Assembly and characterization of the complete mitochondrial genome of Ventilago leiocarpa.

KEY MESSAGE: We reported the mitochondrial genome of Ventilago leiocarpa for the first time. Two and one sites lead to the generation of stop and stat codon through editing were verified. Ventilago leiocarpa, a member of the Rhamnaceae family, is frequently utilized in traditional medicine due to the medicinal properties of its roots. In this study, we successfully assembled the mitogenome of V. leiocarpa using both BGI short reads and Nanopore long reads. This mitogenome has a total length of 331,839 bp. The annotated results showed 36 unique protein-coding, 16 tRNA and 3 rRNA genes in this mitogenome. Furthermore, we confirmed the presence of a branched structure through the utilization of long reads mapping, PCR amplification, and Sanger sequencing. Specifically, the ctg1 can form a single circular molecule or combine with ctg4 to form a linear molecule. Likewise, ctg2 can form a single circular molecule or can be connected to ctg4 to form a linear molecule. Subsequently, through a comparative analysis of the mitogenome and cpgenome sequences, we identified ten mitochondrial plastid sequences (MTPTs), including two complete protein-coding genes and five complete tRNA genes. The existence of MTPTs was verified by long reads. Colinear analysis showed that the mitogenomes of Rosales were highly divergent in structure. Finally, we identified 545 RNA editing sites involving 36 protein-coding genes by Deepred-mt. To validate our findings, we conducted PCR amplification and Sanger sequencing, which confirmed the generation of stop codons in atp9-223 and rps10-391, as well as the generation of a start codon in nad4L-2. This project reported the complex structure and RNA editing event of the V. Leiocarpa mitogenome, which will provide valuable information for the study of mitochondrial gene expression.

Rapid in situ diversification rates in Rhamnaceae explain the parallel evolution of high diversity in temperate biomes from global to local scales.

The macroevolutionary processes that have shaped biodiversity across the temperate realm remain poorly understood and may have resulted from evolutionary dynamics related to diversification rates, dispersal rates, and colonization times, closely coupled with Cenozoic climate change. We integrated phylogenomic, environmental ordination, and macroevolutionary analyses for the cosmopolitan angiosperm family Rhamnaceae to disentangle the evolutionary processes that have contributed to high species diversity within and across temperate biomes. Our results show independent colonization of environmentally similar but geographically separated temperate regions mainly during the Oligocene, consistent with the global expansion of temperate biomes. High global, regional, and local temperate diversity was the result of high in situ diversification rates, rather than high immigration rates or accumulation time, except for Southern China, which was colonized much earlier than the other regions. The relatively common lineage dispersals out of temperate hotspots highlight strong source-sink dynamics across the cosmopolitan distribution of Rhamnaceae. The proliferation of temperate environments since the Oligocene may have provided the ecological opportunity for rapid in situ diversification of Rhamnaceae across the temperate realm. Our study illustrates the importance of high in situ diversification rates for the establishment of modern temperate biomes and biodiversity hotspots across spatial scales.

Dispersal modes affect Rhamnaceae diversification rates in a differentiated manner.

The evolution of dispersal modes has been proposed to promote the diversification of angiosperms. However, little is known about the relative impact of different dispersal modes on plant diversification. We test the association between dispersal modes and diversification rates using Rhamnaceae, the cosmopolitan buckthorn family, as a model. We found that species with diplochory have the highest diversification rates followed by those with myrmecochory and ballistic dispersal, while lineages dispersed by vertebrates and wind have relatively low diversification rates. The difference in diversification rates may be closely linked to the difference in dispersal distance and ecological interactions implied by each dispersal mode. Species which disperse over larger geographical distances may have much higher speciation rates due to the increased chance of establishing isolated populations due to geological barriers or habitat fragmentation. However, long-distance dispersal may also increase the chance of extinction. By contrast, species with short-distance dispersal modes may have low speciation rates. Complex interactions with the surrounding environment may, however, impact diversification rates positively by increasing plant survival and reproductive success.

In-silico and in-vitro assessments of some fabaceae, rhamnaceae, apocynaceae, and anacardiaceae species against Mycobacterium tuberculosis H37Rv and triple-negative breast cancer cells.

Medicinal plants play a huge role in the treatment of various diseases in the Limpopo province (South Africa). Traditionally, concoctions used for treating tuberculosis and cancer are sometimes prepared from plant parts naturally occurring in the region, these include (but not limited to) Schotia brachypetala, Rauvolfia caffra, Schinus molle, Ziziphus mucronate, and Senna petersiana. In this study, the aim was to evaluate the potential antimycobacterial activity of the five medicinal plants against Mycobacterium smegmatis mc2155, Mycobacterium aurum A + , and Mycobacterium tuberculosis H37Rv, and cytotoxic activity against MDA-MB 231 triple-negative breast cancer cells. Phytochemical constituents present in R. caffra and S. molle were tentatively identified by LC-QTOF-MS/MS as these extracts showed antimycobacterial and cytotoxic activity. A rigorous Virtual Screening Workflow (VSW) of the tentatively identified phytocompounds was then employed to identify potential inhibitor/s of M. tuberculosis pantothenate kinase (PanK). Molecular dynamics simulations and post-MM-GBSA free energy calculations were used to determine the potential mode of action and selectivity of selected phytocompounds. The results showed that plant crude extracts generally exhibited poor antimycobacterial activity, except for R. caffra and S. molle which exhibited average efficacy against M. tuberculosis H37Rv with minimum inhibitory concentrations between 0.25-0.125 mg/mL. Only one compound with a favourable ADME profile, namely, norajmaline was returned from the VSW. Norajmaline exhibited a docking score of -7.47 kcal/mol, while, pre-MM-GBSA calculation revealed binding free energy to be -37.64 kcal/mol. All plant extracts exhibited a 50% inhibitory concentration (IC50) of < 30 µg/mL against MDA-MB 231 cells. Flow cytometry analysis of treated MDA-MB 231 cells showed that the dichloromethane extracts from S. petersiana, Z. mucronate, and ethyl acetate extracts from R. caffra and S. molle induced higher levels of apoptosis than cisplatin. It was concluded that norajmaline could emerge as a potential antimycobacterial lead compound. Validation of the antimycobacterial activity of norajmaline will need to be performed in vitro and in vivo before chemical modifications to enhance potency and efficacy are done. S. petersiana, Z. mucronate, R.caffra and S. molle possess strong potential as key contributors in developing new and effective treatments for triple-negative breast cancer in light of the urgent requirement for innovative therapeutic solutions.

Paliurus spina-christi Mill fruit extracts improve glucose uptake and activate the insulin signaling pathways in HepG2 insulin-resistant cells.

BACKGROUND: Paliurus spina-christi Mill. (PSC) fruit is frequently used in the treatment of diabetes mellitus in Mediterranean regions. Here, we investigated the effects of various PSC fruit extracts (PSC-FEs) on glucose consumption and some key mediators of insulin signaling pathways in high glucose and high insulin-induced insulin-resistant HepG2 cells. METHODS: The effects of methanolic, chloroform and total extracts on cell proliferation were assessed by the MTT assay. The potential of non-toxic extracts on glucose utilization in insulin-resistant HepG2 cells was checked using a glucose oxidase assay. AKT and AMP-activated protein kinase (AMPK) pathway activation and mRNA expression levels of insulin receptor (INSR), glucose transporter 1 (GLUT1), and glucose transporters 4 (GLUT4) were determined by western blotting and real-time PCR, respectively. RESULTS: We found that high concentrations of methanolic and both low and high concentrations of total extracts were able to enhance glucose uptake in an insulin-resistant cell line model. Moreover, AKT and AMPK phosphorylation were significantly increased by the high strength of methanolic extract, while total extract raised AMPK activation at low and high concentrations. Also, GLUT 1, GLUT 4, and INSR were elevated by both methanolic and total extracts. CONCLUSIONS: Ultimately, our results shed new light on methanolic and total PSC-FEs as sources of potential anti-diabetic medications, restoring glucose consumption and uptake in insulin-resistant HepG2 cells. These could be at least in part due to re-activating AKT and AMPK signaling pathways and also increased expression of INSR, GLUT1, and GLUT4. Overall, active constituents present in methanolic and total extracts of PCS are appropriate anti-diabetic agents and explain the use of these PSC fruits in traditional medicine for the treatment of diabetes.

A New Ceanothane-Type Triterpenoid Saponin Isolated from Gouania leptostachya DC. var. tonkinensis Pit. and Its Underlying Anti-Inflammatory Effects.

Metabolites from medicinal plants continue to hold significant value in the exploration and advancement of novel pharmaceuticals. In the search for plants containing compounds with anti-inflammatory effects, we observed that the ethanol (EtOH) extract obtained from the aerial components of Gouania leptostachya DC. var. tonkinensis Pit. exhibited substantial suppression of nitric oxide (NO) in vitro. In a phytochemical study on an EtOH extract of G. leptostachya, 11 compounds were purified, including one unreported compound namely gouanioside A (1). Their chemical structures were unambiguously determined through the use of various spectroscopic techniques, such as 1 and 2D NMR, IR, and HR-ESI-MS, and by producing derivatives via chemical reactions. The EtOH extract, fractions, and a new compound exerted inflammatory effects by altering NO synthesis in murine RAW264.7 macrophage cells stimulated with lipopolysaccharide. The underlying inflammatory mechanism of the new compound 1 was also explored through various in vitro experiments. The results of this study indicate the potential usefulness of new compound 1 from G. leptostachya as a treatment for inflammatory diseases.

Pyranonaphthoquinones and Naphthoquinones from the Stem Bark of Ventilago harmandiana and Their Anti-HIV-1 Activity.

Seven previously undescribed compounds, including five pyranonaphthoquinones (ventilanones L-P) and two naphthoquinones (ventilanones Q and R), along with 15 known compounds were isolated from the stem bark of Ventilago harmandiana (Rhamnaceae). The structures were established by extensive analysis of their spectroscopic data. The absolute configuration of ventilanone L was established from single crystal X-ray crystallographic analysis using Cu Kα radiation and from its electronic circular dichroism data. Anti-HIV-1 activity using a syncytium inhibition assay and the cytotoxic activities of some isolated compounds were evaluated. Compounds 12, 13, 15, and 16 showed activity against syncytium formation with half maximal effective concentration (EC50) values ranging from 9.9 to 47 µM (selectivity index (SI) 2.4-4.5).

Hovenianin A Alleviates Hepatic Fibrosis by Inhibiting the PI3K/AKT Pathway in TGF-ß1-Induced HSCs Based on Network Pharmacology and Transcriptomic Analysis.

Hepatic fibrosis is a global health problem, which currently has no FDA approved antifibrotic therapy yet. This study aimed to explore the mechanism of Hovenia genus in the treatment of hepatic fibrosis by an integrative strategy combining network pharmacology analysis, molecular docking, transcriptomics and experimental validation. The traditional Chinese medicine systems pharmacology (TCMSP) database and literatures were used to collect the components of Hovenia genus. Public databases including GeneCards, TTD, PharmGkb were used to acquire the putative targets. The GO and KEGG analysis were applied to explore the underlying mechanisms. Furthermore, The TGF-ß1 induced hepatic stellate cells (HSCs) model were performed to evaluate the anti-hepatic fibrosis activity of Hovenia genus. The RT-qPCR, Western blotting and flow cytometry experiments were used to validate the anti-hepatic fibrosis mechanisms of Hovenianin A. The KEGG analysis of network pharmacology and transcriptomics revealed that the core targets mainly enriched in PI3K-Akt signaling pathways. The cell screening results indicated flavonoids were the main active ingredients of Hovenia. Hovenianin A, a bioactive bisflavonol, was validated to promote the apoptosis of HSCs by inhibiting PI3K-Akt pathway. Molecular docking further corroborated the binding sites between Hovenianin A and AKT1. In summary, Hovenia may have therapeutic effects on liver fibrosis by modulating the PI3K-Akt apoptosis pathway. Our findings may facilitate the development of Hovenia genus, which could help to treat liver fibrosis in the future.

Extracting myricetin and dihydromyricetin simultaneously from Hovenia acerba seed by Ultrasound-Assisted extraction on a lab and small Pilot-Scale.

The flavonoids myricetin and dihydromyricetin are significant components of Hovenia acerba seed. In this work, myricetin and dihydromyricetin were extracted from Hovenia acerba seed using an ultrasound-assisted technique, and the extraction parameters were adjusted using the response surface design approach. HPLC was used to assess the yield of myricetin and dihydromyricetin. According to the data, myricetin and dihydromyricetin yields were 0.53 mg/g and 4.06 mg/g at a 60 % ethanol solution concentration, 180 W of ultrasonic irradiation power, a 20 mL/g ratio of liquid to solid, and a 40 °C optimal extraction temperature. The aforementioned findings are virtually in agreement with the experimental findings suggested by the model. The study mentioned above thus offers a means of separating and developing useful components of natural goods.

Revisiting chloroplast genomic landscape and annotation towards comparative chloroplast genomes of Rhamnaceae.

BACKGROUND: Massive parallel sequencing technologies have enabled the elucidation of plant phylogenetic relationships from chloroplast genomes at a high pace. These include members of the family Rhamnaceae. The current Rhamnaceae phylogenetic tree is from 13 out of 24 Rhamnaceae chloroplast genomes, and only one chloroplast genome of the genus Ventilago is available. Hence, the phylogenetic relationships in Rhamnaceae remain incomplete, and more representative species are needed. RESULTS: The complete chloroplast genome of Ventilago harmandiana Pierre was outlined using a hybrid assembly of long- and short-read technologies. The accuracy and validity of the final genome were confirmed with PCR amplifications and investigation of coverage depth. Sanger sequencing was used to correct for differences in lengths and nucleotide bases between inverted repeats because of the homopolymers. The phylogenetic trees reconstructed using prevalent methods for phylogenetic inference were topologically similar. The clustering based on codon usage was congruent with the molecular phylogenetic tree. The groups of genera in each tribe were in accordance with tribal classification based on molecular markers. We resolved the phylogenetic relationships among six Hovenia species, three Rhamnus species, and two Ventilago species. Our reconstructed tree provides the most complete and reliable low-level taxonomy to date for the family Rhamnaceae. Similar to other higher plants, the RNA editing mostly resulted in converting serine to leucine. Besides, most genes were subjected to purifying selection. Annotation anomalies, including indel calling errors, unaligned open reading frames of the same gene, inconsistent prediction of intergenic regions, and misannotated genes, were identified in the published chloroplast genomes used in this study. These could be a result of the usual imperfections in computational tools, and/or existing errors in reference genomes. Importantly, these are points of concern with regards to utilizing published chloroplast genomes for comparative genomic analysis. CONCLUSIONS: In summary, we successfully demonstrated the use of comprehensive genomic data, including DNA and amino acid sequences, to build a reliable and high-resolution phylogenetic tree for the family Rhamnaceae. Additionally, our study indicates that the revision of genome annotation before comparative genomic analyses is necessary to prevent the propagation of errors and complications in downstream analysis and interpretation.

Three new 8,4'-type oxyneolignans from the seeds of Ziziphus jujuba mill and their antitumor studies.

Ziziphus jujuba Mill. is a deciduous shrub, belonging to the Rhamnaceae family. Phytochemical investigation of Z. jujuba seeds showed the presence of three undescribed 8,4'-type oxyneolignans (1-3). Their structures were elucidated by comprehensive spectroscopic analyses. All isolated compounds were tested for antitumor activity against two human hepatoma cells (Hep3B and HepG2) and exhibited moderate cytotoxicity (IC50: 33.79-49.62 µM).

Fossil flowers of Phylica support a 250 Ma origin for Rhamnaceae.

A new fossil discovery reported by Shi et al. changes our understanding of the biogeographic history of the cosmopolitan family, Rhamnaceae. Flowering shoots of the African genus Phylica (Rhamnaceae) dated at 100 million years ago (Ma) imply a 250 Ma origin of the family in fire-prone Gondwanan vegetation that enabled overland dispersal to all continents where it is currently widespread.

Traveling Wave Ion Mobility-Derived Collision Cross Section Database for Plant Specialized Metabolites: An Application to Ventilago harmandiana Pierre.

The combination of ion mobility mass spectrometry (IM-MS) and chromatography is a valuable tool for identifying compounds in natural products. In this study, using an ultra-performance liquid chromatography system coupled to a high-resolution quadrupole/traveling wave ion mobility spectrometry/time-of-flight MS (UPLC-TWIMS-QTOF), we have established and validated a comprehensive TWCCSN2 and MS database for 112 plant specialized metabolites. The database included 15 compounds that were isolated and purified in-house and are not commercially available. We obtained accurate m/z, retention times, fragment ions, and TWIMS-derived CCS (TWCCSN2) values for 207 adducts (ESI+ and ESI-). The database included novel 158 TWCCSN2 values from 79 specialized metabolites. In the presence of plant matrix, the CCS measurement was reproducible and robust. Finally, we demonstrated the application of the database to extend the metabolite coverage of Ventilago harmandiana Pierre. In addition to pyranonaphthoquinones, a group of known specialized metabolites in V. harmandiana, we identified flavonoids, xanthone, naphthofuran, and protocatechuic acid for the first time through targeted analysis. Interestingly, further investigation using IM-MS of unknown features suggested the presence of organonitrogen compounds and lipid and lipid-like molecules, which is also reported for the first time. Data are available on the MassIVE (https://massive.ucsd.edu, data set identifier MSV000090213).

Cyclopeptide Alkaloids from Discaria chacaye (Rhamnaceae) as Result of Symbiosis with Frankia (Actinomycetales).

Cyclopeptide alkaloids with different biological activities are present in plants of the family Rhamnaceae. Plants of this family grow in a symbiotic relationship with aerobic Gram-positive actinomycetes belonging to the genus Frankia. This goal of this research was a study of the comparative profile of alkaloids present in Discaria chacaye and to establish a connection between the presence or absence of Frankia sp. and the alkaloids. In addition, insecticidal activities of the alkaloidal extract were examined. A total of 24 alkaloids were identified, of which 12 have a benzylisoquinoline skeleton, 9 were cyclopeptides, 2 isoquinolines, and 1 aporphine. The presence of cyclopeptide alkaloids is associated with Frankia nodules in the plant root. The alkaloid extracts showed insecticidal activity with mortality dose-dependence and LD50 values between 44 to 71 µg/mL.

Polysaccharide from Hovenia dulcis (Guaizao) improves pancreatic injury and regulates liver glycometabolism to alleviate STZ-induced type 1 diabetes mellitus in rats.

Hovenia dulcis is a traditional medicinal and edible plant and has a major geographical presence in China. In this study, a polysaccharide purified from H. dulcis (HDPs-2A) was found to ameliorate type 1 diabetes mellitus (T1DM) in streptozotocin-induced diabetic rat. HDPs-2A treatment resulted in significantly lower fasting blood glucose levels, but higher body weight, plasma insulin, and liver glycogen levels. Moreover, HDPs-2A improved dyslipidemia, pancreatic oxidative stress, and reduced serum pro-inflammatory factors. In addition, HDPs-2A up-regulated PDX-1, activated and up-regulated IRS2 expression, and regulated apoptosis and regeneration of islet ß cells to recover islet ß-cell function injury in TIDM rats. HDPs-2A also up-regulated the expression of pancreatic GK and GLUT2 to improve insulin secretion ability of islet ß-cells, ultimately improving the glucose metabolism disorder of T1DM rats. Moreover, HDPs-2A significantly up-regulated the expression of GK and down-regulated the expression of G6Pase in liver to improve liver glycogen synthesis, inhibit liver gluconiogenesis, and improve liver glucose metabolism disorder of T1DM rats. In summary, the hypoglycemic mechanisms of HDPs-2A may include regulating the regeneration and apoptosis of islet ß-cells and activating liver glycometabolism-related signaling pathways in T1DM rats.

Japanese grape (Hovenia dulcis) powder as an antioxidant agent in Bologna sausages.

BACKGROUND: The Japanese grape (Hovenia dulcis Thunberg) has potential as an antioxidant due to its high content of phenolic compounds in the early maturation stages. In this study, the antioxidant sodium erythorbate (CONTROL) was replaced by Japanese grape pseudofruits dehydrated by freeze-drying (FDP) and oven drying (OP), in Bologna sausages. The commercial natural antioxidant licresse (LS), based on licorice, has also been studied. RESULTS: No significant differences (P < 0.05) were observed for the proximate composition and the texture profile of the Bologna sausages. An increase in pH was observed during storage for all formulations. At 28 days, the treatments FDP and OP were darker (lower L* values) and less red (lower a* values), possibly due to the presence of tannins in these samples, which may have bound with the iron present in myoglobin and minimized the oxidation reactions. The use of different antioxidants affected the nitrite contents of the Bologna sausages during storage. Regarding the lipid oxidation, the Japanese grape powder was more effective in delaying the oxidation reactions in Bologna sausages after 14 and 21 days of storage when compared to LS and the CONTROL, respectively. CONCLUSION: The Japanese grape powders were effective in retarding the lipid oxidation of Bologna sausages, possibly due to the presence of bioactive compounds, such as phenolic compounds, tannins, and ascorbic acid, showing the potential of these pseudofruits as antioxidants for use in meat products. © 2022 Society of Chemical Industry.

New cyclopeptide alkaloid of Condalia buxifolia and the absolute stereochemistry of Condaline A.

During the course of a study of Condalia buxifolia (Rhamnaceae), one new cyclopeptide alkaloid condaline B (1), together with six known cyclopeptide alkaloids, condaline A (2), and the scutianines B (3), - D (4) and -E (5), frangulanine (6), and 3,4,28-tris-epi-scutianene N (7), were isolated from the rind bark of Condalia buxifolia. Their structures have been confirmed through spectroscopic analyses such as 1D and 2D NMR experiments. The absolute stereochemistry of condaline A (2), was elucidated by X-ray crystal structure determination of its HI salt. In addition, condaline B (1) was obtained synthetically through a structural transformation of condaline A. Meanwhile, the crude methanol extract, the basic ether fraction, and alkaloids 1-7 were tested against various strains of Gram-positive and Gram-negative bacteria and fungus, showing promising antimicrobial activity.

Characterisation of four new triterpenoid saponins with nitric oxide inhibitory activity from aerial parts of Gouania leptostachya.

Four new triterpenoid saponins (gouaniasides VII-IX [1-3] and joazeiroside C [4]) and one known triterpenoid (5) were isolated from the aerial parts of Gouania leptostachya DC. (Rhamnaceae). Their structures were elucidated via one-dimensional and two-dimensional nuclear magnetic resonance spectroscopy, high-resolution electrospray ionisation-mass spectrometry, and analyses of hydrolytic cleavage results. The anti-inflammatory potential of compounds 1-3 was evaluated according to their ability to inhibit the production of nitric oxide (NO) by RAW 264.7 macrophages. All compounds at noncytotoxic concentrations significantly inhibited NO production by macrophages in a concentration-dependent manner.