Genome mining as a biotechnological tool for the discovery of novel marine natural products

Chu, Leixia; Huang, Jianguo; Mustafa, Muhammad; Deng, Zixin; Gao, Jiangtao

doi:10.1080/07388551.2020.1751056

Cited by 32 publications

(20 citation statements)

References 129 publications

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“…Genomics involves the study of complete DNA sets in organisms, including all its genes, their sequences, arrangements and architecture, providing perspective for looking into biological problems from the most basic code of life DNA. DNA carries instructions for transcription (promoters, untranslated regulatory regions and splicing sites), translation (start and stop codons) and specific functions of a gene (coding sequence) [19]. Genomics features underlying transcriptional and translational regulation, biosynthesis and the transport of plant metabolites can be utilized for systematic mining at single or multiple genome scales for discovering plant signaling metabolites.…”

Section: Genomics-the Source Code For Discovering Plant Signaling Metabolitesmentioning

confidence: 99%

Multi-Omics-Based Discovery of Plant Signaling Molecules

Luo

Zhou

et al. 2022

Metabolites

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Plants produce numerous structurally and functionally diverse signaling metabolites, yet only relatively small fractions of which have been discovered. Multi-omics has greatly expedited the discovery as evidenced by increasing recent works reporting new plant signaling molecules and relevant functions via integrated multi-omics techniques. The effective application of multi-omics tools is the key to uncovering unknown plant signaling molecules. This review covers the features of multi-omics in the context of plant signaling metabolite discovery, highlighting how multi-omics addresses relevant aspects of the challenges as follows: (a) unknown functions of known metabolites; (b) unknown metabolites with known functions; (c) unknown metabolites and unknown functions. Based on the problem-oriented overview of the theoretical and application aspects of multi-omics, current limitations and future development of multi-omics in discovering plant signaling metabolites are also discussed.

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Section: Genomics-the Source Code For Discovering Plant Signaling Metabolitesmentioning

confidence: 99%

Multi-Omics-Based Discovery of Plant Signaling Molecules

Luo

Zhou

et al. 2022

Metabolites

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“…On the one hand, the draft structure of the metabolites needs to be predictable to allow structural confirmation through, e.g., mass spectrometry or NMR, validating the functionality of the hypothetical BGC. Training databases linking biosynthetic enzymes to chemical transformations exist but do not yet reflect the entire biological diversity of natural product biosynthesis, causing limitations in structure prediction [91]. On the other hand, stringent regulation and the low expression of BGCs of interest can lead to low metabolite concentrations, hampering detection and structure confirmation.…”

Section: Genome Miningmentioning

confidence: 99%

Novel Alkaloids from Marine Actinobacteria: Discovery and Characterization

et al. 2021

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The marine environment is an excellent resource for natural products with therapeutic potential. Its microbial inhabitants, often associated with other marine organisms, are specialized in the synthesis of bioactive secondary metabolites. Similar to their terrestrial counterparts, marine Actinobacteria are a prevalent source of these natural products. Here, we discuss 77 newly discovered alkaloids produced by such marine Actinobacteria between 2017 and mid-2021, as well as the strategies employed in their elucidation. While 12 different classes of alkaloids were unraveled, indoles, diketopiperazines, glutarimides, indolizidines, and pyrroles were most dominant. Discoveries were mainly based on experimental approaches where microbial extracts were analyzed in relation to novel compounds. Although such experimental procedures have proven useful in the past, the methodologies need adaptations to limit the chance of compound rediscovery. On the other hand, genome mining provides a different angle for natural product discovery. While the technology is still relatively young compared to experimental screening, significant improvement has been made in recent years. Together with synthetic biology tools, both genome mining and extract screening provide excellent opportunities for continued drug discovery from marine Actinobacteria.

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“…Numerous publications reported the discovery of new secondary metabolites, including 1490 compounds in 2017 [13], 1554 compounds in 2018 [14], and 1490 compounds in 2019 [15]. In general, these secondary metabolites can be grouped into polyketides (PKS), nonribosomal peptides (NRPs), hybrid PKS and NRPs (PKS/NRPs), terpenoids/isoprenoids, ribosomally synthesized and post-translationally modified peptides (RiPPs), and bisindoles [16]. Carotenoids are a class of secondary metabolites belonging to the terpenoids/isoprenoids [17].…”

Section: Introductionmentioning

confidence: 99%

Marine Microbial-Derived Resource Exploration: Uncovering the Hidden Potential of Marine Carotenoids

et al. 2022

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Microbes in marine ecosystems are known to produce secondary metabolites. One of which are carotenoids, which have numerous industrial applications, hence their demand will continue to grow. This review highlights the recent research on natural carotenoids produced by marine microorganisms. We discuss the most recent screening approaches for discovering carotenoids, using in vitro methods such as culture-dependent and culture-independent screening, as well as in silico methods, using secondary metabolite Biosynthetic Gene Clusters (smBGCs), which involves the use of various rule-based and machine-learning-based bioinformatics tools. Following that, various carotenoids are addressed, along with their biological activities and metabolic processes involved in carotenoids biosynthesis. Finally, we cover the application of carotenoids in health and pharmaceutical industries, current carotenoids production system, and potential use of synthetic biology in carotenoids production.

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Genome mining as a biotechnological tool for the discovery of novel marine natural products

Cited by 32 publications

References 129 publications

Multi-Omics-Based Discovery of Plant Signaling Molecules

Multi-Omics-Based Discovery of Plant Signaling Molecules

Novel Alkaloids from Marine Actinobacteria: Discovery and Characterization

Marine Microbial-Derived Resource Exploration: Uncovering the Hidden Potential of Marine Carotenoids

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