Effective prediction of biosynthetic pathway genes involved in bioactive polyphyllins in Paris polyphylla

The genes in polyphyllins pathway mixed with other steroid biosynthetic genes form an extremely complex biosynthetic network in Paris polyphylla with a giant genome. The lack of genomic data and tissue specificity causes the study of the biosynthetic pathway notably difficult. Here, we report an effective method for the prediction of key genes of polyphyllin biosynthesis. Full-length transcriptome from eight different organs via hybrid sequencing of next generation sequencingand third generation sequencing platforms annotated two 2,3-oxidosqualene cyclases (OSCs), 216 cytochrome P450s (CYPs), and 199 UDP glycosyltransferases (UGTs). Combining metabolic differences, gene-weighted co-expression network analysis, and phylogenetic trees, the candidate ranges of OSC, CYP, and UGT genes were further narrowed down to 2, 15, and 24, respectively. Beside the three previously characterized CYPs, we identified the OSC involved in the synthesis of cycloartenol and the UGT (PpUGT73CR1) at the C-3 position of diosgenin and pennogenin in P. polyphylla. This study provides an idea for the investigation of gene cluster deficiency biosynthesis pathways in medicinal plants.

Total In Vitro Biosynthesis of the Thioamitide Thioholgamide and Investigation of the Pathway

Thioholgamides are ribosomally synthesized and post-translationally modified peptides (RiPPs) with potent activity against cancerous cell lines and an unprecedented structure. Despite being one of the most structurally and chemically complex RiPPs, very few biosynthetic steps have been elucidated. Here, we report the complete in vitro reconstitution of the biosynthetic pathway. We demonstrate that thioamidation is the first step and acts as a gatekeeper for downstream processing. Thr dehydration follows thioamidation, and our studies reveal that both these modifications require the formation of protein complexes – ThoH/I and ThoC/D. Harnessing the power of AlphaFold we deduce that ThoD acts as a lyase and also propose putative catalytic residues. ThoF catalyzes the oxidative decarboxylation of the terminal Cys and the subsequent macrocyclization is facilitated by ThoE. This is followed by Ser dehydration, which is also carried out by ThoC/D. ThoG is responsible for histidine bis-N-methylation, which is a prerequisite for His β-hydroxylation – a modification carried out by ThoJ. The last step of the pathway is the removal of the leader peptide by ThoK to afford mature thioholgamide.

Recognized and Emerging Features of Erythropoietic and X-Linked Protoporphyria

Erythropoietic protoporphyria (EPP) and X-linked protoporphyria (XLP) are inherited disorders resulting from defects in two different enzymes of the heme biosynthetic pathway, i.e., ferrochelatase (FECH) and delta-aminolevulinic acid synthase-2 (ALAS2), respectively. The ubiquitous FECH catalyzes the insertion of iron into the protoporphyrin ring to generate the final product, heme. After hemoglobinization, FECH can utilize other metals like zinc to bind the remainder of the protoporphyrin molecules, leading to the formation of zinc protoporphyrin. Therefore, FECH deficiency in EPP limits the formation of both heme and zinc protoporphyrin molecules. The erythroid-specific ALAS2 catalyses the synthesis of delta-aminolevulinic acid (ALA), from the union of glycine and succinyl-coenzyme A, in the first step of the pathway in the erythron. In XLP, ALAS2 activity increases, resulting in the amplified formation of ALA, and iron becomes the rate-limiting factor for heme synthesis in the erythroid tissue. Both EPP and XLP lead to the systemic accumulation of protoporphyrin IX (PPIX) in blood, erythrocytes, and tissues causing the major symptom of cutaneous photosensitivity and several other less recognized signs that need to be considered. Although significant advances have been made in our understanding of EPP and XLP in recent years, a complete understanding of the factors governing the variability in clinical expression and the severity (progression) of the disease remains elusive. The present review provides an overview of both well-established facts and the latest findings regarding these rare diseases.

Flavonoids and Limonoids Profiles Variation in Leaves from Mandarin Cultivars and Its Relationship with Alternate Bearing

Alternate bearing in citrus trees has been extensively studied as a key feature for citrus growers. Although the genetic and the biochemical process occurring during alternate bearing has been studied extensively, there is a lack of information identifying the presence of metabolic indicators during “on” and “off” years. In citrus plants, leaves play a central role in the metabolic pathway triggering the flowering induction process. To investigate the changes during this transition, a liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) analysis of the leaf profiles of 20 compounds (17 polyphenols, two limonoids, and one furanocoumarin), in bearing and non-bearing branches arising from four different mandarin genotypes, was performed. The same metabolites were found in all the genotypes at both stages: both limonoids and 11 polyphenols. Using these compounds, the chemotaxonomic differentiation between cultivars was assessed. The levels of flavanones and limonoids showed differences in both bearing stages and the transition from vegetative to flowering could be shown by the activation of the polyphenol biosynthetic pathway, from precursors like naringenin to metabolic end-points such as narirutin and polymethoxyflavones. Narirutin levels showed significant differences between both stages, suggesting it as a possible marker of the physiological status of the branch.

Human and Mouse Eosinophils Differ in Their Ability to Biosynthesize Eicosanoids, Docosanoids, the Endocannabinoid 2-Arachidonoyl-glycerol and Its Congeners

High eosinophil (EOS) counts are a key feature of eosinophilic asthma. EOS notably affect asthmatic response by generating several lipid mediators. Mice have been utilized in hopes of defining new pharmacological targets to treat asthma. However, many pinpointed targets in mice did not translate into clinics, underscoring that key differences exist between the two species. In this study, we compared the ability of human (h) and mouse (m) EOS to biosynthesize key bioactive lipids derived from arachidonic acid (AA), eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). hEOS were isolated from the blood of healthy subjects and mild asthmatics, while mEOSs were differentiated from the bone marrow. EOSs were treated with fatty acids and lipid mediator biosynthesis assessed by LC-MS/MS. We found that hEOS biosynthesized leukotriene (LT) C4 and LTB4 in a 5:1 ratio while mEOS almost exclusively biosynthesized LTB4. The biosynthesis of the 15-lipoxygenase (LO) metabolites 15-HETE and 12-HETE also differed, with a 15-HETE:12-HETE ratio of 6.3 for hEOS and 0.727 for mEOS. EOS biosynthesized some specialized pro-resolving mediators, and the levels from mEOS were 9-times higher than those of hEOS. In contrast, hEOS produced important amounts of the endocannabinoid 2-arachidonoyl-glycerol (2-AG) and its congeners from EPA and DHA, a biosynthetic pathway that was up to ~100-fold less prominent in mEOS. Our data show that hEOS and mEOS biosynthesize the same lipid mediators but in different amounts. Compared to asthmatics, mouse models likely have an amplified involvement of LTB4 and specialized pro-resolving mediators and a diminished impact of the endocannabinoid 2-arachidonoyl-glycerol and its congeners.

TiO2 nanoparticles and salinity stress in relation to artemisinin production and ADS and DBR2 expression in Artemisia absinthium L.

Artemisia absinthium L. is an important herb that is widely cultivated in different parts of the world for its medicinal properties. The present study evaluated the effects of four concentrations of nanoparticles treatment (0, 10, 20 and 30 mg L-1) and NaCl salinity stress (0, 50, 100 and 150 mM NaCl) and their interactions with respect to the expression of two key genes, i.e. DBR2 and ADS, in the biosynthesis pathway of artemisinin in A. absinthium. Total RNA was extracted and a relative gene expression analysis was carried out using Real-Time PCR. The amount of artemisinin was also determined by HPLC. All the experiments were performed as factorial in a completely randomized design in three replications. The results revealed that salinity stress and nanoparticles treatment and their interaction affected the expressions of these genes significantly. The highest levels of ADS gene expression were observed in the 30 mg L-1 nanoparticles–treated plants in the presence of 150 mM salinity stress and the lowest levels in the 10 mg L-1 nanoparticles–treated plants under 50 mM salinity stress. The maximum DBR2 gene expression was recorded in the 10 mg L-1 nanoparticles–treated plants in the absence of salinity stress and the minimum expression in the 100 mM salinity-stressed plants in the absence of nanoparticles treatment. Moreover, the smallest amounts of artemisinin were observed in the 150 mM salinity-stressed plants in the absence of nanoparticles and the highest amounts in the 30 mg L-1 nanoparticles–treated plants. The maximum amounts of artemisinin and ADS gene expression were reported from the plants in the same nanoparticles treatment and salinity stress conditions. In this regard, the amount of artemisinin was decreased by half in the plants containing the highest DBR2 gene expression. Meanwhile, no significant correlation was observed between these gene expressions and the artemisinin amount in the other nanoparticles–treated plants under different levels of salinity stress. The biosynthetic pathway of secondary metabolites appears to be very complex and dose not directly dependent on these gene expressions.

Bacillimidazoles A−F, Imidazolium-Containing Compounds Isolated from a Marine Bacillus

Chemical investigations of a marine sponge-associated Bacillus revealed six new imidazolium-containing compounds, bacillimidazoles A–F (1–6). Previous reports of related imidazolium-containing natural products are rare. Initially unveiled by timsTOF (trapped ion mobility spectrometry) MS data, extensive HRMS and 1D and 2D NMR analyses enabled the structural elucidation of 1–6. In addition, a plausible biosynthetic pathway to bacillimidazoles is proposed based on isotopic labeling experiments and invokes the highly reactive glycolytic adduct 2,3-butanedione. Combined, the results of structure elucidation efforts, isotopic labeling studies and bioinformatics suggest that 1–6 result from a fascinating intersection of primary and secondary metabolic pathways in Bacillus sp. WMMC1349. Antimicrobial assays revealed that, of 1–6, only compound six displayed discernible antibacterial activity, despite the close structural similarities shared by all six natural products.