Tapping Into Actinobacterial Genomes for Natural Product Discovery

Singh, Tanim Arpit; Passari, Ajit Kumar; Jajoo, Anjana; Bhasin, Sheetal; Gupta, Vijai Kumar; Hashem, Abeer

doi:10.3389/fmicb.2021.655620

Cited by 15 publications

(12 citation statements)

References 79 publications

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“…However, these methods should be handled carefully because mismatches can occur in the prediction of the chemical structures of the clusters. Detailed reviews of each strategy are available in the further mentioned references ( Chavali and Rhee, 2018 ; Singh et al, 2021 ; Almeida et al, 2022 ).…”

Section: Types Of Metabolic Induction In Mixed Culturesmentioning

confidence: 99%

Enhancing chemical and biological diversity by co-cultivation

Selegato

Castro‐Gamboa

2023

Front. Microbiol.

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In natural product research, microbial metabolites have tremendous potential to provide new therapeutic agents since extremely diverse chemical structures can be found in the nearly infinite microbial population. Conventionally, these specialized metabolites are screened by single-strain cultures. However, owing to the lack of biotic and abiotic interactions in monocultures, the growth conditions are significantly different from those encountered in a natural environment and result in less diversity and the frequent re-isolation of known compounds. In the last decade, several methods have been developed to eventually understand the physiological conditions under which cryptic microbial genes are activated in an attempt to stimulate their biosynthesis and elicit the production of hitherto unexpressed chemical diversity. Among those, co-cultivation is one of the most efficient ways to induce silenced pathways, mimicking the competitive microbial environment for the production and holistic regulation of metabolites, and has become a golden methodology for metabolome expansion. It does not require previous knowledge of the signaling mechanism and genome nor any special equipment for cultivation and data interpretation. Several reviews have shown the potential of co-cultivation to produce new biologically active leads. However, only a few studies have detailed experimental, analytical, and microbiological strategies for efficiently inducing bioactive molecules by co-culture. Therefore, we reviewed studies applying co-culture to induce secondary metabolite pathways to provide insights into experimental variables compatible with high-throughput analytical procedures. Mixed-fermentation publications from 1978 to 2022 were assessed regarding types of co-culture set-ups, metabolic induction, and interaction effects.

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Section: Types Of Metabolic Induction In Mixed Culturesmentioning

confidence: 99%

Enhancing chemical and biological diversity by co-cultivation

Selegato

Castro‐Gamboa

2023

Front. Microbiol.

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“…However, the present study showed for the first time that the strain produces a secondary metabolite other than STZ. As a number of novel compounds have been recently identified by the genome-guided approach [4][5][6][7], this approach may become a powerful tool for investigating novel compounds in microorganisms.…”

Section: Discussionmentioning

confidence: 99%

“…Secondary metabolite biosynthetic gene clusters (smBGCs) in actinomycete strains are extracted by in silico analyses using programs such as antiSMASH [3]. Based on the information obtained on smBGCs, secondary metabolites are unveiled using appropriate Microorganisms 2022, 10, 37 2 of 11 procedures, such as biotechnological approaches including heterologous expression and promoter engineering [4][5][6][7].…”

Section: Introductionmentioning

confidence: 99%

Genome Sequence-Guided Finding of Lucensomycin Production by Streptomyces achromogenes Subsp. streptozoticus NBRC14001

et al. 2021

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Information on microbial genome sequences is a powerful resource for accessing natural products with significant activities. We herein report the unveiling of lucensomycin production by Streptomyces achromogenes subsp. streptozoticus NBRC14001 based on the genome sequence of the strain. The genome sequence of strain NBRC14001 revealed the presence of a type I polyketide synthase gene cluster with similarities to a biosynthetic gene cluster for natamycin, which is a polyene macrolide antibiotic that exhibits antifungal activity. Therefore, we investigated whether strain NBRC14001 produces antifungal compound(s) and revealed that an extract from the strain inhibited the growth of Candida albicans. A HPLC analysis of a purified compound exhibiting antifungal activity against C. albicans showed that the compound differed from natamycin. Based on HR-ESI-MS spectrometry and a PubChem database search, the compound was predicted to be lucensomycin, which is a tetraene macrolide antibiotic, and this prediction was supported by the results of a MS/MS analysis. Furthermore, the type I polyketide synthase gene cluster in strain NBRC14001 corresponded well to lucesomycin biosynthetic gene cluster (lcm) in S. cyanogenus, which was very recently reported. Therefore, we concluded that the antifungal compound produced by strain NBRC14001 is lucensomycin.

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“…In terms of activating these silent cryptic genes in vitro, researchers should be made aware that a single BGC can lead to one or more secondary metabolites [33]. In addition, as secondary metabolites have different roles from primary metabolites, they are mainly produced under stressed, unusual or extreme conditions [31].…”

Section: Hidden Potential Of Streptomyces: Metagenomic Insights and E...mentioning

confidence: 99%

Streptomyces: Still the Biggest Producer of New Natural Secondary Metabolites, a Current Perspective

Donald

Pipite

Subramani

et al. 2022

Microbiology Research

102

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There is a real consensus that new antibiotics are urgently needed and are the best chance for combating antibiotic resistance. The phylum Actinobacteria is one of the main producers of new antibiotics, with a recent paradigm shift whereby rare actinomycetes have been increasingly targeted as a source of new secondary metabolites for the discovery of new antibiotics. However, this review shows that the genus Streptomyces is still the largest current producer of new and innovative secondary metabolites. Between January 2015 and December 2020, a significantly high number of novel Streptomyces spp. have been isolated from different environments, including extreme environments, symbionts, terrestrial soils, sediments and also from marine environments, mainly from marine invertebrates and marine sediments. This review highlights 135 new species of Streptomyces during this 6-year period with 108 new species of Streptomyces from the terrestrial environment and 27 new species from marine sources. A brief summary of the different pre-treatment methods used for the successful isolation of some of the new species of Streptomyces is also discussed, as well as the biological activities of the isolated secondary metabolites. A total of 279 new secondary metabolites have been recorded from 121 species of Streptomyces which exhibit diverse biological activity. The greatest number of new secondary metabolites originated from the terrestrial-sourced Streptomyces spp.

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Tapping Into Actinobacterial Genomes for Natural Product Discovery

Cited by 15 publications

References 79 publications

Enhancing chemical and biological diversity by co-cultivation

Enhancing chemical and biological diversity by co-cultivation

Genome Sequence-Guided Finding of Lucensomycin Production by Streptomyces achromogenes Subsp. streptozoticus NBRC14001

Streptomyces: Still the Biggest Producer of New Natural Secondary Metabolites, a Current Perspective

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