Isotope tracer investigations of natural products biosynthesis: the discovery of novel metabolic pathways

Mahmud, Taifo

doi:10.1002/jlcr.1391

Cited by 14 publications

(5 citation statements)

References 58 publications

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“…Isotope labels are frequently used in metabolic and natural product biosynthesis studies where they can be used to track the incorporation of small molecule precursors into complex metabolites in a cellular environment (28)(29)(30)(31). The inherent differences in zero point energies between different isotopes can be used to elucidate the mechanistic details of enzyme catalysed reactions.…”

Section: Take Down Policymentioning

confidence: 99%

Use of isotopically labeled substrates reveals kinetic differences between human and bacterial serine palmitoyltransferase

Harrison

Gable

Niranjanakumari

et al. 2019

Journal of Lipid Research

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Isotope labels are frequently used tools to track metabolites through complex biochemical pathways and to discern the mechanisms of enzyme-catalyzed reactions. Isotopically labeled l-serine is often used to monitor the activity of the first enzyme in sphingolipid biosynthesis, serine palmitoyltransferase (SPT), as well as labeling downstream cellular metabolites. Intrigued by the effect that isotope labels may be having on SPT catalysis, we characterized the impact of different l-serine isotopologues on the catalytic activity of recombinant SPT isozymes from humans and the bacterium Sphingomonas paucimobilis. Our data show that S. paucimobilis SPT activity displays a clear isotope effect with [2,3,3-D]l-serine, whereas the human SPT isoform does not. This suggests that although both human and S. paucimobilis SPT catalyze the same chemical reaction, there may well be underlying subtle differences in their catalytic mechanisms. Our results suggest that it is the activating small subunits of human SPT that play a key role in these mechanistic variations. This study also highlights that it is important to consider the type and location of isotope labels on a substrate when they are to be used in in vitro and in vivo studies.

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Section: Take Down Policymentioning

confidence: 99%

Use of isotopically labeled substrates reveals kinetic differences between human and bacterial serine palmitoyltransferase

Harrison

Gable

Niranjanakumari

et al. 2019

Journal of Lipid Research

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“…Additionally, the model system removes analytical barriers associated with the complex fermentation medium. Past successes using NMR-active isotope labels to study reactions through the use of kinetic isotopes, 9 to elucidate biosynthetic pathways, 10 and in the identification of natural products 11 led us to utilize 13 C- and 15 N-labeled substrates to probe the multicomponent reaction by NMR spectroscopy and mass spectrometry.…”

Section: Resultsmentioning

confidence: 99%

Detailed Mechanistic Study of the Non-enzymatic Formation of the Discoipyrrole Family of Natural Products

Colosimo

MacMillan

2016

J. Am. Chem. Soc.

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Discoipyrroles A–D (DPA–DPD) are recently discovered natural products produced by the marine bacterium Bacillus hunanensis that exhibit anticancer properties in vitro. Initial biosynthetic studies demonstrated that DPA is formed in the liquid fermentation medium of B. hunanensis from three secreted metabolites through an unknown but protein-independent mechanism. The increased identification of natural products that depend on non-enzymatic steps creates a significant need to understand how these different reactions can occur. In this work, we utilized 15N-labeled starting materials and continuous high-sensitivity 1H–15N HMBC NMR spectroscopy to resolve scarce reaction intermediates of the non-enzymatic discoipyrrole reaction as they formed in real time. This information guided supplemental experiments using 13C- and 18O-labeled materials to elucidate the details of DPA’s non-enzymatic biosynthesis, which features a highly concerted pyrrole formation and necessary O2-mediated oxidation. We have illustrated a novel way of using isotopically enhanced two-dimensional NMR spectroscopy to interrogate reaction mechanisms as they occur. In addition, these findings add to our growing knowledge of how multicomponent non-enzymatic reactions can occur through inherently reactive bacterial metabolites.

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“…Due to the lack of a suitable genetic tool to manipulate the acarbose biosynthetic pathway in Actinoplanes sp. SE50/110, earlier studies were limited to isotopic incorporation experiments (29, 67–71) and biochemical characterizations of the putative enzymes in the pathway (31, 38, 72, 73). However, the identification of other acarbose producers (26, 74) as well as the recent development of a genetic method to engineer Actinoplanes sp.…”

Section: Metabolic Engineering Of Pseudo-oligosaccharidesmentioning

confidence: 99%

Biosynthesis and metabolic engineering of pseudo-oligosaccharides

Alanzi

Demessie

Mahmud

2018

Emerging Topics in Life Sciences

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Pseudo-oligosaccharides are microbial-derived secondary metabolites whose chemical structures contain pseudosugars (glycomimetics). Due to their high resemblance to the molecules of life (carbohydrates), most pseudo-oligosaccharides show significant biological activities. Some of them have been used as drugs to treat human and plant diseases. Because of their significant economic value, efforts have been put into understanding their biosynthesis, optimizing their fermentation conditions, and engineering their metabolic pathways to obtain better production yields. A number of unusual enzymes participating in diverse biosynthetic pathways to pseudo-oligosaccharides have been reported. Various methods and conditions to improve the production yields of the target compounds and eliminate byproducts have also been developed. This review article describes recent studies on the biosynthesis, fermentation optimization, and metabolic engineering of high-value pseudo-oligosaccharides.

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Isotope tracer investigations of natural products biosynthesis: the discovery of novel metabolic pathways

Cited by 14 publications

References 58 publications

Use of isotopically labeled substrates reveals kinetic differences between human and bacterial serine palmitoyltransferase

Use of isotopically labeled substrates reveals kinetic differences between human and bacterial serine palmitoyltransferase

Detailed Mechanistic Study of the Non-enzymatic Formation of the Discoipyrrole Family of Natural Products

Biosynthesis and metabolic engineering of pseudo-oligosaccharides

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