Activation of silent biosynthetic gene clusters using transcription factor decoys

Wang, Bin; Guo, Fang; Dong, Shouliang; Zhao, Huimin

doi:10.1038/s41589-018-0187-0

Cited by 96 publications

(87 citation statements)

References 23 publications

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“…The resulting mutants, IsgriM25 and IsgriM38, grown on mannitol soya flour solid medium showed no obvious phenotypical difference compared to the control strain sgriCK (wild type bearing the self-replicable plasmid pKC1139). However, switching to maltose-yeast extract-malt extract (MYM) liquid medium (38) appeared to be lethal for IsgriM25 ( Fig. 3 B and C)-a phenomenon that suggested that sgriM25 may be conditionally essential for the producer.…”

Section: Resultsmentioning

confidence: 99%

Unraveling the iterative type I polyketide synthases hidden in Streptomyces

Wang

Guo

Huang

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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Type I polyketide synthases (T1PKSs) are one of the most extensively studied PKSs, which can act either iteratively or via an assembly-line mechanism. Domains in the T1PKSs can readily be predicted by computational tools based on their highly conserved sequences. However, to distinguish between iterative and noniterative at the module level remains an overwhelming challenge, which may account for the seemingly biased distribution of T1PKSs in fungi and bacteria: small iterative monomodular T1PKSs that are responsible for the enormously diverse fungal natural products exist almost exclusively in fungi. Here we report the discovery of iterative T1PKSs that are unexpectedly both abundant and widespread in Streptomyces. Seven of 11 systematically selected T1PKS monomodules from monomodular T1PKS biosynthetic gene clusters (BGCs) were experimentally confirmed to be iteratively acting, synthesizing diverse branched/nonbranched linear intermediates, and two of them produced bioactive allenic polyketides and citreodiols as end products, respectively. This study indicates the huge potential of iterative T1PKS BGCs from streptomycetes in the discovery of novel polyketides.

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Section: Resultsmentioning

confidence: 99%

Unraveling the iterative type I polyketide synthases hidden in Streptomyces

Wang

Guo

Huang

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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“…The bottleneck of transcriptional silence continues to drive innovation and a plethora of different approaches exist to activate silent pathways [199][200][201] . Advances in analytical techniques (mass spectrometry, NMR imaging and data analysis software) [202][203][204][205] allow us to better detect and characterize compounds produced in minute quantities, a major bottleneck in the field, lifting the veil on 'silent' NPs to further increase the number of unusual molecule leads, in addition to identifying critical pathway intermediates that may aid in deciphering cryptic pathways.…”

Section: Unlocking Nature's Diversitymentioning

confidence: 99%

The hidden enzymology of bacterial natural product biosynthesis

Scott

Piel

2019

Nat Rev Chem

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Bacterial natural products display astounding structural diversity, which, in turn, endows them with a remarkable range of biological activities that are of significant value to modern society. Such structural features are generated by biosynthetic enzymes that construct core scaffolds or perform peripheral modifications, and can thus define natural product families, introduce pharmacophores and permit metabolic diversification. Modern genomics approaches have greatly enhanced our ability to access and characterize natural product pathways via sequence-similaritybased bioinformatics discovery strategies. However, many biosynthetic enzymes catalyse exceptional, unprecedented transformations that continue to defy functional prediction and remain hidden from us in bacterial (meta)genomic sequence data. In this Review, we highlight exciting examples of unusual enzymology that have been uncovered recently in the context of natural product biosynthesis. These suggest that much of the natural product diversity, including entire substance classes, awaits discovery. New approaches to lift the veil on the cryptic chemistries of the natural product universe are also discussed. Bacterial natural products (NPs) are specialized metabolites that encompass an extraordinary breadth of different biological activities, many of which are of considerable value to society. NPs or NP-inspired compounds represent ~65% of all small-molecule approved drugs 1 used in medicine to treat infectious diseases, cancers or as immunosuppressants 2 , and they are also applied extensively in agriculture 3. While NPs have been an extremely productive source of new leads for the chemicals that are integral to modern life, rapid increases in resistance to antibiotics, cancer chemotherapies and pesticides pose significant threats to medicine and agriculture 4,5 .

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“…However, the TFD strategy was used for the first time to activate the cryptic BGCs in Streptomycetes [63]. As it is difficult to exactly predict the regulatory DNA fragments in the BGCs, DNA fragments of approximately 100 base pairs were cloned to both the upstream and downstream of open reading frames (ORFs) in the target BGC.…”

Section: Transcription Factor Decoys Approachmentioning

confidence: 99%

“…This strategy is simpler than other strategies that use deletion or genome editing, such as the deletion of a negative regulator. However, the efficiency of this approach is not high at about 36-50% for the activation of silent BGCs [63]. Therefore, there is still room to improve this strategy by further engineering strategies.…”

Section: Transcription Factor Decoys Approachmentioning

confidence: 99%

Recent Advances in Strategies for Activation and Discovery/Characterization of Cryptic Biosynthetic Gene Clusters in Streptomyces

et al. 2020

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Streptomyces spp. are prolific sources of valuable natural products (NPs) that are of great interest in pharmaceutical industries such as antibiotics, anticancer chemotherapeutics, immunosuppressants, etc. Approximately two-thirds of all known antibiotics are produced by actinomycetes, most predominantly by Streptomyces. Nevertheless, in recent years, the chances of the discovery of novel and bioactive compounds from Streptomyces have significantly declined. The major hindrance for obtaining such bioactive compounds from Streptomyces is that most of the compounds are not produced in significant titers, or the biosynthetic gene clusters (BGCs) are cryptic. The rapid development of genome sequencing has provided access to a tremendous number of NP-BGCs embedded in the microbial genomes. In addition, the studies of metabolomics provide a portfolio of entire metabolites produced from the strain of interest. Therefore, through the integrated approaches of different-omics techniques, the connection between gene expression and metabolism can be established. Hence, in this review we summarized recent advancements in strategies for activating cryptic BGCs in Streptomyces by utilizing diverse state-of-the-art techniques.

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Activation of silent biosynthetic gene clusters using transcription factor decoys

Cited by 96 publications

References 23 publications

Unraveling the iterative type I polyketide synthases hidden in Streptomyces

Unraveling the iterative type I polyketide synthases hidden in Streptomyces

The hidden enzymology of bacterial natural product biosynthesis

Recent Advances in Strategies for Activation and Discovery/Characterization of Cryptic Biosynthetic Gene Clusters in Streptomyces

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