International Journal of Molecular Sciences

Research

Jump to: Review

18 pages, 10362 KiB

Open AccessArticle

Genome-Wide Analysis of Tea FK506-Binding Proteins (FKBPs) Reveals That CsFKBP53 Enhances Cold-Stress Tolerance in Transgenic Arabidopsis thaliana

by Ming-Hui Xu, Jie Tang, Cai-Ning Liu, Wan-Qiao Zhang, Qian Li, Fan Yang and Dan-Dan Liu

Int. J. Mol. Sci. 2025, 26(8), 3575; https://doi.org/10.3390/ijms26083575 - 10 Apr 2025

Viewed by 272

Abstract

FK506-binding proteins (FKBPs) belong to the peptidyl-prolyl cis/trans isomerase (PPIase) superfamily and are involved in a wide range of biological processes including protein folding, hormone signaling, plant growth, and stress responses. However, the FKBPs and their biological functions have not been identified in [...] Read more.

FK506-binding proteins (FKBPs) belong to the peptidyl-prolyl cis/trans isomerase (PPIase) superfamily and are involved in a wide range of biological processes including protein folding, hormone signaling, plant growth, and stress responses. However, the FKBPs and their biological functions have not been identified in tea plants. In this study, 21 FKBP genes were identified using the conserved FK506-binding domain (PF00254) in the tea-plant genome. Their phylogeny, classification, structure, motifs, interactors, and expression patterns were analyzed. Comprehensive qRT-PCR analysis revealed distinct expression patterns of CsFKBPs in different tissues and in response to low temperature. Through a comprehensive genome-wide analysis, we characterized the low-temperature expression dynamics of the CsFKBP53 gene family and demonstrated that its overexpression significantly enhances cold tolerance in Arabidopsis. Notably, the transcript levels of CsFKBP53 exhibited pronounced variability across distinct tea (Camellia sinensis) cultivars under cold-stress conditions. These findings not only underscore the functional conservation of FKBP-type immunophilins across plant lineages but also highlight the biotechnological potential of CsFKBP53 as a genetic modulator of low-temperature resilience in crops. By integrating comparative genomics and functional validation, our study establishes a foundation for leveraging conserved stress-response mechanisms to engineer climate-resilient plants. Full article

(This article belongs to the Special Issue Plant Physiology and Molecular Nutrition)

► Show Figures

Figure 1

19 pages, 5554 KiB

Open AccessArticle

GAPDH Gene Family in Populus deltoides: Genome-Wide Identification, Structural Analysis, and Expression Analysis Under Drought Stress

by Hyemin Lim, Michael Immanuel Jesse Denison, Sathishkumar Natarajan, Kyungmi Lee, Changyoung Oh and Danbe Park

Int. J. Mol. Sci. 2025, 26(1), 335; https://doi.org/10.3390/ijms26010335 - 2 Jan 2025

Viewed by 876

Abstract

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is an enzyme widely involved in glycolysis in animal cells and in non-metabolic processes, including apoptosis and the regulation of gene expression. GAPDH is a ubiquitous protein that plays a pivotal role in plant metabolism and handling of stress responses. [...] Read more.

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is an enzyme widely involved in glycolysis in animal cells and in non-metabolic processes, including apoptosis and the regulation of gene expression. GAPDH is a ubiquitous protein that plays a pivotal role in plant metabolism and handling of stress responses. However, its function in plant stress resistance remains unknown. Identification and systematic analysis of the GAPDH family in Populus deltoides (P. deltoides) have not been performed. Bioinformatics methods were used to analyze the physicochemical characteristics, structural characteristics, phylogenetic relationships, gene structure, motif analysis, and expression of GAPDH gene family members in P. deltoides. We identified 12 GAPDH members in P. deltoides. Five types of PdGAPDH were identified: GAPA, GAPB, GAPC1, GAPC2, and GAPCp. PdGAPDH genes were differentially expressed in leaves, stems, and roots of 1-year-old poplar seedlings. PdGAPDH gene transcripts showed that PdGAPDH2 and PdGAPDH4 were highly expressed in the leaves. In the roots, seven genes—PdGAPDH01, PdGAPDH05, PdGAPDH06, PdGAPDH07, PdGAPDH08, PdGAPDH09, and PdGAPDH12—showed significantly high expression levels. PdGAPDH02, PdGAPDH03, PdGAPDH04, and PdGAPDH11 showed decreased expression under drought conditions and recovered after re-watering. These results lay the foundation for further studies on the drought stress mechanisms of P. deltoides. Full article

(This article belongs to the Special Issue Plant Physiology and Molecular Nutrition)

► Show Figures

Figure 1

20 pages, 3799 KiB

Open AccessArticle

Calcium and Magnesium Regulation of Kernel Sugar Content in Maize: Role of Endogenous Hormones and Antioxidant Enzymes

by Zhaoquan He, Xue Shang, Xiaoze Jin, Xiukang Wang and Yingying Xing

Int. J. Mol. Sci. 2025, 26(1), 200; https://doi.org/10.3390/ijms26010200 - 29 Dec 2024

Cited by 1 | Viewed by 858

Abstract

Ca and Mg are essential micronutrients for plant growth, and they play a crucial role in plant development and responses to adversity by influencing the activities of endogenous hormones and antioxidant enzymes. However, the specific mechanisms through which calcium (Ca) and magnesium (Mg) [...] Read more.

Ca and Mg are essential micronutrients for plant growth, and they play a crucial role in plant development and responses to adversity by influencing the activities of endogenous hormones and antioxidant enzymes. However, the specific mechanisms through which calcium (Ca) and magnesium (Mg) regulate the kernel sugar content through endogenous hormones and antioxidant enzymes remain unclear. In this study, we analyzed the impact of Ca and Mg on the physiology of maize leaves and kernel quality by determining the activities of antioxidant enzymes and endogenous hormones, and the kernel sugar content in maize leaves when supplemented with different levels of Ca and Mg. Our main findings were as follows: (1) Elevated Mg levels augmented superoxide dismutase (SOD) activity, bolstering antioxidant defenses, whereas low Ca and Mg levels diminished SOD activity. High Ca levels enhanced catalase (CAT) activity during kernel development. Low−Ca conditions stimulated gibberellin (GA) synthesis, while high−Ca and high−Mg conditions suppressed it. High Mg levels also elevated abscisic acid (ABA) levels, potentially improving stress tolerance. (2) High Ca levels increased the reducing sugar content in kernels, augmenting the energy supply, while both low and high Mg levels increased soluble sugars, with low Mg levels specifically enhancing the sucrose content, which is a critical energy reserve in plants. (3) CAT exerted a pivotal regulatory role in the sugar accumulation in maize kernels. GA, under the influence of Ca, modulated the sucrose and soluble sugar contents by inhibiting CAT, whereas ABA, under the influence of Mg, promoted CAT activity, thereby affecting the kernel sugar content. This study reveals a new mechanism through which the addition of Ca and Mg regulate the sugar content in maize kernels by affecting endogenous hormones and antioxidant enzyme activities. These findings not only enhance our understanding of the role of micronutrients in plant growth and development but also provide new strategies for improving crop yield and stress tolerance. Full article

(This article belongs to the Special Issue Plant Physiology and Molecular Nutrition)

► Show Figures

Figure 1

22 pages, 9563 KiB

Open AccessArticle

Identification of Kunitz-Type Inhibitor Gene Family of Populus yunnanensis Reveals a Stress Tolerance Function in Inverted Cuttings

by Haiyang Guo, Shaojie Ma, Xiaolin Zhang, Rong Xu, Cai Wang, Shihai Zhang, Lihong Zhao, Dan Li and Dan Zong

Int. J. Mol. Sci. 2025, 26(1), 188; https://doi.org/10.3390/ijms26010188 - 29 Dec 2024

Viewed by 797

Abstract

Plant protease inhibitors are a ubiquitous feature of plant species and exert a substantial influence on plant stress responses. However, the KTI (Kunitz trypsin inhibitor) family responding to abiotic stress has not been fully characterized in Populus yunnanensis. In this study, we [...] Read more.

Plant protease inhibitors are a ubiquitous feature of plant species and exert a substantial influence on plant stress responses. However, the KTI (Kunitz trypsin inhibitor) family responding to abiotic stress has not been fully characterized in Populus yunnanensis. In this study, we conducted a genome-wide study of the KTI family and analyzed their gene structure, gene duplication, conserved motifs, cis-acting elements, and response to stress treatment. A total of 29 KTIs were identified in the P. yunnanensis genome. Based on phylogenetic analysis, the PyKTIs were divided into four groups (1,2, 3, and 4). Promoter sequence analysis showed that the PyKTIs contain many cis-acting elements related to light, plant growth, hormone, and stress responses, indicating that PyKTIs are widely involved in various biological regulatory processes. RNA sequencing and real-time quantitative polymerase chain reaction analysis showed that KTI genes were differentially expressed under the inverted cutting stress of P. yunnanensis. Transcriptome analysis of P. yunnanensis leaves revealed that PyKTI16, PyKTI18, and PyKTI19 were highly upregulated after inverted cutting. Through the GEO query of Populus transcriptome data, KTI genes played a positive defense role in MeJa, drought, time series, and pathogen stress. This study provided comprehensive information for the KTI family in P. yunnanensis, which should be helpful for the functional characterization of P. yunnanensis KTI genes in the future. Full article

(This article belongs to the Special Issue Plant Physiology and Molecular Nutrition)

► Show Figures

Figure 1

19 pages, 10028 KiB

Open AccessArticle

Comparative Analysis of the Chloroplast Genomes of the Melliodendron (Styracaceae) Species: Providing Insights into Molecular Evolution and Phylogenetic Relationships

by Wei Dai, Haozhi Zheng, Menghan Xu, Xingli Zhu, Hui Long, Xiaogang Xu and Yanming Fang

Int. J. Mol. Sci. 2025, 26(1), 177; https://doi.org/10.3390/ijms26010177 - 28 Dec 2024

Viewed by 665

Abstract

Melliodendron xylocarpum is a member of the Styracaceae family, which is well-known for its remarkable ornamental and medicinal properties. In this research, we conducted comparative analysis of the chloroplast genomes from four samples of M. xylocarpum, representing Melliodendron. The results demonstrated that [...] Read more.

Melliodendron xylocarpum is a member of the Styracaceae family, which is well-known for its remarkable ornamental and medicinal properties. In this research, we conducted comparative analysis of the chloroplast genomes from four samples of M. xylocarpum, representing Melliodendron. The results demonstrated that the chloroplast genome of four M. xylocarpum samples ranging from 157,103 bp to 158,357 bp exhibited a typical quadripartite structure, including one large single-copy (LSC) region (90,131 bp to 90,342 bp), one small single-copy (SSC) region (18,467 bp to 18,785 bp), and two inverted repeat regions (IRs) (24,115 bp to 24,261 bp). Different levels of expansion and contraction were observed in the IR region of four M. xylocarpum samples. Besides, accD and ycf1 have been identified under positive selection, potentially linked to the adaptive response of Melliodendron to various environmental changes. Conflicting phylogenetic relationships were identified among various genera within the Styracaceae family in the phylogenetic tree constructed using CDS sequences and complete chloroplast genomes. Furthermore, the significance of a large sample size was also highlighted in this study for enhancing the accuracy of findings from phylogenetic analyses. The findings of this research will provide significant insights for future investigations into the evolutionary trends and conservation of the Melliodendron species. Full article

(This article belongs to the Special Issue Plant Physiology and Molecular Nutrition)

► Show Figures

Figure 1

15 pages, 2497 KiB

Open AccessArticle

Genome–Wide Transcriptional Profiling and Functional Analysis Reveal That OsPHT4;4 Is Critical for the Growth and Development of Rice

by Siyuan Li, Ruiyao Xu, Yaru Qiao, Yanglin Zhong, Xu He, Zhe Zhang, Shiqi Tian, Xue Yang, Lei Wu and Tiancheng Lu

Int. J. Mol. Sci. 2024, 25(23), 13087; https://doi.org/10.3390/ijms252313087 - 5 Dec 2024

Viewed by 808

Abstract

Phosphorus (P) is an essential macronutrient required for various vital processes in crop growth and development, including signal transduction, CO₂ fixation, and photosynthetic phosphorylation. Phosphate transporters (PHTs) in plants play critical roles in the uptake, distribution, and internal transport of Phosphate (Pi). [...] Read more.

Phosphorus (P) is an essential macronutrient required for various vital processes in crop growth and development, including signal transduction, CO₂ fixation, and photosynthetic phosphorylation. Phosphate transporters (PHTs) in plants play critical roles in the uptake, distribution, and internal transport of Phosphate (Pi). Among these transporters, the PHT4 family is widely distributed across plant species; however, the specific functions of many members within this family remain to be fully elucidated. This study focuses on unraveling the function of OsPHT4;4 in Pi utilization and photoprotection. The findings demonstrate that OsPHT4;4 acts as a low-affinity Pi transporter localized to the chloroplast membrane and reveal predominant expression of OsPHT4;4 in leaves, with peak expression during tillering and clear induction by light, exhibiting circadian rhythmicity. The ospht4;4 mutants display stunted growth. Transcriptomic analysis comparing ospht4;4 mutants and wild-types (WT) identified 1482 differentially expressed genes (DEGs), including 729 upregulated genes and 753 downregulated genes. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis reveals enrichment DEGs related to photosynthesis–antenna proteins, carbohydrate metabolism, and phenylpropanoid biosynthesis. These findings suggest that OsPHT4;4 plays crucial roles not only in photosynthesis but also in plant defense as an integral component involved in Pi metabolism. Full article

(This article belongs to the Special Issue Plant Physiology and Molecular Nutrition)

► Show Figures

Figure 1

15 pages, 3358 KiB

Open AccessArticle

Comparative Analysis of Mesocotyl Elongation Ability among Maize Inbred Lines

by Daxing Wen, Xiaoyu Tian, Chenglai Wu and Chunqing Zhang

Int. J. Mol. Sci. 2024, 25(22), 12437; https://doi.org/10.3390/ijms252212437 - 19 Nov 2024

Cited by 1 | Viewed by 788

Abstract

Mesocotyl plays a key role in the seedling emergence of maize; however, the mechanism of mesocotyl elongation is still unclear. Moreover, different maize inbred lines and cultivars have varied mesocotyl lengths positively correlated with deep sowing tolerance. In this study, we selected one [...] Read more.

Mesocotyl plays a key role in the seedling emergence of maize; however, the mechanism of mesocotyl elongation is still unclear. Moreover, different maize inbred lines and cultivars have varied mesocotyl lengths positively correlated with deep sowing tolerance. In this study, we selected one inbred line with long mesocotyl (LM) and two maize inbred lines with short mesocotyl (SM1 and SM2) from more than 400 maize inbred lines. The mesocotyl length of the LM line was about three-fold longer than those of the SM1 and SM2 lines. Microstructure observation showed that the reason for short mesocotyl in the SM1 and SM2 lines was few cell numbers and short cell length, respectively. Subsequently, we used RNA-seq to investigate the mechanism of mesocotyl elongation by regulating cell number and cell length at the transcriptome level. Compared with the LM line, the SM1 line displayed stronger downregulation of Cytochrome P450 and peroxidase genes than the SM2 line. Moreover, plant hormone signal transduction plays a vital role in mesocotyl elongation. Taken together, we propose a model for mesocotyl elongation of maize inbred lines with different cell lengths and cell numbers, which provide new insights into mesocotyl elongation in maize. Full article

(This article belongs to the Special Issue Plant Physiology and Molecular Nutrition)

► Show Figures

Figure 1

20 pages, 3802 KiB

Open AccessArticle

Mining of Oil Content Genes in Recombinant Maize Inbred Lines with Introgression from Temperate and Tropical Germplasm

by Mengfei Shi, Jiachen Sun, Fuyan Jiang, Ranjan K. Shaw, Babar Ijaz and Xingming Fan

Int. J. Mol. Sci. 2024, 25(19), 10813; https://doi.org/10.3390/ijms251910813 - 8 Oct 2024

Cited by 1 | Viewed by 1002

Abstract

The oil content of maize kernels is essential to determine its nutritional and economic value. A multiparent population (MPP) consisting of five recombinant inbred line (RIL) subpopulations was developed to elucidate the genetic basis of the total oil content (TOC) in maize. The [...] Read more.

The oil content of maize kernels is essential to determine its nutritional and economic value. A multiparent population (MPP) consisting of five recombinant inbred line (RIL) subpopulations was developed to elucidate the genetic basis of the total oil content (TOC) in maize. The MPP used the subtropical maize inbred lines CML312 and CML384, along with the tropical maize inbred lines CML395, YML46, and YML32 as the female parents, and Ye107 as the male parent. A genome-wide association study (GWAS) was performed using 429 RILs of the multiparent population across three environments, employing 584,847 high-quality single nucleotide polymorphisms (SNPs). Furthermore, linkage analysis was performed in the five subpopulations to identify quantitative trait loci (QTL) linked to TOC in maize. Through QTL mapping and GWAS, 18 QTLs and 60 SNPs that were significantly associated with TOC were identified. Two novel candidate genes, Zm00001d029550 and Zm00001d029551, related to TOC in maize and located on chromosome 1 were reported, which have not been previously reported. These genes are involved in biosynthesis, lipid signal transduction, plant development and metabolism, and stress responses, potentially influencing maize TOC. Haplotype analysis of Zm00001d029550 and Zm00001d029551 revealed that Hap3 could be considered a superior haplotype for increasing TOC in maize. A co-located SNP (SNP-75791466) on chromosome 1, located 5648 bp and 11,951 bp downstream of the candidate genes Zm00001d029550 and Zm00001d029551, respectively, was found to be expressed in various maize tissues. The highest expression was observed in embryos after pollination, indicating that embryos are the main tissue for oil accumulation in maize. This study provides a theoretical basis for understanding the genetic mechanisms underlying maize TOC and developing high-quality, high-oil maize varieties. Full article

(This article belongs to the Special Issue Plant Physiology and Molecular Nutrition)

► Show Figures

Figure 1

31 pages, 15181 KiB

Open AccessArticle

Transcriptomic and Metabolomic Profiling of Root Tissue in Drought-Tolerant and Drought-Susceptible Wheat Genotypes in Response to Water Stress

by Ling Hu, Xuemei Lv, Yunxiu Zhang, Wanying Du, Shoujin Fan and Lingan Kong

Int. J. Mol. Sci. 2024, 25(19), 10430; https://doi.org/10.3390/ijms251910430 - 27 Sep 2024

Cited by 1 | Viewed by 1460

Abstract

Wheat is the most widely grown crop in the world; its production is severely disrupted by increasing water deficit. Plant roots play a crucial role in the uptake of water and perception and transduction of water deficit signals. In the past decade, the [...] Read more.

Wheat is the most widely grown crop in the world; its production is severely disrupted by increasing water deficit. Plant roots play a crucial role in the uptake of water and perception and transduction of water deficit signals. In the past decade, the mechanisms of drought tolerance have been frequently reported; however, the transcriptome and metabolome regulatory network of root responses to water stress has not been fully understood in wheat. In this study, the global transcriptomic and metabolomics profiles were employed to investigate the mechanisms of roots responding to water stresses using the drought-tolerant (DT) and drought-susceptible (DS) wheat genotypes. The results showed that compared with the control group, wheat roots exposed to polyethylene glycol (PEG) had 25941 differentially expressed genes (DEGs) and more upregulated genes were found in DT (8610) than DS (7141). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the DEGs of the drought-tolerant genotype were preferably enriched in the flavonoid biosynthetic process, anthocyanin biosynthesis and suberin biosynthesis. The integrated analysis of the transcriptome and metabolome showed that in DT, the KEGG pathways, including flavonoid biosynthesis and arginine and proline metabolism, were shared by differentially accumulated metabolites (DAMs) and DEGs at 6 h after treatment (HAT) and pathways including alanine, aspartate, glutamate metabolism and carbon metabolism were shared at 48 HAT, while in DS, the KEGG pathways shared by DAMs and DEGs only included arginine and proline metabolism at 6 HAT and the biosynthesis of amino acids at 48 HAT. Our results suggest that the drought-tolerant genotype may relieve the drought stress by producing more ROS scavengers, osmoprotectants, energy and larger roots. Interestingly, hormone signaling plays an important role in promoting the development of larger roots and a higher capability to absorb and transport water in drought-tolerant genotypes. Full article

(This article belongs to the Special Issue Plant Physiology and Molecular Nutrition)

► Show Figures

Figure 1

15 pages, 2380 KiB

Open AccessArticle

NgAP2a Targets KCS Gene to Promote Lipid Accumulation in Nannochloropsis gaditana

by Yihua Lin, Yanyan Li, Xiaobin Wu, Weinan Xu, Zhengying Zhang, Hongmei Zhu and Hantao Zhou

Int. J. Mol. Sci. 2024, 25(19), 10305; https://doi.org/10.3390/ijms251910305 - 25 Sep 2024

Cited by 2 | Viewed by 957

Abstract

The commercialization of algal lipids and biofuels remains impractical due to the absence of lipogenic strains. As lipogenesis is regulated by a multitude of factors, the success in producing industrially suitable algal strains through conventional methods has been constrained. We present a new [...] Read more.

The commercialization of algal lipids and biofuels remains impractical due to the absence of lipogenic strains. As lipogenesis is regulated by a multitude of factors, the success in producing industrially suitable algal strains through conventional methods has been constrained. We present a new AP2 transcription factor, designated as NgAP2a, which, upon overexpression, leads to a significant increase in lipid storage in Nannochloropsis gaditana while maintaining the integrity of other physiological functions. These provide methodologies for enhancing petroleum output and optimizing the carbon fluxes associated with specific products. An integrated analysis of RNA sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) data has elucidated that the NgAP2a-induced up-regulation of critical genes is implicated in lipogenesis. Specifically, NgAP2a has been demonstrated to directly bind to the M1 motif situated within the promoter region of the KCS gene, thereby promoting the transcriptional activation of genes pertinent to lipid metabolism. In summary, we elucidate a plausible pathway whereby NgAP2a serves as a direct modulator of the KCS gene (Naga_100083g23), thereby influencing the expression levels of genes and molecules associated with lipid biosynthesis. Full article

(This article belongs to the Special Issue Plant Physiology and Molecular Nutrition)

► Show Figures

Figure 1

16 pages, 3787 KiB

Open AccessArticle

Functional Study on the Key Gene LaLBD37 Related to the Lily Bulblets Formation

by Xinru Hou, Kewen Zhang and Yingmin Lyu

Int. J. Mol. Sci. 2024, 25(17), 9456; https://doi.org/10.3390/ijms25179456 - 30 Aug 2024

Cited by 1 | Viewed by 961

Abstract

Oriental hybrid lilies, known for their vibrant colors, diverse flower shapes, and long blooming seasons, require annual bulb propagation in horticultural production. This necessity can lead to higher production costs and limit their use in landscaping. The LA hybrid lily ‘Aladdin’ has shown [...] Read more.

Oriental hybrid lilies, known for their vibrant colors, diverse flower shapes, and long blooming seasons, require annual bulb propagation in horticultural production. This necessity can lead to higher production costs and limit their use in landscaping. The LA hybrid lily ‘Aladdin’ has shown strong self-reproduction capabilities in optimal cultivation environments, producing numerous high-quality underground stem bulblets. This makes it a valuable model for studying bulblet formation in lilies under natural conditions. Through transcriptome data analysis of different developmental stages of ‘Aladdin’ bulblets, the LaLBD37 gene, linked to bulblet formation, was identified. Bioinformatics analysis, subcellular localization studies, and transcriptional activation activity tests were conducted to understand the characteristics of LaLBD37. By introducing the LaLBD37 gene into ‘Sorbonne’ aseptic seedlings via Agrobacterium-mediated transformation, resistant plants were obtained. Positive plants were identified through various methods such as GUS activity detection, PCR, and fluorescence quantitative PCR. Phenotypic changes in positive plants were observed, and various physiological indicators were measured to confirm the role of LaLBD37 in bulblet formation, including soluble sugar content, starch content, sucrose synthase activity, and endogenous hormone levels. The findings suggest that the LaLBD37 gene plays a significant role in promoting the development of lily bulblets, offering insights for enhancing the reproductive capacity of Oriental hybrid lilies and exploring the molecular mechanisms involved in lily bulb regeneration. Full article

(This article belongs to the Special Issue Plant Physiology and Molecular Nutrition)

► Show Figures

Figure 1

24 pages, 3803 KiB

Open AccessArticle

Proteomic Profiling of Cocos nucifera L. Zygotic Embryos during Maturation of Dwarf and Tall Cultivars: The Dynamics of Carbohydrate and Fatty Acid Metabolism

by María Inés Granados-Alegría, Blondy Canto-Canché, Rufino Gómez-Tah, Jean Wildort Félix, Miguel Tzec-Simá, Eliel Ruiz-May and Ignacio Islas-Flores

Int. J. Mol. Sci. 2024, 25(15), 8507; https://doi.org/10.3390/ijms25158507 - 4 Aug 2024

Viewed by 1579

Abstract

There is a limited number of studies analyzing the molecular and biochemical processes regulating the metabolism of the maturation of Cocos nucifera L. zygotic embryos. Our research focused on the regulation of carbohydrate and lipid metabolic pathways occurring at three developmental stages of [...] Read more.

There is a limited number of studies analyzing the molecular and biochemical processes regulating the metabolism of the maturation of Cocos nucifera L. zygotic embryos. Our research focused on the regulation of carbohydrate and lipid metabolic pathways occurring at three developmental stages of embryos from the Mexican Pacific tall (MPT) and the Yucatan green dwarf (YGD) cultivars. We used the TMT-synchronous precursor selection (SPS)-MS3 strategy to analyze the dynamics of proteomes from both embryos; 1044 and 540 proteins were determined for the MPT and YGD, respectively. A comparison of the differentially accumulated proteins (DAPs) revealed that the biological processes (BP) enriched in the MPT embryo included the glyoxylate and dicarboxylate metabolism along with fatty acid degradation, while in YGD, the nitrogen metabolism and pentose phosphate pathway were the most enriched BPs. Findings suggest that the MPT embryos use fatty acids to sustain a higher glycolytic/gluconeogenic metabolism than the YGD embryos. Moreover, the YGD proteome was enriched with proteins associated with biotic or abiotic stresses, e.g., peroxidase and catalase. The goal of this study was to highlight the differences in the regulation of carbohydrate and lipid metabolic pathways during the maturation of coconut YGD and MPT zygotic embryos. Full article

(This article belongs to the Special Issue Plant Physiology and Molecular Nutrition)

► Show Figures

Graphical abstract

19 pages, 17951 KiB

Open AccessArticle

Genome-Wide Identification and Analysis of SUS and AGPase Family Members in Sweet Potato: Response to Excessive Nitrogen Stress during Storage Root Formation

by Shaoxuan Han, Yanhui Lin, Yayi Meng and Chengcheng Si

Int. J. Mol. Sci. 2024, 25(15), 8236; https://doi.org/10.3390/ijms25158236 - 28 Jul 2024

Cited by 2 | Viewed by 1423

Abstract

(1) The development of sweet potato storage roots is impacted by nitrogen (N) levels, with excessive nitrogen often impeding development. Starch synthesis enzymes such as sucrose synthase (SUS) and ADP-glucose pyrophosphorylase (AGPase) are pivotal in this context. Although the effects of excessive nitrogen [...] Read more.

(1) The development of sweet potato storage roots is impacted by nitrogen (N) levels, with excessive nitrogen often impeding development. Starch synthesis enzymes such as sucrose synthase (SUS) and ADP-glucose pyrophosphorylase (AGPase) are pivotal in this context. Although the effects of excessive nitrogen on the formation of sweet potato storage roots are well documented, the specific responses of IbSUSs and IbAGPases have not been extensively reported on. (2) Pot experiments were conducted using the sweet potato cultivar “Pushu 32” at moderate (MN, 120 kg N ha⁻¹) and excessive nitrogen levels (EN, 240 kg N ha⁻¹). (3) Nine IbSUS and nine IbAGPase genes were categorized into three and two distinct subgroups based on phylogenetic analysis. Excessive nitrogen significantly (p < 0.05) suppressed the expression of IbAGPL1, IbAGPL2, IbAGPL4, IbAGPL5, IbAGPL6, IbAGPS1, and IbAGPS2 in fibrous roots and IbSUS2, IbSUS6, IbSUS7, IbSUS8, IbSUS9, IbAGPL2, and IbAGPL4 in storage roots, and then significantly (p < 0.05) decreased the SUS and AGPase activities and starch content of fibrous root and storage root, ultimately reducing the storage root formation of sweet potato. Excessive nitrogen extremely significantly (p < 0.01) enhanced the expression of IbAGPL3, which was strongly negatively correlated with the number and weight of storage roots per plant. (4) IbAGPL3 may be a key gene in the response to excessive nitrogen stress and modifying starch synthesis in sweet potato. Full article

(This article belongs to the Special Issue Plant Physiology and Molecular Nutrition)

► Show Figures

Figure 1

21 pages, 4905 KiB

Open AccessArticle

Differential Transcription Profiling Reveals the MicroRNAs Involved in Alleviating Damage to Photosynthesis under Drought Stress during the Grain Filling Stage in Wheat

by Ruixiang Zhou, Yuhang Song, Xinyu Xue, Ruili Xue, Haifang Jiang, Yi Zhou, Xueli Qi and Yuexia Wang

Int. J. Mol. Sci. 2024, 25(10), 5518; https://doi.org/10.3390/ijms25105518 - 18 May 2024

Cited by 5 | Viewed by 1811

Abstract

To explore the possible novel microRNA (miRNA) regulatory pathways in Zhengmai 1860, a newly cultivated drought-tolerant wheat (Triticum aestivum L.) cultivar, miRNA transcriptome sequencing of the flag leaves of Zhengmai 1860, drought-sensitive variety Zhoumai 18, and drought-resistant variety Bainong 207 was performed [...] Read more.

To explore the possible novel microRNA (miRNA) regulatory pathways in Zhengmai 1860, a newly cultivated drought-tolerant wheat (Triticum aestivum L.) cultivar, miRNA transcriptome sequencing of the flag leaves of Zhengmai 1860, drought-sensitive variety Zhoumai 18, and drought-resistant variety Bainong 207 was performed during the grain filling stage. We also observed changes in the chloroplast ultrastructure, phytohormone levels, and antioxidant- and photosynthesis-related physiological indicators in three wheat varieties. The results showed that the flag leaves of the drought-tolerant variety Zhengmai 1860 had higher chlorophyll contents and net photosynthetic rates than those of Zhoumai 18 under drought stress during the grain filling stage; in addition, the chloroplast structure was more complete. However, there was no significant difference between Zhengmai 1860 and Bainong 207. MiRNA transcriptome analysis revealed that the differential expression of the miRNAs and mRNAs exhibited variable specificity. The KEGG pathway enrichment results indicated that most of the genes were enriched in the MAPK signaling pathway, plant hormone signal transduction, photosynthetic antennae protein, and amino acid and carbohydrate metabolism. In the drought-tolerant cultivar Zhengmai 1860, tae-miR408 was targeted to regulate the allene oxide synthase (AOS) gene, inhibit its expression, reduce the AOS content, and decrease the synthesis of jasmonic acid (JA) and abscisic acid (ABA). The results of this study suggest that Zhengmai 1860 could improve the photosynthetic performance of flag leaves by inhibiting the expression of genes involved in the JA pathway through miRNAs under drought conditions. Moreover, multiple miRNAs may target chlorophyll, antioxidant enzymes, phytohormone signal transduction, and other related pathways; thus, it is possible to provide a more theoretical basis for wheat molecular breeding. Full article

(This article belongs to the Special Issue Plant Physiology and Molecular Nutrition)

► Show Figures

Figure 1

12 pages, 6745 KiB

Open AccessArticle

Cytological, Phytohormone, and Transcriptome Analyses Provide Insights into Persimmon Fruit Shape Formation (Diospyros kaki Thunb.)

by Huawei Li, Yujing Suo, Hui Li, Peng Sun, Weijuan Han and Jianmin Fu

Int. J. Mol. Sci. 2024, 25(9), 4812; https://doi.org/10.3390/ijms25094812 - 28 Apr 2024

Cited by 2 | Viewed by 1147

Abstract

Fruit shape is an important external feature when consumers choose their preferred fruit varieties. Studying persimmon (Diospyros kaki Thunb.) fruit shape is beneficial to increasing its commodity value. However, research on persimmon fruit shape is still in the initial stage. In this [...] Read more.

Fruit shape is an important external feature when consumers choose their preferred fruit varieties. Studying persimmon (Diospyros kaki Thunb.) fruit shape is beneficial to increasing its commodity value. However, research on persimmon fruit shape is still in the initial stage. In this study, the mechanism of fruit shape formation was studied by cytological observations, phytohormone assays, and transcriptome analysis using the long fruit and flat fruit produced by ‘Yaoxianwuhua’ hermaphroditic flowers. The results showed that stage 2–3 (June 11–June 25) was the critical period for persimmon fruit shape formation. Persimmon fruit shape is determined by cell number in the transverse direction and cell length in the longitudinal direction. High IAA, GA₄, ZT, and BR levels may promote long fruit formation by promoting cell elongation in the longitudinal direction, and high GA₃ and ABA levels may be more conducive to flat fruit formation by increasing the cell number in the transverse direction and inhibiting cell elongation in the longitudinal direction, respectively. Thirty-two DEGs related to phytohormone biosynthesis and signaling pathways and nine DEGs related to cell division and cell expansion may be involved in the persimmon fruit shape formation process. These results provide valuable information for regulatory mechanism research on persimmon fruit formation. Full article

(This article belongs to the Special Issue Plant Physiology and Molecular Nutrition)

► Show Figures

Figure 1

16 pages, 6070 KiB

Open AccessArticle

Genome-Wide Identification and Expression Analysis of Kiwifruit Leucine-Rich Repeat Receptor-Like Proteins Reveal Their Roles in Biotic and Abiotic Stress Responses

by Yingying Cao, Congxiao Zhang, Fang Liu, Dawei Li, Aidi Zhang, Li Li and Xiujun Zhang

Int. J. Mol. Sci. 2024, 25(8), 4497; https://doi.org/10.3390/ijms25084497 - 19 Apr 2024

Cited by 2 | Viewed by 1637

Abstract

Leucine-rich repeat receptor-like proteins (LRR-RLPs), a major group of receptor-like proteins in plants, have diverse functions in plant physiology, including growth, development, signal transduction, and stress responses. Despite their importance, the specific roles of kiwifruit LRR-RLPs in response to biotic and [...] Read more.

Leucine-rich repeat receptor-like proteins (LRR-RLPs), a major group of receptor-like proteins in plants, have diverse functions in plant physiology, including growth, development, signal transduction, and stress responses. Despite their importance, the specific roles of kiwifruit LRR-RLPs in response to biotic and abiotic stresses remain poorly understood. In this study, we performed family identification, characterization, transcriptome data analysis, and differential gene expression analysis of kiwifruit LRR-RLPs. We identified totals of 101, 164, and 105 LRR-RLPs in Actinidia chinensis ‘Hongyang’, Actinidia eriantha ‘Huate’, and Actinidia chinensis ‘Red5’, respectively. Synteny analysis revealed that the expansion of kiwifruit LRR-RLPs was primarily attributed to segmental duplication events. Based on RNA-seq data from pathogen-infected kiwifruits, we identified specific LRR-RLP genes potentially involved in different stages of pathogen infection. Additionally, we observed the potential involvement of kiwifruit LRR-RLPs in abiotic stress responses, with upstream transcription factors possibly regulating their expression. Furthermore, protein interaction network analysis unveiled the participation of kiwifruit LRR-RLP in the regulatory network of abiotic stress responses. These findings highlight the crucial roles of LRR-RLPs in mediating both biotic and abiotic stress responses in kiwifruit, offering valuable insights for the breeding of stress-resistant kiwifruit varieties. Full article

(This article belongs to the Special Issue Plant Physiology and Molecular Nutrition)

► Show Figures

Figure 1

16 pages, 11538 KiB

Open AccessArticle

Molecular Mechanism of Different Rooting Capacity between Two Clones of Taxodium hybrid ‘Zhongshanshan’

by Jiaqi Liu, Lei Xuan, Chaoguang Yu, Jianfeng Hua, Ziyang Wang, Yunlong Yin and Zhiquan Wang

Int. J. Mol. Sci. 2024, 25(4), 2427; https://doi.org/10.3390/ijms25042427 - 19 Feb 2024

Cited by 1 | Viewed by 1293

Abstract

The conifer Taxodium hybrid ‘Zhongshanshan’ (T. hybrid ‘Zhongshanshan’) is characterized by rapid growth, strong stress resistance, and high ornamental value and has significant potential for use in afforestation, landscaping, and wood production. The main method of propagating T. hybrid ‘Zhongshanshan’ is tender branch cutting, but [...] Read more.

The conifer Taxodium hybrid ‘Zhongshanshan’ (T. hybrid ‘Zhongshanshan’) is characterized by rapid growth, strong stress resistance, and high ornamental value and has significant potential for use in afforestation, landscaping, and wood production. The main method of propagating T. hybrid ‘Zhongshanshan’ is tender branch cutting, but the cutting rooting abilities of different T. hybrid ‘Zhongshanshan’ clones differ significantly. To explore the causes of rooting ability differences at a molecular level, we analyzed the transcriptome data of cutting base and root tissues of T. hybrid ‘Zhongshanshan 149’ with a rooting rate of less than 5% and T. hybrid ‘Zhongshanshan 118’ with rooting rate greater than 60%, at the developmental time points in this study. The results indicated that differentially expressed genes between the two clones were mainly associated with copper ion binding, peroxidase, and oxidoreductase activity, response to oxidative stress, phenylpropanoid and flavonoid biosynthesis, and plant hormone signal transduction, among others. The expression pattern of ThAP2 was different throughout the development of the adventitive roots of the two clone cuttings. Therefore, this gene was selected for further study. It was shown that ThAP2 was a nuclear-localized transcription factor and demonstrated a positive feedback effect on rooting in transgenic Nicotiana benthamiana cuttings. Thus, the results of this study explain the molecular mechanism of cutting rooting and provide candidate gene resources for developing genetic breeding strategies for optimizing superior clones of T. hybrid ‘Zhongshanshan’. Full article

(This article belongs to the Special Issue Plant Physiology and Molecular Nutrition)

► Show Figures

Figure 1

19 pages, 7820 KiB

Open AccessArticle

SlERF109-like and SlNAC1 Coordinately Regulated Tomato Ripening by Inhibiting ACO1 Transcription

by Chen Sun, Gaifang Yao, Jinghan Zhao, Ruying Chen, Kangdi Hu, Guanghua He and Hua Zhang

Int. J. Mol. Sci. 2024, 25(3), 1873; https://doi.org/10.3390/ijms25031873 - 3 Feb 2024

Cited by 1 | Viewed by 1931

Abstract

As a typical climacteric fruit, tomato (Solanum lycopersicum) is widely used for studying the ripening process. The negative regulation of tomato fruits by transcription factor SlNAC1 has been reported, but its regulatory network was unclear. In the present study, we screened [...] Read more.

As a typical climacteric fruit, tomato (Solanum lycopersicum) is widely used for studying the ripening process. The negative regulation of tomato fruits by transcription factor SlNAC1 has been reported, but its regulatory network was unclear. In the present study, we screened a transcription factor, SlERF109-like, and found it had a stronger relationship with SlNAC1 at the early stage of tomato fruit development through the use of transcriptome data, RT-qPCR, and correlation analysis. We inferred that SlERF109-like could interact with SlNAC1 to become a regulatory complex that co-regulates the tomato fruit ripening process. Results of transient silencing (VIGS) and transient overexpression showed that SlERF109-like and SlNAC1 could regulate chlorophyll degradation-related genes (NYC1, PAO, PPH, SGR1), carotenoids accumulation-related genes (PSY1, PDS, ZDS), ETH-related genes (ACO1, E4, E8), and cell wall metabolism-related genes expression levels (CEL2, EXP, PG, TBG4, XTH5) to inhibit tomato fruit ripening. A dual-luciferase reporter and yeast one-hybrid (Y1H) showed that SlNAC1 could bind to the SlACO1 promoter, but SlERF109-like could not. Furthermore, SlERF109-like could interact with SlNAC1 to increase the transcription for ACO1 by a yeast two-hybrid (Y2H) assay, a luciferase complementation assay, and a dual-luciferase reporter. A correlation analysis showed that SlERF109-like and SlNAC1 were positively correlated with chlorophyll contents, and negatively correlated with carotenoid content and ripening-related genes. Thus, we provide a model in which SlERF109-like could interact with SlNAC1 to become a regulatory complex that negatively regulates the tomato ripening process by inhibiting SlACO1 expression. Our study provided a new regulatory network of tomato fruit ripening and effectively reduced the waste of resources. Full article

(This article belongs to the Special Issue Plant Physiology and Molecular Nutrition)

► Show Figures

Figure 1

13 pages, 4584 KiB

Open AccessArticle

The Impact of Various Organic Phosphorus Carriers on the Uptake and Use Efficiency in Barley

by Yuanfeng Huo, Jingyue Wang, Yinggang Xu, Deyi Hu, Kexian Zhang, Bingjie Chen, Yueyi Wu, Jiaxin Liu, Tianlang Yan, Yang Li, Chaorui Yan, Xuesong Gao, Shu Yuan and Guangdeng Chen

Int. J. Mol. Sci. 2023, 24(24), 17191; https://doi.org/10.3390/ijms242417191 - 6 Dec 2023

Cited by 1 | Viewed by 1587

Abstract

Organic phosphorus (OP) is an essential component of the soil P cycle, which contributes to barley nutrition after its mineralization into inorganic phosphorus (Pi). However, the dynamics of OP utilization in the barley rhizosphere remain unclear. In this study, phytin was screened out [...] Read more.

Organic phosphorus (OP) is an essential component of the soil P cycle, which contributes to barley nutrition after its mineralization into inorganic phosphorus (Pi). However, the dynamics of OP utilization in the barley rhizosphere remain unclear. In this study, phytin was screened out from six OP carriers, which could reflect the difference in OP utilization between a P-inefficient genotype Baudin and a P-efficient genotype CN4027. The phosphorus utilization efficiency (PUE), root morphological traits, and expression of genes associated with P utilization were assessed under P deficiency or phytin treatments. P deficiency resulted in a greater root surface area and thicker roots. In barley fed with phytin as a P carrier, the APase activities of CN4027 were 2–3-fold lower than those of Baudin, while the phytase activities of CN4027 were 2–3-fold higher than those of Baudin. The PUE in CN4027 was mainly enhanced by activating phytase to improve the root absorption and utilization of Pi resulting from OP mineralization, while the PUE in Baudin was mainly enhanced by activating APase to improve the shoot reuse capacity. A phosphate transporter gene HvPHT1;8 regulated P transport from the roots to the shoots, while a purple acid phosphatase (PAP) family gene HvPAPhy_b contributed to the reuse of P in barley. Full article

(This article belongs to the Special Issue Plant Physiology and Molecular Nutrition)

► Show Figures

Figure 1

Review

Jump to: Research

17 pages, 885 KiB

Open AccessReview

Phenotype Assessment and Putative Mechanisms of Ammonium Toxicity to Plants

by Lin-Bei Xie, Li-Na Sun, Zhong-Wei Zhang, Yang-Er Chen, Ming Yuan and Shu Yuan

Int. J. Mol. Sci. 2025, 26(6), 2606; https://doi.org/10.3390/ijms26062606 - 13 Mar 2025

Viewed by 454

Abstract

Ammonium (NH₄⁺) and nitrate (NO₃⁻) are the primary inorganic nitrogen (N) sources that exert influence on plant growth and development. Nevertheless, when NH₄⁺ constitutes the sole or dominant N source, it can inhibit plant growth, [...] Read more.

Ammonium (NH₄⁺) and nitrate (NO₃⁻) are the primary inorganic nitrogen (N) sources that exert influence on plant growth and development. Nevertheless, when NH₄⁺ constitutes the sole or dominant N source, it can inhibit plant growth, a process also known as ammonium toxicity. Over multiple decades, researchers have shown increasing interest in the primary causes, mechanisms, and detoxification strategies of ammonium toxicity. Despite this progress, the current investigations into the mechanisms of ammonium toxicity remain equivocal. This review initially presents a comprehensive assessment of phenotypes induced by ammonium toxicity. Additionally, this review also recapitulates the existing mechanisms of ammonium toxicity, such as ion imbalance, disruption of the phytohormones homeostasis, ROS (reactive oxygen species) burst, energy expenditure, and rhizosphere acidification. We conclude that alterations in carbon–nitrogen (C-N) metabolism induced by high NH₄⁺ may be one of the main reasons for ammonium toxicity and that SnRK1 (Sucrose non-fermenting 1-related kinase) might be involved in this process. The insights proffered in this review will facilitate the exploration of NH₄⁺ tolerance mechanisms and the development of NH₄⁺-tolerant crops in agricultural industries. Full article

(This article belongs to the Special Issue Plant Physiology and Molecular Nutrition)

► Show Figures

Figure 1

13 pages, 732 KiB

Open AccessReview

Interaction of the Transcription Factors BES1/BZR1 in Plant Growth and Stress Response

by Xuehua Cao, Yanni Wei, Biaodi Shen, Linchuan Liu and Juan Mao

Int. J. Mol. Sci. 2024, 25(13), 6836; https://doi.org/10.3390/ijms25136836 - 21 Jun 2024

Cited by 8 | Viewed by 2162

Abstract

Bri1-EMS Suppressor 1 (BES1) and Brassinazole Resistant 1 (BZR1) are two key transcription factors in the brassinosteroid (BR) signaling pathway, serving as crucial integrators that connect various signaling pathways in plants. Extensive genetic and biochemical studies have revealed that BES1 and BZR1, along [...] Read more.

Bri1-EMS Suppressor 1 (BES1) and Brassinazole Resistant 1 (BZR1) are two key transcription factors in the brassinosteroid (BR) signaling pathway, serving as crucial integrators that connect various signaling pathways in plants. Extensive genetic and biochemical studies have revealed that BES1 and BZR1, along with other protein factors, form a complex interaction network that governs plant growth, development, and stress tolerance. Among the interactome of BES1 and BZR1, several proteins involved in posttranslational modifications play a key role in modifying the stability, abundance, and transcriptional activity of BES1 and BZR1. This review specifically focuses on the functions and regulatory mechanisms of BES1 and BZR1 protein interactors that are not involved in the posttranslational modifications but are crucial in specific growth and development stages and stress responses. By highlighting the significance of the BZR1 and BES1 interactome, this review sheds light on how it optimizes plant growth, development, and stress responses. Full article

(This article belongs to the Special Issue Plant Physiology and Molecular Nutrition)

► Show Figures

Figure 1

15 pages, 1061 KiB

Open AccessReview

Nitrate Signaling and Its Role in Regulating Flowering Time in Arabidopsis thaliana

by Mengyun Wang, Jia Wang, Zeneng Wang and Yibo Teng

Int. J. Mol. Sci. 2024, 25(10), 5310; https://doi.org/10.3390/ijms25105310 - 13 May 2024

Cited by 2 | Viewed by 1809

Abstract

Plant growth is coordinated with the availability of nutrients that ensure its development. Nitrate is a major source of nitrogen (N), an essential macronutrient for plant growth. It also acts as a signaling molecule to modulate gene expression, metabolism, and a variety of [...] Read more.

Plant growth is coordinated with the availability of nutrients that ensure its development. Nitrate is a major source of nitrogen (N), an essential macronutrient for plant growth. It also acts as a signaling molecule to modulate gene expression, metabolism, and a variety of physiological processes. Recently, it has become evident that the calcium signal appears to be part of the nitrate signaling pathway. New key players have been discovered and described in Arabidopsis thaliana (Arabidopsis). In addition, knowledge of the molecular mechanisms of how N signaling affects growth and development, such as the nitrate control of the flowering process, is increasing rapidly. Here, we review recent advances in the identification of new components involved in nitrate signal transduction, summarize newly identified mechanisms of nitrate signaling-modulated flowering time in Arabidopsis, and suggest emerging concepts and existing open questions that will hopefully be informative for further discoveries. Full article

(This article belongs to the Special Issue Plant Physiology and Molecular Nutrition)

► Show Figures

Figure 1

Journal Menu

Journal Browser

Plant Physiology and Molecular Nutrition

Share This Special Issue

Special Issue Editors

Special Issue Information

Keywords

Benefits of Publishing in a Special Issue

Related Special Issue

Published Papers (22 papers)

Research

Review

Further Information

Guidelines

MDPI Initiatives

Follow MDPI