Novel bioactive natural products from bacteria via bioprospecting, genome mining and metabolic engineering

Sekurova, Olga N.; Schneider, Olha; Zotchev, Sergey B.

doi:10.1111/1751-7915.13398

Cited by 117 publications

(78 citation statements)

References 124 publications

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“…Hence, their genomes were investigated in order to reveal biosynthetic potential of these isolates. Having information on the BGCs, especially those that may potentially specify biosynthesis of novel compounds, opens possibilities for genome mining that can be applied to trigger gene expression of particular BGCs (Sekurova et al, 2019). Also, comparative genomics can be used to trace transfer of BGCs between isolates, which could be expected to happen considering spatial containment within the sponge.…”

Section: Discussionmentioning

confidence: 99%

Streptomyces spp. From the Marine Sponge Antho dichotoma: Analyses of Secondary Metabolite Biosynthesis Gene Clusters and Some of Their Products

et al. 2020

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Actinomycete bacteria from marine environments represent a potential source for new antibiotics and anti-tumor drugs. Ten strains belonging to the genus Streptomyces isolated from the marine sponge Antho dichotoma collected at the bottom of the Trondheim fjord (Norway) were screened for antibiotic activity. Since only few isolates proved to be bioactive in the conditions tested, we decided to gain an insight into their biosynthetic potential using genome sequencing and analysis. Draft genomes were analyzed for the presence of secondary metabolite biosynthesis gene clusters (BGCs) using antiSMASH software. BGCs specifying both known and potentially novel secondary metabolites were identified, suggesting that these isolates might be sources for new bioactive compounds. The results of this analysis also implied horizontal transfer of several gene clusters between the studied isolates, which was especially evident for the lantibiotic-and thiopeptide-encoding BGCs. The latter implies the significance of particular secondary metabolites for the adaptation of Streptomyces to the spatially enclosed marine environments such as marine sponges. Two bioactive isolates, one showing activity against both yeast and Bacillus subtilis, and one only against yeast were analyzed in details, leading to the identification of cycloheximide, linearmycins, and echinomycins that are presumably responsible for the observed bioactivities.

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Section: Discussionmentioning

confidence: 99%

Streptomyces spp. From the Marine Sponge Antho dichotoma: Analyses of Secondary Metabolite Biosynthesis Gene Clusters and Some of Their Products

et al. 2020

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“…While the strategies used for detecting microbial specialized metabolites are well-established (bioassay-guided, metabolomics, genome mining and sequencing [32][33][34]) those used to elicit the expression of their biosynthetic gene clusters (BGC) have arisen either by more random or intuitive routes such as the one strain-many compounds scheme involving variations of the fermentation protocol, and co-culture systems. The latter approach appears not to have been tested extensively but two examples arising from our Atacama Desert work have produced interesting and unpredictable results.…”

Section: Bioactive Natural Productsmentioning

confidence: 99%

“…Creative cultivation techniques are available for the isolation of rare and novel actinobacteria with large genomes [27,59], though there is a need to marry innovative selective isolation procedures with the ecology of target organisms [60][61][62][63], as demonstrated by adaptations shown by Salinispora and Streptomyces strains [64,65]. There is also a need to obtain complete genome sequences from especially gifted actinobacteria [33,34] for systematic genome mining for new molecules.…”

Section: Genome Analysismentioning

confidence: 99%

“…Genomic-guided identification of new drug targets such as protein-protein interactions also will stimulate natural product bioprospecting given the extent of such interactions in nature. Moreover, as Hug et al [4] point out if production scale cultivation of target organisms compromises the exploitation of a promising natural product, culture-independent strategies that include metagenomics and heterologous expression of BGCs provide exciting approaches for the discovery of novel natural products among biosynthetic dark matter, as does the prospect of coupling genome sequencing with synthetic biology [33,34].…”

Section: Why Bother With Natural Products?mentioning

confidence: 99%

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Dark, rare and inspirational microbial matter in the extremobiosphere: 16 000 m of bioprospecting campaigns

Bull

Goodfellow

2019

Microbiology

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The rationale of our bioprospecting campaigns is that the extremobiosphere, particularly the deep sea and hyper-arid deserts, harbours undiscovered biodiversity that is likely to express novel chemistry and biocatalysts thereby providing opportunities for therapeutic drug and industrial process development. We have focused on actinobacteria because of their frequent role as keystone species in soil ecosystems and their unrivalled track record as a source of bioactive compounds. Population numbers and diversity of actinobacteria in the extremobiosphere are traditionally considered to be low, although they often comprise the dominant bacterial biota. Recent metagenomic evaluation of 'the uncultured microbial majority' has now revealed enormous taxonomic diversity among 'dark' and 'rare' actinobacteria in samples as diverse as sediments from the depths of the Mariana Trench and soils from the heights of the Central Andes. The application of innovative culture and screening options that emphasize rigorous dereplication at each stage of the analysis, and strain prioritization to identify 'gifted' organisms, have been deployed to detect and characterize bioactive hit compounds and sought-after catalysts from this hitherto untapped resource. The rewards include first-in-a-class chemical entities with novel modes of action, as well as a growing microbial seed bank that represents a potentially enormous source of biotechnological and therapeutic innovation.

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“…The type strain of this species, isolate C34 T , is especially gifted sensu Baltz [17] as it has a large genome (7.8 Mb) that includes 31 biosynthetic gene clusters (BGCs) that mainly encode for unknown specialized metabolites [18]. Such gifted Streptomyces strains are pivotal in the search for new drug-leads using state-of-the-art technologies such as genome mining and metabolic engineering [19, 20].…”

Section: Introductionmentioning

confidence: 99%

Streptomyces harenosi sp. nov., a home for a gifted strain isolated from Indonesian sand dune soil

Kusuma

Nouioui

Klenk

et al. 2020

International Journal of Systematic and Evolutionary Microbiology

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A polyphasic study was undertaken to establish the position of a Streptomyces strain, isolate PRKS01-65T, recovered from sand dune soil collected at Parangkusumo, Yogyakarta Province, Java, Indonesia. A combination of chemotaxonomic, cultural and morphological properties confirmed its position in the genus of Streptomyces . Comparative 16S rRNA gene sequence analyses showed that the isolate was most closely related to Streptomyces leeuwenhoekii C34T (99.9 % similarity) and loosely associated with the type strains of Streptomyces chiangmaiensis (98.7 % similarity) and Streptomyces glomeratus (98.9 % similarity). Multilocus sequence analyses based on five conserved housekeeping gene alleles confirmed the close relationship between the isolate and S. leeuwenhoekii C34T, although both strains belonged to a well-supported clade that encompassed the type strains of S. glomeratus , Streptomyces griseomycini , Streptomyces griseostramineus , Streptomyces labedae , Streptomyces lomondensis and Streptomyces spinoverrucosus . A comparison of the draft genome sequence generated for the isolate with corresponding whole genome sequences of its closest phylogenomic neighbours showed that it formed a well-separated lineage with S. leeuwenhoekii C34T. These strains can also be distinguished using a combination of phenotypic properties and by average nucleotide identity and digital DNA–DNA hybridization similarities of 94.3 and 56 %, values consistent with their classification in different species. Based on this wealth of data it is proposed that isolate PRKS01-65T (=NCIMB 15211T=CCMM B1302T=ICEBB-03T) be classified as Streptomyces harenosi sp. nov. The genome of the isolate contains several biosynthetic gene clusters with the potential to produce new natural products.

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Novel bioactive natural products from bacteria via bioprospecting, genome mining and metabolic engineering

Cited by 117 publications

References 124 publications

Streptomyces spp. From the Marine Sponge Antho dichotoma: Analyses of Secondary Metabolite Biosynthesis Gene Clusters and Some of Their Products

Streptomyces spp. From the Marine Sponge Antho dichotoma: Analyses of Secondary Metabolite Biosynthesis Gene Clusters and Some of Their Products

Dark, rare and inspirational microbial matter in the extremobiosphere: 16 000 m of bioprospecting campaigns

Streptomyces harenosi sp. nov., a home for a gifted strain isolated from Indonesian sand dune soil

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