Methods and options for the heterologous production of complex natural products

Zhang, Haoran; Boghigian, Brett A.; Armando, John; Pfeifer, Blaine A.

doi:10.1039/c0np00037j

Cited by 136 publications

(120 citation statements)

References 358 publications

(265 reference statements)

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“…The modular, diverse, and flexible nature of these enzymes offers numerous possibilities for directed manipulation of the biosynthetic pathways for the purpose of new enzymatic insight and molecular variation of the final compound (13)(14)(15). In addition, the growing number of successful cases of heterologous production of such compounds provides parallel opportunities to study biosynthesis within a surrogate host (16,17).…”

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confidence: 99%

Total Biosynthesis and Diverse Applications of the Nonribosomal Peptide-Polyketide Siderophore Yersiniabactin

Ahmadi

Fawaz

Jones

et al. 2015

Appl Environ Microbiol

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Yersiniabactin (Ybt) is a mixed nonribosomal peptide-polyketide natural product natively produced by the pathogen Yersinia pestis. The compound enables iron scavenging capabilities upon host infection and is biosynthesized by a nonribosomal peptide synthetase featuring a polyketide synthase module. This pathway has been engineered for expression and biosynthesis using Escherichia coli as a heterologous host. In the current work, the biosynthetic process for Ybt formation was improved through the incorporation of a dedicated step to eliminate the need for exogenous salicylate provision. When this improvement was made, the compound was tested in parallel applications that highlight the metal-chelating nature of the compound. In the first application, Ybt was assessed as a rust remover, demonstrating a capacity of ϳ40% compared to a commercial removal agent and ϳ20% relative to total removal capacity. The second application tested Ybt in removing copper from a variety of nonbiological and biological solution mixtures. Success across a variety of media indicates potential utility in diverse scenarios that include environmental and biomedical settings.

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confidence: 99%

Total Biosynthesis and Diverse Applications of the Nonribosomal Peptide-Polyketide Siderophore Yersiniabactin

Ahmadi

Fawaz

Jones

et al. 2015

Appl Environ Microbiol

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“…Alternatively, physical contact with an opponent results in the uncovering of hidden clusters by activating defense mechanisms (58). (ii) Genetic engineering is focused primarily on expressing complete gene clusters in heterologous hosts (53,77) or on altering the cellular transcription or protein synthesis machinery. Thus, SM synthesis was enhanced by changing genes with regulatory (12,59), ribosomal (36,49), protein-modifying (57,64), or chromatin-modifying (11,48,61) functions or by adding epigenetic modifiers with DNA methyltransferase or histone deacetylase inhibiting function (26,34,70).…”

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confidence: 99%

Breaking the Silence: Protein Stabilization Uncovers Silenced Biosynthetic Gene Clusters in the Fungus Aspergillus nidulans

Gerke

Bayram

Feussner

et al. 2012

Appl Environ Microbiol

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The genomes of filamentous fungi comprise numerous putative gene clusters coding for the biosynthesis of chemically and structurally diverse secondary metabolites (SMs), which are rarely expressed under laboratory conditions. Previous approaches to activate these genes were based primarily on artificially targeting the cellular protein synthesis apparatus. Here, we applied an alternative approach of genetically impairing the protein degradation apparatus of the model fungus Aspergillus nidulans by deleting the conserved eukaryotic csnE/CSN5 deneddylase subunit of the COP9 signalosome. This defect in protein degradation results in the activation of a previously silenced gene cluster comprising a polyketide synthase gene producing the antibiotic 2,4-dihydroxy-3-methyl-6-(2-oxopropyl)benzaldehyde (DHMBA). The csnE/CSN5 gene is highly conserved in fungi, and therefore, the deletion is a feasible approach for the identification of new SMs. Since its discovery by Fleming in the 1920s, fungal penicillin has saved the lives of millions. Currently, the World Health Organization forecasts that the dramatic increase in antimicrobial resistance all over the world might lead to a disaster and proclaims a need for novel drugs (22). Certain fungi, plants, and bacteria produce various potent secondary metabolites (SMs) that span a wide field of structurally and chemically diverse natural products. With almost 1.5 million species (33), the fungal kingdom is a major reservoir for bioactive natural products as beneficial antibiotics and antitumor drugs but also as deleterious mycotoxins and food contaminants (28,38). Although many fungal SMs have been described and tested, their complete potential is by far not exploited.In recent years, different approaches were applied to find novel bioactive SMs either in new species or in already established model organisms. New geographical spots exhibiting extreme conditions were explored in order to find new species producing as-yet-unknown natural products (37). An alternative approach is the exploration of the full genomic potential of already known species by genomic mining (13,14,30,76). Genomic sequencing revealed that there are many more genes for the biosynthesis of SMs than the metabolites already identified. These genes are often clustered, but most of them are rarely expressed under laboratory conditions (35), making the identification of their chemical products challenging. Two major strategies were applied to activate hidden genes: (i) changing the environment or (ii) genetic engineering (19,35,56). (i) The OSMAC (one strain, many compounds) approach activates silent gene clusters by cultivating microorganisms under different conditions (10, 75). Alternatively, physical contact with an opponent results in the uncovering of hidden clusters by activating defense mechanisms (58). (ii) Genetic engineering is focused primarily on expressing complete gene clusters in heterologous hosts (53, 77) or on altering the cellular transcription or protein synthesis machinery. Thus, SM synthesi...

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“…The advantages and limitations of various well-established industrial hosts, including bacteria, such as Streptomyces spp., Escherichia coli, Pseudomonas spp., Bacillus spp., and fungi, such as Penicillium spp. and Aspergillus spp., for the heterologous production of polyketides, nonribosomal peptides and isoprenoids have recently been reviewed extensively [20]. The currently available host strains are generally good starting points, but are not necessarily optimal: during evolution, organisms are usually not optimized for maximal production titers of secondary metabolites.…”

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confidence: 99%

Design-based re-engineering of biosynthetic gene clusters: plug-and-play in practice

Frasch

Medema

Takano

et al. 2013

Current Opinion in Biotechnology

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Methods and options for the heterologous production of complex natural products

Abstract: This review will detail the motivations, experimental approaches, and growing list of successful cases associated with the heterologous production of complex natural products.

Cited by 136 publications

References 358 publications

Total Biosynthesis and Diverse Applications of the Nonribosomal Peptide-Polyketide Siderophore Yersiniabactin

Total Biosynthesis and Diverse Applications of the Nonribosomal Peptide-Polyketide Siderophore Yersiniabactin

Breaking the Silence: Protein Stabilization Uncovers Silenced Biosynthetic Gene Clusters in the Fungus Aspergillus nidulans

Design-based re-engineering of biosynthetic gene clusters: plug-and-play in practice

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