Omics-based natural product discovery and the lexicon of genome mining

Machado, Henrique; Tuttle, R.N.; Jensen, Paul R.

doi:10.1016/j.mib.2017.10.025

Cited by 54 publications

(50 citation statements)

References 68 publications

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“…The revolutionary developments in genome sequencing and analytical technologies in the last decade have dramatically changed the field of natural product discovery [ 4 ]. Particularly, ecology-driven natural product discovery approaches including the chemical analyses of symbiotic microorganisms, in combination with omics-based dereplication strategies, have become highly efficient approaches to identify new natural products with unique chemical scaffolds and bioactivities [ 5 , 6 , 7 , 8 ]. Most notably, the analysis of insect-microbe symbioses, and more specifically insect-Actinobacteria interactions, have been the focus of a series of recent natural product discovery studies, as bacterial symbionts are required to communicate with the host or participate in host defense using small molecules.…”

Section: Introductionmentioning

confidence: 99%

Natural Products from Actinobacteria Associated with Fungus-Growing Termites

et al. 2018

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The chemical analysis of insect-associated Actinobacteria has attracted the interest of natural product chemists in the past years as bacterial-produced metabolites are sought to be crucial for sustaining and protecting the insect host. The objective of our study was to evaluate the phylogeny and bioprospecting of Actinobacteria associated with fungus-growing termites. We characterized 97 Actinobacteria from the gut, exoskeleton, and fungus garden (comb) of the fungus-growing termite Macrotermes natalensis and used two different bioassays to assess their general antimicrobial activity. We selected two strains for chemical analysis and investigated the culture broth of the axenic strains and fungus-actinobacterium co-cultures. From these studies, we identified the previously-reported PKS-derived barceloneic acid A and the PKS-derived rubterolones. Analysis of culture broth yielded a new dichlorinated diketopiperazine derivative and two new tetracyclic lanthipeptides, named rubrominins A and B. The discussed natural products highlight that insect-associated Actinobacteria are highly prolific natural product producers yielding important chemical scaffolds urgently needed for future drug development programs.

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Section: Introductionmentioning

confidence: 99%

Natural Products from Actinobacteria Associated with Fungus-Growing Termites

et al. 2018

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“…Using different algorithms that compare the new genetic information with 57 virtual enzymatic reactions (such as adenylation, acyltransferase, and acyl-adenylating), this approach provides the possibility of obtaining a correspondence between known natural drugs and possible new ones [20]. (iii) "Integrated Microbial Genomes Atlas of Biosynthetic gene Clusters" (IMG/ABC) [21], launched in 2015, is a large open web database of known predicted microbial BGCs able to associate BGCs with secondary metabolites (SMs) and analyze both BGCs and SMs. In this way, it offers the ability of finding similar function between BGCs present in database and BGCs to be identified [22].…”

Section: Genome Miningmentioning

confidence: 99%

“…Genome mining aims at predicting the genes that encode for new natural compounds of biotechnological interest by using several bioinformatic approaches [21]. The importance of genome mining is based on the urgent need to discover new drug entities due to the increased incidence of severe diseases (such as cancer) and the reduced efficacy of existing drugs [27].…”

Section: The Significance Genome Mining In Drug Discoverymentioning

confidence: 99%

Genome Mining as New Challenge in Natural Products Discovery

et al. 2020

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Drug discovery is based on bioactivity screening of natural sources, traditionally represented by bacteria fungi and plants. Bioactive natural products and their secondary metabolites have represented the main source for new therapeutic agents, used as drug leads for new antibiotics and anticancer agents. After the discovery of the first biosynthetic genes in the last decades, the researchers had in their hands the tool to understand the biosynthetic logic and genetic basis leading to the production of these compounds. Furthermore, in the genomic era, in which the number of available genomes is increasing, genome mining joined to synthetic biology are offering a significant help in drug discovery. In the present review we discuss the importance of genome mining and synthetic biology approaches to identify new natural products, also underlining considering the possible advantages and disadvantages of this technique. Moreover, we debate the associated techniques that can be applied following to genome mining for validation of data. Finally, we review on the literature describing all novel natural drugs isolated from bacteria, fungi, and other living organisms, not only from the marine environment, by a genome-mining approach, focusing on the literature available in the last ten years.

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“…In this review, we summarized a synthetic biology strategy to produce novel secondary metabolites in Streptomyces. Accumulation of genetic information and SM-BGCs aided by recent advances in Next-Generation Sequencing (NGS) has revealed the enormous potential of Streptomyces as a reservoir for novel bioactive compounds and is far outpacing our capacity to explore SM-BGCs and their products [129]. To fully harness Streptomyces' ability to produce valuable secondary metabolites, rational design and efficient synthetic biology tools for Streptomyces are essential.…”

Section: Future Perspectivementioning

confidence: 99%

Synthetic Biology Tools for Novel Secondary Metabolite Discovery in Streptomyces

Lee¹,

Hwang²,

Lee³

et al. 2019

Journal of Microbiology and Biotechnology

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Omics-based natural product discovery and the lexicon of genome mining

Cited by 54 publications

References 68 publications

Natural Products from Actinobacteria Associated with Fungus-Growing Termites

Natural Products from Actinobacteria Associated with Fungus-Growing Termites

Genome Mining as New Challenge in Natural Products Discovery

Synthetic Biology Tools for Novel Secondary Metabolite Discovery in Streptomyces

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