natural product biosynthesis in microorganisms

The members of the order Actinomycetales, especially the genus Streptomyces, produce a number of antibiotics and other bioactive natural products. The genomic analysis of some Streptomyces strains revealed the presence of biosynthetic gene clusters for about 30 secondary metabolites, and these data imply that a single Streptomyces strain can produce more than 30 secondary metabolites (, , ). However, some of these secondary-metabolite genes are not expressed in fermentation culture. To date, various methods (, , , ) have been used to activate genes synthesizing cryptic secondary metabolites. Secondary-metabolite production is affected by environmental factors (, ) such as temperature, the presence of hormone-like chemicals (), and medium composition (). Therefore, to identify new antibiotics, the isolation of new actinomycetes should be accompanied by the study of the effects of different growth conditions on each isolated strain.

natural product biosynthesis in microorganisms.

the in situ biosynthesis of a cryptic natural product from ..
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Triggering cryptic natural product biosynthesis in microorganisms.

Aromatic polyketides are medicinally important natural products produced by type II polyketide synthases (PKSs). Some aromatic PKSs are bimodular and include a dedicated initiation module which synthesizes a non-acetate primer unit. Understanding the mechanism of this initiation module is expected to further enhance the potential for regiospecific modification of bacterial aromatic polyketides. A typical initiation module is comprised of a ketosynthase (KS), an acyl carrier protein (ACP), a malonyl-CoA:ACP transacylase (MAT), an acyl-ACP thioesterase, a ketoreductase (KR), a dehydratase (DH), and an enoyl reductase (ER). Thus far, the identities of the ketoreductase, dehydratase, and enoyl reductase remain a mystery because they are not encoded within the PKS biosynthetic gene cluster. Here we report that SCO1815 from Streptomyces coelicolor A3(2), an uncharacterized homologue of a NADPH-dependent ketoreductase, recognizes and reduces the beta-ketoacyl-ACP intermediate from the initiation module of the R1128 PKS. SCO1815 exhibits moderate specificity for both the acyl chain and the thiol donor. The X-ray crystal structure of SCO1815 was determined to 2.0 A. The structure shows that SCO1815 adopts a Rossmann fold and suggests that a conformational change occurs upon cofactor binding. We propose that a positively charged patch formed by three conserved residues is the ACP docking site. Our findings provide new engineering opportunities for incorporating unnatural primer units into novel polyketides and shed light on the biology of yet another cryptic protein in the S. coelicolor genome.

Triggering cryptic natural product biosynthesis in microorganisms

Natural products, produced chiefly by microorganisms and plants, can be large and structurally complex molecules. These molecules are manufactured by cellular assembly lines, in which enzymes construct the molecules in a stepwise fashion. The means by which enzymes interact and work together in a modular fashion to create diverse structural features has been an active area of research; the work has provided insight into the fine details of biosynthesis. A number of polycyclic aromatic natural products--including several noteworthy anticancer, antibacterial, antifungal, antiviral, antiparasitic, and other medicinally significant substances--are synthesized by polyketide synthases (PKSs) in soil-borne bacteria called actinomycetes. Concerted biosynthetic, enzymological, and structural biological investigations into these modular enzyme systems have yielded interesting mechanistic insights. A core module called the minimal PKS is responsible for synthesizing a highly reactive, protein-bound poly-beta-ketothioester chain. In the absence of other enzymes, the minimal PKS also catalyzes chain initiation and release, yielding an assortment of polycyclic aromatic compounds. In the presence of an initiation PKS module, polyketide backbones bearing additional alkyl, alkenyl, or aryl primer units are synthesized, whereas a range of auxiliary PKS enzymes and tailoring enzymes convert the product of the minimal PKS into the final natural product. In this Account, we summarize the knowledge that has been gained regarding this family of PKSs through recent investigations into the biosynthetic pathways of two natural products, actinorhodin and R1128 (A-D). We also discuss the practical relevance of these fundamental insights for the engineered biosynthesis of new polycyclic aromatic compounds. With a deeper understanding of the biosynthetic process in hand, we can assert control at various stages of molecular construction and thus introduce unnatural functional groups in the process. The metabolic engineer affords a number of new avenues for creating novel molecular structures that will likely have properties akin to their fully natural cousins.

Triggering cryptic natural product ..
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and antibacterial polyketides by Burkholderia gladioli ..

Where possible, we have attempted to highlight these knowledge gaps (e.g., thiosugar biosynthesis, the origin of the allyl moiety of alliin, the trisulfide trigger of calicheamicin); however, there are many natural products that were omitted as their biosynthesis is completely enigmatic.

23/08/2011 · National Academy of Sciences

In bacteria, the biosynthesis of natural products (e.g. antibiotics, enzyme inhibitors, signalling molecules) is directed by groups of genes called Biosynthetic Gene Clusters (BGCs),. The target-directed approach that traces such groups of genes to metabolite production revealed the presence of putative BGCs involved in the synthesis of diverse metabolites. Knowledge of the biosynthetic gene cluster organisation then facilitated the cloning of complete pathways and combined with the current bioinformatics approaches the genome mining concept was born,, which has allowed the interrogation of microbial genomes to determine their biosynthetic abilities. Moreover, in-depth understanding of natural products biosynthesis and the assembly of gene clusters (e.g. polyketides and peptides) was generated via the application of the genomic methods. The combination of genetics-based approaches and mass spectrometry (MS)-based analytical methods has also provided a platform for development of reliable dereplication strategies for natural products discovery and identification. Many cryptic gene clusters that encode secondary metabolism in the most bioactive bacterial members were located through examination of the genomic data. In addition, a significant degree of chemical diversity encoded in silent/cryptic biosynthetic gene clusters were detected in the genomes of such bacteria. Examples include detection of genes coding for synthesis of stambomycin in S. Successful implementation of genome-guided discovery of natural products and biosynthetic pathways from Australia’s untapped microbial megadiversity has also recently been revealed.

Natural products produced by microorganisms ..

Natural products produced by microorganisms are important starting compounds for drug discovery. Secondary metabolites, including antibiotics, have been isolated from different Streptomyces species. The production of these metabolites depends on the culture conditions. Therefore, the development of a new culture method can facilitate the discovery of new natural products. Here, we show that mycolic acid-containing bacteria can influence the biosynthesis of cryptic natural products in Streptomyces species. The production of red pigment by Streptomyces lividans TK23 was induced by coculture with Tsukamurella pulmonis TP-B0596, which is a mycolic acid-containing bacterium. Only living cells induced this pigment production, which was not mediated by any substances. T. pulmonis could induce natural-product synthesis in other Streptomyces strains too: it altered natural-product biosynthesis in 88.4% of the Streptomyces strains isolated from soil. The other mycolic acid-containing bacteria, Rhodococcus erythropolis and Corynebacterium glutamicum, altered biosynthesis in 87.5 and 90.2% of the Streptomyces strains, respectively. The coculture broth of T. pulmonis and Streptomyces endus S-522 contained a novel antibiotic, which we named alchivemycin A. We concluded that the mycolic acid localized in the outer cell layer of the inducer bacterium influences secondary metabolism in Streptomyces, and this activity is a result of the direct interaction between the mycolic acid-containing bacteria and Streptomyces. We used these results to develop a new coculture method, called the combined-culture method, which facilitates the screening of natural products.