Induction of secondary metabolite production by hygromycin B and identification of the 1233A biosynthetic gene cluster with a self-resistance gene

ABSTRACT Recent advances in genome sequencing have revealed a variety of secondary metabolite biosynthetic gene clusters in actinomycetes. Understanding the biosynthetic mechanism controlling secondary metabolite production is important for utilizing these gene clusters. In this study, we focused on the kinanthraquinone biosynthetic gene cluster, which has not been identified yet in Streptomyces sp. SN-593. Based on chemical structure, 5 type II polyketide synthase gene clusters were listed from the genome sequence of Streptomyces sp. SN-593. Among them, a candidate gene cluster was selected by comparing the gene organization with grincamycin, which is synthesized through an intermediate similar to kinanthraquinone. We initially utilized a BAC library for subcloning the kiq gene cluster, performed heterologous expression in Streptomyces lividans TK23, and identified the production of kinanthraquinone and kinanthraquinone B. We also found that heterologous expression of kiqA, which belongs to the DNA-binding response regulator OmpR family, dramatically enhanced the production of kinanthraquinones.

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Bioactive Molecules from Mangrove Streptomyces qinglanensis 172205

Marine Drugs ◽

10.3390/md18050255 ◽

2020 ◽

Vol 18 (5) ◽

pp. 255

Author(s):

Dongbo Xu ◽

Erli Tian ◽

Fandong Kong ◽

Kui Hong

Keyword(s):

Gene Cluster ◽

Secondary Metabolite ◽

Biosynthetic Gene Cluster ◽

Bioactive Molecules ◽

Spectroscopic Methods ◽

Biosynthetic Gene ◽

Electronic Circular Dichroism ◽

Chemical Structures ◽

New Compounds ◽

Antiproliferative Activities

Five new compounds 15R-17,18-dehydroxantholipin (1), (3E,5E,7E)-3-methyldeca-3,5,7-triene-2,9-dione (2) and qinlactone A–C (3–5) were identified from mangrove Streptomyces qinglanensis 172205 with “genetic dereplication,” which deleted the highly expressed secondary metabolite-enterocin biosynthetic gene cluster. The chemical structures were established by spectroscopic methods, and the absolute configurations were determined by electronic circular dichroism (ECD). Compound 1 exhibited strong anti-microbial and antiproliferative bioactivities, while compounds 2–4 showed weak antiproliferative activities.

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Identification of the Biosynthetic Gene Cluster and an Additional Gene for Resistance to the Antituberculosis Drug Capreomycin

Applied and Environmental Microbiology ◽

10.1128/aem.00485-07 ◽

2007 ◽

Vol 73 (13) ◽

pp. 4162-4170 ◽

Cited By ~ 58

Author(s):

Elizabeth A. Felnagle ◽

Michelle R. Rondon ◽

Andrew D. Berti ◽

Heidi A. Crosby ◽

Michael G. Thomas

Keyword(s):

Gene Cluster ◽

Resistance Gene ◽

Aminoglycoside Antibiotic ◽

Biosynthetic Gene Cluster ◽

Multidrug Resistant ◽

23S Rrna ◽

Peptide Antibiotics ◽

Biosynthetic Gene ◽

Essential Components ◽

Initial Work

ABSTRACT Capreomycin (CMN) belongs to the tuberactinomycin family of nonribosomal peptide antibiotics that are essential components of the drug arsenal for the treatment of multidrug-resistant tuberculosis. Members of this antibiotic family target the ribosomes of sensitive bacteria and disrupt the function of both subunits of the ribosome. Resistance to these antibiotics in Mycobacterium species arises due to mutations in the genes coding for the 16S or 23S rRNA but can also arise due to mutations in a gene coding for an rRNA-modifying enzyme, TlyA. While Mycobacterium species develop resistance due to alterations in the drug target, it has been proposed that the CMN-producing bacterium, Saccharothrix mutabilis subsp. capreolus, uses CMN modification as a mechanism for resistance rather than ribosome modification. To better understand CMN biosynthesis and resistance in S. mutabilis subsp. capreolus, we focused on the identification of the CMN biosynthetic gene cluster in this bacterium. Here, we describe the cloning and sequence analysis of the CMN biosynthetic gene cluster from S. mutabilis subsp. capreolus ATCC 23892. We provide evidence for the heterologous production of CMN in the genetically tractable bacterium Streptomyces lividans 1326. Finally, we present data supporting the existence of an additional CMN resistance gene. Initial work suggests that this resistance gene codes for an rRNA-modifying enzyme that results in the formation of CMN-resistant ribosomes that are also resistant to the aminoglycoside antibiotic kanamycin. Thus, S. mutabilis subsp. capreolus may also use ribosome modification as a mechanism for CMN resistance.

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Comparative genomics uncovers genetic diversity and synthetic biology of secondary metabolite production of the genus Trametes

10.21203/rs.2.11205/v1 ◽

2019 ◽

Author(s):

Yan Zhang ◽

Jie Cao ◽

Jingjing Wang ◽

Yajun Cheng ◽

Minghui Zhou ◽

...

Keyword(s):

Genetic Diversity ◽

Synthetic Biology ◽

Secondary Metabolite ◽

Gene Clusters ◽

Glycoside Hydrolases ◽

Secondary Metabolite Production ◽

Crystalline Cellulose ◽

Biosynthetic Gene ◽

Biosynthetic Gene Clusters ◽

Metabolite Production

Abstract It’s well-established that the CAZyme genes of genus Trametes contributed to the degradation processes of polysaccharides, including lignin or crystalline cellulose. However, the comprehensive analysis of the composition of CAZymes and the biosynthetic gene clusters of Trametes genus remain unclear. We conducted comparative analysis, detected the CAZyme genes, and predicted the biosynthetic gene clusters for 9 Trametes strains. Among 82,053 homologous clusters we obtained for genus Trametes, we identified 8,518 core genes, 60,441 accessory genes and 13,094 specific genes. Our results showed that a large proportion of CAZyme genes were catalogued into glycoside hydrolases, glycosyltransferases, and carbohydrate esterases. The predicted BGCs of Trametes genus were divided into 6 strategies and the 9 Trametes strains harbored 47.78 BGCs on average. Our study uncovers the genus Trametes exhibited an open pan-genome structure, provides insights into the genetic diversity and explores the synthetic biology of secondary metabolite production for Trametes genus.

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Transcription Factor Repurposing Offers Insights into Evolution of Biosynthetic Gene Cluster Regulation

mBio ◽

10.1128/mbio.01399-21 ◽

2021 ◽

Author(s):

Wenjie Wang ◽

Milton Drott ◽

Claudio Greco ◽

Dianiris Luciano-Rosario ◽

Pinmei Wang ◽

...

Keyword(s):

Transcription Factor ◽

Secondary Metabolites ◽

Gene Cluster ◽

Gene Clusters ◽

Biosynthetic Gene Cluster ◽

The Other ◽

Biosynthetic Gene ◽

Biosynthetic Gene Clusters ◽

Metabolite Production ◽

Fungal Secondary Metabolites

Fungal secondary metabolites (SMs) are an important source of pharmaceuticals on one hand and toxins on the other. Efforts to identify the biosynthetic gene clusters (BGCs) that synthesize SMs have yielded significant insights into how variation in the genes that compose BGCs may impact subsequent metabolite production within and between species.

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Biosynthetic Gene Cluster Analysis in Micromonospora Species Using ANTISMASH: Secondary Metabolite Genome Mining Pipeline

Methods in Actinobacteriology - Springer Protocols Handbooks ◽

10.1007/978-1-0716-1728-1_32 ◽

2022 ◽

pp. 237-245

Author(s):

Mukesh Kumar Manickasamy ◽

Rajagopal Narayanan ◽

Dhanasekaran Dharmadurai

Keyword(s):

Cluster Analysis ◽

Gene Cluster ◽

Secondary Metabolite ◽

Genome Mining ◽

Biosynthetic Gene Cluster ◽

Biosynthetic Gene

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Boosting Secondary Metabolite Production and Discovery through the Engineering of Novel Microbial Biosensors

BioMed Research International ◽

10.1155/2018/7021826 ◽

2018 ◽

Vol 2018 ◽

pp. 1-11 ◽

Cited By ~ 6

Author(s):

Ulysses Amancio de Frias ◽

Greicy Kelly Bonifacio Pereira ◽

María-Eugenia Guazzaroni ◽

Rafael Silva-Rocha

Keyword(s):

Secondary Metabolites ◽

Secondary Metabolite ◽

Gene Clusters ◽

Secondary Metabolite Production ◽

Special Focus ◽

Biosynthetic Gene ◽

Expression Systems ◽

Biosynthetic Gene Clusters ◽

Metabolite Production ◽

Synthetic Promoters

Bacteria are a source of a large number of secondary metabolites with several biomedical and biotechnological applications. In recent years, there has been tremendous progress in the development of novel synthetic biology approaches both to increase the production rate of secondary metabolites of interest in native producers and to mine and reconstruct novel biosynthetic gene clusters in heterologous hosts. Here, we present the recent advances toward the engineering of novel microbial biosensors to detect the synthesis of secondary metabolites in bacteria and in the development of synthetic promoters and expression systems aiming at the construction of microbial cell factories for the production of these compounds. We place special focus on the potential of Gram-negative bacteria as a source of biosynthetic gene clusters and hosts for pathway assembly, on the construction and characterization of novel promoters for native hosts, and on the use of computer-aided design of novel pathways and expression systems for secondary metabolite production. Finally, we discuss some of the potentials and limitations of the approaches that are currently being developed and we highlight new directions that could be addressed in the field.

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Comparative Genomics Determines Strain-Dependent Secondary Metabolite Production in Streptomyces venezuelae Strains

Biomolecules ◽

10.3390/biom10060864 ◽

2020 ◽

Vol 10 (6) ◽

pp. 864

Author(s):

Woori Kim ◽

Namil Lee ◽

Soonkyu Hwang ◽

Yongjae Lee ◽

Jihun Kim ◽

...

Keyword(s):

Secondary Metabolites ◽

Secondary Metabolite ◽

Gene Clusters ◽

Secondary Metabolite Production ◽

Biosynthetic Gene ◽

Genome Sequences ◽

Biosynthetic Gene Clusters ◽

Streptomyces Venezuelae ◽

Metabolite Production ◽

Non Coding Rna

Streptomyces venezuelae is well known to produce various secondary metabolites, including chloramphenicol, jadomycin, and pikromycin. Although many strains have been classified as S. venezuelae species, only a limited number of strains have been explored extensively for their genomic contents. Moreover, genomic differences and diversity in secondary metabolite production between the strains have never been compared. Here, we report complete genome sequences of three S. venezuelae strains (ATCC 10712, ATCC 10595, and ATCC 21113) harboring chloramphenicol and jadomycin biosynthetic gene clusters (BGC). With these high-quality genome sequences, we revealed that the three strains share more than 85% of total genes and most of the secondary metabolite biosynthetic gene clusters (smBGC). Despite such conservation, the strains produced different amounts of chloramphenicol and jadomycin, indicating differential regulation of secondary metabolite production at the strain level. Interestingly, antagonistic production of chloramphenicol and jadomycin was observed in these strains. Through comparison of the chloramphenicol and jadomycin BGCs among the three strains, we found sequence variations in many genes, the non-coding RNA coding regions, and binding sites of regulators, which affect the production of the secondary metabolites. We anticipate that these genome sequences of closely related strains would serve as useful resources for understanding the complex secondary metabolism and for designing an optimal production process using Streptomyces strains.

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Identification of polyketide biosynthetic gene clusters that harbor self-resistance target genes

10.1101/2020.06.01.128595 ◽

2020 ◽

Author(s):

Gergana A Vandova ◽

Aleksandra Nivina ◽

Chaitan Khosla ◽

Ronald W Davis ◽

Curt R Fisher ◽

...

Keyword(s):

Gene Cluster ◽

Resistance Gene ◽

Resistance Genes ◽

Gene Clusters ◽

Biosynthetic Gene Cluster ◽

The Self ◽

Biosynthetic Gene ◽

Biosynthetic Gene Clusters ◽

Automated Method ◽

Novel Antibiotics

AbstractBackgroundPolyketide secondary metabolites have been a rich source of antibiotic discovery for decades. Thousands of novel polyketide synthase (PKS) gene clusters have been identified in recent years with advances in DNA sequencing. However, experimental characterization of novel and useful PKS activities remains complicated. As a result, computational tools to analyze sequence data are essential to identify and prioritize potentially novel PKS activities. Here we exploit the concept of genetically-encoded self-resistance to identify and rank biosynthetic gene clusters for their potential to encode novel antibiotics.ResultsTo identify PKS genes that are likely to produce an antibacterial compound, we developed an automated method to identify and catalog clusters that harbor potential self-resistance genes. We manually curated a list of known self-resistance genes and searched all NCBI genome databases for homologs of these self-resistance genes in biosynthetic gene clusters. The algorithm takes into account (1) the distance of the potential self-resistance gene to a core enzyme in the biosynthetic gene cluster; (2) the presence of a duplicated housekeeping copy of the self-resistance gene; (3) the presence of close homologs of the biosynthetic gene cluster in diverse species also harboring the putative self-resistance gene; (4) evidence for coevolution of the self-resistance gene and core biosynthetic gene; and (5) self-resistance gene ubiquity. We generated a catalog of 190 unique PKS clusters whose products likely target known enzymes of antibacterial importance. We also present an expanded set of putative self-resistance genes that may be useful in identifying small molecules active against novel microbial targets.ConclusionsWe developed a bioinformatic approach to identify and rank biosynthetic gene clusters that likely harbor self-resistance genes and may produce compounds with antibacterial properties. We compiled a list of putative self-resistance genes for novel antibacterial targets, and of orphan PKS clusters harboring these targets. These catalogues are a resource for discovery of novel antibiotics.

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Heterologous Expression of the Unusual Terreazepine Biosynthetic Gene Cluster Reveals a Promising Approach for Identifying New Chemical Scaffolds

mBio ◽

10.1128/mbio.01691-20 ◽

2020 ◽

Vol 11 (4) ◽

Cited By ~ 2

Author(s):

Lindsay K. Caesar ◽

Matthew T. Robey ◽

Michael Swyers ◽

Md N. Islam ◽

Rosa Ye ◽

...

Keyword(s):

Gene Cluster ◽

Secondary Metabolite ◽

Heterologous Gene Expression ◽

Gene Clusters ◽

Biosynthetic Gene Cluster ◽

Metabolic Enzyme ◽

Biosynthetic Gene ◽

Biosynthetic Gene Clusters ◽

Artificial Chromosomes ◽

Indoleamine 2,3 Dioxygenase

ABSTRACT Advances in genome sequencing have revitalized natural product discovery efforts, revealing the untapped biosynthetic potential of fungi. While the volume of genomic data continues to expand, discovery efforts are slowed due to the time-consuming nature of experiments required to characterize new molecules. To direct efforts toward uncharacterized biosynthetic gene clusters most likely to encode novel chemical scaffolds, we took advantage of comparative metabolomics and heterologous gene expression using fungal artificial chromosomes (FACs). By linking mass spectral profiles with structural clues provided by FAC-encoded gene clusters, we targeted a compound originating from an unusual gene cluster containing an indoleamine 2,3-dioxygenase (IDO). With this approach, we isolate and characterize R and S forms of the new molecule terreazepine, which contains a novel chemical scaffold resulting from cyclization of the IDO-supplied kynurenine. The discovery of terreazepine illustrates that FAC-based approaches targeting unusual biosynthetic machinery provide a promising avenue forward for targeted discovery of novel scaffolds and their biosynthetic enzymes, and it also represents another example of a biosynthetic gene cluster “repurposing” a primary metabolic enzyme to diversify its secondary metabolite arsenal. IMPORTANCE Here, we provide evidence that Aspergillus terreus encodes a biosynthetic gene cluster containing a repurposed indoleamine 2,3-dioxygenase (IDO) dedicated to secondary metabolite synthesis. The discovery of this neofunctionalized IDO not only enabled discovery of a new compound with an unusual chemical scaffold but also provided insight into the numerous strategies fungi employ for diversifying and protecting themselves against secondary metabolites. The observations in this study set the stage for further in-depth studies into the function of duplicated IDOs present in fungal biosynthetic gene clusters and presents a strategy for accessing the biosynthetic potential of gene clusters containing duplicated primary metabolic genes.

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