Harnessing natural product assembly lines: structure, promiscuity, and engineering

Ladner, Christopher C; Williams, Gavin J.

doi:10.1007/s10295-015-1704-8

Cited by 24 publications

(23 citation statements)

References 156 publications

(172 reference statements)

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“…Diversity of Secreted Metabolites. Factors contributing to the extensive metabolite diversity include, e.g., enzyme promiscuity as described for polyketide synthases, which can utilize a variety of starter and extender units (46)(47)(48), alternative cyclization or condensation reactions (49,50), differential regulation of individual enzymes of the biosynthetic machine (51), the release of intermediates and pathway shunt products, biosynthesis mediated by gene products not detected as secondary metabolite biosynthesis genes by antiSMASH, or synthesis by cooperating biosynthetic machines (52). We cannot completely exclude that primary metabolites, and biotransformed or degraded media components, further add to metabolite diversity, although we expect those to be few.…”

Section: Discussion Lc-ms-based Analysis Of the Secreted Metabolome mentioning

confidence: 99%

The secreted metabolome of Streptomyces chartreusis and implications for bacterial chemistry

Senges

Al-Dilaimi

Marchbank

et al. 2018

Proc. Natl. Acad. Sci. U.S.A.

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are known for producing diverse secondary metabolites. Combining genomics with untargeted data-dependent tandem MS and molecular networking, we characterized the secreted metabolome of the tunicamycin producer NRRL 3882. The genome harbors 128 predicted biosynthetic gene clusters. We detected>1,000 distinct secreted metabolites in culture supernatants, only 22 of which were identified based on standards and public spectral libraries. adapts the secreted metabolome to cultivation conditions. A number of metabolites are produced iron dependently, among them 17 desferrioxamine siderophores aiding in iron acquisition. Eight previously unknown members of this long-known compound class are described. A single desferrioxamine synthesis gene cluster was detected in the genome, yet different sets of desferrioxamines are produced in different media. Additionally, a polyether ionophore, differentially produced by the calcimycin biosynthesis cluster, was discovered. This illustrates that metabolite output of a single biosynthetic machine can be exquisitely regulated not only with regard to product quantity but also with regard to product range. Compared with chemically defined medium, in complex medium, total metabolite abundance was higher, structural diversity greater, and the average molecular weight almost doubled. Tunicamycins, for example, were only produced in complex medium. Extrapolating from this study, we anticipate that the larger part of bacterial chemistry, including chemical structures, ecological functions, and pharmacological potential, is yet to be uncovered.

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Section: Discussion Lc-ms-based Analysis Of the Secreted Metabolome mentioning

confidence: 99%

The secreted metabolome of Streptomyces chartreusis and implications for bacterial chemistry

Senges

Al-Dilaimi

Marchbank

et al. 2018

Proc. Natl. Acad. Sci. U.S.A.

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“…Given that biosynthesis pathways often consist of multiple enzymatic cascades to generate the final products, rational engineering of all the enzymes involved in the pathway may not be the most efficient strategy for non-natural product biosynthesis. Therefore, alternative methods such as directed evolution 42 , mutagenesis 25,43 , pathway recombination 30,44 or semi-synthesis 6,45,46 strategies for generating natural product analogues should be systematically explored in greater detail.…”

Section: Purification Of 7-chloro Analogues Of Violacein and Deoxyviomentioning

confidence: 99%

A GenoChemetic strategy for derivatization of the violacein natural product scaffold

Lai¹,

Obled²,

Chee³

et al. 2017

Preprint

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The next frontier in drug discovery could be the semi-synthesis of non-natural, xenobiotic compounds combining both natural product biosynthesis and synthetic chemistry. However, the required tools and underlying engineering principles are yet to be fully understood. One way to investigate non-natural product biosynthesis is to probe the substrate promiscuity of a clinically relevant biosynthesis pathway. Violacein is a bisindole compound produced by the VioABCDE biosynthesis pathway using L-tryptophan as the starting substrate. Previous studies have shown that violacein exhibits antimicrobial properties, and synthetic analogues of violacein might give rise to new targets for therapeutic development to combat antimicrobial resistance. By adding seven types of tryptophan analogues available commercially, 62 new violacein or deoxyviolacein analogues were generated with a synthetic violacein biosynthesis pathway expressed in Escherichia coli, demonstrating the promiscuity of violacein biosynthesis enzymes. Growth inhibition assays against Bacillus subtilis, a Gram-positive bacterium, were carried out to measure growth inhibitory activity of violacein analogues compared to violacein. In addition, we show that four new 7-chloro analogues of violacein or deoxyviolacein can be generated in vivo by combining the rebeccamycin and violacein biosynthesis pathways and purified 7-chloro violacein was found to have similar growth inhibitory activity compared to violacein. Structural studies of VioA revealed active site residues that are important for catalytic activity, and further pathway recombination with VioA homologues in related bisindole pathways may lead to more efficient enzymes that would accept tryptophan analogues more readily.

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“…Isolation of the novel actinoplanic acid C, having a methyl substituent at carbon 4 instead of an ethyl moiety, led us to assume that there is a level of promiscuity associated with the AT domain of module 14. Promiscuity of AT domains is frequently observed with various type I PKS products (21). In these cases, the rate of incorporation of a certain extender-CoA moiety largely depends on relative availability of the competing substrates from the cellular pool.…”

Section: Actinoplanic Acid Pks Module 14 Is Promiscuous Incorporatinmentioning

confidence: 99%

Discovery of the actinoplanic acid pathway in Streptomyces rapamycinicus reveals a genetically conserved synergism with rapamycin

Mrak

Krastel

Lukančič

et al. 2018

Journal of Biological Chemistry

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Harnessing natural product assembly lines: structure, promiscuity, and engineering

Cited by 24 publications

References 156 publications

The secreted metabolome of Streptomyces chartreusis and implications for bacterial chemistry

The secreted metabolome of Streptomyces chartreusis and implications for bacterial chemistry

A GenoChemetic strategy for derivatization of the violacein natural product scaffold

Discovery of the actinoplanic acid pathway in Streptomyces rapamycinicus reveals a genetically conserved synergism with rapamycin

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