Physiological and Biochemical Mechanisms and Cytology of Cold Tolerance in Brassica napus

Ecophysiological, transcriptomic and metabolomic analyses shed light on the response mechanism of Bruguiera gymnorhiza to upwelling stress

Mangroves, due to their unique habitats, endure dual stressors from land to ocean and ocean to land directions. While extensive researches have been conducted on land-ocean stressors, studies on ocean-land stressors like upwelling are considerably scarce. In this study, ecophysiological, transcriptome, and metabolome analyses were conducted to determine the responses of mangrove plant (Bruguiera gymnorhiza, B. gymnorhiza) to upwelling stress. The results suggested that upwelling stress in B. gymnorhiza induces oxidative stress and membrane damage, which are mitigated by the synergistic actions of antioxidant enzymes and osmoprotectants. Transcriptomic and metabolomic analyses revealed that upregulated genes related to oxidation-reduction and carbohydrate metabolism, along with accumulated metabolites such as amino acids, lipids, phenols, and organic acids, contribute to enhancing antioxidant capacity and maintaining osmotic balance. Further analysis identified key KEGG pathways involved in the response to upwelling stress, including amino acid metabolism, carbohydrate and energy metabolism, flavonoid biosynthesis, and plant hormone signal transduction. These findings provide vital information into the multi-level response mechanisms of mangrove plants to upwelling stress.

Comparative Metabolome and Transcriptome Analysis of Rapeseed (Brassica napus L.) Cotyledons in Response to Cold Stress

Cold stress affects the seed germination and early growth of winter rapeseed, leading to yield losses. We employed transmission electron microscopy, physiological analyses, metabolome profiling, and transcriptome sequencing to understand the effect of cold stress (0 °C, LW) on the cotyledons of cold-tolerant (GX74) and -sensitive (XY15) rapeseeds. The mesophyll cells in cold-treated XY15 were severely damaged compared to slightly damaged cells in GX74. The fructose, glucose, malondialdehyde, and proline contents increased after cold stress in both genotypes; however, GX74 had significantly higher content than XY15. The pyruvic acid content increased after cold stress in GX74, but decreased in XY15. Metabolome analysis detected 590 compounds, of which 32 and 74 were differentially accumulated in GX74 (CK vs. cold stress) and XY15 (CK vs. cold stressed). Arachidonic acid and magnoflorine were the most up-accumulated metabolites in GX74 subjected to cold stress compared to CK. There were 461 and 1481 differentially expressed genes (DEGs) specific to XY15 and GX74 rapeseeds, respectively. Generally, the commonly expressed genes had higher expressions in GX74 compared to XY15 in CK and cold stress conditions. The expression changes in DEGs related to photosynthesis-antenna proteins, chlorophyll biosynthesis, and sugar biosynthesis-related pathways were consistent with the fructose and glucose levels in cotyledons. Compared to XY15, GX74 showed upregulation of a higher number of genes/transcripts related to arachidonic acid, pyruvic acid, arginine and proline biosynthesis, cell wall changes, reactive oxygen species scavenging, cold-responsive pathways, and phytohormone-related pathways. Taken together, our results provide a detailed overview of the cold stress responses in rapeseed cotyledons.

Transcriptome Analysis of Potato Leaves under Oxidative Stress

Potato (Solanum tuberosum L.) is a major global food crop, and oxidative stress can significantly impact its growth. Previous studies have shown that its resistance to oxidative stress is mainly related to transcription factors, post-translational modifications, and antioxidant enzymes in vivo, but the specific molecular mechanisms remain unclear. In this study, we analyzed the transcriptome data from potato leaves treated with H2O2 and Methyl viologen (MV), and a control group, for 12 h. We enriched 8334 (CK vs. H2O2) and 4445 (CK vs. MV) differentially expressed genes (DEGs), respectively, and randomly selected 15 DEGs to verify the sequencing data by qRT-PCR. Gene ontology (GO) enrichment analysis showed that the DEGs were mainly concentrated in cellular components and related to molecular function, and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that most of the DEGs were related to metabolic pathways, plant hormone signal transduction, MAPK-signaling pathway, and plant-pathogen interactions. In addition, several candidate transcription factors, mainly including MYB, WRKY, and genes associated with Ca2+-mediated signal transduction, were also found to be differentially expressed. Among them, the plant hormone genes Soltu.DM.03G022780 and Soltu.DM.06G019360, the CNGC gene Soltu.DM.06G006320, the MYB transcription factors Soltu.DM.06G004450 and Soltu.DM.09G002130, and the WRKY transcription factor Soltu.DM.06G020440 were noticeably highly expressed, which indicates that these are likely to be the key genes in the regulation of oxidative stress tolerance. Overall, these findings lay the foundation for further studies on the molecular mechanisms of potato leaves in response to oxidative stress.

Sensing, signalling, and regulatory mechanism of cold-stress tolerance in plants

Cold stress is a crucial environmental factor influencing growth and distribution and possessing yield penalties. To survive in the cold, plants have evolved to use a range of molecular mechanisms. The major regulatory pathway under low-temperature stress involves the conversion of external stimulus into an internal signal that triggers a defence mechanism through a transcriptional cascade to counter stress. Cold-receptive mechanism and cell signalling involve cold-related signalling molecules, sensors, calcium signals, MAPK cascade, and ICE-COR-CBF pathway that modulate signal transduction in plants. Of these, the ICE-CBF-COR signalling is considered to be an important regulator for cold-stress acclimation. ICE stimulates acclimation to cold and plays a pivotal role in regulating CBF-mediated cold-tolerance mechanism. Thus, CBFs regulate COR gene expression by binding to its promoter. Similarly, the C-repeat binding factor-dependent signalling cascade also stimulates osmotic stress-regulatory gene expression. This review elucidates the regulatory mechanism underlying cold stress, i.e., signal molecules, cold receptors, signal-transduction pathways, metabolic regulation under cold stress, and crosstalk of regulatory pathways with other abiotic stresses in plants. The results may pave the way for crop improvement in low-temperature environments.

NO and GSH Alleviate the Inhibition of Low-Temperature Stress on Cowpea Seedlings

Low-temperature stress in early spring seriously affects the growth and development of cowpea seedlings. To study the alleviative effect of the exogenous substances nitric oxide (NO) and glutathione (GSH) on cowpea (Vigna unguiculata (Linn.) Walp.) seedlings under 8 °C low-temperature stress, 200 μmol·L^-1 NO and 5 mmol·L^-1 GSH were sprayed on cowpea seedlings whose second true leaf was about to unfold to enhance the tolerance of cowpea seedlings to low temperature. Spraying NO and GSH can eliminate excess superoxide radicals (O₂^-) and hydrogen peroxide (H₂O₂) to varying degrees, reduce the content of malondialdehyde and relative conductivity, delay the degradation of photosynthetic pigments, increase the content of osmotic regulating substances such as soluble sugar, soluble protein, and proline, and improve the activity of antioxidant enzymes such as superoxide dismutase, peroxidase, catalase, ascorbate peroxidase, dehydroascorbate reductase, and monodehydroascorbate reductase. This study revealed that the mixed use of NO and GSH played an important role in alleviating low temperature stress, and the effect of spraying NO alone was better than that of spraying GSH.

Identification of Competing Endogenous RNAs (ceRNAs) Network Associated with Drought Tolerance in Medicago truncatula with Rhizobium Symbiosis

Drought, bringing the risks of agricultural production losses, is becoming a globally environmental stress. Previous results suggested that legumes with nodules exhibited superior drought tolerance compared with the non-nodule group. To investigate the molecular mechanism of rhizobium symbiosis impacting drought tolerance, transcriptome and sRNAome sequencing were performed to identify the potential mRNA-miRNA-ncRNA dynamic network. Our results revealed that seedlings with active nodules exhibited enhanced drought tolerance by reserving energy, synthesizing N-glycans, and medicating systemic acquired resistance due to the early effects of symbiotic nitrogen fixation (SNF) triggered in contrast to the drought susceptible with inactive nodules. The improved drought tolerance might be involved in the decreased expression levels of miRNA such as mtr_miR169l-5p, mtr_miR398b, and mtr_miR398c and its target genes in seedlings with active nodules. Based on the negative expression pattern between miRNA and its target genes, we constructed an mRNA-miR169l-ncRNA ceRNA network. During severe drought stress, the lncRNA alternative splicings TCONS_00049507 and TCONS_00049510 competitively interacted with mtr_miR169l-5p, which upregulated the expression of NUCLEAR FACTOR-Y (NF-Y) transcription factor subfamily NF-YA genes MtNF-YA2 and MtNF-YA3 to regulate their downstream drought-response genes. Our results emphasized the importance of SNF plants affecting drought tolerance. In conclusion, our work provides insight into ceRNA involvement in rhizobium symbiosis contributing to drought tolerance and provides molecular evidence for future study.

Transcriptome Profiling of Stem-Differentiating Xylem in Response to Abiotic Stresses Based on Hybrid Sequencing in Cunninghamia lanceolata

Cunninghamia lanceolata (C. lanceolata) belongs to Gymnospermae, which are fast-growing and have desirable wood properties. However, C. lanceolata's stress resistance is little understood. To unravel the physiological and molecular regulation mechanisms under environmental stresses in the typical gymnosperm species of C. lanceolata, three-year-old plants were exposed to simulated drought stress (polyethylene glycol 8000), salicylic acid, and cold treatment at 4 °C for 8 h, 32 h, and 56 h, respectively. Regarding the physiological traits, we observed a decreased protein content and increased peroxidase upon salicylic acid and polyethylene glycol treatment. Superoxide dismutase activity either decreased or increased at first and then returned to normal under the stresses. Regarding the molecular regulation, we used both nanopore direct RNA sequencing and short-read sequencing to reveal a total of 5646 differentially expressed genes in response to different stresses, of which most had functions in lignin catabolism, pectin catabolism, and xylan metabolism, indicating that the development of stem-differentiating xylem was affected upon stress treatment. Finally, we identified a total of 51 AP2/ERF, 29 NAC, and 37 WRKY transcript factors in C. lanceolata. The expression of most of the NAC TFs increased under cold stress, and the expression of most of the WRKY TFs increased under cold and SA stress. These results revealed the transcriptomics responses in C. lanceolata to short-term stresses under this study's experimental conditions and provide preliminary clues about stem-differentiating xylem changes associated with different stresses.

Functional Characterization of MaZIP4, a Gene Regulating Copper Stress Tolerance in Mulberry (Morus atropurpurea R.)

ZIP4 (zinc transporter 4) plays important roles in transporting Cu²⁺ ions in plants, which may contribute to the maintenance of plant metal homeostasis in growth, plant development and normal physiological metabolism. However, ZIP4 transporters have not been described in mulberry and the exact function of ZIP4 transporters in regulating the homeostasis of Cu in mulberry remains unclear. In this study, a new ZIP4 gene (MaZIP4) was isolated and cloned from Morus atropurpurea R. Phylogenetic analysis of amino sequences suggested that the amino-acid sequence of the MaZIP4 protein shows high homology with other ZIP4 proteins of Morus notabilis, Trema orientale, Ziziphus jujube and Cannabis sativa. In addition, a MaZIP4 silenced line was successfully constructed using virus-induced gene silencing (VIGS). The analysis of MaZIP4 expression by quantitative real-time PCR in mulberry showed that the level of MaZIP4 expression increased with increasing Cu concentration until the Cu concentration reached 800 ppm. Relative to the blank (WT) and the negative controls, malondialdehyde (MDA) levels increased significantly and rose with increasing Cu concentration in the MaZIP4 silenced line, whereas the soluble protein and proline content, superoxide dismutase (SOD) and peroxidase (POD) activities of these transgenic plants were lower. These results indicated that MaZIP4 may play an important role in the resistance of mulberry to Cu stress.

Integrated methylome and transcriptome analysis unravel the cold tolerance mechanism in winter rapeseed(Brassica napus L.)

BACKGROUND

Cytosine methylation, the main type of DNA methylation, regulates gene expression in plant response to environmental stress. The winter rapeseed has high economic and ecological value in China's Northwest, but the DNA methylation pattern of winter rapeseed during freezing stress remains unclear.

RESULT

This study integrated the methylome and transcriptome to explore the genome-scale DNA methylation pattern and its regulated pathway of winter rapeseed, using freezing-sensitive (NF) and freezing-resistant (NS) cultivars.The average methylation level decreased under freezing stress, and the decline in NF was stronger than NS after freezing stress. The CG methylation level was the highest among the three contexts of CG, CHG, and CHH. At the same time, the CHH proportion was high, and the methylation levels were highest 2 kb up/downstream, followed by the intron region. The C sub-genomes methylation level was higher than the A sub-genomes. The methylation levels of chloroplast and mitochondrial DNA were much lower than the B. napus nuclear DNA, the SINE methylation level was highest among four types of transposable elements (TEs), and the preferred sequence of DNA methylation did not change after freezing stress. A total of 1732 differentially expressed genes associated with differentially methylated genes (DMEGs) were identified in two cultivars under 12 h and 24 h in three contexts by combining whole-genome bisulfite sequencing( and RNA-Seq data. Function enrichment analysis showed that most DMEGs participated in linoleic acid metabolism, alpha-linolenic acid metabolism, carbon fixation in photosynthetic organisms, flavonoid biosynthesis, and plant hormone signal transduction pathways. Meanwhile, some DMEGs encode core transcription factors in plant response to stress.

CONCLUSION

Based on the findings of DNA methylation, the freezing tolerance of winter rapeseed is achieved by enhanced signal transduction, lower lipid peroxidation, stronger cell stability, increased osmolytes, and greater reactive oxygen species (ROS) scavenging. These results provide novel insights into better knowledge of the methylation regulation of tolerance mechanism in winter rapeseed under freezing stress.

Transcriptomic Analysis Reveals Potential Gene Regulatory Networks Under Cold Stress of Loquat (Eriobotrya japonica Lindl.)

Loquat (Eriobotrya japonica Lindl. ) is one of the most economically important evergreen fruit crops in China, while it often suffered the injury of cold stress in winter and earlier spring, and the annual yield loss of loquat fruits caused by cold or freezing stress was immeasurable. However, knowledge about the physiological response and molecular mechanism under cold stress is still limited. To investigate the potential regulation mechanism pre- and post-cold stress in loquat and the changes in physiological indicators, a comparative transcriptome analysis was performed against a cold-resistant cv. "Huoju" and a cold-sensitive cv. "Ninghaibai". The results of physiological indicators related to cold resistance indicated that rachis was most sensitive to cold stress and was considered as the representative organ to directly evaluate cold resistance of loquat based on subordinate function analysis. Here, we compared the transcriptome profiles of rachis pre- and under cold stress in "Huoju" and "Ninghaibai". A total of 4,347 and 3,513 differentially expressed genes (DEGs) were detected in "Ninghaibai" and "Huoju", among which 223 and 166 were newly identified genes, respectively, most of them were functionally enriched in plant hormone signal transduction (Huoju: 142; Ninghaibai: 200), and there were higher plant hormone content and related DEG expression levels in "Huoju" than that of "Ninghaibai". Moreover, a total of 3,309 differentially expressed transcription factors (DETFs) were identified, and some DEGs and DETFs were screened to be subjected to co-expression network analysis based on the gene expression profile data. Some candidate DEGs, including UDP-glycosyltransferase (UGT), glycosyltransferase (GT), sugar phosphate/phosphate translocator (SPT), sugar transport protein (STP), proline-rich receptor-like protein kinase (PERK), and peroxidise (POD), were significantly affected by cold stress, and the expression level of these genes obtained from real-time quantitative RT-PCR was consistent with the pattern of transcriptome profile, which suggested that these genes might play the vital roles in cold resistance of loquat. Our results provide an invaluable resource for the identification of specific genes and TFs and help to clarify gene transcription during the cold stress response of loquat.

Genome-Wide Identification and Analysis of the Ascorbate Peroxidase (APX) Gene Family of Winter Rapeseed (Brassica rapa L.) Under Abiotic Stress

Winter Brassica rapa (B. rapa) is an important oilseed crop in northern China, but the mechanism of its cold resistance remains unclear. Ascorbate peroxidase (APX) plays important roles in the response of this plant to abiotic stress and in scavenging free radicals. In this study, the roles of APX proteins in the cold response and superoxide metabolism pathways in rapeseed species were investigated, and a comprehensive analysis of phylogeny, chromosome distribution, motif identification, sequence structure, gene duplication, and RNA-seq expression profiles in the APX gene family was conducted. Most BrAPX genes were specifically expressed under cold stress and behaved significantly differently in cold-tolerant and weakly cold-resistant varieties. Quantitative real-time-PCR (qRT-PCR) was also used to verify the differences in expression between these two varieties under cold, freezing, drought and heat stress. The expression of five BrAPX genes was significantly upregulated in growth cones at 3 h of cold stress, while their expression was significantly lower at 24 h than at 3 h. The expression of Bra015403 and Bra003918 was significantly higher in “Longyou-7” growth cones than in other treatments. Five BrAPXs (Bra035235, Bra003918, Bra033040, Bra017120, and Bra031934) were closely associated with abiotic stress responses in B. rapa. These candidate genes may play important roles in the response of B. rapa to low temperature stress and provide new information for the elucidation of the cold resistance mechanism in B. rapa.

Phosphoproteomics of cold stress-responsive mechanisms in Rhododendron chrysanthum

BACKGROUND

As an alpine plant, Rhododendron chrysanthum (R. chrysanthum) has evolved cold resistance mechanisms and become a valuable plant resource with the responsive mechanism of cold stress.

METHODS AND RESULTS

We adopt the phosphoproteomic and proteomic analysis combining with physiological measurement to illustrate the responsive mechanism of R. chrysanthum seedling under cold (4 °C) stress. After chilling for 12 h, 350 significantly changed proteins and 274 significantly changed phosphoproteins were detected. Clusters of Orthologous Groups (COG) analysis showed that significantly changed phosphoproteins and proteins indicated cold changed energy production and conversion and signal transduction.

CONCLUSIONS

The results indicated photosynthesis was inhibited under cold stress, but cold induced calcium-mediated signaling, reactive oxygen species (ROS) homeostasis and other transcription regulation factors could protect plants from the destruction caused by cold stress. These data provide the insight to the cold stress response and defense mechanisms of R. chrysanthum leaves at the phosphoproteome level.

Effect of heat stress on oxidative damage and antioxidant defense system in white clover (Trifolium repens L.)

This study leads to advances in the field of heat tolerance among different plant species. We concluded that a coordinated, increased antioxidant defense system enabled white clover to reduce heat-induced oxidative damage. The rise in global ambient temperature has a wide range of effects on plant growth, and, therefore, on the activation of various molecular defenses before the appearance of heat damage. Elevated temperatures result in accelerated generation of reactive oxygen species (ROS), causing an imbalance between ROS production and the ability of scavenging systems to detoxify and remove the reactive intermediates. The aim of this study was to determine the role of antioxidant defense systems in the alleviation of heat stress (HS) consequences in white clover (Trifolium repens L.), which is cultivated worldwide. We evaluated how temperature and time parameters contribute to the thermotolerance of white clover at different growth stages. We revealed HS protection in white clover from 37 to 40 °C, with 40 °C providing the greatest protection of 3-day-old seedlings and 28-day-old adult plants. Heat-provoked oxidative stress in white clover was confirmed by substantial changes in electrolyte leakage, malondialdehyde (MDA), and chlorophyll content, as well as superoxide anion (O₂^·-) and hydrogen peroxide (H₂O₂) production. Furthermore, superoxide dismutase (SOD) and ascorbate peroxidase (APX) as well as a high level of GSH non-enzymatic antioxidant were the most responsive, and were associated with acquired thermotolerance through the regulation of ROS generation. We demonstrated, by studying protoplast transient gene expression, direct genetic evidence of endogenous antioxidant-related genes that confer HS tolerance in white clover. Our present study clearly establishes that oxidative stress ensues from HS, which triggers the induction of antioxidant defense systems for ROS scavenging in white clover.

C-coordinated O-carboxymethyl chitosan Cu(II) complex exerts antifungal activity by disrupting the cell membrane integrity of Phytophthora capsici Leonian

Damage to the cell membrane is an effective method to prevent drug resistance in plant fungal diseases. Here, we proposed a negative remodeling model of the cell membrane structure induced by the C-coordinated O-carboxymethyl chitosan Cu (II) complex (O-CSLn-Cu). FITC-labeled O-CSLn-Cu (FITC-O-CSLn-Cu) was first synthesized via a nucleophilic substitution reaction and confirmed by FT-IR. FITC-labeled O-CSLn-Cu could pass through the fungal cell membrane, as detected by confocal laser scanning microscopy (CLSM) coupled with fluorescein isothiocyanate (FITC)-fluorescence. O-CSLn-Cu treatment led to apparent morphological changes in the membranes of P. capsici Leonian and giant unilamellar vesicles (GUVs) by transmission electron microscopy (TEM). Then, we performed component analysis of the cell membrane from the P. capsici Leonian affected by O-CSLn-Cu with a particular interest in membrane physicochemical properties. Many unsaturated fatty acids (UFAs) and key enzymes promoting UFA synthesis of the cell membrane were downregulated. Similarly, a large number of membrane proteins responsible for substance transport and biochemical reactions were downregulated. Furthermore, O-CSLn-Cu treatments increased plasma membrane permeability with significant leakage of intercellular electrolytes, soluble proteins and sugars, and lipid peroxidation with decreasing membrane fluidity. Finally, aquaporin 10 was proven to be a potential molecular target sensitive to antimicrobial agents according to composition analysis of membrane structure and immunohistochemistry.