Biosynthetic Cluster Research Articles

Molecular Biodiversity in Fusarium subglutinans and F. temperatum: A Valuable Tool to Distinguish the Two Sister Species and Determine the Beauvericin Chemotype

Fusarium subglutinans and F. temperatum are widely distributed maize pathogens recognized as distinct species with a species-specific chemotype based on patterns of mycotoxins. Recent comparative genomic analysis revealed that genomes of both species carry a complete beauvericin (Bea) biosynthetic genes cluster, but the key gene Bea1 in F. subglutinans is not functional likely due to a large insertion (NRPS22ins) and multiple mutations (SNP298 and SNP528). We used the recently published genome sequences for these species to develop PCR markers for investigating the distribution of three main mutations in the Bea1 gene in a large collection of strains of both species from around the world. We also designed a PCR assay for a rapid and reliable discrimination of both species in the evaluation of crop exposure to mycotoxins. Overall, our results showed that SNP528 was the most common mutation, followed by NRPS22ins and SNP298. Moreover, phylogenetic analyses suggest that non-synonymous SNPs have occurred first, and that the resulting inactivation of BEA production has caused the accumulation of other polymorphisms, including the NRPS22ins, in the entire gene-coding region. The screening for genetic differences between these species could guide future crop management strategies.

PePalA/B/C are required for virulence and patulin biosynthesis by regulating the PePacC-processing proteolytic activity in Penicillium expansum

Abstract Background The Pal/Rim signaling pathway is crucial for fungal responses to ambient pH conditions. It comprises the transcription factor PacC/Rim101 and six upstream Pal proteins. While the role of PacC has been extensively studied, there is limited information on the functions of the upstream Pal proteins. Results In the genome of Penicillium expansum, genes encoding the endosomal membrane complex (PalA/B/C) were identified. Among these, only the expression of PePalB, not PePalA or PePalC, is pH-dependent. Subcellular localization and functional analyses showed that PePalA/B/C are localized to the cytosol and peripheral punctate structures. Deletion of PePalA/B/C resulted in reduced growth and conidiation of P. expansum across various pH conditions. The virulence of the ΔPePalA/B/C mutant was significantly reduced in pear and apple fruits. Additionally, the mutants exhibited a loss of patulin production under both acidic and alkaline conditions and the down-regulation of genes in the patulin biosynthetic cluster. pH shift experiments further demonstrated that PePalA/B/C are essential for both the PePacC expression and the pH-dependent proteolytic activation of PePacC. Conclusions These findings highlight the significant roles of PePalA/B/C in regulating growth, conidiation, virulence, and patulin production in P. expansum, thereby enhancing our understanding of the regulatory mechanisms underlying the Pal/Rim signaling pathway.

Phenazines are involved in the antagonism of a novel subspecies of Pseudomonas chlororaphis strain S1Bt23 against Pythium ultimum

Long-term use of chemical fungicides to control plant diseases caused by fungi and oomycetes has led to pathogen resistance and negative impacts on public health and environment. There is a global search for eco-friendly methods and antagonistic bacteria are emerging as alternatives. We isolated a potent antagonistic bacterial strain (S1Bt23) from woodland soil in Québec, Canada. Taxonomic characterization by 16S rRNA, multi-locus sequence analysis, pairwise whole-genome comparisons, phylogenomics and phenotypic data identified strain S1Bt23 as a novel subspecies within Pseudomonas chlororaphis. In dual culture studies, strain S1Bt23 exhibited potent mycelial growth inhibition (60.2–66.7%) against Pythium ultimum. Furthermore, strain S1Bt23 was able to significantly bioprotect potato tuber slices from the development of necrosis inducible by P. ultimum. Annotations of the whole genome sequence of S1Bt23 revealed the presence of an arsenal of secondary metabolites including the complete phenazine biosynthetic cluster (phzABCDEFG). Thin-layer (TLC) and high-performance liquid (HPLC) chromatographic analyses of S1Bt23 extracts confirmed the production of phenazines, potent antifungal compounds. CRISPR/Cas9-mediated deletion of phzB (S1Bt23ΔphzB) or phzF (S1Bt23ΔphzF) gene abrogated phenazine production based on TLC and HPLC analyses. Also, S1Bt23ΔphzB and S1Bt23ΔphzF mutants lost antagonistic activity and bioprotection ability of potato tubers against P. ultimum. This demonstrated that phenazines are involved in the antagonistic activity of S1Bt23 against P. ultimum. Finally, based on genotypic and phenotypic data, we taxonomically conclude that S1Bt23 represents a novel subspecies for which the name Pseudomonas chlororaphis subsp. phenazini is proposed.

The tropical marine actinomycete Nocardiopsis dassonvillei NCIM 5124 as novel source of ectoine: Genomic and transcriptomic insights

Since ectoine is a high-value product, overviewing strategies for identifying novel microbial sources becomes relevant. In the current study, by following a genome mining approach, the ectoine biosynthetic cluster in a tropical marine strain of Nocardiopsis dassonvillei (NCIM 5124) was located and compared with related organisms. Transcriptome analysis of Control and Test samples (with 0 and 5% NaCl, respectively) was carried out to understand salt induced stress response at the molecular level. There were 4950 differentially expressed genes with 25 transcripts being significantly upregulated in Test samples. NaCl induced upregulation of the ectoine biosynthesis cluster and some other genes (stress response, chaperone/Clp protease, cytoplasm, ribonucleoprotein and protein biosynthesis). The production of ectoine as a stress response molecule was experimentally validated via LCMS analysis. The investigation sheds light on the responses exhibited by this actinomycete in coping up with salt stress and provides a foundation for understanding salt induced molecular interactions.

TetR family regulator AbrT controls lincomycin production and morphological development in Streptomyces lincolnensis

BackgroundThe TetR family of transcriptional regulators (TFRs), serving as crucial regulators of diverse cellular processes, undergo conformational changes induced by small-molecule ligands, which either inhibit or activate them to modulate target gene expression. Some ligands of TFRs in actinomycetes and their regulatory effects have been identified and studied; however, regulatory mechanisms of the TetR family in the lincomycin-producing Streptomyces lincolnensis remain poorly understood.ResultsIn this study, we found that AbrT (SLCG_1979), a TetR family regulator, plays a pivotal role in regulating lincomycin production and morphological development in S. lincolnensis. Deletion of abrT gene resulted in increased lincomycin A (Lin-A) production, but delayed mycelium formation and sporulation on solid media. AbrT directly or indirectly repressed the expression of lincomycin biosynthetic (lin) cluster genes and activated that of the morphological developmental genes amfC, whiB, and ftsZ. We demonstrated that AbrT bound to two motifs (5′-CGCGTACTCGTA-3′ and 5′-CGTACGATAGCT-3′) present in the bidirectional promoter between abrT and SLCG_1980 genes. This consequently repressed abrT itself and its adjacent gene SLCG_1980 that encodes an arabinose efflux permease. D-arabinose, not naturally occurring as L-arabinose, was identified as the effector molecule of AbrT, reducing its binding affinity to abrT-SLCG_1980 intergenic region. Furthermore, based on functional analysis of the AbrT homologue in Saccharopolyspora erythraea, we inferred that the TetR family regulator AbrT may play an important role in regulating secondary metabolism in actinomycetes.ConclusionsAbrT functions as a regulator for governing lincomycin production and morphological development of S. lincolnensis. Our findings demonstrated that D-arabinose acts as a ligand of AbrT to mediate the regulation of lincomycin biosynthesis in S. lincolnensis. Our findings provide novel insights into ligand-mediated regulation in antibiotic biosynthesis.

Expanding the Pseudomonas diversity of the wheat rhizosphere: four novel species antagonizing fungal phytopathogens and with plant-beneficial properties.

Plant-beneficial Pseudomonas bacteria hold the potential to be used as inoculants in agriculture to promote plant growth and health through various mechanisms. The discovery of new strains tailored to specific agricultural needs remains an open area of research. In this study, we report the isolation and characterization of four novel Pseudomonas species associated with the wheat rhizosphere. Comparative genomic analysis with all available Pseudomonas type strains revealed species-level differences, substantiated by both digital DNA-DNA hybridization and average nucleotide identity, underscoring their status as novel species. This was further validated by the phenotypic differences observed when compared to their closest relatives. Three of the novel species belong to the P. fluorescens species complex, with two representing a novel lineage in the Pseudomonas phylogeny. Functional genome annotation revealed the presence of specific features contributing to rhizosphere colonization, including flagella and components for biofilm formation. The novel species have the genetic potential to solubilize nutrients by acidifying the environment, releasing alkaline phosphatases and their metabolism of nitrogen species, indicating potential as biofertilizers. Additionally, the novel species possess traits that may facilitate direct promotion of plant growth through the modulation of the plant hormone balance, including the ACC deaminase enzyme and auxin metabolism. The presence of biosynthetic clusters for toxins such as hydrogen cyanide and non-ribosomal peptides suggests their ability to compete with other microorganisms, including plant pathogens. Direct inoculation of wheat roots significantly enhanced plant growth, with two strains doubling shoot biomass. Three of the strains effectively antagonized fungal phytopathogens (Thielaviopsis basicola, Fusarium oxysporum, and Botrytis cinerea), demonstrating their potential as biocontrol agents. Based on the observed genetic and phenotypic differences from closely related species, we propose the following names for the four novel species: Pseudomonas grandcourensis sp. nov., type strain DGS24T ( = DSM 117501T = CECT 31011T), Pseudomonas purpurea sp. nov., type strain DGS26T ( = DSM 117502T = CECT 31012T), Pseudomonas helvetica sp. nov., type strain DGS28T ( = DSM 117503T = CECT 31013T) and Pseudomonas aestiva sp. nov., type strain DGS32T ( = DSM 117504T = CECT 31014T).

Unveiling Nature’s Secrets: Activating Silent Biosynthetic Genes Clusters in Fungi and Bacteria

Microorganisms such as fungi and bacteria are prosperous producers of secondary metabolites; moreover, they are home to a large number of silent biosynthetic gene clusters, but they are all poorly expressed. Thus, these resultant compounds remain cryptic or unknown. However, since these cluster products have many bioactivities, stimulating their production and gaining access to their related structures are considered a top priority. Here, we summarize the three strategies that have been the topic of current trends. Regulating of genetic investigation, heterogeneous and refactoring cluster expression, as well as elicitor and coculture screening are the strategies utilized to unlock the expression of biosynthetic gene clusters (BGCs). These all help to triggers the manufacturing of innovative metabolites having various functions.

The Utilization of Bacillus subtilis to Design Environmentally Friendly Living Paints with Anti-Mold Properties.

The anti-fungal properties of the probiotic bacterium Bacillus subtilis have been studied extensively in agriculture and ecology, but their applications in the built environment remain to be determined. Our work aims to utilize this biological component to introduce new diverse anti-mold properties into paint. "Mold" refers to the ubiquitous fungal species that generate visible multicellular filaments commonly found in household dust. The development of mold leads to severe health problems for occupants, including allergic response, hypersensitivity pneumonitis, and asthma, which have significant economic and clinical outcomes. We here demonstrate the robust effect of a commercial paint enhanced with Bacillus subtilis cells against the common mold agent, Aspergillus niger, and identify three biosynthetic clusters essential for this effect. Our results lay the foundation for bio-convergence and synthetic biology approaches to introduce renewable and environmentally friendly bio-anti-fungal agents into the built environment.

Discovery of novel cellobiose lipid gene clusters from Basidiomycetes: How chemical variation is reflected in gene cluster architecture.

Cellobiose lipids are surface-active compounds or biological detergents produced by distinct Basidiomycetes yeasts, of which the most and best-described ones belong to the Ustilaginomycetes class. The molecules display slight variation in congener type, which is linked to the hydroxylation position of the long fatty acid, acetylation profile of the cellobiose unit, and presence or absence of the short fatty acid. In general, this variation is strain specific. Although cellobiose lipid biosynthesis has been described for about 11 yeast species, hitherto only two types of biosynthetic gene clusters are identified, and this for only three species. This work adds six more biosynthetic gene clusters and describes for the first time a novel type of cellobiose lipid biosynthetic cluster with a simplified architecture related to specific cellobiose lipids synthesized by Trichosporonaceae family members.

Influence of Cluster-Situated Regulator PteF in Filipin Biosynthetic Cluster on Avermectin Biosynthesis in Streptomyces avermitilis.

Crosstalk regulation is widespread in Streptomyces species. Elucidating the influence of a specific regulator on target biosynthetic gene clusters (BGCs) and cell metabolism is crucial for strain improvement through regulatory protein engineering. PteF and PteR are two regulators that control the biosynthesis of filipin, which competes for building blocks with avermectins in Streptomyces avermitilis. However, little is known about the effects of PteF and PteR on avermectin biosynthesis. In this study, we investigated their impact on avermectin biosynthesis and global cell metabolism. The deletion of pteF resulted in a 55.49% avermectin titer improvement, which was 23.08% higher than that observed from pteR deletion, suggesting that PteF plays a more significant role in regulating avermectin biosynthesis, while PteF hardly influences the transcription level of genes in avermectin and other polyketide BGCs. Transcriptome data revealed that PteF exhibited a global regulatory effect. Avermectin production enhancement could be attributed to the repression of the tricarboxylic acid cycle and fatty acid biosynthetic pathway, as well as the enhancement of pathways supplying acyl-CoA precursors. These findings provide new insights into the role of PteF on avermectin biosynthesis and cell metabolism, offering important clues for designing and building efficient metabolic pathways to develop high-yield avermectin-producing strains.

Differential gene expression of Hymenoscyphus fraxineus grown on Fraxinus excelsior and F. mandshurica supplemented media

AbstractAsh dieback is caused by the invasive fungal species Hymenoscyphus fraxineus and leads to the loss of the common ash (Fraxineus excelsior) in many areas. In contrast, the pathogen seems to colonize the local ash species Fraxinus mandshurica (Manchurian ash) symptom-free in its native environment East Asia. In order to gain insight into the differences in the substrate dependence of the pathogen, two H. fraxineus strains (1511 and 1431) were grown in media supplemented with leave material of F. excelsior or F. mandshurica and without supplement. A total of 95 and 916 genes were upregulated in media containing F. excelsior leaf material for strain 1431, compared to F. mandshurica and media without plant supplementation. The differential expression analysis of strain 1511 revealed 483 and 875 upregulated genes. Oxidative phosphorylation is highly upregulated in strain 1431 cultivated in F. excelsior-supplemented media indicating an active metabolism but probably also linked to the release of reactive oxygen species. In both strains during growth on F. excelsior, transcripts with similarity to genes of toxin biosynthetic pathways of other Ascomycota are enriched. In strain 1511, a gene cluster with similarity to depudecin cluster is upregulated in addition. For both strains, the upregulated genes, if grown in media supplemented with leaf material from F. excelsior, include a gene of the biosynthetic cluster of phytotoxin viridiol. The results suggest increased metabolic activity and toxin production in the presence of F. excelsior tissue compared to F. mandshurica.

A myo-inositol dehydrogenase involved in aminocyclitol biosynthesis of hygromycin A.

Hygromycin A is a broad-spectrum antibiotic that contains a furanose, cinnamic acid, and aminocyclitol moieties. The biosynthesis of the aminocyclitol has been proposed to proceed through six enzymatic steps from glucose 6-phosphate through myo-inositol to the final methylenedioxy-containing aminocyclitol. Although there is some in vivo evidence for this proposed pathway, biochemical support for the individual enzyme activities is lacking. In this study, we verify the activity for one enzyme in this pathway. We show that Hyg17 is a myo-inositol dehydrogenase that has a unique substrate scope when compared to other myo-inositol dehydrogenases. Furthermore, we analyze sequences from the protein family containing Hyg17 and discuss genome mining strategies that target this protein family to identify biosynthetic clusters for natural product discovery.

Prodigiosin: An In-depth Exploration of a Bioactive Compound from Serratia sp.

Background:: The rising interest in natural pigments as alternatives is a result of the expanding usage of synthetic colorants and the negative consequences that go along with them. Noble natural pigments with higher stability and productivity are becoming popular in the food industry, and their diverse biological characteristics make them valuable for pharmaceutical applications. Microbes, especially gram-negative and positive bacteria, are considered attractive sources for replacing synthetic dyes. Prodigiosin, a tripyrrole red pigment produced as secondary metabolites by these bacteria, exhibits unusual properties and has potential as an effective proapoptotic agent against cancer and multi-drug resistant cells. Objective:: This review aims to highlight the characteristics of prodigiosin and explore its potential applications as a therapeutic drug. Results:: The review investigates the biosynthetic cluster genes of prodigiosin identified using the EZ-Tn5 transposon approach in different bacteria, including the pig gene cluster in Serratia sp., red gene cluster in S. coelicolor, and hap gene cluster in Hahella chejuensis. It is also described compound nature for producing host survival physiology. Prodigiosin has a common pyrrolyl Promethean structure and is a member of the tripyrrole family. Numerous tri-pyrrole derivatives have been used in antibiotics and have demonstrated promise as pro-apoptotic agents against cancer and drug-resistant cells. Conclusion:: Prodigiosin is an intriguing subject for investigating biosynthesis and exploitation through biotechnological methods due to its distinctive properties and potential as a medicinal medication. Future investigation and bioengineering on producing strains may synthesize functional derivatives with diverse applications.

Enhanced protein secretion in reduced genome strains of Streptomyces lividans

BackgroundS. lividans TK24 is a popular host for the production of small molecules and the secretion of heterologous protein. Within its large genome, twenty-nine non-essential clusters direct the biosynthesis of secondary metabolites. We had previously constructed ten chassis strains, carrying deletions in various combinations of specialized metabolites biosynthetic clusters, such as those of the blue actinorhodin (act), the calcium-dependent antibiotic (cda), the undecylprodigiosin (red), the coelimycin A (cpk) and the melanin (mel) clusters, as well as the genes hrdD, encoding a non-essential sigma factor, and matAB, a locus affecting mycelial aggregation. Genome reduction was aimed at reducing carbon flow toward specialized metabolite biosynthesis to optimize the production of secreted heterologous protein.ResultsTwo of these S. lividans TK24 derived chassis strains showed ~ 15% reduction in biomass yield, 2-fold increase of their total native secretome mass yield and enhanced abundance of several secreted proteins compared to the parental strain. RNAseq and proteomic analysis of the secretome suggested that genome reduction led to cell wall and oxidative stresses and was accompanied by the up-regulation of secretory chaperones and of secDF, a Sec-pathway component. Interestingly, the amount of the secreted heterologous proteins mRFP and mTNFα, by one of these strains, was 12 and 70% higher, respectively, than that secreted by the parental strain.ConclusionThe current study described a strategy to construct chassis strains with enhanced secretory abilities and proposed a model linking the deletion of specialized metabolite biosynthetic clusters to improved production of secreted heterologous proteins.

Bioengineering Phaeodactylum tricornutum, a marine diatom, for cannabinoid biosynthesis

Over the last few years, phytocannabinoids have been studied for their bioactive properties as potential drug candidates to treat or alleviate symptoms of several diseases. The isolation of single and pure cannabinoid (CB) from their natural source, i.e., Cannabis plants results in a low yield, diluted among hundreds of other plant metabolites. The use of biotechnological platforms to produce single CBs is appealing to the pharmaceutical industry. Therefore, our aim was to develop a sustainable system using the model diatom Phaeodactylum tricornutum to produce cannabigerolic acid (CBGA), the precursor to several CBs such as well-known cannabidiol (CBD) and delta-9-tetrahydrocannabinol (THC). We engineered P. tricornutum to express a mutant version of the Streptomyces sp. strain CL190's naptherpin biosynthetic cluster gene B NphB (Y288A/G286S, nphB), a non-Cannabis aromatic prenyltransferase enzyme, either by random integrated chromosomal expression (RICE) or extrachromosomal expression (EE), to maximize the success of protein production. The gene of nphB was linked to the reporter cyan fluorescent protein (CFP) and introduced in P. tricornutum. Clones were characterized by CFP fluorescence intensity, protein synthesis, enzymatic activity, and production of CBGA. We present, for the first time in diatoms, the successful production of a CB, CBGA up to 4.1 (± 0.2) mg/kg of microalgal fresh biomass weight. This work shows the potential of P. tricornutum as a sustainable controlled heterologous platform for CBs production, plant bioactive compounds, and relevant pharmaceuticals.

Whole-genome sequence of Bacillus velezensis strain R22 isolated from Oryza sativa rhizosphere in Bulgaria.

Bacillus velezensis R22 was isolated from a rice rhizosphere in Bulgaria. Its genome (assembled into 14 scaffolds) has a size of 4.08 Mbp and a G + C content of 46.35%. Nine full biosynthetic clusters for antimicrobials were predicted, among them two new gene clusters probably encoding polyketides named macrolactin R22 and velezensin.

Characteristics of marine strain Streptomyces sp. with antimicrobial and cytotoxic activity

The Black Sea is a unique water basin consisting of a thin superficial oxygenic layer with moderate salinity, and a deep anoxic water mass. The microbiota of the Black Sea remains relatively understudied, which makes it interesting first of all from the most practical point of view of the search for producers of new biologically active compounds. A strain of actinobacteria Streptomyces sp. ONU 561 was isolated from the surface of mussel shells collected in the coastal zone of Odesa. It demonstrated a wide range of antagonistic activity, inhibiting the growth of a set of opportunistic pathogens, including representatives of Staphylococcus aureus, Escherichia coli, Proteus vulgaris, and Klebsiella pneumoniae. In addition, bacteria of this strain were able to inhibit the growth of all tested strains of mycelial fungi, including representatives of Aspergillus niger, A. flavus and Fusarium oxysporum species, and Candida albicans yeast. A significant cytotoxic effect was revealed in the cell cultures of human malignant cells – human rhabdomyosarcoma (RD) and human laryngeal adenocarcinoma (Hep-2). Analysis of the exometabolome of the strain did not explain these effects.The strain was comprehensively characterized, including physiological, biochemical, and morphological traits. The complete genome of the strain was sequenced using Illumina HiSeq 4000 (2x150) and ONT and annotated using NCBI PGAP. Its genome has a size of 8 359 197 bp. GC content – 71.59%. Using antiSMASH 7.0, 35 biosynthetic clusters were revealed. The indices of digital DNA-DNA hybridization and orthoANI for all of the type strains with Streptomyces sp. ONU 561 are much lower than threshold values for the species separation. The obtained results, including a comparative analysis of the genome, indicate the possible affiliation of the strain Streptomyces sp. ONU 561 to a new species and the potential ability of these actinobacteria to synthesize previously unknown antibiotic compounds.

"Revealing the genetic arsenal of Bacillus firmus TNAU1: Unleashing nematicidal and plant growth promotion traits"

Bacillus firmus is a promising nematicidal bacterium that also confers plant growth promotion, nutrient acquisition and antimicrobial activities. In the present study, attempts were made for whole genome sequencing of B. firmus TNAU1 isolated from the rhizosphere region of cucumber. The results confirmed that the isolate was B. firmus which contained a single circular genome of 5,370,919 bp (5.3 Mb) in length with an average GC content of 41.16 %. Annotation was performed using PATRIC tool to explore the subsystem analysis, specialty genes, Enzyme Commission (EC) numbers, Gene Ontology (GO) mappings, KEGG pathways of B. firmus TNAU1. A total of 5804 coding sequence (CDS) genes that encode proteins were predicted based on the KEGG and clusters of orthologous groups (COGs) database. Comparative genomic analysis was performed to discover the unique features and their relationship with other available B. firmus strains. Blastp analysis revealed that TNAU 1 genome assemblies had 26 homologs corresponding to nematode-virulent proteases and various genes responsible for plant growth promotion which includes indole acetic acid (IAA) production, nitrate transport, phosphorus and potassium solubilization. Four secondary metabolite biosynthetic clusters encoding antibiotics and siderophore production were confirmed through comparative genomics. B. firmus TNAU1 was evaluated for its antagonistic activity against root-knot nematode Meloidogyne incognita of tomato. The results exhibited that B. firmus inhibited the egg hatching and mortality of juveniles by 96% over control under in vitro conditions and greenhouse experiments confirmed that the TNAU1 strain not only had the potential to suppress the soil and root population of M. incognita (70% reduction over control), but also triggered the plant growth parameters of tomato.

Modern Approaches to the Genome Editing of Antibiotic Biosynthetic Clusters in Actinomycetes.

Representatives of the phylum Actinomycetota are one of the main sources of secondary metabolites, including antibiotics of various classes. Modern studies using high-throughput sequencing techniques enable the detection of dozens of potential antibiotic biosynthetic genome clusters in many actinomycetes; however, under laboratory conditions, production of secondary metabolites amounts to less than 5% of the total coding potential of producer strains. However, many of these antibiotics have already been described. There is a continuous "rediscovery" of known antibiotics, and new molecules become almost invisible against the general background. The established approaches aimed at increasing the production of novel antibiotics include: selection of optimal cultivation conditions by modifying the composition of nutrient media; co-cultivation methods; microfluidics, and the use of various transcription factors to activate silent genes. Unfortunately, these tools are non-universal for various actinomycete strains, stochastic in nature, and therefore do not always lead to success. The use of genetic engineering technologies is much more efficient, because they allow for a directed and controlled change in the production of target metabolites. One example of such technologies is mutagenesis-based genome editing of antibiotic biosynthetic clusters. This targeted approach allows one to alter gene expression, suppressing the production of previously characterized molecules, and thereby promoting the synthesis of other unknown antibiotic variants. In addition, mutagenesis techniques can be successfully applied both to new producer strains and to the genes of known isolates to identify new compounds.

Widespread biosynthesis of 16-carbon terpenoids in bacteria.

Terpenoids are the most diverse group of specialized metabolites with numerous applications. Their biosynthesis is based on the five-carbon isoprene building block and, as a result, almost all terpenoids isolated to date are based on backbones that contain multiples of five carbon atoms. Intrigued by the discovery of an unusual bacterial terpenoid with a 16-carbon skeleton, here we investigate whether the biosynthesis of 16-carbon terpenoids is more widespread than this single example. We mine bacterial genomic information and identify potential C16 biosynthetic clusters in more than 700 sequenced genomes. We study selected clusters using a yeast synthetic biology platform and reveal that the encoded synthases produce at least 47 different noncanonical terpenoids. By thorough chemical analysis, we explain the structures of 13 C16 metabolites, most of which possess intricate highly strained bi- and tricyclic backbones. Our results unveil the existence of an extensive class of terpenoids in bacteria.