Integrated Transcriptome and Proteome Analysis Provides Insights into Anthocyanin Accumulation in the Leaves of Red-Leaved Poplars

2021 ◽  
Author(s):  
Xinghao Chen ◽  
Hanqi Liu ◽  
Shijie Wang ◽  
Chao Zhang ◽  
Minsheng Yang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Candidate Genes ◽  
Molecular Mechanism ◽  
Populus Deltoides ◽  
Proteome Analysis ◽  
Anthocyanin Synthesis ◽  
Total Chlorophyll ◽  
Anthocyanin Accumulation ◽  
Proteome Expression ◽  
Red Coloration

Abstract The red-leaved poplar cultivars ‘Quanhong’ and ‘Xuanhong’ are bud mutations of Populus deltoides cv. ‘Zhonglin 2025’. These cultivars are valued for their beautiful shape, lack of flying catkins, and ornamental leaf colors. However, the understanding of the molecular mechanism of anthocyanin accumulation in the leaves of red-leaved poplars is still unclear. Here, we profiled the changes of pigment content, transcriptome and proteome expression in the leaves of three poplar cultivars and the results showed that the ratios of anthocyanin to total chlorophyll in both red-leaved poplars were higher than that in ‘Zhonglin 2025’, indicating that the anthocyanin was highly accumulated in the leaves of red-leaved poplars. Based on the results of integrated transcriptome and proteome analysis, 15 and 11 differentially expressed genes/proteins involved in anthocyanin synthesis were screened in ‘Quanhong’ and ‘Xuanhong’, respectively, including the CHS, F3H, and DFR genes. Among the 120 transcription factors, 3 (HY5, HYH, and TTG2), may be directly involved in the regulation of anthocyanin synthesis in both red-leaved poplars. This study screens the candidate genes involved in anthocyanin accumulation in the leaves of red-leaved poplars and lays a foundation for further exploring the molecular mechanism of leaf red coloration in red-leaved poplars.

scholarly journals Integrated transcriptome and proteome analysis provides insights into leaf color differences between red-leaved poplar cultivars (‘Quanhong’ and ‘Xuanhong’) and ‘Zhonglin 2025’ (Populus deltoides cv. ‘Zhonglin 2025’)

2020 ◽  
Author(s):  
Xinghao Chen ◽  
Hanqi Liu ◽  
Shijie Wang ◽  
Chao Zhang ◽  
Minsheng Yang ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Populus Deltoides ◽  
Proteome Analysis ◽  
Differentially Expressed ◽  
Anthocyanin Synthesis ◽  
Integrated Analysis ◽  
Physiological Indicators ◽  
Protein Levels ◽  
Color Differences ◽  
Leaf Coloration

Abstract BackgroundThe red-leaved poplar cultivars ‘Quanhong’ and ‘Xuanhong’ are bud mutations of Populus deltoides cv. ‘Zhonglin 2025’. These cultivars are valued for their beautiful shape, lack of flying catkins, and ornamental leaf colors. The molecular mechanism that leads to different leaf colors between these red-leaved poplars and ‘Zhonglin 2025’ remains unclear.ResultsIn this study, we analyzed growth and physiological indicators in the ‘Quanhong’, ‘Xuanhong’, and ‘Zhonglin 2025’ poplar cultivars, and performed transcriptome and proteome analysis of their leaves. The results showed that plant height and ground diameter were significantly lower in both red-leaved poplars than in ‘Zhonglin 2025’, indicating that their growth and development were markedly inhibited. The ratio of anthocyanin to total chlorophyll and photosynthetic capacity of the leaves were higher and lower, respectively, in the red-leaved cultivars than in ‘Zhonglin 2025’. At the transcript and protein levels, 6,792 differentially expressed genes (DEGs) and 2,786 differentially expressed proteins (DEPs) were screened in the ‘Quanhong’ cultivar, respectively, and 4,398 DEGs and 2,333 DEPs were screened in the ‘Xuanhong’ cultivar, respectively. We screened 769 DEGs/DEPs in ‘Quanhong’ and 399 DEGs/DEPs in ‘Xuanhong’ in an integrated transcriptomics/proteomics analysis. Based on the results of this integrated analysis, 15 and 11 genes/proteins involved in anthocyanin synthesis were further identified in ‘Quanhong’ and ‘Xuanhong’, respectively, including the CHS , F3H , and DFR genes. Among the 120 transcription factors, 3 (HY5, HYH, and TTG2), may be directly involved in the regulation of anthocyanin synthesis in both red-leaved poplars.ConclusionsBy comparing the proteomes and transcriptomes of red-leaved poplar cultivars and ‘Zhonglin 2025’, we identified the key genes and proteins related to red leaf coloration. The findings of this study provided insights that may aid further studies of the molecular mechanism of leaf red coloration in red-leaved poplars.

scholarly journals Improving the Anthocyanin Accumulation of Hypocotyls in Radish Sprouts by Hemin-induced NO

2020 ◽  
Author(s):  
Nana Su ◽  
Ze Liu ◽  
Hui Chen ◽  
Mengyang Niu ◽  
Jin Cui
Keyword(s):  
Nitric Oxide ◽  
Transcription Factors ◽  
Anthocyanin Biosynthesis ◽  
Reductase Activity ◽  
Specific Inhibitor ◽  
Anthocyanin Synthesis ◽  
Zinc Protoporphyrin ◽  
Anthocyanin Content ◽  
Anthocyanin Accumulation ◽  
Radish Sprouts

Abstract Background: The biosynthesis of anthocyanin in the hypocotyls of radish (Raphanus sativus L.) sprouts was enhanced by hemin in our preliminary experiments, but the underlying mechanism is unclear. Here, we found that NO (nitric oxide) exerted an essential role in Hemin-regulated anthocyanin biosynthesis, which was supported by the following results.Results: Hemin boosted anthocyanin as well as NO content. NO-scavenger cPTIO (carboxy-PTIO) significantly attenuated hemin-induced increase of anthocyanin content, transcripts of anthocyanin synthesis related genes and positive transcription factors, implying that NO played a prominent role during hemin-induced anthocyanin biosynthesis. Hemin specific inhibitor ZnPP (Zinc Protoporphyrin) strongly reduced anthocyanin content, while, NO donor SNP (Sodium Nitroprusside) addition considerably reversed this inhibition and by contrast, resulted in a significant increase in anthocyanin accumulation, closely paralleling the transcripts of structural genes and transcription factors. Moreover, NO content, NR (nitrate reductase) activity and expression level of NOA (nitric oxide associated factor) were up-regulated by Hemin. Conclusions:Those consequences indicated that NO might work downstream in Hemin-heightened anthocyanin accumulation in radish sprouts.

scholarly journals Transcriptome Analysis Reveals Candidate Genes Related to Anthocyanin Biosynthesis in Different Carrot Genotypes and Tissues

Plants ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 344 ◽  
Author(s):  
Geng Meng ◽  
Sabine K. Clausen ◽  
Søren K. Rasmussen
Keyword(s):  
Candidate Genes ◽  
High Performance ◽  
Anthocyanin Biosynthesis ◽  
High Performance Liquid Chromatographic ◽  
Anthocyanin Synthesis ◽  
Natural Food ◽  
Sequencing Analysis ◽  
Anthocyanin Accumulation ◽  
Glutathione S Transferase ◽  
The Individual

Black carrots are characterized by a significant amount of anthocyanins, which are not only a good source of natural food colorant, but can also provide many health benefits to humans. In the present work, taproots of different carrot genotypes were used to identify the candidate genes related to anthocyanin synthesis, with particular a focus on R2R3MYB, bHLH transcription factors, and glutathione S-transferase gene (GST). The RNA-sequencing analysis (RNA-Seq) showed that DcMYB6 and DcMYB7 had a genotypic dependent expression and they are likely involved in the regulation of anthocyanin biosynthesis. They were specifically upregulated in solid black taproots, including both black phloem and xylem. DcbHLH3 (LOC108204485) was upregulated in all black samples compared with the orange ones. We also found that GST1 (LOC108205254) might be an important anthocyanin transporter, and its upregulated expression resulted in the increasing of vacuolar anthocyanin accumulation in black samples. Moreover, high performance liquid chromatographic (HPLC) analysis and liquid chromatography coupled to mass spectrometry (LC-MS) were used to identify the individual anthocyanin in the purple tissues of two carrot cultivars. The results showed that five main anthocyanin compounds and the most abundant anthocyanin were the same in different tissues, while the second-highest anthocyanin between three tissues was different, even in the same cultivar. In conclusion, this study combined anthocyanin profiles and comparative transcriptomic analysis to identify candidate genes involved in anthocyanin biosynthesis in carrots, thus providing a better foundation for improving anthocyanin accumulation in carrots as a source of colorants.

MYB_SH[AL]QKY[RF] transcription factors MdLUX and MdPCL-like promote anthocyanin accumulation through DNA hypomethylation and MdF3H activation in apple

2020 ◽  
Author(s):  
Wen-Fang Li ◽  
Gai-Xing Ning ◽  
Cun-Wu Zuo ◽  
Ming-Yu Chu ◽  
Shi-Jin Yang ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Transcription Factors ◽  
Promoter Region ◽  
Anthocyanin Biosynthesis ◽  
Apple Fruit ◽  
Anthocyanin Synthesis ◽  
Mrna Levels ◽  
Anthocyanin Accumulation ◽  
Dna Hypomethylation ◽  
Fruit Skin

Abstract Heritable DNA methylation is a highly conserved epigenetic mark that is important for many biological processes. In a previous transcriptomic study on the fruit skin pigmentation of apple (Malus domestica Borkh.) cv. ‘Red Delicious’ (G0) and its four continuous-generation bud sport mutants including ‘Starking Red’ (G1), ‘Starkrimson’ (G2), ‘Campbell Redchief’ (G3) and ‘Vallee spur’ (G4), we identified MYB transcription factors (TFs) MdLUX and MdPCL-like involved in regulating anthocyanin synthesis. However, how these TFs ultimately determine the fruit skin colour traits remain elusive. Here, bioinformatics analysis revealed that MdLUX and MdPCL-like contained a well-conserved motif SH[AL]QKY[RF] in their C-terminal region and were located in the nucleus of onion epidermal cells. Overexpression of MdLUX and MdPCL-like in ‘Golden Delicious’ fruits, ‘Gala’ calli and Arabidopsis thaliana promoted the accumulation of anthocyanin, whereas MdLUX and MdPCL-like suppression inhibited anthocyanin accumulation in ‘Red Fuji’ apple fruit skin. Yeast one-hybrid assays revealed that MdLUX and MdPCL-like may bind to the promoter region of the anthocyanin biosynthesis gene MdF3H. Dual-luciferase assays indicated that MdLUX and MdPCL-like activated MdF3H. The whole-genome DNA methylation study revealed that the methylation levels of the mCG context at the upstream (i.e., promoter region) of MdLUX and MdPCL-like were inversely correlated with their mRNA levels and anthocyanin accumulation. Hence, the data suggest that MYB_SH[AL]QKY[RF] TFs MdLUX and MdPCL-like promote anthocyanin biosynthesis in apple fruit skins through the DNA hypomethylation of their promoter regions and the activation of the structural flavonoid gene MdF3H.

scholarly journals Exploring the Molecular Mechanism of Blue Flower Color Formation in Hydrangea macrophylla cv. “Forever Summer”

2021 ◽  
Vol 12 ◽  
Author(s):  
Jiqing Peng ◽  
Xujie Dong ◽  
Chao Xue ◽  
Zhiming Liu ◽  
Fuxiang Cao
Keyword(s):  
Transcription Factors ◽  
Molecular Mechanism ◽  
Color Change ◽  
Anthocyanin Biosynthesis ◽  
Flower Color ◽  
Anthocyanin Synthesis ◽  
Blue Flower ◽  
Biosynthesis Pathway ◽  
Color Formation ◽  
Hydrangea Macrophylla

Hydrangea macrophylla has a large inflorescence and rich colors, which has made it one of the most popular ornamental flowers worldwide. Thus far, the molecular mechanism of flower color formation in H. macrophylla flowers is unknown. By comparing the pigment content and transcriptome data of the bud period (FSF1), discoloration period (FSF2) and full-bloom stage (FSF3) of infertile blue flowers of H. macrophylla cv. “Forever Summer,” we found that genes associated with anthocyanin production were most associated with the formation of blue infertile flowers throughout development. The anthocyanin biosynthesis pathway is the main metabolic pathway associated with flower color formation, and the carotenoid biosynthesis pathway appeared to have almost no contribution to flower color. There was no competition between the flavonoid and flavonol and anthocyanin biosynthesis pathways for their substrate. At FSF1, the key genes CHS and CHI in the flavonoid biosynthesis pathway were up-regulated, underlying the accumulation of a substrate for anthocyanin synthesis. By FSF3, the downstream genes F3H, C3′5′H, CYP75B1, DFR, and ANS in the anthocyanin biosynthesis pathway were almost all up-regulated, likely promoting the synthesis and accumulation of anthocyanins and inducing the color change of infertile flowers. By analyzing protein–protein interaction networks and co-expression of transcription factors as well as differentially expressed structural genes related to anthocyanin synthesis, we identified negatively regulated transcription factors such as WER-like, MYB114, and WDR68. Their site of action may be the key gene DFR in the anthocyanin biosynthesis pathway. The potential regulatory mechanism of flower color formation may be that WER-like, MYB114, and WDR68 inhibit or promote the synthesis of anthocyanins by negatively regulating the expression of DFR. These results provide an important basis for studying the infertile flower color formation mechanism in H. macrophylla and the development of new cultivars with other colors.

scholarly journals Genome-wide characterization and analysis of bHLH transcription factors related to anthocyanin biosynthesis in spine grapes (Vitis davidii)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ming Li ◽  
Lei Sun ◽  
Hong Gu ◽  
Dawei Cheng ◽  
XiZhi Guo ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Candidate Genes ◽  
Grape Berry ◽  
Synthesis Process ◽  
Anthocyanin Synthesis ◽  
Bhlh Transcription Factor ◽  
Transcription Factor Family ◽  
Bhlh Transcription Factors

AbstractAs one of the largest transcription factor family, basic helix-loop-helix (bHLH) transcription factor family plays an important role in plant metabolism, physiology and growth. Berry color is one of the important factors that determine grape quality. However, the bHLH transcription factor family’s function in anthocyanin synthesis of grape berry has not been studied systematically. We identified 115 bHLH transcription factors in grape genome and phylogenetic analysis indicated that bHLH family could be classified into 25 subfamilies. First, we screened six candidate genes by bioinformatics analysis and expression analysis. We found one of the candidate genes VdbHLH037 belonged to III (f) subfamily and interacted with genes related to anthocyanin synthesis through phylogenetic analysis and interaction network prediction. Therefore, we speculated that VdbHLH037 participated in the anthocyanin synthesis process. To confirm this, we transiently expressed VdbHLH037 in grape and Arabidopsis transformation. Compared with the control, transgenic materials can accumulate more anthocyanins. These results provide a good base to study the function of the VdbHLH family in anthocyanin synthesis of grape berry.

scholarly journals Transcriptome profiling analysis of muscle tissue reveals potential candidate genes affecting water holding capacity in Chinese Simmental beef cattle

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Lili Du ◽  
Tianpeng Chang ◽  
Bingxing An ◽  
Mang Liang ◽  
Xinghai Duan ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Candidate Genes ◽  
Molecular Mechanism ◽  
Meat Quality ◽  
Relevant Literature ◽  
Transcriptome Profiling ◽  
Water Holding Capacity ◽  
Potential Candidate ◽  
Protein Protein Interaction ◽  
Water Holding

AbstractWater holding capacity (WHC) is an important sensory attribute that greatly influences meat quality. However, the molecular mechanism that regulates the beef WHC remains to be elucidated. In this study, the longissimus dorsi (LD) muscles of 49 Chinese Simmental beef cattle were measured for meat quality traits and subjected to RNA sequencing. WHC had significant correlation with 35 kg water loss (r = − 0.99, p < 0.01) and IMF content (r = 0.31, p < 0.05), but not with SF (r = − 0.20, p = 0.18) and pH (r = 0.11, p = 0.44). Eight individuals with the highest WHC (H-WHC) and the lowest WHC (L-WHC) were selected for transcriptome analysis. A total of 865 genes were identified as differentially expressed genes (DEGs) between two groups, of which 633 genes were up-regulated and 232 genes were down-regulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment revealed that DEGs were significantly enriched in 15 GO terms and 96 pathways. Additionally, based on protein–protein interaction (PPI) network, animal QTL database (QTLdb), and relevant literature, the study not only confirmed seven genes (HSPA12A, HSPA13, PPARγ, MYL2, MYPN, TPI, and ATP2A1) influenced WHC in accordance with previous studies, but also identified ATP2B4, ACTN1, ITGAV, TGFBR1, THBS1, and TEK as the most promising novel candidate genes affecting the WHC. These findings could offer important insight for exploring the molecular mechanism underlying the WHC trait and facilitate the improvement of beef quality.

scholarly journals Differences in Anthocyanin Accumulation Profiles between Teinturier and Non-Teinturier Cultivars during Ripening

Foods ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 1073
Author(s):  
Meng-Bo Tian ◽  
Lin Yuan ◽  
Ming-Yuan Zheng ◽  
Zhu-Mei Xi
Keyword(s):  
Gene Expression ◽  
Plant Secondary Metabolites ◽  
Anthocyanin Synthesis ◽  
Anthocyanin Content ◽  
Anthocyanin Accumulation ◽  
Total Anthocyanin ◽  
Total Anthocyanin Content ◽  
The Individual ◽  
Relative Gene ◽  
High Expression Level

Anthocyanins are vital components of plant secondary metabolites, and are also the most important coloring substances in wine. Teinturier cultivars are rich in anthocyanins. However, the differences in anthocyanin accumulation and profiles between teinturier and non-teinturier cultivars have not been reported. In this study, Yan 73 and Dunkelfelder were selected as the experimental materials, and three non-teinturier cultivars were used for comparison. LC-MS and qRT-PCR were used to determine the individual anthocyanin contents and the relative gene expression. The results show that the total anthocyanin content of the teinturier cultivars was considerably higher than that in non-teinturier cultivars, and the levels of individual anthocyanins increased gradually during ripening. Lower ratios of modified anthocyanins were found in the teinturier cultivars, which was not only due to the high expression level of VvUFGT and VvGST4, but also due to the relatively low expression of VvOMT in these cultivars. Cluster analysis of gene expression and anthocyanin accumulation showed that VvUFGT is related to anthocyanin accumulation, and that AM1 is related to the synthesis and transport of methylated anthocyanins. Our results will be useful for further clarifying the pathways of anthocyanin synthesis, modification, and transport in teinturier cultivars.

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