Search Results (49)

Phosphorus (P), as one of the essential bulk elements for plant growth and development, plays an important role in root growth, accumulation of secondary metabolites, and regulation of gene expression. In Salvia miltiorrhiza Bunge (S. miltiorrhiza), an important medicinal plant, the accumulation of its active components is closely related to the level of phosphorus supply, but the molecular regulatory mechanism of phosphorus treatment in the growth and secondary metabolism of S. miltiorrhiza is not clear. In this study, we investigated the effects of low phosphorus (P2), moderate phosphorus (P4), and high phosphorus (P6) treatment on the growth and development of S. miltiorrhiza. seedlings, the accumulation of bioactive compounds, and their transcriptional regulation using transcriptomic and metabolomic analyses, and identified the key regulatory genes in the biosynthesis pathways of tanshinone and salvianolic acid. The findings revealed that S. miltiorrhiza biomass exhibited a “peaked” response to phosphorus concentration, peaking at 0.625 mmol·L⁻¹. At this optimal concentration, all four batches achieved maximum root length, root weight, and leaf weight: Batch I (11.3 cm, 2.34 g, 1.62 g), Batch II (12.7 cm, 2.67 g, 1.89 g), Batch III (13.8 cm, 2.85 g, 2.04 g), and Batch IV (15.6 cm, 3.51 g, 2.44 g). Both lower and higher concentrations resulted in growth inhibition and reduced bioactive compound accumulation. Transcription factors associated with root growth and development included bHLH, MYB, and WRKY; in particular, the bZIP23 transcription factor was highly expressed under abnormal phosphorus supply conditions. In addition, the biosynthetic pathways of tanshinone and salvianolic acid were elucidated, and key genes related to the synthesis pathways (CPS, KSL, CYP, PAL, HPPR, and RAS) were identified. The expression of several TFs (such as SmCPS1, SmCYP76AH3, SmCYP76AH1, SmGGPPS1, and SmRAS1) was found to be correlated with tanshinone and salvianolic acid synthesis. The present study provides a theoretical basis for further revealing the molecular mechanism of phosphorus regulation of growth, development, and secondary metabolism of S. miltiorrhiza and provides potential targets for efficient cultivation and molecular breeding of S. miltiorrhiza. Full article

The Aspergillus genus is an important group of filamentous fungi, and the various biological activities of its secondary metabolites (SMs) have great biosynthetic potential. Despite over 4200 SMs having been isolated from Aspergillus spp., their metabolic potential remains unexplored due to the presence of numerous silent biosynthetic gene clusters (BGCs) in their genomes. Fortunately, over the last two decades, the global transcriptional regulator (GTR) engineering strategy has emerged as a powerful tool for activating these cryptic BGCs in order to synthesize previously undiscovered SMs from Aspergillus spp. This review highlights recent advances in fungal GTR engineering techniques, the regulatory mechanisms of GTRs, and current challenges and future perspectives for their application in natural product discovery in the genus Aspergillus. 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

Fungal secondary metabolism (SM) is highly correlated with physiological processes that are typically regulated by pleiotropic regulators. In this study, we purposefully altered PratfA, a crucial regulator associated with oxidative stress in Penicillium raistrickii CGMCC 3.1066. After the knockout of PratfA, a novel polyketide (PK) raistrilide A (1) and the known nonribosomal peptide (NRP) tunicoidine (2) subsequently disappeared. Notably, compound 1 is a rare octaketone derivative and contains two unsubstituted cis-double bonds, demonstrating its unique biosynthetic mechanism. The knockout of PratfA resulted in the disappearance of 1–2 and greatly increased the susceptibility of ΔPratfA mutant strain to oxidative stress, rendering it nearly impossible to survive in such environments. At present, the OE⸬PratfA strain showed no phenotypic or oxidative stress sensitivity differences compared to the wild-type strain. Our findings highlight that the oxidative-stress-related transcription factor (TF) PratfA influences SM pathways in P. raistrickii. The manipulation of regulatory factors can guide the discovery of novel natural products (NPs). Full article

Fungi have played a pivotal role in human history, from the dangers of fungal toxins to the revolutionary discovery of penicillin. Fungal secondary metabolites (SMs), such as polyketides (PKs) and terpenes, have attracted considerable interest due to their diverse biological activities. Botrytis deweyae, an endophytic fungus, exhibits behaviors that are notably distinct from those of its necrotrophic relatives within the genus Botrytis. This study explores the importance of terpenes and PK gene clusters and their conservation between species. In addition, new putative biosynthetic gene clusters corresponding to those families were identified. Consequently, the new PKS BdPKS22-26 were also identified in other Botrytis species and other fungi. In addition, those new gene clusters identified in this work show differences in the degree of conservation and are phylogenetically closely related to some of the 21 PKSs previously described in the reference strain Botrytis cinerea B05.10. Moreover, a new gene cluster related to terpenes in B. deweyae B1 and B. cinerea B05.10 was also identified that had never been detected before. This new gene cluster is well conserved among other Botrytis species in many phylogenetically distant fungal lineages. Understanding the genetic basis and conservation of these putative biosynthetic gene clusters sheds light on the metabolic potential and ecological roles of B. deweyae and related fungal species. Full article

Background: Mastocytosis (MS) is a rare disease that can involve various organs, including the bone. Given the incidence of the disease in the global population, MS poses a challenge for physicians, and early therapeutic intervention in the initial stages could significantly impact the quality of life of affected patients. Objective: The aim of this scoping review was to provide an overview of secondary osteoporosis in systemic mastocytosis (SM), focusing on the heterogeneity of its manifestations, the benefits of early diagnosis, and appropriate pharmacological treatment. Design: A technical expert panel (TEP) consisting of 8 physicians with expertise in metabolic bone diseases conducted the review following the PRISMA-ScR model. A strength of this study is that it provides various therapeutic approaches for patients with bone involvement in SM, although the limited available literature on the topic constituted a limitation. The TEP sought evidence regarding the following diagnostic and therapeutic modalities in the management of SM: “bisphosphonate therapy”, “zoledronic acid therapy”, “denosumab therapy”, “IFN-alpha therapy”, and “IFN-alpha therapy in combination with pamidronate”. Results: Clinical data showed a correlation between densitometric outcomes, serum tryptase levels, and mast cell infiltration in the bone marrow, between increased bone mineral density and the presence of osteosclerosis in cases of advanced SM, between the severity of osteoporosis and hypertryptasemia, and also provided results on the long-term effects of bisphosphonate therapy, the therapeutic efficacy of zoledronic acid administration, the positive effect of denosumab on the reduction of serum tryptase levels (even if is proved in a limited numbers of cases) and the prevention of new fractures, and the effect of IFN-alpha in more severe cases of SM, either alone or in combination with pamidronate. Conclusions: Studies have demonstrated the effectiveness of various treatments depending on the form of mastocytosis, whether indolent systemic or advanced systemic, in the prognosis of the disease. However, this role should be further investigated in additional clinical studies, considering the limited data on the use of these interventions. Full article

The bitter rot of apple is caused by Colletotrichum spp. and is a serious pre-harvest disease that can manifest in postharvest losses on harvested fruit. In this study, we obtained genome sequences from four different species, C. chrysophilum, C. noveboracense, C. nupharicola, and C. fioriniae, that infect apple and cause diseases on other fruits, vegetables, and flowers. Our genomic data were obtained from isolates/species that have not yet been sequenced and represent geographic-specific regions. Genome sequencing allowed for the construction of phylogenetic trees, which corroborated the overall concordance observed in prior MLST studies. Bioinformatic pipelines were used to discover CAZyme, effector, and secondary metabolic (SM) gene clusters in all nine Colletotrichum isolates. We found redundancy and a high level of similarity across species regarding CAZyme classes and predicted cytoplastic and apoplastic effectors. SM gene clusters displayed the most diversity in type and the most common cluster was one that encodes genes involved in the production of alternapyrone. Our study provides a solid platform to identify targets for functional studies that underpin pathogenicity, virulence, and/or quiescence that can be targeted for the development of new control strategies. With these new genomics resources, exploration via omics-based technologies using these isolates will help ascertain the biological underpinnings of their widespread success and observed geographic dominance in specific areas throughout the country. Full article

Plasmids are mobile genetic elements known to carry secondary metabolic genes that affect the fitness and survival of microbes in the environment. Well-studied cases of plasmid-encoded secondary metabolic genes in marine habitats include toxin/antitoxin and antibiotic biosynthesis/resistance genes. Here, we examine metagenome-assembled genomes (MAGs) from the permanently-stratified water column of the Cariaco Basin for integrated plasmids that encode biosynthetic gene clusters of secondary metabolites (smBGCs). We identify 16 plasmid-borne smBGCs in MAGs associated primarily with Planctomycetota and Pseudomonadota that encode terpene-synthesizing genes, and genes for production of ribosomal and non-ribosomal peptides. These identified genes encode for secondary metabolites that are mainly antimicrobial agents, and hence, their uptake via plasmids may increase the competitive advantage of those host taxa that acquire them. The ecological and evolutionary significance of smBGCs carried by prokaryotes in oxygen-depleted water columns is yet to be fully elucidated. Full article

In 1999, the first biosynthetic gene cluster (BGC), synthesizing the virulence factor DHN melanin, was characterized in Aspergillus fumigatus. Since then, 19 additional BGCs have been linked to specific secondary metabolites (SMs) in this species. Here, we provide a comprehensive timeline of A. fumigatus BGC discovery and find that initial advances centered around the commonly expressed SMs where chemical structure informed rationale identification of the producing BGC (e.g., gliotoxin, fumigaclavine, fumitremorgin, pseurotin A, helvolic acid, fumiquinazoline). Further advances followed the transcriptional profiling of a ΔlaeA mutant, which aided in the identification of endocrocin, fumagillin, hexadehydroastechrome, trypacidin, and fumisoquin BGCs. These SMs and their precursors are the commonly produced metabolites in most A. fumigatus studies. Characterization of other BGC/SM pairs required additional efforts, such as induction treatments, including co-culture with bacteria (fumicycline/neosartoricin, fumigermin) or growth under copper starvation (fumivaline, fumicicolin). Finally, four BGC/SM pairs were discovered via overexpression technologies, including the use of heterologous hosts (fumicycline/neosartoricin, fumihopaside, sphingofungin, and sartorypyrone). Initial analysis of the two most studied A. fumigatus isolates, Af293 and A1160, suggested that both harbored ca. 34–36 BGCs. An examination of 264 available genomes of A. fumigatus located only four additional new BGCs, suggesting the secondary metabolome across A. fumigatus isolates is remarkably conserved. Based on our analysis, around 20 of the genetically characterized BGCs within the A. fumigatus species complex still lack a known chemical product. Such BGCs remain the final hurdle in fully understanding the secondary metabolism in this important species. Full article

With its quality, intensity, and photoperiod, light is a decisive abiotic factor that directly influences plant biomass and the accumulation of specialized metabolites (SMs). Photosynthetically active radiation (PAR) has significant effects on primary and secondary plant metabolism and thus influences the morphological characteristics of plants and their antioxidant systems. The aim of this study was to investigate the effects of blue, red, and a 50:50 combination of blue and red LED lighting on the SM content in broccoli, mustard, and garden cress microgreens grown in an indoor farm using the zero-acreage farming technique (ZFarming). This research aims to provide valuable insights into the optimization of light spectra to improve the nutritional quality of microgreens, with a focus on sustainable and space-saving cultivation methods. After eight days, the samples were cut in the cotyledon phenophase and analyzed in a fresh state. The microgreens grown under the blue spectrum LED lighting had the highest content of ascorbic acid (112.70 mg·100 g fw⁻¹), total phenolics (412.39 mg GAE·100 g fw⁻¹), and the highest antioxidant capacity (2443.62 µmol TE·L⁻¹). The results show that the highest content of SMs in all the studied microgreens species was accumulated under the blue spectrum LED lighting. This study underlines the favorable influence of the blue spectrum (400–500 nm) on the nutrient content, especially the enhancement of SMs, in the microgreens investigated. Furthermore, the use of supplemental LED lighting proves to be a sustainable and effective means of producing microgreens with superior nutritional properties through the innovative practice of the zero-acreage farming technique. Full article

Traumatic brain injury (TBI) is a significant source of disability in the United States and around the world and may lead to long-lasting cognitive deficits and a decreased quality of life for patients across injury severities. Following the primary injury phase, TBI is characterized by complex secondary cascades that involve altered homeostasis and metabolism, faulty signaling, neuroinflammation, and lipid dysfunction. The objectives of the present study were to (1) assess potential correlations between lipidome and cytokine changes after closed-head mild TBI (mTBI), and (2) examine the reproducibility of our acute lipidomic profiles following TBI. Cortices from 54 Sprague Dawley male and female rats were analyzed by ultra-high-performance liquid chromatography mass spectrometry (LC-MS) in both positive and negative ionization modes and multiplex cytokine analysis after single (smTBI) or repetitive (rmTBI) closed-head impacts, or sham conditions. Tissue age was a variable, given that two cohorts (n = 26 and n = 28) were initially run a year-and-a-half apart, creating inter-batch variations. We annotated the lipidome datasets using an in-house data dictionary based on exact masses of precursor and fragment ions and removed features with statistically significant differences between sham control batches. Our results indicate that lipids with high-fold change between injury groups moderately correlate with the cytokines eotaxin, IP-10, and TNF-α. Additionally, we show a significant decrease in the pro-inflammatory markers IL-1β and IP-10, TNF-α, and RANTES in the rmTBI samples relative to the sham control. We discuss the major challenges in correlating high dimensional lipidomic data with functional cytokine profiles and the implications for understanding the biological significance of two related but disparate analysis modes in the study of TBI, an inherently heterogeneous neurological disorder. Full article

Protein tyrosine phosphatases (PTPs) are ubiquitous in living organisms and are promising drug targets for cancer, diabetes/obesity, and autoimmune disorders. In this study, a histone deacetylase inhibitor called suberoylanilide hydroxamic acid (SAHA) was added to a culture of marine fungi (Aspergillus sydowii DL1045) to identify potential drug candidates related to PTP inhibition. Then, the profile of the induced metabolites was characterized using an integrated metabolomics strategy. In total, 46% of the total SMs were regulated secondary metabolites (SMs), among which 20 newly biosynthesized metabolites (10% of the total SMs) were identified only in chemical epigenetic regulation (CER) broth. One was identified as a novel compound, and fourteen compounds were identified from Aspergillus sydowii first. SAHA derivatives were also biotransformed by A. sydowii DL1045, and five of these derivatives were identified. Based on the bioassay, some of the newly synthesized metabolites exhibited inhibitory effects on PTPs. The novel compound sydowimide A (A11) inhibited Src homology region 2 domain-containing phosphatase-1 (SHP1), T-cell protein tyrosine phosphatase (TCPTP) and leukocyte common antigen (CD45), with IC₅₀ values of 1.5, 2.4 and 18.83 μM, respectively. Diorcinol (A3) displayed the strongest inhibitory effect on SHP1, with an IC₅₀ value of 0.96 μM. The structure–activity relationship analysis and docking studies of A3 analogs indicated that the substitution of the carboxyl group reduced the activity of A3. Research has demonstrated that CER positively impacts changes in the secondary metabolic patterns of A. sydowii DL1045. The compounds produced through this approach will provide valuable insights for the creation and advancement of novel drug candidates related to PTP inhibition. Full article

The natural fermentation of antibiotics, along with semi-synthetic and synthetic approaches, is one of the most important methods for their production. The majority of the antibiotic market comes from the fermentation of high-yielding (HY) fungal strains. These strains have been obtained since the 1950s from wild-type (WT) isolates as a result of classical strain improvement (CSI) programs primarily involving multi-round random mutagenesis and screening. However, the molecular basis leading to high-yield production was unknown. In recent years, due to the application of multiomic approaches, key changes that occur in CSI programs, with WT strains that become HY industrial producers of a particular antibiotic, have begun to be understood. It becomes obvious that, during CSI, certain universal events are selected, which lead both to a direct increase in the production of the target metabolite and affect other vital processes of the cell (side mutations). These key events include: the upregulation of the target biosynthetic gene cluster (BGC), changes in the system of global regulation, disruption of alternative BGCs, the rearrangement of energy fluxes in favor of the target SM (secondary metabolite), changes in the regulation of the response to stress, and the redirection of primary metabolic pathways to obtain more precursors for target production. This knowledge opens up the possibility of both introducing targeted changes using genetic engineering methods when creating new producers and increasing the production of CSI strains as a result of fermentation with low-molecular compounds, targeted to compensate for the effects of side mutations. Full article

Tyrosine aminotransferase (TAT, E.C. 2.6.1.5) is a pyridoxal phosphate-dependent aminotransferase that is widely found in living organisms. It catalyzes the transfer of the amino group on tyrosine to α-ketoglutarate to produce 4-hydroxyphenylpyruvic acid (4-HPP) and is the first enzyme for tyrosine degradation. Three SmTATs have been identified in the genome of Salvia miltiorrhiza (a model medicinal plant), but their information is very limited. Here, the expression profiles of the three SmTAT genes (SmTAT1, SmTAT2, and SmTAT3) were studied. All three genes expressed in different tissues and responded to methyl jasmonate stimuli. SmTAT proteins are localized in the cytoplasm. The recombinant SmTATs were subjected to in vitro biochemical properties. All three recombinant enzymes had TAT activities and SmTAT1 had the highest catalytic activity for tyrosine, followed by SmTAT3. Also, SmTAT1 preferred the direction of tyrosine deamination to 4-HPP, while SmTAT2 preferred transamination of 4-HPP to tyrosine. In parallel, transient overexpression of SmTATs in tobacco leaves revealed that all three SmTAT proteins catalyzed tyrosine to 4-HPP in vivo, with SmTAT1 exhibiting the highest enzymatic activity. Overall, our results lay a foundation for the production of tyrosine-derived secondary metabolites via metabolic engineering or synthetic biology in the future. Full article

The soil-borne pathogen Fusarium pseudograminearum is capable of causing a highly destructive crown disease in wheat. The purpose of this study was to characterize the biological functions, such as of virulence and secondary metabolites (SMs), of a putative RNA-Pol II transcription elongation factor, FpRtfA, in F. pseudograminearum. The current study revealed that the deletion of FpRtfA reduced radial growth compared to wild type in F. pseudograminearum. In addition, FpRtfA was found important to conidiation and response to metal ions and oxidative stress. More importantly, the virulence to the wheat stem base or head was decreased when FpRtfA was deleted. Using genome-wide gene expression profiling, FpRtfA was found to regulate several processes related to the above phenotype, such as the carbohydrate metabolic process, and the response to oxidative stress and oxidoreductase activity, especially for SMs. Further, we proved that FpRtfA exerts its regulatory effect on the virulence of pathogens by modulating the expression of the PKS gene, but not the generation of DON. In conclusion, FpRtfA has important roles in growth, asexual development, and the response to metal ions and oxidative stress. More importantly, FpRtfA is required for SMs and full virulence in F. pseudograminearum. Full article