CytC2. CytC3 is a nonheme iron halogenase that will generate both gamma-chloro- and gamma,gamma-dichloroaminobutyryl-S-CytC2 from aminobutyryl-S-CytC2. CytC4, a thioesterase, hydrolytically releases the dichloroaminobutyrate, a known streptomycete antibiotic. Thus, this short four-protein pathway is likely the biosynthetic source of this amino acid antimetabolite. This four-enzyme system analogously converts the proS-methyl group of valine to the dichloromethyl product regio- and stereospecifically.     

Discovery of a two-component monooxygenase SnoaW/SnoaL2 involved in nogalamycin biosynthesis

Nogalamycin is an anthracycline polyketide antibiotic that contains two deoxysugars, at positions C-1 and C-7. Previous biosynthetic studies conducted in vivo affiliated snoaL2 with an unusual C-1 hydroxylation reaction, but in vitro activity was not established. Here, we demonstrate that inactivation of either snoaL2 or snoaW resulted in accumulation of two nonhydroxylated metabolites, nogalamycinone and a novel anthracycline 3',4'-demethoxy-nogalose-nogalamycinone. The C-1 hydroxylation activity was successfully reconstructed in vitro in the presence of the two enzymes, NAD(P)H and the substrates. Based on relative reaction efficiencies, 3',4'-demethoxy-nogalose-nogalamycinone was identified as the likely natural substrate. A biosynthetic model was established where the atypical short-chain alcohol dehydrogenase SnoaW reduces the anthraquinone to a dihydroquinone using NADPH, which enables activation of oxygen and formation of a hydroperoxy intermediate. Finally, protonation of the intermediate by SnoaL2 yields the 1-hydroxylated product.     

Glycoprotein synthesis as a function of epithelial cell arrangement: biosynthesis and release of glycoproteins by human breast and prostate cells in organ culture.

We demonstrate that a technique is available to investigate glycoprotein synthesis in organ cultures of human breast and prostate surgical specimens where the 3-dimensional epithelial cell arrangement remains intact. Malignant breast and prostate epithelium maintained their capacity to synthesize glycoproteins for at least 3 days as followed by the incorporation of [3H]glucosamine into macromolecules. Over 70% of incorporation was by malignant cells as judged by autoradiography. Labeled glycoproteins were released into glandular lumina and consequently into the culture fluid. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed predominantly one group of macrmolecules released with an apparent molecular weight of 48,000 +/- 6,000 daltons. This glycoprotein was found in all of the breast specimens studied, which included 1 medullary, 1 infiltrating lobular, and 8 infiltrating duct carcinomas. The pattern was independent of the availability of estrogen receptors. A similar glycoprotein was also observed in the culture media from a Grade I and a Grade II well-differentiated infiltrating prostate carcinoma. Incorporation was below the level of detection in 4 of 6 cases of benign prostatic hyperplasia. A more complex pattern of labeled glycoproteins was found in the media of a Grade II and a Grade III poorly-differentiated prostate carcinoma. The established human mammary carcinoma cell line MCF-7 synthesized and released a similar 48,000 molecular weight glycoprotein but additional components with larger molecular weights were also released. An intriguing interpretation that 3-dimensional tissue integrity restricts some glycoprotein synthesis is discussed. Cells grown in 2-dimensional monolayers could escape from such a topographic restriction and express additional families of glycoproteins.     

The role of cep15 in the biosynthesis of chloroeremomycin: reactivation of an ancestral catalytic function

The gene clusters of several glycopeptides contain genes that encode COG2120 domain zinc-dependent N-acetylglucosaminyl deacetylases. Recently, a COG2120 protein encoded in the chloroeremomycin gene cluster, Cep15, has been postulated to possess nucleotidyltransferase activity. Here, we demonstrate that Cep15 possesses no catalytic activity and does not have a clear role in chloroeremomycin biosynthesis. This result strongly suggests that cep15 and bal2 are evolutionary artifacts and may be pseudogenes. Comparative sequence analysis with the closely related active Orf2* deacetylase (teicoplanin biosynthesis) reveals an asparagine in place of a metal-binding histidine in the "pseudo-active site" of Cep15. Substitution of this histidine by asparagine in Orf2* abolishes deacetylase activity. Remarkably, the Cep15 N164H mutant is an active deacetylase. To our knowledge, this is the first example of reactivating an ancestral enzymatic role for a bacterial protein by point mutagenesis.     

Dihydrophenylalanine: a prephenate-derived Photorhabdus luminescens antibiotic and intermediate in dihydrostilbene biosynthesis

2,5-Dihydrophenylalanine (H(2)Phe) is a multipotent nonproteinogenic amino acid produced by various Actinobacteria and Gammaproteobacteria. Although the metabolite was discovered over 40 years ago, details of its biosynthesis have remained largely unknown. We show here that L-H(2)Phe is a secreted metabolite in Photorhabdus luminescens cultures and a precursor of a recently described 2,5-dihydrostilbene. Bioinformatic analysis suggested?a candidate gene cluster for the processing of prephenate to H(2)Phe, and gene knockouts validated that three adjacent genes plu3042-3044 were required for H(2)Phe production. Biochemical experiments validated Plu3043 as a nonaromatizing prephenate decarboxylase generating an endocyclic dihydro-hydroxyphenylpyruvate. Plu3042 acted next to transaminate the Plu3043 product, precluding spontaneous exocyclic double-bond isomerization and yielding 2,5-dihydrotyrosine. The enzymatic products most plausibly on path to H(2)Phe illustrate the versatile metabolic rerouting of prephenate from aromatic amino acid synthesis to antibiotic synthesis.     

The biosynthesis of spinosyn in Saccharopolyspora spinosa: synthesis of the cross-bridging precursor and identification of the function of SpnJ

Spinosyns are glycosylated polyketide-derived macrolides possessing a perhydro-as-indacene core that is presumably formed via a series of intramolecular cross-bridging reactions. The unusual structure of the spinosyn aglycone suggests an intriguing biosynthetic pathway for its formation, which is expected to be initiated by the oxidation of the 15-OH group of the mature polyketide precursor and may involve a Diels-Alder-type [4 + 2] cycloaddition reaction. Three possible routes, which differ in the order of oxidation and cyclization events, can be envisioned for the biosynthesis of the core structure. Sequence analysis of the spinosyn biosynthetic gene cluster led to the speculation of spnJ as the possible oxidase gene. To explore the early stage of intramolecular ring formation, we cloned and expressed the spnJ gene and purified the SpnJ protein which shows the characteristics of flavoproteins. Two possible substrates for SpnJ, the linear mature polyketide precursor and the corresponding cyclized macrolactone, were also synthesized. TLC and HPLC analysis of the incubation mixture of these compounds with SpnJ revealed that only the synthesized macrolactone could be converted to the corresponding ketone. This result clearly indicated that macrolactone formation proceeds 15-OH oxidation since the linear polyketide is not a substrate for SpnJ. The experiments described herein detail a convergent synthesis of spinosyn macrolactone and validate the catalytic function of SpnJ as a flavin-dependent oxidase. More significantly, we have established the spinosyn macrolactone as the immediate precursor of the tricyclic nucleus of spinosyns.     

青蒿素生物合成的研究III: 青蒿素和青蒿素B生物合成中的关键性中间体-青蒿素

以[15-^3H]青蒿酸为前体用青蒿匀聚浆体进行青蒿素和青蒿素B的生物合成.实验结果表明, 在青蒿植物由MVA生物合成青蒿素和青蒿素B的途径中, 青蒿酸是关键性中间体.