Genome Mining Research Articles (Page 1)

Flavin-dependent halogenases (FDHs) are a class of enzymes renowned for their regioselective ability to precisely insert halogen atoms into small aromatic compounds. Halogen incorporation can enhance the physicochemical and biological properties of molecules, making them valuable for agrochemical and pharmaceutical applications. Through bioinformatic mining of bacterial genomes, we discovered and functionally characterized SnFDHal, an efficient tryptophan 5-halogenase from Streptomyces noursei NRRL B-1714. This halogenase operates across a broad pH range and exhibits a melting temperature of 46.7°C at both pH 6 and pH 8, which is comparable to thermophilic halogenases such as Th-Hal and BorH, and notably higher than those of mesophilic counterparts. Steady-state kinetic analysis revealed that SnFDHal displays superior catalytic efficiency for the chlorination of L-tryptophan compared to other FDHs reported to date. Structural modeling of its active site suggests that a conserved bulky phenylalanine residue (F49) promotes halogenation at the C-5 position of L-tryptophan, consistent with experimental findings. The combination of high catalytic efficiency and thermostability positions SnFDHal as a promising biocatalyst for applications in agrochemical and pharmaceutical industries.

Terpenes are the largest category of specialised metabolites. Aerobic endospore-forming bacteria (AEFB), a diverse group of microorganisms, can thrive in various habitats and produce specialised metabolites, including terpenes. This study investigates the potential for terpene biosynthesis in 10 AEFB strain whole-genome sequences by performing a bioinformatics analyses to identify genes associated with these isoprene biosynthesis pathways. Specifically, we focused on the sequences coding for enzymes in the methylerythritol-phosphate (MEP) pathway and the polyprenyl synthase family, which play crucial roles in synthesising terpene precursors together with terpene synthases. A comparative analysis revealed the unique genetic architecture of these biosynthetic gene clusters (BGCs). Our results indicated that some strains possessed the complete genetic machinery required to produce terpenes such as squalene, hopanoids, and carotenoids. We also reconstructed phylogenetic trees based on the amino acid sequences of terpene synthases, which aligned with the phylogenetic relationships inferred from the whole-genome sequences, suggesting that the production of terpenes is an ancestor property in AEFB. Our findings highlight the importance of genome mining as a powerful tool for discovering new biological activities. Furthermore, this research lays the groundwork for future investigations to enhance our understanding of terpene biosynthesis in AEFB and the potential applications of these Brazilian environmental strains.

To expand the availability of promiscuous oleate hydratases (OAHs) for the asymmetric hydration of unactivated alkenes via sequence-based genome mining combined with targeted amino acid substitution. From 100 screened OAHs, 13 candidates were chosen, all exhibiting hydration activity toward oleic acid. These enzymes also showed significant activity with 1-decene (2mM), with AuOAH, CkOAH, AiOAH, and CeaOAH producing (S)-2-decanol at concentrations of 822, 603, 495, and 461μM, respectively. AuOAH, CeaOAH, and CkOAH further demonstrated notable activity with short-chain 1-heptene (2mM), generating (S)-2-heptanol concentrations of 156, 115, and 133μM, respectively. AuOAH, sourced from Acinetobacter ursingii for its relatively high activity and broad substrate range, was purified and characterized, showing turnover rates of 0.43-3.21nmolmin-1mg-1 for 1-alkenes (C7-C13). The optimization of reaction conditions for whole-cell asymmetric hydration of 1-decene in recombinant E. coli (AuOAH) demonstrated that exogenous illumination with 561.5nm light (9.4µmolm-2s-1) increased 1-decene conversion by approximately 1.5-fold. Similar light-induced enhancements (1.3-2.2-fold) were observed in OAHs from various sources. Under optimized conditions, recombinant E. coli (AuOAH) achieved 13.2-78.7% conversion for various unactivated alkenes (C7-C13) in an aqueous/organic two-phase system, with ee values ≥ 98%. This study significantly enriches the enzymatic toolbox for asymmetric alkene hydration and illustrates the beneficial effect of light illumination on OAH-catalyzed hydration.

Genome mining of tailoring enzymes from biosynthetic gene clusters for synthetic biology: A case study with fungal methyltransferases.

Development of a salt-enhanced promoter strategy for activating silent biosynthetic gene clusters from streptomycetes.

Molecular profiling of the Australian plague locust pathobiome reveals a microbial driver of population suppression.

Genome mining of carbohydrate-active enzymes (CAZyme) and poly-γ-glutamic acid (γ-PGA) synthesis by Bacillus velezensis (WA11) directly from lignocellulosic biomass-based substrate

Discovery of a novel antibacterial protein from Lactobacillus acidophilus using integrated genomic mining, molecular dynamics, and functional assays

The increasing prevalence of type 2 diabetes has driven an increasing demand for safe and effective α-glucosidase inhibitors (AGIs). Given prior findings of α-glucosidase inhibitory activity in Paenibacillus spp., this study aims to evaluate the biosynthetic capacity and inhibitory potential of Paenibacillus sp. JNUCC 31. Genomic annotation of the strain JNUCC 31 revealed multiple biosynthetic gene clusters associated with secondary metabolite biosynthesis. Fatty acid profiling initially identified anteiso-C15:0 (57.32%) as the dominant fatty acid via GC-MS. Subsequently, the ethyl acetate extract from fermented cultures, which exhibited the highest α-glucosidase inhibitory activity (52.4 ± 0.7%), was purified and five known compounds were isolated: adenosine, uridine, 4-hydroxybenzaldehyde, dibutyl phthalate (DBP), and 1-acetyl-β-carboline. Among these, adenosine, uridine, and DBP have been previously reported as α-glucosidase inhibitors. Enzyme kinetics confirmed that uridine (Ki = 153.35µM) functions as a competitive inhibitor, while adenosine (Ki = 90.88µM) and DBP (Ki = 516.22µM) act via a mixed-type inhibition mechanism. Molecular docking and molecular dynamics simulations demonstrated stable binding of these active compounds to human maltase-glucoamylase (MGAM, PDB ID: 2QMJ) and microbial isomaltase (PDB ID: 3A4A). Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) analysis indicated favorable binding free energies (− 14.18 to − 36.5 kcal/mol), with key residues such as Trp406 (MGAM), Tyr158 and Gln279 (isomaltase) playing major roles in binding stabilization. Collectively, these findings highlight the strain JNUCC 31 as a promising microbial source of antidiabetic lead compounds.Supplementary InformationThe online version contains supplementary material available at 10.1038/s41598-025-21753-5.

Streptomyces are significant producers of antimicrobial secondary metabolites. In this study, a Streptomyces rochei FE-3-1was isolated from the rhizosphere of rice plants, and its metabolites exhibited potent antagonistic activity against plant pathogen Pyricularia oryzae. However, the genome sequence of the strain has not been reported to date. Whole genome sequencing and genome mining were conducted to comprehensively characterize the strain's main features. The results showed that the total size of the genome is 8,247,561 bp with 72.51% G + C content. Among a total of 7158 genes, 169 predicted RNA genes were identified including 67 transfer RNA (tRNA) genes, 18 ribosomal RNA (rRNA) genes and 84 small RNA (sRNA) genes, as well as 14 genomic islands were predicted. A total of 31 biosynthetic gene clusters were detected within the genome of Streptomyces rochei FE-3-1, and at least four of these gene clusters are associated with known potent antimicrobials. These findings provide a solid theoretical foundation for utilizing strain FE-3-1 in developing biofertilizers or biopesticides within the field of biotechnology.

Streptomyces are significant producers of antimicrobial secondary metabolites. In this study, a Streptomyces rochei FE-3–1was isolated from the rhizosphere of rice plants, and its metabolites exhibited potent antagonistic activity against plant pathogen Pyricularia oryzae. However, the genome sequence of the strain has not been reported to date. Whole genome sequencing and genome mining were conducted to comprehensively characterize the strain’s main features. The results showed that the total size of the genome is 8,247,561 bp with 72.51% G + C content. Among a total of 7158 genes, 169 predicted RNA genes were identified including 67 transfer RNA (tRNA) genes, 18 ribosomal RNA (rRNA) genes and 84 small RNA (sRNA) genes, as well as 14 genomic islands were predicted. A total of 31 biosynthetic gene clusters were detected within the genome of Streptomyces rochei FE-3–1, and at least four of these gene clusters are associated with known potent antimicrobials. These findings provide a solid theoretical foundation for utilizing strain FE-3–1 in developing biofertilizers or biopesticides within the field of biotechnology.

BackgroundPlectropomus leopardus is a hermaphrodite fish with a unique pattern of gonadal development. However, the molecular mechanism of sexual differentiation in this species remains unclear. The Doublesex and Mab-3 related transcription factor (dmrt) gene family are known to play a crucial role in gonad differentiation and development. Notably, systematic investigations into the composition and function of the dmrt gene family in this hermaphrodite fish remain conspicuously lacking.MethodsIn this study, we systematically identified members of the dmrt gene family through genomic database mining in P. leopardus. Tissue and stage-specific expression profiles of dmrt paralogs were quantitatively analyzed using reverse transcription quantitative PCR (qPCR), revealing sexually dimorphic expression patterns in the gonads at various developmental stages. Furthermore, the expression distribution of dmrt2a at different developmental stages was explored using fluorescence in situ hybridization (FISH). Subsequently, dmrt2a was interfered with using RNAi technology, and the regulatory effect of dmrt2a on oocytes was verified by combining FISH and TUNEL assays.ResultsIn this study, we identified six members of the dmrt gene family in P. leopardus and designated them as dmrt1, dmrt2a, dmrt2b, dmrt3, dmrta1 and dmrta2 based on the homology analysis results, respectively. Whole-tissue expression analysis revealed that the dmrt genes exhibit tissue-specific expression pattern in P. leopardus. Notably, dmrt1 and dmrt2a are highly expressed in the gonads, suggesting their potential role in gonadal development. Further qPCR results showed that dmrt genes are differentially expressed between males and females at different developmental stages. Among them, dmrt2a is highly expressed in the ovary at different developmental stages and is found to be a pivotal factor in ovarian development. FISH was used to further verify the expression of dmrt2a in oocytes. In addition, knockdown of dmrt2a in gonads caused oocyte apoptosis and decreased oocyte number, demonstrating the critical role of dmrt2a in oocyte development.ConclusionsThis study demonstrates that dmrt2a plays a crucial regulatory role in the development of the oocytes in P. leopardus, supplementing the understanding of the functional roles of the dmrt gene family in vertebrate sex differentiation. These findings will help to understand the properties and functions of the dmrt genes in P. leopardus and provide a solid basis for further studies on the functional mechanisms of dmrt genes in hermaphroditic fish.Supplementary InformationThe online version contains supplementary material available at 10.1186/s13293-025-00769-6.

Abstract Terpenoids represent the most structurally diverse class of natural products on Earth. Terpene synthases are key enzymes for constructing the complex and varied terpene skeletons by catalyzing the formation of multiple carbon–carbon bonds. Phomactatriene and verticillene family natural products are both classified as bicyclic diterpenoids, sharing a unique bicyclo[9.3.1]pentadecane skeleton. In this study, we used genome mining to identify the phomactatriene synthase SiPS from bacteria, together with two verticillene synthases, LxVS and AxVS. Our DFT calculations revealed that the rearrangement pathways for compounds in the phomactatriene and verticillene families follow a shared biosynthetic route. Furthermore, through comparative structural model analyses of the phomactatriene and verticillene synthases, we employed molecular modelling and site‐directed mutagenesis to facilitate functional interconversion between these distinct terpene synthases. This work enhances our understanding of terpene biosynthesis and the potential for engineering terpene synthases for biotechnological applications.

The draft genome of a multi-drug-resistant Nocardia anissiorum, designated JW2, isolated from soil, and exhibiting considerable resistance to anti-microbial agents produced by different Streptomyces species is provided. Genome mining counts for 35 biosynthetic gene clusters. A total of 37% of the identified BGCs have no similarity in the MiBIG database.

BackgroundPhenylspirodrimanes (PSDs) are a unique class of meroterpenoids that have been extensively studied due to their diverse biological activities. These metabolites are supposedly biosynthesized through the farnesylation of orsellinate. However, the molecular basis has not yet been elucidated.ResultsHerein, using a combination of genome mining, bioinformatic alignment, and gene deletion approach, we characterized the dedicated gene cluster psd responsible for biosynthesizing PSDs in the fungus Stachybotrys sp. CPCC 401591. RNA sequencing-based transcriptomic analyses broadened our understanding of the genetic basis, regulation, and mechanisms of PSDs biosynthesis. Furthermore, based on the chemical structures of PSD derivatives characterized and deduced gene functions of the cluster psd, a hypothetical metabolic pathway for biosynthesizing chartarlactam K (1) was proposed. These results revealed the underlying mechanism of phenylspirodrimanes generation, and these findings might facilitate downstream metabolic engineering studies of PSDs or the production of new chemical entities.ConclusionsGenome discovery and gene deletion experiments unveiled a previously uncharacterized biosynthetic gene cluster psd involved in the biosynthesizing PSD derivatives in Stachybotrys sp. CPCC 401591. In addition, based on the gene cluster data and transcriptomic analyses, a hypothetical biosynthetic pathway of 1 was put forward.Graphical Supplementary InformationThe online version contains supplementary material available at 10.1186/s12934-025-02853-3.

Terpenoids represent the most structurally diverse class of natural products on Earth. Terpene synthases are key enzymes for constructing the complex and varied terpene skeletons by catalyzing the formation of multiple carbon-carbon bonds. Phomactatriene and verticillene family natural products are both classified as bicyclic diterpenoids, sharing a unique bicyclo[9.3.1]pentadecane skeleton. In this study, we used genome mining to identify the phomactatriene synthase SiPS from bacteria, together with two verticillene synthases, LxVS and AxVS. Our DFT calculations revealed that the rearrangement pathways for compounds in the phomactatriene and verticillene families follow a shared biosynthetic route. Furthermore, through comparative structural model analyses of the phomactatriene and verticillene synthases, we employed molecular modelling and site-directed mutagenesis to facilitate functional interconversion between these distinct terpene synthases. This work enhances our understanding of terpene biosynthesis and the potential for engineering terpene synthases for biotechnological applications.

We report the draft genome sequence of Enterobacter roggenkampii strain B1-01, isolated from the roots of bamboo in Cagayan, Philippines. The assembled genome is 4.6 Mb in size, with a G + C content of 56.2% and 4,305 protein-coding genes. Genome mining identified genes involved in plant growth promotion and secondary metabolite production.

Biosynthetic gene clusters (BGCs) of bioactive natural products occasionally encode resistant versions of the proteins they inhibit, offering opportunities for resistance gene-guided genome mining to uncover natural products with predictable modes of action. In this study, we developed a genome mining tool designed to identify fungal BGCs harboring putative resistance genes. Applying this tool to approximately 2500 fungal genomes, we identified a BGC designated as the pts cluster, which encodes an acetolactate synthase (ALS) homologue. Functional characterization of the pts cluster resulted in the identification of pterrespiramide A (1), featuring unique spirotetramate and cis-decalin moieties. Consistent with the predicted activity, 1 was confirmed as an ALS inhibitor and exhibited both antifungal and herbicidal activities. This study illuminates the potential of resistance gene-guided genome mining as a powerful strategy for accelerating the discovery of previously undescribed bioactive natural products.

DMAT-type prenyltransferases (PTases) are essential for the biosynthesis of structurally diverse hybrid terpenoids. Here, we report the discovery and functional characterization of DiaB, a previously uncharacterized fungal PTase identified through genome mining. Heterologous expression of the dia gene cluster in Aspergillus oryzae NSAR1 led to the production of five new meroterpenoids. In vivo and in vitro studies revealed that DiaB is a PTase that catalyzes the regiospecific O-farnesylation of free l-threonine and l-serine, a previously unknown activity for this enzyme class in fungi. The functions of all enzymes in the cluster were elucidated, revealing a novel pathway to prenylated amino acids. This work expands the substrate scope of DMAT-type PTases and provides a new biocatalytic tool for meroterpenoid diversification.

Rare actinomycetes belonging to the genus Nocardia are opportunistic pathogens responsible for nocardiosis, especially in immunocompromised individuals. Despite their pathogenicity, they possess diverse metabolic pathways and therefore are potential sources of novel bioactive secondary metabolites, with implications for drug discovery. However, the biosynthetic potential of many Nocardia strains has not been determined. In this study, we evaluated the antibiotic production abilities of 119 Nocardia strains through co-culturing with Staphylococcus aureus. Among the tested strains, Nocardia tsunamiensis IFM 10818 exhibited strong inhibitory activity against S. aureus, indicating the presence of antibacterial compounds. Subsequent chemical analysis revealed that this strain produces nargenicin A1, a macrolide antibiotic previously identified in other Nocardia strains. To better understand the biosynthetic potential of N. tsunamiensis IFM 10818, we performed whole-genome sequencing. Comparative genomic analysis revealed its phylogenetic placement within the genus Nocardia, demonstrating its close relationship with Nocardia crassostreae. Importantly, we assessed the prevalence of the biosynthetic gene cluster (BGC) responsible for nargenicin A1 production within the genus. These findings confirm that N. tsunamiensis IFM 10818 is a previously unreported producer of nargenicin A1. This study highlights the utility of genome mining and functional screening in discovering bioactive compounds from underexplored microbial taxa. Further exploration of Nocardia genomes may reveal additional cryptic BGCs with pharmaceutical potential.IMPORTANCEThe macrolide nargenicin A1, produced by certain Nocardia strains, exhibits a range of biological activities, most notably strong antibacterial effects against methicillin-resistant Staphylococcus aureus. The identification of a high-yielding producer strain is essential to support future pharmaceutical development and commercial production. In this study, we identified Nocardia tsunamiensis IFM 10818 as a prolific producer of nargenicin A1. This strain exhibited significant inhibitory activity against S. aureus in co-culture assays, and a chemical analysis confirmed the production of nargenicin A1. Genome sequencing of N. tsunamiensis IFM 10818 allowed for the identification of the biosynthetic gene cluster responsible for nargenicin biosynthesis, reinforcing the potential for industrial applications. These findings highlight the promise of Nocardia species as untapped sources of valuable secondary metabolites and emphasize the importance of strain screening and genomic analyses in the discovery and development of new antibiotics.