Genome-wide characterization and analysis of WRKY transcription factors in Panax ginseng.

BACKGROUND: Panax ginseng is a well-known medicinal plant worldwide. As an herbal medicine, ginseng is also known for its long lifecycle, which can reach several decades. WRKY proteins play regulatory roles in many aspects of biological processes in plants, such as responses to biotic or abiotic stress, plant development, and adaptation to environmental challenges. Genome-wide analyses of WRKY genes in P. ginseng have not been reported. RESULTS: In this study, 137 PgWRKY genes were identified from the ginseng genome. Phylogenetic analysis showed that the PgWRKYs could be clustered into three primary groups and five subgroups. Most of the PgWRKY gene promoters contained several kinds of hormone- and stress-related cis-regulatory elements. The expression patterns of PgWRKY genes in 14 different tissues were analyzed based on the available public RNA-seq data. The responses of the PgWRKY genes to heat, cold, salt and drought treatment were also investigated. Most of the PgWRKY genes were expressed differently after heat treatment, and expression trends changed significantly under drought and cold treatment but only slightly under salt treatment. The coexpression analysis of PgWRKY genes with the ginsenoside biosynthesis pathway genes identified 11 PgWRKYs that may have a potential regulatory role in the biosynthesis process of ginsenoside. CONCLUSIONS: This work provides insights into the evolution, modulation and distribution of the WRKY gene family in ginseng and extends our knowledge of the molecular basis along with modulatory mechanisms of WRKY transcription factors in ginsenoside biosynthesis.

Candidate genes involved in the biosynthesis of lignan in Schisandra chinensis fruit based on transcriptome and metabolomes analysis.

Schisandra chinensis Turcz. (Baill.) is a plant species with fruits that have been well known in Far Eastern medicine for a long time. It has traditionally been used as a stimulating and fortifying agent in cases of physical exhaustion and to inhibit fatigue. The major bioactive compounds found in S. chinensis are lignans with a dibenzocyclooctadiene skeleton, but little is known about their biosynthesis in plants. S. chinensis is the ideal medicinal plant for studying the biosynthesis of lignans, especially the dibenzocyclooctadiene skeleton. Genomic information for this important herbal plant is unavailable. To better understand the lignan biosynthesis pathway, we generated transcriptome sequences from the fruit during ripening and performed de novo sequence assembly, yielding 136 843 unique transcripts with N50 of 1778 bp. Putative functions could be assigned to 41 824 transcripts (51.57%) based on BLAST searches against annotation databases including GO (Gene ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes). Furthermore, 22 candidate cytochrome P450 genes and 15 candidate dirigent proteins genes that were most likely involved in the lignan biosynthesis pathway were discovered based on transcriptome sequencing of S. chinensis. The genomic data obtained from S. chinensis, especially the identification of putative genes involved in the lignan biosynthesis pathway, will facilitate our understanding of lignan biosynthesis at the molecular level. The lignan metabolite profiles were analyzed by metabolomes, the accumulation patterns of 30 metabolites involved in the lignan pathway were studied. Co-expression network of lignan contents and transcriptional changes showed 355 strong correlations (correlation coefficient, R2 > 0.9) between 21 compounds and 153 transcripts. Furthermore, the comprehensive analysis and characterization of the genes involved in lignan pathways and the metabolite profiles of lignans are expected to provide better insight regarding the diversity of the chemical composition, synthetic characteristics, and regulatory mechanisms of this medical herb.

De novo transcriptome analysis of gene responses to pest feeding in leaves of Panax ginseng C. A. Meyer.

The aim of the present study was to investigate the transcriptomic differences between Panax ginseng [Renshen (RS)] plants bitten by pests (n=3, test group; samples defined as RS11­13) or not (n=3, control group; samples defined as RS1­3) using de novo RNA sequencing on an Illumina HiSeq™ 2000 platform. A total of 51,097,386 (99.6%), 49,310,564 (99.5%), 59,192,372 (99.6%), 60,338,540 (99.5%), 56,976,410 (99.6%) and 54,226,588 (99.6%) clean reads were obtained for RS11, RS12, RS13, RS1, RS2 and RS3, respectively. De novo assembly generated 370,267 unigenes, 927 of which were differentially expressed genes (DEGs), including 782 significantly upregulated and 145 significantly downregulated genes. Function enrichment analysis revealed that these DEGs were located in 28 significantly enriched Kyoto Encyclopedia of Genes and Genomes pathways, including phenylpropanoid biosynthesis (for example, TRINITY_DN30766_c0_g2_i1, encoding peroxidase 20) and mitogen­activated protein kinase (MAPK) signaling (TRINITY_DN85589_c0_g1_i1, encoding WRKY transcription factor 75). Weighted gene co­expression network analysis identified modules including TRINITY_DN85589_c0_g1_i1, TRINITY_DN58279_c0_g1_i1 [encoding aspartyl protease (AP)] and TRINITY_DN74866_c0_g2_i1 [encoding 12­oxophytodienoate reductase (OPR)] that may be the most significantly associated with pest responses. In this module, TRINITY_DN85589_c0_g1_i1 may co­express with TRINITY_DN58279_c0_g1_i1 or TRINITY_DN74866_c0_g2_i1. WRYK and AP have been suggested to promote the activity of antioxidant peroxidase. Collectively, the findings from the present study suggested that a MAPK­WRKY­OPR/AP­peroxidase signaling pathway may be a potentially important mechanism underlying defense responses against pests in ginseng plants.

Comparison of USPIO-enhanced MRI and Gd-DTPA enhancement during the subacute stage of focal cerebral ischemia in rats.

BACKGROUND: Being one class of magnetic resonance imaging (MRI) contrast agents, ultrasmall superparamagnetic particles of iron oxides (USPIO) bear the potential to study neuroinflammation following stroke, but there is still debate over whether the iron oxides particles may enter the brain tissue passively over a damaged blood-brain barrier (BBB). PURPOSE: To compare the enhancement patterns of USPIO and gadopentate dimeglumine (Gd-DTPA) during the subacute stage of focal cerebral ischemia, to examine the relationship between USPIO enhancement and BBB disturbance, as well as with neuroinflammatory cell response. MATERIAL AND METHODS: Multiple MR sequences were obtained on days 3 and 6 after transient middle cerebral artery occlusion induced in rats with and without the application of USPIO and Gd-DTPA. The enhancement patterns of the two contrast agents were compared and correlated to histology, including IgG for BBB permeability, Prussian Blue staining for iron particle detection, and CD68 immunohistochemistry staining to identify macrophage/microglia. RESULTS: Gd-DTPA enhancement depicted BBB breakdown being in line with IgG leakage. The USPIO enhanced images demonstrated both diffuse and focal signal alteration in ischemic lesions. The diffuse enhanced pattern had a similar spatial and temporal profile as with Gd-DTPA enhancement. In addition, focal enhanced signal loss was visible on T1-, T2-, and T2*-weighted images, with a peak tendency of MR signal loss, macrophage/microglia concentration and iron particle accumulation at a later phase of the study. CONCLUSION: After focal cerebral ischemia, Gd-DTPA-enhanced MRI showed a higher sensitivity in detecting BBB alterations than did USPIO enhancement. USPIO provided complementary information regarding inflammatory cell activity in neuroinflammatory to cerebral ischemia that had not been visualized using conventional Gd-DTPA. The assessment using multiple MR parameters may identify intracellular and extracellular USPIO in vivo.

[Effect of forsythia suspense extract on phagocytosis of peritoneal macrophages and NO production in vitro].

AIM: To investigate the effect of forsythia suspensa (FS) extract on phagocytosis of peritoneal macrophages and NO production in vitro. METHODS: The peritoneal macrophagess were isolated from BALB/c mice. After stained with CFDA-SE, the DH5alpha were co-cultured with peritoneal macrophagess for 3 h. The effect of FS extract on cyto-phagocytesis in vitro was analyzed by flow cytometry. The peritoneal macrophages were stimulated and activated by LPS in vitro. The effect of FS extract on NO production of the peritoneal macrophages in vitro was measured by NO assay kit. RESULTS: FCM analysis showed that FS extract significantly promoted the phagocytosis of peritoneal macrophages at the final concentration of 40, 80, 160 mg/L, respectively (P<0.05). It also decreased the production of NO at different concentration induced by LPS (P<0.05). CONCLUSION: FS extract can promote phagocytosis of peritoneal macrophages and inhibit NO production in vitro.