scholarly journals Combined Analysis of Volatile Terpenoid Metabolism and Transcriptome Reveals Transcription Factors Related to Terpene Synthase in Two Cultivars of Dendrobium officinale Flowers

2021 ◽  
Vol 12 ◽  
Author(s):  
Ninghong Li ◽  
Yingxue Dong ◽  
Min Lv ◽  
Li Qian ◽  
Xu Sun ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Transcriptome Analysis ◽  
Dendrobium Officinale ◽  
Terpene Synthase ◽  
Traditional Chinese Herbal Medicine ◽  
Medicinal Value ◽  
Volatile Terpenoids ◽  
Terpenoid Metabolism ◽  
Regulatory Effects ◽  
Main Components

Dendrobium officinale is a kind of traditional Chinese herbal medicine. Its flowers could be used as health care tea for its aroma flavor and medicinal value. Most recent studies demonstrated that terpenoids are the main components of the aromatic compounds in the flowers, but the biosynthesis of terpenoids is poorly understood in D. officinale. In the experiment, the flowers from two cultivars of D. officinale with different smells were collected. The transcriptome analysis and combined volatile terpenoids determination were performed to identify the genes related to the biosynthesis of the terpenoids. The results showed that the different products of volatile terpenoids are α-thujene, linalool, α-terpineol, α-phellandrene, γ-muurolene, α-patchoulene, and δ-elemene in two cultivar flowers. The transcriptome analysis detected 25,484 genes in the flowers. And 18,650 differentially expressed genes were identified between the two cultivars. Of these genes, 253 genes were mapped to the terpenoid metabolism pathway. Among these genes, 13 terpene synthase (TPS) genes may have correlations with AP2/ERF, WRKY, MYB, bHLH, and bZIP transcription factors by weighted gene co-expression network analysis (WGCNA). The transcription factors have regulatory effects on TPS genes. These results may provide ideas for the terpenoid biosynthesis and regulatory network of D. officinale flowers.

scholarly journals Aging affects artemisinin synthesis in Artemisia annua

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jiao Li ◽  
Xiao-Hui Chu ◽  
Xiao-Yu Wang ◽  
Bao-Min Feng ◽  
Zong-Xia Yu
Keyword(s):  
Transcription Factors ◽  
Clinical Application ◽  
Small Rna ◽  
Transcriptome Analysis ◽  
Artemisia Annua ◽  
Malaria Treatment ◽  
Biosynthesis Pathway ◽  
Regulatory Effects ◽  
Effective Component

AbstractArtemisinin (ART) is the most effective component in malaria treatment, however, the extremely low content restricts its clinical application. Therefore, it is urgent to increase the yield of ART. ART gradually accumulates with aging, small RNA (sRNA) and transcriptome analysis were applied on the leaves of 2-week-old (2 w) and 3-month-old (3 m) A. annua respectively. Among all the annotated sRNAs, 125 were upregulated and 128 downregulated in the 3 m sample compared to the 2 w one. Whereas 2183 genes were upregulated and 2156 downregulated. Notably, the level of miR156 and several annotated miRNAs gradually decreased while SPLs increased. In addition, the genes on ART biosynthesis pathway were significantly upregulated including ADS, CYP71AV1, ADH1, DBR2 and ALDH1, and so were the positive transcription factors like AaERF1, AaORA and AaWRKY1 indicating that age influences the ART biosynthesis by activating the expression of the synthesizing genes as well as positive transcription factors. This study contributes to reveal the regulatory effects of age on ART biosynthesis both in sRNA and transcription levels.

scholarly journals Cytological Observation and Transcriptome Comparative Analysis of Self-Pollination and Cross-Pollination in Dendrobium Officinale

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 432
Author(s):  
Yaling Chen ◽  
Benchang Hu ◽  
Fantao Zhang ◽  
Xiangdong Luo ◽  
Jiankun Xie
Keyword(s):  
Pollen Tubes ◽  
The Self ◽  
Dendrobium Officinale ◽  
Self Incompatibility ◽  
Related Gene ◽  
Cytological Observation ◽  
Lectin Receptor ◽  
Cross Pollination ◽  
Self Pollination ◽  
Medicinal Value

Dendrobium officinale is a rare and traditional medicinal plant with high pharmacological and nutritional value. The self-incompatibility mechanism of D. officinale reproductive isolation was formed in the long-term evolution process, but intraspecific hybridization of different germplasm resources leads to a large gap in the yield, quality, and medicinal value of D. officinale. To investigate the biological mechanism of self-incompatibility in D. officinale, cytological observation and the transcriptome analysis was carried out on the samples of self-pollination and cross-pollination in D. officinale. Results for self-pollination showed that the pollen tubes could grow in the style at 2 h, but most of pollen tubes stopped growing at 4 h, while a large number of cross-pollinated pollen tubes grew along the placental space to the base of ovary, indicating that the self-incompatibility of D. officinale may be gametophyte self-incompatibility. A total of 63.41 G basesum of D. officinale style samples from non-pollinated, self-pollination, and cross-pollination by RNA-seq were obtained, and a total of 1944, 1758, and 475 differentially expressed genes (DEGs) in the comparison of CK (non-pollinated) vs. HF (cross-pollination sample), CK vs. SF (self-pollination sample) and SF vs. HF were identified, respectively. Forty-one candidate genes related to self-incompatibility were found by function annotation of DEGs, including 6 Ca2+ signal genes, 4 armed repeat containing (ARC) related genes, 11 S-locus receptor kinase (SRK) related genes, 2 Exo70 family genes, 9 ubiquitin related genes, 1 fatty acid related gene, 6 amino acid-related genes, 1 pollen-specific leucine-rich repeat extensin-like protein (LRX) related gene and 1 lectin receptor-like kinases (RLKs) related gene, showed that self-incompatibility mechanism of D. officinale involves the interaction of multiple genes and pathways. The results can provide a basis for the study of the self-incompatibility mechanism of D. officinale, and provide ideas for the preservation and utilization of high-quality resources of D. officinale.

Analysis of the transcription factors and their regulatory roles during a step-by-step differentiation of induced pluripotent stem cells into hepatocyte-like cells

2019 ◽  
Vol 15 (6) ◽  
pp. 383-398 ◽  
Author(s):  
Yannick Tauran ◽  
Stéphane Poulain ◽  
Myriam Lereau-Bernier ◽  
Mathieu Danoy ◽  
Marie Shinohara ◽  
...  
Keyword(s):  
Stem Cells ◽  
Transcription Factors ◽  
Induced Pluripotent Stem Cells ◽  
Transcriptome Analysis ◽  
Pluripotent Stem Cells ◽  
Original Method ◽  
Induced Pluripotent

Human induced pluripotent stem cells have been investigated through a sequential in vitro step-by-step differentiation into hepatocyte-like cells using nanoCAGE, an original method for promoters, transcription factors, and transcriptome analysis.

scholarly journals Comprehensive Transcriptome Analysis Revealed the Effects of the Light Quality, Light Intensity, and Photoperiod on Phlorizin Accumulation in Lithocarpus polystachyus Rehd.

Forests ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 995 ◽  
Author(s):  
Yantong Zhang ◽  
Limei Lin ◽  
Yuehong Long ◽  
Hongyu Guo ◽  
Zhuo Wang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Light Intensity ◽  
Light Exposure ◽  
Southern China ◽  
Green Light ◽  
Differentially Expressed ◽  
Chromatography Method ◽  
Pal Activity ◽  
Study Results ◽  
Regulatory Effects

Lithocarpus polystachyus Rehd. is an important medicinal plant species grown in southern China, with phlorizin as its main active substance. The effects of light conditions on phlorizin biosynthesis in L. polystachyus remain unclear. Thus, we analyzed the transcriptomes of L. polystachyus plants cultivated under diverse light qualities, light intensities, and photoperiods. The light treatments resulted in 5977–8027 differentially expressed genes (DEGs), which were functionally annotated based on the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Genes encoding transcription factors from 89 families were differentially expressed after the light treatments, implying these transcription factors are photoresponsive. Phenylalanine ammonia lyase (PAL) and 4-coumarate-CoA ligase (4CL) are the key enzymes for the accumulation of phlorizin. The transcription levels of PAL2, PAL, 4CL1 (DN121614), 4CLL7, and 4CL1 (DN102161) were positively correlated with phlorizin accumulation, suggesting that these genes are important for phlorizin biosynthesis. An ultra-high-performance liquid chromatography method was used to quantify the phlorizin content. Phlorizin accumulated in response to the green light treatment and following appropriate decreases in the light intensity or appropriate increases in the duration of the light exposure. The green light, 2000 lx, and 3000 lx treatments increased the PAL activity of L. polystachyus, but the regulatory effects of the light intensity treatments on PAL activity were relatively weak. This study represents the first comprehensive analysis of the light-induced transcriptome of L. polystachyus. The study results may form the basis of future studies aimed at elucidating the molecular mechanism underlying phlorizin biosynthesis in L. polystachyus. Moreover, this study may be relevant for clarifying the regulatory effects of light on the abundance of bioactive components in medicinal plants.

scholarly journals Transcriptome analysis of Pueraria candollei var. mirifica for gene discovery in the biosyntheses of isoflavones and miroestrol

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Nithiwat Suntichaikamolkul ◽  
Kittitya Tantisuwanichkul ◽  
Pinidphon Prombutara ◽  
Khwanlada Kobtrakul ◽  
Julie Zumsteg ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Transcriptome Analysis ◽  
De Novo ◽  
Biosynthetic Genes ◽  
Pueraria Candollei ◽  
Isoflavone Synthase ◽  
Young Leaves ◽  
Plausible Mechanism ◽  
Polymerase Chain ◽  
R2r3 Myb

Abstract Background Pueraria candollei var. mirifica, a Thai medicinal plant used traditionally as a rejuvenating herb, is known as a rich source of phytoestrogens, including isoflavonoids and the highly estrogenic miroestrol and deoxymiroestrol. Although these active constituents in P. candollei var. mirifica have been known for some time, actual knowledge regarding their biosynthetic genes remains unknown. Results Miroestrol biosynthesis was reconsidered and the most plausible mechanism starting from the isoflavonoid daidzein was proposed. A de novo transcriptome analysis was conducted using combined P. candollei var. mirifica tissues of young leaves, mature leaves, tuberous cortices, and cortex-excised tubers. A total of 166,923 contigs was assembled for functional annotation using protein databases and as a library for identification of genes that are potentially involved in the biosynthesis of isoflavonoids and miroestrol. Twenty-one differentially expressed genes from four separate libraries were identified as candidates involved in these biosynthetic pathways, and their respective expressions were validated by quantitative real-time reverse transcription polymerase chain reaction. Notably, isoflavonoid and miroestrol profiling generated by LC-MS/MS was positively correlated with expression levels of isoflavonoid biosynthetic genes across the four types of tissues. Moreover, we identified R2R3 MYB transcription factors that may be involved in the regulation of isoflavonoid biosynthesis in P. candollei var. mirifica. To confirm the function of a key-isoflavone biosynthetic gene, P. candollei var. mirifica isoflavone synthase identified in our library was transiently co-expressed with an Arabidopsis MYB12 transcription factor (AtMYB12) in Nicotiana benthamiana leaves. Remarkably, the combined expression of these proteins led to the production of the isoflavone genistein. Conclusions Our results provide compelling evidence regarding the integration of transcriptome and metabolome as a powerful tool for identifying biosynthetic genes and transcription factors possibly involved in the isoflavonoid and miroestrol biosyntheses in P. candollei var. mirifica.

scholarly journals Beneficial Regulatory Effects of Polymethoxyflavone—Rich Fraction from Ougan (Citrus reticulata cv. Suavissima) Fruit on Gut Microbiota and Identification of Its Intestinal Metabolites in Mice

Antioxidants ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 831
Author(s):  
Jiebiao Chen ◽  
Yue Wang ◽  
Tailin Zhu ◽  
Sijia Yang ◽  
Jinping Cao ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
High Performance ◽  
Citrus Fruit ◽  
Intestinal Content ◽  
Citrus Reticulata ◽  
Citrus Fruits ◽  
Human Gut ◽  
16S Ribosomal Dna ◽  
Regulatory Effects ◽  
Main Components

Polymethoxyflavones (PMFs) are special flavonoids in citrus fruits that have been suggested to be beneficial to human health. However, whether PMFs in citrus fruit alter human gut microbiota is not well understood. The aim of the present study was to investigate the effects of PMF-rich fraction from Ougan (Citrus reticulata cv. Suavissima) on gut microbiota and evaluate the intestinal metabolic profile of PMFs in Institute of Cancer Research mice. The main components of the PMF-rich fraction were nobiletin, tangeretin, and 5-demethylnobiletin. The composition of the gut microbiota was analyzed using 16S ribosomal DNA sequencing. The results showed that after oral administration, the composition of mice gut microbiota was significantly altered. The relative abundance of two probiotics, Lactobacillus and Bifidobacterium, were found to increase significantly. A total of 21 metabolites of PMFs were detected in mice intestinal content by high performance liquid chromatography electrospray ionization tandem mass spectrometry, and they were generated through demethylation, demethoxylation, hydroxylation, and glucuronidation. Our results provided evidence that PMFs have potential beneficial regulatory effects on gut microbiota that in turn metabolize PMFs, which warrants further investigation in human clinical trials.

scholarly journals Analogous and Diverse Functions of APSES-Type Transcription Factors in the Morphogenesis of the Entomopathogenic Fungus Metarhizium rileyi

2020 ◽  
Vol 86 (8) ◽  
Author(s):  
Caiyan Xin ◽  
Jinping Zhang ◽  
Siji Nian ◽  
Guangxi Wang ◽  
Zhongkang Wang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Transcriptome Analysis ◽  
Entomopathogenic Fungus ◽  
Regulatory Mechanisms ◽  
Sequencing Analysis ◽  
Fungal Virulence ◽  
Content Type ◽  
Dimorphic Transition ◽  
Metarhizium Rileyi ◽  
Fungal Morphogenesis

ABSTRACT APSES-type transcription factors (TFs) have analogous and diverse functions in the regulation of fungal morphogenesis processes. However, little is known about these functions in microsclerotium formation. In this study, we characterized two orthologous APSES genes (MrStuA and MrXbp) in the entomopathogenic fungus Metarhizium rileyi. Deletion of either MrStuA or MrXbp impaired dimorphic transition, conidiation, fungal virulence, and microsclerotium formation. Compared with the wild-type strain, ΔMrStuA and ΔMrXbp mutants were hypersensitive to thermal and oxidative stress. Furthermore, transcriptome sequencing analysis revealed that MrStuA and MrXbp independently regulate their own distinctive subsets of signaling pathways during dimorphic transition and microsclerotium formation, but they also show an overlapping regulation of genes during these two distinct morphogenesis processes. These results provide a global insight into vital roles of MrStuA and MrXbp in M. rileyi and aid in dissection of the interacting regulatory mechanisms of dimorphism transition and microsclerotium development. IMPORTANCE Transcription factors (TFs) are core components of the signaling pathway and play an important role in transcriptional regulation of gene expression during fungal morphogenesis processes. A prevailing theory suggests an interplay between different TFs regulating microsclerotial differentiation; however, the persisting issue remains that these interplay mechanisms are not clear. Here, we analyzed two members of the APSES-type TFs in Metarhizium rileyi using a gene deletion strategy and transcriptome analysis. Mutants were significantly impaired in microsclerotium formation and dimorphic transition. Transcriptome analysis provided evidence for interacting regulatory mechanisms by the two TFs in microsclerotium formation and dimorphic transition. Furthermore, we investigated their overlapping roles in mediating the expression of genes required for different fungal morphogenesis processes. Characterization of TFs in this study will aid in dissecting the interplay between regulatory mechanisms in fungal morphogenesis processes.

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