scholarly journals Transcriptome and Metabolome-based Analysis of Anthocyanidin Biosynthesis in Purple Pepper

2021 ◽  
Author(s):  
Yaning Meng ◽  
Hongxiao Zhang ◽  
Yanqin Fan ◽  
Libin Yan
Keyword(s):  
Metabolic Pathways ◽  
Promoter Region ◽  
Biosynthetic Pathway ◽  
Transcriptome Data ◽  
Structural Genes ◽  
Green Pepper ◽  
Color Formation ◽  
Kegg Analysis ◽  
Key Genes ◽  
Metabolome Data

Abstract In order to clarify the profile of gene expression and metabolites for color formation and the molecular mechanism of anthocyanidin accumulation in purple pepper fruits, we analyzed the anthocyanidin metabolome data of the fruits of 2 purple pepper lines and 1 green pepper line and detected a total of 5 anthocyanidin-like metabolites, of which delphin chloride was unique to purple pepper fruits and 3 other anthocyanidin-like substances shared the metabolic pathway ko00942 and were up-regulated. Based on the transcriptome data, three pathways (ko00360, ko00400, and ko00941) related to anthocyanidin metabolism were identified through KEGG analysis. Three enzymes (DFR, ANS, and UFGT) and three transcription factors (MYB, BHLH, and WD40) in the purple pepper anthocyanidin biosynthetic pathway were up-regulated. We proposed a model to explain the regulation of pepper anthocyanidin biosynthesis: MYB, BHLH, and WD40 formed a ternary complex and bound to the specific cis-acting elements in the promoter region of the structural genes related to anthocyanidin biosynthesis to directly regulate their transcription, which resulted in the accumulation of a large amount of anthocyanidin metabolites including delphinidin 3-O-glucoside, delphinidin 3-O-rutinoside, and delphin chloride, giving color to pepper fruits. This study clarified the metabolic pathways and key genes affecting the color of purple pepper fruits and provided new insights into the synthesis and accumulation of anthocyanidins in pepper fruits.

scholarly journals Comparative analysis of transcrptome profiling to identify genes involved in bulged surface of pear fruits (Pyrus bretschneideri Rehd. cv. Yuluxiangli)

2020 ◽  
Author(s):  
Baopeng Ding ◽  
Chaohui Hu ◽  
Yuqin Song ◽  
Ruijie Hao ◽  
Xinxin Feng ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Promoter Region ◽  
Theoretical Basis ◽  
Transcriptional Factor ◽  
Growth Retardant ◽  
Vascular Bundles ◽  
Kegg Analysis ◽  
The Family ◽  
Negative Role ◽  
Division Cell

Abstract Background: Pear (Pyrus spp.) belongs to the genus Pyrus, in the family Rosaceae. Some varieties of pear fruits exhibit bulged surface, which seriously affect the quality and commodity value. In this study, we performed anatomical, physiological and transcriptomic analysis, to explore the mechanism of paclobutrazol (PBZ) on the bulged surface of pear fruits. Results: The vascular bundles of flesh were more evenly distributed and the cells arranged more compactly with smaller size. However, the auxin (IAA) content of flesh decreased significantly when treated with PBZ. Further, the GO and KEGG analysis of differentially expressed genes (DEGs) showed that auxin, phenylpropanoid metabolic pathways and transcriptional factor genes were significantly enriched on the relieved bulged surface of pear fruits. The promoter region analysis of selected DEGs showed that some genes contained auxin responded cis-elements. Conclusion: We conclude that PBZ might play a negative role in the cell division, cell elongation and vascular bundle development on bulged surface of pear fruits through the involvement of auxin related genes. This study will provide theoretical basis for the regulation of bulged surface of pear fruits by growth retardant agent.

scholarly journals Identification and quantification of target metabolites combined with transcriptome of two rheum species focused on anthraquinone and flavonoids biosynthesis

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Jing Liu ◽  
Liang Leng ◽  
Yan Liu ◽  
Han Gao ◽  
Wei Yang ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Biosynthetic Pathway ◽  
Multiple Reaction Monitoring ◽  
Perennial Herb ◽  
Reaction Monitoring ◽  
Transcriptome Data ◽  
Quadrupole Mass ◽  
Peak Intensity ◽  
Flavonoids Biosynthesis ◽  
Important Medicinal Plant

AbstractRheum emodi is a perennial herb and an important medicinal plant, with anthraquinones and flavonoids as its main bioactive compounds. However, there is little knowledge about the biosynthetic pathway of anthraquinones in rhubarbs. In this study, we qualitatively and quantitatively assessed 62 pharmacological metabolites in rhubarb using dynamic multiple reaction monitoring (dMRM) of triple-quadrupole mass spectrometry (QqQ-MS), including 21 anthraquinones, 17 flavonoids, 6 stilbenes, 12 gallate esters, 3 tannins, and 3 others. Besides, the metabolomics results showed significant differences among all the 60 metabolites, except for gallic acid and piceatannol-O-β-glucoside. The combined transcriptome data of R. palmatum L. (RPL) and R. officinale Baill. (ROB) showed that 21,691 unigenes were annotated in the metabolic pathways. Taken together, 17 differentially expressed genes (DEGs) were associated with the anthraquinone biosynthetic pathway. Additionally, a significant correlation between anthraquinone peak intensity and DEG expression level existed, validating that DEGs contribute to the anthraquinone biosynthetic pathway. RT-qPCR results showed that the cluster-14354.38156 gene may catalyze the O-methylation of emodin to produce physcion. This study provides a useful resource for further studies on secondary metabolism in rhubarb and the combination analysis of transcriptome and metabolome, which can help with the discovery of enzyme genes involved in metabolite biosynthesis.

scholarly journals Characterization and Action Mechanism Analysis of VvmiR156b/c/d-VvSPL9 Module Responding to Multiple-Hormone Signals in the Modulation of Grape Berry Color Formation

Foods ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 896
Author(s):  
Ziwen Su ◽  
Xicheng Wang ◽  
Xuxian Xuan ◽  
Zilu Sheng ◽  
Haoran Jia ◽  
...  
Keyword(s):  
Color Change ◽  
Grape Berry ◽  
Anthocyanin Synthesis ◽  
Structural Genes ◽  
Expression Levels ◽  
Color Formation ◽  
Grape Berries ◽  
Ripening Stages ◽  
Color Conversion ◽  
Hormone Signals

In recent years, more and more reports have shown that the miR156-SPL module can participate in the regulation of anthocyanin synthesis in plants. However, little is known about how this module responds to hormonal signals manipulating this process in grapes. In this study, exogenous GA, ABA, MeJA, and NAA were used to treat the ‘Wink’ grape berries before color conversion, anthocyanin and other related quality physiological indexes (such as sugar, aroma) were determined, and spatio-temporal expression patterns of related genes were analyzed. The results showed that the expression levels of VvmiR156b/c/d showed a gradually rising trend with the ripening and color formation of grape berries, and the highest expression levels were detected at day 28 after treatment, while the expression level of VvSPL9 exhibited an opposite trend as a whole, which further verifies that VvmiR156b/c/d can negatively regulate VvSPL9. Besides, VvmiR156b/c/d was positively correlated with anthocyanin content and related genes levels, while the expression pattern of VvSPL9 showed a negative correlation. Analysis of promoter cis-elements and GUS staining showed that VvmiR156b/c/d contained a large number of hormone response cis-elements (ABA, GA, SA, MeJA, and NAA) and were involved in hormone regulation. Exogenous ABA and MeJA treatments significantly upregulated the expression levels of VvmiR156b/c/d and anthocyanin structural genes in the early stage of color conversion and made grape berries quickly colored. Interestingly, GA treatment downregulated the expression levels of VvmiR156b/c/d and anthocyanin structural genes in the early color-change period, but significantly upregulated in the middle color-change and ripening stages, therefore GA mainly modulated grape berry coloring in the middle- and late-ripening stages. Furthermore, NAA treatment downregulated the expression levels of VvmiR156b/c/d and anthocyanin structural genes and delayed the peak expression of genes. Meanwhile, to further recognize the potential functions of VvmiR156b/c/d, the mature tomato transient trangenetic system was utilized in this work. Results showed that transient overexpression of VvmiR156b/c/d in tomato promoted fruit coloring and overexpression of VvSPL9 inhibited fruit coloration. Finally, a regulatory network of the VvmiR156b/c/d-VvSPL9 module responsive to hormones modulating anthocyanin synthesis was developed. In conclusion, VvmiR156b/c/d-mediated VvSPL9 participated in the formation of grape color in response to multi-hormone signals.

scholarly journals Transcriptome and Metabolome Dynamics Explain Aroma Differences between Green and Red Prickly Ash Fruit

Foods ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 391
Author(s):  
Xitong Fei ◽  
Yichen Qi ◽  
Yu Lei ◽  
Shujie Wang ◽  
Haichao Hu ◽  
...  
Keyword(s):  
Redundancy Analysis ◽  
Biosynthetic Pathway ◽  
Expression Patterns ◽  
Gas Chromatography Mass Spectrometry ◽  
Zanthoxylum Armatum ◽  
Aroma Characteristics ◽  
Main Factors ◽  
Key Genes ◽  
Zanthoxylum Bungeanum ◽  
Aroma Components

Green prickly ash (Zanthoxylum armatum) and red prickly ash (Zanthoxylum bungeanum) fruit have unique flavor and aroma characteristics that affect consumers’ purchasing preferences. However, differences in aroma components and relevant biosynthesis genes have not been systematically investigated in green and red prickly ash. Here, through the analysis of differentially expressed genes (DEGs), differentially abundant metabolites, and terpenoid biosynthetic pathways, we characterize the different aroma components of green and red prickly ash fruits and identify key genes in the terpenoid biosynthetic pathway. Gas chromatography-mass spectrometry (GC-MS) was used to identify 41 terpenoids from green prickly ash and 61 terpenoids from red prickly ash. Piperitone was the most abundant terpenoid in green prickly ash fruit, whereas limonene was most abundant in red prickly ash. Intergroup correlation analysis and redundancy analysis showed that HDS2, MVK2, and MVD are key genes for terpenoid synthesis in green prickly ash, whereas FDPS2 and FDPS3 play an important role in the terpenoid synthesis of red prickly ash. In summary, differences in the composition and content of terpenoids are the main factors that cause differences in the aromas of green and red prickly ash, and these differences reflect contrasting expression patterns of terpenoid synthesis genes.

scholarly journals Comparative transcriptome analysis reveals key genes associated with pigmentation in radish (Raphanus sativus L.) skin and flesh

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jifang Zhang ◽  
Jian Zhao ◽  
Qunyun Tan ◽  
Xiaojun Qiu ◽  
Shiyong Mei
Keyword(s):  
Transcription Factors ◽  
Raphanus Sativus ◽  
Regulatory Networks ◽  
Anthocyanin Biosynthesis ◽  
Comparative Transcriptome ◽  
Structural Genes ◽  
Key Genes ◽  
Transcript Profiles ◽  
Species Specific ◽  
Anthocyanin Biosynthetic Genes

AbstractRadish (Raphanus sativus) is an important vegetable worldwide that exhibits different flesh and skin colors. The anthocyanins responsible for the red and purple coloring in radishes possess nutritional value and pharmaceutical potential. To explore the structural and regulatory networks related to anthocyanin biosynthesis and identify key genes, we performed comparative transcriptome analyses of the skin and flesh of six colored radish accessions. The transcript profiles showed that each accession had a species-specific transcript profile. For radish pigmentation accumulation, the expression levels of anthocyanin biosynthetic genes (RsTT4, RsC4H, RsTT7, RsCCOAMT, RsDFR, and RsLDOX) were significantly upregulated in the red- and purple-colored accessions, but were downregulated or absent in the white and black accessions. The correlation test, combined with metabolome (PCC > 0.95), revealed five structural genes (RsTT4, RsDFR, RsCCOAMT, RsF3H, and RsBG8L) and three transcription factors (RsTT8-1, RsTT8-2, and RsPAR1) to be significantly correlated with flavonoids in the skin of the taproot. Four structural genes (RsBG8L, RsDFR, RsCCOAMT, and RsLDOX) and nine transcription factors (RsTT8-1, RsTT8-2, RsMYB24L, RsbHLH57, RsPAR2L, RsbHLH113L, RsOGR3L, RsMYB24, and RsMYB34L) were found to be significantly correlated with metabolites in the flesh of the taproot. This study provides a foundation for future studies on the gene functions and genetic diversity of radish pigmentation and should aid in the cultivation of new valuable radish varieties.

scholarly journals Combined Transcriptome and Metabolome Integrated Analysis of Acer mandshuricum to Reveal Candidate Genes Involved in Anthocyanin Accumulation

2021 ◽  
Author(s):  
Shikai Zhang ◽  
Wang Zhan ◽  
Anran Sun ◽  
Ying Xie ◽  
Zhiming Han ◽  
...  
Keyword(s):  
Regulatory Mechanism ◽  
Color Change ◽  
Anthocyanin Biosynthesis ◽  
Integrated Analysis ◽  
Anthocyanin Accumulation ◽  
Structural Genes ◽  
Leaf Color ◽  
Accumulation Pattern ◽  
Color Formation ◽  
Red Color

Abstract The red color formation of Acer mandshuricum leaves is caused by the accumulation of anthocyanins primarily, but the molecular mechanism researches which underlie anthocyanin biosynthesis in A. mandshuricum were still lacking. Therefore, we combined the transcriptome and metabolome and analyzed the regulatory mechanism and accumulation pattern of anthocyanins in leaf color change periods in three different leaf color states. In our results, 26 anthocyanins were identified. Notably, the metabolite cyanidin 3-O-glucoside was found that significantly correlated with the color formation, was the predominant metabolite in anthocyanin biosynthesis of A. mandshuricum. By the way, two key structural genes ANS (Cluster-20561.86285) and BZ1 (Cluster-20561.99238) in anthocyanidin biosynthesis pathway were significantly up-regulated in RL, suggesting that they might enhance accumulation of cyanidin 3-O-glucoside which is their downstream metabolite, and contributed the red formation of A. mandshuricum leaves. Additionally, most TFs (e.g., MYBs, bZIPs and bHLHs) were detected differentially expressed in three leaf color stages that could participate in anthocyanin accumulation. This study sheds light on the anthocyanin molecular regulation of anthocyanidin bio-synthesis and accumulation underlying the different leaf color change periods in A. mandshuricum, and it could provide basic theory and new insight for the leaf color related genetic improvement of A. mandshuricum.

Dependence of heme biosynthesis on iron-sulfur cluster biogenesis: human ALAD is an unrecognized iron-sulfur protein

2020 ◽  
Author(s):  
Gang Liu ◽  
Debangsu Sil ◽  
Wing-Hang Tong ◽  
Nunziata Maio ◽  
J. Martin Bollinger ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Biosynthetic Pathway ◽  
Aminolevulinic Acid ◽  
Heme Biosynthesis ◽  
Second Step ◽  
Iron Sulfur Cluster ◽  
Sulfur Cluster ◽  
Iron Sulfur ◽  
Sulfur Protein ◽  
Iron Sulfur Protein

Abstract Heme biosynthesis and iron-sulfur cluster (ISC) biogenesis are two major mammalian metabolic pathways that require iron. It has long been known that these two pathways interconnect, but the previously described interactions do not fully explain why heme biosynthesis depends on intact ISC biogenesis. Herein we have identified a previously unrecognized connection between these two pathways through our discovery that human aminolevulinic acid dehydratase (ALAD), which catalyzes the second step of heme biosynthesis, is an Fe-S protein. We found that several highly conserved cysteines and an Ala306-Phe307-Arg308 motif of human ALAD are important for [Fe4S4] cluster acquisition and coordination. The enzymatic activity of human ALAD was greatly reduced upon loss of its Fe-S cluster, which resulted in reduced heme biosynthesis in human cells. Our findings explain why heme biosynthesis depends on intact ISC biogenesis, as ALAD provides an early Fe-S-dependent checkpoint in the heme biosynthetic pathway.

scholarly journals GuUGT, a glycosyltransferase from Glycyrrhiza uralensis , exhibits glycyrrhetinic acid 3- and 30-O-glycosylation

2019 ◽  
Vol 6 (10) ◽  
pp. 191121 ◽  
Author(s):  
Ying Huang ◽  
Da Li ◽  
Jinhe Wang ◽  
Yi Cai ◽  
Zhubo Dai ◽  
...  
Keyword(s):  
Biosynthetic Pathway ◽  
Glycyrrhetinic Acid ◽  
Glycyrrhiza Uralensis ◽  
Transcriptome Data ◽  
Bioactive Components ◽  
Triterpenoid Saponins ◽  
Genes Encoding ◽  
Engineered Yeast ◽  
Biochemical Analyses

Glycyrrhiza uralensis is a well-known herbal medicine that contains triterpenoid saponins as the predominant bioactive components, and these compounds include glycyrrhetinic acid (GA)-glycoside derivatives. Although two genes encoding UDP-glycosyltransferases (UGTs) that glycosylate these derivates have been functionally characterized in G. uralensis , the mechanisms of glycosylation by other UGTs remain unknown. Based on the available transcriptome data, we isolated a UGT with expression in the roots of G. uralensis . This UGT gene possibly encodes a glucosyltransferase that glycosylates GA derivatives at the 3-OH site. Biochemical analyses revealed that the recombinant UGT enzyme could transfer a glucosyl moiety to the free 3-OH or 30-COOH groups of GA. Furthermore, engineered yeast harbouring genes involved in the biosynthetic pathway for GA-glycoside derivates produced GA-3- O -β-D-glucoside, implying that the enzyme has GA 3-O-glucosyltransferase activity in vivo . Our results could provide a frame for understand the function of the UGT gene family, and also is important for further studies of triterpenoids biosynthesis in G. uralensis .

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