International Journal of Molecular Sciences

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22 pages, 8956 KiB

Open AccessArticle

Genome-Wide Characterization, Comparative Analysis, and Expression Profiling of SWEET Genes Family in Four Cymbidium Species (Orchidaceae)

by Yonglu Wei, Jie Li, Jianpeng Jin, Jie Gao, Qi Xie, Chuqiao Lu, Genfa Zhu and Fengxi Yang

Int. J. Mol. Sci. 2025, 26(9), 3946; https://doi.org/10.3390/ijms26093946 - 22 Apr 2025

Abstract

The SWEET (Sugar Will Eventually be Exported Transporters) protein family plays a key role in plant growth, adaptation, and stress responses by facilitating soluble sugar transport. However, their functions in Cymbidium remain poorly understood. This study identified 59 SWEET genes across four Cymbidium [...] Read more.

The SWEET (Sugar Will Eventually be Exported Transporters) protein family plays a key role in plant growth, adaptation, and stress responses by facilitating soluble sugar transport. However, their functions in Cymbidium remain poorly understood. This study identified 59 SWEET genes across four Cymbidium species, encoding conserved MtN3/saliva domains. Despite variations in exon-intron structures, gene motifs and domains were highly conserved. Phylogenetic analysis grouped 95 SWEET proteins from six species into four clades, with gene expansion driven by whole-genome, segmental, and tandem duplications. Cis-element analysis and expression profiling across 72 samples revealed diverse regulatory patterns. Notably, SWEET genes showed peak expression in floral development, leaf morph variations, and diurnal rhythms. qRT-PCR and transcription factor binding analysis further highlighted their regulatory roles in floral patterning, leaf variation, and metabolic rhythms. These findings provide a foundation for future studies on SWEET gene function and their potential molecular breeding value in orchids. Full article

(This article belongs to the Special Issue Transcriptional Regulation in Plant Development: 2nd Edition)

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17 pages, 5041 KiB

Open AccessArticle

Physiological and Transcriptional Responses of Sesame (Sesamum indicum L.) to Waterlogging Stress

by Yadong Fan, Chengqi Cui, Yanyang Liu, Ke Wu, Zhenwei Du, Xiaolin Jiang, Fengli Zhao, Ruping Zhang, Jingjing Wang, Hongxian Mei and Haiyang Zhang

Int. J. Mol. Sci. 2025, 26(6), 2603; https://doi.org/10.3390/ijms26062603 - 13 Mar 2025

Viewed by 473

Abstract

Waterlogging stress significantly impacts the growth and productivity of crops. As a traditional oil crop, sesame (Sesamum indicum L.) suffers substantial damage due to waterlogging stress. However, the mechanism underlying waterlogging stress in sesame is still unclear. In this study, we investigated [...] Read more.

Waterlogging stress significantly impacts the growth and productivity of crops. As a traditional oil crop, sesame (Sesamum indicum L.) suffers substantial damage due to waterlogging stress. However, the mechanism underlying waterlogging stress in sesame is still unclear. In this study, we investigated the physiological indicators of two sesame genotypes under waterlogging stress. The results revealed that the activity of antioxidant enzymes in sesame was affected, with the contents of malondialdehyde (MDA) and hydrogen peroxide (H₂O₂) significantly increased. Additionally, transcriptional analysis identified a total of 15,143 differentially expressed genes (DEGs). Among them, 759 DEGs exhibited consistent differential expression across all time points, representing the core waterlogging-responsive genes. Gene Ontology (GO) enrichment analysis indicated that the DEGs were primarily associated with hypoxia, stimulus response, and oxidoreductase enzyme activities. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that these DEGs were mainly enriched in the metabolic and biosynthesis of secondary metabolites, glycolysis/gluconeogenesis, phenylpropanoid biosynthesis, MAPK signaling pathway-plant, carbon fixation by Calvin cycle, plant hormone signal transduction, and plant-pathogen interaction pathways. Furthermore, transcription factors (TFs) such as AP2/ERF, bHLH, bZIP, and WRKY may play key roles in the transcriptional changes induced by waterlogging stress. Combined with weighted gene co-expression network analysis (WGCNA) analysis and K-means clustering, a total of 5 hub genes and 56 genes were identified, including F-box protein (Sin09950 and Sin12912), bZIP (Sin04465, Sin00091), WRKY (Sin01376, Sin06113), and so on. In brief, this study explored the regulatory network involved in waterlogging stress in sesame at the transcriptome level, providing valuable insights into unraveling the molecular mechanisms of waterlogging stress and facilitating the breeding of improved waterlogging-tolerant sesame varieties. Full article

(This article belongs to the Special Issue Transcriptional Regulation in Plant Development: 2nd Edition)

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16 pages, 2890 KiB

Open AccessArticle

Metabolome and Transcriptome Analyses Reveal the Correlation Between Fructan Changes and Phytohormone Regulation During Tuber Sprouting of Helianthus tuberosus L.

by Ya Wen, Zhenjie Zhou, Xiaozhu Guo, Juan Li, Gui Wang and Xuemei Sun

Int. J. Mol. Sci. 2025, 26(5), 1864; https://doi.org/10.3390/ijms26051864 - 21 Feb 2025

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Abstract

Jerusalem artichoke (Helianthus tuberosus L.) reproduces asexually through tubers, which are rich in fructan-type carbohydrates and serve as the primary processing organ. Plant hormones may regulate the sprouting process of tubers, but the changes in fructans and their regulatory mechanisms in relation [...] Read more.

Jerusalem artichoke (Helianthus tuberosus L.) reproduces asexually through tubers, which are rich in fructan-type carbohydrates and serve as the primary processing organ. Plant hormones may regulate the sprouting process of tubers, but the changes in fructans and their regulatory mechanisms in relation to hormones remain unclear. This study utilized two varieties of Jerusalem artichoke, “Qingyu No.1” and “Qingyu No.3”, to analyze the changes in the proportion of carbohydrates (especially fructans) in total sugars during the sprouting process. Metabolomic and transcriptomic analyses were conducted at three selected sprouting stages. The results indicated that during tuber sprouting, carbohydrates such as fructans play a regulatory role through conversion activities. Multi-omics analysis revealed that jasmonic acid and salicylic acid promote Jerusalem artichoke sprouting through metabolism and are involved in the plant hormone signal transduction process. Differentially expressed genes related to hormone signaling were screened and divided into three groups based on expression levels. It was found that the proportion of carbohydrates is highly correlated with the expression of hormone-related genes in the sprouts, suggesting that plant hormones may regulate carbohydrate metabolism during the sprouting of Jerusalem artichoke tubers. In conclusion, these results preliminarily elucidate the regulatory mechanisms of plant hormones in Jerusalem artichoke tuber sprouting, aiming to provide a theoretical basis for the production and processing of Jerusalem artichoke. Full article

(This article belongs to the Special Issue Transcriptional Regulation in Plant Development: 2nd Edition)

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18 pages, 6015 KiB

Open AccessArticle

Overexpression of TCP5 or Its Dominant Repressor Form, TCP5-SRDX, Causes Male Infertility in Arabidopsis

by Tingting Li, Ping Tian, Xinxin Wang, Mengyao Li and Shuping Xing

Int. J. Mol. Sci. 2025, 26(5), 1813; https://doi.org/10.3390/ijms26051813 - 20 Feb 2025

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Abstract

TCP transcription factors have long been known to play a crucial role in leaf development, but their significance in reproduction has recently been revealed. TCP5 is a member of class II of the TCP family, which predominantly regulates cell differentiation. This study used [...] Read more.

TCP transcription factors have long been known to play a crucial role in leaf development, but their significance in reproduction has recently been revealed. TCP5 is a member of class II of the TCP family, which predominantly regulates cell differentiation. This study used overexpression and SRDX fusion to evaluate the role of TCP5 in anther development. TCP5 overexpression resulted in lower fertility, primarily due to anther non-dehiscence. We also observed reduced lignin accumulation in the anther endothecium. In addition, TCP5 overexpression resulted in smaller anthers with fewer pollen sacs and pollen due to early-anther defects before meiosis. TCP5 showed expression in early anthers, including the epidermis, endothecium, middle layer, tapetum, sporogenous cells (pollen mother cells), and vascular bundles. Conversely, during meiosis, the TCP5 signal was only detected in the tapetum, PMCs, and vascular bundles. The TCP5 signal disappeared after meiosis, and no signal was observed in mature anthers. Interestingly, the TCP5-SRDX transgenic plants were also sterile, at least for the early-arising flowers, if not all of them. TCP5-SRDX expression also resulted in undersized anthers with fewer pollen sacs and pollen. However, the lignin accumulation in most of these anthers was comparable to that of the wild type, allowing these anthers to open. The qRT-PCR results revealed that several genes associated with secondary cell wall thickening had altered expression profiles in TCP5 overexpression transgenics, which supported the non-dehiscent anther phenotype. Furthermore, the expression levels of numerous critical anther genes were down-regulated in both TCP5 overexpression and TCP5-SRDX plants, indicating a comparable anther phenotype in these transgenic plants. These findings not only suggest that an appropriate TCP5 expression level is essential for anther development and plant fertility, but also improve our understanding of TCP transcription factor functioning in plant male reproduction and contribute information that may allow us to manipulate fertility and breeding in crops. Full article

(This article belongs to the Special Issue Transcriptional Regulation in Plant Development: 2nd Edition)

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16 pages, 5378 KiB

Open AccessArticle

Comprehensive Analysis of CaFAD Genes Involved in Fatty Acid Accumulation in Coffea arabica and Functional Characterization of CaFAD8 in Transgenic Arabidopsis thaliana

by Zhenwei Zhang, Xuejun Li, Meijun Qi, Sumera Anwar, Butian Wang and Yu Ge

Int. J. Mol. Sci. 2025, 26(3), 1023; https://doi.org/10.3390/ijms26031023 - 25 Jan 2025

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Abstract

The quality of Coffee arabica L. beans, particularly the aroma, is a key determinant of commercial value. Fatty acids, as precursors of volatile aroma compounds, play a crucial role in this quality. Screening and identification of their related genes are of particular significance. [...] Read more.

The quality of Coffee arabica L. beans, particularly the aroma, is a key determinant of commercial value. Fatty acids, as precursors of volatile aroma compounds, play a crucial role in this quality. Screening and identification of their related genes are of particular significance. This study identified 21 members of the CaFAD gene family in the C. arabica genome using bioinformatics tools. Gene duplication events observed in the CaFAD gene family were likely driven by natural selection and mutation pressure, with natural selection being more prominent. Transcriptome sequencing, qRT-PCR, and fatty acid profiling across four fruit developmental stages revealed that CaFAD8 was closely associated with fatty acid synthesis regulation. Fatty acid content was initially high but decreased during the later stages, while CaFAD8 expression showed an inverse pattern. Subcellular localization indicated that CaFAD8 functions primarily on the inner membrane. CaFAD8-OE heterologous expression experiment in Arabidopsis thaliana reduced the total fatty acid content in seeds but increased unsaturated fatty acids, including oleic, linoleic, and linolenic acids. These findings suggest that CaFAD8 promotes fatty acid unsaturation and provides insights into fatty acid metabolism in C. arabica. This study offers a foundation for understanding CaFAD gene regulation and supports breeding strategies for high-oil C. arabica varieties. Full article

(This article belongs to the Special Issue Transcriptional Regulation in Plant Development: 2nd Edition)

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18 pages, 2200 KiB

Open AccessArticle

Comparative Transcriptomic Analysis Reveals New Insights into Spawn Aging in Agaricus bisporus: Mitochondrial Dysfunction

by Lili Shu, Zhiheng Zeng, Meiyuan Chen, Jiazhi Zhao, Xiaoyan Zhang, Jianqing Dai, Zhixin Cai, Yuanping Lu, Zhiheng Qiu and Hui Zeng

Int. J. Mol. Sci. 2025, 26(2), 849; https://doi.org/10.3390/ijms26020849 - 20 Jan 2025

Viewed by 765

Abstract

Spawn aging poses a substantial challenge to the Agaricus bisporus industry. This study focuses on the role of mitochondrial dysfunction in the aging process of A. bisporus spawn. We conducted a comprehensive comparative transcriptome analysis to elucidate the molecular mechanisms underlying A. bisporus [...] Read more.

Spawn aging poses a substantial challenge to the Agaricus bisporus industry. This study focuses on the role of mitochondrial dysfunction in the aging process of A. bisporus spawn. We conducted a comprehensive comparative transcriptome analysis to elucidate the molecular mechanisms underlying A. bisporus spawn aging. A total of 1620 genes with significant expression changes between the normal and aged spawn were identified, including 917 up-regulated genes and 703 down-regulated genes. Our results revealed a notable down-regulation of genes involved in carbohydrate metabolism, mitochondrial energy metabolism, reactive oxygen species (ROS) scavenging, repair mechanisms for oxidative stress-induced damage, fatty acid β-oxidation, and amino acid degradation in aged A. bisporus spawn. Additionally, we observed a decreased expression of genes involved in critical signal transduction pathways associated with mitochondrial function in aged mycelium as well as genes responsible for maintaining mitochondrial stability. The up-regulated genes in aged spawn mainly affect mitochondrial fission and programmed cell death, impacting mitochondrial function. Overall, the present study first provides evidence for the pivotal role of mitochondrial dysfunction in the aging process of A. bisporus spawn and contributes to the development of targeted strategies to enhance mitochondrial function, mitigate spawn aging, and improve the yield and quality of A. bisporus cultivation. Full article

(This article belongs to the Special Issue Transcriptional Regulation in Plant Development: 2nd Edition)

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13 pages, 8604 KiB

Open AccessArticle

Identification and Candidate Gene Analysis of Brcl1, a Novel Gene Confers a Leaf Curled Phenotype in Brassica rapa L.

by Lihui Wang, Huishan Liu, Yunxia Sun, Wei Wang, Chao Li, Yuanwei Liu, Zhiyong Liu, Ruiqin Ji, Shengnan Huang, Gaoyang Qu and Yugang Wang

Int. J. Mol. Sci. 2025, 26(2), 732; https://doi.org/10.3390/ijms26020732 - 16 Jan 2025

Viewed by 623

Abstract

Leaf shape is an important determinant of photosynthesis, yield and quality in plants. In this study, we obtained a curled leaf mutant, cl1, from an ethyl methanesulfonate (EMS)-induced mutagenesis population. It was designated the Brcl1^YS locus. Bulk segregant RNA sequencing combined [...] Read more.

Leaf shape is an important determinant of photosynthesis, yield and quality in plants. In this study, we obtained a curled leaf mutant, cl1, from an ethyl methanesulfonate (EMS)-induced mutagenesis population. It was designated the Brcl1^YS locus. Bulk segregant RNA sequencing combined with recombinant screening identified the candidate interval responsible for Brcl1^YS in a 97.5 kb region on chromosome A02. Twelve genes were identified within the candidate region. Sequence differences and co-separation verification confirmed that BraA02g017030.3C was the most promising candidate gene underlying the Brcl1^YS locus. It is homologous to Arabidopsis AT1G66350 (RGL1), which has been shown to act as a negative regulator of the gibberellin pathway. Combined with cell morphology observation, it is speculated that the loss of function of Brcl1^YS results in differences in cell development, ultimately leading to changes in leaf morphology. The results will contribute to the understanding of the molecular mechanisms underlying leaf curling in B. rapa. Full article

(This article belongs to the Special Issue Transcriptional Regulation in Plant Development: 2nd Edition)

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18 pages, 10098 KiB

Open AccessArticle

Integrated Genetic Diversity and Multi-Omics Analysis of Colour Formation in Safflower

by Yonghua Qin, Kangjun Fan, Aidiya Yimamu, Peng Zhan, Lu Lv, Gang Li, Jiao Liu, Zunhong Hu, Xingchu Yan, Xueli Hu, Hong Liu and Rui Qin

Int. J. Mol. Sci. 2025, 26(2), 647; https://doi.org/10.3390/ijms26020647 - 14 Jan 2025

Cited by 1 | Viewed by 774

Abstract

Safflower (Carthamus tinctorius L.) is a medicinal and edible cash crop that is widely cultivated worldwide. However, the genetic diversity of safflower germplasm resources and the reasons for the variations in safflower flower colour remain unclear. In this study, we used a [...] Read more.

Safflower (Carthamus tinctorius L.) is a medicinal and edible cash crop that is widely cultivated worldwide. However, the genetic diversity of safflower germplasm resources and the reasons for the variations in safflower flower colour remain unclear. In this study, we used a combination of agronomic traits and Indel markers to assess the genetic diversity of 614 safflower germplasm resources. The results showed that most of the evaluated agronomic traits had high variability. The mean values of the Shannon’s information index (I) and polymorphism information content (PIC) in 50 pairs of Indel markers were 0.551 and 0.296, respectively. The population structure, neighbour-joining phylogeny, and principal coordinate analyses classified all genotypes into four subgroups, and 214 safflower core germplasms were constructed. Multiple analyses of genetic diversity parameters, range conformity, and the percentage of variance difference showed that the core germplasm did not differ significantly and could represent the original germplasm better. Transcriptome and metabolome analyses revealed that flavonoid synthesis-related genes, including CHS, F3H, ANS, and BZ1, were differentially expressed in different coloured safflowers. Most significantly, different genes and metabolite compounds in white safflowers were enriched upstream from the phenylpropanoid metabolic pathway to the production of naringenin, whereas those in red safflowers were concentrated in the downstream pathway from eriodictyol. Meanwhile, the preliminary quantification of anthocyanins and carotenoids extracted from red, orange, and white types of safflower showed that the level of both anthocyanins and carotenoids were highest in red types. This work provides new insights into the formation of different safflower flower colours and in the conservation and management of safflower germplasm. Full article

(This article belongs to the Special Issue Transcriptional Regulation in Plant Development: 2nd Edition)

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26 pages, 7287 KiB

Open AccessArticle

Mitochondrial Genome Insights into Evolution and Gene Regulation in Phragmites australis

by Jipeng Cui, Qianhui Yang, Jiyue Zhang, Chuanli Ju and Suxia Cui

Int. J. Mol. Sci. 2025, 26(2), 546; https://doi.org/10.3390/ijms26020546 - 10 Jan 2025

Viewed by 980

Abstract

As a globally distributed perennial Gramineae, Phragmites australis can adapt to harsh ecological environments and has significant economic and environmental values. Here, we performed a complete assembly and annotation of the mitogenome of P. australis using genomic data from the PacBio and BGI [...] Read more.

As a globally distributed perennial Gramineae, Phragmites australis can adapt to harsh ecological environments and has significant economic and environmental values. Here, we performed a complete assembly and annotation of the mitogenome of P. australis using genomic data from the PacBio and BGI platforms. The P. australis mitogenome is a multibranched structure of 501,134 bp, divided into two circular chromosomes of 325,493 bp and 175,641 bp, respectively. A sequence-simplified succinate dehydrogenase 4 gene was identified in this mitogenome, which is often translocated to the nuclear genome in the mitogenomes of gramineous species. We also identified tissue-specific mitochondrial differentially expressed genes using RNAseq data, providing new insights into understanding energy allocation and gene regulatory strategies in the long-term adaptive evolution of P. australis mitochondria. In addition, we studied the mitogenome features of P. australis in more detail, including repetitive sequences, gene Ka/Ks analyses, codon preferences, intracellular gene transfer, RNA editing, and multispecies phylogenetic analyses. Our results provide an essential molecular resource for understanding the genetic characterisation of the mitogenome of P. australis and provide a research basis for population genetics and species evolution in Arundiaceae. Full article

(This article belongs to the Special Issue Transcriptional Regulation in Plant Development: 2nd Edition)

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17 pages, 5618 KiB

Open AccessArticle

Comprehensive Identification of AREB Gene Family in Populus euphratica Oliv. and Functional Analysis of PeAREB04 in Drought Tolerance

by Binglei Liu, Jianhao Sun, Chen Qiu, Xiaoli Han and Zhijun Li

Int. J. Mol. Sci. 2025, 26(2), 518; https://doi.org/10.3390/ijms26020518 - 9 Jan 2025

Viewed by 621

Abstract

The transcription factors in the ABA Response Element Binding (AREB) protein family were differentially regulated under multiple stress conditions; however, functional analyses of AREB in Populus euphratica Oliv. had not been conducted previously. In the present study, the comprehensive identification of the P. [...] Read more.

The transcription factors in the ABA Response Element Binding (AREB) protein family were differentially regulated under multiple stress conditions; however, functional analyses of AREB in Populus euphratica Oliv. had not been conducted previously. In the present study, the comprehensive identification of the P. euphratica AREB gene family and the function of PeAREB04 in response to drought stress in P. euphratica were elucidated. A comprehensive analysis of the PeAREB family was first performed, followed by the determination of their expression patterns under drought stress. Bioinformatics analysis revealed that thirteen AREB genes were identified across the P. euphratica genome, with these genes distributed across eight chromosomes in a seemingly random pattern. Phylogenetic analysis indicated that the PeAREB genes could be categorized into four distinct branches. Cis-acting element analysis revealed that most PeAREB genes contained multiple hormone- and stress-responsive elements. Transcriptomic sequencing of P. euphratica seedlings under drought stress showed that most PeAREB genes responded rapidly to drought stress in either the leaves or roots. One gene, PeAREB04, was selected for further functional validation due to its significant upregulation in both leaves and roots under drought stress. Overexpression of PeAREB04 in Arabidopsis thaliana resulted in a high survival rate, reduced water loss in isolated leaves, and a significant reduction in stomatal aperture under natural drought conditions. Drought stress simulations using mannitol further demonstrated that overexpression of PeAREB04 significantly enhanced root elongation. These findings indicate that the identification of the PeAREB gene family and the characterization of PeAREB04’s role in drought stress have been largely accomplished. Furthermore, the PeAREB04 gene demonstrates considerable potential as a key target for future genetic engineering strategies aimed at enhancing plant drought resistance. Full article

(This article belongs to the Special Issue Transcriptional Regulation in Plant Development: 2nd Edition)

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16 pages, 9890 KiB

Open AccessArticle

Genome-Wide Identification and Expression Analysis of HSP70 Gene Family Under High-Temperature Stress in Lettuce (Lactuca sativa L.)

by Qian Wang, Wenjing Sun, Yipei Duan, Yikun Xu, Huiyu Wang, Jinghong Hao, Yingyan Han and Chaojie Liu

Int. J. Mol. Sci. 2025, 26(1), 102; https://doi.org/10.3390/ijms26010102 - 26 Dec 2024

Cited by 1 | Viewed by 855

Abstract

The heat shock protein 70 (HSP70) family plays an important role in the growth and development of lettuce and in the defense response to high-temperature stress; however, its bioinformatics analysis in lettuce has been extremely limited. Genome-wide bioinformatics analysis methods such as chromosome [...] Read more.

The heat shock protein 70 (HSP70) family plays an important role in the growth and development of lettuce and in the defense response to high-temperature stress; however, its bioinformatics analysis in lettuce has been extremely limited. Genome-wide bioinformatics analysis methods such as chromosome location, phylogenetic relationships, gene structure, collinearity analysis, and promoter analysis were performed in the LsHSP70 gene family, and the expression patterns in response to high-temperature stress were analyzed. The mechanism of LsHSP70-19 in heat resistance in lettuce was studied by virus-induced gene silencing (VIGS) and transient overexpression techniques. The results showed that a total of 37 LsHSP70 genes were identified by the Hidden Markov Model (HMM) and Protein Family Database (Pfam). These 37 LsHSP70 genes were classified into groups A, B, C, and D by phylogenetic relationships. They were mainly localized on seven chromosomes except for chromosome 3; gene structure analysis showed that LsHSP70 contained 1–9 exons, and the protein structure domains of genes in the same group were highly conserved. The covariance analysis showed that nine pairs of LsHSP70 genes existed between LsHSP70 members, and lettuce LsHSP70 and sunflower HaHSP70 had been more conserved in the evolutionary process. The promoter analysis showed that there were a large number of cis-acting elements related to phytohormones, growth, development, stress, and light response in LsHSP70. In addition, the results of the expression pattern analysis for all LsHSP70 genes under high-temperature stress showed that 28 out of 37 LsHSP70 genes were able to respond to heat stress, and only LsHSP70-8, LsHSP70-14, LsHSP70-19, LsHSP70-23, and LsHSP70-24 were able to respond rapidly to heat stress (2 h). The expression of LsHSP70-19 was higher at different periods under high-temperature stress; the overexpression of LsHSP70-19, the plant fresh weight, and the root weight were better than the control (CK); and the heat resistance was better. These results suggest that LsHSP70-19 may play an important role under high-temperature stress in lettuce. Full article

(This article belongs to the Special Issue Transcriptional Regulation in Plant Development: 2nd Edition)

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24 pages, 14115 KiB

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Regulatory Mechanism of Exogenous ABA on Gibberellin Signaling and Antioxidant Responses in Rhododendron chrysanthum Pall. Under UV-B Stress

by Wang Yu, Kun Cao, Hongwei Xu and Xiaofu Zhou

Int. J. Mol. Sci. 2024, 25(24), 13651; https://doi.org/10.3390/ijms252413651 - 20 Dec 2024

Viewed by 655

Abstract

In the present work, we examined the effects of exogenous abscisic acid (ABA) under ultraviolet B (UV-B) exposure on gibberellin (GA) production, signaling, and antioxidant-related genes in Rhododendron chrysanthum Pall (R. chrysanthum). Using transcriptomics, acetylated proteomics, and widely targeted metabolomics, the [...] Read more.

In the present work, we examined the effects of exogenous abscisic acid (ABA) under ultraviolet B (UV-B) exposure on gibberellin (GA) production, signaling, and antioxidant-related genes in Rhododendron chrysanthum Pall (R. chrysanthum). Using transcriptomics, acetylated proteomics, and widely targeted metabolomics, the effects of UV-B stress on R. chrysanthum and the regulatory effects of exogenous ABA on it were revealed from multiple perspectives. The findings revealed that R. chrysanthum’s antioxidant enzyme genes were differentially expressed by UV-B radiation and were substantially enriched in the glutathione metabolic pathway. Exogenous ABA supplementation boosted plant resistance to UV-B damage and further enhanced the expression of antioxidant enzyme genes. Furthermore, under UV-B stress, glutathione reductase, glutathione peroxidase, and L-ascorbate peroxidase were found to be the primary antioxidant enzymes controlled by exogenous ABA. In addition, gibberellin content was altered due to UV-B and exogenous ABA treatments, with greater effects on GA3 and GA53. The acetylation proteomics study’s outcomes disclosed that the three main oxidative enzymes’ acetylation modifications were dramatically changed during UV-B exposure, which may have an impact on the antioxidant enzymes’ functions and activities. The protective impact of exogenous ABA and gibberellin on R. chrysanthum’s photosynthetic system was further established by measuring the parameters of chlorophyll fluorescence. This research offers a theoretical foundation for the development of breeding highly resistant plant varieties as well as fresh insights into how hormone levels and antioxidant systems are regulated by plants in response to UV-B damage. Full article

(This article belongs to the Special Issue Transcriptional Regulation in Plant Development: 2nd Edition)

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15 pages, 8738 KiB

Open AccessArticle

Unraveling the Molecular Mechanisms by Which the miR171b-SCL6 Module Regulates Maturation in Lilium

by Qing Li, Meiqi Song, Yachen Wang, Ping Lu, Wei Ge and Kezhong Zhang

Int. J. Mol. Sci. 2024, 25(17), 9156; https://doi.org/10.3390/ijms25179156 - 23 Aug 2024

Cited by 1 | Viewed by 983

Abstract

Lilium is one of the most widely cultivated ornamental bulbous plants in the world. Although research has shown that variable temperature treatments can accelerate the development process from vegetative to reproductive growth in Lilium, the molecular regulation mechanisms of this development are [...] Read more.

Lilium is one of the most widely cultivated ornamental bulbous plants in the world. Although research has shown that variable temperature treatments can accelerate the development process from vegetative to reproductive growth in Lilium, the molecular regulation mechanisms of this development are not clear. In this study, Lbr-miR171b and its target gene, LbrSCL6, were selected and validated using transgenic functional verification, subcellular localization, and transcriptional activation. This study also investigated the differential expression of Lbr-miR171b and LbrSCL6 in two temperature treatment groups (25 °C and 15 °C). Lbr-miR171b expression significantly increased after the temperature change, whereas that of LbrSCL6 exhibited the opposite trend. Through in situ hybridization experiments facilitated by the design of hybridization probes targeting LbrSCL6, a reduction in LbrSCL6 expression was detected following variable temperature treatment at 15 °C. The transgenic overexpression of Lbr-miR171b in plants promoted the phase transition, while LbrSCL6 overexpression induced a delay in the phase transition. In addition, LbrWOX4 interacted with LbrSCL6 in yeast two-hybrid and bimolecular fluorescence complementation assays. In conclusion, these results explain the molecular regulatory mechanisms governing the phase transition in Lilium. Full article

(This article belongs to the Special Issue Transcriptional Regulation in Plant Development: 2nd Edition)

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16 pages, 3346 KiB

Open AccessArticle

Gibberellin Signaling through RGA Suppresses GCN5 Effects on Arabidopsis Developmental Stages

by Christina Balouri, Stylianos Poulios, Dimitra Tsompani, Zoe Spyropoulou, Maria-Christina Ketikoglou, Athanasios Kaldis, John H. Doonan and Konstantinos E. Vlachonasios

Int. J. Mol. Sci. 2024, 25(12), 6757; https://doi.org/10.3390/ijms25126757 - 19 Jun 2024

Cited by 1 | Viewed by 2115

Abstract

Histone acetyltransferases (HATs) modify the amino-terminal tails of the core histone proteins via acetylation, regulating chromatin structure and transcription. GENERAL CONTROL NON-DEREPRESSIBLE 5 (GCN5) is a HAT that specifically acetylates H3K14 residues. GCN5 has been associated with cell division and differentiation, meristem function, [...] Read more.

Histone acetyltransferases (HATs) modify the amino-terminal tails of the core histone proteins via acetylation, regulating chromatin structure and transcription. GENERAL CONTROL NON-DEREPRESSIBLE 5 (GCN5) is a HAT that specifically acetylates H3K14 residues. GCN5 has been associated with cell division and differentiation, meristem function, root, stem, foliar, and floral development, and plant environmental response. The flowers of gcn5 plants display a reduced stamen length and exhibit male sterility relative to the wild-type plants. We show that these effects may arise from gibberellin (GA)-signaling defects. The signaling pathway of bioactive GAs depends on the proteolysis of their repressors, DELLA proteins. The repressor GA (RGA) DELLA protein represses plant growth, inflorescence, and flower and seed development. Our molecular data indicate that GCN5 is required for the activation and H3K14 acetylation of genes involved in the late stages of GA biosynthesis and catabolism. We studied the genetic interaction of the RGA and GCN5; the RGA can partially suppress GCN5 action during the whole plant life cycle. The reduced elongation of the stamen filament of gcn5–6 mutants is reversed in the rga–t2;gcn5–6 double mutants. RGAs suppress the GCN5 effect on the gene expression and histone acetylation of GA catabolism and GA signaling. Interestingly, the RGA and RGL2 do not suppress ADA2b function, suggesting that ADA2b acts downstream of GA signaling and is distinct from GCN5 activity. In conclusion, we propose that the action of GCN5 on stamen elongation is partially mediated by RGA and GA signaling. Full article

(This article belongs to the Special Issue Transcriptional Regulation in Plant Development: 2nd Edition)

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