Omics and multi-omics approaches to study the biosynthesis of secondary metabolites in microorganisms

Palazzotto, Emilia; Weber, Tilmann

doi:10.1016/j.mib.2018.03.004

Cited by 109 publications

(62 citation statements)

References 70 publications

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“…Pertinent organizations (for instance, shellfisheries, shoreline establishments, and other fish-related businesses) are heavily affected with evaluated yearly expense of United States dollars (USD) $895 million around the world utilized for monitoring and carrying out mitigation plans for saxitoxin-producing dinoflagellates [6]. Lately, studies of natural product biosynthesis were revolutionized by the unbiased and non-targeted universal detection, identification, and measurement of molecular fractions consisting of genes (genomics), messenger RNA (mRNA) (transcriptomics), proteins (proteomics), and metabolites (metabolomics), collectively dubbed as "omics" [23,24]. This is due to the capacity of omics technology and integrated methodologies to extract and appraise biomolecules at a global scale rather than targeting the individual genes, proteins, or metabolites via a traditional reductionist approach ( Figure 1).…”

Section: Structure Of Saxitoxin (Stx)mentioning

confidence: 99%

Biosynthesis of Saxitoxin in Marine Dinoflagellates: An Omics Perspective

et al. 2020

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Saxitoxin is an alkaloid neurotoxin originally isolated from the clam Saxidomus giganteus in 1957. This group of neurotoxins is produced by several species of freshwater cyanobacteria and marine dinoflagellates. The saxitoxin biosynthesis pathway was described for the first time in the 1980s and, since then, it was studied in more than seven cyanobacterial genera, comprising 26 genes that form a cluster ranging from 25.7 kb to 35 kb in sequence length. Due to the complexity of the genomic landscape, saxitoxin biosynthesis in dinoflagellates remains unknown. In order to reveal and understand the dynamics of the activity in such impressive unicellular organisms with a complex genome, a strategy that can carefully engage them in a systems view is necessary. Advances in omics technology (the collective tools of biological sciences) facilitated high-throughput studies of the genome, transcriptome, proteome, and metabolome of dinoflagellates. The omics approach was utilized to address saxitoxin-producing dinoflagellates in response to environmental stresses to improve understanding of dinoflagellates gene–environment interactions. Therefore, in this review, the progress in understanding dinoflagellate saxitoxin biosynthesis using an omics approach is emphasized. Further potential applications of metabolomics and genomics to unravel novel insights into saxitoxin biosynthesis in dinoflagellates are also reviewed.

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Section: Structure Of Saxitoxin (Stx)mentioning

confidence: 99%

Biosynthesis of Saxitoxin in Marine Dinoflagellates: An Omics Perspective

et al. 2020

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“…Confirmed or potential producers of new antimicrobial agents are further analysed by diverse "omics" approaches [342,[354][355][356][357]. The downstream evaluation of the collected data sets using bioinformatics tools enables for example the identification of the BGC for the product of interest and/or provides an overview on the overall biosynthetic potential of target strain (genome mining) [9,[358][359][360].…”

Section: Strategies and Tools For The Discovery Of Natural Productsmentioning

confidence: 99%

Actinomycete-Derived Polyketides as a Source of Antibiotics and Lead Structures for the Development of New Antimicrobial Drugs

Robertsen

Musiol-Kroll

2019

Antibiotics

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Actinomycetes are remarkable producers of compounds essential for human and veterinary medicine as well as for agriculture. The genomes of those microorganisms possess several sets of genes (biosynthetic gene cluster (BGC)) encoding pathways for the production of the valuable secondary metabolites. A significant proportion of the identified BGCs in actinomycetes encode pathways for the biosynthesis of polyketide compounds, nonribosomal peptides, or hybrid products resulting from the combination of both polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs). The potency of these molecules, in terms of bioactivity, was recognized in the 1940s, and started the “Golden Age” of antimicrobial drug discovery. Since then, several valuable polyketide drugs, such as erythromycin A, tylosin, monensin A, rifamycin, tetracyclines, amphotericin B, and many others were isolated from actinomycetes. This review covers the most relevant actinomycetes-derived polyketide drugs with antimicrobial activity, including anti-fungal agents. We provide an overview of the source of the compounds, structure of the molecules, the biosynthetic principle, bioactivity and mechanisms of action, and the current stage of development. This review emphasizes the importance of actinomycetes-derived antimicrobial polyketides and should serve as a “lexicon”, not only to scientists from the Natural Products field, but also to clinicians and others interested in this topic.

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“…Exploiting multi-omics data sets is now a pivotal step in discovering novel antibiotics (Palazzotto and Weber, 2018). Albright et al, 2014, demonstrate a clear methodology for screening strains for novel antibiotic metabolites based on multiomics data (Albright et al, 2014).…”

Section: Completing the Multi-omics Picture: Metabolomicsmentioning

confidence: 99%

The Progress of Multi-Omics Technologies: Determining Function in Lactic Acid Bacteria Using a Systems Level Approach

2020

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Lactic Acid Bacteria (LAB) have long been recognized as having a significant impact ranging from commercial to health domains. A vast amount of research has been carried out on these microbes, deciphering many of the pathways and components responsible for these desirable effects. However, a large proportion of this functional information has been derived from a reductionist approach working with pure culture strains. This provides limited insight into understanding the impact of LAB within intricate systems such as the gut microbiome or multi strain starter cultures. Whole genome sequencing of strains and shotgun metagenomics of entire systems are powerful techniques that are currently widely used to decipher function in microbes, but they also have their limitations. An available genome or metagenome can provide an image of what a strain or microbiome, respectively, is potentially capable of and the functions that they may carry out. A top-down, multi-omics approach has the power to resolve the functional potential of an ecosystem into an image of what is being expressed, translated and produced. With this image, it is possible to see the real functions that members of a system are performing and allow more accurate and impactful predictions of the effects of these microorganisms. This review will discuss how technological advances have the potential to increase the yield of information from genomics, transcriptomics, proteomics and metabolomics. The potential for integrated omics to resolve the role of LAB in complex systems will also be assessed. Finally, the current software approaches for managing these omics data sets will be discussed.

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Omics and multi-omics approaches to study the biosynthesis of secondary metabolites in microorganisms

Cited by 109 publications

References 70 publications

Biosynthesis of Saxitoxin in Marine Dinoflagellates: An Omics Perspective

Biosynthesis of Saxitoxin in Marine Dinoflagellates: An Omics Perspective

Actinomycete-Derived Polyketides as a Source of Antibiotics and Lead Structures for the Development of New Antimicrobial Drugs

The Progress of Multi-Omics Technologies: Determining Function in Lactic Acid Bacteria Using a Systems Level Approach

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