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PQQ increases actinorhodin production by enhancing cofactor biosynthesis and modulating intracellular TAG level a, Pathway enrichment analysis of the upregulated proteins. The ratio indicates the fraction of upregulated proteins enriched in a pathway versus all the proteins in the particular pathway. b, Actinorhodin production curve and glucose consumption curve for S. coelicolor with and without the pqq gene cluster. Mean concentrations with error bars showing s.d. are plotted (n = 3, three biologically independent samples). ACT, actinorhodin. c–e, Introduction of the pqq BGC increased the levels of ATP (c), NADH/NAD⁺ (d) and NADPH/NADP⁺ (e). DW, dry weight. Mean concentrations with error bars showing s.d. are plotted (n = 3, three biologically independent samples). Multiple comparison significance was tested to **P < 0.05, ***P < 0.01 by an unpaired two-sided Student’s t-test. f, Introduction of the pqq BGC increased TAG formation and degradation efficiency. Mean concentrations with error bars showing s.d. are plotted (n = 3, three biologically independent samples). g, The labelled and unlabelled amount of actinorhodin at different time points during fermentation after supplementation of ¹³C-labelled glucose. Mean concentrations with error bars showing s.d. are plotted (n = 4, three biologically independent samples). Multiple comparison significance was tested to **P < 0.05, ***P < 0.01 by an unpaired two-sided Student’s t-test. Source data
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Streptomyces has the largest repertoire of natural product biosynthetic gene clusters (BGCs), yet developing a universal engineering strategy for each Streptomyces species is challenging. Given that some Streptomyces species have larger BGC repertoires than others, we proposed that a set of genes co-evolved with BGCs to support biosynthetic profici...
Citations
... Therefore, it is imperative to reconfigure this intricate network with the aim of achieving optimal production. In the past decade, numerous target screening strategies have been developed to identify independent regulatory targets that can enhance production 27 . However, there is currently a lack of reliable theory or data-driven guidance on how to effectively combine these targets to achieve synergistic improvement. ...
Non-ribosomal peptides (NRPs) are pharmaceutically important natural products that include numerous clinical drugs. However, the biosynthesis of these NRPs is intricately regulated and improving production through manipulation of multiple regulatory targets remains largely empirical. We here develop a screening-based, multi-target rational combination strategy and demonstrate its effectiveness in enhancing the titers of three NRP drugs ˗ daptomycin, thaxtomin A and surfactin. Initially, we devise a reliable colorimetric analog co-expression and co-biosynthesis reporter system for screening high-yielding phenotypes. Subsequently, through coupling CRISPR interference to induce genome-wide differential expression, we identify dozens of repressors that inhibit the biosynthesis of these NRPs. To address the challenge of multi-target combination, we further developed a dual-target screen approach and introduced an interplay map based on the synergy coefficient of each pairwise interaction. Employing this strategy, we engineer the final strains with multi-target synergistic combination and achieve the titer improvement of the three NRPs. Our work provides a rational multi-target combination strategy for production improvement of NRPs.
... Moreover, we achieved tunable product profiles of RimPKS-TRs through substrate CoA pool engineering. PKS pathways are often tightly regulated in nature, as shown by the wide presence of PKS pathway-specific transcription regulators within the BGCs 58 and the more recent discovery of pyrroloquinoline quinone gene clusters that co-evolved with PKS BGCs and enhanced natural product production 59 . Another common PKS-related regulation approach prioritizes regulating CoA substrate biosynthesis, investigation of which has benefited the identification of key steps in the engineering of such PKSs. ...
Medium- and branched-chain diols and amino alcohols are important industrial solvents, polymer building blocks, cosmetics and pharmaceutical ingredients, yet biosynthetically challenging to produce. Here we present an approach that uses a modular polyketide synthase (PKS) platform for the efficient production of these compounds. This platform takes advantage of a versatile loading module from the rimocidin PKS and nicotinamide adenine dinucleotide phosphate-dependent terminal thioreductases. Reduction of the terminal aldehyde with alcohol dehydrogenases enables the production of diols, oxidation enables the production of hydroxy acids and specific transaminases allow the production of various amino alcohols. Furthermore, replacement of the malonyl-coenzyme A-specific acyltransferase in the extension module with methyl- or ethylmalonyl-coenzyme A-specific acyltransferase enables the production of branched-chain diols, amino alcohols and carboxylic acids in high titres. Use of our PKS platform in Streptomyces albus demonstrated the high tunability and efficiency of the platform.
... PQQ acts as a redox cofactor in alcohol or glucose dehydrogenase reactions in many Gram-negative bacteria. The addition of PQQ or the introduction of the pqq gene cluster has been shown to effectively enhance polyketides production [40]. Subsequently, an attempt was performed to add PQQ at various concentrations (0.04 μM, 28 μM, and 280 μM) at the early stage of fermentation (20 h). ...
... This regulator likely balances cellular growth with product synthesis (Wu et al., 2021). Additionally, maintaining balanced levels of cofactors such as NADPH is vital for the production of isoprene (Liu et al., 2019a) and polyketides (Wang et al., 2024), both of which are integral components of numerous quinones. ...
Pigments, as coloured secondary metabolites, endow the world with a rich palette of colours. They primarily originate from plants and microorganisms and play crucial roles in their survival and adaptation processes. In this article, we categorize pigments based on their chemical structure into flavonoids, carotenoids, pyrroles, quinones, azaphilones, melanins, betalains, flavins, and others. We further meticulously describe the colours, sources, and biosynthetic pathways, including key enzymatic steps and regulatory networks that control pigment production, in both plants and microorganisms. In particular, we highlight the role of transport proteins and transcription factors in fine‐tuning these pathways. Finally, we introduce the use of pigments in practical production and research, aiming to provide new insights and directions for the application of coloured compounds in diverse fields, such as agriculture, industry, and medicine.
... Beyond dereplication, StreptomeDB has been instrumental in metabolite annotation. For instance, Wang et al. ( 14 ) employed Strep-tomeDB NPs to confirm the identities of metabolites whose production increased following the integration of the pyrroloquinoline quinone BGC into various Streptomyces strains. Additionally, StreptomeDB has been used for structure-based virtual screening. ...
Streptomycetes remain an important bacterial source of natural products (NPs) with significant therapeutic promise, particularly in the fight against antimicrobial resistance. Herein, we present StreptomeDB 4.0, a substantial update of the database that includes expanded content and several new features. Currently, StreptomeDB 4.0 contains over 8500 NPs originating from ∼3900 streptomycetes, manually annotated from ∼7600 PubMed-indexed peer-reviewed articles. The database was enhanced by two in-house developments: (i) automated literature-mined NP-protein relationships (hyperlinked to the CPRiL web server) and (ii) pharmacophore-based NP-protein interactions (predicted with the ePharmaLib dataset). Moreover, genome mining was supplemented through hyperlinks to the widely used antiSMASH database. To facilitate NP structural dereplication, interactive visualization tools were implemented, namely the JSpecView applet and plotly.js charting library for predicted nuclear magnetic resonance and mass spectrometry spectral data, respectively. Furthermore, both the backend database and the frontend web interface were redesigned, and several software packages, including PostgreSQL and Django, were updated to the latest versions. Overall, this comprehensive database serves as a vital resource for researchers seeking to delve into the metabolic intricacies of streptomycetes and discover novel therapeutics, notably antimicrobial agents. StreptomeDB is publicly accessible at https://www.pharmbioinf.uni-freiburg.de/streptomedb.
... Combined with rational bioinformatics design, engineering modifications can lead to more intelligent and diversified directions. For example, Wang et al. performed pan-genome analysis on Streptomyces, discovering the pqq gene co-evolving with polyketide BGCs, which enhanced the production of at least 16,385 metabolites and activated many unknown BGCs [161]. ...
... By utilizing elicitor screening and imaging mass spectrometry under approximately 500 conditions, this approach revealed novel secondary metabolites from bacteria, including the discovery of nine cryptic metabolites with potential therapeutic bioactivities, such as a new glycopeptide chemotype with potent antiviral properties. Another study demonstrated the identification of genes co-evolved with BGCs in Streptomyces strains through phylogenomic analysis (Wang et al. 2024). Engineering the pyrroloquinoline quinone gene cluster into multiple strains resulted in significant enhancements in metabolite production, including known natural products and activated silent BGCs, thereby showcasing a novel and universal strategy to boost polyketide productivity. ...
Extreme environments such as hyperarid, hypersaline, hyperthermal environments, and the deep sea harbor diverse microbial communities, which are specially adapted to extreme conditions and are known as extremophiles. These extremophilic organisms have developed unique survival strategies, making them ideal models for studying microbial diversity, evolution, and adaptation to adversity. They also play critical roles in biogeochemical cycles. Additionally, extremophiles often produce novel bioactive compounds in response to corresponding challenging environments. Recent advances in technologies, including genomic sequencing and untargeted metabolomic analysis, have significantly enhanced our understanding of microbial diversity, ecology, evolution, and the genetic and physiological characteristics in extremophiles. The integration of advanced multi-omics technologies into culture-dependent research has notably improved the efficiency, providing valuable insights into the physiological functions and biosynthetic capacities of extremophiles. The vast untapped microbial resources in extreme environments present substantial opportunities for discovering novel natural products and advancing our knowledge of microbial ecology and evolution. This review highlights the current research status on extremophilic microbiomes, focusing on microbial diversity, ecological roles, isolation and cultivation strategies, and the exploration of their biosynthetic potential. Moreover, we emphasize the importance and potential of discovering more strain resources and metabolites, which would be boosted greatly by harnessing the power of multi-omics data.
... Nevertheless, it appears plausible to leverage F 420 -dependent enzymes to explore their potential in identifying secondary metabolites from similar or related classes of natural products. A recent study highlighted the significance of such an approach, wherein the production of the redox cofactor pyrroloquinoline quinone [58] in several Streptomyces strains resulted in enhanced production of natural products, as well as the activation of dormant BGCs [59]. ...
... Extensive genomic studies and atlas analyses of biosynthetic gene clusters have revealed that certain bacterial and fungal taxa are more adept than others at producing a diverse array of natural products, hinting at the existence of productivity-related key genes. 4 ...
Encoded within many microbial genomes, biosynthetic gene clusters (BGCs) underlie the synthesis of various secondary metabolites that often mediate ecologically important functions. Several studies and bioinformatics methods developed over the past decade have advanced our understanding of both microbial pangenomes and BGC evolution. In this minireview, we first highlight challenges in broad evolutionary analysis of BGCs, including delineation of BGC boundaries and clustering of BGCs across genomes. We further summarize key findings from microbial comparative genomics studies on BGC conservation across taxa and habitats and discuss the potential fitness effects of BGCs in different settings. Afterward, recent research showing the importance of genomic context on the production of secondary metabolites and the evolution of BGCs is highlighted. These studies draw parallels to recent, broader, investigations on gene-to-gene associations within microbial pangenomes. Finally, we describe mechanisms by which microbial pangenomes and BGCs evolve, ranging from the acquisition or origination of entire BGCs to micro-evolutionary trends of individual biosynthetic genes. An outlook on how expansions in the biosynthetic capabilities of some taxa might support theories that open pangenomes are the result of adaptive evolution is also discussed. We conclude with remarks about how future work leveraging longitudinal metagenomics across diverse ecosystems is likely to significantly improve our understanding on the evolution of microbial genomes and BGCs.
