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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: closed (20 January 2025) | Viewed by 9212

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Prof. Dr. Zhou Li

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Guest Editor

College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
Interests: abiotic stress; gene function; omics; metabolic regulation; stress signal transduction; molecular mechanism; grass species; stress physiology
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Special Issue Information

Dear Colleagues,

Plants suffer from various environmental stresses including abiotic stresses such as drought, heat, cold, and ionic stress (salt, aluminum, and cadmium), as well as biotic stresses (insects, parasites, viruses, fungi, or bacteria), which limits their plant growth and development. The frequency and intensity of environmental stresses are increasing due to global warming. Multiple adaptive strategies to counter environmental stresses have been elucidated in plants, including osmotic balance, lipids signaling and metabolism, and antioxidant defense systems, etc. The rapid development of new technologys such as gene editing, genomics, phenomics, etc., will provide illuminating insights into the adaptation of plants to diverse stresses and the interaction of environmental stresses and plants.

In this Special Issue for IJMS, we will focus on physiological, metabolic, and molecular mechanisms when plants respond to abiotic and biotic stresses. Transgenic technology and omics studies based on transcriptomics, proteomics, ionomics, metabolomics, genomics, or phenomics are important approaches to reveal plant adaptation to environmental stress. Research papers and up-to-date review articles are all welcome.

Dr. Zhou Li
Guest Editor

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Keywords

abiotic stress
biotic stress
adaptation
gene function
omics
metabolic regulation
stress signal
molecular mechanism

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Published Papers (8 papers)

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Research

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26 pages, 11679 KiB

Open AccessArticle

Evaluation of Salt-Tolerant Germplasms and Identification of Salt Tolerance-Related Proteins in Upland Cotton at the Seedling Stage

by Xiawen Li, Abdul Rehman, Zhenzhen Wang, Hongge Li, Jun Ma, Xiongming Du, Zhen Peng and Shoupu He

Int. J. Mol. Sci. 2025, 26(5), 1982; https://doi.org/10.3390/ijms26051982 - 25 Feb 2025

Viewed by 473

Abstract

Currently, developing cotton cultivation in saline–alkali soils is a vital focus for restructuring the cotton industry in China. The seedling stage, specifically the three-leaf stage, is a crucial period for assessing the salt tolerance of cotton. This research examined 430 natural populations of upland cotton, including 45 semi-wild germlines of Gossypium purpurascens. We measured the phenotypic responses of salt stress injury on seedlings as well as potassium (K), calcium (Ca), sodium (Na), and magnesium (Mg) concentrations in the roots, stems, and leaves following a 72 h exposure. The comprehensive salt tolerance index (CSTI) was determined using a membership function, principal component analysis, and cluster analysis based on 48 phenotypic traits related to salt tolerance. The results revealed significant variations in the phenotypic traits of the ion group under salt stress. Salt stress greatly affected the relative contents of Mg, K, and Ca ions in the aboveground parts of cotton, and correlations were observed among the 48 indices. The CSTI was calculated using seven principal component indexes, identifying 30 salt-tolerant, 114 weakly salt-tolerant, 39 salt-sensitive, and 4 highly sensitive materials based on cluster analysis. Among the 45 G. purpurascens cotton resources, 28 were weakly salt-tolerant, while 17 were salt-sensitive. Through TMT (Tandem Mass Tag)-based quantitative analysis, we identified 3107 unique peptides among 28,642 detected peptides, resulting in 203,869 secondary mass spectra, with 50,039 spectra successfully matched to peptides. Additionally, we identified several salt tolerance-related pathways (carbon metabolism; glutathione metabolism; the biosynthesis of amino acids, etc.) and proteins classified within the CAZy (Carbohydrate-Active EnZYme) family and expansin proteins. The results of this study concerning salt-tolerant materials provide a crucial theoretical foundation for the identification and evaluation of salt-tolerant breeding parents in cultivated cotton. Full article

(This article belongs to the Special Issue New Insights into Environmental Stresses and Plants)

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15 pages, 6048 KiB

Open AccessArticle

Mitogen-Activated Protein Kinases 3/6 Reduce Auxin Signaling via Stabilizing Indoleacetic Acid-Induced Proteins 8/9 in Plant Abiotic Stress Adaptation

by Chunyan Wang, Xiaoxuan Li, Han Zhao, Xiankui Cui, Wenhong Xu, Ke Li, Yang Xu, Zipeng Yu, Luyao Yu and Rui Guo

Int. J. Mol. Sci. 2025, 26(5), 1964; https://doi.org/10.3390/ijms26051964 - 24 Feb 2025

Viewed by 521

Abstract

The balance between plant growth and stress response is a key issue in the field of biology. In this process, mitogen-activated protein kinase 3 (MPK3) and MPK6 contribute to the construction of plants’ defense system during stress tolerance, while auxin, a growth-promoting hormone, is the key to maintaining plant growth. Nevertheless, the antagonistic or cooperative relationship between MPK3/6-mediated stress response and auxin-mediated plant growth remains unclear. Here, we demonstrate that stress-activated MPK3/6 interact with the auxin signaling repressors indoleacetic acid-induced protein 8 (IAA8) and IAA9, two key targets for regulating the auxin signaling output during stress responses. Protein phosphorylation mass spectrometry followed by a co-analysis with in vitro phosphorylation experiments revealed that MPK3/6 phosphorylated the S91, T94, and S152 residues of IAA8 and the S88 residue of IAA9. Phosphorylation significantly enhanced the protein stability of IAA8/9, thereby maintaining basal auxin signaling during plant stress adaptation. Collectively, MPK3/6-IAA8/9 are key modules that are turned on during plant stress adaptation to precisely reduce auxin signaling output, thereby preventing plants from improper vigorous growth under stress conditions. Full article

(This article belongs to the Special Issue New Insights into Environmental Stresses and Plants)

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20 pages, 4466 KiB

Open AccessArticle

Establishment and Validation of an Efficient Agrobacterium Tumefaciens-Mediated Transient Transformation System for Salix Psammophila

by Yanfei Yang, Zhicheng Chen, Jinna Zhao, Guangshun Zheng, Fei Wang, Shaofeng Li, Xingrong Ren and Jianbo Li

Int. J. Mol. Sci. 2024, 25(23), 12934; https://doi.org/10.3390/ijms252312934 - 1 Dec 2024

Viewed by 1478

Abstract

Salix psammophila, C. Wang & Chang Y. Yang, a desert-adapted shrub, is recognized for its exceptional drought tolerance and plays a vital role in ecosystem maintenance. However, research on S. psammophila has been limited due to the lack of an efficient and reliable genetic transformation method, including gene functional studies. The Agrobacterium-mediated transient overexpression assay is a rapid and powerful tool for analyzing gene function in plant vivo. In this study, tissue culture seedlings of S. psammophila were utilized as the recipient materials, and the plant expression vector pCAMBIA1301, containing the GUS reporter gene, was transferred into the seedlings via an Agrobacterium-mediated method. To enhance the efficiency of the system, the effects of secondary culture time, Agrobacterium concentration, infection time, and co-culture duration on the transient transformation efficiency of S. psammophila were explored. The optimal combination for the instantaneous transformation of S. psammophila tissue culture seedlings mediated by Agrobacterium was determined as follows: a secondary culture time of 30 d, a value of OD₆₀₀ of 0.8, an infection time of 3 h, and a co-culture duration of 48 h. Subsequently, the effectiveness of the transformation system was validated using the S. psammophila drought response gene SpPP2C80. To further confirm the accuracy of the system, SpPP2C80-overexpressing Arabidopsis was constructed and drought resistance analysis was performed. The results were consistent with the transient overexpression of SpPP2C80 in S. psammophila tissue culture seedlings, indicating that this system can be effectively employed for studying gene function in S. psammophila. These findings provide essential information for investigating gene function in non-model plants and pave the way for advancements in molecular biology research in S. psammophila. Full article

(This article belongs to the Special Issue New Insights into Environmental Stresses and Plants)

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25 pages, 2327 KiB

Open AccessArticle

DRB1, DRB2 and DRB4 Are Required for an Appropriate miRNA-Mediated Molecular Response to Osmotic Stress in Arabidopsis thaliana

by Joseph L. Pegler, Jackson M. J. Oultram, Christopher P. L. Grof and Andrew L. Eamens

Int. J. Mol. Sci. 2024, 25(23), 12562; https://doi.org/10.3390/ijms252312562 - 22 Nov 2024

Cited by 1 | Viewed by 925

Abstract

Arabidopsis thaliana (Arabidopsis) double-stranded RNA binding (DRB) proteins DRB1, DRB2 and DRB4 perform essential roles in microRNA (miRNA) production, with many of the produced miRNAs mediating aspects of the molecular response of Arabidopsis to abiotic stress. Exposure of the drb1, drb2 and drb4 mutants to mannitol stress showed drb2 to be the most sensitive to this form of osmotic stress. Profiling of the miRNA landscapes of mannitol-stressed drb1, drb2 and drb4 seedlings via small RNA sequencing, and comparison of these to the profile of mannitol-stressed wild-type Arabidopsis plants, revealed that the ability of the drb1 and drb2 mutants to mount an appropriate miRNA-mediated molecular response to mannitol stress was defective. RT-qPCR was next used to further characterize seven miRNA/target gene expression modules, with this analysis identifying DRB1 as the primary DRB protein required for miR160, miR164, miR167 and miR396 production. In addition, via its antagonism of DRB1 function, DRB2 was shown by RT-qPCR to play a secondary role in regulating the production of these four miRNAs. This analysis further showed that DRB1, DRB2 and DRB4 are all required to regulate the production of miR399 and miR408, and that DRB4 is the primary DRB protein required to produce the non-conserved miRNA, miR858. Finally, RT-qPCR was used to reveal that each of the seven characterized miRNA/target gene expression modules responded differently to mannitol-induced osmotic stress in each of the four assessed Arabidopsis lines. In summary, this research has identified mannitol-stress-responsive miRNA/target gene expression modules that can be molecularly manipulated in the future to generate novel Arabidopsis lines with increased tolerance to this form of osmotic stress. Full article

(This article belongs to the Special Issue New Insights into Environmental Stresses and Plants)

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20 pages, 9797 KiB

Open AccessArticle

Integrated Metabolomics and Transcriptomics Provide Key Molecular Insights into Floral Stage-Driven Flavonoid Pathway in Safflower

by Lili Yu, Naveed Ahmad, Weijie Meng, Shangyang Zhao, Yue Chang, Nan Wang, Min Zhang, Na Yao, Xiuming Liu and Jian Zhang

Int. J. Mol. Sci. 2024, 25(22), 11903; https://doi.org/10.3390/ijms252211903 - 6 Nov 2024

Cited by 2 | Viewed by 1389

Abstract

Safflower (Carthamus tinctorius L.) is a traditional Chinese medicinal herb renowned for its high flavonoid content and significant medicinal value. However, the dynamic changes in safflower petal flavonoid profiles across different flowering phases present a challenge in optimizing harvest timing and medicinal use. To enhance the utilization of safflower, this study conducted an integrated transcriptomic and metabolomic analysis of safflower petals at different flowering stages. Our findings revealed that certain flavonoids were more abundant during the fading stage, while others peaked during full bloom. Specifically, seven metabolites, including p-coumaric acid, naringenin chalcone, naringenin, dihydrokaempferol, apigenin, kaempferol, and quercetin, accumulated significantly during the fading stage. In contrast, dihydromyricetin and delphinidin levels were notably reduced. Furthermore, key genes in the flavonoid biosynthesis pathway, such as 4CL, DFR, and ANR, exhibited up-regulated expression with safflower’s flowering progression, whereas CHI, F3H, and FLS were down-regulated. Additionally, exposure to UV-B stress at full bloom led to an up-regulation of flavonoid content and altered the expression of key flavonoid biosynthetic genes over time. This study not only elucidates the regulatory mechanisms underlying flavonoid metabolism in safflower but also provides insights for maximizing its medicinal and industrial applications. Full article

(This article belongs to the Special Issue New Insights into Environmental Stresses and Plants)

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19 pages, 21126 KiB

Open AccessArticle

Transcriptome Regulation Mechanisms Difference between Female and Male Buchloe dactyloides in Response to Drought Stress and Rehydration

by Muye Liu, Yalan Su, Ke Teng, Xifeng Fan, Yueseng Yue, Guozeng Xiao and Lingyun Liu

Int. J. Mol. Sci. 2024, 25(17), 9653; https://doi.org/10.3390/ijms25179653 - 6 Sep 2024

Viewed by 1039

Abstract

Drought, a pervasive global challenge, significantly hampers plant growth and crop yields, with drought stress being a primary inhibitor. Among resilient species, Buchloe dactyloides, a warm-season and dioecious turfgrass, stands out for its strong drought resistance and minimal maintenance requirements, making it a favored choice in ecological management and landscaping. However, there is limited research on the physiological and molecular differences in drought resistance between male and female B. dactyloides. To decipher the transcriptional regulation dynamics of these sexes in response to drought, RNA-sequencing analysis was conducted using the ‘Texoka’ cultivar as a model. A 14-day natural drought treatment, followed by a 7-day rewatering period, was applied. Notably, distinct physiological responses emerged between genders during and post-drought, accompanied by a more pronounced differential expression of genes (DEGs) in females compared to males. Further, KEGG and GO enrichment analysis revealed different DEGs enrichment pathways of B. dactyloides in response to drought stress. Analysis of the biosynthesis and signaling transduction pathways showed that drought stress significantly enhanced the biosynthesis and signaling pathway of ABA in both female and male B. dactyloides plants, contrasting with the suppression of IAA and JA pathways. Also, we discovered BdMPK8-like as a potential enhancer of drought tolerance in yeast, highlighting novel mechanisms. This study demonstrated the physiological and molecular mechanisms differences between male and female B. dactyloides in response to drought stress, providing a theoretical basis for the corresponding application of female and male B. dactyloides. Additionally, it enriches our understanding of drought resistance mechanisms in dioecious plants, opening avenues for future research and genetic improvement. Full article

(This article belongs to the Special Issue New Insights into Environmental Stresses and Plants)

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21 pages, 10213 KiB

Open AccessArticle

Low-Temperature Regulates the Cell Structure and Chlorophyll in Addition to Cellulose Metabolism of Postharvest Red Toona sinensis Buds across Different Seasons

by Qian Zhao, Fu Wang, Yifei Wang, Xiulai Zhong, Shunhua Zhu, Xinqi Zhang, Shuyao Li, Xiujuan Lei, Zhenyuan Zang, Guofei Tan and Jian Zhang

Int. J. Mol. Sci. 2024, 25(14), 7719; https://doi.org/10.3390/ijms25147719 - 14 Jul 2024

Viewed by 1431

Abstract

Postharvest fibrosis and greening of Toona sinensis buds significantly affect their quality during storage. This study aimed to clarify the effects of low-temperature storage on postharvest red TSB quality harvested in different seasons. Red TSB samples were collected from Guizhou province, China, 21 days after the beginning of spring (Lichun), summer (Lixia), and autumn (Liqiu), and stored at 4 °C in dark conditions. We compared and analyzed the appearance, microstructure, chlorophyll and cellulose content, and expression levels of related genes across different seasons. The results indicated that TSB harvested in spring had a bright, purple-red color, whereas those harvested in summer and autumn were green. All samples lost water and darkened after 1 day of storage. Severe greening occurred in spring-harvested TSB within 3 days, a phenomenon not observed in summer and autumn samples. Microstructural analysis revealed that the cells in the palisade and spongy tissues of spring and autumn TSB settled closely during storage, while summer TSB cells remained loosely aligned. Xylem cells were smallest in spring-harvested TSB and largest in autumn. Prolonged storage led to thickening of the secondary cell walls and pith cell autolysis in the petioles, enlarging the cavity area. Chlorophyll content was higher in leaves than in petioles, while cellulose content was lower in petioles across all seasons. Both chlorophyll and cellulose content increased with storage time. Gene expression analysis showed season-dependent variations and significant increases in the expression of over half of the chlorophyll-related and cellulose-related genes during refrigeration, correlating with the observed changes in chlorophyll and cellulose content. This research provides valuable insights for improving postharvest storage and freshness preservation strategies for red TSB across different seasons. Full article

(This article belongs to the Special Issue New Insights into Environmental Stresses and Plants)

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Review

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17 pages, 3385 KiB

Open AccessReview

The Role of E3 Ubiquitin Ligase Gene FBK in Ubiquitination Modification of Protein and Its Potential Function in Plant Growth, Development, Secondary Metabolism, and Stress Response

by Yuting Wu, Yankang Zhang, Wanlin Ni, Qinghuang Li, Min Zhou and Zhou Li

Int. J. Mol. Sci. 2025, 26(2), 821; https://doi.org/10.3390/ijms26020821 - 19 Jan 2025

Viewed by 1078

Abstract

As a crucial post-translational modification (PTM), protein ubiquitination mediates the breakdown of particular proteins, which plays a pivotal role in a large number of biological processes including plant growth, development, and stress response. The ubiquitin-proteasome system (UPS) consists of ubiquitin (Ub), ubiquitinase, deubiquitinating enzyme (DUB), and 26S proteasome mediates more than 80% of protein degradation for protein turnover in plants. For the ubiquitinases, including ubiquitin-activating enzyme (E1), ubiquitin-conjugating enzyme (E2), and ubiquitin ligase (E3), the FBK (F-box Kelch repeat protein) is an essential component of multi-subunit E3 ligase SCF (Skp1-Cullin 1-F-box) involved in the specific recognition of target proteins in the UPS. Many FBK genes have been identified in different plant species, which regulates plant growth and development through affecting endogenous phytohormones as well as plant tolerance to various biotic and abiotic stresses associated with changes in secondary metabolites such as phenylpropanoid, phenolic acid, flavonoid, lignin, wax, etc. The review summarizes the significance of the ubiquitination modification of protein, the role of UPS in protein degradation, and the possible function of FBK genes involved in plant growth, development, secondary metabolism, and stress response, which provides a systematic and comprehensive understanding of the mechanism of ubiquitination and potential function of FBKs in plant species. Full article

(This article belongs to the Special Issue New Insights into Environmental Stresses and Plants)

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