Low-temperature perception leading to gene expression and cold tolerance in higher plants

Noninvasive Abiotic Stress Phenotyping of Vascular Plant in Each Vegetative Organ View

The last decades have witnessed a rapid development of noninvasive plant phenotyping, capable of detecting plant stress scale levels from the subcellular to the whole population scale. However, even with such a broad range, most phenotyping objects are often just concerned with leaves. This review offers a unique perspective of noninvasive plant stress phenotyping from a multi-organ view. First, plant sensing and responding to abiotic stress from the diverse vegetative organs (leaves, stems, and roots) and the interplays between these vital components are analyzed. Then, the corresponding noninvasive optical phenotyping techniques are also provided, which can prompt the practical implementation of appropriate noninvasive phenotyping techniques for each organ. Furthermore, we explore methods for analyzing compound stress situations, as field conditions frequently encompass multiple abiotic stressors. Thus, our work goes beyond the conventional approach of focusing solely on individual plant organs. The novel insights of the multi-organ, noninvasive phenotyping study provide a reference for testing hypotheses concerning the intricate dynamics of plant stress responses, as well as the potential interactive effects among various stressors.

Effect of cold stress on photosynthetic physiological characteristics and molecular mechanism analysis in cold-resistant cotton (ZM36) seedlings

Low temperature and cold damage seriously hinder the growth, development, and morphogenesis of cotton seedlings. However, the response mechanism of cotton seedlings under cold stress still lacks research. In this study, transcriptome sequencing, gas exchange parameters, and rapid chlorophyll fluorescence parameters were analyzed in leaves of cold-tolerant upland cotton variety "ZM36" under different temperature stress [25°C (T25, CK), 15°C (T15), 10°C (T10), and 4°C (T4)]. The results showed that the net photosynthetic rate (Pn), stomatal conductance (Gs), transpiration rate (Tr), PSII potential maximum photochemical efficiency (Fv/Fm), and performance index (PIabs) of cotton leaves significantly decreased, and the intercellular CO2 concentration (Ci) and Fo/Fm significantly increased under cold stress. The transcriptome sequencing analysis showed that a total of 13,183 DEGs were involved in the response of cotton seedlings at each temperature point (T25, T15, T10, and T4), mainly involving five metabolic pathways-the phosphatidylinositol signaling system, photosynthesis, photosynthesis antenna protein, carbon fixation in photosynthetic organisms, and carotenoid synthesis. The 1,119 transcription factors were discovered among all the DEGs. These transcription factors involve 59 families, of which 15.8% of genes in the NAC family are upregulated. Through network regulatory analysis, the five candidate genes GhUVR8 (GH_A05G3668), GhPLATZ (GH_A09G2161), GhFAD4-1 (GH_A01G0758), GhNFYA1 (GH_A02G1336), and GhFAD4-2 (GH_D01G0766) were identified in response to cold stress. Furthermore, suppressing the expression level of GhPLATZ by virus-induced gene silencing led to the reduction of low temperature resistance, implying GhPLATZ as a positive regulator of low temperature tolerance. The findings of the study revealed a piece of the complex response mechanism of the cold-tolerant variety "ZM36" to different cold stresses and excavated key candidate genes for low temperature response, which provided support for accelerating the selection and breeding of cotton varieties with low temperature tolerance.

Identification and analysis of MAPK cascade gene families of Camellia oleifera and their roles in response to cold stress

BACKGROUND

Low-temperature severely limits the growth and development of Camellia oleifera (C. oleifera). The mitogen-activated protein kinase (MAPK) cascade plays a key role in the response to cold stress.

METHODS AND RESULTS

Our study aims to identify MAPK cascade genes in C. oleifera and reveal their roles in response to cold stress. In our study, we systematically identified and analyzed the MAPK cascade gene families of C. oleifera, including their physical and chemical properties, conserved motifs, and multiple sequence alignments. In addition, we characterized the interacting networks of MAPKK kinase (MAPKKK)-MAPK kinase (MAPKK)-MAPK in C. oleifera. The molecular mechanism of cold stress resistance of MAPK cascade genes in wild C. oleifera was analyzed by differential gene expression and real-time quantitative reverse transcription-PCR (qRT-PCR).

CONCLUSION

In this study, 21 MAPKs, 4 MAPKKs and 55 MAPKKKs genes were identified in the leaf transcriptome of C. oleifera. According to the phylogenetic results, MAPKs were divided into 4 groups (A, B, C and D), MAPKKs were divided into 3 groups (A, B and D), and MAPKKKs were divided into 2 groups (MEKK and Raf). Motif analysis showed that the motifs in each subfamily were conserved, and most of the motifs in the same subfamily were basically the same. The protein interaction network based on Arabidopsis thaliana (A. thaliana) homologs revealed that MAPK, MAPKK, and MAPKKK genes were widely involved in C. oleifera growth and development and in responses to biotic and abiotic stresses. Gene expression analysis revealed that the CoMAPKKK5/CoMAPKKK43/CoMAPKKK49-CoMAPKK4-CoMAPK8 module may play a key role in the cold stress resistance of wild C. oleifera at a high-elevation site in Lu Mountain (LSG). This study can facilitate the mining and utilization of genetic resources of C. oleifera with low-temperature tolerance.

Advances in membrane-tethered NAC transcription factors in plants

Transcription factors are central components in cell signal transduction networks and are critical regulators for gene expression. It is estimated that approximately 10% of all transcription factors are membrane-tethered. MTFs (membrane-bound transcription factors) are latent transcription factors that are inherently anchored in the cellular membrane in a dormant form. When plants encounter environmental stimuli, they will be released from the membrane by intramembrane proteases or by the ubiquitin proteasome pathway and then were translocated to the nucleus. The capacity to instantly activate dormant transcription factors is a critical strategy for modulating diverse cellular functions in response to external or internal signals, which provides an important transcriptional regulatory network in response to sudden stimulus and improves plant survival. NTLs (NTM1-like) are a small subset of NAC (NAM, ATAF1/2, CUC2) transcription factors, which contain a conserved NAC domain at the N-terminus and a transmembrane domain at the C-terminus. In the past two decades, several NTLs have been identified from several species, and most of them are involved in both development and stress response. In this review, we review the reports and findings on NTLs in plants and highlight the mechanism of their nuclear import as well as their functions in regulating plant growth and stress response.

MrERF039 transcription factor plays an active role in the cold response of Medicago ruthenica as a sugar molecular switch

Cold stress severely restricts plant development, causing significant agricultural losses. We found a critical transcription factor network in Medicago ruthenica was involved in plant adaptation to low-temperature. APETALA2/ethylene responsive factor (AP2/ERF) transcription factor MrERF039 was transcriptionally induced by cold stress in M. ruthenica. Overexpression of MrERF039 significantly increased the glucose and maltose content, thereby improving the tolerance of M. ruthenica. MrERF039 could bind to the DRE cis-acting element in the MrCAS15A promoter. Additionally, the methyl group of the 14th amino acid in MrERF039 was required for binding. Transcriptome analysis showed that MrERF039 acted as a sugar molecular switch, regulating numerous sugar transporters and sugar metabolism-related genes. In addition, we found that MrERF039 could directly regulate β-amylase gene, UDP glycosyltransferase gene, and C2H2 zinc finger protein gene expression. In conclusion, these findings suggest that high expression of MrERF039 can significantly improve the cold tolerance of M. ruthenica root tissues during cold acclimation. Our results provide a new theoretical basis and candidate genes for breeding new legume forage varieties with high resistance.

Major quality regulation network of flavonoid synthesis governing the bioactivity of black wolfberry

Black wolfberry (Lycium ruthenicum Murr.) contains various bioactive metabolites represented by flavonoids, which are quite different among production regions. However, the underlying regulation mechanism of flavonoid biosynthesis governing the bioactivity of black wolfberry remains unclear. Presently, we compared the bioactivity of black wolfberry from five production regions. Multi-omics were performed to construct the regulation network associated with the fruit bioactivity. The detailed regulation mechanisms were identified using genetic and molecular methods. Typically, Qinghai (QH) fruit exhibited higher antioxidant and anti-inflammatory activities. The higher medicinal activity of QH fruit was closely associated with the accumulation of eight flavonoids, especially Kaempferol-3-O-rutinoside (K3R) and Quercetin-3-O-rutinoside (rutin). Flavonoid biosynthesis was found to be more active in QH fruit, and the upregulation of LrFLS, LrCHS, LrF3H and LrCYP75B1 caused the accumulation of K3R and rutin, leading to high medicinal bioactivities of black wolfberry. Importantly, transcription factor LrMYB94 was found to regulate LrFLS, LrCHS and LrF3H, while LrWRKY32 directly triggered LrCYP75B1 expression. Moreover, LrMYB94 interacted with LrWRKY32 to promote LrWRKY32-regulated LrCYP75B1 expression and rutin synthesis in black wolfberry. Transgenic black wolfberry overexpressing LrMYB94/LrWRKY32 contained higher levels of K3R and rutin, and exhibited high medicinal bioactivities. Importantly, the LrMYB94/LrWRKY32-regulated flavonoid biosynthesis was light-responsive, showing the importance of light intensity for the medicinal quality of black wolfberry. Overall, our results elucidated the regulation mechanisms of K3R and rutin synthesis, providing the basis for the genetic breeding of high-quality black wolfberry.

microRNAs: Key Regulators in Plant Responses to Abiotic and Biotic Stresses via Endogenous and Cross-Kingdom Mechanisms

Dramatic shifts in global climate have intensified abiotic and biotic stress faced by plants. Plant microRNAs (miRNAs)-20-24 nucleotide non-coding RNA molecules-form a key regulatory system of plant gene expression; playing crucial roles in plant growth; development; and defense against abiotic and biotic stress. Moreover, they participate in cross-kingdom communication. This communication encompasses interactions with other plants, microorganisms, and insect species, collectively exerting a profound influence on the agronomic traits of crops. This article comprehensively reviews the biosynthesis of plant miRNAs and explores their impact on plant growth, development, and stress resistance through endogenous, non-transboundary mechanisms. Furthermore, this review delves into the cross-kingdom regulatory effects of plant miRNAs on plants, microorganisms, and pests. It proceeds to specifically discuss the design and modification strategies for artificial miRNAs (amiRNAs), as well as the protection and transport of miRNAs by exosome-like nanovesicles (ELNVs), expanding the potential applications of plant miRNAs in crop breeding. Finally, the current limitations associated with harnessing plant miRNAs are addressed, and the utilization of synthetic biology is proposed to facilitate the heterologous expression and large-scale production of miRNAs. This novel approach suggests a plant-based solution to address future biosafety concerns in agriculture.

R-loops act as regulatory switches modulating transcription of COLD-responsive genes in rice

COLD is a major naturally occurring stress that usually causes complex symptoms and severe yield loss in crops. R-loops function in various cellular processes, including development and stress responses, in plants. However, how R-loops function in COLD responses is largely unknown in COLD susceptible crops like rice (Oryza sativa L.). We conducted DRIP-Seq along with other omics data (RNA-Seq, DNase-Seq and ChIP-Seq) in rice with or without COLD treatment. COLD treatment caused R-loop reprogramming across the genome. COLD-biased R-loops had higher GC content and novel motifs for the binding of distinct transcription factors (TFs). Moreover, R-loops can directly/indirectly modulate the transcription of a subset of COLD-responsive genes, which can be mediated by R-loop overlapping TF-centered or cis-regulatory element-related regulatory networks and lncRNAs, accounting for c. 60% of COLD-induced expression of differential genes in rice, which is different from the findings in Arabidopsis. We validated two R-loop loci with contrasting (negative/positive) roles in the regulation of two individual COLD-responsive gene expression, as potential targets for enhanced COLD resistance. Our study provides detailed evidence showing functions of R-loop reprogramming during COLD responses and provides some potential R-loop loci for genetic and epigenetic manipulation toward breeding of rice varieties with enhanced COLD tolerance.

A comprehensive analysis of transcriptomic data for comparison of cold tolerance in two Brassica napus genotypes

Brassica napus is an important oil crop and cold stress severely limits its productivity. To date, several studies have reported the regulatory genes and pathways involved in cold-stress responses in B. napus. However, transcriptome-scale identification of the regulatory genes is still lacking. In this study, we performed comparative transcriptome analysis of cold-tolerant C18 (CT - C18) and cold-sensitive C6 (CS - C6) Brassica napus genotypes under cold stress for 7 days, with the primary purpose of identifying cold-responsive transcription in B. napus. A total of 6061 TFs belonging to 58 families were annotated in the B. napus genome, of which 3870 were expressed under cold stress in both genotypes. Among these, 451 TFs were differentially expressed (DE), with 21 TF genes expressed in both genotypes. Most TF members of the MYB (26), bHLH (23), and NAC (17) families were significantly expressed in the CT - C18 genotype compared with the CS - C6 B. napus genotype. GO classification showed a significant role in transcription regulation, DNA-binding transcription factor activity, response to chitin, and the ethylene-activated signaling pathway. KEGG pathway annotation revealed these TFs are involved in regulating more pathways, resulting in more tolerance. In conclusion, the results provide insights into the molecular regulation mechanisms of B. napus in response to freezing treatment, expanding our understanding of the complex molecular mechanisms in plants' response to freezing stress.

Unravelling chilling-stress resistance mechanisms in endangered Mangrove plant Lumnitzera littorea (Jack) Voigt

Lumnitzera littorea (Jack) Voigt is one of the most endangered mangrove species in China. Previous studies have showed the impact of chilling stress on L. littorea and the repsonses at physiological and biochemical levels, but few attentions have been paid at molecular level. In this study, we conducted genome-wide investigation of transcriptional and post-transcriptional dynamics in L. littorea in response to chilling stress (8 °C day/5 °C night). In the seedlings of L. littorea, chilling sensing and signal transducing, photosystem II regeneration and peroxidase-mediated reactive oxygen species (ROS) scavenging were substantially enhanced to combat the adverse impact induced by chilling exposure. We further revealed that alternative polyadenylation (APA) events participated in chilling stress-responsive processes, including energy metabolism and steroid biosynthesis. Furthermore, APA-mediated miRNA regulations downregulated the expression of the genes involved in fatty acid biosynthesis and elongation, and protein phosphorylation, reflecting the important role of post-transcriptional regulation in modulating chilling tolerance in L. littorea. Our findings present a molecular view to the adaptive characteristics of L. littorea and shed light on the conservation genomic approaches of endangered mangrove species.

Comparative physiological, antioxidant and proteomic investigation reveal robust response to cold stress in Digitalis purpurea L

BACKGROUND OF THE STUDY

Digitalis purpurea (L) is an important medicinal plant growing at Alpine region of Himalayas and withstands low temperatures and harsh climatic conditions existing at high altitude. It serves as an ideal plant system to decipher the tolerance to cold stress (CS) in plants from high altitudes.

METHODS AND RESULTS

To understand the complexity of plant response to CS, we performed a comparative physiological and biochemical study complemented with proteomics in one-month-old D. purpurea grown at 25 °C (control) and 4 °C (CS). We observed an enhanced accumulation of different osmo-protectants (glycine betaine, soluble sugar and proline) and higher transcription (mRNA levels) of various antioxidant enzymes with an increased antioxidant enzyme activity in D. purpurea when exposed to CS. Furthermore, higher concentrations of non-enzymatic antioxidants (flavonoids, phenolics) was also associated with the response to CS. Differential proteomic analysis revealed the role of various proteins primarily involved in redox reactions, protein stabilization, quinone and sterol metabolism involved in CS response in D. purpurea..

CONCLUSION

Our results provide a framework for better understanding the physiological and molecular mechanism of CS response in D. purpurea at high altitudes.

CpCAF1 from Chimonanthus praecox Promotes Flowering and Low-Temperature Tolerance When Expressed in Arabidopsis thaliana

CCR4-associated factor I (CAF1) is a deadenylase that plays a critical role in the initial step of mRNA degradation in most eukaryotic cells, and in plant growth and development. Knowledge of CAF1 proteins in woody plants remains limited. Wintersweet (Chimonanthus praecox) is a highly ornamental woody plant. In this study, CpCAF1 was isolated from wintersweet. CpCAF1 belongs to the DEDDh (Asp-Glu-Asp-Asp-His) subfamily of the DEDD (Asp-Glu-Asp-Asp) nuclease family. The amino acid sequence showed highest similarity to the homologous gene of Arabidopsis thaliana. In transgenic Arabidopsis overexpressing CpCAF1, the timing of bolting, formation of the first rosette, and other growth stages were earlier than those of the wild-type plants. Root, lateral branch, rosette leaf, and silique growth were positively correlated with CpCAF1 expression. FLOWERING LOCUS T (FT) and SUPPRESSOROF OVEREXPRESSION OF CO 1 (SOC1) gene expression was higher while EARLY FLOWERING3 (ELF3) and FLOWERING LOCUS C (FLC) gene expression of transgenic Arabidopsis was lower than the wild type grown for 4 weeks. Plant growth and flowering occurrences were earlier in transgenic Arabidopsis overexpressing CpCAF1 than in the wild-type plants. The abundance of the CpCAF1 transcript grew steadily, and significantly exceeded the initial level under 4 °C in wintersweet after initially decreasing. After low-temperature exposure, transgenic Arabidopsis had higher proline content and stronger superoxide dismutase activity than the wild type, and the malondialdehyde level in transgenic Arabidopsis was decreased significantly by 12 h and then increased in low temperature, whereas it was directly increased in the wild type. A higher potassium ion flux in the root was detected in transgenic plants than in the wild type with potassium deficiency. The CpCAF1 promoter was a constitutive promoter that contained multiple cis-acting regulatory elements. The DRE, LTR, and MYB elements, which play important roles in response to low temperature, were identified in the CpCAF1 promoter. These findings indicate that CpCAF1 is involved in flowering and low-temperature tolerance in wintersweet, and provide a basis for future genetic and breeding research on wintersweet.

Seven plant capacities to adapt to abiotic stress

Abiotic stresses such as drought and heat continue to impact crop production in a warming world. This review distinguishes seven inherent capacities that enable plants to respond to abiotic stresses and continue growing, although at a reduced rate, to achieve a productive yield. These are the capacities to selectively take up essential resources, store them and supply them to different plant parts, generate the energy required for cellular functions, conduct repairs to maintain plant tissues, communicate between plant parts, manage existing structural assets in the face of changed circumstances, and shape-shift through development to be efficient in different environments. By illustration, we show how all seven plant capacities are important for reproductive success of major crop species during drought, salinity, temperature extremes, flooding, and nutrient stress. Confusion about the term 'oxidative stress' is explained. This allows us to focus on the strategies that enhance plant adaptation by identifying key responses that can be targets for plant breeding.

Coping with the cold: unveiling cryoprotectants, molecular signaling pathways, and strategies for cold stress resilience

Low temperature stress significantly threatens crop productivity and economic sustainability. Plants counter this by deploying advanced molecular mechanisms to perceive and respond to cold stress. Transmembrane proteins initiate these responses, triggering a series of events involving secondary messengers such as calcium ions (Ca2+), reactive oxygen species (ROS), and inositol phosphates. Of these, calcium signaling is paramount, activating downstream phosphorylation cascades and the transcription of cold-responsive genes, including cold-regulated (COR) genes. This review focuses on how plants manage freeze-induced damage through dual strategies: cold tolerance and cold avoidance. Tolerance mechanisms involve acclimatization to decreasing temperatures, fostering gradual accumulation of cold resistance. In contrast, avoidance mechanisms rely on cryoprotectant molecules like potassium ions (K+), proline, glycerol, and antifreeze proteins (AFPs). Cryoprotectants modulate intracellular solute concentration, lower the freezing point, inhibit ice formation, and preserve plasma membrane fluidity. Additionally, these molecules demonstrate antioxidant activity, scavenging ROS, preventing protein denaturation, and subsequently mitigating cellular damage. By forming extensive hydrogen bonds with water molecules, cryoprotectants also limit intercellular water movement, minimizing extracellular ice crystal formation, and cell dehydration. The deployment of cryoprotectants is a key adaptive strategy that bolsters plant resilience to cold stress and promotes survival in freezing environments. However, the specific physiological and molecular mechanisms underlying these protective effects remain insufficiently understood. Therefore, this review underscores the need for further research to elucidate these mechanisms and assess their potential impact on crop productivity and sustainability, contributing to the progressive discourse in plant biology and environmental science.

ISSR molecular markers and anatomical structures can assist in rapid and directional screening of cold-tolerant seedling mutants of medicinal and ornamental plant in Plumbago indica L

Plumbago indica L. is a perennial herb with ornamental and anticancer medicinal functions widely distributed in the tropics. It is affected by temperature and cannot bloom normally in colder subtropical regions, which seriously affects its ornamental value. To create low-temperature resistance mutants and enrich new germplasm resources, this study used tissue culture and chemical reagent (0.5 mmol/L NaN₃) and low-temperature stress (0°C, full darkness for 48h) induction to target and screen for cold-resistance mutants. The results showed that the ISSR band polymorphism ratio of the 24 suspected mutant materials was 87.5%. The DNA profiles of the 9 mutants initially identified were altered. The content of plumbagin in the stems and leaves of the mutants was examined, and it was found that the accumulation in the leaves of the mutant SA24 could be as high as 3.84 times that of the control, which was 0.5991%. There were significant differences in the anatomical structures of roots, stems and leaves. The mutants mostly exhibited reduced root diameter (only 0.17-0.69 times that of CK), increased stem diameter (up to 2.19 times that of CK), enlarged mesophyll cells, increased thickness (up to 1.83 times that of CK) and high specificity, which are thought to be important for the different cold resistance obtained by the mutants. In the cold resistance experiment, four cold-tolerant mutants were successfully screened according to their morphological characteristics and physiological indexes, and the mutagenesis efficiency could be as high as 2.22% and did not affect the accumulation of plumbagin in their stems and leaves, even higher than CK. The responses of the screened mutants SA15, SA19, SA23 and SA24 to low temperature showed slower leaf wilting, higher light energy conversion efficiency, less accumulation of MDA content, increased enzymatic activities of antioxidant enzymes (SOD, CAT, POD) and more accumulation of soluble sugars and proline content. These characteristics are consistent with the response of cold-resistance plants to low temperatures. The cold- resistance mutants cultivated in soil were observed of agronomic and ornamental traits for one year, mainly manifested as delayed flowering and delayed entry into the senescence stage. This study provides a more rapid and accurate technique for identifying and screening cold-tolerant mutants, and lays the foundation for future experiments on the creation of new cold-resistant varieties.

The alteration of proteins and metabolites in leaf apoplast and the related gene expression associated with the adaptation of Ammopiptanthus mongolicus to winter freezing stress

Ammopiptanthus mongolicus, an evergreen broad-leaved plant, can tolerate severe freezing stress (temperatures as low as -20 °C in winter). The apoplast is the space outside the plasma membrane that plays an important role in plant responses to environmental stress. Here, we investigated, using a multi-omics approach, the dynamic alterations in the levels of proteins and metabolites in the apoplast and related gene expression changes involved in the adaptation of A. mongolicus to winter freezing stress. Of the 962 proteins identified in the apoplast, the abundance of several PR proteins, including PR3 and PR5, increased significantly in winter, which may contribute to winter freezing-stress tolerance by functioning as antifreeze proteins. The increased abundance of the cell-wall polysaccharides and cell wall-modifying proteins, including PMEI, XTH32, and EXLA1, may enhance the mechanical properties of the cell wall in A. mongolicus. Accumulation of flavonoids and free amino acids in the apoplast may be beneficial for ROS scavenging and the maintenance of osmotic homeostasis. Integrated analyses revealed gene expression changes associated with alterations in the levels of apoplast proteins and metabolites. Our study improved the current understanding of the roles of apoplast proteins and metabolites in plant adaptation to winter freezing stress.

Low-temperature and circadian signals are integrated by the sigma factor SIG5

Chloroplasts are a common feature of plant cells and aspects of their metabolism, including photosynthesis, are influenced by low-temperature conditions. Chloroplasts contain a small circular genome that encodes essential components of the photosynthetic apparatus and chloroplast transcription/translation machinery. Here, we show that in Arabidopsis, a nuclear-encoded sigma factor that controls chloroplast transcription (SIGMA FACTOR5) contributes to adaptation to low-temperature conditions. This process involves the regulation of SIGMA FACTOR5 expression in response to cold by the bZIP transcription factors ELONGATED HYPOCOTYL5 and ELONGATED HYPOCOTYL5 HOMOLOG. The response of this pathway to cold is gated by the circadian clock, and it enhances photosynthetic efficiency during long-term cold and freezing exposure. We identify a process that integrates low-temperature and circadian signals, and modulates the response of chloroplasts to low-temperature conditions.

Assessment of proline function in higher plants under extreme temperatures

Climate change and abiotic stress factors are key players in crop losses worldwide. Among which, extreme temperatures (heat and cold) disturb plant growth and development, reduce productivity and, in severe cases, lead to plant death. Plants have developed numerous strategies to mitigate the detrimental impact of temperature stress. Exposure to stress leads to the accumulation of various metabolites, e.g. sugars, sugar alcohols, organic acids and amino acids. Plants accumulate the amino acid 'proline' in response to several abiotic stresses, including temperature stress. Proline abundance may result from de novo synthesis, hydrolysis of proteins, reduced utilization or degradation. Proline also leads to stress tolerance by maintaining the osmotic balance (still controversial), cell turgidity and indirectly modulating metabolism of reactive oxygen species. Furthermore, the crosstalk of proline with other osmoprotectants and signalling molecules, e.g. glycine betaine, abscisic acid, nitric oxide, hydrogen sulfide, soluble sugars, helps to strengthen protective mechanisms in stressful environments. Development of less temperature-responsive cultivars can be achieved by manipulating the biosynthesis of proline through genetic engineering. This review presents an overview of plant responses to extreme temperatures and an outline of proline metabolism under such temperatures. The exogenous application of proline as a protective molecule under extreme temperatures is also presented. Proline crosstalk and interaction with other molecules is also discussed. Finally, the potential of genetic engineering of proline-related genes is explained to develop 'temperature-smart' plants. In short, exogenous application of proline and genetic engineering of proline genes promise ways forward for developing 'temperature-smart' future crop plants.

Mdm-miR160-MdARF17-MdWRKY33 module mediates freezing tolerance in apple

Apple (Malus domestica) trees are vulnerable to freezing temperatures. Cold resistance in woody perennial plants can be improved through biotechnological approaches. However, genetic engineering requires a thorough understanding of the molecular mechanisms of the tree's response to cold. In this study, we demonstrated that the Mdm-miR160-MdARF17-MdWRKY33 module is crucial for apple freezing tolerance. Mdm-miR160 plays a negative role in apple freezing tolerance, whereas MdARF17, one of the targets of Mdm-miR160, is a positive regulator of apple freezing tolerance. RNA sequencing analysis revealed that in apple, MdARF17 mediates the cold response by influencing the expression of cold-responsive genes. EMSA and ChIP-qPCR assays demonstrated that MdARF17 can bind to the promoter of MdWRKY33 and promotes its expression. Overexpression of MdWRKY33 enhanced the cold tolerance of the apple calli. In addition, we found that the Mdm-miR160-MdARF17-MdWRKY33 module regulates cold tolerance in apple by regulating reactive oxygen species (ROS) scavenging, as revealed by (i) increased H₂ O₂ levels and decreased peroxidase (POD) and catalase (CAT) activities in Mdm-miR160e OE plants and MdARF17 RNAi plants and (ii) decreased H₂ O₂ levels and increased POD and CAT activities in MdmARF17 OE plants and MdWRKY33 OE calli. Taken together, our study uncovered the molecular roles of the Mdm-miR160-MdARF17-MdWRKY33 module in freezing tolerance in apple, thus providing support for breeding of cold-tolerant apple cultivars.

Comprehensive Transcriptome Analysis of Responses during Cold Stress in Wheat (Triticum aestivum L.)

Wheat production is often impacted by pre-winter freezing damage and cold spells in later spring. To study the influences of cold stress on wheat seedlings, unstressed Jing 841 was sampled once at the seedling stage, followed by 4 °C stress treatment for 30 days and once every 10 days. A total of 12,926 differentially expressed genes (DEGs) were identified from the transcriptome. K-means cluster analysis found a group of genes related to the glutamate metabolism pathway, and many genes belonging to the bHLH, MYB, NAC, WRKY, and ERF transcription factor families were highly expressed. Starch and sucrose metabolism, glutathione metabolism, and plant hormone signal transduction pathways were found. Weighted Gene Co-Expression Network Analysis (WGCNA) identified several key genes involved in the development of seedlings under cold stress. The cluster tree diagram showed seven different modules marked with different colors. The blue module had the highest correlation coefficient for the samples treated with cold stress for 30 days, and most genes in this module were rich in glutathione metabolism (ko00480). A total of eight DEGs were validated using quantitative real-time PCR. Overall, this study provides new insights into the physiological metabolic pathways and gene changes in a cold stress transcriptome, and it has a potential significance for improving freezing tolerance in wheat.

Combined lncRNA and mRNA Expression Profiles Identified the lncRNA–miRNA–mRNA Modules Regulating the Cold Stress Response in Ammopiptanthus nanus

Long non-coding RNAs (lncRNAs) have been shown to play critical regulatory roles in plants. Ammopiptanthus nanus can survive under severe low-temperature stress, and lncRNAs may play crucial roles in the gene regulation network underlying the cold stress response in A. nanus. To investigate the roles of lncRNAs in the cold stress response of A. nanus, a combined lncRNA and mRNA expression profiling under cold stress was conducted. Up to 4890 novel lncRNAs were identified in A. nanus and 1322 of them were differentially expressed under cold stress, including 543 up-regulated and 779 down-regulated lncRNAs. A total of 421 lncRNAs were found to participate in the cold stress response by forming lncRNA–mRNA modules and regulating the genes encoding the stress-related transcription factors and enzymes in a cis-acting manner. We found that 31 lncRNAs acting as miRNA precursors and 8 lncRNAs acting as endogenous competitive targets of miRNAs participated in the cold stress response by forming lncRNA–miRNA–mRNA regulatory modules. In particular, a cold stress-responsive lncRNA, TCONS00065739, which was experimentally proven to be an endogenous competitive target of miR530, contributed to the cold stress adaptation by regulating TZP in A. nanus. These results provide new data for understanding the biological roles of lncRNAs in response to cold stress in plants.

Exogenous application of salicylic acid improves freezing stress tolerance in alfalfa

Freezing stress is one of the most detrimental environmental factors that can seriously impact the growth, development, and distribution of alfalfa (Medicago sativa L.). Exogenous salicylic acid (SA) has been revealed as a cost-effective method of improving defense against freezing stress due to its predominant role in biotic and abiotic stress resistance. However, how the molecular mechanisms of SA improve freezing stress resistance in alfalfa is still unclear. Therefore, in this study, we used leaf samples of alfalfa seedlings pretreatment with 200 μM and 0 μM SA, which were exposed to freezing stress (-10°C) for 0, 0.5, 1, and 2h and allowed to recover at normal temperature in a growth chamber for 2 days, after which we detect the changes in the phenotypical, physiological, hormone content, and performed a transcriptome analysis to explain SA influence alfalfa in freezing stress. The results demonstrated that exogenous SA could improve the accumulation of free SA in alfalfa leaves primarily through the phenylalanine ammonia-lyase pathway. Moreover, the results of transcriptome analysis revealed that the mitogen-activated protein kinase (MAPK) signaling pathway-plant play a critical role in SA alleviating freezing stress. In addition, the weighted gene co-expression network analysis (WGCNA) found that MPK3, MPK9, WRKY22 (downstream target gene of MPK3), and TGACG-binding factor 1 (TGA1) are candidate hub genes involved in freezing stress defense, all of which are involved in the SA signaling pathway. Therefore, we conclude that SA could possibly induce MPK3 to regulate WRKY22 to participate in freezing stress to induced gene expression related to SA signaling pathway (NPR1-dependent pathway and NPR1-independent pathway), including the genes of non-expresser of pathogenesis-related gene 1 (NPR1), TGA1, pathogenesis-related 1 (PR1), superoxide dismutase (SOD), peroxidase (POD), ascorbate peroxidase (APX), glutathione-S-transferase (GST), and heat shock protein (HSP). This enhanced the production of antioxidant enzymes such as SOD, POD, and APX, which increases the freezing stress tolerance of alfalfa plants.

Effect of Hot- and Cold-Water Treatment on Broccoli Bioactive Compounds, Oxidative Stress Parameters and Biological Effects of Their Extracts

The goal of this work was to define resistant and susceptible variables of young broccoli (Brassica oleracea L. convar. botrytis (L.) Alef. var. cymosa Duch.) plants treated with cold and hot water. Additionally, we wanted to single out variables that could potentially be used as biomarkers of cold/hot-water stress in broccoli. Hot water changed more variables (72%) of young broccoli than cold water (24%) treatment. Hot water increased the concentration of vitamin C for 33%, hydrogen peroxide for 10%, malondialdehyde for 28%, and proline for 147%. Extracts of broccoli stressed with hot water were significantly more efficient in the inhibition of α-glucosidase (65.85 ± 4.85% compared to 52.00 ± 5.16% of control plants), while those of cold-water-stressed broccoli were more efficient in the inhibition of α-amylase (19.85 ± 2.70% compared to 13.26 ± 2.36% of control plants). Total glucosinolates and soluble sugars were affected by hot and cold water in an opposite way, which is why they could be used as biomarkers of hot/cold-water stress in broccoli. The possibility of using temperature stress to grow broccoli enriched with compounds of interest to human health should be further investigated.

Comparative transcriptome analysis reveals the regulatory mechanisms of two tropical water lilies in response to cold stress

BACKGROUND

Tropical water lily is an aquatic plant with high ornamental value, but it cannot overwinter naturally at high latitudes. The temperature drop has become a key factor restricting the development and promotion of the industry.

RESULTS

The responses of Nymphaea lotus and Nymphaea rubra to cold stress were analyzed from the perspective of physiology and transcriptomics. Under the cold stress, Nymphaea rubra had obvious leaf edge curling and chlorosis. The degree of peroxidation of its membrane was higher than that of Nymphaea lotus, and the content of photosynthetic pigments also decreased more than that of Nymphaea lotus. The soluble sugar content, SOD enzyme activity and CAT enzyme activity of Nymphaea lotus were higher than those of Nymphaea rubra. This indicated that there were significant differences in the cold sensitivity of the two varieties. GO enrichment and KEGG pathway analysis showed that many stress response genes and pathways were affected and enriched to varying degrees under the cold stress, especially plant hormone signal transduction, metabolic pathways and some transcription factor genes were from ZAT gene family or WKRY gene family. The key transcription factor ZAT12 protein in the cold stress response process has a C₂H₂ conserved domain, and the protein is localized in the nucleus. Under the cold stress, overexpression of the NlZAT12 gene in Arabidopsis thaliana increased the expression of some cold-responsive protein genes. The content of reactive oxygen species and MDA in transgenic Arabidopsis thaliana was lower, and the content of soluble sugar was higher, indicating that overexpression of NlZAT12 can improve the cold tolerance of Arabidopsis thaliana.

CONCLUSION

We demonstrate that ethylene signalling and reactive oxygen species signalling play critical roles in the response of the two cultivars to cold stress. The key gene NlZAT12 for improving cold tolerance was identified. Our study provides a theoretical basis for revealing the molecular mechanism of tropical water lily in response to cold stress.

Limitation of sucrose biosynthesis shapes carbon partitioning during plant cold acclimation

Cold acclimation is a multigenic process by which many plant species increase their freezing tolerance. Stabilization of photosynthesis and carbohydrate metabolism plays a crucial role in cold acclimation. To study regulation of primary and secondary metabolism during cold acclimation of Arabidopsis thaliana, metabolic mutants with deficiencies in either starch or flavonoid metabolism were exposed to 4°C. Photosynthesis was determined together with amounts of carbohydrates, anthocyanins, organic acids and enzyme activities of the central carbohydrate metabolism. Starch deficiency was found to significantly delay soluble sugar accumulation during cold acclimation, while starch overaccumulation did not affect accumulation dynamics but resulted in lower total amounts of \sucrose and glucose. Anthocyanin amounts were lowered in both starch deficient and overaccumulating mutants. Vice versa, flavonoid deficiency did not result in a changed starch amount, which suggested a unidirectional signalling link between starch and flavonoid metabolism. Mathematical modelling of carbon metabolism indicated kinetics of sucrose biosynthesis to be limiting for carbon partitioning in leaf tissue during cold exposure. Together with cold-induced dynamics of citrate, fumarate and malate amounts, this provided evidence for a central role of sucrose phosphate synthase activity in carbon partitioning between biosynthetic and dissimilatory pathways which stabilizes photosynthesis and metabolism at low temperature.

Progress and Prospects of the Molecular Basis of Soybean Cold Tolerance

Cold stress is a major factor influencing the geographical distribution of soybean growth and causes immense losses in productivity. Understanding the molecular mechanisms that the soybean has undergone to survive cold temperatures will have immense value in improving soybean cold tolerance. This review focuses on the molecular mechanisms involved in soybean response to cold. We summarized the recent studies on soybean cold-tolerant quantitative trait loci (QTLs), transcription factors, associated cold-regulated (COR) genes, and the regulatory pathways in response to cold stress. Cold-tolerant QTLs were found to be overlapped with the genomic region of maturity loci of E1, E3, E4, pubescence color locus of T, stem growth habit gene locus of Dt1, and leaf shape locus of Ln, indicating that pleiotropic loci may control multiple traits, including cold tolerance. The C-repeat responsive element binding factors (CBFs) are evolutionarily conserved across species. The expression of most GmDREB1s was upregulated by cold stress and overexpression of GmDREB1B;1 in soybean protoplast, and transgenic Arabidopsis plants can increase the expression of genes with the DRE core motif in their promoter regions under cold stress. Other soybean cold-responsive regulators, such as GmMYBJ1, GmNEK1, GmZF1, GmbZIP, GmTCF1a, SCOF-1 and so on, enhance cold tolerance by regulating the expression of COR genes in transgenic Arabidopsis. CBF-dependent and CBF-independent pathways are cross-talking and work together to activate cold stress gene expression. Even though it requires further dissection for precise understanding, the function of soybean cold-responsive transcription factors and associated COR genes studied in Arabidopsis shed light on the molecular mechanism of cold responses in soybeans and other crops. Furthermore, the findings may also provide practical applications for breeding cold-tolerant soybean varieties in high-latitude and high-altitude regions.

Brassinosteroid signaling positively regulates abscisic acid biosynthesis in response to chilling stress in tomato

Brassinosteroids (BRs) and abscisic acid (ABA) are essential regulators of plant growth and stress tolerance. Although the antagonistic interaction of BRs and ABA is proposed to ensure the balance between growth and defense in model plants, the crosstalk between BRs and ABA in response to chilling in tomato (Solanum lycopersicum), a warm-climate horticultural crop, is unclear. Here, we determined that overexpression of the BR biosynthesis gene DWARF (DWF) or the key BR signaling gene BRASSINAZOLE-RESISTANT1 (BZR1) increases ABA levels in response to chilling stress via positively regulating the expression of the ABA biosynthesis gene 9-CIS-EPOXYCAROTENOID DIOXYGENASE1 (NCED1). BR-induced chilling tolerance was mostly dependent on ABA biosynthesis. Chilling stress or high BR levels decreased the abundance of BRASSINOSTEROID-INSENSITIVE2 (BIN2), a negative regulator of BR signaling. Moreover, we observed that chilling stress increases BR levels and results in the accumulation of BZR1. BIN2 negatively regulated both the accumulation of BZR1 protein and chilling tolerance by suppressing ABA biosynthesis. Our results demonstrate that BR signaling positively regulates chilling tolerance via ABA biosynthesis in tomato. The study has implications in production of warm-climate crops in horticulture.

A comparative transcriptomic analysis reveals a coordinated mechanism activated in response to cold acclimation in common vetch (Vicia sativa L.)

BACKGROUND

Due to its strong abiotic stress tolerance, common vetch is widely cultivated as a green manure and forage crop in grass and crop rotation systems. The comprehensive molecular mechanisms activated in common vetch during cold adaptation remain unknown.

RESULTS

We investigated physiological responses and transcriptome profiles of cold-sensitive (Lanjian No. 1) and cold-tolerant (Lanjian No. 3) cultivars during cold acclimation to explore the molecular mechanisms of cold acclimation. In total, 2681 and 2352 differentially expressed genes (DEGs) were identified in Lanjian No. 1 and Lanjian No. 3, respectively; 7532 DEGs were identified in both lines. DEGs involved in "plant hormone signal transduction" were significantly enriched during cold treatment, and 115 DEGs involved in cold-processed hormone signal transduction were identified. Common vetch increased the level of indoleacetic acid (IAA) by upregulating the transcriptional regulator Aux/IAA and downregulating GH3, endowing it with stronger cold tolerance. An auxin-related DEG was overexpressed in yeast and shown to possess a biological function conferring cold tolerance.

CONCLUSION

This study identifies specific genes involved in Ca²⁺ signaling, redox regulation, circadian clock, plant hormones, and transcription factors whose transcriptional differentiation during cold acclimation may improve cold tolerance and contributes to the understanding of common and unique molecular mechanisms of cold acclimation in common vetch. The candidate genes identified here also provide valuable resources for further functional genomic and breeding studies.

Biochemical and Transcriptional Responses in Cold-Acclimated and Non-Acclimated Contrasting Camelina Biotypes under Freezing Stress

Cold-acclimated and non-acclimated contrasting Camelina (Camelina sativa L.) biotypes were investigated for changes in stress-associated biomarkers, including antioxidant enzyme activity, lipid peroxidation, protein, and proline content. In addition, a well-known freezing tolerance pathway participant known as C-repeat/DRE-binding factors (CBFs), an inducer of CBF expression (ICE1), and a cold-regulated (COR6.6) genes of the ICE-CBF-COR pathway were studied at the transcriptional level on the doubled-haploid (DH) lines. Freezing stress had significant effects on all studied parameters. The cold-acclimated DH34 (a freezing-tolerant line) showed an overall better performance under freezing stress than non-acclimated plants. The non-cold-acclimated DH08 (a frost-sensitive line) showed the highest electrolyte leakage after freezing stress. The highest activity of antioxidant enzymes (glutathione peroxidase, superoxide dismutase, and catalase) was also detected in non-acclimated plants, whereas the cold-acclimated plants showed lower enzyme activities upon stress treatment. Cold acclimation had a significantly positive effect on the total protein and proline content of stressed plants. The qRT-PCR analysis revealed significant differences in the expression and cold-inducibility of CsCBF1-3, CsICE1, and CsCOR6.6 genes among the samples of different treatments. The highest expression of all CBF genes was recorded in the non-acclimated frost-tolerant biotype after freezing stress. Interestingly a significantly higher expression of COR6.6 was detected in cold-acclimated samples of both frost-sensitive and -tolerant biotypes after freezing stress. The presented results provide more insights into freezing tolerance mechanisms in the Camelina plant from both a biochemical point of view and the expression of the associated genes.

Cold Tolerance of ScCBL6 Is Associated with Tonoplast Transporters and Photosynthesis in Arabidopsis

Plants that are adapted to harsh environments offer enormous opportunity to understand stress responses in ecological systems. Stipa capillacea is widely distributed in the frigid and arid region of the Tibetan Plateau, but its signal transduction system under cold stress has not been characterized. In this study, we isolated a cDNA encoding the signal transduction protein, ScCBL6, from S. capillacea, and evaluated its role in cold tolerance by ectopically expressing it in Arabidopsis. Full-length ScCBL6 encode 227 amino acids, and are clustered with CBL6 in Stipa purpurea and Oryza sativa in a phylogenetic analysis. Compared with tolerance in wild-type (WT) plants, ScCBL6-overexpressing plants (ScCBL6-OXP) were more tolerant to cold stress but not to drought stress, as confirmed by their high photosynthetic capacity (Fv/Fm) and survival rate under cold stress. We further compared their cold-responsive transcriptome profiles by RNA sequencing. In total, 3931 genes were differentially expressed by the introduction of ScCBL6. These gene products were involved in multiple processes such as the immune system, lipid catabolism, and secondary metabolism. A KEGG pathway analysis revealed that they were mainly enriched in plant hormone signal transduction and biomacromolecule metabolism. Proteins encoded by differentially expressed genes were predicted to be localized in chloroplasts, mitochondria, and vacuoles, suggesting that ScCBL6 exerts a wide range of functions. Based on its tonoplast subcellular location combined with integrated transcriptome and physiological analyses of ScCBL6-OXP, we inferred that ScCBL6 improves plant cold stress tolerance in Arabidopsis via the regulation of photosynthesis, redox status, and tonoplast metabolite transporters.

Freeze dehydration vs. supercooling of mesophyll cells: Impact of cell wall, cellular and tissue traits on the extent of water displacement

The extent of freeze dehydration of mesophyll cells in response to extracellular ice varies from supercooling to severe freezing cytorrhysis. The structural factors involved are poorly understood. In a comparison of mesophyll cells of 11 species, the factors "cell wall", "cellular" and "tissue" traits were investigated. The extent of freeze dehydration was quantified as reduction in the sectional area during controlled freezing in the presence of ice. The cell wall thickness, cell size, cell area and the relative area of intercellular spaces were determined. The modulus of elasticity was determined by psychrometry. To grasp the relationships between factors and with freeze dehydration, we applied a principal component analysis. The first two components explain 84% of the variance in the dataset. The first principal component correlated negatively with the extent of freeze dehydration and relative area of intercellular spaces, and positively with the squared cell wall thickness to cell size ratio, elasticity and cell wall thickness. The cell size parameters determined the second principal component. Supercooling appeared preferable in cells with a high squared cell wall thickness to cell size ratio and a low relative area of intercellular spaces. Such factors are hypothesised to affect the magnitude of negative turgor pressure being built up below the turgor loss point. Negative turgor pressure slows dehydration by reducing the water potential gradient to the extracellular ice. With high levels of freeze dehydration, sufficient intercellular spaces for extracellular ice accommodation are needed. The low relative area of intercellular spaces increases cell-to-cell contact area and could support tissue stability.

Integrated Transcriptome and Metabolome Analysis of Color Change and Low-Temperature Response during Flowering of Prunus mume

In China, Prunus mume is a famous flowering tree that has been cultivated for 3000 years. P. mume grows in tropical and subtropical regions, and most varieties lack cold resistance; thus, it is necessary to study the low-temperature response mechanism of P. mume to expand the scope of its cultivation. We used the integrated transcriptomic and metabolomic analysis of a cold-resistant variety of P. mume 'Meiren', to identify key genes and metabolites associated with low temperatures during flowering. The 'Meiren' cultivar responded in a timely manner to temperature by way of a low-temperature signal transduction pathway. After experiencing low temperatures, the petals fade and wilt, resulting in low ornamental value. At the same time, in the cold response pathway, the activities of related transcription factors up- or downregulate genes and metabolites related to low temperature-induced proteins, osmotic regulators, protective enzyme systems, and biosynthesis and metabolism of sugars and acids. Our findings promote research on the adaptation of P. mume to low temperatures during wintering and early flowering for domestication and breeding.

Molecular and Physiological Mechanisms to Mitigate Abiotic Stress Conditions in Plants

Agriculture production faces many abiotic stresses, mainly drought, salinity, low and high temperature. These abiotic stresses inhibit plants' genetic potential, which is the cause of huge reduction in crop productivity, decrease potent yields for important crop plants by more than 50% and imbalance agriculture's sustainability. They lead to changes in the physio-morphological, molecular, and biochemical nature of the plants and change plants' regular metabolism, which makes them a leading cause of losses in crop productivity. These changes in plant systems also help to mitigate abiotic stress conditions. To initiate the signal during stress conditions, sensor molecules of the plant perceive the stress signal from the outside and commence a signaling cascade to send a message and stimulate nuclear transcription factors to provoke specific gene expression. To mitigate the abiotic stress, plants contain several methods of avoidance, adaption, and acclimation. In addition to these, to manage stress conditions, plants possess several tolerance mechanisms which involve ion transporters, osmoprotectants, proteins, and other factors associated with transcriptional control, and signaling cascades are stimulated to offset abiotic stress-associated biochemical and molecular changes. Plant growth and survival depends on the ability to respond to the stress stimulus, produce the signal, and start suitable biochemical and physiological changes. Various important factors, such as the biochemical, physiological, and molecular mechanisms of plants, including the use of microbiomes and nanotechnology to combat abiotic stresses, are highlighted in this article.

Temporal regulation of cold transcriptional response in switchgrass

Switchgrass low-land ecotypes have significantly higher biomass but lower cold tolerance compared to up-land ecotypes. Understanding the molecular mechanisms underlying cold response, including the ones at transcriptional level, can contribute to improving tolerance of high-yield switchgrass under chilling and freezing environmental conditions. Here, by analyzing an existing switchgrass transcriptome dataset, the temporal cis-regulatory basis of switchgrass transcriptional response to cold is dissected computationally. We found that the number of cold-responsive genes and enriched Gene Ontology terms increased as duration of cold treatment increased from 30 min to 24 hours, suggesting an amplified response/cascading effect in cold-responsive gene expression. To identify genomic sequences likely important for regulating cold response, machine learning models predictive of cold response were established using k-mer sequences enriched in the genic and flanking regions of cold-responsive genes but not non-responsive genes. These k-mers, referred to as putative cis-regulatory elements (pCREs) are likely regulatory sequences of cold response in switchgrass. There are in total 655 pCREs where 54 are important in all cold treatment time points. Consistent with this, eight of 35 known cold-responsive CREs were similar to top-ranked pCREs in the models and only these eight were important for predicting temporal cold response. More importantly, most of the top-ranked pCREs were novel sequences in cold regulation. Our findings suggest additional sequence elements important for cold-responsive regulation previously not known that warrant further studies.

Temperature modulation of CAMTA3 gene induction activity is mediated through the DNA binding domain

The calmodulin-binding transcription activator (CAMTA) proteins of Arabidopsis thaliana play a major role in cold acclimation, contributing to the rapid induction of the C-REPEAT BINDING FACTOR (CBF) genes and other genes that impart freezing tolerance in plants exposed to cold temperature (4°C). The goal of this study was to better understand how the gene induction activity of CAMTA3 is modulated by temperature. Our results indicate that a severely truncated version of CAMTA3, CAMTA3³³⁴ , which includes the N-terminal CG-1 DNA binding domain and a newly identified transcriptional activation domain (TAD), was able to rapidly induce the expression of CBF2 and two newly identified target genes, EXPANSIN-LIKE A1 (EXPL1) and NINE-CIS-EPOXYCAROTENOID DIOXYGENASE 3 (NCED3), in response to cold temperature. Additionally, CAMTA3³³⁴ was able to restore freezing tolerance when expressed in a camta23 double mutant. The ability of CAMTA3 and CAMTA3³³⁴ to induce target genes at cold temperature did not involve increased levels of these proteins or increased binding of these proteins to target gene promoters in cold-treated plants. Rather, domain-swapping experiments indicated that the CAMTA3 CG-1 domain conferred temperature dependence to the ability of the CAMTA3 TAD to induce gene expression. The CG-1 domain also enabled the TAD to induce the expression of target genes at a moderate temperature (22°C) in response to cycloheximide treatment, consistent with the TAD activity not being intrinsically temperature dependent. We propose a working model in which the temperature modulation of CAMTA3 gene induction activity occurs independently from the C-terminal calmodulin-binding domains that previously have been proposed to activate CAMTA3 transcriptional activity in response to cold temperature.

Repeated colonization of alpine habitats by Arabidopsis arenosa viewed through freezing resistance and ice management strategies

Success or failure of plants to cope with freezing temperatures can critically influence plant distribution and adaptation to new habitats. Especially in alpine environments, frost is a likely major selective force driving adaptation. In Arabidopsis arenosa (L.) Lawalrée, alpine populations have evolved independently in different mountain ranges, enabling studying mechanisms of acclimation and adaptation to alpine environments. We tested for heritable, parallel differentiation in freezing resistance, cold acclimation potential and ice management strategies using eight alpine and eight foothill populations. Plants from three European mountain ranges (Niedere Tauern, Făgăraș and Tatra Mountains) were grown from seeds of tetraploid populations in four common gardens, together with diploid populations from the Tatra Mountains. Freezing resistance was assessed using controlled freezing treatments and measuring effective quantum yield of photosystem II, and ice management strategies by infrared video thermography and cryomicroscopy. The alpine ecotype had a higher cold acclimation potential than the foothill ecotype, whereby this differentiation was more pronounced in tetraploid than diploid populations. However, no ecotypic differentiation was found in one region (Făgăraș), where the ancient lineage had a different evolutionary history. Upon freezing, an ice lens within a lacuna between the palisade and spongy parenchyma tissues was formed by separation of leaf tissues, a mechanism not previously reported for herbaceous species. The dynamic adjustment of freezing resistance to temperature conditions may be particularly important in alpine environments characterized by large temperature fluctuations. Furthermore, the formation of an extracellular ice lens may be a useful strategy to avoid tissue damage during freezing.

Cold-induced [Ca2+]cyt elevations function to support osmoregulation in marine diatoms

Diatoms are a group of microalgae that are important primary producers in a range of open ocean, freshwater, and intertidal environments. The latter can experience substantial long- and short-term variability in temperature, from seasonal variations to rapid temperature shifts caused by tidal immersion and emersion. As temperature is a major determinant in the distribution of diatom species, their temperature sensory and response mechanisms likely have important roles in their ecological success. We examined the mechanisms diatoms use to sense rapid changes in temperature, such as those experienced in the intertidal zone. We found that the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana exhibit a transient cytosolic Ca2+ ([Ca2+]cyt) elevation in response to rapid cooling, similar to those observed in plant and animal cells. However, [Ca2+]cyt elevations were not observed in response to rapid warming. The kinetics and magnitude of cold-induced [Ca2+]cyt elevations corresponded with the rate of temperature decrease. We did not find a role for the [Ca2+]cyt elevations in enhancing cold tolerance but showed that cold shock induces a Ca2+-dependent K+ efflux and reduces mortality of P. tricornutum during a simultaneous hypo-osmotic shock. As intertidal diatom species may routinely encounter simultaneous cold and hypo-osmotic shocks during tidal cycles, we propose that cold-induced Ca2+ signaling interacts with osmotic signaling pathways to aid in the regulation of cell volume. Our findings provide insight into the nature of temperature perception in diatoms and highlight that cross-talk between signaling pathways may play an important role in their cellular responses to multiple simultaneous stressors.

Physiological genetic variation in tomato fruit chilling tolerance during postharvest storage

Storage at low temperatures is a common practice to prolong postharvest life of fruit and vegetables with a minimal negative impact on human/environmental health. Storage at low temperatures, however, can be restricted due to produce susceptibility to non-freezing chilling temperatures, when injuries such as physiological disorders and decays may result in unmarketable produce. We have investigated tomato fruit response to postharvest chilling stress in a recombinant inbred line (RIL) population developed from a cross between a chilling-sensitive cultivated tomato (Solanum lycopersicum L.) breeding line and a chilling-tolerant inbred accession of the tomato wild species S. pimpinellifolium L. Screening of the fruit of 148 RILs under cold storage (1.5°C) indicated presence of significant variations in chilling tolerance, manifested by varying degrees of fruit injury. Two extremely contrasting groups of RILs were identified, chilling-tolerant and chilling-sensitive RILs. The RILs in the two groups were further investigated under chilling stress conditions, and several physiological parameters, including weight loss, chlorophyll fluorescence parameters Fv/Fm, and Performance Index (PI), were determined to be efficient markers for identifying response to chilling stress in postharvest fruit. The Fv/Fm values reflected the physiological damages endured by the fruit after cold storage, and PI was a sensitive marker for early changes in photosystem II function. These two parameters were early indicators of chilling response before occurrence of visible chilling injuries. Antioxidant activities and ascorbic acid content were significantly higher in the chilling-tolerant than the chilling-sensitive lines. Further, the expression of C-repeat/DREB binding factors (CBFs) genes swiftly changed within 1-hr of fruit exposure to the chilling temperature, and the SlCBF1 transcript level was generally higher in the chilling-tolerant than chilling-sensitive lines after 2-hr exposure to the low temperature. This research demonstrates the presence of potential genetic variation in fruit chilling tolerance in the tomato RIL population. Further investigation of the RIL population is underway to better understand the genetic, physiological, and biochemical mechanisms involved in postharvest fruit chilling tolerance in tomato.

Dynamic changes in the transcriptome landscape of Arabidopsis thaliana in response to cold stress

Plants must reprogram gene expression to adapt constantly changing environmental temperatures. With the increased occurrence of extremely low temperatures, the negative effects on plants, especially on growth and development, from cold stress are becoming more and more serious. In this research, strand-specific RNA sequencing (ssRNA-seq) was used to explore the dynamic changes in the transcriptome landscape of Arabidopsis thaliana exposed to cold temperatures (4°C) at different times. In total, 7,623 differentially expressed genes (DEGs) exhibited dynamic temporal changes during the cold treatments. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that the DEGs were enriched in cold response, secondary metabolic processes, photosynthesis, glucosinolate biosynthesis, and plant hormone signal transduction pathways. Meanwhile, long non-coding RNAs (lncRNAs) were identified after the assembly of the transcripts, from which 247 differentially expressed lncRNAs (DElncRNAs) and their potential target genes were predicted. 3,621 differentially alternatively spliced (DAS) genes related to RNA splicing and spliceosome were identified, indicating enhanced transcriptome complexity due to the alternative splicing (AS) in the cold. In addition, 739 cold-regulated transcription factors (TFs) belonging to 52 gene families were identified as well. This research analyzed the dynamic changes of the transcriptome landscape in response to cold stress, which reveals more complete transcriptional patterns during short- and long-term cold treatment and provides new insights into functional studies of that how plants are affected by cold stress.

A natural antisense RNA improves chrysanthemum cold tolerance by regulating the transcription factor DgTCP1

Long noncoding RNAs (lncRNAs) are widely involved in the regulation of plant growth and development, but their mechanism of action in response to cold stress in plants remains unclear. Here, we found an lncRNA transcribed from the antisense strand of DgTCP1 (class I Teosinte branched1/Cycloidea/Proliferating [TCP] transcription factor) of chrysanthemum (Chrysanthemum morifolium Ramat.), named DglncTCP1. During the response of chrysanthemum to cold stress, overexpression of DgTCP1 improved the cold tolerance of chrysanthemum, while the DgTCP1 editing line (dgtcp1) showed decreased tolerance to cold stress. Overexpression of DglncTCP1 also increased the cold tolerance of chrysanthemum, while the DglncTCP1 amiRNA lines (DglncTCP1 amiR-18/38) also showed decreased tolerance to cold stress. Additionally, the overexpression of DglncTCP1 upregulated the expression of DgTCP1. This indicated that DglncTCP1 may play a cis-regulatory role in the regulatory process of DgTCP1 in cold tolerance. DglncTCP1 acts as a scaffold to recruit the histone modification protein DgATX (ARABIDOPSIS TRITHORAX from chrysanthemum) to DgTCP1 to enhance H3K4me3 levels, thereby activating DgTCP1 expression. Moreover, DgTCP1 can directly target DgPOD (peroxidase gene from chrysanthemum) to promote its expression and reduce reactive oxygen species accumulation, thereby improving the cold tolerance of chrysanthemum. In conclusion, these results suggest that natural antisense lncRNA plays a key role in improving the cold tolerance of chrysanthemum.

Transcriptome-based gene regulatory network analyses of differential cold tolerance of two tobacco cultivars

BACKGROUND

Cold is one of the main abiotic stresses that severely affect plant growth and development, and crop productivity as well. Transcriptional changes during cold stress have already been intensively studied in various plant species. However, the gene networks involved in the regulation of differential cold tolerance between tobacco varieties with contrasting cold resistance are quite limited.

RESULTS

Here, we conducted multiple time-point transcriptomic analyses using Tai tobacco (TT, cold susceptibility) and Yan tobacco (YT, cold resistance) with contrasting cold responses. We identified similar DEGs in both cultivars after comparing with the corresponding control (without cold treatment), which were mainly involved in response to abiotic stimuli, metabolic processes, kinase activities. Through comparison of the two cultivars at each time point, in contrast to TT, YT had higher expression levels of the genes responsible for environmental stresses. By applying Weighted Gene Co-Expression Network Analysis (WGCNA), we identified two main modules: the pink module was similar while the brown module was distinct between the two cultivars. Moreover, we obtained 100 hub genes, including 11 important transcription factors (TFs) potentially involved in cold stress, 3 key TFs in the brown module and 8 key TFs in the pink module. More importantly, according to the genetic regulatory networks (GRNs) between TFs and other genes or TFs by using GENIE3, we identified 3 TFs (ABI3/VP1, ARR-B and WRKY) mainly functioning in differential cold responses between two cultivars, and 3 key TFs (GRAS, AP2-EREBP and C2H2) primarily involved in cold responses.

CONCLUSION

Collectively, our study provides valuable resources for transcriptome- based gene network studies of cold responses in tobacco. It helps to reveal how key cold responsive TFs or other genes are regulated through network. It also helps to identify the potential key cold responsive genes for the genetic manipulation of tobacco cultivars with enhanced cold tolerance in the future.

Antagonist Temperature Variation Affects the Photosynthetic Parameters and Secondary Metabolites of Ocimum basilicum L. and Salvia officinalis L

Climate change is one of the main challenges for actual and future generations. Global warming affects plants and animals and is responsible for considerable crop loss. This study studied the influence of antagonist successive stresses, cold-heat and heat-cold, on two medicinal plants Ocimum basilicum L. and Salvia officinalis L. The photosynthetic parameters decreased for plants under the variation of subsequent stress. Net assimilation rates and stomatal conductance to water vapor are more affected in the case of plants under cold-heat consecutive stress than heat-cold successive stress. Emissions of volatile organic compounds have been enhanced for plants under successive stress when compared with control plants. Chlorophyll concentrations for plants under successive stress decreased for basil and sage plants. The total phenolic and flavonoid contents were not affected by the successive stresses when compared with the plants under only one type of treatment.

Meta-analysis of transcriptomic responses to cold stress in plants

Transcriptomic analyses are needful tools to gain insight into the molecular mechanisms underlying plant responses to abiotic stresses. The aim of this study was to identify key genes differentially regulated in response to chilling stress in various plant species with different levels of tolerance to low temperatures. A meta-analysis was performed using the RNA-Seq data of published studies whose experimental conditions were comparable. The results confirmed the importance of ethylene in the hormonal cross-talk modulating the defensive responses against chilling stress, especially in sensitive species. The transcriptomic activity of five Ethylene Response Factors genes and a REDOX Responsive Transcription Factor 1 involved in hormone-related pathways belonging to ethylene metabolism and signal transduction were induced. Transcription activity of two genes encoding for heat shock factors was enhanced, together with various genes associated with developmental processes. Several transcription factor families showed to be commonly induced between different plant species. Protein-protein interaction networks highlighted the role of the photosystems I and II, as well as genes encoding for HSF and WRKY transcription factors. A model of gene regulatory network underlying plant responses to chilling stress was developed, allowing the delivery of new candidate genes for genetic improvement of crops towards low temperatures tolerance.

The miR164a-NAM3 module confers cold tolerance by inducing ethylene production in tomato

Because of a high sensitivity to cold, both the yield and quality of tomato (Solanum lycopersicum L.) are severely restricted by cold stress. The NAC transcription factor (TF) family has been characterized as an important player in plant growth, development, and the stress response, but the role of NAC TFs in cold stress and their interaction with other post-transcriptional regulators such as microRNAs in cold tolerance remains elusive. Here, we demonstrated that SlNAM3, the predicted target of Sl-miR164a/b-5p, improved cold tolerance as indicated by a higher maximum quantum efficiency of photosystem II (Fv/Fm), lower relative electrolyte leakage, and less wilting in SlNAM3-overexpression plants compared to wild-type. Further genetic and molecular confirmation revealed that Sl-miR164a/b-5p functioned upstream of SlNAM3 by inhibiting the expression of the latter, thus playing a negative role in cold tolerance. Interestingly, this role is partially mediated by an ethylene-dependent pathway because either Sl-miR164a/b-5p silencing or SlNAM3 overexpression improved cold tolerance in the transgenic lines by promoting ethylene production. Moreover, silencing of the ethylene synthesis genes, SlACS1A, SlACS1B, SlACO1, and SlACO4, resulted in a significant decrease in cold tolerance. Further experiments demonstrated that NAM3 activates SlACS1A, SlACS1B, SlACO1, and SlACO4 transcription by directly binding to their promoters. Taken together, the present study identified the miR164a-NAM3 module conferring cold tolerance in tomato plants via the direct regulation of SlACS1A, SlACS1B, SlACO1, and SlACO4 expression to induce ethylene synthesis.

Sulfenylation of ENOLASE2 facilitates H2O2-conferred freezing tolerance in Arabidopsis

H₂O₂ affects the expression of genes that are involved in plant responses to diverse environmental stresses; however, the underlying mechanisms remain elusive. Here, we demonstrate that H₂O₂ enhances plant freezing tolerance through its effect on a protein product of low expression of osmotically responsive genes2 (LOS2). LOS2 is translated into a major product, cytosolic enolase2 (ENO2), and sometimes an alternative product, the transcription repressor c-Myc-binding protein (MBP-1). ENO2, but not MBP-1, promotes cold tolerance by binding the promoter of C-repeat/DRE binding factor1 (CBF1), a central transcription factor in plant cold signaling, thus activating its expression. Overexpression of CBF1 restores freezing sensitivity of a LOS2 loss-of-function mutant. Furthermore, cold-induced H₂O₂ increases nuclear import and transcriptional binding activity of ENO2 by sulfenylating cysteine 408 and thereby promotes its oligomerization. Collectively, our results illustrate how H₂O₂ activates plant cold responses by sulfenylating ENO2 and promoting its oligomerization, leading to enhanced nuclear translocation and transcriptional activation of CBF1.

Genome-wide identification of cold-tolerance genes and functional analysis of IbbHLH116 gene in sweet potato

Sweet potato (Ipomoea batatas L.) originated from South America; therefore, it is vulnerable to low temperature. Here, the evolutionary analysis of 22 cold-responsive genes in 35 plant species revealed that the identified MYC-type basic helix-loop-helix (bHLH) transcription factors exhibit diverse structures. We found that the number of bHLH gene family members was significantly lower than that of cold-tolerant species. We further systematically evaluated the gene structure, promoter analysis, synteny analysis, and expression pattern of 28 bHLH gene family members in sweet potato. The basic helix-loop-helix protein 116 (IbbHLH116) has the closest phylogeny to the AtICE1 protein of A. thaliana. However, the IbbHLH116 protein from cold-tolerant variety FS18 showed a 37.90% of sequence homology with AtICE1 protein. Subcellular localization analysis showed that IbbHLH116 is localized in the nucleus. The transcripts of IbbHLH116 were highly accumulated in cold-tolerant genotype FS18, particularly in new leaves and stems, compared to the cold-sensitive genotype NC1 under cold stress. Overexpression of IbbHLH116 in the wild type (Col-0) A. thaliana significantly enhanced cold tolerance in transgenic plants by regulating activities of oxidative protective enzymes, such as peroxidase (POD), superoxide dismutase (SOD), and the contents of malondialdehyde (MDA), proline and soluble proteins. Moreover, overexpression of IbbHLH116 in ice1 mutant A. thaliana fully rescued the cold-sensitive phenotype by promoting the expression of C-repeat binding factors 3 (CBF3). Overexpression of IbbHLH116 in the sweet potato callus also induced the expression of CBF3 under low temperature. These results imply that IbbHLH116 can perform the function of the ICE1 gene in conferring cold tolerance in sweet potato.

Transcriptome analysis of the winter wheat Dn1 in response to cold stress

BACKGROUND

Heilongjiang Province has a long and cold winter season (the minimum temperature can reach -30 ℃), and few winter wheat varieties can safely overwinter. Dongnongdongmai1 (Dn1) is the first winter wheat variety that can safely overwinter in Heilongjiang Province. This variety fills the gap for winter wheat cultivation in the frigid region of China and greatly increases the land utilization rate. To understand the molecular mechanism of the cold response, we conducted RNA-sequencing analysis of Dn1 under cold stress.

RESULTS

Approximately 120,000 genes were detected in Dn1 under cold stress. The numbers of differentially expressed genes (DEGs) in the six comparison groups (0 ℃ vs. 5 ℃, -5 ℃ vs. 5 ℃, -10 ℃ vs. 5 ℃, -15 ℃ vs. 5 ℃, -20 ℃ vs. 5 ℃ and -25 ℃ vs. 5 ℃) were 11,313, 8313, 15,636, 13,671, 14,294 and 13,979, respectively. Gene Ontology functional annotation suggested that the DEGs under cold stress mainly had "binding", "protein kinase" and "catalytic" activities and were involved in "oxidation-reduction", "protein phosphorylation" and "carbohydrate metabolic" processes. Kyoto Encyclopedia of Genes and Genomes enrichment analysis indicated that the DEGs performed important functions in cold signal transduction and carbohydrate metabolism. In addition, major transcription factors (AP2/ERF, bZIP, NAC, WRKY, bHLH and MYB) participating in the Dn1 cold stress response were activated by low temperature.

CONCLUSION

This is the first study to explore the Dn1 transcriptome under cold stress. Our study comprehensively analysed the key genes involved in cold signal transduction and carbohydrate metabolism in Dn1 under cold stress. The results obtained by transcriptome analysis could help to further explore the cold resistance mechanism of Dn1 and provide basis for breeding of cold-resistant crops.

Temperature-phase transcriptomics reveals that hormones and sugars in the phloem of grape participate in tolerance during cold acclimation

Most of the upregulated genes contributed to the accumulation of soluble sugars and ABA in the phloem of 'Vitis amurensis' compared to 'Merlot' during cold acclimation. Extreme cold is one of the dominant abiotic factors affecting grape yield and quality. However, the changes in sugars, phytohormones, and gene expression in the branch phloem of different tolerant grape varieties during cold acclimation remain elusive. The data supported that with decreasing temperature, the contents of fructose, sucrose, and ABA in the phloem of Vitis amurensis (cold-tolerant, T) and 'Merlot' (cold-sensitive, S) increased during cold acclimation, and these indicators were higher in T than in S. Furthermore, the activities of sucrose synthetase, sucrose phosphate synthetase, and acid invertase peaked in the early phase of cold acclimation (approximately 5 °C) compared to other phases (approximately 28 °C, 0 °C, - 5 °C and - 10 °C). Moreover, the RNA sequencing results helped identify a total of 11,343 differentially expressed genes in the phloem of T and S, among which 4912 were upregulated and 6431 were downregulated. In the abscisic acid pathway, CRTISO, PSPY1-1, CYCP707A4-2, PYL4-1, PYL4-2, P2C08, SAPK2, TARAB1, and DBF3 were more highly expressed in T than in S. In the starch and sucrose metabolism pathway, HXK1, PGMP, GLGL1, SUS6, VCINV, BGL11, SSY1, GPS, BAM1 and BAM3 were also more highly expressed in T than in S. Moreover, the genes related to oxidative phosphorylation, such as NDHF, ND4, ND1, NAD7, NAD2, ATPB, YMF19, ATP9, PMA1 and AHA8, were upregulated in T. These results will be beneficial for understanding the potential differences in tolerance across two different cold-tolerant grapes with respect to sugar metabolism and gene expression.

Expression Level Dominance and Homeolog Expression Bias Upon Cold Stress in the F1 Hybrid Between the Invasive Sphagneticola trilobata and the Native S. calendulacea in South China, and Implications for Its Invasiveness

The role of hybridization is significant in biological invasion, and thermotolerance is a trait critical to range expansions. The South American Sphagneticola trilobata is now widespread in South China, threatening the native S. calendulacea by competition and hybridization. Furthermore, upon formation, their F1 hybrid can quickly replace both parents. In this study, the three taxa were used as a model to investigate the consequences of hybridization on cold tolerance, particularly the effect of subgenome dominance in the hybrid. Upon chilling treatments, physiological responses and transcriptome profiles were compared across different temperature points to understand their differential responses to cold. While both parents showed divergent responses, the hybrid’s responses showed an overall resemblance to S. calendulacea, but the contribution of homeolog expression bias to cold stress was not readily evident in the F1 hybrid possibly due to inherent bias that comes with the sampling location. Our findings provided insights into the role of gene expression in differential cold tolerance, and further contribute to predicting the invasive potential of other hybrids between S. trilobata and its congeners around the world.