Hydroxytryptophan biosynthesis by a family of heme-dependent enzymes in bacteria.

Hydroxytryptophan serves as a chemical precursor to a variety of bioactive specialized metabolites, including the human neurotransmitter serotonin and the hormone melatonin. Although the human and animal routes to hydroxytryptophan have been known for decades, how bacteria catalyze tryptophan indole hydroxylation remains a mystery. Here we report a class of tryptophan hydroxylases that are involved in various bacterial metabolic pathways. These enzymes utilize a histidine-ligated heme cofactor and molecular oxygen or hydrogen peroxide to catalyze regioselective hydroxylation on the tryptophan indole moiety, which is mechanistically distinct from their animal counterparts from the nonheme iron enzyme family. Through genome mining, we also identify members that can hydroxylate the tryptophan indole ring at alternative positions. Our results not only reveal a conserved way to synthesize hydroxytryptophans in bacteria but also provide a valuable enzyme toolbox for biocatalysis. As proof of concept, we assemble a highly efficient pathway for melatonin in a bacterial host.

Discovery of a Bacterial Hydrazine Transferase That Constructs the N-Aminolactam Pharmacophore in Albofungin Biosynthesis.

Structural motifs containing nitrogen-nitrogen (N-N) bonds are prevalent in a large number of clinical drugs and bioactive natural products. Hydrazine (N2H4) serves as a widely utilized building block for the preparation of these N-N-containing molecules in organic synthesis. Despite its common use in chemical processes, no enzyme has been identified to catalyze the incorporation of free hydrazine in natural product biosynthesis. Here, we report that a hydrazine transferase catalyzes the condensation of N2H4 and an aromatic polyketide pathway intermediate, leading to the formation of a rare N-aminolactam pharmacophore in the biosynthesis of broad-spectrum antibiotic albofungin. These results expand the current knowledge on the biosynthetic mechanism for natural products with N-N units and should facilitate future development of biocatalysts for the production of N-N-containing chemicals.

Albiflorin ameliorates thioacetamide-induced hepatic fibrosis: The involvement of NURR1-mediated inflammatory signaling cascades in hepatic stellate cells activation.

Thioacetamide (TAA) within the liver generates hepatotoxic metabolites that can be induce hepatic fibrosis, similar to the clinical pathological features of chronic human liver disease. The potential protective effect of Albiflorin (ALB), a monoterpenoid glycoside found in Paeonia lactiflora Pall, against hepatic fibrosis was investigated. The mouse hepatic fibrosis model was induced with an intraperitoneal injection of TAA. Hepatic stellate cells (HSCs) were subjected to treatment with transforming growth factor-beta (TGF-ß), while lipopolysaccharide/adenosine triphosphate (LPS/ATP) was added to stimulate mouse peritoneal macrophages (MPMs), leading to the acquisition of conditioned medium. For TAA-treated mice, ALB reduced ALT, AST, HYP levels in serum or liver. The administration of ALB reduced histopathological abnormalities, and significantly regulated the expressions of nuclear receptor-related 1 protein (NURR1) and the P2X purinoceptor 7 receptor (P2×7r) in liver. ALB could suppress HSCs epithelial-mesenchymal transition (EMT), extracellular matrix (ECM) deposition, and pro-inflammatory factor level. ALB also remarkably up-regulated NURR1, inhibited P2×7r signaling pathway, and worked as working as C-DIM12, a NURR1 agonist. Moreover, deficiency of NURR1 in activated HSCs and Kupffer cells weakened the regulatory effect of ALB on P2×7r inhibition. NURR1-mediated inhibition of inflammatory contributed to the regulation of ALB ameliorates TAA-induced hepatic fibrosis, especially based on involving in the crosstalk of HSCs-macrophage. Therefore, ALB plays a significant part in the mitigation of TAA-induced hepatotoxicity this highlights the potential of ALB as a protective intervention for hepatic fibrosis.

Regulation of the Nur77-P2X7r Signaling Pathway by Nodakenin: A Potential Protective Function against Alcoholic Liver Disease.

Alcoholic liver disease (ALD) is the main factor that induces liver-related death worldwide and represents a common chronic hepatopathy resulting from binge or chronic alcohol consumption. This work focused on revealing the role and molecular mechanism of nodakenin (NK) in ALD associated with hepatic inflammation and lipid metabolism through the regulation of Nur77-P2X7r signaling. In this study, an ALD model was constructed through chronic feeding of Lieber-DeCarli control solution with or without NK treatment. Ethanol (EtOH) or NK was administered to AML-12 cells, after which Nur77 was silenced. HepG2 cells were exposed to ethanol (EtOH) and subsequently treated with recombinant Nur77 (rNur77). Mouse peritoneal macrophages (MPMs) were treated with lipopolysaccharide/adenosine triphosphate (LPS/ATP) and NK, resulting in the generation of conditioned media. In vivo, histopathological alterations were markedly alleviated by NK, accompanied by reductions in serum triglyceride (TG), aspartate aminotransferase (AST), and alanine aminotransferase (ALT) levels and the modulation of Lipin-1, SREBP1, and Nur77 levels in comparison to the EtOH-exposed group (p < 0.001). Additionally, NK reduced the production of P2X7r and NLRP3. NK markedly upregulated Nur77, inhibited P2X7r and Lipin-1, and promoted the function of Cytosporone B, a Nur77 agonist (p < 0.001). Moreover, Nur77 deficiency weakened the regulatory effect of NK on P2X7r and Lipin-1 inhibition (p < 0.001). In NK-exposed MPMs, cleaved caspase-1 and mature IL-1ß expression decreased following LPS/ATP treatment (p < 0.001). NK also decreased inflammatory-factor production in primary hepatocytes stimulated with MPM supernatant. NK ameliorated ETOH-induced ALD through a reduction in inflammation and lipogenesis factors, which was likely related to Nur77 activation. Hence, NK is a potential therapeutic approach to ALD.

Conserved Enzymatic Cascade for Bacterial Azoxy Biosynthesis.

Azoxy compounds exhibit a wide array of biological activities and possess distinctive chemical properties. Although there has been considerable interest in the biosynthetic mechanisms of azoxy metabolites, the enzymatic basis responsible for azoxy bond formation has remained largely enigmatic. In this study, we unveil the enzyme cascade that constructs the azoxy bond in valanimycin biosynthesis. Our research demonstrates that a pair of metalloenzymes, comprising a membrane-bound hydrazine synthase and a nonheme diiron azoxy synthase, collaborate to convert an unstable pathway intermediate to an azoxy product through a hydrazine-azo-azoxy pathway. Additionally, by characterizing homologues of this enzyme pair from other azoxy metabolite pathways, we propose that this two-enzyme cascade could represent a conserved enzymatic strategy for azoxy bond formation in bacteria. These findings provide significant mechanistic insights into biological N-N bond formation and should facilitate the targeted isolation of bioactive azoxy compounds through genome mining.

Functional Characterization of Laccase Isozyme (PoLcc1) from the Edible Mushroom Pleurotus ostreatus Involved in Lignin Degradation in Cotton Straw.

Fungal laccases play important roles in the degradation of lignocellulose. In this study, the laccase producing cotton straw medium for Pleurotus ostreatus was optimized by single-factor and orthogonal experiments, and to investigate the role of Lacc1 gene, one of the laccase-encoding genes, in the degradation of cotton straw lignin, an overexpression strain of Lacc1 gene was constructed, which was analyzed for the characteristics of lignin degradation. The results demonstrated that the culture conditions with the highest lignin degradation efficiency of the P. ostreatus were the cotton straw particle size of 0.75 mm, a solid-liquid ratio of 1:3 and containing 0.25 g/L of Tween in the medium, as well as an incubation temperature of 26 °C. Two overexpression strains (OE L1-1 and OE L1-4) of Lacc1 gene were obtained, and the gene expression increased 12.08- and 33.04-fold, respectively. The results of 1H-NMR and FTIR analyses of significant changes in lignin structure revealed that Lacc1 gene accelerated the degradation of lignin G-units and involved in the cleavage of ß-O-4 linkages and the demethylation of lignin units. These findings will help to improve the efficiency of biodelignification and expand our understanding of its mechanism.

Convergent biosynthetic transformations to a bacterial specialized metabolite.

Microbes produce specialized metabolites to thrive in their natural habitats. However, it is rare that a given specialized metabolite is biosynthesized via pathways with distinct intermediates and enzymes. Here, we show that the core assembly mechanism of the antibiotic indolmycin in marine gram-negative Pseudoalteromonas luteoviolacea is distinct from its counterpart in terrestrial gram-positive Streptomyces species, with a molecule that is a shunt product in the Streptomyces pathway employed as a biosynthetic substrate for a novel metal-independent N-demethylindolmycin synthase in the P. luteoviolacea pathway. To provide insight into this reaction, we solved the 1.5 Å resolution structure in complex with product and identified the active site residues. Guided by our biosynthetic insights, we then engineered the Streptomyces indolmycin producer for titer improvement. This study provides a paradigm for understanding how two unique routes to a microbial specialized metabolite can emerge from convergent biosynthetic transformations.

Enzymatic Tailoring in Luzopeptin Biosynthesis Involves Cytochrome†P450-Mediated Carbon-Nitrogen Bond Desaturation for Hydrazone Formation.

Luzopeptins and related decadepsipeptides are bisintercalator nonribosomal peptides featuring rare acyl-substituted tetrahydropyridazine-3-carboxylic acid (Thp) subunits that are critical to their biological activities. Herein, we reconstitute the biosynthetic tailoring pathway in luzopeptin A biosynthesis through in vivo genetic and in vitro biochemical approaches. Significantly, we revealed a multitasking cytochrome P450 enzyme that catalyzes four consecutive oxidations including the highly unusual carbon-nitrogen bond desaturation, forming the hydrazone-bearing 4-OH-Thp residues. Moreover, we identified a membrane-bound acyltransferase that likely mediates the subsequent O-acetylation extracellularly, as a potential self-protective strategy for the producer strain. Further genome mining of novel decadepsipeptides and an associated P450 enzyme have provided mechanistic insights into the P450-mediated carbon-nitrogen bond desaturation. Our results not only reveal the molecular basis of pharmacophore formation in bisintercalator decadepsipeptides, but also expand the catalytic versatility of P450 family enzymes.

The Biosynthetic Gene Cluster of Pyrazomycin-A C-Nucleoside Antibiotic with a Rare Pyrazole Moiety.

Pyrazomycin is a rare C-nucleoside antibiotic containing a naturally occurring pyrazole ring, the biosynthetic origin of which has remained obscure for decades. In this study we report the identification of the gene cluster responsible for pyrazomycin biosynthesis in Streptomyces candidus NRRL 3601, revealing that the StrR-family regulator PyrR is the cluster-situated transcriptional activator governing pyrazomycin biosynthesis. Furthermore, our results from in vivo reconstitution and stable-isotope feeding experiments provide support for the hypothesis that PyrN is a new nitrogen-nitrogen bond-forming enzyme that catalyzes the linkage of the ϵ-NH2 nitrogen atom of l-N6 -OH-lysine and the α-NH2 nitrogen atom of l-glutamic acid. This study lays the foundation for further genetic and biochemical characterization of pyrazomycin pathway enzymes involved in constructing the characteristic pyrazole ring.

An HPLC method for simultaneous quantitative determination of seven secoiridoid glucosides separated from the roots of Ilex pubescens.

A simple and specific high-performance liquid chromatographic method has been developed and validated to simultaneously determine seven secoiridoid glucosides for the first time. Three of them were separated from the ethanolic extract of the roots of Ilex pubescens for the first time, namely nuezhenide A, ligusides B and oleonuezhenide. In quantitative analysis, all of the calibration curves showed good linear regression (r > 0.999) within the tested ranges, and the mean recoveries of three different concentrations ranged from 97.6 to 101.2%. The limit of detection and limit of quantification were <4.18 and 11.63 ng mL-1 , respectively. The relative standard deviation for repeatability and the precision of seven analytes were <3.4 and 1.9%, respectively. The established method was successfully applied to simultaneous determination of seven secoiridoid glucosides in 11 batches of samples collected from different habitats in China.

Nitric oxide synthase-guided genome mining identifies a cytochrome P450 enzyme for olefin nitration in bacterial specialized metabolism.

The biological signaling molecule nitric oxide (NO) has recently emerged as a metabolic precursor for the creation of microbial natural products with diversified structures and biological activities. Within the biosynthetic gene clusters (BGCs) of these compounds, genes associated with NO production pathways have been pinpointed. In this study, we employ a nitric oxide synthase (NOS)-guided genome mining strategy for the targeted discovery of NO-derived bacterial natural products and NO-utilizing biocatalysts. We show that a conserved NOS-containing BGC, distributed across several actinobacterial genomes, is responsible for the biosynthesis of lajollamycin, a unique nitro-tetraene-containing antibiotic whose biosynthetic mechanism remains elusive. Through a combination of in vivo and in vitro studies, we unveil the first cytochrome P450 enzyme capable of catalyzing olefin nitration in natural product biosynthesis. These results not only expand the current knowledge about biosynthetic nitration processes but also offer an efficient way for targeted identification of NO-utilizing metabolic pathways and novel nitrating biocatalysts.

Effects of moderate drought extension on bacterial network structure in the rhizosphere soil of Leymus chinensis in semi-arid grasslands.

Introduction: Grasslands are home to complex bacterial communities whose dynamic interactions play a crucial role in organic matter and nutrient cycling. However, there is limited understanding regarding the impact of changes in rainfall amount and the duration of dry intervals on bacterial interactions. Methods: To assess the impact of changes in precipitation volume and dry intervals on bacterial co-occurrence networks, we carried out precipitation manipulation experiments in the Eastern Eurasian Steppe of China. Results and Discussion: We found that alterations in precipitation and dry intervals did not significantly affect bacterial alpha and beta diversity. However, we observed significant changes in the co-occurrence network structure of bacteria in the rhizosphere ecosystem, with the 12-day dry interval showing the most notable reduction in the number of degrees, edges, and clustering coefficient. Additionally, the study identified putative keystone taxa and observed that the moderately prolonged dry intervals between precipitation events had a major effect on the robustness of bacterial networks. The complexity and stability of the network were found to be positively correlated, and were primarily influenced by soil water content, phosphorous, and aboveground biomass, followed by available phosphorus (AP) and total biomass. These findings have the potential to enhance our comprehension of how bacterial co-occurrence pattern react to variations in dry intervals, by regulating their interactions in water-limited ecosystems. This, in turn, could aid in predicting the impact of precipitation regime alterations on ecosystem nutrient cycling, as well as the feedback between ecosystem processes and global climate change.

Heterologous Reconstitution of Toxoflavin Biosynthesis Reveals Key Pathway Intermediates and a Cofactor-Independent Oxidase.

Bacterial azapteridine-containing phytotoxin toxoflavin is a causal agent of rice grain rot. Here, we heterologously reconstitute Bukholderia toxoflavin biosynthesis in Escherichia coli and identify key pathway intermediates, including the hitherto unknown ribityl-dedimethyl-toxoflavin. Furthermore, we characterized a cofactorless oxidase that converts ribityl-dedimethyl-toxoflavin to ribose and dedimethyl-toxoflavin, the latter of which then undergoes stepwise methylations to form toxoflavin. These findings provide new insights into the biosynthetic pathways of toxoflavin and related triazine metabolites.

Targeted genome mining for microbial antitumor agents acting through DNA intercalation.

Microbial natural products have been one of the most important sources for drug development. In the current postgenomic era, sequence-driven approaches for natural product discovery are becoming increasingly popular. Here, we develop an effective genome mining strategy for the targeted discovery of microbial metabolites with antitumor activities. Our method employs uvrA-like genes as genetic markers, which have been identified in the biosynthetic gene clusters (BGCs) of several chemotherapeutic drugs of microbial origin and confer self-resistance to the corresponding producers. Through systematic genomic analysis of gifted actinobacteria genera, identification of uvrA-like gene-containing BGCs, and targeted isolation of products from a BGC prioritized for metabolic analysis, we identified a new tetracycline-type DNA intercalator timmycins. Our results thus provide a new genome mining strategy for the efficient discovery of antitumor agents acting through DNA intercalation.

Taurine postponed the replicative senescence of rat bone marrow-derived multipotent stromal cells in vitro.

The aging of many mammalian tissues is associated with replicative decline in somatic stem cells. Postponing this decline is a direct way of anti-aging. Bone marrow-derived multipotent stromal cells (BMSCs) hold promise for an increasing list of therapeutic uses due to their multilineage potential. Clinical application of BMSCs requires abundant cells that can be overcome by ex vivo expansion of cells, but often facing the replicative senescence problem. We demonstrated that taurine exhibited anti-replicative senescence effect on rat BMSCs by promoting colony forming unit-fibroblast formation and cell proliferation, shortening cell population doubling time, enormously inhibiting senescence-associated beta-galactosidase activity and slowing the loss of differentiation potential, while having no significant effect on the maximum passage number and total culture time, and slight influences on the cell surface CD molecules expressions. Taurine is a quite safe antioxidant and nutrient extensively used in food addition and clinical treatment. These suggested that taurine is a promising anti-replicative senescence additive for ex vivo expansion of BMSCs in experimental and clinical cell therapies.

Ligninolytic characteristics of Pleurotus ostreatus cultivated in cotton stalk media.

Biodelignification is widely regarded as a low-efficiency process because it is usually slow and difficult to control. To improve its efficiency and understand its mechanism, the present study analyzed the delignification characteristics of Pleurotus ostreatus grown on a cotton stalk medium. The results demonstrated that all strains of P. ostreatus can selectively degrade the cotton stalk lignin. When cultured in a cotton stalk medium for 60 days, P. ostreatus degraded lignin primarily during its mycelium growth with up to 54.04% lignin degradation and produced laccase and manganese dependent peroxidase with high activity levels at the peaks of 70.17 U/ml and 62.39 U/ml, respectively, but no detectable lignin peroxidase. The results of nuclear magnetic resonance spectroscopy and Fourier transform infrared spectroscopy analyses of significant changes in lignin structure revealed that syringyl (S) lignin units were more degraded than guaiacyl (G) lignin units, with a significantly elevated G/S ratio. The Gas Chromatography-Mass Spectrometer analysis of low-molecular-weight compounds revealed that the delignification resulted in the formation of alcohols, organic acids, benzodiazepines, and alkanes. Identified benzodiazepines implied the degradation of G and S units of lignin. These findings will help to improve the efficiency of biodelignification and expand our understanding of its mechanism.

Decreased precipitation reduced the complexity and stability of bacterial co-occurrence patterns in a semiarid grassland.

Introduction: Grasslands harbor complex bacterial communities, whose dynamic interactions are considered critical for organic matter and nutrient cycling. However, less is known about how changes in precipitation impact bacterial interactions. Methods: We conducted precipitation manipulation experiments in the Eastern Eurasian Steppe in China and constructed co-occurrence networks for bacterial communities. Results: The network topological features of the bacterial communities exhibited considerable differences among increased precipitation, control, and decreased precipitation gradients. The bacterial co-occurrence pattern in the increased precipitation gradient was the most complex and stable, with a large network size, followed by those of the control and decreased precipitation gradients. Soil moisture (SM) was the primary factor influencing the complexity, size, and stability of bacterial networks across different precipitation gradients, followed by total nitrogen (TN), belowground biomass, aboveground biomass, and total carbon (TC). Discussion: Our results indicate that drought conditions reduce the complexity and stability of the bacterial community, and future changes in precipitation will greatly reshape bacterial interactions in semiarid grasslands. Overall, these findings could enhance our understanding of how microbes respond to changing precipitation patterns by regulating their interactions in water-limited ecosystems and will improve our ability to predict the impacts of precipitation regime change on ecosystem nutrient cycling and feedback between ecosystem processes and global climate change.

Molecular basis of enzymatic nitrogen-nitrogen formation by a family of zinc-binding cupin enzymes.

Molecules with a nitrogen-nitrogen (N-N) bond in their structures exhibit various biological activities and other unique properties. A few microbial proteins are recently emerging as dedicated N-N bond forming enzymes in natural product biosynthesis. However, the details of these biochemical processes remain largely unknown. Here, through in vitro biochemical characterization and computational studies, we report the molecular basis of hydrazine bond formation by a family of di-domain enzymes. These enzymes are widespread in bacteria and sometimes naturally exist as two standalone enzymes. We reveal that the methionyl-tRNA synthase-like domain/protein catalyzes ATP-dependent condensation of two amino acids substrates to form a highly unstable ester intermediate, which is subsequently captured by the zinc-binding cupin domain/protein and undergoes redox-neutral intramolecular rearrangement to give the N-N bond containing product. These results provide important mechanistic insights into enzymatic N-N bond formation and should facilitate future development of novel N-N forming biocatalyst.

Nitric oxide as a source for bacterial triazole biosynthesis.

The heterocycle 1,2,3-triazole is among the most versatile chemical scaffolds and has been widely used in diverse fields. However, how nature creates this nitrogen-rich ring system remains unknown. Here, we report the biosynthetic route to the triazole-bearing antimetabolite 8-azaguanine. We reveal that its triazole moiety can be assembled through an enzymatic and non-enzymatic cascade, in which nitric oxide is used as a building block. These results expand our knowledge of the physiological role of nitric oxide synthase in building natural products with a nitrogen-nitrogen bond, and should also inspire the development of synthetic biology approaches for triazole production.

New phenanthrene and 9, 10-dihydrophenanthrene derivatives from the stems of Dendrobium officinale with their cytotoxic activities.

Two new phenanthrene and 9, 10-dihydrophenanthrene derivatives (1-2) with six known congeners (3-8) were isolated from the extraction of stems of Dendrobium officinale. Compounds 1 and 2 were based on carbon skeleton in which phenanthrene and 9, 10-dihydrophenanthrene moiety were linked with a phenylpropane unit through a dioxane bridge, respectively. Their structures were determined by comprehensive NMR spectroscopic data, the absolute configuration of new compounds were determined by comparing their experimental and calculated ECD for the first time. All the compounds were investigated contains two cancer cell lines (HI-60, THP-1). All the isolates showed cytotoxicity, especially compound 4 showed markedly cytotoxic activities against HI-60 and THP-1 cell lines with IC50 values of 11.96 and 8.92 µM.