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Advanced Plant Molecular Responses to Abiotic Stresses

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: 20 May 2025 | Viewed by 7676

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Dr. Dong-Gwan Kim

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1. Department of Bioindustry and Bioresource Engineering, Department of Bioindustry and Bioresource Engineering, Sejong University, Seoul, Republic of Korea
2. Plant Engineering Research Institute, Sejong University, Seoul 143-747, Republic of Korea
Interests: environmental stresses to plant; phytoremediation; CRISPR/Cas9; plant molecular biology; plant physiology

Special Issue Information

Dear Colleagues,

Plants always encounter stressful circumstances from germination to death, such as light, water, salts, temperature, and nutrient and biotic stresses, primarily affecting the plant’s growth, development, and progeny. But, the plant itself always overcomes these stresses through molecular responses, which means recognition, signal transduction, transcription factor activation/deactivation responses, and finally gene expression. Plant gene expression helps to register or be tolerant and even overcome stressful environments. In addition, plant hormones are crucial compounds for regulating these kinds of target gene expressions.

This Special Issue aims to provide an advanced molecular mechanism on plant abiotic stress acclimation or adaptation with a special focus on the plant abiotic stress registance mechanism. I am confident that this Special Issue will help expand the understanding of the tolerance or overcome mechanism of abiotic stress in plants and further expand the molecular biological basis for researchers studying plant stress. We welcome all research papers or reviews containing molecular biological data.

Dr. Dong-Gwan Kim
Guest Editor

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Keywords

abiotic stress responses (heat, drought, salinity, nutrient deficiency, oxygen quality, flooding, light, etc.)
genetically modified plants
CRISPR/Cas-mediated stress overcome
microplastic/nanoparticle stresses
bioinformatic studies
miRNAs and other noncoding RNAs involved in abiotic stresses in plants
secondary metabolite synthesis

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Published Papers (10 papers)

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Research

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15 pages, 4045 KiB

Open AccessArticle

Comprehensive Evaluation and Construction of Drought Resistance Index System in Hulless Barley Seedlings

by Liping Niu, La Bo, Shuaihao Chen, Zhongmengyi Qin, Dawa Dondup, Lhundrup Namgyal, Xiruo Quzong, Zhuo Ga, Yanming Zhang, Yafei Shi and Xin Hou

Int. J. Mol. Sci. 2025, 26(8), 3799; https://doi.org/10.3390/ijms26083799 - 17 Apr 2025

Viewed by 157

Abstract

With global climate change ongoing, the frequency and intensity of extreme weather events have increased annually. Hulless barley (Hordeum vulgare L. var. nudum), a primary crop cultivated in the Qinghai–Tibet Plateau mountains, frequently encounters multiple abiotic stresses including low temperature, high salinity, and drought. Among these stresses, drought has emerged as a critical environmental constraint affecting sustainable agricultural development worldwide. Establishing a drought resistance evaluation system for the hulless barley germplasm during its seedling stages could provide a theoretical foundation for screening and breeding drought-tolerant cultivars to address climate change challenges. This study employed two drought-sensitive (YC85 and YC88) and two drought-tolerant (ZY1252 and ZY1100) cultivars to develop an effective drought resistance evaluation protocol for hulless barley. Our findings identified several reliable indicators for assessing drought tolerance at the seedling stage: fresh mass, chlorophyll fluorescence parameters (F_v/F_m, NPQ, and R_FD), photosynthetic parameters (E and gsw), and reactive oxygen species (ROS) levels. The established evaluation system was subsequently applied to three uncharacterized cultivars (ZY673, ZY1403, and KL14). The results classified all three as drought-sensitive, with ZY1403 exhibiting the highest sensitivity. Our work has established a comprehensive drought resistance evaluation framework for Tibetan hulless barley. Furthermore, this study provides valuable insights for optimizing cultivation practices and water resource management strategies, offering theoretical guidance for agricultural adaptation to climate change. Full article

(This article belongs to the Special Issue Advanced Plant Molecular Responses to Abiotic Stresses)

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21 pages, 6156 KiB

Open AccessArticle

Cloning and Functional Analysis of ZFP5 from Amorpha fruticosa for Enhancing Drought and Saline–Alkali Resistance in Tobacco

by Ziang Liu, Yu Yang, Lihua Yang, Bochun Wang, Xiaotong Gao, Shuchao Huang, Xiufeng Li, Chengjun Yang and Qingjie Guan

Int. J. Mol. Sci. 2025, 26(8), 3792; https://doi.org/10.3390/ijms26083792 - 17 Apr 2025

Viewed by 122

Abstract

Drought and soil salinization significantly constrain agricultural productivity, driving the need for molecular breeding strategies to enhance stress resistance. Zinc finger proteins play a critical role in plant response to abiotic stress. In this study, a gene encoding a C2H2-type zinc finger protein (AfZFP5) was cloned from Amorpha fruticosa, a species known for its strong adaptability. qRT-PCR analysis revealed that AfZFP5 expression is regulated by sorbitol, H₂O₂, NaCl, and NaHCO₃. And all four treatments can cause upregulation of AFZFP5 expression in the roots or leaves of Amorpha fruticosa within 48 h. Transgenic tobacco lines overexpressing AfZFP5 demonstrated enhanced tolerance to drought and salt–alkali stress at germination, seedling, and vegetative stages. Compared to wild-type plants, transgenic lines exhibited significantly higher germination rates, root lengths, and fresh weights when treated with sorbitol, NaCl, and NaHCO₃. Under natural drought and salt–alkali stress conditions, transgenic plants showed elevated activities of superoxide dismutase (SOD) and peroxidase (POD), and upregulated expression of oxidative stress-related kinase genes (NtSOD, NtPOD) during the vegetative stage. Additionally, transgenic tobacco displayed lower malondialdehyde (MDA) content and reduced staining levels with 3,3′diaminobenzidine (DAB) and Nitro blue tetrazolium (NBT), indicating enhanced reactive oxygen species (ROS) scavenging capacity by AfZFP5 upon salt–alkali stress. Under simulated drought with PEG6000 and salt–alkali stress, chlorophyll fluorescence intensity and Fv/Fm values in transgenic tobacco were significantly higher than in wild-type plants during the vegetative stage, suggesting that AfZFP5 mitigates stress-induced damage to the photosynthetic system. This study highlights the role of AfZFP5 in conferring drought and salt–alkali stress tolerance, providing genetic resources and a theoretical foundation for breeding stress-resistance crops. Full article

(This article belongs to the Special Issue Advanced Plant Molecular Responses to Abiotic Stresses)

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21 pages, 7423 KiB

Open AccessArticle

Cytosolic and Nucleosolic Calcium-Regulated Long Non-Coding RNAs and Their Target Protein-Coding Genes in Response to Hyperosmolarity and Salt Stresses in Arabidopsis thaliana

by Doudou Wang, Kaifeng Zheng, Wenfen Long, Liang Zhao, Wanjie Li, Xiuhua Xue and Shengcheng Han

Int. J. Mol. Sci. 2025, 26(5), 2086; https://doi.org/10.3390/ijms26052086 - 27 Feb 2025

Viewed by 447

Abstract

Long non-coding RNAs (lncRNAs) are involved in plant biotic and abiotic stress responses, in which Ca²⁺ also plays a significant role. There is diversity in the regulation of different gene expressions by cytosolic Ca²⁺ ([Ca²⁺]_cyt) and nucleosolic Ca²⁺ ([Ca²⁺]_nuc). However, no studies have yet explored the interrelationship between lncRNAs and calcium signaling, nor how calcium signaling regulates the expression of lncRNAs. Here, we use transgenic materials PV-NES and NLS-PV, which simulate [Ca²⁺]_cyt- and [Ca²⁺]_nuc-deficient mutants, respectively, and wild type (WT) materials in response to hyperosmolarity (250 mM sorbitol) or salt stresses (125 mM NaCl) at different time points to obtain RNA-seq data, respectively. Then, we proceed with the screening of lncRNAs, adding 688 new lncRNAs to the known Arabidopsis lncRNA database. Subsequently, through the analysis of differentially expressed lncRNA genes, it was found that cytosolic or nucleosolic calcium signals have distinct regulatory effects on differentially expressed lncRNAs (DElncRNAs) and differentially expressed protein-coding genes (DEPCGs) treated with high-concentration NaCl and sorbitol at different times. Furthermore, through weighted correlation network analysis (WGCNA), it is discovered that under hyperosmolarity and salt stresses, lncRNA-associated PCGs are related to the cell wall structure, the plasma membrane component, and osmotic substances through trans-regulation. In addition, by screening for cis-regulatory target PCGs of Ca²⁺-regulated lncRNAs related to osmotic stress, we obtain a series of lncRNA-PCG pairs related to water transport, cell wall components, and lateral root formation. Therefore, we expand the existing Arabidopsis lncRNA database and obtain a series of lncRNAs and PCGs regulated by [Ca²⁺]_cyt or [Ca²⁺]_nuc in response to salt and hyperosmolarity stress, providing a new perspective for subsequent research on lncRNAs. We also explore the trans- and cis-regulated target PCGs of lncRNAs regulated by calcium signaling, providing new insights for further studying salt stress and osmotic stress. Full article

(This article belongs to the Special Issue Advanced Plant Molecular Responses to Abiotic Stresses)

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20 pages, 7275 KiB

Open AccessArticle

OsEL2 Regulates Rice Cold Tolerance by MAPK Signaling Pathway and Ethylene Signaling Pathway

by Jiacheng Wu, Xufeng Cao, Xingzhuo Sun, Yulin Chen, Peng Zhang, Yanting Li, Chuan Ma, Lingli Wu, Xin Liang, Qiuping Fu, Lihua Li, Jianqing Zhu, Xiaomei Jia, Xiaoying Ye, Jun Zhu and Rongjun Chen

Int. J. Mol. Sci. 2025, 26(4), 1633; https://doi.org/10.3390/ijms26041633 - 14 Feb 2025

Viewed by 585

Abstract

Low temperature stress represents a significant abiotic stress factor affecting rice yields. While the structure and some of the functions of cell cycle protein-dependent protein kinase inhibitor (CKI) family proteins have been the subject of study, their relevance to cold tolerance in rice has been less investigated. In this study, we cloned OsEL2 (LOC_Os03g01740) and constructed anti-expression lines of this gene. The resulting lines exhibited significant cold sensitivity and displayed greater oxidative damage than wild type Nippobare (Nip). However, the activities of antioxidant enzymes, such as catalase (CAT), were significantly elevated in OsEL2-AX plants in comparison to Nip following exposure to 4 °C stress. RNA sequencing revealed the presence of 18,822 differential genes, with the majority of them being expressed with temporal specificity. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that a considerable number of differentially expressed genes (DEGs) are involved in the metabolism of amino acids, lipids, and terpenoids. Weighted gene co-expression network analysis (WGCNA) revealed a close relationship between the genes in the turquoise and light green modules and rice cold tolerance traits. These genes were predominantly enriched in terpene metabolism and the metabolism of various plant secondary metabolites, suggesting that OsEL2 influences rice cold tolerance through the metabolism of these two classes of substances. An analysis of the genes within these two modules using transcription factor (TF) enrichment and KEGG enrichment revealed that they are predominantly regulated by mitogen-activated protein kinase (MAPK) and ethylene signaling pathways. Furthermore, we found that tryptophan metabolism, phenylalanine metabolism, and monoterpene synthesis were enriched in down-regulated pathway enrichment analysis. In addition, we also found that the MAPK signaling pathway was enriched in the KEGG enrichment analysis of AX2 with Nip. The results demonstrate that anti-expression of OsEL2 is associated with a notable decline in rice tolerance to cold stress. Full article

(This article belongs to the Special Issue Advanced Plant Molecular Responses to Abiotic Stresses)

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19 pages, 5241 KiB

Open AccessArticle

Quantitative Proteomic Analysis of Lysine Malonylation in Response to Salicylic Acid in the Roots of Platycodon grandiflorus

by Wanyue Ding, Yingying Duan, Yuqing Wang, Jizhou Fan, Weiyi Rao and Shihai Xing

Int. J. Mol. Sci. 2025, 26(3), 1392; https://doi.org/10.3390/ijms26031392 - 6 Feb 2025

Viewed by 785

Abstract

Salicylic acid, as a plant hormone, significantly affects the physiological and biochemical indexes of soluble sugar, malondialdehyde content, peroxidase, and superoxide dismutase enzyme activity in Platycodon grandiflorus. Lysine malonylation is a post-translational modification that involves various cellular functions in plants, though it is rarely studied, especially in medicinal plants. In this study, the aim was to perform a comparative quantitative proteomic study of malonylation modification on P. grandiflorus root proteins after salicylic acid treatment using Western blot with specific antibodies, affinity enrichment and LC-MS/MS analysis methods. The analysis identified 1907 malonyl sites for 809 proteins, with 414 proteins and 798 modification sites quantified with high confidence. Post-treatment, 361 proteins were upregulated, and 310 were downregulated. Bioinformatics analysis revealed that malonylation in P. grandiflorus is primarily involved in photosynthesis and carbon metabolism. Physiological and biochemical analysis showed that salicylic acid treatment increased the malondialdehyde levels, soluble protein, superoxide dismutase, and peroxidase activity but did not significantly affect the total saponins content in P. grandiflorus. These findings provide an important basis for exploring the molecular mechanisms of P. grandiflorus following salicylic acid treatment and enhance understanding of the biological function of protein lysine malonylation in plants. Full article

(This article belongs to the Special Issue Advanced Plant Molecular Responses to Abiotic Stresses)

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18 pages, 3461 KiB

Open AccessArticle

Chemical Composition, Physiological and Morphological Variations in Salvia subg. Perovskia Populations in Response to Different Salinity Levels

by Zahra Ghaffari, Mehdi Rahimmalek, Mohammad R. Sabzalian, Ahmad Arzani, Razieh Kiani, Shima Gharibi, Katarzyna Wróblewska and Antoni Szumny

Int. J. Mol. Sci. 2024, 25(23), 12566; https://doi.org/10.3390/ijms252312566 - 22 Nov 2024

Cited by 1 | Viewed by 930

Abstract

This study evaluated the salinity tolerance of five populations of Salvia subg. Perovskia (S. abrotanoides and S. yadngii). The aims of the study were to assess essential oil components, as well as growth and physiological parameters of two Salvia species in response to salt stress. Four different levels of salinity (0, 60, 90, and 120 mM NaCl) were applied. The effects of various concentrations of NaCl on essential oil content, composition, growth, water relation, proline, lipid peroxidation (MDA), hydrogen peroxide content, and antioxidant enzyme activity, as well as Na and K contents in leaves and the roots were evaluated. The results revealed that root dry weight loss was higher than that of shoots, indicating root vulnerability due to direct exposure to the salt stress. The lowest and highest oil content was obtained in PATKH (0.6%) at 60 mM and PABAD (0.6%) in 90 mM to 2.16% in PABSM population under 120 mM NaCl. Based on GC-MS analysis, 1,8-cineol (11.64 to 22.02%), camphor (2.67 to 27.14%), bornyl acetate (2.12 to 11.07%), borneol (2.38 to 24.37%), β-caryophyllene (3.24 to 7.58%), α-humulene (2.97 to 7.92%), and δ-3-carene (5.31 to 26.65%) were the most abundant compounds. Based on the principal component analysis (PCA), the most salinity-tolerant populations belonged to P. abrotanoides species. These populations are characterized by high root stress tolerance index (STI), root elements, and relative water content (RWC) with elevated levels of salinity stress. Finally, the findings might be useful in unraveling the salinity tolerance mechanisms for integrating stress tolerance with medicinal qualities in future studies. Full article

(This article belongs to the Special Issue Advanced Plant Molecular Responses to Abiotic Stresses)

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18 pages, 9697 KiB

Open AccessArticle

Characterization of Cytoskeletal Profilin Genes in Plasticity Elongation of Mesocotyl and Coleoptile of Maize Under Diverse Abiotic Stresses

by Xiaoqiang Zhao, Siqi Sun, Zhenzhen Shi, Fuqiang He, Guoxiang Qi, Xin Li and Yining Niu

Int. J. Mol. Sci. 2024, 25(21), 11693; https://doi.org/10.3390/ijms252111693 - 30 Oct 2024

Viewed by 798

Abstract

The plasticity elongation of mesocotyl (MES) and coleoptile (COL) largely determines the morphology of maize seedlings under abiotic stresses. The profilin (PRF) proteins play a pivotal role in cytoskeleton dynamics and plant development via regulating actin polymerization. However, little is known about whether and how the expression of the ZmPRF gene family regulates MES and COL elongation in maize under adverse abiotic stresses. Here, a total of eight ZmPRF gene members were identified in the maize genome. They were mainly located in the cytoplasm, chloroplast, and mitochondrion, and clearly divided into four classes, based on phylogenetic analysis. Segmental duplication was the main driver for the expansion of ZmPRF genes. Ka/Ks analysis indicated that most ZmPRF genes were intensely purified and selected. Promoter cis-element analysis suggested their potential roles in response to growth and development, stress adaption, hormone response, and light response. The protein–protein interaction network and two independent RNA-sequencing analyses revealed that eight ZmPRF genes and their thirty-seven interacting genes showed varied expression patterns in MES and COL of three maize genotypes under different sowing depths, 24-epibrassinolide application, and light spectral-quality treatments, of which ZmPRF3.3 was a potential core conserved gene for breeding application. Moreover, the quantitative real-time PCR (qRT-PCR) verified that the relative expression levels of most ZmPRF genes in MES and COL under above treatments were significantly correlated with the plasticity elongation of MES and COL in maize. Therefore, these results perform a comprehensive overview of the ZmPRF family and will provide valuable information for the validation of the function of ZmPRF genes in maize development under diverse abiotic stress. Full article

(This article belongs to the Special Issue Advanced Plant Molecular Responses to Abiotic Stresses)

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41 pages, 6783 KiB

Open AccessArticle

Stress-Responsive Gene Expression, Metabolic, Physiological, and Agronomic Responses by Consortium Nano-Silica with Trichoderma against Drought Stress in Bread Wheat

by Ghalia S. Aljeddani, Ragaa A. Hamouda, Amal M. Abdelsattar and Yasmin M. Heikal

Int. J. Mol. Sci. 2024, 25(20), 10954; https://doi.org/10.3390/ijms252010954 - 11 Oct 2024

Viewed by 1652

Abstract

The exploitation of drought is a critical worldwide challenge that influences wheat growth and productivity. This study aimed to investigate a synergistic amendment strategy for drought using the single and combined application of plant growth-promoting microorganisms (PGPM) (Trichoderma harzianum) and biogenic silica nanoparticles (SiO₂NPs) from rice husk ash (RHA) on Saudi Arabia’s Spring wheat Summit cultivar (Triticum aestivum L.) for 102 DAS (days after sowing). The significant improvement was due to the application of 600 ppm SiO₂NPs and T. harzianum + 600 ppm SiO₂NPs, which enhanced the physiological properties of chlorophyll a, carotenoids, total pigments, osmolytes, and antioxidant contents of drought-stressed wheat plants as adaptive strategies. The results suggest that the expression of the studied genes (TaP5CS1, TaZFP34, TaWRKY1, TaMPK3, TaLEA, and the wheat housekeeping gene TaActin) in wheat remarkably enhanced wheat tolerance to drought stress. We discovered that the genes and metabolites involved significantly contributed to defense responses, making them potential targets for assessing drought tolerance levels. The drought tolerance indices of wheat were revealed by the mean productivity (MP), stress sensitivity index (SSI), yield stability index (YSI), and stress tolerance index (STI). We employed four databases, such as BAR, InterPro, phytozome, and the KEGG pathway, to predict and decipher the putative domains in prior gene sequencing. As a result, we discovered that these genes may be involved in a range of important biological functions in specific tissues at different developmental stages, including response to drought stress, proline accumulation, plant growth and development, and defense response. In conclusion, the sole and/or dual T. harzianum application to the wheat cultivar improved drought tolerance strength. These findings could be insightful data for wheat production in Saudi Arabia under various water regimes. Full article

(This article belongs to the Special Issue Advanced Plant Molecular Responses to Abiotic Stresses)

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14 pages, 3283 KiB

Open AccessArticle

Genome-Wide Identification of Glutathione S-Transferase Family from Dendrobium officinale and the Functional Characterization of DoGST5 in Cadmium Tolerance

by Wu Jiang, Tao Wang, Man Zhang, Xiaojing Duan, Jiadong Chen, Yingying Liu, Zhengming Tao and Qiaosheng Guo

Int. J. Mol. Sci. 2024, 25(15), 8439; https://doi.org/10.3390/ijms25158439 - 2 Aug 2024

Cited by 2 | Viewed by 1254

Abstract

Glutathione S-transferases (GSTs) are members of a protein superfamily with diverse physiological functions, including cellular detoxification and protection against oxidative damage. However, there is limited research on GSTs responding to cadmium (Cd) stress. This study classified 46 GST genes in Dendrobium officinale (D. officinale) into nine groups using model construction and domain annotation. Evolutionary analysis revealed nine subfamilies with diverse physical and chemical properties. Prediction of subcellular localization revealed that half of the GST members were located in the cytoplasm. According to the expression analysis of GST family genes responding to Cd stress, DoGST5 responded significantly to Cd stress. Transient expression of DoGST5-GFP in tobacco leaves revealed that DoGST5 was localized in the cytoplasm. DoGST5 overexpression in Arabidopsis enhanced Cd tolerance by reducing Cd-induced H₂O₂ and O₂⁻ levels. These findings demonstrate that DoGST5 plays a critical role in enhancing Cd tolerance by balancing reactive oxygen species (ROS) levels, offering potential applications for improving plant adaptability to heavy metal stress. Full article

(This article belongs to the Special Issue Advanced Plant Molecular Responses to Abiotic Stresses)

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Review

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31 pages, 5408 KiB

Open AccessReview

Drought Stress in Roses: A Comprehensive Review of Morphophysiological, Biochemical, and Molecular Responses

by Hmmam Zarif, Chunguo Fan, Guozhen Yuan, Rui Zhou, Yufei Chang, Jingjing Sun, Jun Lu, Jinyi Liu and Changquan Wang

Int. J. Mol. Sci. 2025, 26(9), 4272; https://doi.org/10.3390/ijms26094272 - 30 Apr 2025

Abstract

Climate change poses significant threats to agriculture globally, particularly in arid and semi-arid regions where drought stress (DS) is most severe, disrupting ecosystems and constraining progress in agriculture and horticulture. Roses, valued for their aesthetic appeal, are highly susceptible to abiotic stresses, especially DS, which markedly reduces flower quantity and quality. Under DS conditions, roses exhibit diverse morphological, physiological, biochemical, and molecular adaptations that vary across species. This review examines the effects of DS on rose growth, yield, and physiological traits, including gas exchange, photosynthesis, phytohormone dynamics, and water and nutrient relationships, alongside their biochemical and molecular responses. Furthermore, DS impacts the biosynthesis of secondary metabolites, notably reducing the yield and quality of essential oils in roses, which are critical for their commercial value in perfumery and aromatherapy. Additionally, the impact of DS on rose flower quality and post-harvest longevity is assessed. By elucidating these diverse responses, this review provides a framework for understanding DS effects on roses and offers insights to develop strategies for mitigating its adverse impacts. Full article

(This article belongs to the Special Issue Advanced Plant Molecular Responses to Abiotic Stresses)

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