International Journal of Molecular Sciences

2024

Jump to: 2023, 2022, 2021, 2020, 2019

20 pages, 8723 KiB

Open AccessArticle

Protein Structural Modeling and Transport Thermodynamics Reveal That Plant Cation–Chloride Cotransporters Mediate Potassium–Chloride Symport

by Sam W. Henderson, Saeed Nourmohammadi and Maria Hrmova

Int. J. Mol. Sci. 2024, 25(23), 12955; https://doi.org/10.3390/ijms252312955 - 2 Dec 2024

Viewed by 428

Abstract

Plant cation–chloride cotransporters (CCCs) are proposed to be Na⁺-K⁺-2Cl⁻ transporting membrane proteins, although evolutionarily, they associate more closely with K⁺-Cl⁻ cotransporters (KCCs). Here, we investigated grapevine (Vitis vinifera L.) VvCCC using 3D protein modeling, [...] Read more.

Plant cation–chloride cotransporters (CCCs) are proposed to be Na⁺-K⁺-2Cl⁻ transporting membrane proteins, although evolutionarily, they associate more closely with K⁺-Cl⁻ cotransporters (KCCs). Here, we investigated grapevine (Vitis vinifera L.) VvCCC using 3D protein modeling, bioinformatics, and electrophysiology with a heterologously expressed protein. The 3D protein modeling revealed that the signatures of ion binding sites in plant CCCs resembled those of animal KCCs, which was supported by phylogenomic analyses and ancestral sequence reconstruction. The conserved features of plant CCCs and animal KCCs included predicted K⁺ and Cl⁻-binding sites and the absence of a Na⁺-binding site. Measurements with VvCCC-injected Xenopus laevis oocytes with VvCCC localizing to plasma membranes indicated that the oocytes had depleted intracellular Cl⁻ and net ⁸⁶Rb fluxes, which agreed with thermodynamic predictions for KCC cotransport. The ⁸⁶Rb uptake by VvCCC-injected oocytes was Cl⁻-dependent, did not require external Na⁺, and was partially inhibited by the non-specific CCC-blocker bumetanide, implying that these properties are typical of KCC transporters. A loop diuretic-insensitive Na⁺ conductance in VvCCC-injected oocytes may account for earlier observations of Na⁺ uptake by plant CCC proteins expressed in oocytes. Our data suggest plant CCC membrane proteins are likely to function as K⁺-Cl⁻ cotransporters, which opens the avenues to define their biophysical properties and roles in plant physiology. Full article

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16 pages, 1366 KiB

Open AccessArticle

Influence of ZnSO₄ and Methyl Jasmonate on the Metabolites and Bioactivity Present in Lemon-Fruit Membrane Vesicles

by Maria Gomez-Molina, Micaela Carvajal and Paula Garcia-Ibañez

Int. J. Mol. Sci. 2024, 25(23), 12917; https://doi.org/10.3390/ijms252312917 - 30 Nov 2024

Viewed by 564

Abstract

Membrane vesicles isolated from vegetable tissues have shown promise in encapsulation technologies used in industries like food and cosmetics, offering innovative approaches to product development. However, their associated linked metabolites have not been studied. Lemon vesicle research not only adds value to the [...] Read more.

Membrane vesicles isolated from vegetable tissues have shown promise in encapsulation technologies used in industries like food and cosmetics, offering innovative approaches to product development. However, their associated linked metabolites have not been studied. Lemon vesicle research not only adds value to the lemon crop (Citrus × limon L.), one of the most widely cultivated fruit trees in the world, is a source of bioactive compounds such as phenolics and organic acids. In this study, the influence of elicitation with ZnSO₄ and methyl jasmonate, which modulate the bioactive metabolites, on fruit membrane vesicle bond metabolites was studied. The study showed that foliar application of ZnSO₄ increased phenolic compounds as caffeic, sinapic, and chlorogenic acids and the flavonoid hesperidin by about 20% in lemons. Furthermore, a clear interaction between vesicles and citrate and ascorbate that were increased by methyl jasmonate were associated with their higher bioactivity. This was related to the double intrinsic in vitro antioxidant activities of these vesicles. Full article

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24 pages, 8631 KiB

Open AccessArticle

Genetic Diversity and Genome-Wide Association Study of Total Phenolics, Flavonoids, and Antioxidant Properties in Potatoes (Solanum tuberosum L.)

by Haroon Rasheed, Bowen Deng, Daraz Ahmad and Jinsong Bao

Int. J. Mol. Sci. 2024, 25(23), 12795; https://doi.org/10.3390/ijms252312795 - 28 Nov 2024

Viewed by 293

Abstract

Genetic diversity of nutritional quality traits is crucial for potato breeding efforts to develop better varieties for the diverse market demands. In this study, the genetic diversity of 104 potato genotypes was estimated based on nutritional quality traits such as color parameters, total [...] Read more.

Genetic diversity of nutritional quality traits is crucial for potato breeding efforts to develop better varieties for the diverse market demands. In this study, the genetic diversity of 104 potato genotypes was estimated based on nutritional quality traits such as color parameters, total phenolic content, total flavonoid content, 2,2-Diphenyl-1-picrylhydrazyl (DPPH), and 2,2-azino-bis-(3-ethylbezothiazoline-6-sulphonic acid) radical scavenging potential across two environments. The results indicated that environment II, Hangzhou 2020, exhibited higher bioactive compounds and antioxidant properties than environment I, Hangzhou 2019. The colored potato accessions exhibited higher levels of total phenolic content, total flavonoid content, DPPH, and ABTS activities than the white potato accessions, indicating the superiority of the colored to white potato accessions. The genome sequencing identified 1,101,368 high-quality single-nucleotide polymorphisms (SNPs), and 141,656 insertion/deletions (Indels). A population structure analysis revealed that genotypes can be divided into two subpopulations. Genome-wide association studies (GWAS) identified 128 significant SNPs associated with potato’s color, total phenolic content, total flavonoid content, and antioxidant properties. Thus, the study provides new opportunities for strategic breeding and marker-assisted selection of ideal varieties and favorable alleles to enhance bioactive compounds and health-beneficial properties. Full article

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17 pages, 7986 KiB

Open AccessArticle

Metabolome and Transcriptome Analyses Reveal Metabolomic Variations and Key Transcription Factors Involved in Lipid Biosynthesis During Seed Development in Carya illinoinensis

by Kaikai Zhu, Lu Wei, Hammad Hussain, Pengpeng Tan, Guo Wei, Juan Zhao, Sichen Zhou, Hui Liu and Fangren Peng

Int. J. Mol. Sci. 2024, 25(21), 11571; https://doi.org/10.3390/ijms252111571 - 28 Oct 2024

Viewed by 607

Abstract

Plant oils are a large group of neutral lipids that play a vital role in the food and oleochemical industries. The pecan (Carya illinoinensis) is a promising woody oil crop known for its high-quality sources of essential fatty acids and various [...] Read more.

Plant oils are a large group of neutral lipids that play a vital role in the food and oleochemical industries. The pecan (Carya illinoinensis) is a promising woody oil crop known for its high-quality sources of essential fatty acids and various bioactive compounds that may aid in preventing heart diseases. However, there is still a lack of understanding regarding the accumulation of lipids and the molecular mechanism of lipid biosynthesis during seed development. This study aims to analyze the metabolite variations and molecular mechanisms of lipid biosynthesis by integrating untargeted metabolomics and transcriptomics during pecan seed development. A total of 293 differentially accumulated metabolites were identified and further categorized into 13 groups, with lipids and lipid-like molecules constituting the largest group. The oil content and fatty acid compositions of pecan embryos were assessed at three stages of seed development. Oleic acid (c18:1) and linoleic acid (c18:2n6) were found to be the most abundant unsaturated fatty acid components in pecan embryos. Additionally, a comprehensive analysis revealed 15,990 differentially expressed genes, with a focus on the key genes related to lipid metabolism. Furthermore, the study identified 1201 transcription factors from differentially expressed genes. These transcription factors were divided into 65 families, with different members in the same family exhibiting different expression patterns during seed development. The expression patterns of ten transcription factor genes during seed development were verified by qRT–PCR. Two key genes, CiABI3 and CiFUS3 were further cloned and found to be localized in the nucleus. This study used metabolome and transcriptome analysis during key periods of pecan seed development to identify the key genes associated with seed development and fatty acid biosynthesis. Full article

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15 pages, 1073 KiB

Open AccessReview

Establishment and Maintenance of Heat-Stress Memory in Plants

by Shuzhi Zheng, Weishuang Zhao, Zimeng Liu, Ziyue Geng, Qiang Li, Binhui Liu, Bing Li and Jiaoteng Bai

Int. J. Mol. Sci. 2024, 25(16), 8976; https://doi.org/10.3390/ijms25168976 - 18 Aug 2024

Viewed by 1355

Abstract

Among the rich repertoire of strategies that allow plants to adapt to high-temperature stress is heat-stress memory. The mechanisms underlying the establishment and maintenance of heat-stress memory are poorly understood, although the chromatin opening state appears to be an important structural basis for [...] Read more.

Among the rich repertoire of strategies that allow plants to adapt to high-temperature stress is heat-stress memory. The mechanisms underlying the establishment and maintenance of heat-stress memory are poorly understood, although the chromatin opening state appears to be an important structural basis for maintaining heat-stress memory. The chromatin opening state is influenced by epigenetic modifications, making DNA and histone modifications important entry points for understanding heat-shock memory. Current research suggests that traditional heat-stress signaling pathway components might be involved in chromatin opening, thereby promoting the establishment of heat-stress memory in plants. In this review, we discuss the relationship between chromatin structure-based maintenance and the establishment of heat-stress memory. We also discuss the association between traditional heat-stress signals and epigenetic modifications. Finally, we discuss potential research ideas for exploring plant adaptation to high-temperature stress in the future. Full article

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18 pages, 3731 KiB

Open AccessArticle

Metabolomic and Proteomic Analyses to Reveal the Role of Plant-Derived Smoke Solution on Wheat under Salt Stress

by Setsuko Komatsu, Azzahrah Diniyah, Wei Zhu, Masataka Nakano, Shafiq Ur Rehman, Hisateru Yamaguchi, Keisuke Hitachi and Kunihiro Tsuchida

Int. J. Mol. Sci. 2024, 25(15), 8216; https://doi.org/10.3390/ijms25158216 - 27 Jul 2024

Viewed by 939

Abstract

Salt stress is a serious problem, because it reduces the plant growth and seed yield of wheat. To investigate the salt-tolerant mechanism of wheat caused by plant-derived smoke (PDS) solution, metabolomic and proteomic techniques were used. PDS solution, which repairs the growth inhibition [...] Read more.

Salt stress is a serious problem, because it reduces the plant growth and seed yield of wheat. To investigate the salt-tolerant mechanism of wheat caused by plant-derived smoke (PDS) solution, metabolomic and proteomic techniques were used. PDS solution, which repairs the growth inhibition of wheat under salt stress, contains metabolites related to flavonoid biosynthesis. Wheat was treated with PDS solution under salt stress and proteins were analyzed using a gel-free/label-free proteomic technique. Oppositely changed proteins were associated with protein metabolism and signal transduction in biological processes, as well as mitochondrion, endoplasmic reticulum/Golgi, and plasma membrane in cellular components with PDS solution under salt stress compared to control. Using immuno-blot analysis, proteomic results confirmed that ascorbate peroxidase increased with salt stress and decreased with additional PDS solution; however, H⁺-ATPase displayed opposite effects. Ubiquitin increased with salt stress and decreased with additional PDS solution; nevertheless, genomic DNA did not change. As part of mitochondrion-related events, the contents of ATP increased with salt stress and recovered with additional PDS solution. These results suggest that PDS solution enhances wheat growth suppressed by salt stress through the regulation of energy metabolism and the ubiquitin-proteasome system related to flavonoid metabolism. Full article

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20 pages, 2723 KiB

Open AccessReview

Small Peptides: Orchestrators of Plant Growth and Developmental Processes

by Shuaiqi Lu and Fei Xiao

Int. J. Mol. Sci. 2024, 25(14), 7627; https://doi.org/10.3390/ijms25147627 - 11 Jul 2024

Viewed by 1467

Abstract

Small peptides (SPs), ranging from 5 to 100 amino acids, play integral roles in plants due to their diverse functions. Despite their low abundance and small molecular weight, SPs intricately regulate critical aspects of plant life, including cell division, growth, differentiation, flowering, fruiting, [...] Read more.

Small peptides (SPs), ranging from 5 to 100 amino acids, play integral roles in plants due to their diverse functions. Despite their low abundance and small molecular weight, SPs intricately regulate critical aspects of plant life, including cell division, growth, differentiation, flowering, fruiting, maturation, and stress responses. As vital mediators of intercellular signaling, SPs have garnered significant attention in plant biology research. This comprehensive review delves into SPs’ structure, classification, and identification, providing a detailed understanding of their significance. Additionally, we summarize recent findings on the biological functions and signaling pathways of prominent SPs that regulate plant growth and development. This review also offers a perspective on future research directions in peptide signaling pathways. Full article

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18 pages, 4285 KiB

Open AccessArticle

Exploring Seaweed and Glycine Betaine Biostimulants for Enhanced Phenolic Content, Antioxidant Properties, and Gene Expression of Vitis vinifera cv. “Touriga Franca” Berries

by Eliana Monteiro, Gabriella De Lorenzis, Valentina Ricciardi, Miguel Baltazar, Sandra Pereira, Sofia Correia, Helena Ferreira, Fernando Alves, Isabel Cortez, Berta Gonçalves and Isaura Castro

Int. J. Mol. Sci. 2024, 25(10), 5335; https://doi.org/10.3390/ijms25105335 - 14 May 2024

Cited by 1 | Viewed by 1124

Abstract

Climate change will pose a challenge for the winemaking sector worldwide, bringing progressively drier and warmer conditions and increasing the frequency and intensity of weather extremes. The short-term adaptation strategy of applying biostimulants through foliar application serves as a crucial measure in mitigating [...] Read more.

Climate change will pose a challenge for the winemaking sector worldwide, bringing progressively drier and warmer conditions and increasing the frequency and intensity of weather extremes. The short-term adaptation strategy of applying biostimulants through foliar application serves as a crucial measure in mitigating the detrimental effects of environmental stresses on grapevine yield and berry quality. The aim of this study was to evaluate the effect of foliar application of a seaweed-based biostimulant (A. nodosum—ANE) and glycine betaine (GB) on berry quality, phenolic compounds, and antioxidant activity and to elucidate their action on the secondary metabolism. A trial was installed in a commercial vineyard (cv. “Touriga Franca”) in the Cima Corgo (Upper Corgo) sub-region of the Douro Demarcated Region, Portugal. A total of four foliar sprayings were performed during the growing season: at flowering, pea size, bunch closer, and veraison. There was a positive effect of GB in the berry quality traits. Both ANE and GB increased the synthesis of anthocyanins and other phenolics in berries and influenced the expression of genes related to the synthesis and transport of anthocyanins (CHS, F3H, UFGT, and GST). So, they have the potential to act as elicitors of the secondary metabolism, leading to improved grape quality, and also to set the foundation for sustainable agricultural practices in the long run. Full article

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25 pages, 6343 KiB

Open AccessArticle

GhMYB52 Like: A Key Factor That Enhances Lint Yield by Negatively Regulating the Lignin Biosynthesis Pathway in Fibers of Upland Cotton (Gossypium hirsutum L.)

by Yang Yang, Xue Zhou, Xi Zhu, Bo Ding, Linzhu Jiang, Huiming Zhang, Silu Li, Shuyan Cao, Mi Zhang, Yan Pei and Lei Hou

Int. J. Mol. Sci. 2024, 25(9), 4921; https://doi.org/10.3390/ijms25094921 - 30 Apr 2024

Cited by 1 | Viewed by 1111

Abstract

In the context of sustainable agriculture and biomaterial development, understanding and enhancing plant secondary cell wall formation are crucial for improving crop fiber quality and biomass conversion efficiency. This is especially critical for economically important crops like upland cotton (Gossypium hirsutum L.), [...] Read more.

In the context of sustainable agriculture and biomaterial development, understanding and enhancing plant secondary cell wall formation are crucial for improving crop fiber quality and biomass conversion efficiency. This is especially critical for economically important crops like upland cotton (Gossypium hirsutum L.), for which fiber quality and its processing properties are essential. Through comprehensive genome-wide screening and analysis of expression patterns, we identified a particularly high expression of an R2R3 MYB transcription factor, GhMYB52 Like, in the development of the secondary cell wall in cotton fiber cells. Utilizing gene-editing technology to generate a loss-of-function mutant to clarify the role of GhMYB52 Like, we revealed that GhMYB52 Like does not directly contribute to cellulose synthesis in cotton fibers but instead represses a subset of lignin biosynthesis genes, establishing it as a lignin biosynthesis inhibitor. Concurrently, a substantial decrease in the lint index, a critical measure of cotton yield, was noted in parallel with an elevation in lignin levels. This study not only deepens our understanding of the molecular mechanisms underlying cotton fiber development but also offers new perspectives for the molecular improvement of other economically important crops and the enhancement of biomass energy utilization. Full article

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23 pages, 7639 KiB

Open AccessArticle

Changes in Phytohormones and Transcriptomic Reprogramming in Strawberry Leaves under Different Light Qualities

by Peng Li, Zhiqiang Wang, Xiaodi Wang, Fengzhi Liu and Haibo Wang

Int. J. Mol. Sci. 2024, 25(5), 2765; https://doi.org/10.3390/ijms25052765 - 27 Feb 2024

Viewed by 1346

Abstract

Strawberry plants require light for growth, but the frequent occurrence of low-light weather in winter can lead to a decrease in the photosynthetic rate (Pn) of strawberry plants. Light-emitting diode (LED) systems could be used to increase Pn. However, the changes in the [...] Read more.

Strawberry plants require light for growth, but the frequent occurrence of low-light weather in winter can lead to a decrease in the photosynthetic rate (Pn) of strawberry plants. Light-emitting diode (LED) systems could be used to increase Pn. However, the changes in the phytohormones and transcriptomic reprogramming in strawberry leaves under different light qualities are still unclear. In this study, we treated strawberry plants with sunlight, sunlight covered with a 50% sunshade net, no light, blue light (460 nm), red light (660 nm), and a 50% red/50% blue LED light combination for 3 days and 7 days. Our results revealed that the light quality has an effect on the contents of Chl a and Chl b, the minimal fluorescence (F₀), and the Pn of strawberry plants. The light quality also affected the contents of abscisic acid (ABA), auxin (IAA), trans-zeatin-riboside (tZ), jasmonic acid (JA), and salicylic acid (SA). RNA sequencing (RNA-seq) revealed that differentially expressed genes (DEGs) are significantly enriched in photosynthesis antenna proteins, photosynthesis, carbon fixation in photosynthetic organisms, porphyrin and chlorophyll metabolisms, carotenoid biosynthesis, tryptophan metabolism, phenylalanine metabolism, zeatin biosynthesis, and linolenic acid metabolism. We then selected the key DEGs based on the results of a weighted gene co-expression network analysis (WGCNA) and drew nine metabolic heatmaps and protein–protein interaction networks to map light regulation. Full article

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19 pages, 6228 KiB

Open AccessArticle

Comparative Analysis of Chloroplast Genome of Meconopsis (Papaveraceae) Provides Insights into Their Genomic Evolution and Adaptation to High Elevation

by Shuqi Zhao, Xiaoman Gao, Xiaolei Yu, Tao Yuan, Guiyu Zhang, Chenlai Liu, Xinzhong Li, Pei Wei, Xiaoyan Li and Xing Liu

Int. J. Mol. Sci. 2024, 25(4), 2193; https://doi.org/10.3390/ijms25042193 - 12 Feb 2024

Cited by 6 | Viewed by 1818

Abstract

The Meconopsis species are widely distributed in the Qinghai-Tibet Plateau, Himalayas, and Hengduan Mountains in China, and have high medicinal and ornamental value. The high diversity of plant morphology in this genus poses significant challenges for species identification, given their propensity for highland [...] Read more.

The Meconopsis species are widely distributed in the Qinghai-Tibet Plateau, Himalayas, and Hengduan Mountains in China, and have high medicinal and ornamental value. The high diversity of plant morphology in this genus poses significant challenges for species identification, given their propensity for highland dwelling, which makes it a question worth exploring how they cope with the harsh surroundings. In this study, we recently generated chloroplast (cp) genomes of two Meconopsis species, Meconopsis paniculata (M. paniculata) and M. pinnatifolia, and compared them with those of ten Meconopsis cp genomes to comprehend cp genomic features, their phylogenetic relationships, and what part they might play in plateau adaptation. These cp genomes shared a great deal of similarities in terms of genome size, structure, gene content, GC content, and codon usage patterns. The cp genomes were between 151,864 bp and 154,997 bp in length, and contain 133 predictive genes. Through sequence divergence analysis, we identified three highly variable regions (trnD-psbD, ccsA-ndhD, and ycf1 genes), which could be used as potential markers or DNA barcodes for phylogenetic analysis. Between 22 and 38 SSRs and some long repeat sequences were identified from 12 Meconopsis species. Our phylogenetic analysis confirmed that 12 species of Meconopsis clustered into a monophyletic clade in Papaveraceae, which corroborated their intrageneric relationships. The results indicated that M. pinnatifolia and M. paniculata are sister species in the phylogenetic tree. In addition, the atpA and ycf2 genes were positively selected in high-altitude species. The functions of these two genes might be involved in adaptation to the extreme environment in the cold and low CO₂ concentration conditions at the plateau. Full article

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24 pages, 2940 KiB

Open AccessArticle

DNA Barcoding and Fertilization Strategies in Sideritis syriaca subsp. syriaca, a Local Endemic Plant of Crete with High Medicinal Value

by Konstantinos Paschalidis, Dimitrios Fanourakis, Georgios Tsaniklidis, Ioannis Tsichlas, Vasileios A. Tzanakakis, Fotis Bilias, Eftihia Samara, Ioannis Ipsilantis, Katerina Grigoriadou, Ioulietta Samartza, Theodora Matsi, Georgios Tsoktouridis and Nikos Krigas

Int. J. Mol. Sci. 2024, 25(3), 1891; https://doi.org/10.3390/ijms25031891 - 4 Feb 2024

Cited by 3 | Viewed by 2461

Abstract

Herein, we applied DNA barcoding for the genetic characterization of Sideritis syriaca subsp. syriaca (Lamiaceae; threatened local Cretan endemic plant) using seven molecular markers of cpDNA. Five fertilization schemes were evaluated comparatively in a pilot cultivation in Crete. Conventional inorganic fertilizers (ChFs), integrated [...] Read more.

Herein, we applied DNA barcoding for the genetic characterization of Sideritis syriaca subsp. syriaca (Lamiaceae; threatened local Cretan endemic plant) using seven molecular markers of cpDNA. Five fertilization schemes were evaluated comparatively in a pilot cultivation in Crete. Conventional inorganic fertilizers (ChFs), integrated nutrient management (INM) fertilizers, and two biostimulants were utilized (foliar and soil application). Plant growth, leaf chlorophyll fluorescence, and color were assessed and leaf content of chlorophyll, key antioxidants (carotenoids, flavonoids, phenols), and nutrients were evaluated. Fertilization schemes induced distinct differences in leaf shape, altering quality characteristics. INM-foliar and ChF-soil application promoted yield, without affecting tissue water content or biomass partitioning to inflorescences. ChF-foliar application was the most stimulatory treatment when the primary target was enhanced antioxidant contents while INM-biostimulant was the least effective one. However, when the primary target is yield, INM, especially by foliar application, and ChF, by soil application, ought to be employed. New DNA sequence datasets for the plastid regions of petB/petD, rpoC1, psbK-psbI, and atpF/atpH were deposited in the GenBank for S. syriaca subsp. syriaca while the molecular markers rbcL, trnL/trnF, and psbA/trnH were compared to those of another 15 Sideritis species retrieved from the GenBank, constructing a phylogenetic tree to show their genetic relatedness. Full article

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16 pages, 7547 KiB

Open AccessArticle

Identification and Expression Patterns of WOX Transcription Factors under Abiotic Stresses in Pinus massoniana

by Dengbao Wang, Zimo Qiu, Tao Xu, Sheng Yao, Mengyang Zhang, Xiang Cheng, Yulu Zhao and Kongshu Ji

Int. J. Mol. Sci. 2024, 25(3), 1627; https://doi.org/10.3390/ijms25031627 - 28 Jan 2024

Cited by 3 | Viewed by 1545

Abstract

WUSCHEL-related homeobox (WOX) transcription factors (TFs) play a crucial role in regulating plant development and responding to various abiotic stresses. However, the members and functions of WOX proteins in Pinus massoniana remain unclear. In this study, a total of 11 WOX genes were [...] Read more.

WUSCHEL-related homeobox (WOX) transcription factors (TFs) play a crucial role in regulating plant development and responding to various abiotic stresses. However, the members and functions of WOX proteins in Pinus massoniana remain unclear. In this study, a total of 11 WOX genes were identified, and bioinformatics methods were used for preliminary identification and analysis. The phylogenetic tree revealed that most PmWOXs were distributed in ancient and WUS clades, with only one member found in the intermediate clade. We selected four highly conserved WOX genes within plants for further expression analysis. These genes exhibited expressions across almost all tissues, while PmWOX2, PmWOX3, and PmWOX4 showed high expression levels in the callus, suggesting their potential involvement in specific functions during callus development. Expression patterns under different abiotic stresses indicated that PmWOXs could participate in resisting multiple stresses in P. massoniana. The identification and preliminary analysis of PmWOXs lay the foundation for further research on analyzing the resistance molecular mechanism of P. massoniana to abiotic stresses. Full article

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2023

Jump to: 2024, 2022, 2021, 2020, 2019

14 pages, 2399 KiB

Open AccessArticle

Biochemical Analysis to Understand the Flooding Tolerance of Mutant Soybean Irradiated with Gamma Rays

by Setsuko Komatsu, Tiantian Zhou and Yuhi Kono

Int. J. Mol. Sci. 2024, 25(1), 517; https://doi.org/10.3390/ijms25010517 - 30 Dec 2023

Viewed by 1156

Abstract

Flooding stress, which reduces plant growth and seed yield, is a serious problem for soybean. To improve the productivity of flooded soybean, flooding-tolerant soybean was produced by gamma-ray irradiation. Three-day-old wild-type and mutant-line plants were flooded for 2 days. Protein, RNA, and genomic [...] Read more.

Flooding stress, which reduces plant growth and seed yield, is a serious problem for soybean. To improve the productivity of flooded soybean, flooding-tolerant soybean was produced by gamma-ray irradiation. Three-day-old wild-type and mutant-line plants were flooded for 2 days. Protein, RNA, and genomic DNA were then analyzed based on oppositely changed proteins between the wild type and the mutant line under flooding stress. They were associated with cell organization, RNA metabolism, and protein degradation according to proteomic analysis. Immunoblot analysis confirmed that the accumulation of beta-tubulin/beta-actin increased in the wild type under flooding stress and recovered to the control level in the mutant line; however, alpha-tubulin increased in both the wild type and the mutant line under stress. Ubiquitin was accumulated and genomic DNA was degraded by flooding stress in the wild type; however, they were almost the same as control levels in the mutant line. On the other hand, the gene expression level of RNase H and 60S ribosomal protein did not change in either the wild type or the mutant line under flooding stress. Furthermore, chlorophyll a/b decreased and increased in the wild type and the mutant line, respectively, under flooding stress. These results suggest that the regulation of cell organization and protein degradation might be an important factor in the acquisition of flooding tolerance in soybean. Full article

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20 pages, 4886 KiB

Open AccessArticle

Genome-Wide Identification and Characterization of Gibberellic Acid-Stimulated Arabidopsis Gene Family in Pineapple (Ananas comosus)

by Mingzhe Yang, Chaoyang Liu, Wei Zhang, Jing Wu, Ziqin Zhong, Wen Yi, Hui Liu, Yan Leng, Weisheng Sun, Aiping Luan and Yehua He

Int. J. Mol. Sci. 2023, 24(23), 17063; https://doi.org/10.3390/ijms242317063 - 2 Dec 2023

Cited by 2 | Viewed by 1632

Abstract

The gibberellic acid-stimulated Arabidopsis (GASA) gene family plays a crucial role in growth, development, and stress response, and it is specific to plants. This gene family has been extensively studied in various plant species, and its functional role in pineapple has yet to [...] Read more.

The gibberellic acid-stimulated Arabidopsis (GASA) gene family plays a crucial role in growth, development, and stress response, and it is specific to plants. This gene family has been extensively studied in various plant species, and its functional role in pineapple has yet to be characterized. In this study, 15 AcGASA genes were identified in pineapple through a genome-wide scan and categorized into three major branches based on a phylogenetic tree. All AcGASA proteins share a common structural domain with 12 cysteine residues, but they exhibit slight variations in their physicochemical properties and motif composition. Predictions regarding subcellular localization suggest that AcGASA proteins are present in the cell membrane, Golgi apparatus, nucleus, and cell wall. An analysis of gene synteny indicated that both tandem and segmental repeats have a significant impact on the expansion of the AcGASA gene family. Our findings demonstrate the differing regulatory effects of these hormones (GA, NAA, IAA, MeJA, and ABA) on the AcGASA genes. We analyzed the expression profiles of GASA genes in different pineapple tissue parts, and the results indicated that AcGASA genes exhibit diverse expression patterns during the development of different plant tissues, particularly in the regulation of floral organ development. This study provides a comprehensive understanding of GASA family genes in pineapple. It serves as a valuable reference for future studies on the functional characterization of GASA genes in other perennial herbaceous plants. Full article

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20 pages, 4018 KiB

Open AccessArticle

SMALL PLANT AND ORGAN 1 (SPO1) Encoding a Cellulose Synthase-like Protein D4 (OsCSLD4) Is an Important Regulator for Plant Architecture and Organ Size in Rice

by Lei Qiao, Qilong Wu, Liuzhen Yuan, Xudong Huang, Yutao Yang, Qinying Li, Nida Shahzad, Haifeng Li and Wenqiang Li

Int. J. Mol. Sci. 2023, 24(23), 16974; https://doi.org/10.3390/ijms242316974 - 30 Nov 2023

Viewed by 1325

Abstract

Plant architecture and organ size are considered as important traits in crop breeding and germplasm improvement. Although several factors affecting plant architecture and organ size have been identified in rice, the genetic and regulatory mechanisms remain to be elucidated. Here, we identified and [...] Read more.

Plant architecture and organ size are considered as important traits in crop breeding and germplasm improvement. Although several factors affecting plant architecture and organ size have been identified in rice, the genetic and regulatory mechanisms remain to be elucidated. Here, we identified and characterized the small plant and organ 1 (spo1) mutant in rice (Oryza sativa), which exhibits narrow and rolled leaf, reductions in plant height, root length, and grain width, and other morphological defects. Map-based cloning revealed that SPO1 is allelic with OsCSLD4, a gene encoding the cellulose synthase-like protein D4, and is highly expressed in the roots at the seedling and tillering stages. Microscopic observation revealed the spo1 mutant had reduced number and width in leaf veins, smaller size of leaf bulliform cells, reduced cell length and cell area in the culm, and decreased width of epidermal cells in the outer glume of the grain. These results indicate the role of SPO1 in modulating cell division and cell expansion, which modulates plant architecture and organ size. It is showed that the contents of endogenous hormones including auxin, abscisic acid, gibberellin, and zeatin tested in the spo1 mutant were significantly altered, compared to the wild type. Furthermore, the transcriptome analysis revealed that the differentially expressed genes (DEGs) are significantly enriched in the pathways associated with plant hormone signal transduction, cell cycle progression, and cell wall formation. These results indicated that the loss of SPO1/OsCSLD4 function disrupted cell wall cellulose synthase and hormones homeostasis and signaling, thus leading to smaller plant and organ size in spo1. Taken together, we suggest the functional role of SPO1/OsCSLD4 in the control of rice plant and organ size by modulating cell division and expansion, likely through the effects of multiple hormonal pathways on cell wall formation. Full article

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16 pages, 5619 KiB

Open AccessArticle

Transcriptome-Wide Identification of TCP Transcription Factor Family Members in Pinus massoniana and Their Expression in Regulation of Development and in Response to Stress

by Mengyang Zhang, Romaric Hippolyte Agassin, Zichen Huang, Dengbao Wang, Sheng Yao and Kongshu Ji

Int. J. Mol. Sci. 2023, 24(21), 15938; https://doi.org/10.3390/ijms242115938 - 3 Nov 2023

Cited by 3 | Viewed by 1507

Abstract

Pinus massoniana is an important coniferous tree species for barren mountain afforestation with enormous ecological and economic significance. It has strong adaptability to the environment. TEOSINTE BRANCHED 1/CYCLOIDEA/PCF (TCP) transcription factors (TFs) play crucial roles in plant stress response, hormone signal transduction, and [...] Read more.

Pinus massoniana is an important coniferous tree species for barren mountain afforestation with enormous ecological and economic significance. It has strong adaptability to the environment. TEOSINTE BRANCHED 1/CYCLOIDEA/PCF (TCP) transcription factors (TFs) play crucial roles in plant stress response, hormone signal transduction, and development processes. At present, TCP TFs have been widely studied in multiple plant species, but research in P. massoniana has not been carried out. In this study, 13 PmTCP TFs were identified from the transcriptomes of P. massoniana. The phylogenetic results revealed that these PmTCP members were divided into two categories: Class I and Class II. Each PmTCP TF contained a conserved TCP domain, and the conserved motif types and numbers were similar in the same subgroup. According to the transcriptional profiling analysis under drought stress conditions, it was found that seven PmTCP genes responded to drought treatment to varying degrees. The qRT-PCR results showed that the majority of PmTCP genes were significantly expressed in the needles and may play a role in the developmental stage. Meanwhile, the PmTCPs could respond to several stresses and hormone treatments at different levels, which may be important for stress resistance. In addition, PmTCP7 and PmTCP12 were nuclear localization proteins, and PmTCP7 was a transcriptional suppressor. These results will help to explore the regulatory factors related to the growth and development of P. massoniana, enhance its stress resistance, and lay the foundation for further exploration of the physiological effects on PmTCPs. Full article

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19 pages, 7608 KiB

Open AccessArticle

Virome Analysis of Aconitum carmichaelii Reveals Infection by Eleven Viruses, including Two Potentially New Species

by Jie Yang, Ping-Xiu Lan, Yun Wang, Jin-Ming Li, Ruhui Li, Steve Wylie, Xiao-Jiao Chen, Gen-Hua Yang, Hong Cai and Fan Li

Int. J. Mol. Sci. 2023, 24(21), 15558; https://doi.org/10.3390/ijms242115558 - 25 Oct 2023

Viewed by 1561

Abstract

Aconitum carmichaelii is a herbaceous herb indigenous to China that has been cultivated for traditional medicine for centuries. Virus-like symptoms of A. carmichaelii plants were observed on leaves in some A. carmichaelii plantations in Zhanyi and Wuding Counties, Yunnan Province, southwest China. High-throughput [...] Read more.

Aconitum carmichaelii is a herbaceous herb indigenous to China that has been cultivated for traditional medicine for centuries. Virus-like symptoms of A. carmichaelii plants were observed on leaves in some A. carmichaelii plantations in Zhanyi and Wuding Counties, Yunnan Province, southwest China. High-throughput sequencing (HTS) was performed on 28 symptomatic plants, and the results revealed infection with 11 viruses, including 2 novel viruses and 9 previously described viruses: Aconitum amalgavirus 1 (AcoAV-1), aconite virus A (AcVA), cucumber mosaic virus (CMV), currant latent virus (CuLV), apple stem grooving virus (ASGV), chilli veinal mottle virus (ChiVMV), tomato spotted wilt orthotospovirus (TSWV), tobacco vein distorting virus (TVDV), and potato leafroll virus (PLRV). Two novel viruses tentatively named Aconitum potyvirus 1 and Aconitum betapartitivirus 1, were supported by sequence and phylogenetic analysis results of their genomes. We proposed the names Potyvirus aconiti and Betapartitivirus aconiti. RT-PCR assays of 142 plants revealed the predominance and widespread distribution of CMV, AcVA, and AcoPV-1 in plantations. The detection of isolates of CuLV, ASGV, ChiVMV, TSWV, TVDV, and PLRV infections for the first time in A. carmichaelii expands their known host ranges. Full article

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19 pages, 2344 KiB

Open AccessArticle

OXPHOS Organization and Activity in Mitochondria of Plants with Different Life Strategies

by Irina V. Ukolova and Gennadii B. Borovskii

Int. J. Mol. Sci. 2023, 24(20), 15229; https://doi.org/10.3390/ijms242015229 - 16 Oct 2023

Cited by 1 | Viewed by 1283

Abstract

The study of the supramolecular organization of the mitochondrial oxidative phosphorylation system (OXPHOS) in various eukaryotes has led to the accumulation of a considerable amount of data on the composition, stoichiometry, and architecture of its constituent superstructures. However, the link between the features [...] Read more.

The study of the supramolecular organization of the mitochondrial oxidative phosphorylation system (OXPHOS) in various eukaryotes has led to the accumulation of a considerable amount of data on the composition, stoichiometry, and architecture of its constituent superstructures. However, the link between the features of system arrangement and the biological characteristics of the studied organisms has been poorly explored. Here, we report a comparative investigation into supramolecular and functional OXPHOS organization in the mitochondria of etiolated shoots of winter wheat (Triticum aestivum L.), maize (Zea mays L.), and pea (Pisum sativum L.). Investigations based on BN-PAGE, in-gel activity assays, and densitometric analysis revealed both similarities and specific OXPHOS features apparently related to the life strategies of each species. Frost-resistant winter wheat was distinguished by highly stable basic I₁III₂IVa/b respirasomes and V₂ dimers, highly active complex I, and labile complex IV, which were probably essential for effective OXPHOS adaptation during hypothermia. Maize, a C4 plant, had the highly stable dimers IV₂ and V₂, less active complex I, and active alternative NAD(P)H dehydrogenases. The latter fact could contribute to successful chloroplast–mitochondrial cooperation, which is essential for highly efficient photosynthesis in this species. The pea OXPHOS contained detergent-resistant high-molecular respirasomes I_1–2III₂IV_n, highly active complexes IV and V, and stable succinate dehydrogenase, suggesting an active energy metabolism in organelles of this plant. The results and conclusions are in good agreement with the literature data on the respiratory activity of mitochondria from these species and are summarized in a proposed scheme of organization of OXPHOS fragments. Full article

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17 pages, 5539 KiB

Open AccessArticle

Genome-Wide Identification and Characterization of the YTH Domain-Containing RNA-Binding Protein Family in Liriodendron chinense

by Sheng Yao, Jingjing Zhang, Xiang Cheng, Dengbao Wang, Wenya Yu, Kongshu Ji and Qiong Yu

Int. J. Mol. Sci. 2023, 24(20), 15189; https://doi.org/10.3390/ijms242015189 - 14 Oct 2023

Cited by 3 | Viewed by 1795

Abstract

N⁶-methyladenosine (m⁶A) is becoming one of the most important RNA modifications in plant growth and development, including defense, cell differentiation, and secondary metabolism. YT521-B homology (YTH) domain-containing RNA-binding proteins, identified as m⁶A readers in epitranscriptomics, could affect [...] Read more.

N⁶-methyladenosine (m⁶A) is becoming one of the most important RNA modifications in plant growth and development, including defense, cell differentiation, and secondary metabolism. YT521-B homology (YTH) domain-containing RNA-binding proteins, identified as m⁶A readers in epitranscriptomics, could affect the fate of m⁶A-containing RNA by recognizing and binding the m⁶A site. Therefore, the identification and study of the YTH gene family in Liriodendron chinense (L. chinense) can provide a molecular basis for the study of the role of m⁶A in L. chinense, but studies on the YTH gene in L. chinense have not been reported. We identified nine putative YTH gene models in the L. chinense genome, which can be divided into DF subgroups and DC subgroups. Domain sequence analysis showed that the LcYTH protein had high sequence conservation. A LcYTH aromatic cage bag is composed of tryptophan and tryptophan (WWW). PrLDs were found in the protein results of YTH, suggesting that these genes may be involved in the process of liquid–liquid phase separation. LcYTH genes have different tissue expression patterns, but the expression of LcYTHDF2 is absolutely dominant in all tissues. In addition, the expression of the LcYTH genes is changed in response to ABA and MeJA. In this study, We identified and analyzed the expression pattern of LcYTH genes. Our results laid a foundation for further study of the function of the LcYTH gene and further genetic and functional analyses of m⁶A RNA modification in forest trees. Full article

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13 pages, 6107 KiB

Open AccessArticle

Cloning of PmMYB6 in Pinus massoniana and an Analysis of Its Function

by Yuan He, Qingqing Hao, Peizhen Chen, Yiyun Qin, Manqing Peng, Sheng Yao, Xin He, Qiong Yu, Romaric Hippolyte Agassin and Kongshu Ji

Int. J. Mol. Sci. 2023, 24(18), 13766; https://doi.org/10.3390/ijms241813766 - 6 Sep 2023

Cited by 2 | Viewed by 1864

Abstract

Phenylpropanoids are crucial for the growth and development of plants and their interaction with the environment. As key transcriptional regulators of plant growth and development, MYB-like transcription factors play a vital role in the biosynthesis of phenylpropanoid metabolites. In this study, we functionally [...] Read more.

Phenylpropanoids are crucial for the growth and development of plants and their interaction with the environment. As key transcriptional regulators of plant growth and development, MYB-like transcription factors play a vital role in the biosynthesis of phenylpropanoid metabolites. In this study, we functionally characterized PmMYB6, a Pinus massoniana gene that encodes an R2R3-MYB transcription factor. It was confirmed by qPCR that PmMYB6 was highly expressed in the flowers, xylem, and phloem of P. massoniana. By overexpressing PmMYB6 in tobacco and poplar, we found that transgenic plants had enlarged xylem, increased content of lignin and flavonoids, and up-regulated expression of several enzyme genes of the phenylpropane metabolism pathway to different degrees. The above research results indicate that PmMYB6 is involved in the metabolic flux distribution of different branches of the phenylpropane metabolic pathway, and the results may provide clues for the regulation of metabolic fluxes between flavonoids and the lignin biosynthesis pathways of P. massoniana, as well as provide a basis for the molecular breeding of P. massoniana. Full article

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15 pages, 3303 KiB

Open AccessArticle

Proteomic Analysis Reveals Salt-Tolerant Mechanism in Soybean Applied with Plant-Derived Smoke Solution

by Setsuko Komatsu, Taiki Kimura, Shafiq Ur Rehman, Hisateru Yamaguchi, Keisuke Hitachi and Kunihiro Tsuchida

Int. J. Mol. Sci. 2023, 24(18), 13734; https://doi.org/10.3390/ijms241813734 - 6 Sep 2023

Cited by 2 | Viewed by 1776

Abstract

Salt stress of soybean is a serious problem because it reduces plant growth and seed yield. To investigate the salt-tolerant mechanism of soybean, a plant-derived smoke (PDS) solution was used. Three-day-old soybeans were subjected to PDS solution under 100 mM NaCl for 2 [...] Read more.

Salt stress of soybean is a serious problem because it reduces plant growth and seed yield. To investigate the salt-tolerant mechanism of soybean, a plant-derived smoke (PDS) solution was used. Three-day-old soybeans were subjected to PDS solution under 100 mM NaCl for 2 days, resulting in PDS solution improving soybean root growth, even under salt stress. Under the same condition, proteins were analyzed using the proteomic technique. Differential abundance proteins were associated with transport/formaldehyde catabolic process/sucrose metabolism/glutathione metabolism/cell wall organization in the biological process and membrane/Golgi in the cellular component with or without PDS solution under salt stress. Immuno-blot analysis confirmed that osmotin, alcohol dehydrogenase, and sucrose synthase increased with salt stress and decreased with additional PDS solution; however, H⁺ATPase showed opposite effects. Cellulose synthase and xyloglucan endotransglucosylase/hydrolase increased with salt and decreased with additional PDS solution. Furthermore, glycoproteins decreased with salt stress and recovered with additional treatment. As mitochondrion-related events, the contents of ATP and gamma-aminobutyric acid increased with salt stress and recovered with additional treatment. These results suggest that PDS solution improves the soybean growth by alleviating salt stress. Additionally, the regulation of energy metabolism, protein glycosylation, and cell wall construction might be an important factor for the acquisition of salt tolerance in soybean. Full article

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15 pages, 4289 KiB

Open AccessArticle

Association Mapping and Expression Analysis of the Genes Involved in the Wood Formation of Poplar

by Yaolin Wang, Heng Zhang, Sheng Zhu, Tengfei Shen, Huixin Pan and Meng Xu

Int. J. Mol. Sci. 2023, 24(16), 12662; https://doi.org/10.3390/ijms241612662 - 10 Aug 2023

Viewed by 1871

Abstract

Xylogenesis is a complex and sequential biosynthetic process controlled by polygenes. Deciphering the genetic architecture of this complex quantitative trait could provide valuable information for increasing wood biomass and improving its properties. Here, we performed genomic resequencing of 64 24-year-old trees (64 hybrids [...] Read more.

Xylogenesis is a complex and sequential biosynthetic process controlled by polygenes. Deciphering the genetic architecture of this complex quantitative trait could provide valuable information for increasing wood biomass and improving its properties. Here, we performed genomic resequencing of 64 24-year-old trees (64 hybrids of section Aigeiros and their parents) grown in the same field and conducted full-sib family-based association analyses of two growth and six woody traits using GEMMA as a choice of association model selection. We identified 1342 significantly associated single nucleotide polymorphisms (SNPs), 673 located in the region upstream and downstream of 565 protein-encoding genes. The transcriptional regulation network of secondary cell wall (SCW) biosynthesis was further constructed based on the published data of poplar miRNA, transcriptome, and degradome. These provided a certain scientific basis for the in-depth understanding of the mechanism of poplar timber formation and the molecular-assisted breeding in the future. Full article

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18 pages, 10534 KiB

Open AccessArticle

Genome-Wide Identification, Characterization, and Expression Analysis of Long-Chain Acyl-CoA Synthetases in Carya illinoinensis under Different Treatments

by Wenjuan Ma, Kaikai Zhu, Juan Zhao, Mengyun Chen, Lu Wei, Zhenbing Qiao, Pengpeng Tan and Fangren Peng

Int. J. Mol. Sci. 2023, 24(14), 11558; https://doi.org/10.3390/ijms241411558 - 17 Jul 2023

Cited by 3 | Viewed by 1749

Abstract

As crucial enzymes in the lipid metabolic network, long-chain acyl-CoA synthases (LACSs) are members of the acyl-activated enzyme superfamily and play a crucial role in epidermal wax synthesis, plant lipid anabolic metabolism, and stress tolerance. In this study, 11 pecan LACS genes were [...] Read more.

As crucial enzymes in the lipid metabolic network, long-chain acyl-CoA synthases (LACSs) are members of the acyl-activated enzyme superfamily and play a crucial role in epidermal wax synthesis, plant lipid anabolic metabolism, and stress tolerance. In this study, 11 pecan LACS genes were identified and categorized into five groups and located on nine chromosomes. The significant degree of conservation in the AtLACS and CiLACS protein sequences was demonstrated by multiple sequence alignment and conserved motif analysis. Cis-acting element analysis identified numerous stress-responsive and hormone-inducible elements in the promoter regions of CiLACS genes. The expression levels of CiLACS9 and CiLACS9-1 were considerably up-regulated under salt and drought stress, according to the qRT-RCR study. Treatment with ABA also led to increased expression levels of CiLACS1, CiLACS1-1, CiLACS2, and CiLACS9-1. Notably, CiLACS4, CiLACS4-1, CiLACS9, and CiLACS9-1 exhibited peak expression levels at 135 days after anthesis and are likely to have been crucial in the accumulation of seed kernel oil. Moreover, the CiLACS9 gene was shown to be located in the cytoplasm. These findings offer a theoretical framework for clarifying the roles of LACS genes in the processes of pecan kernel oil synthesis and response to abiotic stressors. Full article

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32 pages, 20479 KiB

Open AccessArticle

Canonical and Alternative Auxin Signaling Systems in Mono-, Di-, and Tetraploid Potatoes

by Sergey N. Lomin, Oksana O. Kolachevskaya, Dmitry V. Arkhipov and Georgy A. Romanov

Int. J. Mol. Sci. 2023, 24(14), 11408; https://doi.org/10.3390/ijms241411408 - 13 Jul 2023

Cited by 1 | Viewed by 1545

Abstract

It has long been known that the phytohormone auxin plays a promoting role in tuber formation and stress tolerance in potatoes. Our study aimed to identify and characterize the complete sets of auxin-related genes that presumably constitute the entire auxin signaling system in [...] Read more.

It has long been known that the phytohormone auxin plays a promoting role in tuber formation and stress tolerance in potatoes. Our study aimed to identify and characterize the complete sets of auxin-related genes that presumably constitute the entire auxin signaling system in potato (Solanum tuberosum L.). The corresponding genes were retrieved from sequenced genomes of the doubled monoploid S. tuberosum DM1-3-516-R44 (DM) of the Phureja group, the heterozygous diploid line RH89-039-16 (RH), and the autotetraploid cultivar Otava. Both canonical and noncanonical auxin signaling pathways were considered. Phylogenetic and domain analyses of deduced proteins were supplemented by expression profiling and 3D molecular modeling. The canonical and ABP1-mediated pathways of auxin signaling appeared to be well conserved. The total number of potato genes/proteins presumably involved in canonical auxin signaling is 46 and 108 in monoploid DM and tetraploid Otava, respectively. Among the studied potatoes, spectra of expressed genes obviously associated with auxin signaling were partly cultivar-specific and quite different from analogous spectrum in Arabidopsis. Most of the noncanonical pathways found in Arabidopsis appeared to have low probability in potato. This was equally true for all cultivars used irrespective of their ploidy. Thus, some important features of the (noncanonical) auxin signaling pathways may be variable and species-specific. Full article

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12 pages, 5726 KiB

Open AccessArticle

Complete Chloroplast Genomes and Comparative Analyses of Three Paraphalaenopsis (Aeridinae, Orchidaceae) Species

by Jinliao Chen, Fei Wang, Zhuang Zhao, Minghe Li, Zhongjian Liu and Donghui Peng

Int. J. Mol. Sci. 2023, 24(13), 11167; https://doi.org/10.3390/ijms241311167 - 6 Jul 2023

Cited by 15 | Viewed by 2090

Abstract

Paraphalaenopsis, a genus of perennial herbs from the family Orchidaceae, contains a number of ornamental species. However, there is no information on the chloroplast genomes of Paraphalaenopsis, which limits our studies of this genus. In this study, we reported the chloroplast [...] Read more.

Paraphalaenopsis, a genus of perennial herbs from the family Orchidaceae, contains a number of ornamental species. However, there is no information on the chloroplast genomes of Paraphalaenopsis, which limits our studies of this genus. In this study, we reported the chloroplast genomes of three species of Paraphalaenopsis (P. labukensis, P. denevel, and P. laycockii ‘Semi-alba’) and performed comprehensive comparative analysis. These three chloroplast genomes showed a typical quadripartile structure. Their lengths ranged from 147,311 bp to 149,240 bp. Each genome contained 120 unique genes, including 74 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Comparative analysis revealed major differences in sequence divergence in the three chloroplast genomes. In addition, six hypervariable regions were identified (psbM-trnD^GUC, psbB, ccsA, trnK^UUU, trnS^GCU-trnG^UCC, rps16-trnQ^UUG) that can be used as DNA molecular markers. Phylogenetic relationships were determined using the chloroplast genomes of 28 species from 12 genera of Aeridinae. Results suggested that Paraphalaenopsis was a clade of Aeridinae that was sister to the Holcoglossum-Vanda clade, with 100% bootstrap support within Aeridinae. The findings of this study provided the foundation for future studies on the phylogenetic analysis of Aeridinae. Full article

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21 pages, 4174 KiB

Open AccessArticle

Transcriptome Screening of Long Noncoding RNAs and Their Target Protein-Coding Genes Unmasks a Dynamic Portrait of Seed Coat Coloration Associated with Anthocyanins in Tibetan Hulless Barley

by Kaifeng Zheng, Xiaozhuo Wu, Xiuhua Xue, Wanjie Li, Zitao Wang, Jinyuan Chen, Yanfen Zhang, Feng Qiao, Heping Zhao, Fanfan Zhang and Shengcheng Han

Int. J. Mol. Sci. 2023, 24(13), 10587; https://doi.org/10.3390/ijms241310587 - 24 Jun 2023

Cited by 4 | Viewed by 1857

Abstract

Many plants have the capability to accumulate anthocyanins for coloration, and anthocyanins are advantageous to human health. In the case of hulless barley (Hordeum vulgare L. var. nudum), investigation into the mechanism of anthocyanin formation is limited to the level of protein-coding [...] Read more.

Many plants have the capability to accumulate anthocyanins for coloration, and anthocyanins are advantageous to human health. In the case of hulless barley (Hordeum vulgare L. var. nudum), investigation into the mechanism of anthocyanin formation is limited to the level of protein-coding genes (PCGs). Here, we conducted a comprehensive bioinformatics analysis to identify a total of 9414 long noncoding RNAs (lncRNAs) in the seed coats of purple and white hulless barley along a developmental gradient. Transcriptome-wide profiles of lncRNAs documented several properties, including GC content fluctuation, uneven length, a diverse range of exon numbers, and a wide variety of transcript classifications. We found that certain lncRNAs in hulless barley possess detectable sequence conservation with Hordeum vulgare and other monocots. Furthermore, both differentially expressed lncRNAs (DElncRNAs) and PCGs (DEPCGs) were concentrated in the later seed development stages. On the one hand, DElncRNAs could potentially cis-regulate DEPCGs associated with multiple metabolic pathways, including flavonoid and anthocyanin biosynthesis in the late milk and soft dough stages. On the other hand, there was an opportunity for trans-regulated lncRNAs in the color-forming module to affect seed coat color by upregulating PCGs in the anthocyanin pathway. In addition, the interweaving of hulless barley lncRNAs and diverse TFs may function in seed coat coloration. Notably, we depicted a dynamic portrait of the anthocyanin synthesis pathway containing hulless barley lncRNAs. Therefore, this work provides valuable gene resources and more insights into the molecular mechanisms underlying anthocyanin accumulation in hulless barley from the perspective of lncRNAs, which facilitate the development of molecular design breeding in crops. Full article

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15 pages, 2624 KiB

Open AccessArticle

Exploring Redox Modulation of Plant UDP-Glucose Pyrophosphorylase

by Daniel Decker, Juliette Aubert, Malgorzata Wilczynska and Leszek A. Kleczkowski

Int. J. Mol. Sci. 2023, 24(10), 8914; https://doi.org/10.3390/ijms24108914 - 17 May 2023

Cited by 3 | Viewed by 2196

Abstract

UDP-glucose (UDPG) pyrophosphorylase (UGPase) catalyzes a reversible reaction, producing UDPG, which serves as an essential precursor for hundreds of glycosyltransferases in all organisms. In this study, activities of purified UGPases from sugarcane and barley were found to be reversibly redox modulated in vitro [...] Read more.

UDP-glucose (UDPG) pyrophosphorylase (UGPase) catalyzes a reversible reaction, producing UDPG, which serves as an essential precursor for hundreds of glycosyltransferases in all organisms. In this study, activities of purified UGPases from sugarcane and barley were found to be reversibly redox modulated in vitro through oxidation by hydrogen peroxide or oxidized glutathione (GSSG) and through reduction by dithiothreitol or glutathione. Generally, while oxidative treatment decreased UGPase activity, a subsequent reduction restored the activity. The oxidized enzyme had increased K_m values with substrates, especially pyrophosphate. The increased K_m values were also observed, regardless of redox status, for UGPase cysteine mutants (Cys102Ser and Cys99Ser for sugarcane and barley UGPases, respectively). However, activities and substrate affinities (K_ms) of sugarcane Cys102Ser mutant, but not barley Cys99Ser, were still prone to redox modulation. The data suggest that plant UGPase is subject to redox control primarily via changes in the redox status of a single cysteine. Other cysteines may also, to some extent, contribute to UGPase redox status, as seen for sugarcane enzymes. The results are discussed with respect to earlier reported details of redox modulation of eukaryotic UGPases and regarding the structure/function properties of these proteins. Full article

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22 pages, 4340 KiB

Open AccessArticle

Comparison and Characterization of Phenotypic and Genomic Mutations Induced by a Carbon-Ion Beam and Gamma-ray Irradiation in Soybean (Glycine max (L.) Merr.)

by Zhuo Feng, Yan Du, Jingmin Chen, Xia Chen, Weibin Ren, Lulu Wang and Libin Zhou

Int. J. Mol. Sci. 2023, 24(10), 8825; https://doi.org/10.3390/ijms24108825 - 16 May 2023

Cited by 4 | Viewed by 2154

Abstract

Soybean (Glycine max (L.) Merr.) is a nutritious crop that can provide both oil and protein. A variety of mutagenesis methods have been proposed to obtain better soybean germplasm resources. Among the different types of physical mutagens, carbon-ion beams are considered to [...] Read more.

Soybean (Glycine max (L.) Merr.) is a nutritious crop that can provide both oil and protein. A variety of mutagenesis methods have been proposed to obtain better soybean germplasm resources. Among the different types of physical mutagens, carbon-ion beams are considered to be highly efficient with high linear energy transfer (LET), and gamma rays have also been widely used for mutation breeding. However, systematic knowledge of the mutagenic effects of these two mutagens during development and on phenotypic and genomic mutations has not yet been elucidated in soybean. To this end, dry seeds of Williams 82 soybean were irradiated with a carbon-ion beam and gamma rays. The biological effects of the M₁ generation included changes in survival rate, yield and fertility. Compared with gamma rays, the relative biological effectiveness (RBE) of the carbon-ion beams was between 2.5 and 3.0. Furthermore, the optimal dose for soybean was determined to be 101 Gy to 115 Gy when using the carbon-ion beam, and it was 263 Gy to 343 Gy when using gamma rays. A total of 325 screened mutant families were detected from out of 2000 M₂ families using the carbon-ion beam, and 336 screened mutant families were found using gamma rays. Regarding the screened phenotypic M₂ mutations, the proportion of low-frequency phenotypic mutations was 23.4% when using a carbon ion beam, and the proportion was 9.8% when using gamma rays. Low-frequency phenotypic mutations were easily obtained with the carbon-ion beam. After screening the mutations from the M₂ generation, their stability was verified, and the genome mutation spectrum of M₃ was systemically profiled. A variety of mutations, including single-base substitutions (SBSs), insertion–deletion mutations (INDELs), multinucleotide variants (MNVs) and structural variants (SVs) were detected with both carbon-ion beam irradiation and gamma-ray irradiation. Overall, 1988 homozygous mutations and 9695 homozygous + heterozygous genotype mutations were detected when using the carbon-ion beam. Additionally, 5279 homozygous mutations and 14,243 homozygous + heterozygous genotype mutations were detected when using gamma rays. The carbon-ion beam, which resulted in low levels of background mutations, has the potential to alleviate the problems caused by linkage drag in soybean mutation breeding. Regarding the genomic mutations, when using the carbon-ion beam, the proportion of homozygous-genotype SVs was 0.45%, and that of homozygous + heterozygous-genotype SVs was 6.27%; meanwhile, the proportions were 0.04% and 4.04% when using gamma rays. A higher proportion of SVs were detected when using the carbon ion beam. The gene effects of missense mutations were greater under carbon-ion beam irradiation, and the gene effects of nonsense mutations were greater under gamma-ray irradiation, which meant that the changes in the amino acid sequences were different between the carbon-ion beam and gamma rays. Taken together, our results demonstrate that both carbon-ion beam and gamma rays are effective techniques for rapid mutation breeding in soybean. If one would like to obtain mutations with a low-frequency phenotype, low levels of background genomic mutations and mutations with a higher proportion of SVs, carbon-ion beams are the best choice. Full article

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13 pages, 4375 KiB

Open AccessArticle

Genome-Wide Identification and Analysis of OsSPXs Revealed Its Genetic Influence on Cold Tolerance of Dongxiang Wild Rice (DXWR)

by Cheng Huang, Jilin Wang, Dianwen Wang, Jingjing Chang, Hongping Chen, Dazhou Chen, Wei Deng and Chunjie Tian

Int. J. Mol. Sci. 2023, 24(10), 8755; https://doi.org/10.3390/ijms24108755 - 15 May 2023

Cited by 2 | Viewed by 1936

Abstract

SPX-domain proteins (small proteins with only the SPX domain) have been proven to be involved in phosphate-related signal transduction and regulation pathways. Except for OsSPX1 research showing that it plays a role in the process of rice adaptation to cold stress, the potential [...] Read more.

SPX-domain proteins (small proteins with only the SPX domain) have been proven to be involved in phosphate-related signal transduction and regulation pathways. Except for OsSPX1 research showing that it plays a role in the process of rice adaptation to cold stress, the potential functions of other SPX genes in cold stress are unknown. Therefore, in this study, we identified six OsSPXs from the whole genome of DXWR. The phylogeny of OsSPXs has a strong correlation with its motif. Transcriptome data analysis showed that OsSPXs were highly sensitive to cold stress, and real-time PCR verified that the levels of OsSPX1, OsSPX2, OsSPX4, and OsSPX6 in cold-tolerant materials (DXWR) during cold treatment were higher than that of cold-sensitive rice (GZX49). The promoter region of DXWR OsSPXs contains a large number of cis-acting elements related to abiotic stress tolerance and plant hormone response. At the same time, these genes have expression patterns that are highly similar to cold-tolerance genes. This study provides useful information about OsSPXs, which is helpful for the gene-function research of DXWR and genetic improvements during breeding. Full article

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12 pages, 752 KiB

Open AccessReview

Cross-Kingdom Regulation of Plant-Derived miRNAs in Modulating Insect Development

by Xuepeng Chi, Zhe Wang, Ying Wang, Zhenguo Liu, Hongfang Wang and Baohua Xu

Int. J. Mol. Sci. 2023, 24(9), 7978; https://doi.org/10.3390/ijms24097978 - 28 Apr 2023

Cited by 6 | Viewed by 2573

Abstract

MicroRNAs (miRNAs), a class of non-coding small RNAs, are crucial regulatory factors in plants and animals at the post-transcriptional level. These tiny molecules suppress gene expression by complementary oligonucleotide binding to sites in the target messenger. Recently, the discovery of plant-derived miRNAs with [...] Read more.

MicroRNAs (miRNAs), a class of non-coding small RNAs, are crucial regulatory factors in plants and animals at the post-transcriptional level. These tiny molecules suppress gene expression by complementary oligonucleotide binding to sites in the target messenger. Recently, the discovery of plant-derived miRNAs with cross-kingdom abilities to regulate gene expression in insects has promoted exciting discussion, although some controversies exist regarding the modulation of insect development by plant-derived miRNAs. Here, we review current knowledge about the mechanisms of miRNA biogenesis, the roles of miRNAs in coevolution between insects and plants, the regulation of insect development by plant-derived miRNAs, the cross-kingdom transport mechanisms of plant-derived miRNAs, and cross-kingdom regulation. In addition, the controversy regarding the modulation of insect development by plant-derived miRNAs also was discussed. Our review provides new insights for understanding complex plant–insect interactions and discovering new strategies for pest management and even crop genetic improvement. Full article

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23 pages, 819 KiB

Open AccessReview

From Transgenesis to Genome Editing in Crop Improvement: Applications, Marketing, and Legal Issues

by Daniela Marone, Anna Maria Mastrangelo and Grazia Maria Borrelli

Int. J. Mol. Sci. 2023, 24(8), 7122; https://doi.org/10.3390/ijms24087122 - 12 Apr 2023

Cited by 14 | Viewed by 6090

Abstract

The biotechnological approaches of transgenesis and the more recent eco-friendly new breeding techniques (NBTs), in particular, genome editing, offer useful strategies for genetic improvement of crops, and therefore, recently, they have been receiving increasingly more attention. The number of traits improved through transgenesis [...] Read more.

The biotechnological approaches of transgenesis and the more recent eco-friendly new breeding techniques (NBTs), in particular, genome editing, offer useful strategies for genetic improvement of crops, and therefore, recently, they have been receiving increasingly more attention. The number of traits improved through transgenesis and genome editing technologies is growing, ranging from resistance to herbicides and insects to traits capable of coping with human population growth and climate change, such as nutritional quality or resistance to climatic stress and diseases. Research on both technologies has reached an advanced stage of development and, for many biotech crops, phenotypic evaluations in the open field are already underway. In addition, many approvals regarding main crops have been granted. Over time, there has been an increase in the areas cultivated with crops that have been improved through both approaches, but their use in various countries has been limited by legislative restrictions according to the different regulations applied which affect their cultivation, marketing, and use in human and animal nutrition. In the absence of specific legislation, there is an on-going public debate with favorable and unfavorable positions. This review offers an updated and in-depth discussion on these issues. Full article

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29 pages, 1980 KiB

Open AccessReview

Hairy Root Cultures as a Source of Phenolic Antioxidants: Simple Phenolics, Phenolic Acids, Phenylethanoids, and Hydroxycinnamates

by Janusz Malarz, Yulia V. Yudina and Anna Stojakowska

Int. J. Mol. Sci. 2023, 24(8), 6920; https://doi.org/10.3390/ijms24086920 - 7 Apr 2023

Cited by 12 | Viewed by 3174

Abstract

Plant-derived antioxidants are intrinsic components of human diet and factors implicated in tolerance mechanisms against environmental stresses in both plants and humans. They are being used as food preservatives and additives or ingredients of cosmetics. For nearly forty years, Rhizobium rhizogenes-transformed roots [...] Read more.

Plant-derived antioxidants are intrinsic components of human diet and factors implicated in tolerance mechanisms against environmental stresses in both plants and humans. They are being used as food preservatives and additives or ingredients of cosmetics. For nearly forty years, Rhizobium rhizogenes-transformed roots (hairy roots) have been studied in respect to their usability as producers of plant specialized metabolites of different, primarily medical applications. Moreover, the hairy root cultures have proven their value as a tool in crop plant improvement and in plant secondary metabolism investigations. Though cultivated plants remain a major source of plant polyphenolics of economic importance, the decline in biodiversity caused by climate changes and overexploitation of natural resources may increase the interest in hairy roots as a productive and renewable source of biologically active compounds. The present review examines hairy roots as efficient producers of simple phenolics, phenylethanoids, and hydroxycinnamates of plant origin and summarizes efforts to maximize the product yield. Attempts to use Rhizobium rhizogenes-mediated genetic transformation for inducing enhanced production of the plant phenolics/polyphenolics in crop plants are also mentioned. Full article

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20 pages, 10614 KiB

Open AccessArticle

Metabolic Composition and Quality Traits of Polygonatum cyrtonema Hua from Different Germplasms and Age Sections Based on Widely Targeted Metabolomics Analysis

by Qingshuang Wang, Jingjie Ban, Roudi Cai, Xueying Zhang, Chunwang Lai, Yan Chen, Xiaoli Li, Cuirong Chen, Yukun Chen, Zihao Zhang, Zhongxiong Lai and Yuling Lin

Int. J. Mol. Sci. 2023, 24(7), 6077; https://doi.org/10.3390/ijms24076077 - 23 Mar 2023

Cited by 6 | Viewed by 1960

Abstract

Polygonatum rhizomes are rich in various compounds with many biological activities and are widely used in functional foods and pharmaceutical products. In order to screen for superior Polygonatum cyrtonema Hua (P. cyrtonema) germplasm and also to elucidate the nutritional and medicinal values [...] Read more.

Polygonatum rhizomes are rich in various compounds with many biological activities and are widely used in functional foods and pharmaceutical products. In order to screen for superior Polygonatum cyrtonema Hua (P. cyrtonema) germplasm and also to elucidate the nutritional and medicinal values of rhizomes, the metabolic composition and quality traits of rhizomes from different germplasms and age sections of P. cyrtonema were analysed by widely targeted metabolomics, and the molecular mechanism of triacylglycerol synthesis was explored. The results showed that the different germplasms and age sections of P. cyrtonema were rich in different nutritional and medicinal components. Of these, the broad-leaved green stem (GK) germplasm is rich in polysaccharides, alkaloids, and lipids; the pointed-leaved green stem (JL) germplasm is rich in flavonoids, steroids, and amino acids, while the pointed-leaved purple stem (JZ) germplasm contains more phenolic acids. The one-year (AT) age section is rich in polysaccharides, steroids, organic acids, and lipids; the three years (CT) age section contains more flavonoids, alkaloids, and amino acid metabolites. Lipids were significantly enriched in the broad-leaved green stem germplasm and the one-year age section. Interestingly, the highest accumulation of triacylglycerols, an important component of lipids, was also found in the GK germplasm and the AT age section. Nineteen, 14, and 13 members of the glycerol-3-phosphate acyltransferase (GPAT), lysophosphatidic acid acyltransferase (LPAT), and diacylglycerol acyltransferase (DGAT) gene families, respectively, involved in triacylglycerol synthesis were also identified. The quantitative real-time PCR (qRT-PCR) results further suggested that the differentially expressed PcDGAT1, PcDGAT2.4, PcGPAT9.1, PcLPAT2.9, and PcLPAT4.3 genes may play important roles in triacylglycerol synthesis in P. cyrtonema. Therefore, this study provides a new theoretical reference for product development and the breeding of new varieties of Polygonatum species. Full article

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13 pages, 2100 KiB

Open AccessReview

“B” Regulatory Subunits of PP2A: Their Roles in Plant Development and Stress Reactions

by Csaba Máthé, Csongor Freytag, Adrienn Kelemen, Márta M-Hamvas and Tamás Garda

Int. J. Mol. Sci. 2023, 24(6), 5147; https://doi.org/10.3390/ijms24065147 - 7 Mar 2023

Cited by 5 | Viewed by 2356

Abstract

Protein phosphatase PP2A is an enzyme complex consisting of C (catalytic), A (scaffold) and B (regulatory) subunits. B subunits are a large family of proteins that regulate activity, substrate specificity and subcellular localization of the holoenzyme. Knowledge on the molecular functions of PP2A [...] Read more.

Protein phosphatase PP2A is an enzyme complex consisting of C (catalytic), A (scaffold) and B (regulatory) subunits. B subunits are a large family of proteins that regulate activity, substrate specificity and subcellular localization of the holoenzyme. Knowledge on the molecular functions of PP2A in plants is less than for protein kinases, but it is rapidly increasing. B subunits are responsible for the large diversity of PP2A functioning. This paper intends to give a survey on their multiple regulatory mechanisms. Firstly, we give a short description on our current knowledge in terms of “B”-mediated regulation of metabolic pathways. Next, we present their subcellular localizations, which extend from the nucleus to the cytosol and membrane compartments. The next sections show how B subunits regulate cellular processes from mitotic division to signal transduction pathways, including hormone signaling, and then the emerging evidence for their regulatory (mostly modulatory) roles in both abiotic and biotic stress responses in plants. Knowledge on these issues should be increased in the near future, since it contributes to a better understanding of how plant cells work, it may have agricultural applications, and it may have new insights into how vascular plants including crops face diverse environmental challenges. Full article

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14 pages, 7902 KiB

Open AccessArticle

Genome-Wide Association Analysis of Fruit Shape-Related Traits in Areca catechu

by Hao Ding, Guangzhen Zhou, Long Zhao, Xinyu Li, Yicheng Wang, Chengcai Xia, Zhiqiang Xia and Yinglang Wan

Int. J. Mol. Sci. 2023, 24(5), 4686; https://doi.org/10.3390/ijms24054686 - 28 Feb 2023

Cited by 4 | Viewed by 2530

Abstract

The areca palm (Areca catechu L.) is one of the most economically important palm trees in tropical areas. To inform areca breeding programs, it is critical to characterize the genetic bases of the mechanisms that regulate areca fruit shape and to identify [...] Read more.

The areca palm (Areca catechu L.) is one of the most economically important palm trees in tropical areas. To inform areca breeding programs, it is critical to characterize the genetic bases of the mechanisms that regulate areca fruit shape and to identify candidate genes related to fruit-shape traits. However, few previous studies have mined candidate genes associated with areca fruit shape. Here, the fruits produced by 137 areca germplasms were divided into three categories (spherical, oval, and columnar) based on the fruit shape index. A total of 45,094 high-quality single-nucleotide polymorphisms (SNPs) were identified across the 137 areca cultivars. Phylogenetic analysis clustered the areca cultivars into four subgroups. A genome-wide association study that used a mixed linear model identified the 200 loci that were the most significantly associated with fruit-shape traits in the germplasms. In addition, 86 candidate genes associated with areca fruit-shape traits were further mined. Among the proteins encoded by these candidate genes were UDP-glucosyltransferase 85A2, the ABA-responsive element binding factor GBF4, E3 ubiquitin-protein ligase SIAH1, and LRR receptor-like serine/threonine-protein kinase ERECTA. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis showed that the gene that encoded UDP-glycosyltransferase, UGT85A2, was significantly upregulated in columnar fruits as compared to spherical and oval fruits. The identification of molecular markers that are closely related to fruit-shape traits not only provides genetic data for areca breeding, but it also provides new insights into the shape formation mechanisms of drupes. Full article

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13 pages, 1075 KiB

Open AccessReview

Crucial Abiotic Stress Regulatory Network of NF-Y Transcription Factor in Plants

by Han Zhang, Shujing Liu, Tianmeng Ren, Mengxue Niu, Xiao Liu, Chao Liu, Houling Wang, Weilun Yin and Xinli Xia

Int. J. Mol. Sci. 2023, 24(5), 4426; https://doi.org/10.3390/ijms24054426 - 23 Feb 2023

Cited by 27 | Viewed by 3820

Abstract

Nuclear Factor-Y (NF-Y), composed of three subunits NF-YA, NF-YB and NF-YC, exists in most of the eukaryotes and is relatively conservative in evolution. As compared to animals and fungi, the number of NF-Y subunits has significantly expanded in higher plants. The NF-Y complex [...] Read more.

Nuclear Factor-Y (NF-Y), composed of three subunits NF-YA, NF-YB and NF-YC, exists in most of the eukaryotes and is relatively conservative in evolution. As compared to animals and fungi, the number of NF-Y subunits has significantly expanded in higher plants. The NF-Y complex regulates the expression of target genes by directly binding the promoter CCAAT box or by physical interaction and mediating the binding of a transcriptional activator or inhibitor. NF-Y plays an important role at various stages of plant growth and development, especially in response to stress, which attracted many researchers to explore. Herein, we have reviewed the structural characteristics and mechanism of function of NF-Y subunits, summarized the latest research on NF-Y involved in the response to abiotic stresses, including drought, salt, nutrient and temperature, and elaborated the critical role of NF-Y in these different abiotic stresses. Based on the summary above, we have prospected the potential research on NF-Y in response to plant abiotic stresses and discussed the difficulties that may be faced in order to provide a reference for the in-depth analysis of the function of NF-Y transcription factors and an in-depth study of plant responses to abiotic stress. Full article

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16 pages, 2542 KiB

Open AccessArticle

Small Cellular Particles from European Spruce Needle Homogenate

by Marko Jeran, Anna Romolo, Vesna Spasovski, Matej Hočevar, Urban Novak, Roman Štukelj, Vid Šuštar, Matic Kisovec, Apolonija Bedina Zavec, Ksenija Kogej, Aleš Iglič, Polonca Trebše and Veronika Kralj-Iglič

Int. J. Mol. Sci. 2023, 24(5), 4349; https://doi.org/10.3390/ijms24054349 - 22 Feb 2023

Cited by 1 | Viewed by 2364

Abstract

Small cellular particles (SCPs) are being considered for their role in cell-to-cell communication. We harvested and characterized SCPs from spruce needle homogenate. SCPs were isolated by differential ultracentrifugation. They were imaged by scanning electron microscope (SEM) and cryogenic transmission electron microscope (cryo TEM), [...] Read more.

Small cellular particles (SCPs) are being considered for their role in cell-to-cell communication. We harvested and characterized SCPs from spruce needle homogenate. SCPs were isolated by differential ultracentrifugation. They were imaged by scanning electron microscope (SEM) and cryogenic transmission electron microscope (cryo TEM), assessed for their number density and hydrodynamic diameter by interferometric light microscopy (ILM) and flow cytometry (FCM), total phenolic content (TPC) by UV-vis spectroscopy, and terpene content by gas chromatography-mass spectrometry (GC-MS). The supernatant after ultracentrifugation at 50,000× g contained bilayer-enclosed vesicles whereas in the isolate we observed small particles of other types and only a few vesicles. The number density of cell-sized particles (CSPs) (larger than 2 μm) and meso-sized particles (MSPs) (cca 400 nm–2 µm) was about four orders of magnitude lower than the number density of SCPs (sized below 500 nm). The average hydrodynamic diameter of SCPs measured in 10,029 SCPs was 161 ± 133 nm. TCP decreased considerably due to 5-day aging. Volatile terpenoid content was found in the pellet after 300× g. The above results indicate that spruce needle homogenate is a source of vesicles to be explored for potential delivery use. Full article

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17 pages, 345 KiB

Open AccessReview

Unraveling the Diverse Roles of Neglected Genes Containing Domains of Unknown Function (DUFs): Progress and Perspective

by Peiyun Lv, Jinlu Wan, Chunting Zhang, Aiman Hina, G M Al Amin, Naheeda Begum and Tuanjie Zhao

Int. J. Mol. Sci. 2023, 24(4), 4187; https://doi.org/10.3390/ijms24044187 - 20 Feb 2023

Cited by 15 | Viewed by 4224

Abstract

Domain of unknown function (DUF) is a general term for many uncharacterized domains with two distinct features: relatively conservative amino acid sequence and unknown function of the domain. In the Pfam 35.0 database, 4795 (24%) gene families belong to the DUF type, yet, [...] Read more.

Domain of unknown function (DUF) is a general term for many uncharacterized domains with two distinct features: relatively conservative amino acid sequence and unknown function of the domain. In the Pfam 35.0 database, 4795 (24%) gene families belong to the DUF type, yet, their functions remain to be explored. This review summarizes the characteristics of the DUF protein families and their functions in regulating plant growth and development, generating responses to biotic and abiotic stress, and other regulatory roles in plant life. Though very limited information is available about these proteins yet, by taking advantage of emerging omics and bioinformatic tools, functional studies of DUF proteins could be utilized in future molecular studies. Full article

17 pages, 5205 KiB

Open AccessArticle

Evolutionary Analysis of Respiratory Burst Oxidase Homolog (RBOH) Genes in Plants and Characterization of ZmRBOHs

by Haiyang Zhang, Xu Wang, An Yan, Jie Deng, Yanping Xie, Shiyuan Liu, Debin Liu, Lin He, Jianfeng Weng and Jingyu Xu

Int. J. Mol. Sci. 2023, 24(4), 3858; https://doi.org/10.3390/ijms24043858 - 14 Feb 2023

Cited by 13 | Viewed by 3400

Abstract

The respiratory burst oxidase homolog (RBOH), as the key producer of reactive oxygen species (ROS), plays an essential role in plant development. In this study, a bioinformatic analysis was performed on 22 plant species, and 181 RBOH homologues were identified. A typical RBOH [...] Read more.

The respiratory burst oxidase homolog (RBOH), as the key producer of reactive oxygen species (ROS), plays an essential role in plant development. In this study, a bioinformatic analysis was performed on 22 plant species, and 181 RBOH homologues were identified. A typical RBOH family was identified only in terrestrial plants, and the number of RBOHs increased from non-angiosperms to angiosperms. Whole genome duplication (WGD)/segmental duplication played a key role in RBOH gene family expansion. Amino acid numbers of 181 RBOHs ranged from 98 to 1461, and the encoded proteins had molecular weights from 11.1 to 163.6 kDa, respectively. All plant RBOHs contained a conserved NADPH_Ox domain, while some of them lacked the FAD_binding_8 domain. Plant RBOHs were classified into five main subgroups by phylogenetic analysis. Most RBOH members in the same subgroup showed conservation in both motif distribution and gene structure composition. Fifteen ZmRBOHs were identified in maize genome and were positioned in eight maize chromosomes. A total of three pairs of orthologous genes were found in maize, including ZmRBOH6/ZmRBOH8, ZmRBOH4/ZmRBOH10 and ZmRBOH15/ZmRBOH2. A Ka/Ks calculation confirmed that purifying selection was the main driving force in their evolution. ZmRBOHs had typical conserved domains and similar protein structures. cis-element analyses together with the expression profiles of the ZmRBOH genes in various tissues and stages of development suggested that ZmRBOH was involved in distinct biological processes and stress responses. Based on the RNA-Seq data and qRT-PCR analysis, the transcriptional response of ZmRBOH genes was examined under various abiotic stresses, and most of ZmRBOH genes were up-regulated by cold stress. These findings provide valuable information for further revealing the biological roles of ZmRBOH genes in plant development and abiotic stress responses. Full article

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14 pages, 3629 KiB

Open AccessArticle

Transcription Factor SiDi19-3 Enhances Salt Tolerance of Foxtail Millet and Arabidopsis

by Shenghui Xiao, Yiman Wan, Shiming Guo, Jiayin Fan, Qing Lin, Chengchao Zheng and Changai Wu

Int. J. Mol. Sci. 2023, 24(3), 2592; https://doi.org/10.3390/ijms24032592 - 30 Jan 2023

Cited by 4 | Viewed by 2122

Abstract

Salt stress is an important limiting factor of crop production. Foxtail millet (Setaria italica L.) is an important model crop for studying tolerance to various abiotic stressors. Therefore, examining the response of foxtail millet to salt stress at the molecular level is [...] Read more.

Salt stress is an important limiting factor of crop production. Foxtail millet (Setaria italica L.) is an important model crop for studying tolerance to various abiotic stressors. Therefore, examining the response of foxtail millet to salt stress at the molecular level is critical. Herein, we discovered that SiDi19-3 interacts with SiPLATZ12 to control salt tolerance in transgenic Arabidopsis and foxtail millet seedlings. SiDi19-3 overexpression increased the transcript levels of most Na⁺/H⁺ antiporter (NHX), salt overly sensitive (SOS), and calcineurin B-like protein (CBL) genes and improved the salt tolerance of foxtail millet and Arabidopsis. Six SiDi19 genes were isolated from foxtail millet. Compared with roots, stems, and leaves, panicles and seeds had higher transcript levels of SiDi19 genes. All of them responded to salt, alkaline, polyethylene glycol, and/or abscisic acid treatments with enhanced expression levels. These findings indicate that SiDi19-3 and other SiDi19 members regulate salt tolerance and other abiotic stress response in foxtail millet. Full article

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17 pages, 16457 KiB

Open AccessArticle

Functional Characterization of Potato UBC13-UEV1s Genes Required for Ubiquitin Lys63 Chain to Polyubiquitination

by Weigang Liu, Xun Tang, Xue Fu, Huanhuan Zhang, Cunlan Zhu, Ning Zhang and Huaijun Si

Int. J. Mol. Sci. 2023, 24(3), 2412; https://doi.org/10.3390/ijms24032412 - 26 Jan 2023

Viewed by 1893

Abstract

Ubiquitin-conjugating enzymes (E2s/UBC) are components of the ubiquitin proteasome system (UPS), and the ubiquitin-conjugating enzyme variant (UEV) is one of E2s (ubiquitin-conjugating enzymes, UBC) subfamily. The UEVs and UBC13 play an auxiliary role in mediating Lys63-linked polyUb chain assembly, which is correlated with [...] Read more.

Ubiquitin-conjugating enzymes (E2s/UBC) are components of the ubiquitin proteasome system (UPS), and the ubiquitin-conjugating enzyme variant (UEV) is one of E2s (ubiquitin-conjugating enzymes, UBC) subfamily. The UEVs and UBC13 play an auxiliary role in mediating Lys63-linked polyUb chain assembly, which is correlated with target protein non-proteolytic functions, such as DNA repair or response to stress. However, the collaborative mechanism of StUBC13 (homologue of AtUBC13) and StUEVs (the UEVs in potato) involved in potato are not fully understood understood. Here, we identified two StUBC13 and seven StUEVs from potato genome. We analyzed protein motif and conserved domain, gene structure, phylogenetic features, cis-acting elements of StUBC13 and StUEVs. Subsequently, we screened StUBC13 partners protein and verified interaction between StUBC13 and StUEVs using yeast two-hybrid, split luciferase complementation (SLC) and bimolecular fluorescence complementation (BiFC) approach. The expression profile and qRT-PCR analysis suggested that StUBC13 and StUEVs gene exhibited a tissue-specific expression and were induced by different stress. Overall, this investigative study provides a comprehensive reference and view for further functional research on StUBC13 and StUEV1s in potato. Full article

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15 pages, 5435 KiB

Open AccessArticle

Genome-Wide Identification of Kiwifruit SGR Family Members and Functional Characterization of SGR2 Protein for Chlorophyll Degradation

by Juan Luo, Muhammad Abid, Yi Zhang, Xinxia Cai, Jing Tu, Puxin Gao, Zupeng Wang and Hongwen Huang

Int. J. Mol. Sci. 2023, 24(3), 1993; https://doi.org/10.3390/ijms24031993 - 19 Jan 2023

Cited by 5 | Viewed by 2272

Abstract

The STAY-GREEN (SGR) proteins play an important role in chlorophyll (Chl) degradation and are closely related to plant photosynthesis. However, the availability of inadequate studies on SGR motivated us to conduct a comprehensive study on the identification and functional dissection of SGR superfamily [...] Read more.

The STAY-GREEN (SGR) proteins play an important role in chlorophyll (Chl) degradation and are closely related to plant photosynthesis. However, the availability of inadequate studies on SGR motivated us to conduct a comprehensive study on the identification and functional dissection of SGR superfamily members in kiwifruit. Here, we identified five SGR genes for each of the kiwifruit species [Actinidia chinensis (Ac) and Actinidia eriantha (Ae)]. The phylogenetic analysis showed that the kiwifruit SGR superfamily members were divided into two subfamilies the SGR subfamily and the SGRL subfamily. The results of transcriptome data and RT-qPCR showed that the expression of the kiwifruit SGRs was closely related to light and plant developmental stages (regulated by plant growth regulators), which were further supported by the presence of light and the plant hormone-responsive cis-regulatory element in the promoter region. The subcellular localization analysis of the AcSGR2 protein confirmed its localization in the chloroplast. The Fv/Fm, SPAD value, and Chl contents were decreased in overexpressed AcSGR2, but varied in different cultivars of A. chinensis. The sequence analysis showed significant differences within AcSGR2 proteins. Our findings provide valuable insights into the characteristics and evolutionary patterns of SGR genes in kiwifruit, and shall assist kiwifruit breeders to enhance cultivar development. Full article

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22 pages, 3692 KiB

Open AccessArticle

Biology of Two-Spotted Spider Mite (Tetranychus urticae): Ultrastructure, Photosynthesis, Guanine Transcriptomics, Carotenoids and Chlorophylls Metabolism, and Decoyinine as a Potential Acaricide

by Ambra S. Parmagnani, Giuseppe Mannino, Carla Brillada, Mara Novero, Luca Dall’Osto and Massimo E. Maffei

Int. J. Mol. Sci. 2023, 24(2), 1715; https://doi.org/10.3390/ijms24021715 - 15 Jan 2023

Cited by 3 | Viewed by 2897

Abstract

Two-Spotted Spider Mites (TSSMs, Tetranychus urticae Koch 1836 (Acari: Tetranychidae)) is one of the most important pests in many crop plants, and their feeding activity is based on sucking leaf cell contents. The purpose of this study was to evaluate the interaction between [...] Read more.

Two-Spotted Spider Mites (TSSMs, Tetranychus urticae Koch 1836 (Acari: Tetranychidae)) is one of the most important pests in many crop plants, and their feeding activity is based on sucking leaf cell contents. The purpose of this study was to evaluate the interaction between TSSMs and their host Lima bean (Phaseolus lunatus) by analyzing the metabolomics of leaf pigments and the transcriptomics of TSSM guanine production. We also used epifluorescence, confocal laser scanning, and transmission electron microscopies to study the morphology and structure of TSSMs and their excreta. Finally, we evaluated the potential photosynthetic ability of TSSMs and the activity and content of Ribulose-1,5-bisphosphate Carboxylase/Oxigenase (RubisCO). We found that TSSMs express several genes involved in guanine production, including Guanosine Monophosphate Synthetase (GMPS) and decoyinine (DCY), a potential inhibitor of GMPS, was found to reduce TSSMs proliferation in infested Lima bean leaves. Despite the presence of intact chloroplasts and chlorophyll in TSSMs, we demonstrate that TSSMs do not retain any photosynthetic activity. Our results show for the first time the transcriptomics of guanine production in TSSMs and provide new insight into the catabolic activity of TSSMs on leaf chlorophyll and carotenoids. Finally, we preliminary demonstrate that DCY has an acaricidal potential against TSSMs. Full article

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18 pages, 1385 KiB

Open AccessReview

Basic Helix-Loop-Helix Transcription Factors: Regulators for Plant Growth Development and Abiotic Stress Responses

by Zhi-Fang Zuo, Hyo-Yeon Lee and Hong-Gyu Kang

Int. J. Mol. Sci. 2023, 24(2), 1419; https://doi.org/10.3390/ijms24021419 - 11 Jan 2023

Cited by 20 | Viewed by 4176

Abstract

Plant basic helix-loop-helix (bHLH) transcription factors are involved in many physiological processes, and they play important roles in the abiotic stress responses. The literature related to genome sequences has increased, with genome-wide studies on the bHLH transcription factors in plants. Researchers have detailed [...] Read more.

Plant basic helix-loop-helix (bHLH) transcription factors are involved in many physiological processes, and they play important roles in the abiotic stress responses. The literature related to genome sequences has increased, with genome-wide studies on the bHLH transcription factors in plants. Researchers have detailed the functionally characterized bHLH transcription factors from different aspects in the model plant Arabidopsis thaliana, such as iron homeostasis and abiotic stresses; however, other important economic crops, such as rice, have not been summarized and highlighted. The bHLH members in the same subfamily have similar functions; therefore, unraveling their regulatory mechanisms will help us to identify and understand the roles of some of the unknown bHLH transcription factors in the same subfamily. In this review, we summarize the available knowledge on functionally characterized bHLH transcription factors according to four categories: plant growth and development; metabolism synthesis; plant signaling, and abiotic stress responses. We also highlight the roles of the bHLH transcription factors in some economic crops, especially in rice, and discuss future research directions for possible genetic applications in crop breeding. Full article

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2022

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19 pages, 4655 KiB

Open AccessArticle

Accumulation of Anthocyanins in Detached Leaves of Kalanchoë blossfeldiana: Relevance to the Effect of Methyl Jasmonate on This Process

by Marian Saniewski, Joanna Szablińska-Piernik, Agnieszka Marasek-Ciołakowska, Joanna Mitrus, Justyna Góraj-Koniarska, Lesław B. Lahuta, Wiesław Wiczkowski, Kensuke Miyamoto, Junichi Ueda and Marcin Horbowicz

Int. J. Mol. Sci. 2023, 24(1), 626; https://doi.org/10.3390/ijms24010626 - 30 Dec 2022

Cited by 3 | Viewed by 2128

Abstract

Accumulation of anthocyanins in detached leaves and in excised stems of Kalanchoë blossfeldiana kept under natural light conditions in the presence or absence of methyl jasmonate (JA-Me) was investigated. When the abaxial surface of detached leaves was held lower than the adaxial surface [...] Read more.

Accumulation of anthocyanins in detached leaves and in excised stems of Kalanchoë blossfeldiana kept under natural light conditions in the presence or absence of methyl jasmonate (JA-Me) was investigated. When the abaxial surface of detached leaves was held lower than the adaxial surface (the normal or natural position) under natural light conditions, anthocyanins were not accumulated on the abaxial side of the leaves. In contrast, when the adaxial surface of detached leaves was held lower than the abaxial surface (inverted position), anthocyanins were highly accumulated on the abaxial side of the leaves. These phenomena were independent of the growth stage of K. blossfeldiana as well as photoperiod. Application of JA-Me in lanolin paste significantly inhibited anthocyanin accumulation induced on the abaxial side of detached leaves held in an inverted position in a dose-dependent manner. Anthocyanin accumulation in the excised stem in response to natural light was also significantly inhibited by JA-Me in lanolin paste. Possible mechanisms of anthocyanin accumulation on the abaxial side of detached K. blossfeldiana leaves held in an inverted position under natural light conditions and the inhibitory effect of JA-Me on this process are described. The accompanying changes in the content of primary metabolites and histological analyses were also described. Full article

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26 pages, 3502 KiB

Open AccessArticle

A Multi-Year, Multi-Cultivar Approach to Differential Expression Analysis of High- and Low-Protein Soybean (Glycine max)

by Julia C. Hooker, Nour Nissan, Doris Luckert, Martin Charette, Gerardo Zapata, François Lefebvre, Ramona M. Mohr, Ketema A. Daba, Thomas D. Warkentin, Mehri Hadinezhad, Brent Barlow, Anfu Hou, Ashkan Golshani, Elroy R. Cober and Bahram Samanfar

Int. J. Mol. Sci. 2023, 24(1), 222; https://doi.org/10.3390/ijms24010222 - 23 Dec 2022

Cited by 4 | Viewed by 2707

Abstract

Soybean (Glycine max (L.) Merr.) is among the most valuable crops based on its nutritious seed protein and oil. Protein quality, evaluated as the ratio of glycinin (11S) to β-conglycinin (7S), can play a role in food and feed quality. To help [...] Read more.

Soybean (Glycine max (L.) Merr.) is among the most valuable crops based on its nutritious seed protein and oil. Protein quality, evaluated as the ratio of glycinin (11S) to β-conglycinin (7S), can play a role in food and feed quality. To help uncover the underlying differences between high and low protein soybean varieties, we performed differential expression analysis on high and low total protein soybean varieties and high and low 11S soybean varieties grown in four locations across Eastern and Western Canada over three years (2018–2020). Simultaneously, ten individual differential expression datasets for high vs. low total protein soybeans and ten individual differential expression datasets for high vs. low 11S soybeans were assessed, for a total of 20 datasets. The top 15 most upregulated and the 15 most downregulated genes were extracted from each differential expression dataset and cross-examination was conducted to create shortlists of the most consistently differentially expressed genes. Shortlisted genes were assessed for gene ontology to gain a global appreciation of the commonly differentially expressed genes. Genes with roles in the lipid metabolic pathway and carbohydrate metabolic pathway were differentially expressed in high total protein and high 11S soybeans in comparison to their low total protein and low 11S counterparts. Expression differences were consistent between East and West locations with the exception of one, Glyma.03G054100. These data are important for uncovering the genes and biological pathways responsible for the difference in seed protein between high and low total protein or 11S cultivars. Full article

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17 pages, 5988 KiB

Open AccessArticle

Study on ZmRPN10 Regulating Leaf Angle in Maize by RNA-Seq

by Xiangzhuo Ji, Bingbing Jin, Zelong Zhuang, Fangguo Chang, Fang Wang and Yunling Peng

Int. J. Mol. Sci. 2023, 24(1), 189; https://doi.org/10.3390/ijms24010189 - 22 Dec 2022

Cited by 2 | Viewed by 2174

Abstract

Ubiquitin/proteasome-mediated proteolysis (UPP) plays a crucial role in almost all aspects of plant growth and development, proteasome subunit RPN10 mediates ubiquitination substrate recognition in the UPP process. The recognition pathway of ubiquitinated UPP substrate is different in different species, which indicates that the [...] Read more.

Ubiquitin/proteasome-mediated proteolysis (UPP) plays a crucial role in almost all aspects of plant growth and development, proteasome subunit RPN10 mediates ubiquitination substrate recognition in the UPP process. The recognition pathway of ubiquitinated UPP substrate is different in different species, which indicates that the mechanism and function of RPN10 are different in different species. However, the homologous ZmRPN10 in maize has not been studied. In this study, the changing of leaf angle and gene expression in leaves in maize wild-type B73 and mutant rpn10 under exogenous brassinosteroids (BRs) were investigated. The regulation effect of BR on the leaf angle of rpn10 was significantly stronger than that of B73. Transcriptome analysis showed that among the differentially expressed genes, CRE1, A-ARR and SnRK2 were significantly up-regulated, and PP2C, BRI1 AUX/IAA, JAZ and MYC2 were significantly down-regulated. This study revealed the regulation mechanism of ZmRPN10 on maize leaf angle and provided a promising gene resource for maize breeding. Full article

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20 pages, 4936 KiB

Open AccessArticle

GA-Mediated Disruption of RGA/BZR1 Complex Requires HSP90 to Promote Hypocotyl Elongation

by Panagiota Konstantinia Plitsi, Despina Samakovli, Loukia Roka, Aggeliki Rampou, Konstantinos Panagiotopoulos, Konstantinos Koudounas, Ioannis Isaioglou, Kosmas Haralampidis, Stamatis Rigas, Polydefkis Hatzopoulos and Dimitra Milioni

Int. J. Mol. Sci. 2023, 24(1), 88; https://doi.org/10.3390/ijms24010088 - 21 Dec 2022

Cited by 3 | Viewed by 2464

Abstract

Circuitries of signaling pathways integrate distinct hormonal and environmental signals, and influence development in plants. While a crosstalk between brassinosteroid (BR) and gibberellin (GA) signaling pathways has recently been established, little is known about other components engaged in the integration of the two [...] Read more.

Circuitries of signaling pathways integrate distinct hormonal and environmental signals, and influence development in plants. While a crosstalk between brassinosteroid (BR) and gibberellin (GA) signaling pathways has recently been established, little is known about other components engaged in the integration of the two pathways. Here, we provide supporting evidence for the role of HSP90 (HEAT SHOCK PROTEIN 90) in regulating the interplay of the GA and BR signaling pathways to control hypocotyl elongation of etiolated seedlings in Arabidopsis. Both pharmacological and genetic depletion of HSP90 alter the expression of GA biosynthesis and catabolism genes. Major components of the GA pathway, like RGA (REPRESSOR of ga1–3) and GAI (GA-INSENSITIVE) DELLA proteins, have been identified as physically interacting with HSP90. Interestingly, GA-promoted DELLA degradation depends on the ATPase activity of HSP90, and inhibition of HSP90 function stabilizes the DELLA/BZR1 (BRASSINAZOLE-RESISTANT 1) complex, modifying the expression of downstream transcriptional targets. Our results collectively reveal that HSP90, through physical interactions with DELLA proteins and BZR1, modulates DELLA abundance and regulates the expression of BZR1-dependent transcriptional targets to promote plant growth. Full article

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