scholarly journals BrmiR828 Targets BrPAP1, BrMYB82, and BrTAS4 Involved in the Light Induced Anthocyanin Biosynthetic Pathway in Brassica rapa

2020 ◽  
Vol 21 (12) ◽  
pp. 4326
Author(s):  
Bo Zhou ◽  
Jingtong Leng ◽  
Yanyun Ma ◽  
Pengzhen Fan ◽  
Yuhua Li ◽  
...  
Keyword(s):  
Brassica Rapa ◽  
Biosynthetic Pathway ◽  
Anthocyanin Biosynthesis ◽  
Transcript Level ◽  
Transcript Abundance ◽  
Light Irradiation ◽  
Dark Treatment ◽  
Anthocyanin Biosynthetic Pathway ◽  
Post Transcriptional Regulation ◽  
Gene 4

Comprehensive research in various plants shows that the metabolic pathway of anthocyanin biosynthesis is affected by environmental factors and regulated by microRNAs through post-transcriptional regulation. In seedlings of Brassica rapa Tsuda, the accumulation of anthocyanin is induced by light. However, the roles of BrmiR828 in the light-induced synthesis of anthocyanin in Brassica rapa remain to be explored. Here, a primary transcript of BrmiR828 was identified to be located on the chromosomes of the A03 sub-genome. Five candidate MYB family genes were predicted as targets of BrmiR828 in the database of Brassica rapa (BRAD, V1.1) by using psRNATarget. The transcript abundance of mature BrmiR828 was reduced in seedlings of Brassica rapa Tsuda under blue light irradiation comparing with dark treatment. However, Real-time PCR showed the transcript level of the five candidate targets, Bra004162, Bra022602, Bra001917, Bra029113, and Bra039763 was up-regulated when the seedlings exposed to blue or UV-A light. Trans-acting siRNA gene 4 (BrTAS4) was also identified to have a higher transcript level under blue and UV-A light irradiation than that in dark treatment. RNA ligase mediated 5′amplification of cDNA ends (RLM-5′ RACE) showed that BrmiR828 can splice the mRNA of Bra039763, Bra022602, and BrTAS4 on binding sites. Phylogenetic analysis of candidate BrMYBs targets along with MYBs from Arabidopsis thaliana showed that Bra039763, Bra004162, Bra001917, Bra029113, and Bra022602 are classified to the same group with AtMYB75, AtMYB114, AtMYB90, AtMYB113, and AtMYB82 which are involved in the anthocyanin biosynthetic pathway. As a result, light-induced down-regulation of BrmiR828 can target BrTAS4, BrPAP1 (Bra039763), MYB82 (Bra022602) to negatively regulate their transcript levels leading to the accumulation of MYB transcription factors that positively regulate anthocyanin biosynthesis in light-exposed seedlings of Brassica rapa.

scholarly journals The MIR-Domain of PbbHLH2 Is Involved in Regulation of the Anthocyanin Biosynthetic Pathway in ”Red Zaosu” (PyrusBretschneideri Rehd.) Pear Fruit

2021 ◽  
Vol 22 (6) ◽  
pp. 3026
Author(s):  
Xieyu Li ◽  
Fangxin Xiang ◽  
Wei Han ◽  
Bingqing Qie ◽  
Rui Zhai ◽  
...  
Keyword(s):  
Biosynthetic Pathway ◽  
Anthocyanin Biosynthesis ◽  
Bimolecular Fluorescence Complementation ◽  
Anthocyanin Content ◽  
Pear Fruit ◽  
Fruit Peel ◽  
Interaction Domain ◽  
Dihydroflavonol Reductase ◽  
Anthocyanin Biosynthetic Pathway ◽  
R2r3 Myb

The N-terminal of Myc-like basic helix-loop-helix transcription factors (bHLH TFs) contains an interaction domain, namely the MYB-interacting region (MIR), which interacts with the R2R3-MYB proteins to regulate genes involved in the anthocyanin biosynthetic pathway. However, the functions of MIR-domain bHLHs in this pathway are not fully understood. In this study, PbbHLH2 containing the MIR-domain was identified and its function investigated. The overexpression of PbbHLH2 in ”Zaosu” pear peel increased the anthocyanin content and the expression levels of late biosynthetic genes. Bimolecular fluorescence complementation showed that PbbHLH2 interacted with R2R3-MYB TFs PbMYB9, 10, and 10b in onion epidermal cells and confirmed that MIR-domain plays important roles in the interaction between the MIR-domain bHLH and R2R3-MYB TFs. Moreover, PbbHLH2 bound and activated the dihydroflavonol reductase promoter in yeast one-hybrid (Y1H) and dual-luciferase assays. Taken together these results suggested that the MIR domain of PbbHLH2 regulated anthocyanin biosynthesis in pear fruit peel.

scholarly journals iTRAQ-Based Protein Profiling Provides Insights into the Mechanism of Light-Induced Anthocyanin Biosynthesis in Chrysanthemum (Chrysanthemum × morifolium)

Genes ◽  
2019 ◽  
Vol 10 (12) ◽  
pp. 1024
Author(s):  
Yan Hong ◽  
Mengling Li ◽  
Silan Dai
Keyword(s):  
Biosynthetic Pathway ◽  
Developmental Stages ◽  
Anthocyanin Biosynthesis ◽  
Expression Patterns ◽  
Flower Color ◽  
Chrysanthemum Morifolium ◽  
Light Signal ◽  
Protein Profiling ◽  
Differentially Expressed ◽  
Anthocyanin Biosynthetic Pathway

The generation of chrysanthemum (Chrysanthemum × morifolium) flower color is mainly attributed to the accumulation of anthocyanins. Light is one of the key environmental factors that affect the anthocyanin biosynthesis, but the deep molecular mechanism remains elusive. In our previous study, a series of light-induced structural and regulatory genes involved in the anthocyanin biosynthetic pathway in the chrysanthemum were identified using RNA sequencing. In the present study, differentially expressed proteins that are in response to light with the capitulum development of the chrysanthemum ‘Purple Reagan’ were further identified using isobaric tags for relative and absolute quantification (iTRAQ) technique, and correlation between the proteomic and the transcriptomic libraries was analyzed. In general, 5106 raw proteins were assembled based on six proteomic libraries (three capitulum developmental stages × two light treatments). As many as 160 proteins were differentially expressed between the light and the dark libraries with 45 upregulated and 115 downregulated proteins in response to shading. Comparative analysis between the pathway enrichment and the gene expression patterns indicated that most of the proteins involved in the anthocyanin biosynthetic pathway were downregulated after shading, which was consistent with the expression patterns of corresponding encoding genes; while five light-harvesting chlorophyll a/b-binding proteins were initially downregulated after shading, and their expressions were enhanced with the capitulum development thereafter. As revealed by correlation analysis between the proteomic and the transcriptomic libraries, GDSL esterase APG might also play an important role in light signal transduction. Finally, a putative mechanism of light-induced anthocyanin biosynthesis in the chrysanthemum was proposed. This study will help us to clearly identify light-induced proteins associated with flower color in the chrysanthemum and to enrich the complex mechanism of anthocyanin biosynthesis for use in cultivar breeding.

scholarly journals Discovery of Anthocyanin Biosynthetic Pathway in Cosmos caudatus Kunth. Using Omics Analysis

Agronomy ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 661
Author(s):  
Darvien Gunasekaran ◽  
Noor Idayu Tahir ◽  
Muhamad Afiq Akbar ◽  
Syazwani Basir ◽  
Ismanizan Ismail ◽  
...  
Keyword(s):  
Biosynthetic Pathway ◽  
Anthocyanin Biosynthesis ◽  
Natural Colorant ◽  
Gene Pathway ◽  
Cosmos Caudatus ◽  
Anthocyanin Biosynthetic Pathway ◽  
Medicinal Value ◽  
Expression Studies ◽  
Genes Encoding ◽  
Nutritional Compounds

Cosmos caudatus Kunth. or “king’s salad” contains high values of nutritional compounds that act as health promoters. Although widely consumed for its medicinal value, information on phytochemical contents and their biosynthesis in the species is scarce. Among the interesting compounds are the anthocyanins that possess a dual role; an antioxidant and natural colorant. A complete anthocyanin biosynthetic pathway in C. caudatus was elucidated using transcriptomics, metabolomics, and anatomical approaches in this study. The transcriptomic analysis revealed genes encoding enzymes in the anthocyanin biosynthetic pathway and the genes encoding the transcription factors relevant to the latter pathway. A total of 11 anthocyanins of cyanidin, pelargonidin, and delphinidin derivatives that are significantly abundant in the species were identified, correlating with the anthocyanin mainstream gene pathway. The occurrence of anthocyanin was further validated by light microscopy. Anthocyanin pigments in C. caudatus were detected at the epidermal layer of the leaf, stem, and flower, and at the cortex of stem and root. To our knowledge, this is the first work that has delineated the complete anthocyanin biosynthetic pathway in Malaysia’s underutilized plant, C. caudatus Kunth. This study correlated multi-omics data that will help integrate systems biology and synthetic biology, for a detailed understanding of the molecular mechanism and characterization of the anthocyanin biosynthesis using heterologous expression studies.

scholarly journals The Purple Leaf (pl6) Mutation Regulates Leaf Color by Altering the Anthocyanin and Chlorophyll Contents in Rice

Plants ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 1477
Author(s):  
Asadullah Khan ◽  
Sanaullah Jalil ◽  
Huan Cao ◽  
Yohannes Tsago ◽  
Mustapha Sunusi ◽  
...  
Keyword(s):  
Gamma Ray ◽  
Anthocyanin Biosynthesis ◽  
Light Attenuation ◽  
Transcript Level ◽  
Underlying Mechanism ◽  
Anthocyanin Accumulation ◽  
Morphological Marker ◽  
Chlorophyll Contents ◽  
Rice Mutant ◽  
Purple Coloration

The anthocyanin biosynthesis attracts strong interest due to the potential antioxidant value and as an important morphological marker. However, the underlying mechanism of anthocyanin accumulation in plant tissues is not clearly understood. Here, a rice mutant with a purple color in the leaf blade, named pl6, was developed from wild type (WT), Zhenong 41, with gamma ray treatment. By map-based cloning, the OsPL6 gene was located on the short arm of chromosome 6. The multiple mutations, such as single nucleotide polymorphism (SNP) at −702, −598, −450, an insertion at −119 in the promoter, three SNPs and one 6-bp deletion in the 5′-UTR region, were identified, which could upregulate the expression of OsPL6 to accumulate anthocyanin. Subsequently, the transcript level of structural genes in the anthocyanin biosynthesis pathway, including OsCHS, OsPAL, OsF3H and OsF3′H, was elevated significantly. Histological analysis revealed that the light attenuation feature of anthocyanin has degraded the grana and stroma thylakoids, which resulted in poor photosynthetic efficiency of purple leaves. Despite this, the photoabatement and antioxidative activity of anthocyanin have better equipped the pl6 mutant to minimize the oxidative damage. Moreover, the contents of abscisic acid (ABA) and cytokanin (CK) were elevated along with anthocyanin accumulation in the pl6 mutant. In conclusion, our results demonstrate that activation of OsPL6 could be responsible for the purple coloration in leaves by accumulating excessive anthocyanin and further reveal that anthocyanin acts as a strong antioxidant to scavenge reactive oxygen species (ROS) and thus play an important role in tissue maintenance.

scholarly journals The Flavonoid Biosynthesis Network in Plants

2021 ◽  
Vol 22 (23) ◽  
pp. 12824
Author(s):  
Weixin Liu ◽  
Yi Feng ◽  
Suhang Yu ◽  
Zhengqi Fan ◽  
Xinlei Li ◽  
...  
Keyword(s):  
Biosynthetic Pathway ◽  
Current Knowledge ◽  
Anthocyanin Biosynthesis ◽  
Basic Structure ◽  
Ring Structure ◽  
Flavonoid Biosynthesis ◽  
Comprehensive Overview ◽  
Flavonoid Biosynthetic Pathway ◽  
Intermediate Metabolites ◽  
Important Intermediate

Flavonoids are an important class of secondary metabolites widely found in plants, contributing to plant growth and development and having prominent applications in food and medicine. The biosynthesis of flavonoids has long been the focus of intense research in plant biology. Flavonoids are derived from the phenylpropanoid metabolic pathway, and have a basic structure that comprises a C15 benzene ring structure of C6-C3-C6. Over recent decades, a considerable number of studies have been directed at elucidating the mechanisms involved in flavonoid biosynthesis in plants. In this review, we systematically summarize the flavonoid biosynthetic pathway. We further assemble an exhaustive map of flavonoid biosynthesis in plants comprising eight branches (stilbene, aurone, flavone, isoflavone, flavonol, phlobaphene, proanthocyanidin, and anthocyanin biosynthesis) and four important intermediate metabolites (chalcone, flavanone, dihydroflavonol, and leucoanthocyanidin). This review affords a comprehensive overview of the current knowledge regarding flavonoid biosynthesis, and provides the theoretical basis for further elucidating the pathways involved in the biosynthesis of flavonoids, which will aid in better understanding their functions and potential uses.

scholarly journals DeepShape: estimating isoform-level ribosome abundance and distribution with Ribo-seq data

2019 ◽  
Vol 20 (S24) ◽  
Author(s):  
Hongfei Cui ◽  
Hailin Hu ◽  
Jianyang Zeng ◽  
Ting Chen
Keyword(s):  
Transcript Level ◽  
Transcript Abundance ◽  
Ribosome Profiling ◽  
Computational Method ◽  
Translational Efficiency ◽  
Rna Seq ◽  
Basic Step ◽  
Synonymous Codons ◽  
Abundance And Distribution ◽  
Different Characteristics

Abstract Background Ribosome profiling brings insight to the process of translation. A basic step in profile construction at transcript level is to map Ribo-seq data to transcripts, and then assign a huge number of multiple-mapped reads to similar isoforms. Existing methods either discard the multiple mapped-reads, or allocate them randomly, or assign them proportionally according to transcript abundance estimated from RNA-seq data. Results Here we present DeepShape, an RNA-seq free computational method to estimate ribosome abundance of isoforms, and simultaneously compute their ribosome profiles using a deep learning model. Our simulation results demonstrate that DeepShape can provide more accurate estimations on both ribosome abundance and profiles when compared to state-of-the-art methods. We applied DeepShape to a set of Ribo-seq data from PC3 human prostate cancer cells with and without PP242 treatment. In the four cell invasion/metastasis genes that are translationally regulated by PP242 treatment, different isoforms show very different characteristics of translational efficiency and regulation patterns. Transcript level ribosome distributions were analyzed by “Codon Residence Index (CRI)” proposed in this study to investigate the relative speed that a ribosome moves on a codon compared to its synonymous codons. We observe consistent CRI patterns in PC3 cells. We found that the translation of several codons could be regulated by PP242 treatment. Conclusion In summary, we demonstrate that DeepShape can serve as a powerful tool for Ribo-seq data analysis.

scholarly journals Fetal expression of genes related to metabolic function is impacted by supplementation of ground beef and sucrose during gestation in a swine model

2020 ◽  
Vol 98 (8) ◽  
Author(s):  
Ashley S Hoyle ◽  
Ana Clara B Menezes ◽  
Megan A Nelson ◽  
Kendall C Swanson ◽  
Kimberly A Vonnahme ◽  
...  
Keyword(s):  
Metabolic Diseases ◽  
Fetal Liver ◽  
Ground Beef ◽  
Transcript Level ◽  
Transcript Abundance ◽  
Mrna Abundance ◽  
Late Gestation ◽  
Swine Model ◽  
Metabolic Function ◽  
Longissimus Dorsi Muscle

Abstract To determine the effects of maternal supplementation on the mRNA abundance of genes associated with metabolic function in fetal muscle and liver, pregnant sows (Landrace × Yorkshire; initial body weight (BW) 221.58 ± 33.26 kg; n = 21) fed a complete gestation diet (corn–soybean meal based diet, CSM) were randomly assigned to 1 of 4 isocaloric supplementation treatments: control (CON, 378 g/d CSM, n = 5), sucrose (SUGAR, 255 g/d crystalized sugar, n = 5), cooked ground beef (BEEF, 330 g/d n = 6), or BEEF + SUGAR (B+S, 165 g/d cooked ground beef and 129 g/d crystalized sugar, n = 5), from days 40 to 110 of gestation. Sows were euthanized on day 111 of gestation. Two male and 2 female fetuses of median BW were selected from each litter, and samples of the longissimus dorsi muscle and liver were collected. Relative transcript level was quantified via qPCR with HPRT1 as the reference gene for both muscle and liver samples. The following genes were selected and analyzed in the muscle: IGF1R, IGF2, IGF2R, GYS-1, IRS-1, INSR, SREBP-1C, and LEPR; while the following were analyzed in the liver: IGF2, IGF2R, FBFase, G6PC, PC, PCK1, FGF21, and LIPC. No effect of fetal sex by maternal treatment interaction was observed in mRNA abundance of any of the genes evaluated (P > 0.11). In muscle, the maternal nutritional treatment influenced (P = 0.02) IGF2 mRNA abundance, with B+S and SUGAR fetuses having lower abundance than CON, which was not different from BEEF. Additionally, SREBP-1 mRNA abundance was greater (P < 0.01) for B+S compared with CON, BEEF, or SUGAR fetuses; and females tended (P = 0.06) to have an increased abundance of SREBP-1 than males. In fetal liver, IGF2R mRNA abundance was greater (P = 0.01) for CON and BEEF than SUGAR and B+S; while FBPase mRNA abundance was greater (P = 0.03) for B+S compared with the other groups. In addition, maternal nutritional tended (P = 0.06) to influence LIPC mRNA abundance, with increased abundance in CON compared with SUGAR and B+S. These data indicate limited changes in transcript abundance due to substitution of supplemental sugar by ground beef during mid to late gestation. However, the differential expression of FBPase and SREBP-1c in response to the simultaneous supplementation of sucrose and ground beef warrants further investigations, since these genes may play important roles in determining the offspring susceptibility to metabolic diseases.

Expression characterisation of cyclophilin BrROC1 during light treatment and abiotic stresses response in Brassica rapa subsp. rapa ‘Tsuda’

2018 ◽  
Vol 45 (12) ◽  
pp. 1223 ◽  
Author(s):  
Haifang Yan ◽  
Bo Zhou ◽  
Wei He ◽  
Yuzhe Nie ◽  
Yuhua Li
Keyword(s):  
Blue Light ◽  
Brassica Rapa ◽  
Abiotic Stresses ◽  
Expression Patterns ◽  
Transcript Level ◽  
Light Treatment ◽  
Anthocyanin Synthesis ◽  
Root Epidermis ◽  
High Or Low Temperature ◽  
Level Analysis

ROC1 is a prototypic peptidyl prolyl cis/trans isomerase (PPIase) of the plant cytosol belonging to the large subfamily of cyclophilins that are associated with diverse functions through foldase, scaffolding, chaperoning or other unknown activities. Although many functions of plant cyclophilins have been reported, the molecular basis of stress-responsive expression of plant cyclophilins is still largely unknown. To characterise the roles of BrROC1 during light treatment and their responses in various abiotic stresses, we identified BrROC1 genes and characterised their expression patterns in Brassica rapa subsp. rapa ‘Tsuda’. Our results showed that BrROC1 genes are multi-family genes. Transcript level analysis showed BrROC1-2 expressed higher than BrROC1-1 in 0 to 6-day-old seedlings under natural light. Moreover, BrROC1-2 genes were also induced to highly express in the cotyledon, upper hypocotyls and lower hypocotyls of seedlings under UV-A and blue-light treatment. In addition, the transcript level of BrROC1-1 was higher in pigment tissues than that in unpigment tissues (cotyledon and lower hypocotyl) under UV-A and blue-light treatment. Furthermore, when the unpigment epidermis (shaded light) of 2-month-old ‘Tsuda’ turnip roots was exposed to UV-A light, transcript levels of the BrROC1-1 and BrROC1-2 were significantly increased with time prolongation. These two BrROC1 genes might be involved in UV-A-induced anthocyanin synthesis in the root epidermis of ‘Tsuda’ turnip, which accumulates high levels of anthocyanin. These two BrROC1 genes were also induced to be regulated by abiotic stresses such as high or low temperature, dehydration, osmotic and salt stresses. Then, the results indicate that BrROC1 genes are involved in light induction response and may play important roles in adaptation of plants to various environmental stresses.

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