Search Results (189)

To identify differentially abundant polyketide synthases (PKSs) and to characterize the biochemical consequences of brevetoxin biosynthesis, bottom-up, TMT-based quantitative proteomics and redox proteomics were conducted to compare two strains of the Florida red tide dinoflagellate Karenia brevis, which differ significantly in their brevetoxin content. Forty-eight PKS enzymes potentially linked to brevetoxin production were identified, with thirty-eight showing up to 16-fold higher abundance in the high-toxin strain. A pronounced shift toward a more oxidized redox state was observed in this strain’s proteome. Notably, 25 antioxidant-related proteins were significantly elevated, including alternative oxidase (AOX), which increased by 17-fold. These results elucidate the cellular consequences of toxin biosynthesis in K. brevis, offer new leads for the study of brevetoxin biosynthesis, and suggest a novel red tide mitigation approach targeting high toxin-producing strains. Full article

Colorectal cancer (CRC) is a multifactorial disease increasingly recognized for its complex interplay with the gut microbiota. The disruption of microbial homeostasis—dysbiosis—has profound implications for intestinal barrier integrity and host immune function. Pathogenic bacterial species such as Fusobacterium nucleatum, Escherichia coli harboring polyketide synthase (pks) island, and enterotoxigenic Bacteroides fragilis are implicated in CRC through mechanisms involving mucosal inflammation, epithelial barrier disruption, and immune evasion. These pathogens promote pro-tumorigenic inflammation, enhance DNA damage, and suppress effective anti-tumor immunity. Conversely, commensal and probiotic bacteria, notably Lactobacillus and Bifidobacterium species, exert protective effects by preserving epithelial barrier function and priming host immune responses. These beneficial microbes can promote the maturation of dendritic cells, stimulate CD8⁺ T cell cytotoxicity, and modulate regulatory T cell populations, thereby enhancing anti-tumor immunity. The dichotomous role of the microbiota underscores its potential as both a biomarker and a therapeutic target in CRC. Recent advances in studies have explored microbiota-modulating strategies—ranging from dietary interventions and prebiotics to fecal microbiota transplantation (FMT) and microbial consortia—as adjuncts to conventional therapies. Moreover, the composition of the gut microbiome has been shown to influence the responses to immunotherapy and chemotherapy, raising the possibility of microbiome-informed precision oncology therapy. This review synthesizes the current findings on the pathogenic and protective roles of bacteria in CRC and evaluates the translational potential of microbiome-based interventions in shaping future therapeutic paradigms. Full article

A novel actinobacterial strain, designated E54^T, was isolated from a hyper-arid desert soil sample collected from the Kumtagh Desert in Dunhuang, Gansu Province, China. Phylogenetic analysis based on 16S rRNA gene sequences placed strain E54^T within the genus Lentzea, showing highest similarity to Lentzea waywayandensis DSM 44232^T (98.9%) and Lentzea flava NBRC 15743^T (98.5%). However, whole-genome comparisons revealed that the average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between E54^T and these related strains were below the thresholds for species delineation. Strain E54^T exhibited typical morphological characteristics of the genus Lentzea, forming a branched substrate. It grew optimally at 28–30 °C, pH 7.0–9.0, and tolerated up to 10% NaCl. The cell wall contained meso-diaminopimelic acid, the predominant menaquinone was MK-9(H₄), and major fatty acids included iso-C_16:0. The polar lipid profile comprised diphosphatidyl glycerol, phosphatidyl ethanolamine, phosphatidyl inositol, hydroxyphosphatidyl ethanolamine, and an unidentified lipid. The characteristic amino acid type of the cell wall was meso-DAP. Whole-cell hydrolysis experiments revealed the characteristic cell wall sugar fractions: ribose and galactose. The genome of strain E54^T is approximately 8.0 Mb with a DNA G+C content of 69.38 mol%. Genome mining revealed 39 biosynthetic gene clusters (BGCs), including non-ribosomal peptide synthetases (NRPS), polyketide synthases (PKS), terpenes, and siderophores. Comparative antiSMASH-based genome analysis across 38 Lentzea strains further demonstrated the genus’ remarkable biosynthetic diversity. NRPS and type I PKS (T1PKS) were the most prevalent BGC types, indicating a capacity to synthesize structurally complex and pharmacologically relevant metabolites. Together, these findings underscore the untapped biosynthetic potential of the genus Lentzea and support the proposal of strain E54^T as a novel species. The strain E54^T (=JCM 34936^T = GDMCC 4.216^T) should represent a novel species, for which the name Lentzea xerophila sp. nov. is proposed. Full article

Trichoderma spp. produce diverse secondary metabolites with biological activity. This study explored the antimicrobial, antibiofilm, antioxidant, and cytotoxic properties of metabolites from two native Trichoderma strains, 10BR1 and UEPA AR12, isolated from rhizospheric soils. Organic extracts from both strains demonstrated broad-spectrum antimicrobial activity, inhibiting Gram-positive and Gram-negative bacteria, as well as various Candida species, with notable efficacy against Staphylococcus aureus (MICs: 15.6–31.25 µg/mL). The extracts also showed antibiofilm activity, with UEPA AR12 exhibiting the highest inhibition against Escherichia coli (81.8%), Enterococcus faecalis (92.8%), Candida albicans (87.9%), and Candida parapsilosis (89.3%). Antioxidant activity, assessed via DPPH assay, revealed a dose-dependent radical scavenging effect (12.88% to 39.67% at 7.8–1000 µg/mL). Cytotoxicity assays indicated that UEPA AR12 extracts were more cytotoxic (IC₅₀: 202.5–234.3 µg/mL) than 10BR1 (IC₅₀: 368.7–602.1 µg/mL) in non-tumor cells, with similar trends in tumor cells (Huh7). HPLC/MS analysis identified 21 metabolites in the extracts. Genomic analyses, supported by rpb2 gene and phylogenetic clustering, confirmed that both strains were T. afroharzianum. FUNGISMASH revealed multiple biosynthetic gene clusters, predominantly Type I polyketide synthase (T1PKS). Additionally, targeted genomic analyses did not detect mycotoxin-related genes. These findings highlight the antimicrobial, antibiofilm, and antioxidant potentials of these strains, positioning them as sources of bioactive metabolites for pharmaceutical applications. Full article

Polyketides (PKs) are a widespread class of secondary metabolites with recognised pharmacological properties. These molecules are abundantly produced in the marine environment, especially by dinoflagellate-photosynthetic organisms able to produce several PKs, including neurotoxins, cytotoxins, and immunomodulating agents. The biosynthesis of these compounds is driven by a conserved enzymatic process involving polyketide synthase complexes. Different genera of dinoflagellates produce PKs. Among them, dinoflagellates of the genus Amphidinium are of particular interest due to its ability to produce the following two major families of PKs: amphidinolides and amphidinols. These compounds display remarkable biological activities, including anticancer, antimicrobial, and antifungal effects, making them attractive targets for pharmaceutical research and development. However, the natural yield of Amphidinium-derived polyketides (APKs) is generally low, limiting their potential for sustainable molecular farming. This challenge has prompted interest in developing biotechnological strategies to enhance their production. This review aims to define the current state of studies about APKs, starting from their initial discoveries to the recent understanding of their biosynthetic pathways. Additionally, it summarizes the structures of compounds discovered, highlights their biotechnological potential, and discusses novel trends in their production. Full article

Background: Mithramycin (MTM) is a polyketide anti-cancer natural product previously identified as an EWS-FLI1 inhibitor. This oncogenic transcription factor is a canonical target for drug development in Ewing sarcoma. However, poor pharmacokinetics have been identified as a critical liability of MTM, preventing its further development. Through semisynthetic chemical modifications, we identified mithramycin SA-Trp (MTMSA-Trp) as being a pharmacologically superior congener. To explore their pharmacokinetic (PK) differences, this study examined the plasma PKs and plasma protein binding (PPB) of MTM and MTMSA-Trp in mice, rats, and monkeys. Methods: Protein binding was investigated by rapid equilibrium dialysis in plasma from mice, rats, monkeys, and humans. The pharmacokinetics were investigated at milligram- and microgram-level doses in mice and rats. The pharmacokinetics in monkeys were investigated using the cassette dosing approach at two microgram-level doses. The MTMSA-Trp pharmacokinetic linearity was evaluated in mice at 0.3, 1, 3, and 10 mg/kg doses. All samples were analyzed using LC-MS/MS. Results: Plasma protein binding was higher for MTMSA-Trp (1–4% unbound) than for MTM (10–30% unbound) across species, except in athymic nude mice (1–4% unbound and <1% for mithramycin and MTMSA-Trp, respectively). In mice and rats, MTMSA-Trp had significantly lower clearance than MTM at both milligram and microgram doses; however, the difference in plasma exposure was more pronounced at milligram doses. Consistent with the rodent PK results, cassette microdosing in monkeys showed that the clearance of MTMSA-Trp was lower than that of MTM, but the differences were less pronounced. In the dose proportionality study, MTMSA-Trp showed linear pharmacokinetics at 1, 3, and 10 mg/kg doses. Conclusions: MTMSA-Trp has significantly lower clearance than MTM in rodent models. This is a significant improvement compared to the parent drug, MTM, and warrants further evaluation of PKs in non-rodent models to enable the prediction of MTMSA-Trp PK in humans. Full article

This study investigated Morchella importuna strain degeneration during repeated subculturing and employed metabolomics, transcriptomics, and other techniques to explore its molecular mechanisms. Significant metabolic and transcriptional differences were observed between normal mycelia (NM) and degenerated mycelia (DG). Metabolomic analysis revealed 699 differentially expressed metabolites (DEMs) that were predominantly enriched in secondary metabolite biosynthesis pathways, particularly flavonoids and indole alkaloids. Total flavonoid content was markedly higher in NM than in DG, with most flavonoid compounds showing reduced levels in degenerated strains. Transcriptomic profiling revealed 2691 differentially expressed genes (DEGs), primarily associated with metabolic pathways and genetic information processing. Integrated analysis showed that metabolic dynamics were regulated by DEGs, with pyruvate metabolism being significantly enriched. The FunBGCeX tool identified biosynthetic gene clusters (BGCs) in the M. importuna genome, highlighting the critical role of the non-reducing polyketide synthase (NR-PKS) gene in flavonoid biosynthesis. This gene exhibited significantly downregulated expression in DG strains. These findings indicate that M. importuna degeneration resulted from systemic dysregulation of gene expression networks and metabolic pathway reorganization. The results presented herein also provide theoretical insights into degeneration mechanisms and potential prevention strategies for this edible fungus. Full article

Soil, rhizosphere, and plant-associated microorganisms can enhance plant growth and health. A genomic analysis of these microbes revealed the key characteristics contributing to their beneficial effects. Following a field survey in Panama, four bacterial isolates with plant growth-promoting traits (PGPT) in rice (Oryza sativa L.) were identified. In this study, we sequenced, assembled, and annotated the genomes of Lysinibacillus fusiformis C6 and 24, and Bacillus cereus D23 and 59. The C6 genome was 4,754,472 bp long with 10 contigs, 37.62% guanine-cytosine (GC) content, and 4657 coding sequences (CDS). The 24 genome was 4,683,219 bp with five contigs, 37.65% GC content, and 4550 CDS. The D23 genome was 6,199,908 bp long with 18 contigs, 34.84% GC content, and 6141 CDS. The 59 genome was 6,194,462 bp with 21 contigs, 34.87% GC content, and 6122 CDS. Digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) confirmed that C6 and 24 belong to Lysinibacillus fusiformis, whereas D23 and 59 belong to the Bacillus cereus species. Further results revealed that these bacteria contained genes characteristic of plant growth-promoting bacteria, such as siderophore, phytohormone auxin (IAA) production, and nitrogen-fixing abilities that promote plant growth. Moreover, the antiSMASH database identified gene clusters involved in secondary metabolite production (biosynthetic gene clusters), such as betalactone, NRPS-like, NRP-siderophore, terpene, and RiPP-like clusters. Moreover, diverse and novel biosynthetic clusters (BCGs) have included non-ribosomal peptides (NRPs), polyketides (PKs), bacteriocins, and ribosomally synthesized and post-transcriptionally modified peptides (RiPPs). This work offers new insights into the genomic basis of the studied strains’ plant growth-promoting capabilities. Full article

The long-term coexistence of sea cucumber-associated microorganisms with their host enables them to jointly withstand the unique marine ecological environment, and possess great potential for producing various natural products. However, under conventional laboratory conditions, most biosynthetic gene clusters (BGCs) in these microorganisms remain silent, necessitating the establishment of effective activation strategies for exploring bioactive secondary metabolites (SMs). Histone acetylation status regulates chromatin structure and plays a crucial role in cellular physiology and fungal secondary metabolism. Penicillium sclerotiorum SD-36 was isolated from sea cucumbers in our previous study. Genome sequencing results indicate that this strain harbors as many as 52 BGCs, suggesting it holds a wealth of genetic resources essential for synthesizing diverse SMs. Here, we describe the impact of a class 1 histone deacetylase (HDAC), PsHos2, on secondary metabolism of sea cucumber-associated Penicillium sclerotiorum SD-36. The colony morphology and SM profile of ΔPsHos2 exhibited significant changes, with the emergence of multiple new compound peaks. Six compounds, including five azaphilones, which are characterized by a pyranoquinone core structure, were isolated from ΔPsHos2, and seventeen unreported potential azaphilone-related nodes were obtained using molecular networking based on LC-MS/MS. Transcriptome analysis revealed that PsHos2 influenced the expression of 44 BGC core genes. Specifically, seven genes within cluster 86.1, the putative BGC for azaphilones, were upregulated, including two polyketide synthase (PKS) genes. The results indicate that regulation based on class 1 HDACs is an important strategy for enhancing SM synthesis in sea cucumber-associated fungi and expanding the resources of marine natural products. Full article

Phlebopus portentosus is an edible and medicinal ectomycorrhizal mushroom with delicious and high nutritional value. However, the mechanism of secondary metabolite biosynthesis in P. portentosus is still unclear. In this study, the genomics, metabolomics, and transcriptomics were integrated to reveal the biosynthesis mechanism of secondary metabolites in P. portentosus under different cultivation conditions. The 31.4 Mb genome of P. portentosus YAF023 with 15 scaffolds was assembled by Illumina and Nanopore sequencing and annotated, and 206 cytochrome P450s, 201 carbohydrate-active enzymes, 186 transcription factors, 18 terpene synthases (TPSs), and 5 polyketide synthases (PKSs) were identified. Multi-omics analysis showed that PpPKS1 is probably involved in the biosynthesis of Ethyl orsellinate; PpPKS2 and PpPKS5 are probably involved in the synthesis of 6-Methylsalicylic acid and Cytochalasin Z5, respectively; PpTRI5 was involved in the tetracyclic sesquiterpene β-type trichodiene compounds; and PpSTCs was involved in the synthesis of β-copaene analogs or derivatives. Co-expression network analysis and binding site prediction of the promoter regions suggested that PpHOX4 and PpHSF1 regulated the gene expression of PpPKS1, and Ppzf-C2H2 32 and PpHSF5 regulated the gene expression of PpSTCs 8, and PpSTCs 3, respectively. This study will provide an important foundation for further development and utilization of secondary metabolites of P. portentosus. Full article

The growing threat of antibiotic resistance has made treating bacterial and fungal infections increasingly difficult. With the discovery of new antibiotics slowing down, alternative strategies are urgently needed. Siderophores, small iron-chelating molecules produced by microorganisms, play a crucial role in iron acquisition and serve as virulence factors in many pathogens. Because iron is essential for microbial survival, targeting siderophore biosynthesis and transport presents a promising approach to combating drug-resistant infections. This review explores the key genetic and biochemical mechanisms involved in siderophore production, emphasizing potential drug targets within these pathways. Three major biosynthetic routes are examined: nonribosomal peptide synthetase (NRPS)-dependent, polyketide synthase (PKS)-based, and NRPS-independent (NIS) pathways. Additionally, microbial iron uptake mechanisms and membrane-associated transport systems are discussed, providing insights into their role in sustaining pathogenic growth. Recent advances in inhibitor development have shown that blocking critical enzymes in siderophore biosynthesis can effectively impair microbial growth. By disrupting these pathways, new antimicrobial strategies can be developed, offering alternatives to traditional antibiotics and potentially reducing the risk of resistance. A deeper understanding of siderophore biosynthesis and its regulation not only reveals fundamental microbial processes but also provides a foundation for designing targeted therapeutics. Leveraging these insights could lead to novel drugs that overcome antibiotic resistance, offering new hope in the fight against persistent infections. Full article

Cystic fibrosis (CF) patients experience higher risks of colorectal cancer but the pathogenesis is unclear. In the general population, polyketide synthase-positive (pks⁺) E. coli is implicated in intestinal carcinogenesis via the production of colibactin; however, the relevance in CF is unknown. In this study, we investigate pks⁺E. coli prevalence in CF and potential associations between pks⁺E. coli, gastrointestinal inflammation, and microbiome dynamics with fecal calprotectin and 16SrRNA gene taxonomic data. Cross-sectional analysis demonstrated no difference in pks⁺E. coli carriage between CF patients and healthy controls, 21/55 (38%) vs. 26/55 (47%), p = 0.32. Pks⁺E. coli was not associated with significant differences in mean (SD) calprotectin concentration (124 (154) vs. 158 (268) mg/kg; p = 0.60), microbial richness (159 (76.5) vs. 147 (70.4); p = 0.50) or Shannon diversity index (2.78 (0.77) vs. 2.65 (0.74); p = 0.50) in CF. Additionally, there was no association with exocrine pancreatic status (p = 0.2) or overall antibiotic use (p = 0.6). Longitudinally, CF subjects demonstrated intra-individual variation in pks⁺E. coli presence but no significant difference in overall prevalence. Future investigation into the effects of repeat exposure on risk profile and analysis of older CF cohorts is necessary to identify if associations with colorectal cancer exist. Full article

Monacolin K (MK), a secondary metabolite produced by Monascus spp. with the ability to inhibit cholesterol production, is structurally identical to lovastatin produced by Aspergillus terreus. In the lovastatin biosynthetic pathway, the polyketide synthase (PKS) encoded by lovB must work together with the enoyl reductase encoded by lovC to ensure lovastatin production. However, it is unclear whether mokA and mokE in the MK gene cluster of Monascus spp., both of which are highly homologous to lovB and lovC, respectively, also have the same functions for MK biosynthesis. In the current study, the high-yielding MK M. pilosus MS-1 was used as the research object, and it was found that the enoyl reductase domain of MokA may be non-functional due to the lack of amino acids at active sites, a function that may be compensated for by MokE in the MK synthesis pathway. Then, the mokE-deleted (ΔmokE), -complemented (ΔmokE::mokE), and -overexpressed (PgpdA-mokE) strains were constructed, and the results showed that ΔmokE did not produce MK, and ΔmokE::mokE restored MK synthesis, while the ability of PgpdA-mokE to produce MK was increased by 32.1% compared with the original strain MS-1. These results suggest that the MokA synthesized by Monascus spp. must be assisted by MokE to produce MK, just as lovastatin produced by A. terreus, which provides clues for further genetic engineering to improve the yield of MK in Monascus spp. Full article

Nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) play crucial roles in the development and pathogenicity of the entomopathogenic fungus Beauveria bassiana. However, they are among the few biosynthetic gene clusters with unknown functions in B. bassiana. To investigate the role of the hybrid PKS–NRPS synthetase gene BBA_09856 in B. bassiana, we constructed a mutant strain, ∆BBA09856-WT, by deleting the BBA_09856 gene through Agrobacterium-mediated transformation. We then analyzed the biological characteristics of the mutant strain and the virulence of the mutant strain toward Ostrinia furnacalis larvae, as well as its antagonistic effects against the phytopathogen Botrytis cinerea. We found that the average growth rate of the three mutant strains, ∆BBA09856-WT, was significantly higher compared to the wild-type (WT) strain on the 15th day of culture on potato dextrose agar (PDA) plates (7.01 cm vs. 6.30 cm, p < 0.01). Additionally, the average spore production(3.16 × 10⁷/cm² vs. 9.95 × 10⁶/cm², p < 0.001) and germination rate (82.50% vs. 54.72%, 12 h, p < 0.001) were significantly different between the three mutant strains, ∆BBA09856-WT, and the WT strain. The average survival rates of O. furnacalis infected with the WT strain and the three mutant strains, ∆BBA09856-WT, after 8 days were 61.66%, and 30.00%, respectively, indicating that the pathogenicity of the tested mutant strains was significantly greater than that of the WT strain. The results of the dual culture test indicated that the inhibitory rates of the WT and ∆BBA09856-WT strains against B. cinerea were 40.25% and 47.65%, respectively (p < 0.001). Similarly, in the dual culture test, the WT strain reduced the growth of B. cinerea by 9.90%, while the ∆BBA09856-WT exhibited a significantly greater inhibition rate of 28.29% (p < 0.05). The diameters of disease spots, measured 6 d after inoculation with B. cinerea in the tomato treatment groups, revealed significant differences in endophytic colonization between the WT and ∆BBA09856-WT strains in the WT+Bc and ∆BBA09856-WT+Bc treatment groups (15.26 mm vs. 12.16 mm, p < 0.01). Notably, ∆BBA09856-WT exhibited enhanced virulence toward O. furnacalis larvae and increased antagonistic activity against B. cinerea. Our results indicate that the gene BBA_09856 may have a negative correlation with the development and virulence of B. bassiana toward the insect pest O. furnacalis larvae, as well as its antagonism against B. cinerea. These findings suggest that molecular techniques, such as gene editing, could be employed to develop superior strains of B. bassiana for the biological control of plant diseases and insect pests. Full article

This study presents the first comprehensive genomic analysis of Cryptoporus qinlingensis, a classical folk medicine and newly identified macrofungus from the Qinling Mountains. Utilizing advanced sequencing technologies, including PacBio HiFi and Hi-C, we achieved a high-quality chromosome-level genome assembly. The genome, sized at 39.1 Mb, exhibits a heterozygosity of 0.21% and contains 21.2% repetitive sequences. Phylogenetic analysis revealed a recent divergence of C. qinlingensis from Dichomitus squalens approximately 212.26 million years ago (MYA), highlighting the rapid diversification within the Polyporaceae family. Comparative genomic studies indicate significant gene family contraction in C. qinlingensis, suggesting evolutionary adaptations. The identification of a tetrapolar mating system, along with the analysis of CAZymes and P450 genes, underscores the genomic complexity and ecological adaptability of this species. Furthermore, the discovery of 30 biosynthetic gene clusters (BGCs) related to secondary metabolites, including polyketide synthase (PKS), non-ribosomal peptide synthetase (NRPS), and terpene synthesis enzymes, opens new avenues for exploring bioactive compounds with potential medicinal applications. This research not only enriches our understanding of the Cryptoporus genus but also provides a valuable foundation for future studies aiming to harness the therapeutic potential of C. qinlingensis and to further explore its ecological and evolutionary significance. Full article