Genome Mining as New Challenge in Natural Products Discovery

Albarano, Luisa; Esposito, Roberta; Ruocco, Nadia; Costantini, Maria

doi:10.3390/md18040199

Cited by 111 publications

(76 citation statements)

References 79 publications

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“…The development of sequencing, computational and storage capacities reduced the financial and time investment needed for new discoveries of biotechnological interest. This is now enabled with genome mining, the process of extracting information from genome sequences to detect biosynthetic pathways of bioactive natural products and their possible functional and chemical interactions (Trivella and de Felicio, 2018;Albarano et al, 2020). It is used to investigate key enzymes of biosynthetic pathways and predict the chemical products encoded by biosynthetic genes.…”

Section: Marine Biodiscovery Areasmentioning

confidence: 99%

The Essentials of Marine Biotechnology

Barbier²,

et al. 2021

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Coastal countries have traditionally relied on the existing marine resources (e.g., fishing, food, transport, recreation, and tourism) as well as tried to support new economic endeavors (ocean energy, desalination for water supply, and seabed mining). Modern societies and lifestyle resulted in an increased demand for dietary diversity, better health and well-being, new biomedicines, natural cosmeceuticals, environmental conservation, and sustainable energy sources. These societal needs stimulated the interest of researchers on the diverse and underexplored marine environments as promising and sustainable sources of biomolecules and biomass, and they are addressed by the emerging field of marine (blue) biotechnology. Blue biotechnology provides opportunities for a wide range of initiatives of commercial interest for the pharmaceutical, biomedical, cosmetic, nutraceutical, food, feed, agricultural, and related industries. This article synthesizes the essence, opportunities, responsibilities, and challenges encountered in marine biotechnology and outlines the attainment and valorization of directly derived or bio-inspired products from marine organisms. First, the concept of bioeconomy is introduced. Then, the diversity of marine bioresources including an overview of the most prominent marine organisms and their potential for biotechnological uses are described. This is followed by introducing methodologies for exploration of these resources and the main use case scenarios in energy, food and feed, agronomy, bioremediation and climate change, cosmeceuticals, bio-inspired materials, healthcare, and well-being sectors. The key aspects in the fields of legislation and funding are provided, with the emphasis on the importance of communication and stakeholder engagement at all levels of biotechnology development. Finally, vital overarching concepts, such as the quadruple helix and Responsible Research and Innovation principle are highlighted as important to follow within the marine biotechnology field. The authors of this review are collaborating under the European Commission-funded Cooperation in Science and Technology (COST) Action Ocean4Biotech – European transdisciplinary networking platform for marine biotechnology and focus the study on the European state of affairs.

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Section: Marine Biodiscovery Areasmentioning

confidence: 99%

The Essentials of Marine Biotechnology

Barbier²,

et al. 2021

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“…Required is the development of novel cultivation and screening tools for rare, barely studied taxa [159] . On the other hand, bioinformatics tools are limited as they can only detect BGCs based on known sequences, leading to potential mischaracterisation or failure to detect new families [160] , [161] . However, with the advent of new molecular and computational technologies, the future of LPs discovery will undoubtedly expand, providing unsurpassed knowledge on the ecological roles of these important secondary metabolites [138] .…”

Section: Discovery Of New Lps: Where Are We Going?mentioning

confidence: 99%

The ecological roles of microbial lipopeptides: Where are we going?

Gutiérrez-Chávez

Benaud

Ferrari

2021

Computational and Structural Biotechnology Journal

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Lipopeptides (LPs) are secondary metabolites produced by a diversity of bacteria and fungi. Their unique chemical structure comprises both a peptide and a lipid moiety. LPs are of major biotechnological interest owing to their emulsification, antitumor, immunomodulatory, and antimicrobial activities. To date, these versatile compounds have been applied across multiple industries, from pharmaceuticals through to food processing, cosmetics, agriculture, heavy metal, and hydrocarbon bioremediation. The variety of LP structures and the diversity of the environments from which LP-producing microorganisms have been isolated suggest important functions in their natural environment. However, our understanding of the ecological role of LPs is limited. In this review, the mode of action and the role of LPs in motility, antimicrobial activity, heavy metals removal and biofilm formation are addressed. We include discussion on the need to characterise LPs from a diversity of microorganisms, with a focus on taxa inhabiting ‘extreme’ environments. We introduce the use of computational target fishing and molecular dynamics simulations as powerful tools to investigate the process of interaction between LPs and cell membranes. Together, these advances will provide new understanding of the mechanism of action of novel LPs, providing greater insights into the roles of LPs in the natural environment.

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“…Indeed, genome analysis has uncovered universal microbial processes to down-regulate or silence biosynthetic gene clusters [ 174 ]. In fact, genome mining studies suggest 92–96% of fungal secondary metabolite biosynthesis is routinely turned off [ 175 , 176 ] through epigenetic regulators and absence of triggers from other organisms [ 177 ], presumably to reduce energetic costs during times when the products do not add to fitness. Furthermore, as argued in Table 2 , chemical complexity may depend on community interactions that transform compounds [ 3 ], sometimes through enzymes or shunt metabolites (e.g.…”

Section: Introductionmentioning

confidence: 99%

Deep learning approaches for natural product discovery from plant endophytic microbiomes

Aghdam

Brown

2021

Environmental Microbiome

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Plant microbiomes are not only diverse, but also appear to host a vast pool of secondary metabolites holding great promise for bioactive natural products and drug discovery. Yet, most microbes within plants appear to be uncultivable, and for those that can be cultivated, their metabolic potential lies largely hidden through regulatory silencing of biosynthetic genes. The recent explosion of powerful interdisciplinary approaches, including multi-omics methods to address multi-trophic interactions and artificial intelligence-based computational approaches to infer distribution of function, together present a paradigm shift in high-throughput approaches to natural product discovery from plant-associated microbes. Arguably, the key to characterizing and harnessing this biochemical capacity depends on a novel, systematic approach to characterize the triggers that turn on secondary metabolite biosynthesis through molecular or genetic signals from the host plant, members of the rich ‘in planta’ community, or from the environment. This review explores breakthrough approaches for natural product discovery from plant microbiomes, emphasizing the promise of deep learning as a tool for endophyte bioprospecting, endophyte biochemical novelty prediction, and endophyte regulatory control. It concludes with a proposed pipeline to harness global databases (genomic, metabolomic, regulomic, and chemical) to uncover and unsilence desirable natural products.

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Genome Mining as New Challenge in Natural Products Discovery

Cited by 111 publications

References 79 publications

The Essentials of Marine Biotechnology

The Essentials of Marine Biotechnology

The ecological roles of microbial lipopeptides: Where are we going?

Deep learning approaches for natural product discovery from plant endophytic microbiomes

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