The Experts below are selected from a list of 258 Experts worldwide ranked by ideXlab platform
Mohammad R. Seyedsayamdost - One of the best experts on this subject based on the ideXlab platform.
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Reporter‐Guided Transposon Mutant Selection for Activation of Silent Gene Clusters in Burkholderia thailandensis
Chembiochem : a European journal of chemical biology, 2020Co-Authors: Dainan Mao, Aya Yoshimura, Rurun Wang, Mohammad R. SeyedsayamdostAbstract:Most natural product biosynthetic Gene clusters that can be observed bioinformatically are Silent. This insight has prompted the development of several methodologies for inducing their expression. One of the more recent methods, termed reporter-guided mutant selection (RGMS), entails creation of a library of mutants that is then screened for the desired phenotype via reporter Gene expression. Herein, we apply a similar approach to Burkholderia thailandensis and, using transposon mutaGenesis, mutagenize three strains, each carrying a fluorescent reporter in the malleilactone (mal), capistruin (cap), or an unidentified ribosomal peptide (tomm) Gene cluster. We show that even a small library of
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reporter guided transposon mutant selection for activation of Silent Gene clusters in burkholderia thailandensis
ChemBioChem, 2020Co-Authors: Dainan Mao, Aya Yoshimura, Rurun Wang, Mohammad R. SeyedsayamdostAbstract:Most natural product biosynthetic Gene clusters that can be observed bioinformatically are Silent. This insight has prompted the development of several methodologies for inducing their expression. One of the more recent methods, termed reporter-guided mutant selection (RGMS), entails creation of a library of mutants that is then screened for the desired phenotype via reporter Gene expression. Herein, we apply a similar approach to Burkholderia thailandensis and, using transposon mutaGenesis, mutagenize three strains, each carrying a fluorescent reporter in the malleilactone (mal), capistruin (cap), or an unidentified ribosomal peptide (tomm) Gene cluster. We show that even a small library of <500 mutants can be used to induce expression of each cluster. We also explore the mechanism of activation and find that inhibition of pyrimidine biosynthesis is linked to the induction of the mal cluster. Both a transposon insertion into pyrF as well as small-molecule-mediated inhibition of PyrF trigger malleilactone biosynthesis. Our results pave the way toward the broad application of RGMS and related approaches to Burkholderia spp.
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recent advances in activating Silent biosynthetic Gene clusters in bacteria
Current Opinion in Microbiology, 2018Co-Authors: Dainan Mao, Bethany K. Okada, Mohammad R. SeyedsayamdostAbstract:The explosion of microbial genome sequences has shown that bacteria harbor an immense, largely untapped potential for the biosynthesis of diverse natural products, which have traditionally served as an important source of pharmaceutical compounds. Most of the biosynthetic Genes that can be detected bioinformatically are not, or only weakly, expressed under standard laboratory growth conditions. Herein we review three recent approaches that have been developed for inducing these so-called Silent biosynthetic Gene cluster: insertion of constitutively active promoters using CRISPR-Cas9, high-throughput elicitor screening for identification of small molecule inducers, and reporter-guided mutant selection for creation of overproducing strains. Together with strategies implemented previously, these approaches promise to unleash the products of Silent Gene clusters in years to come.
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discovery of a cryptic antifungal compound from streptomyces albus j1074 using high throughput elicitor screens
Journal of the American Chemical Society, 2017Co-Authors: Behnam Nazari, Leah B. Bushin, Kyuho Moon, Mohammad R. SeyedsayamdostAbstract:An important unresolved issue in microbial secondary metabolite production is the abundance of biosynthetic Gene clusters that are not expressed under typical laboratory growth conditions. These so-called Silent or cryptic Gene clusters are sources of new natural products, but how they are silenced, and how they may be rationally activated are areas of ongoing investigation. We recently devised a chemoGenetic high-throughput screening approach (“HiTES”) to discover small molecule elicitors of Silent biosynthetic Gene clusters. This method was successfully applied to a Gram-negative bacterium; it has yet to be implemented in the prolific antibiotic-producing streptomycetes. Herein we have developed a high-throughput transcriptional assay format in Streptomyces spp. by leveraging eGFP, inserted both at a neutral site and inside the biosynthetic cluster of interest, as a read-out for secondary metabolite synthesis. Using this approach, we successfully used HiTES to activate a Silent Gene cluster in Streptomy...
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Mapping the Trimethoprim-Induced Secondary Metabolome of Burkholderia thailandensis
ACS chemical biology, 2016Co-Authors: Bethany K. Okada, Dainan Mao, Leah B. Bushin, Mohammad R. SeyedsayamdostAbstract:While bacterial genomes typically contain numerous secondary metabolite biosynthetic Gene clusters, only a small fraction of these are expressed at any given time. The remaining majority is inactive or Silent, and methods that awaken them would greatly expand our repertoire of bioactive molecules. We recently devised a new approach for identifying inducers of Silent Gene clusters and proposed that the clinical antibiotic trimethoprim acted as a global activator of secondary metabolism in Burkholderia thailandensis. Herein, we report that trimethoprim triggers the production of over 100 compounds that are not observed under standard growth conditions, thus drastically modulating the secondary metabolic output of B. thailandensis. Using MS/MS networking and NMR, we assign structures to ∼40 compounds, including a group of new molecules, which we call acybolins. With methods at hand for activation of Silent Gene clusters and rapid identification of small molecules, the hidden secondary metabolomes of bacteria can be interrogated.
Axel A Brakhage - One of the best experts on this subject based on the ideXlab platform.
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Warum Mikroorganismen Naturstoffe produzieren
BIOspektrum, 2020Co-Authors: Mario K. C. Krespach, Maria C. Stroe, Axel A BrakhageAbstract:A key role in the communication between fungi and bacteria is played by natural products. Many of their encoding Gene clusters are Silent under standard laboratory conditions. Interspecies “talk” between microorganisms represents an ecological trigger to activate such Silent Gene clusters and leads to the formation of novel natural products by the involved species. The understanding of both the activation of Silent Gene clusters and the ecological function of the produced compounds is of importance to reveal functional microbial interactions required to shape microbiomes.
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Targeted induction of a Silent fungal Gene cluster encoding the bacteria-specific germination inhibitor fumigermin.
eLife, 2020Co-Authors: Maria C. Stroe, Kirstin Scherlach, Christian Hertweck, Tina Netzker, Thomas Krüger, Vito Valiante, Axel A BrakhageAbstract:Microorganisms produce numerous secondary metabolites (SMs) with various biological activities. Many of their encoding Gene clusters are Silent under standard laboratory conditions because for their activation they need the ecological context, such as the presence of other microorganisms. The true ecological function of most SMs remains obscure, but understanding of both the activation of Silent Gene clusters and the ecological function of the produced compounds is of importance to reveal functional interactions in microbiomes. Here, we report the identification of an as-yet uncharacterized Silent Gene cluster of the fungus Aspergillus fumigatus, which is activated by the bacterium Streptomyces rapamycinicus during the bacterial-fungal interaction. The resulting natural product is the novel fungal metabolite fumigermin, the biosynthesis of which requires the polyketide synthase FgnA. Fumigermin inhibits germination of spores of the inducing S. rapamycinicus, and thus helps the fungus to defend resources in the shared habitat against a bacterial competitor.
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engineering fungal secondary metabolism a roadmap to novel compounds
Journal of Biotechnology, 2013Co-Authors: Axel A Brakhage, Daniel H ScharfAbstract:Natural products play important roles not only in the environment but also as useful compounds in various applications like in medicine or plant protection. An enormous number of such compounds have derived from microorganisms colonizing various habitats. Traditionally, new isolates of bacteria or fungi have been screened for their potential to produce biologically active compounds. In the post genomic era, however, there is a growing number of novel methods based on Genetic engineering to obtain new metabolites. In this review, we summarize the recent progress made in the development of novel promising approaches for natural product discovery in fungi using genome mining, activation of Silent Gene clusters, heterologous expression of biosynthesis Genes, exchange of enzyme modules as well as redesign of metabolic flux.
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regulation of fungal secondary metabolism
Nature Reviews Microbiology, 2013Co-Authors: Axel A BrakhageAbstract:Fungi produce a multitude of low-molecular-mass compounds known as secondary metabolites, which have roles in a range of cellular processes such as transcription, development and intercellular communication. In addition, many of these compounds now have important applications, for instance, as antibiotics or immunosuppressants. Genome mining efforts indicate that the capability of fungi to produce secondary metabolites has been substantially underestimated because many of the fungal secondary metabolite biosynthesis Gene clusters are Silent under standard cultivation conditions. In this Review, I describe our current understanding of the regulatory elements that modulate the transcription of Genes involved in secondary metabolism. I also discuss how an improved knowledge of these regulatory elements will ultimately lead to a better understanding of the physiological and ecological functions of these important compounds and will pave the way for a novel avenue to drug discovery through targeted activation of Silent Gene clusters.
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Fungal secondary metabolites - strategies to activate Silent Gene clusters.
Fungal genetics and biology : FG & B, 2010Co-Authors: Axel A Brakhage, Volker SchroeckhAbstract:Filamentous fungi produce a multitude of low molecular weight bioactive compounds. The increasing number of fungal genome sequences impressively demonstrated that their biosynthetic potential is far from being exploited. In fungi, the Genes required for the biosynthesis of a secondary metabolite are clustered. Many of these bioinformatically newly discovered secondary metabolism Gene clusters are Silent under standard laboratory conditions. Consequently, no product can be found. This review summarizes the current strategies that have been successfully applied during the last years to activate these Silent Gene clusters in filamentous fungi, especially in the genus Aspergillus. The techniques take advantage of genome mining, vary from the simple search for compounds with bioinformatically predicted physicochemical properties up to methods that exploit a probable interaction of microorganisms. Until now, the majority of successful approaches have been based on molecular biology like the Generation of Gene "knock outs", promoter exchange, overexpression of transcription factors or other pleiotropic regulators. Moreover, strategies based on epiGenetics opened a new avenue for the elucidation of the regulation of secondary metabolite formation and will certainly continue to play a significant role for the elucidation of cryptic natural products. The conditions under which a given Gene cluster is naturally expressed are largely unknown. One technique is to attempt to simulate the natural habitat by co-cultivation of microorganisms from the same ecosystem. This has already led to the activation of Silent Gene clusters and the identification of novel compounds in Aspergillus nidulans. These simulation strategies will help discover new natural products in the future, and may also provide fundamental new insights into microbial communication.
Dainan Mao - One of the best experts on this subject based on the ideXlab platform.
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Reporter‐Guided Transposon Mutant Selection for Activation of Silent Gene Clusters in Burkholderia thailandensis
Chembiochem : a European journal of chemical biology, 2020Co-Authors: Dainan Mao, Aya Yoshimura, Rurun Wang, Mohammad R. SeyedsayamdostAbstract:Most natural product biosynthetic Gene clusters that can be observed bioinformatically are Silent. This insight has prompted the development of several methodologies for inducing their expression. One of the more recent methods, termed reporter-guided mutant selection (RGMS), entails creation of a library of mutants that is then screened for the desired phenotype via reporter Gene expression. Herein, we apply a similar approach to Burkholderia thailandensis and, using transposon mutaGenesis, mutagenize three strains, each carrying a fluorescent reporter in the malleilactone (mal), capistruin (cap), or an unidentified ribosomal peptide (tomm) Gene cluster. We show that even a small library of
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reporter guided transposon mutant selection for activation of Silent Gene clusters in burkholderia thailandensis
ChemBioChem, 2020Co-Authors: Dainan Mao, Aya Yoshimura, Rurun Wang, Mohammad R. SeyedsayamdostAbstract:Most natural product biosynthetic Gene clusters that can be observed bioinformatically are Silent. This insight has prompted the development of several methodologies for inducing their expression. One of the more recent methods, termed reporter-guided mutant selection (RGMS), entails creation of a library of mutants that is then screened for the desired phenotype via reporter Gene expression. Herein, we apply a similar approach to Burkholderia thailandensis and, using transposon mutaGenesis, mutagenize three strains, each carrying a fluorescent reporter in the malleilactone (mal), capistruin (cap), or an unidentified ribosomal peptide (tomm) Gene cluster. We show that even a small library of <500 mutants can be used to induce expression of each cluster. We also explore the mechanism of activation and find that inhibition of pyrimidine biosynthesis is linked to the induction of the mal cluster. Both a transposon insertion into pyrF as well as small-molecule-mediated inhibition of PyrF trigger malleilactone biosynthesis. Our results pave the way toward the broad application of RGMS and related approaches to Burkholderia spp.
-
recent advances in activating Silent biosynthetic Gene clusters in bacteria
Current Opinion in Microbiology, 2018Co-Authors: Dainan Mao, Bethany K. Okada, Mohammad R. SeyedsayamdostAbstract:The explosion of microbial genome sequences has shown that bacteria harbor an immense, largely untapped potential for the biosynthesis of diverse natural products, which have traditionally served as an important source of pharmaceutical compounds. Most of the biosynthetic Genes that can be detected bioinformatically are not, or only weakly, expressed under standard laboratory growth conditions. Herein we review three recent approaches that have been developed for inducing these so-called Silent biosynthetic Gene cluster: insertion of constitutively active promoters using CRISPR-Cas9, high-throughput elicitor screening for identification of small molecule inducers, and reporter-guided mutant selection for creation of overproducing strains. Together with strategies implemented previously, these approaches promise to unleash the products of Silent Gene clusters in years to come.
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Mapping the Trimethoprim-Induced Secondary Metabolome of Burkholderia thailandensis
ACS chemical biology, 2016Co-Authors: Bethany K. Okada, Dainan Mao, Leah B. Bushin, Mohammad R. SeyedsayamdostAbstract:While bacterial genomes typically contain numerous secondary metabolite biosynthetic Gene clusters, only a small fraction of these are expressed at any given time. The remaining majority is inactive or Silent, and methods that awaken them would greatly expand our repertoire of bioactive molecules. We recently devised a new approach for identifying inducers of Silent Gene clusters and proposed that the clinical antibiotic trimethoprim acted as a global activator of secondary metabolism in Burkholderia thailandensis. Herein, we report that trimethoprim triggers the production of over 100 compounds that are not observed under standard growth conditions, thus drastically modulating the secondary metabolic output of B. thailandensis. Using MS/MS networking and NMR, we assign structures to ∼40 compounds, including a group of new molecules, which we call acybolins. With methods at hand for activation of Silent Gene clusters and rapid identification of small molecules, the hidden secondary metabolomes of bacteria can be interrogated.
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mapping the trimethoprim induced secondary metabolome of burkholderia thailandensis
ACS Chemical Biology, 2016Co-Authors: Bethany K. Okada, Dainan Mao, Leah B. Bushin, Mohammad R. SeyedsayamdostAbstract:While bacterial genomes typically contain numerous secondary metabolite biosynthetic Gene clusters, only a small fraction of these are expressed at any given time. The remaining majority is inactive or Silent, and methods that awaken them would greatly expand our repertoire of bioactive molecules. We recently devised a new approach for identifying inducers of Silent Gene clusters and proposed that the clinical antibiotic trimethoprim acted as a global activator of secondary metabolism in Burkholderia thailandensis. Herein, we report that trimethoprim triggers the production of over 100 compounds that are not observed under standard growth conditions, thus drastically modulating the secondary metabolic output of B. thailandensis. Using MS/MS networking and NMR, we assign structures to ∼40 compounds, including a group of new molecules, which we call acybolins. With methods at hand for activation of Silent Gene clusters and rapid identification of small molecules, the hidden secondary metabolomes of bacteria...
Bethany K. Okada - One of the best experts on this subject based on the ideXlab platform.
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recent advances in activating Silent biosynthetic Gene clusters in bacteria
Current Opinion in Microbiology, 2018Co-Authors: Dainan Mao, Bethany K. Okada, Mohammad R. SeyedsayamdostAbstract:The explosion of microbial genome sequences has shown that bacteria harbor an immense, largely untapped potential for the biosynthesis of diverse natural products, which have traditionally served as an important source of pharmaceutical compounds. Most of the biosynthetic Genes that can be detected bioinformatically are not, or only weakly, expressed under standard laboratory growth conditions. Herein we review three recent approaches that have been developed for inducing these so-called Silent biosynthetic Gene cluster: insertion of constitutively active promoters using CRISPR-Cas9, high-throughput elicitor screening for identification of small molecule inducers, and reporter-guided mutant selection for creation of overproducing strains. Together with strategies implemented previously, these approaches promise to unleash the products of Silent Gene clusters in years to come.
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Mapping the Trimethoprim-Induced Secondary Metabolome of Burkholderia thailandensis
ACS chemical biology, 2016Co-Authors: Bethany K. Okada, Dainan Mao, Leah B. Bushin, Mohammad R. SeyedsayamdostAbstract:While bacterial genomes typically contain numerous secondary metabolite biosynthetic Gene clusters, only a small fraction of these are expressed at any given time. The remaining majority is inactive or Silent, and methods that awaken them would greatly expand our repertoire of bioactive molecules. We recently devised a new approach for identifying inducers of Silent Gene clusters and proposed that the clinical antibiotic trimethoprim acted as a global activator of secondary metabolism in Burkholderia thailandensis. Herein, we report that trimethoprim triggers the production of over 100 compounds that are not observed under standard growth conditions, thus drastically modulating the secondary metabolic output of B. thailandensis. Using MS/MS networking and NMR, we assign structures to ∼40 compounds, including a group of new molecules, which we call acybolins. With methods at hand for activation of Silent Gene clusters and rapid identification of small molecules, the hidden secondary metabolomes of bacteria can be interrogated.
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mapping the trimethoprim induced secondary metabolome of burkholderia thailandensis
ACS Chemical Biology, 2016Co-Authors: Bethany K. Okada, Dainan Mao, Leah B. Bushin, Mohammad R. SeyedsayamdostAbstract:While bacterial genomes typically contain numerous secondary metabolite biosynthetic Gene clusters, only a small fraction of these are expressed at any given time. The remaining majority is inactive or Silent, and methods that awaken them would greatly expand our repertoire of bioactive molecules. We recently devised a new approach for identifying inducers of Silent Gene clusters and proposed that the clinical antibiotic trimethoprim acted as a global activator of secondary metabolism in Burkholderia thailandensis. Herein, we report that trimethoprim triggers the production of over 100 compounds that are not observed under standard growth conditions, thus drastically modulating the secondary metabolic output of B. thailandensis. Using MS/MS networking and NMR, we assign structures to ∼40 compounds, including a group of new molecules, which we call acybolins. With methods at hand for activation of Silent Gene clusters and rapid identification of small molecules, the hidden secondary metabolomes of bacteria...
Leah B. Bushin - One of the best experts on this subject based on the ideXlab platform.
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discovery of a cryptic antifungal compound from streptomyces albus j1074 using high throughput elicitor screens
Journal of the American Chemical Society, 2017Co-Authors: Behnam Nazari, Leah B. Bushin, Kyuho Moon, Mohammad R. SeyedsayamdostAbstract:An important unresolved issue in microbial secondary metabolite production is the abundance of biosynthetic Gene clusters that are not expressed under typical laboratory growth conditions. These so-called Silent or cryptic Gene clusters are sources of new natural products, but how they are silenced, and how they may be rationally activated are areas of ongoing investigation. We recently devised a chemoGenetic high-throughput screening approach (“HiTES”) to discover small molecule elicitors of Silent biosynthetic Gene clusters. This method was successfully applied to a Gram-negative bacterium; it has yet to be implemented in the prolific antibiotic-producing streptomycetes. Herein we have developed a high-throughput transcriptional assay format in Streptomyces spp. by leveraging eGFP, inserted both at a neutral site and inside the biosynthetic cluster of interest, as a read-out for secondary metabolite synthesis. Using this approach, we successfully used HiTES to activate a Silent Gene cluster in Streptomy...
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Mapping the Trimethoprim-Induced Secondary Metabolome of Burkholderia thailandensis
ACS chemical biology, 2016Co-Authors: Bethany K. Okada, Dainan Mao, Leah B. Bushin, Mohammad R. SeyedsayamdostAbstract:While bacterial genomes typically contain numerous secondary metabolite biosynthetic Gene clusters, only a small fraction of these are expressed at any given time. The remaining majority is inactive or Silent, and methods that awaken them would greatly expand our repertoire of bioactive molecules. We recently devised a new approach for identifying inducers of Silent Gene clusters and proposed that the clinical antibiotic trimethoprim acted as a global activator of secondary metabolism in Burkholderia thailandensis. Herein, we report that trimethoprim triggers the production of over 100 compounds that are not observed under standard growth conditions, thus drastically modulating the secondary metabolic output of B. thailandensis. Using MS/MS networking and NMR, we assign structures to ∼40 compounds, including a group of new molecules, which we call acybolins. With methods at hand for activation of Silent Gene clusters and rapid identification of small molecules, the hidden secondary metabolomes of bacteria can be interrogated.
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mapping the trimethoprim induced secondary metabolome of burkholderia thailandensis
ACS Chemical Biology, 2016Co-Authors: Bethany K. Okada, Dainan Mao, Leah B. Bushin, Mohammad R. SeyedsayamdostAbstract:While bacterial genomes typically contain numerous secondary metabolite biosynthetic Gene clusters, only a small fraction of these are expressed at any given time. The remaining majority is inactive or Silent, and methods that awaken them would greatly expand our repertoire of bioactive molecules. We recently devised a new approach for identifying inducers of Silent Gene clusters and proposed that the clinical antibiotic trimethoprim acted as a global activator of secondary metabolism in Burkholderia thailandensis. Herein, we report that trimethoprim triggers the production of over 100 compounds that are not observed under standard growth conditions, thus drastically modulating the secondary metabolic output of B. thailandensis. Using MS/MS networking and NMR, we assign structures to ∼40 compounds, including a group of new molecules, which we call acybolins. With methods at hand for activation of Silent Gene clusters and rapid identification of small molecules, the hidden secondary metabolomes of bacteria...
