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21 pages, 6926 KiB

Open AccessArticle

Multi-Omics Analysis Reveals That Anthocyanin Degradation and Phytohormone Changes Regulate Red Color Fading in Rapeseed (Brassica napus L.) Petals

by Lan Huang, Baogang Lin, Pengfei Hao, Kaige Yi, Xi Li and Shuijin Hua

Int. J. Mol. Sci. 2024, 25(5), 2577; https://doi.org/10.3390/ijms25052577 - 23 Feb 2024

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Abstract

Flower color is an important trait for the ornamental value of colored rapeseed (Brassica napus L.), as the plant is becoming more popular. However, the color fading of red petals of rapeseed is a problem for its utilization. Unfortunately, the mechanism for [...] Read more.

Flower color is an important trait for the ornamental value of colored rapeseed (Brassica napus L.), as the plant is becoming more popular. However, the color fading of red petals of rapeseed is a problem for its utilization. Unfortunately, the mechanism for the process of color fading in rapeseed is unknown. In the current study, a red flower line, Zhehuhong, was used as plant material to analyze the alterations in its morphological and physiological characteristics, including pigment and phytohormone content, 2 d before flowering (T1), at flowering (T2), and 2 d after flowering (T3). Further, metabolomics and transcriptomics analyses were also performed to reveal the molecular regulation of petal fading. The results show that epidermal cells changed from spherical and tightly arranged to totally collapsed from T1 to T3, according to both paraffin section and scanning electron microscope observation. The pH value and all pigment content except flavonoids decreased significantly during petal fading. The anthocyanin content was reduced by 60.3% at T3 compared to T1. The content of three phytohormones, 1-aminocyclopropanecarboxylic acid, melatonin, and salicylic acid, increased significantly by 2.2, 1.1, and 30.3 times, respectively, from T1 to T3. However, auxin, abscisic acid, and jasmonic acid content decreased from T1 to T3. The result of metabolomics analysis shows that the content of six detected anthocyanin components (cyanidin, peonidin, pelargonidin, delphinidin, petunidin, and malvidin) and their derivatives mainly exhibited a decreasing trend, which was in accordance with the trend of decreasing anthocyanin. Transcriptomics analysis showed downregulation of genes involved in flavonol, flavonoid, and anthocyanin biosynthesis. Furthermore, genes regulating anthocyanin biosynthesis were preferentially expressed at early stages, indicating that the degradation of anthocyanin is the main issue during color fading. The corresponding gene-encoding phytohormone biosynthesis and signaling, JASMONATE-ZIM-DOMAIN PROTEIN, was deactivated to repress anthocyanin biosynthesis, resulting in fading petal color. The results clearly suggest that anthocyanin degradation and phytohormone regulation play essential roles in petal color fading in rapeseed, which is a useful insight for the breeding of colored rapeseed. Full article

(This article belongs to the Special Issue Advanced Research of Plant Secondary Metabolism)

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18 pages, 13927 KiB

Open AccessArticle

Pigment Diversity in Leaves of Caladium × hortulanum Birdsey and Transcriptomic and Metabolic Comparisons between Red and White Leaves

by Yiwei Zhou, Yechun Xu, Gen-Fa Zhu, Jianjun Tan, Jingyi Lin, Lishan Huang, Yuanjun Ye and Jinmei Liu

Int. J. Mol. Sci. 2024, 25(1), 605; https://doi.org/10.3390/ijms25010605 - 03 Jan 2024

Cited by 1 | Viewed by 715

Abstract

Leaf color is a key ornamental characteristic of cultivated caladium (Caladium × hortulanum Birdsey), a plant with diverse leaf colors. However, the genetic improvement of leaf color in cultivated caladium is hindered by the limited understanding of leaf color diversity and regulation. [...] Read more.

Leaf color is a key ornamental characteristic of cultivated caladium (Caladium × hortulanum Birdsey), a plant with diverse leaf colors. However, the genetic improvement of leaf color in cultivated caladium is hindered by the limited understanding of leaf color diversity and regulation. In this study, the chlorophyll and anthocyanin content of 137 germplasm resources were measured to explore the diversity and mechanism of leaf color formation in cultivated caladium. Association analysis of EST-SSR markers and pigment traits was performed, as well as metabolomics and transcriptomics analysis of a red leaf variety and its white leaf mutant. We found significant differences in chlorophyll and anthocyanin content among different color groups of cultivated caladium, and identified three, eight, three, and seven EST-SSR loci significantly associated with chlorophyll-a, chlorophyll-b, total chlorophyll and total anthocyanins content, respectively. The results further revealed that the white leaf mutation was caused by the down-regulation of various anthocyanins (such as cyanidin-3-O-rutinoside, quercetin-3-O-glucoside, and others). This change in concentration is likely due to the down-regulation of key genes (four PAL, four CHS, six CHI, eight F3H, one F3′H, one FLS, one LAR, four DFR, one ANS and two UFGT) involved in anthocyanin biosynthesis. Concurrently, the up-regulation of certain genes (one FLS and one LAR) that divert the anthocyanin precursors to other pathways was noted. Additionally, a significant change in the expression of numerous transcription factors (12 NAC, 12 bZIP, 23 ERF, 23 bHLH, 19 MYB_related, etc.) was observed. These results revealed the genetic and metabolic basis of leaf color diversity and change in cultivated caladium, and provided valuable information for molecular marker-assisted selection and breeding of leaf color in this ornamental plant. Full article

(This article belongs to the Special Issue Advanced Research of Plant Secondary Metabolism)

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17 pages, 3183 KiB

Open AccessArticle

Genome-Wide Identification of PAP1 Direct Targets in Regulating Seed Anthocyanin Biosynthesis in Arabidopsis

by Yuan Guo, Dong Li, Tiantian Liu, Yuxin Li, Jiajia Liu, Mingyuan He, Xiaohui Cui, Zijin Liu and Mingxun Chen

Int. J. Mol. Sci. 2023, 24(22), 16049; https://doi.org/10.3390/ijms242216049 - 07 Nov 2023

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Abstract

Anthocyanins are widespread water-soluble pigments in the plant kingdom. Anthocyanin accumulation is activated by the MYB-bHLH-WD40 (MBW) protein complex. In Arabidopsis, the R2R3-MYB transcription factor PAP1 activates anthocyanin biosynthesis. While prior research primarily focused on seedlings, seeds received limited attention. This study [...] Read more.

Anthocyanins are widespread water-soluble pigments in the plant kingdom. Anthocyanin accumulation is activated by the MYB-bHLH-WD40 (MBW) protein complex. In Arabidopsis, the R2R3-MYB transcription factor PAP1 activates anthocyanin biosynthesis. While prior research primarily focused on seedlings, seeds received limited attention. This study explores PAP1’s genome-wide target genes in anthocyanin biosynthesis in seeds. Our findings confirm that PAP1 is a positive regulator of anthocyanin biosynthesis in Arabidopsis seeds. PAP1 significantly increased anthocyanin content in developing and mature seeds in Arabidopsis. Transcriptome analysis at 12 days after pollination reveals the upregulation of numerous genes involved in anthocyanin accumulation in 35S:PAP1 developing seeds. Chromatin immunoprecipitation and dual luciferase reporter assays demonstrate PAP1’s direct promotion of ten key genes and indirect upregulation of TT8, TTG1, and eight key genes during seed maturation, thus enhancing seed anthocyanin accumulation. These findings enhance our understanding of PAP1’s novel role in regulating anthocyanin accumulation in Arabidopsis seeds. Full article

(This article belongs to the Special Issue Advanced Research of Plant Secondary Metabolism)

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15 pages, 7347 KiB

Open AccessArticle

Molecular Regulatory Network of Anthocyanin Accumulation in Black Radish Skin as Revealed by Transcriptome and Metabonome Analysis

by Jing Zhang, Zi-Xuan Zhang, Bo-Yue Wen, Ya-Jie Jiang, Xia He, Rui Bai, Xin-Ling Zhang, Wen-Chen Chai, Xiao-Yong Xu, Jin Xu, Lei-Ping Hou and Mei-Lan Li

Int. J. Mol. Sci. 2023, 24(17), 13663; https://doi.org/10.3390/ijms241713663 - 04 Sep 2023

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Abstract

To understand the coloring mechanism in black radish, the integrated metabolome and transcriptome analyses of root skin from a black recombinant inbred line (RIL 1901) and a white RIL (RIL 1911) were carried out. A total of 172 flavonoids were detected, and the [...] Read more.

To understand the coloring mechanism in black radish, the integrated metabolome and transcriptome analyses of root skin from a black recombinant inbred line (RIL 1901) and a white RIL (RIL 1911) were carried out. A total of 172 flavonoids were detected, and the analysis results revealed that there were 12 flavonoid metabolites in radish root skin, including flavonols, flavones, and anthocyanins. The relative concentrations of most flavonoids in RIL 1901 were higher than those in RIL 1911. Meanwhile, the radish root skin also contained 16 types of anthocyanins, 12 of which were cyanidin and its derivatives, and the concentration of cyanidin 3-o-glucoside was very high at different development stages of black radish. Therefore, the accumulation of cyanidin and its derivatives resulted in the black root skin of radish. In addition, a module positively related to anthocyanin accumulation and candidate genes that regulate anthocyanin synthesis was identified by the weighted gene co-expression network analysis (WGCNA). Among them, structural genes (RsCHS, RsCHI, RsDFR, and RsUGT75C1) and transcription factors (TFs) (RsTT8, RsWRKY44L, RsMYB114, and RsMYB308L) may be crucial for the anthocyanin synthesis in the root skin of black radish. The anthocyanin biosynthesis pathway in the root skin of black radish was constructed based on the expression of genes related to flavonoid and anthocyanin biosynthesis pathways (Ko00941 and Ko00942) and the relative expressions of metabolites. In conclusion, this study not only casts new light on the synthesis and accumulation of anthocyanins in the root skin of black radish but also provides a molecular basis for accelerating the cultivation of new black radish varieties. Full article

(This article belongs to the Special Issue Advanced Research of Plant Secondary Metabolism)

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15 pages, 4825 KiB

Open AccessArticle

Acceptors and Effectors Alter Substrate Inhibition Kinetics of a Plant Glucosyltransferase NbUGT72AY1 and Its Mutants

by Jieren Liao, Veronika Lederer, Alba Bardhi, Zhiwei Zou, Timothy D. Hoffmann, Guangxin Sun, Chuankui Song, Thomas Hoffmann and Wilfried Schwab

Int. J. Mol. Sci. 2023, 24(11), 9542; https://doi.org/10.3390/ijms24119542 - 31 May 2023

Viewed by 1279

Abstract

One of the main obstacles in biocatalysis is the substrate inhibition (SI) of enzymes that play important roles in biosynthesis and metabolic regulation in organisms. The promiscuous glycosyltransferase UGT72AY1 from Nicotiana benthamiana is strongly substrate-inhibited by hydroxycoumarins (inhibitory constant Ki < 20 µM), [...] Read more.

One of the main obstacles in biocatalysis is the substrate inhibition (SI) of enzymes that play important roles in biosynthesis and metabolic regulation in organisms. The promiscuous glycosyltransferase UGT72AY1 from Nicotiana benthamiana is strongly substrate-inhibited by hydroxycoumarins (inhibitory constant Ki < 20 µM), but only weakly inhibited when monolignols are glucosylated (Ki > 1000 µM). Apocarotenoid effectors reduce the inherent UDP-glucose glucohydrolase activity of the enzyme and attenuate the SI by scopoletin derivatives, which could also be achieved by mutations. Here, we studied the kinetic profiles of different phenols and used the substrate analog vanillin, which has shown atypical Michaelis–Menten kinetics in previous studies, to examine the effects of different ligands and mutations on the SI of NbUGT72AY1. Coumarins had no effect on enzymatic activity, whereas apocarotenoids and fatty acids strongly affected SI kinetics by increasing the inhibition constant Ki. Only the F87I mutant and a chimeric version of the enzyme showed weak SI with the substrate vanillin, but all mutants exhibited mild SI when sinapaldehyde was used as an acceptor. In contrast, stearic acid reduced the transferase activity of the mutants to varying degrees. The results not only confirm the multi-substrate functionality of NbUGT72AY1, but also reveal that the enzymatic activity of this protein can be fine-tuned by external metabolites such as apocarotenoids and fatty acids that affect SI. Since these signals are generated during plant cell destruction, NbUGT72AY1 likely plays an important role in plant defense by participating in the production of lignin in the cell wall and providing direct protection through the formation of toxic phytoalexins. Full article

(This article belongs to the Special Issue Advanced Research of Plant Secondary Metabolism)

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19 pages, 7695 KiB

Open AccessArticle

Cytotoxic Steroidal Saponins Containing a Rare Fructosyl from the Rhizomes of Paris polyphylla var. latifolia

by Tian-Yi Li, Yang Du, Min-Chang Wang, Ke Liu, Yang Liu, Yu Cao, Yuan-Yuan Wang, Wen-Wen Chen, Xiao-Ying Qian, Peng-Cheng Qiu, Hai-Feng Tang and Yun-Yang Lu

Int. J. Mol. Sci. 2023, 24(8), 7149; https://doi.org/10.3390/ijms24087149 - 12 Apr 2023

Cited by 2 | Viewed by 1593

Abstract

A phytochemical investigation of the steroidal saponins from the rhizomes of Paris polyohylla var. latifolia led to the discovery and characterization of three new spirostanol saponins, papolatiosides A–C (1–3), and nine known compounds (4–12). Their [...] Read more.

A phytochemical investigation of the steroidal saponins from the rhizomes of Paris polyohylla var. latifolia led to the discovery and characterization of three new spirostanol saponins, papolatiosides A–C (1–3), and nine known compounds (4–12). Their structures were established via extensive spectroscopic data analysis and chemical methods. Interestingly, compounds 1 and 2 possessed a fructosyl in their oligosaccharide moiety, which is rare in natural product and was firstly reported in family Melanthiaceae. The cytotoxicity of these saponins against several human cancer cell lines was evaluated by a CCK-8 experiment. As a result, compound 1 exhibited a significant cytotoxic effect on LN229, U251, Capan-2, HeLa, and HepG2 cancer cells with IC₅₀ values of 4.18 ± 0.31, 3.85 ± 0.44, 3.26 ± 0.34, 3.30 ± 0.38 and 4.32 ± 0.51 μM, respectively. In addition, the result of flow cytometry analysis indicated that compound 1 could induce apoptosis of glioma cells LN229. The underlying mechanism was explored by network pharmacology and western bolt experiments, which indicated that compound 1 could induce glioma cells LN229 apoptosis by regulating the EGFR/PI3K/Akt/mTOR pathway. Full article

(This article belongs to the Special Issue Advanced Research of Plant Secondary Metabolism)

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23 pages, 8831 KiB

Open AccessArticle

Characterization of the WRKY Gene Family Related to Anthocyanin Biosynthesis and the Regulation Mechanism under Drought Stress and Methyl Jasmonate Treatment in Lycoris radiata

by Ning Wang, Guowei Song, Fengjiao Zhang, Xiaochun Shu, Guanghao Cheng, Weibing Zhuang, Tao Wang, Yuhang Li and Zhong Wang

Int. J. Mol. Sci. 2023, 24(3), 2423; https://doi.org/10.3390/ijms24032423 - 26 Jan 2023

Cited by 7 | Viewed by 2090

Abstract

Lycoris radiata, belonging to the Amaryllidaceae family, is a well-known Chinese traditional medicinal plant and susceptible to many stresses. WRKY proteins are one of the largest families of transcription factors (TFs) in plants and play significant functions in regulating physiological metabolisms and [...] Read more.

Lycoris radiata, belonging to the Amaryllidaceae family, is a well-known Chinese traditional medicinal plant and susceptible to many stresses. WRKY proteins are one of the largest families of transcription factors (TFs) in plants and play significant functions in regulating physiological metabolisms and abiotic stress responses. The WRKY TF family has been identified and investigated in many medicinal plants, but its members and functions are not identified in L. radiata. In this study, a total of 31 L. radiata WRKY (LrWRKY) genes were identified based on the transcriptome-sequencing data. Next, the LrWRKYs were divided into three major clades (Group I–III) based on the WRKY domains. A motif analysis showed the members within same group shared a similar motif component, indicating a conservational function. Furthermore, subcellular localization analysis exhibited that most LrWRKYs were localized in the nucleus. The expression pattern of the LrWRKY genes differed across tissues and might be important for Lycoris growth and flower development. There were large differences among the LrWRKYs based on the transcriptional levels under drought stress and MeJA treatments. Moreover, a total of 18 anthocyanin components were characterized using an ultra-performance liquid chromatography-electrospray ionization tandem mass spectrometry (UPLC-ESI-MS/MS) analysis and pelargonidin-3-O-glucoside-5-O-arabinoside as well as cyanidin-3-O-sambubioside were identified as the major anthocyanin aglycones responsible for the coloration of the red petals in L. radiata. We further established a gene-to-metabolite correlation network and identified LrWRKY3 and LrWRKY27 significant association with the accumulation of pelargonidin-3-O-glucoside-5-O-arabinoside in the Lycoris red petals. These results provide an important theoretical basis for further exploring the molecular basis and regulatory mechanism of WRKY TFs in anthocyanin biosynthesis and in response to drought stress and MeJA treatment. Full article

(This article belongs to the Special Issue Advanced Research of Plant Secondary Metabolism)

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13 pages, 2528 KiB

Open AccessArticle

An ABCG-Type Transporter Facilitates ABA Influx and Regulates Camptothecin Biosynthesis in Camptotheca acuminata

by Yanyan Wang, Yang Wang, Hefei Bai, Yuqian Han and Fang Yu

Int. J. Mol. Sci. 2022, 23(24), 16120; https://doi.org/10.3390/ijms232416120 - 17 Dec 2022

Cited by 2 | Viewed by 1186

Abstract

Camptothecin (CPT) and its derivatives from Camptotheca acuminata have antitumor effects as a DNA topoisomerase I inhibitor. Previous studies have shown that application of exogenous abscisic acid (ABA) significantly promoted the accumulation level of CPT and induced the expression of CPT biosynthetic genes, [...] Read more.

Camptothecin (CPT) and its derivatives from Camptotheca acuminata have antitumor effects as a DNA topoisomerase I inhibitor. Previous studies have shown that application of exogenous abscisic acid (ABA) significantly promoted the accumulation level of CPT and induced the expression of CPT biosynthetic genes, which revealed that ABA signaling is effectively involved in regulating CPT biosynthesis in C. acuminata. In this study, an ABA transporter, CaABAT, which encodes a plasma membrane protein belonging to the ABCG subfamily, was identified in C. acuminata, and its ABA import activity was confirmed by transport assay in yeast cells. Real-time PCR analysis showed that CaABAT was predominately expressed in C. acuminata leaves and its expression could be significantly upregulated by exogenous ABA treatment. Silencing of CaABAT down-regulated the expression of ABA response genes, which indicated that translocation of ABA by CaABAT should initiate changes in plant physiological status in response to ABA signaling, thus leading to decreased expression of CPT biosynthesis pathway genes and low accumulation levels of CPT in C. acuminata. Full article

(This article belongs to the Special Issue Advanced Research of Plant Secondary Metabolism)

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8 pages, 9604 KiB

Open AccessArticle

Key Amino Acids for Transferase Activity of GDSL Lipases

by Takanori Yamashiro, Akira Shiraishi, Koji Nakayama and Honoo Satake

Int. J. Mol. Sci. 2022, 23(23), 15141; https://doi.org/10.3390/ijms232315141 - 01 Dec 2022

Cited by 1 | Viewed by 1150

Abstract

The Gly-Asp-Ser-Leu (GDSL) motif of esterase/lipase family proteins (GELPs) generally exhibit esterase activity, whereas transferase activity is markedly preferred in several GELPs, including the Tanacetum cinerariifolium GDSL lipase TciGLIP, which is responsible for the biosynthesis of the natural insecticide, pyrethrin I. This transferase [...] Read more.

The Gly-Asp-Ser-Leu (GDSL) motif of esterase/lipase family proteins (GELPs) generally exhibit esterase activity, whereas transferase activity is markedly preferred in several GELPs, including the Tanacetum cinerariifolium GDSL lipase TciGLIP, which is responsible for the biosynthesis of the natural insecticide, pyrethrin I. This transferase activity is due to the substrate affinity regulated by the protein structure and these features are expected to be conserved in transferase activity-exhibiting GELPs (tr-GELPs). In this study, we identified two amino acid residues, [N/R]208 and D484, in GELP sequence alignments as candidate key residues for the transferase activity of tr-GELPs by two-entropy analysis. Molecular phylogenetic analysis demonstrated that each tr-GELP is located in the clusters for non-tr-GELPs, and most GELPs conserve at least one of the two residues. These results suggest that the two conserved residues are required for the acquisition of transferase activity in the GELP family. Furthermore, substrate docking analyses using ColabFold-generated structure models of both natives and each of the two amino acids-mutated TciGLIPs also revealed numerous docking models for the proper access of substrates to the active site, indicating crucial roles of these residues of TciGLIP in its transferase activity. This is the first report on essential residues in tr-GELPs for the transferase activity. Full article

(This article belongs to the Special Issue Advanced Research of Plant Secondary Metabolism)

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Review

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27 pages, 2953 KiB

Open AccessReview

Brassinosteroid Promotes Grape Berry Quality-Focus on Physicochemical Qualities and Their Coordination with Enzymatic and Molecular Processes: A Review

by Jiajia Li, Yi Quan, Lei Wang and Shiping Wang

Int. J. Mol. Sci. 2023, 24(1), 445; https://doi.org/10.3390/ijms24010445 - 27 Dec 2022

Cited by 6 | Viewed by 1956

Abstract

Brassinosteroid (BR) is an important endogenous phytohormone that plays a significant role in fruit quality regulation. The regulation of BR biosynthesis and its physiological effects have been well-studied in various fruits. External quality (fruit longitudinal and transverse diameters, firmness, single berry weight, color) [...] Read more.

Brassinosteroid (BR) is an important endogenous phytohormone that plays a significant role in fruit quality regulation. The regulation of BR biosynthesis and its physiological effects have been well-studied in various fruits. External quality (fruit longitudinal and transverse diameters, firmness, single berry weight, color) and internal quality (sugars, aroma, anthocyanin, stress-related metabolites) are important parameters that are modified during grape berry development and ripening. Grapevines are grown all over the world as a cash crop and utilized for fresh consumption, wine manufacture, and raisin production. In this paper, the biosynthesis and signaling transduction of BR in grapevine were summarized, as well as the recent developments in understanding the role of BR in regulating the external quality (fruit longitudinal and transverse diameters, firmness, single berry weight, and color) and internal quality (sugars, organic acids, aroma substances, anthocyanins, antioxidants) of grapes. Additionally, current advancements in exogenous BR strategies for improving grape berries quality were examined from the perspectives of enzymatic activity and transcriptional regulation. Furthermore, the interaction between BR and other phytohormones regulating the grape berry quality was also discussed, aiming to provide a reliable reference for better understanding the potential value of BR in the grape/wine industry. Full article

(This article belongs to the Special Issue Advanced Research of Plant Secondary Metabolism)

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