Disordered cold regulated15 proteins protect chloroplast membranes during freezing through binding and folding, but do not stabilize chloroplast enzymes in vivo

HOS15-mediated turnover of PRR7 enhances freezing tolerance

Arabidopsis PSEUDORESPONSE REGULATOR7 (PRR7) is a core component of the circadian oscillator which also plays a crucial role in freezing tolerance. PRR7 undergoes proteasome-dependent degradation to discretely phase maximal expression in early evening. While its repressive activity on downstream genes is integral to cold regulation, the mechanism of the conditional regulation of the PRR7 abundance is unknown. We used mutant analysis, protein interaction and ubiquitylation assays to establish that the ubiquitin ligase adaptor, HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE 15 (HOS15), controls the protein accumulation pattern of PRR7 through direct protein-protein interactions at low temperatures. Freezing tolerance and electrolyte leakage assays show that PRR7 enhances cold temperature sensitivity, supported by ChIP-qPCR at C-REPEAT BINDING FACTOR1 (CBF1) and COLD-REGULATED 15A (COR15A) promoters where PRR7 levels were higher in hos15 mutants. HOS15 mediates PRR7 turnover through enhanced ubiquitylation at low temperature in the dark. Under the same conditions, increased PRR7 association with the promoters of CBFs and COR15A in hos15 correlates with decreased CBF1 and COR15A transcription and enhanced freezing sensitivity. We propose a novel mechanism whereby HOS15-mediated degradation of PRR7 provides an intersection between the circadian system and other cold acclimation pathways that lead to increased freezing tolerance.

Altering cold-regulated gene expression decouples the salicylic acid-growth trade-off in Arabidopsis

In Arabidopsis (Arabidopsis thaliana), overproduction of salicylic acid (SA) increases disease resistance and abiotic stress tolerance but penalizes growth. This growth-defense trade-off has hindered the adoption of SA-based disease management strategies in agriculture. However, investigation of how SA inhibits plant growth has been challenging because many SA-hyperaccumulating Arabidopsis mutants have developmental defects due to the pleiotropic effects of the underlying genes. Here, we heterologously expressed a bacterial SA synthase gene in Arabidopsis and observed that elevated SA levels decreased plant growth and reduced the expression of cold-regulated (COR) genes in a dose-dependent manner. Growth suppression was exacerbated at below-ambient temperatures. Severing the SA-responsiveness of individual COR genes was sufficient to overcome the growth inhibition caused by elevated SA at ambient and below-ambient temperatures while preserving disease- and abiotic-stress-related benefits. Our results show the potential of decoupling SA-mediated growth and defense trade-offs for improving crop productivity.

Heavy metal toxicity leads to accumulation of insoluble proteins and induces endoplasmic reticulum stress-specific unfolded protein response in Arabidopsis thaliana

Unfolded protein accumulation in the endoplasmic reticulum (ER) triggers ER stress, leading to a unique transcriptomic response called unfolded protein response (UPR). While ER stress is linked to various environmental stresses, its role in plant responses to heavy metal toxicity remains unclear. This study aimed to elucidate if heavy metals Fe, Zn, Cu, and As induce ER stress in plants. For this purpose, Arabidopsis thaliana seedlings were treated with Fe (200, 400 µM), Zn (500, 700 µM), Cu (25, 50 µM), and As (250, 500 µM) for 7 days, which resulted in 50-70% decrease in plant growth. All treatments increased insoluble protein levels, indicating unfolded protein accumulation, with the highest induction observed for 50 µM Cu treatment (fivefold). Expressions of genes involved in the perception and signaling of ER stress (IRE1, bZIP28, bZIP60, bZIP17) indicate that Zn toxicity specifically induces bZIP28 but not the IRE1 branch of UPR. All metals except Fe also induced genes associated with protein folding in the ER (BIP1, BIP3, and CNX) and ER-associated protein degradation (ERAD) (HRD1). This finding indicates Zn, Cu, and As but not Fe cause ER stress in plants. Furthermore, increased expression of ER oxidoreductase 1 (ERO1) suggests that metal toxicity also disrupts oxidative protein folding in the ER lumen. This study enhances our understanding of the intricate interplay between essential nutrients, metal toxicity, protein folding machinery, and ER stress, demonstrating that heavy metal toxicity has an ER stress component in plants alongside its established effects on energy metabolism, membrane integrity, and oxidative stress.

HOS15-mediated turnover of PRR7 enhances freezing tolerance

Arabidopsis PSEUDO RESPONSE REGULATOR7 (PRR7) is a core component of the circadian oscillator which also plays a crucial role in freezing tolerance. PRR7 undergoes proteasome-dependent degradation to discretely phase maximal expression in early evening. While its transcriptional repressive activity on downstream genes is integral to cold regulation, the mechanism of the conditional regulation of the PRR7 protein activity is unknown. We used double mutant analysis, protein interaction and ubiquitylation assays to establish that the ubiquitin ligase adaptor, HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE 15 (HOS15), controls the protein accumulation pattern of PRR7 through direct protein-protein interactions. Freezing tolerance and electrolyte leakage assays show that PRR7 enhances cold temperature sensitivity, supported by ChIP-qPCR at C-REPEAT BINDING FACTOR (CBF) and COLD REGULATED 15A (COR15A) promoters where PRR7 levels were higher in hos15 mutants. We establish that HOS15 mediates PRR7 protein turnover through enhanced ubiquitylation at low temperature in the dark. Under the same conditions, increased PRR7 association with the promoter regions of CBFs and COR15A in hos15 correlates with decreased CBF1 and COR15A transcription and enhanced freezing sensitivity. We propose a novel mechanism whereby HOS15-mediated regulation of PRR7 provides an intersection between the circadian system and other cold acclimation pathways leading to freezing tolerance through upregulation of CBF1 and COR15A.

Functional in vitro diversity of an intrinsically disordered plant protein during freeze-thawing is encoded by its structural plasticity

Intrinsically disordered late embryogenesis abundant (LEA) proteins play a central role in the tolerance of plants and other organisms to dehydration brought upon, for example, by freezing temperatures, high salt concentration, drought or desiccation, and many LEA proteins have been found to stabilize dehydration-sensitive cellular structures. Their conformational ensembles are highly sensitive to the environment, allowing them to undergo conformational changes and adopt ordered secondary and quaternary structures and to participate in formation of membraneless organelles. In an interdisciplinary approach, we discovered how the functional diversity of the Arabidopsis thaliana LEA protein COR15A found in vitro is encoded in its structural repertoire, with the stabilization of membranes being achieved at the level of secondary structure and the stabilization of enzymes accomplished by the formation of oligomeric complexes. We provide molecular details on intra- and inter-monomeric helix-helix interactions, demonstrate how oligomerization is driven by an α-helical molecular recognition feature (α-MoRF) and provide a rationale that the formation of noncanonical, loosely packed, right-handed coiled-coils might be a recurring theme for homo- and hetero-oligomerization of LEA proteins.

Au-Based Nanoparticles Enhance Low Temperature Tolerance in Wheat by Regulating Some Physiological Parameters and Gene Expression

One of the key problems of biology is how plants adapt to unfavorable conditions, such as low temperatures. A special focus is placed on finding ways to increase tolerance in important agricultural crops like wheat. Au-based nanoparticles (Au-NPs) have been employed extensively in this area in recent years. Au-NPs can be produced fast and easily using low-cost chemical reagents. When employed in microdoses, Au-NPs are often non-toxic to plants, animals, and people. In addition, Au-NPs mainly have favorable impacts on plants. In this study, we investigated the effect of Au-NP seed nanopriming (diameter 15.3 nm, Au concentration 5-50 µg mL-1) on cold tolerance, as well as some physiological, biochemical and molecular parameters, of cold-sustainable wheat (Triticum aestivum L.) genotype Zlata. The treatment with Au-NPs improved tolerance to low temperatures in control conditions and after cold hardening. Au-NPs treatment boosted the intensity of growth processes, the quantity of photosynthetic pigments, sucrose in leaves, and the expressions of encoded RuBisCo and Wcor15 genes. The potential mechanisms of Au-NPs' influence on the cold tolerance of wheat varieties were considered.

Protein Disorder in Plant Stress Adaptation: From Late Embryogenesis Abundant to Other Intrinsically Disordered Proteins

Global climate change has caused severe abiotic and biotic stresses, affecting plant growth and food security. The mechanical understanding of plant stress responses is critical for achieving sustainable agriculture. Intrinsically disordered proteins (IDPs) are a group of proteins without unique three-dimensional structures. The environmental sensitivity and structural flexibility of IDPs contribute to the growth and developmental plasticity for sessile plants to deal with environmental challenges. This article discusses the roles of various disordered proteins in plant stress tolerance and resistance, describes the current mechanistic insights into unstructured proteins such as the disorder-to-order transition for adopting secondary structures to interact with specific partners (i.e., cellular membranes, membrane proteins, metal ions, and DNA), and elucidates the roles of liquid-liquid phase separation driven by protein disorder in stress responses. By comparing IDP studies in animal systems, this article provides conceptual principles of plant protein disorder in stress adaptation, reveals the current research gaps, and advises on the future research direction. The highlighting of relevant unanswered questions in plant protein disorder research aims to encourage more studies on these emerging topics to understand the mechanisms of action behind their stress resistance phenotypes.

A Novel Isoprene Synthase from the Monocot Tree Copernicia prunifera (Arecaceae) Confers Enhanced Drought Tolerance in Transgenic Arabidopsis

The capacity to emit isoprene, among other stresses, protects plants from drought, but the molecular mechanisms underlying this trait are only partly understood. The Arecaceae (palms) constitute a very interesting model system to test the involvement of isoprene in enhancing drought tolerance, as their high isoprene emissions may have contributed to make them hyperdominant in neotropical dry forests, characterized by recurrent and extended periods of drought stress. In this study we isolated and functionally characterized a novel isoprene synthase, the gene responsible for isoprene biosynthesis, from Copernicia prunifera, a palm from seasonally dry tropical forests. When overexpressed in the non-emitter Arabidopsis thaliana, CprISPS conferred significant levels of isoprene emission, together with enhanced tolerance to water limitation throughout plant growth and development, from germination to maturity. CprISPS overexpressors displayed higher germination, cotyledon/leaf greening, water usage efficiency, and survival than WT Arabidopsis under various types of water limitation. This increased drought tolerance was accompanied by a marked transcriptional up-regulation of both ABA-dependent and ABA-independent key drought response genes. Taken together, these results demonstrate the capacity of CprISPS to enhance drought tolerance in Arabidopsis and suggest that isoprene emission could have evolved in Arecaceae as an adaptive mechanism against drought.

Plant dehydrins and dehydrin-like proteins: characterization and participation in abiotic stress response

Abiotic stress has a significant impact on plant growth and development. It causes changes in the subcellular organelles, which, due to their stress sensitivity, can be affected. Cellular components involved in the abiotic stress response include dehydrins, widely distributed proteins forming a class II of late embryogenesis abundant protein family with characteristic properties including the presence of evolutionarily conserved sequence motifs (including lysine-rich K-segment, N-terminal Y-segment, and often phosphorylated S motif) and high hydrophilicity and disordered structure in the unbound state. Selected dehydrins and few poorly characterized dehydrin-like proteins participate in cellular stress acclimation and are also shown to interact with organelles. Through their functioning in stabilizing biological membranes and binding reactive oxygen species, dehydrins and dehydrin-like proteins contribute to the protection of fragile organellar structures under adverse conditions. Our review characterizes the participation of plant dehydrins and dehydrin-like proteins (including some organellar proteins) in plant acclimation to diverse abiotic stress conditions and summarizes recent updates on their structure (the identification of dehydrin less conserved motifs), classification (new proposed subclasses), tissue- and developmentally specific accumulation, and key cellular activities (including organellar protection under stress acclimation). Recent findings on the subcellular localization (with emphasis on the mitochondria and plastids) and prospective applications of dehydrins and dehydrin-like proteins in functional studies to alleviate the harmful stress consequences by means of plant genetic engineering and a genome editing strategy are also discussed.

Cold-responsive transcription factors in Arabidopsis and rice: A regulatory network analysis using array data and gene co-expression network

Plant growth and development can be influenced by cold stress. Responses of plants to cold are regulated in part by transcription factors (TFs) and microRNAs, which their determination would be necessary in comprehension of the corresponding molecular cues. Here, transcriptomes of Arabidopsis and rice were analyzed to computationally determine TFs and microRNAs that are differentially responsive to cold treatment, and their co-expression networks were established. Among 181 Arabidopsis and 168 rice differentially expressed TF genes, 37 (26 novel) were up- and 16 (8 novel) were downregulated. Common TF encoding genes were from ERF, MYB, bHLH, NFY, bZIP, GATA, HSF and WRKY families. NFY A4/C2/A10 were the significant hub TFs in both plants. Phytohormone responsive cis-elements such as ABRE, TGA, TCA and LTR were the common cis-elements in TF promoters. Arabidopsis had more responsive TFs compared to rice possibly due to its greater adaptation to ranges geographical latitudes. Rice had more relevant miRNAs probably because of its bigger genome size. The interacting partners and co-expressed genes were different for the common TFs so that of the downstream regulatory networks and the corresponding metabolic pathways. Identified cold-responsive TFs in (A + R) seemed to be more engaged in energy metabolism esp. photosynthesis, and signal transduction, respectively. At post-transcriptional level, miR5075 showed to target many identified TFs in rice. In comparison, the predictions showed that identified TFs are being targeted by diverse groups of miRNAs in Arabidopsis. Novel TFs, miRNAs and co-expressed genes were introduced as cold-responsive markers that can be harnessed in future studies and development of crop tolerant varieties.

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.

Genome wide identification of GDSL gene family explores a novel GhirGDSL26 gene enhancing drought stress tolerance in cotton

BACKGROUND

Current climate change scenarios are posing greater threats to the growth and development of plants. Thus, significant efforts are required that can mitigate the negative effects of drought on the cotton plant. GDSL esterase/lipases can offer an imperative role in plant development and stress tolerance. However, thesystematic and functional roles of the GDSL gene family, particularly in cotton under water deficit conditions have not yet been explored.

RESULTS

In this study, 103, 103, 99, 198, 203, 239, 249, and 215 GDSL proteins were identified in eight cotton genomes i.e., Gossypium herbaceum (A1), Gossypium arboretum (A2), Gossypium raimondii (D5), Gossypium hirsutum (AD1), Gossypium barbadense (AD2), Gossypium tomentosum (AD3), Gossypium mustelinum (AD4), Gossypium darwinii (AD5), respectively. A total of 198 GDSL genes of Gossypium hirsutum were divided into eleven clades using phylogenetic analysis, and the number of GhirGDSL varied among different clades. The cis-elements analysis showed that GhirGDSL gene expression was mainly related to light, plant hormones, and variable tense environments. Combining the results of transcriptome and RT-qPCR, GhirGDSL26 (Gh_A01G1774), a highly up-regulated gene, was selected for further elucidating its tole in drought stress tolerance via estimating physiological and biochemical parameters. Heterologous expression of the GhirGDSL26 gene in Arabidopsis thaliana resulted in a higher germination and survival rates, longer root lengths, lower ion leakage and induced stress-responsive genes expression under drought stress. This further highlighted that overexpressed plants had a better drought tolerance as compared to the wildtype plants. Moreover, 3, 3'-diaminobenzidine (DAB) and Trypan staining results indicated reduced oxidative damage, less cell membrane damage, and lower ion leakage in overexpressed plants as compared to wild type. Silencing of GhirGDSL26 in cotton via VIGS resulting in a susceptible phenotype, higher MDA and H₂O₂ contents, lower SOD activity, and proline content.

CONCLUSION

Our results demonstrated that GhirGDSL26 plays a critical role in cotton drought stress tolerance. Current findings enrich our knowledge of GDSL genes in cotton and provide theoretical guidance and excellent gene resources for improving drought tolerance in cotton.

LEAfing through literature: late embryogenesis abundant proteins coming of age-achievements and perspectives

To deal with increasingly severe periods of dehydration related to global climate change, it becomes increasingly important to understand the complex strategies many organisms have developed to cope with dehydration and desiccation. While it is undisputed that late embryogenesis abundant (LEA) proteins play a key role in the tolerance of plants and many anhydrobiotic organisms to water limitation, the molecular mechanisms are not well understood. In this review, we summarize current knowledge of the physiological roles of LEA proteins and discuss their potential molecular functions. As these are ultimately linked to conformational changes in the presence of binding partners, post-translational modifications, or water deprivation, we provide a detailed summary of current knowledge on the structure-function relationship of LEA proteins, including their disordered state in solution, coil to helix transitions, self-assembly, and their recently discovered ability to undergo liquid-liquid phase separation. We point out the promising potential of LEA proteins in biotechnological and agronomic applications, and summarize recent advances. We identify the most relevant open questions and discuss major challenges in establishing a solid understanding of how these intriguing molecules accomplish their tasks as cellular sentinels at the limits of surviving water scarcity.

Coronatine Enhances Chilling Tolerance of Tomato Plants by Inducing Chilling-Related Epigenetic Adaptations and Transcriptional Reprogramming

Low temperature is an important environmental factor limiting the widespread planting of tropical and subtropical crops. The application of plant regulator coronatine, which is an analog of Jasmonic acid (JA), is an effective approach to enhancing crop's resistance to chilling stress and other abiotic stresses. However, the function and mechanism of coronatine in promoting chilling resistance of tomato is unknown. In this study, coronatine treatment was demonstrated to significantly increase tomato chilling tolerance. Coronatine increases H3K4me3 modifications to make greater chromatin accessibility in multiple chilling-activated genes. Corresponding to that, the expression of CBFs, other chilling-responsive transcription factor (TF) genes, and JA-responsive genes is significantly induced by coronatine to trigger an extensive transcriptional reprogramming, thus resulting in a comprehensive chilling adaptation. These results indicate that coronatine enhances the chilling tolerance of tomato plants by inducing epigenetic adaptations and transcriptional reprogramming.

Discovery of cold-resistance genes in Vitis amurensis using bud-based quantitative trait locus mapping and RNA-seq

Background

In cold regions, low temperature is the main limiting factor affecting grape production. As an important breeding resource, V. amurensis Rupr. has played a crucial role in the discovery of genes which confer cold resistance in grapes. Thus far, many cold-resistance genes have been reported based on the study of V. amurensis. In order to identify more candidate genes related to cold resistance in V. amurensis, QTL mapping and RNA-seq was conducted based on the hybrid population and different cold-resistance cultivars in this study.

Results

In this study, highly cold-resistant grape cultivar ‘Shuangyou’ (SY) which belongs to V. amurensis, and cold-sensitive cultivar ‘Red Globe’ (RG) which belongs to Vitis vinifera L. were used to identify cold resistance genes. Cold-resistance quantitative trait locus (QTL) mapping was performed based on genetic population construction through interspecific crossing of ‘Shuangyou’ and ‘Red Globe’. Additionally, transcriptome analysis was conducted for the dormant buds of these two cultivars at different periods. Based on transcriptome analysis and QTL mapping, many new structural genes and transcription factors which relate to V. amurensis cold resistance were discovered, including CORs (VaCOR413IM), GSTs (VaGST-APIC, VaGST-PARB, VaGSTF9 and VaGSTF13), ARFs (VaIAA27 and VaSAUR71), ERFs (VaAIL1), MYBs (VaMYBR2, VaMYBLL and VaMYB3R-1) and bHLHs (VaICE1 and VabHLH30).

Conclusions

This discovery of candidate cold-resistance genes will provide an important theoretical reference for grape cold-resistance mechanisms, research, and cold-resistant grape cultivar breeding in the future.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08788-y.

GmWRKY21, a Soybean WRKY Transcription Factor Gene, Enhances the Tolerance to Aluminum Stress in Arabidopsis thaliana

The WRKY transcription factors (TFs) are one of the largest families of TFs in plants and play multiple roles in plant growth and development and stress response. In this study, GmWRKY21 encoding a WRKY transcription factor was functionally characterized in Arabidopsis and soybean. The GmWRKY21 protein containing a highly conserved WRKY domain and a C₂H₂ zinc-finger structure is located in the nucleus and has the characteristics of transcriptional activation ability. The GmWRKY21 gene presented a constitutive expression pattern rich in the roots, leaves, and flowers of soybean with over 6-fold of relative expression levels and could be substantially induced by aluminum stress. As compared to the control, overexpression of GmWRKY21 in Arabidopsis increased the root growth of seedlings in transgenic lines under the AlCl₃ concentrations of 25, 50, and 100 μM with higher proline and lower MDA accumulation. The results of quantitative real-time polymerase chain reaction (qRT-PCR) showed that the marker genes relative to aluminum stress including ALMT, ALS3, MATE, and STOP1 were induced in GmWRKY21 transgenic plants under AlCl₃ treatment. The stress-related genes, such as KIN1, COR15A, COR15B, COR47, GLOS3, and RD29A, were also upregulated in GmWRKY21 transgenic Arabidopsis under aluminum stress. Similarly, stress-related genes, such as GmCOR47, GmDREB2A, GmMYB84, GmKIN1, GmGST1, and GmLEA, were upregulated in hair roots of GmWRKY21 transgenic plants. In summary, these results suggested that the GmWRKY21 transcription factor may promote the tolerance to aluminum stress mediated by the pathways regulating the expression of the acidic aluminum stress-responsive genes and abiotic stress-responsive genes.

Specific CBF transcription factors and cold-responsive genes fine-tune the early triggering response after acquisition of cold priming and memory

Plants need to adapt to fluctuating temperatures throughout their lifetime. Previous research showed that Arabidopsis memorizes a first cold stress (priming) and improves its primed freezing tolerance further when subjected to a second similar stress after a lag phase. This study investigates primary metabolomic and transcriptomic changes during early cold priming or triggering after 3 days at 4°C interrupted by a memory phase. DREB1 family transcription factors DREB1C/CBF2, DREB1D/CBF4, DREB1E/DDF2, and DREB1F/DDF1 were strongly significantly induced throughout the entire triggering. During triggering, genes encoding Late Embryogenesis Abundant (LEA), antifreeze proteins or detoxifiers of reactive oxygen species (ROS) were higher expressed compared with priming. Examples of early triggering responders were xyloglucan endotransglucosylase/hydrolase genes encoding proteins involved in cell wall remodeling, while late responders were identified to act in fine-tuning the stress response and developmental regulation. Induction of non-typical members of the DREB subfamily of ERF/AP2 transcription factors, the relatively small number of induced CBF regulon genes and a slower accumulation of selected cold stress associated metabolites indicate that a cold triggering stimulus might be sensed as milder stress in plants compared with priming. Further, strong induction of CBF4 throughout triggering suggests a unique function of this gene for the response to alternating temperatures.

Molecular basis of priming-induced acquired tolerance to multiple abiotic stresses in plants

The growth, survival, and productivity of plants are constantly challenged by diverse abiotic stresses. When plants are exposed to stress for the first time, they can capture molecular information and store it as a form of memory, which enables them to competently and rapidly respond to subsequent stress(es). This process is referred to as a priming-induced or acquired stress response. In this review, we discuss how (i) the storage and retrieval of the information from stress memory modulates plant physiological, cellular, and molecular processes in response to subsequent stress(es), (ii) the intensity, recurrence, and duration of priming stimuli influences the outcomes of the stress response, and (iii) the varying responses at different plant developmental stages. We highlight current understanding of the distinct and common molecular processes manifested at the epigenetic, (post-)transcriptional, and post-translational levels mediated by stress-associated molecules and metabolites, including phytohormones. We conclude by emphasizing how unravelling the molecular circuitry underlying diverse priming-stimuli-induced stress responses could propel the use of priming as a management practice for crop plants. This practice, in combination with precision agriculture, could aid in increasing yield quantity and quality to meet the rapidly rising demand for food.

The F-box E3 ubiquitin ligase AtSDR is involved in salt and drought stress responses in Arabidopsis

F-box protein genes have been shown to play vital roles in plant development and stress respones. In Arabidopsis, there are more than 600 F-box proteins, and most of their functions are unclear. The present study shows that the F-box (SKP1-Cullin/CDC53-F-box) gene At5g15710 (Salt and Drought Responsiveness, SDR) is involved in abiotic stress responses in Arabidopsis. SDR is expressed in all tissues of Arabidopsis and is upregulated by salt and heat stresses and ABA treatment but downregulated by drought stress. Subcellular localization analysis shows that the SDR protein colocalizes with the nucleus. 35S:AntiSDR plants are hypersensitive to salt stress, but 35S:SDR plants display a salt-tolerant phenotype. Furthermore, 35S:SDR plants are hypersensitive to drought stress, while 35S:AntiSDR plants are significantly more drought tolerant. Overall, our results suggest that SDR is involved in salt and drought stress responses in Arabidopsis.

Unraveling the complexity of faba bean (Vicia faba L.) transcriptome to reveal cold-stress-responsive genes using long-read isoform sequencing technology

Faba bean (Vicia faba L.), a globally important grain legume providing a stable source of dietary protein, was one of the earliest plant cytogenetic models. However, the lack of draft genome annotations and unclear structural information on mRNA transcripts have impeded its genetic improvement. To address this, we sequenced faba bean leaf transcriptome using the PacBio single-molecule long-read isoform sequencing platform. We identified 28,569 nonredundant unigenes, ranging from 108 to 9669 bp, with a total length of 94.5 Mb. Many unigenes (3597, 12.5%) had 2-20 isoforms, indicating a highly complex transcriptome. Approximately 96.5% of the unigenes matched sequences in public databases. The predicted proteins and transcription factors included NB-ARC, Myb_domain, C3H, bHLH, and heat shock proteins, implying that this genome has an abundance of stress resistance genes. To validate our results, we selected WCOR413-15785, DHN2-12403, DHN2-14197, DHN2-14797, COR15-14478, and HVA22-15 unigenes from the ICE-CBF-COR pathway to analyze their expression patterns in cold-treated samples via qRT-PCR. The expression of dehydrin-related genes was induced by cold stress. The assembled data provide the first insights into the deep sequencing of full-length RNA from faba bean at the single-molecule level. This study provides an important foundation to improve gene modeling and protein prediction.

Natural Variation among Arabidopsis Accessions in the Regulation of Flavonoid Metabolism and Stress Gene Expression by Combined UV Radiation and Cold

Plants are constantly exposed to stressful environmental conditions. Plant stress reactions were mainly investigated for single stress factors. However, under natural conditions plants may be simultaneously exposed to different stresses. Responses to combined stresses cannot be predicted from the reactions to the single stresses. Flavonoids accumulate in Arabidopsis thaliana during exposure to UV-A, UV-B or cold, but the interactions of these factors on flavonoid biosynthesis were unknown. We therefore investigated the interaction of UV radiation and cold in regulating the expression of well-characterized stress-regulated genes, and on transcripts and metabolites of the flavonoid biosynthetic pathway in 52 natural Arabidopsis accessions that differ widely in their freezing tolerance. The data revealed interactions of cold and UV on the regulation of stress-related and flavonoid biosynthesis genes, and on flavonoid composition. In many cases, plant reactions to a combination of cold and UV were unique under combined stress and not predictable from the responses to the single stresses. Strikingly, all correlations between expression levels of flavonoid biosynthesis genes and flavonol levels were abolished by UV-B exposure. Similarly, correlations between transcript levels of flavonoid biosynthesis genes or flavonoid contents, and freezing tolerance were lost in the presence of UV radiation, while correlations with the expression levels of cold-regulated genes largely persisted. This may indicate different molecular cold acclimation responses in the presence or absence of UV radiation.

Growth-defense trade-offs and yield loss in plants with engineered cell walls

As a major component of plant secondary cell walls, lignin provides structural integrity and rigidity, and contributes to primary defense by providing a physical barrier to pathogen ingress. Genetic modification of lignin biosynthesis has been adopted to reduce the recalcitrance of lignified cell walls to improve biofuel production, tree pulping properties and forage digestibility. However, lignin-modification is often, but unpredictably, associated with dwarf phenotypes. Hypotheses suggested to explain this include: collapsed vessels leading to defects in water and solute transport; accumulation of molecule(s) that are inhibitory to plant growth or deficiency of metabolites that are critical for plant growth; activation of defense pathways linked to cell wall integrity sensing. However, there is still no commonly accepted underlying mechanism for the growth defects. Here, we discuss recent data on transcriptional reprogramming in plants with modified lignin content and their corresponding suppressor mutants, and evaluate growth-defense trade-offs as a factor underlying the growth phenotypes. New approaches will be necessary to estimate how gross changes in transcriptional reprogramming may quantitatively affect growth. Better understanding of the basis for yield drag following cell wall engineering is important for the biotechnological exploitation of plants as factories for fuels and chemicals.

Arabidopsis cold-regulated plasma membrane protein Cor413pm1 is a regulator of ABA response

Cold-regulated (COR) genes are considered downstream functional genes in the cold-response pathway. However, we identified a plasma membrane-type, AtCor413pm1, as a regulatory gene for the abscisic acid (ABA) response, and found that ABA induced it predominantly in Arabidopsis roots, vasculature, stipules, and guard cells. Differentially expressed genes combined with qPCR analysis revealed the expressions of three ABA-responsive genes (AtDTX50, AtABR1, and AtCIPK20) were significantly altered in the ABA-treated atcor413pm1 mutant, compared to the wild-type. Furthermore, the ABA-induced transient Ca²⁺ oscillation in the plasma membrane of atcor413pm1 roots was different from that observed in the wild-type. Our results revealed that AtCor413pm1 might play a role in the cross-talk between the ABA and stress response pathways.

Stabilization of Dry Sucrose Glasses by Four LEA_4 Proteins from Arabidopsis thaliana

Cells of many organisms and organs can withstand an (almost) total water loss (anhydrobiosis). Sugars play an essential role in desiccation tolerance due to their glass formation ability during dehydration. In addition, intrinsically disordered LEA proteins contribute to cellular survival under such conditions. One possible mechanism of LEA protein function is the stabilization of sugar glasses. However, little is known about the underlying mechanisms. Here we used FTIR spectroscopy to investigate sucrose (Suc) glass stability dried from water or from two buffer components in the presence of four recombinant LEA and globular reference proteins. Buffer ions influenced the strength of the Suc glass in the order Suc < Suc/Tris < Suc/NaP. LEA proteins strengthened the sugar H-bonded network and the molecular structure in the glassy state. The position of νOH peak and the wavenumber–temperature coefficient (WTC_g) provided similar information about the H-bonded network. Protein aggregation of LEA proteins was reduced in the desiccation-induced Suc glassy state. Detailed knowledge about the role of LEA proteins in the stabilization of dry sugar glasses yields information about their role in anhydrobiosis. This may open the possibility to use such proteins in biotechnical applications requiring dry storage of biologicals such as proteins, cells or tissues.

Measuring Freezing Tolerance of Leaves and Rosettes: Electrolyte Leakage and Chlorophyll Fluorescence Assays

Quantitative assessment of freezing tolerance is essential to unravel plant adaptations to cold temperatures. Not only the survival of whole plants, but also impairment of detached leaves or small rosettes after a freeze-thaw cycle can be used to accurately quantify plant freezing tolerance in terms of LT₅₀ values. Here we describe two methods to determine the freezing tolerance of detached leaves or rosettes using a full or selected set of freezing temperatures and an additional method using chlorophyll fluorescence as a different physiological parameter. Firstly, we illustrate how to assess the integrity of (predominantly) the plasma membrane during freezing using an electrolyte leakage assay. Secondly, we provide a chlorophyll fluorescence imaging protocol to determine the freezing tolerance of the photosynthetic apparatus.

Target enzymes are stabilized by AfrLEA6 and a gain of α-helix coincides with protection by a group 3 LEA protein during incremental drying

Anhydrobiotic organisms accumulate late embryogenesis abundant (LEA) proteins, a family of intrinsically disordered proteins (IDPs) reported to improve cellular tolerance to water stress. Here we show that AfrLEA6, a Group 6 LEA protein only recently discovered in animals, protects lactate dehydrogenase (LDH), citrate synthase (CS) and phosphofructokinase (PFK) against damage during desiccation. In some cases, protection is enhanced by trehalose, a naturally-occurring protective solute. An open question is whether gain of secondary structure by LEA proteins during drying is a prerequisite for this stabilizing function. We used incremental drying (equilibration to a series of relative humidities, RH) to test the ability of AfrLEA2, a Group 3 LEA protein, to protect desiccation-sensitive PFK. AfrLEA2 was chosen due to its exceptional ability to protect PFK. In parallel, circular dichroism (CD) spectra were obtained for AfrLEA2 across the identical range of relative water contents. Protection of PFK by AfrLEA2, above that observed with trehalose and BSA, coincides with simultaneous gain of α-helix in AfrLEA2. At 100% RH, the CD spectrum for AfrLEA2 is typical of random coil, while at decreasing RH, the spectrum shows higher ellipticity at 191 nm and minima at 208 and 220 nm, diagnostic of α-helix. This study provides experimental evidence linking the gain of α-helix with stabilization of a target protein across a graded series of hydration states. Mechanistically, it is intriguing that certain other functions of these IDPs, like preventing aggregation of target proteins, can occur in fully hydrated cells and apparently do not require gain of α-helix.

Transcriptomics of Biostimulation of Plants Under Abiotic Stress

Plant biostimulants are compounds, living microorganisms, or their constituent parts that alter plant development programs. The impact of biostimulants is manifested in several ways: via morphological, physiological, biochemical, epigenomic, proteomic, and transcriptomic changes. For each of these, a response and alteration occur, and these alterations in turn improve metabolic and adaptive performance in the environment. Many studies have been conducted on the effects of different biotic and abiotic stimulants on plants, including many crop species. However, as far as we know, there are no reviews available that describe the impact of biostimulants for a specific field such as transcriptomics, which is the objective of this review. For the commercial registration process of products for agricultural use, it is necessary to distinguish the specific impact of biostimulants from that of other legal categories of products used in agriculture, such as fertilizers and plant hormones. For the chemical or biological classification of biostimulants, the classification is seen as a complex issue, given the great diversity of compounds and organisms that cause biostimulation. However, with an approach focused on the impact on a particular field such as transcriptomics, it is perhaps possible to obtain a criterion that allows biostimulants to be grouped considering their effects on living systems, as well as the overlap of the impact on metabolism, physiology, and morphology occurring between fertilizers, hormones, and biostimulants.

Functional Characterization of Cotton C-Repeat Binding Factor Genes Reveal Their Potential Role in Cold Stress Tolerance

Low temperature is a common biological abiotic stress in major cotton-growing areas. Cold stress significantly affects the growth, yield, and yield quality of cotton. Therefore, it is important to develop more robust and cold stress-resilient cotton germplasms. In response to climate change and erratic weather conditions, plants have evolved various survival mechanisms, one of which involves the induction of various stress responsive transcript factors, of which the C-repeat-binding factors (CBFs) have a positive effect in enhancing plants response to cold stress. In this study, genomewide identification and functional characterization of the cotton CBFs were carried out. A total of 29, 28, 25, 21, 30, 26, and 15 proteins encoded by the CBF genes were identified in seven Gossypium species. A phylogenetic evaluation revealed seven clades, with Clades 1 and 6 being the largest. Moreover, the majority of the proteins encoded by the genes were predicted to be located within the nucleus, while some were distributed in other parts of the cell. Based on the transcriptome and RT-qPCR analysis, Gthu17439 (GthCBF4) was highly upregulated and was further validated through forward genetics. The Gthu17439 (GthCBF4) overexpressed plants exhibited significantly higher tolerance to cold stress, as evidenced by the higher germination rate, increased root growth, and high-induction levels of stress-responsive genes. Furthermore, the overexpressed plants under cold stress had significantly reduced oxidative damage due to a reduction in hydrogen peroxide (H₂O₂) production. Moreover, the overexpressed plants under cold stress had minimal cell damage compared to the wild types, as evidenced by the Trypan and 3,3'-Diaminobenzidine (DAB) staining effect. The results showed that the Gthu17439 (GthCBF4) could be playing a significant role in enhancing cold stress tolerance in cotton and can be further exploited in developing cotton germplasm with improved cold-stress tolerance.

Cold Stress Activates the Expression of Genes of the Chloroplast Transcription Apparatus in Arabidopsis thaliana Plants

The physiological and molecular responses of Arabidopsis thaliana plants to cold stress were studied. Exposure to a low non-freezing temperature (4°C, 5 days) caused a decrease in the physiological functions and activity of a number of photosynthetic genes and elevation in expression of the cold stress gene COR15a, the product of which protects chloroplasts. It was shown for the first time that in parallel to a general inhibition of physiological functions under hypothermia, an increase in the expression of most genes for the chloroplast transcription apparatus was observed. This is obviously one of the compensatory mechanisms of adaptation aimed to maintain cellular homeostasis and physiological functions under hypothermia.

Cold-regulated gene LeCOR413PM2 confers cold stress tolerance in tomato plants

Tomato (Lycopersicon esculentum Mill) is an important food plant that has been used as a model plant in genetic evolution and molecular biology research. The plant is originated from the tropics; thus, it is sensitive to cold. Its growth and development can be easily affected by cold stress. In this study, cold-regulated gene LeCOR413PM2 was cloned from tomato leaves and then used to generate two types of transgenic tomato plants: LeCOR413PM2-overexpressing transgenic plants and RNA-interference-expressing transgenic plants. The functions and expression of LeCOR413PM2 gene in response to cold stress were subsequently assessed. The results showed that LeCOR413PM2 localized in the plasma membrane. Expression of LeCOR413PM2 gene in the leaf of transgenic tomato plant was highest compared to that in other organs (i.e., root, stem, flower and fruit); it was elevated when plants were treated with cold stress. Overexpression of LeCOR413PM2 gene was found to not only reduce damage to cell membrane, accumulation of ROS, and photoinhibition of PSII, but also maintain high activity of antioxidant enzymes and content of osmotic regulators. The results also reveal that high activities of antioxidant enzymes were caused by the up-regulation of their gene expressions. This study demonstrates that the overexpression of LeCOR413PM2 could increase cold tolerance of transgenic tomato plants, while the suppressed expression of LeCOR413PM2 by RNA interference could increase the sensitivity of plants to cold.

The N-Terminal Region of Soybean PM1 Protein Protects Liposomes during Freeze-Thaw

Late embryogenesis abundant (LEA) group 1 (LEA_1) proteins are intrinsically disordered proteins (IDPs) that play important roles in protecting plants from abiotic stress. Their protective function, at a molecular level, has not yet been fully elucidated, but several studies suggest their involvement in membrane stabilization under stress conditions. In this paper, the soybean LEA_1 protein PM1 and its truncated forms (PM1-N: N-terminal half; PM1-C: C-terminal half) were tested for the ability to protect liposomes against damage induced by freeze-thaw stress. Turbidity measurement and light microscopy showed that full-length PM1 and PM1-N, but not PM1-C, can prevent freeze-thaw-induced aggregation of POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) liposomes and native thylakoid membranes, isolated from spinach leaves (Spinacia oleracea). Particle size distribution analysis by dynamic light scattering (DLS) further confirmed that PM1 and PM1-N can prevent liposome aggregation during freeze-thaw. Furthermore, PM1 or PM1-N could significantly inhibit membrane fusion of liposomes, but not reduce the leakage of their contents following freezing stress. The results of proteolytic digestion and circular dichroism experiments suggest that PM1 and PM1-N proteins bind mainly on the surface of the POPC liposome. We propose that, through its N-terminal region, PM1 functions as a membrane-stabilizing protein during abiotic stress, and might inhibit membrane fusion and aggregation of vesicles or other endomembrane structures within the plant cell.

Late Embryogenesis Abundant Protein-Client Protein Interactions

The intrinsically disordered proteins belonging to the LATE EMBRYOGENESIS ABUNDANT protein (LEAP) family have been ascribed a protective function over an array of intracellular components. We focus on how LEAPs may protect a stress-susceptible proteome. These examples include instances of LEAPs providing a shield molecule function, possibly by instigating liquid-liquid phase separations. Some LEAPs bind directly to their client proteins, exerting a holdase-type chaperonin function. Finally, instances of LEAP-client protein interactions have been documented, where the LEAP modulates (interferes with) the function of the client protein, acting as a surreptitious rheostat of cellular homeostasis. From the examples identified to date, it is apparent that client protein modulation also serves to mitigate stress. While some LEAPs can physically bind and protect client proteins, some apparently bind to assist the degradation of the client proteins with which they associate. Documented instances of LEAP-client protein binding, even in the absence of stress, brings to the fore the necessity of identifying how the LEAPs are degraded post-stress to render them innocuous, a first step in understanding how the cell regulates their abundance.

A Chloroplast COR413 Protein From Physcomitrella patens Is Required for Growth Regulation Under High Light and ABA Responses

COR413 genes belong to a poorly characterized group of plant-specific cold-regulated genes initially identified as part of the transcriptional activation machinery of plants during cold acclimation. They encode multispanning transmembrane proteins predicted to target the plasma membrane or the chloroplast inner membrane. Despite being ubiquitous throughout the plant kingdom, little is known about their biological function. In this study, we used reverse genetics to investigate the relevance of a predicted chloroplast localized COR413 protein (PpCOR413im) from the moss Physcomitrella patens in developmental and abiotic stress responses. Expression of PpCOR413im was strongly induced by abscisic acid (ABA) and by various environmental stimuli, including low temperature, hyperosmosis, salinity and high light. In vivo subcellular localization of PpCOR413im-GFP fusion protein revealed that this protein is localized in chloroplasts, confirming the in silico predictions. Loss-of-function mutants of PpCOR413im exhibited growth and developmental alterations such as growth retardation, reduced caulonema formation and hypersensitivity to ABA. Mutants also displayed altered photochemistry under various abiotic stresses, including dehydration and low temperature, and exhibited a dramatic growth inhibition upon exposure to high light. Disruption of PpCOR413im also caused altered chloroplast ultrastructure, increased ROS accumulation, and enhanced starch and sucrose levels under high light or after ABA treatment. In addition, loss of PpCOR413im affected both nuclear and chloroplast gene expression in response to ABA and high light, suggesting a role for this gene downstream of ABA in the regulation of growth and environmental stress responses. Developmental alterations exhibited by PpCOR413im knockout mutants had remarkable similarities to those exhibited by hxk1, a mutant lacking a major chloroplastic hexokinase, an enzyme involved in energy homeostasis. Based on these findings, we propose that PpCOR413im is involved in coordinating energy metabolism with ABA-mediated growth and developmental responses.

Overexpression of Isoprene Synthase Affects ABA- and Drought-Related Gene Expression and Enhances Tolerance to Abiotic Stress

Isoprene is the most abundant single biogenic volatile compound emitted by plants. Despite the relevance of this molecule to plant abiotic resistance and its impact on global atmospheric chemistry, little is known about the details of its mechanism of action. Here, we characterized through both physiological and molecular methods the mechanisms of action of isoprene using model transgenic arabidopsis lines overexpressing a monocot isoprene synthase gene. Our results demonstrated the effect that isoprene had on ABA signaling at different tissue-specific, spatial, and temporal scales. In particular, we found that isoprene enhanced stomatal sensitivity to ABA through upregulation of RD29B signaling gene. By contrast, isoprene decreased sensitivity to ABA in germinating seeds and roots, suggesting tissue-specific mechanisms of action. In leaves, isoprene caused the downregulation of COR15A and P5CS genes, suggesting that the enhanced tolerance to water-deprivation stress observed in isoprene-emitting plants may be mediated chiefly by an enhanced membrane integrity and tolerance to osmotic stress.

Similar Yet Different-Structural and Functional Diversity among Arabidopsis thaliana LEA_4 Proteins

The importance of intrinsically disordered late embryogenesis abundant (LEA) proteins in the tolerance to abiotic stresses involving cellular dehydration is undisputed. While structural transitions of LEA proteins in response to changes in water availability are commonly observed and several molecular functions have been suggested, a systematic, comprehensive and comparative study of possible underlying sequence-structure-function relationships is still lacking. We performed molecular dynamics (MD) simulations as well as spectroscopic and light scattering experiments to characterize six members of two distinct, lowly homologous clades of LEA_4 family proteins from Arabidopsis thaliana. We compared structural and functional characteristics to elucidate to what degree structure and function are encoded in LEA protein sequences and complemented these findings with physicochemical properties identified in a systematic bioinformatics study of the entire Arabidopsis thaliana LEA_4 family. Our results demonstrate that although the six experimentally characterized LEA_4 proteins have similar structural and functional characteristics, differences concerning their folding propensity and membrane stabilization capacity during a freeze/thaw cycle are obvious. These differences cannot be easily attributed to sequence conservation, simple physicochemical characteristics or the abundance of sequence motifs. Moreover, the folding propensity does not appear to be correlated with membrane stabilization capacity. Therefore, the refinement of LEA_4 structural and functional properties is likely encoded in specific patterns of their physicochemical characteristics.

Plasma Membrane Aquaporin Members PIPs Act in Concert to Regulate Cold Acclimation and Freezing Tolerance Responses in Arabidopsis thaliana

Aquaporins play a major role in plant water uptake at both optimal and environmentally stressed conditions. However, the functional specificity of aquaporins under cold remains obscure. To get a better insight to the role of aquaporins in cold acclimation and freezing tolerance, we took an integrated approach of physiology, transcript profiling and cell biology in Arabidopsis thaliana. Cold acclimation resulted in specific upregulation of PIP1;4 and PIP2;5 aquaporin (plasma membrane intrinsic proteins) expression, and immunoblotting analysis confirmed the increase in amount of PIP2;5 protein and total amount of PIPs during cold acclimation, suggesting that PIP2;5 plays a major role in tackling the cold milieu. Although single mutants of pip1;4 and pip2;5 or their double mutant showed no phenotypic changes in freezing tolerance, they were more sensitive in root elongation and cell survival response under freezing stress conditions compared with the wild type. Consistently, a single mutation in either PIP1;4 or PIP2;5 altered the expression of a number of aquaporins both at the transcriptional and translational levels. Collectively, our results suggest that aquaporin members including PIP1;4 and PIP2;5 function in concert to regulate cold acclimation and freezing tolerance responses.

Season specificity in the cold-induced calcium signal and the volatile chemicals in the atmosphere

Cold-induced Ca²⁺ signals in plants are widely accepted to be involved in cold acclimation. Surprisingly, despite using Arabidopsis plants grown in a growth chamber, we observed a clear seasonal change in cold-induced Ca²⁺ signals only in roots. Ca²⁺ signals were captured using Arabidopsis expressing Yellow Cameleon 3.60. In winter, two Ca²⁺ signal peaks were observed during a cooling treatment from 20 to 0°C, but in summer only one small peak was observed under the same cooling condition. In the spring and autumn seasons, an intermediate type of Ca²⁺ signal, which had a delayed first peak and smaller second peaks compared with the those of the winter type, was observed. Volatile chemicals and/or particles in the air from the outside may affect plants in the growth chamber. This idea is supported by the fact that incubation of plants with activated carbon changed the intermediate-type Ca²⁺ signal to the summer-type. The seasonality was also observed in the freezing tolerance of plants cold-acclimated in a low-temperature chamber. The solar radiation intensity was weakly correlated, not only with the seasonal characteristics of the Ca²⁺ signal but also with freezing tolerance. It has been reported that the ethylene concentration in the atmosphere seasonally changes depending on the solar radiation intensity. Ethylene gas and 1-aminocyclopropane-1-carboxylic acid treatment affected the Ca²⁺ signals, the shape of which became a shape close to, but not the same as, the winter type from the other types, indicating that ethylene may be one of several factors influencing the cold-induced Ca²⁺ signal.

Acclimation, priming and memory in the response of Arabidopsis thaliana seedlings to cold stress

Because stress experiences are often recurrent plants have developed strategies to remember a first so-called priming stress to eventually respond more effectively to a second triggering stress. Here, we have studied the impact of discontinuous or sustained cold stress (4 °C) on in vitro grown Arabidopsis thaliana seedlings of different age and their ability to get primed and respond differently to a later triggering stress. Cold treatment of 7-d-old seedlings induced the expression of cold response genes but did not cause a significantly enhanced freezing resistance. The competence to increase the freezing resistance in response to cold was associated with the formation of true leaves. Discontinuous exposure to cold only during the night led to a stepwise modest increase in freezing tolerance provided that the intermittent phase at ambient temperature was less than 32 h. Seedlings exposed to sustained cold treatment developed a higher freezing tolerance which was further increased in response to a triggering stress during three days after the priming treatment had ended indicating cold memory. Interestingly, in all scenarios the primed state was lost as soon as the freezing tolerance had reached the level of naïve plants indicating that an effective memory was associated with an altered physiological state. Known mutants of the cold stress response (cbfs, erf105) and heat stress memory (fgt1) did not show an altered behaviour indicating that their roles do not extend to memory of cold stress in Arabidopsis seedlings.

Repair of sub-lethal freezing damage in leaves of Arabidopsis thaliana

BACKGROUND

The detrimental effects of global climate change direct more attention to the survival and productivity of plants during periods of highly fluctuating temperatures. In particular in temperate climates in spring, temperatures can vary between above-zero and freezing temperatures, even during a single day. Freeze-thaw cycles cause cell membrane lesions that can lead to tissue damage and plant death. Whereas the processes of cold acclimation and freeze-thaw injury are well documented, not much is known about the recovery of plants after a freezing event. We therefore addressed the following questions: i. how does the severity of freezing damage influence repair; ii. how are respiration and content of selected metabolites influenced during the repair process; and iii. how do transcript levels of selected genes respond during repair?

RESULTS

We have investigated the recovery from freezing to sub-lethal temperatures in leaves of non-acclimated and cold acclimated Arabidopsis thaliana plants over a period of 6 days. Fast membrane repair and recovery of photosynthesis were observed 1 day after recovery (1D-REC) and continued until 6D-REC. A substantial increase in respiration accompanied the repair process. In parallel, concentrations of sugars and proline, acting as compatible solutes during freezing, remained unchanged or declined, implicating these compounds as carbon and nitrogen sources during recovery. Similarly, cold-responsive genes were mainly down regulated during recovery of cold acclimated leaves. In contrast, genes involved in cell wall remodeling and ROS scavenging were induced during recovery. Interestingly, also the expression of genes encoding regulatory proteins, such as 14-3-3 proteins, was increased suggesting their role as regulators of repair processes.

CONCLUSIONS

Recovery from sub-lethal freezing comprised membrane repair, restored photosynthesis and increased respiration rates. The process was accompanied by transcriptional changes including genes encoding regulatory proteins redirecting the previous cold response to repair processes, e.g. to cell wall remodeling, maintenance of the cellular proteome and to ROS scavenging. Understanding of processes involved in repair of freeze-thaw injury increases our knowledge on plant survival in changing climates with highly fluctuating temperatures.

A maize stress-responsive Di19 transcription factor, ZmDi19-1, confers enhanced tolerance to salt in transgenic Arabidopsis

ZmDi19-1 can be induced by various abiotic stresses and enhance the salt tolerance of transgenic Arabidopsis thaliana. Drought-induced protein 19 (Di19) is an essential zinc finger family member that plays vital roles in regulating multiple stress responses. Here, the Di19 family gene in maize (Zea mays) ZmDi19-1 was characterized. We determined that ZmDi19-1 is constitutively expressed in root, stem, leaf and other maize tissues under normal conditions. In addition, ZmDi19-1 expression was induced by PEG and NaCl stresses. The subcellular localization revealed that ZmDi19-1 is a nuclear membrane protein. In yeast cells, ZmDi19-1 displayed transcriptional activity and could bind to the TACA(A/G)T sequence, which was corroborated using the dual luciferase reporter assay system. The overexpression of ZmDi19-1 in Arabidopsis thaliana enhanced the plants' tolerance to salt stress. Compared with wild-type, the Arabidopsis ZmDi19-1-overexpressing lines had higher relative water and proline contents, and lower malondialdehyde contents, in leaves under salt-stress conditions. The transcriptome analysis revealed 1414 upregulated and 776 downregulated genes, and an RNA-seq analysis identified some differentially expressed genes, which may be downstream of ZmDi19-1, involved in salt-stress responses. The data demonstrated that ZmDi19-1 responds to salt stress and may impact the expression of stress-related genes in Arabidopsis.

A novel cold-regulated protein isolated from Saussurea involucrata confers cold and drought tolerance in transgenic tobacco (Nicotiana tabacum)

Adverse environmental conditions, such as cold and drought, can inhibit plant growth, development, and productivity. The isolation and characterization of stress response genes from stress-tolerant plants can provide a better understanding of the underlying adaptive mechanisms. In this study, a novel cold-regulated gene, SikCOR413PM1, was isolated from Saussurea involucrata Kar. et Kir., which is a plant that survives at the high altitudes and in the low temperatures of alpine slopes in northwestern China. SikCOR413PM1 was induced in response to cold and drought in S. involucrata, and phylogenetic analysis revealed that the gene groups with a COR gene encoding a COR413PM protein family member. Subcellular localization of a SikCOR413PM1-green fluorescent fusion protein showed that SikCOR413PM1 was localized to the plasma membrane. A transgenic tobacco (Nicotiana tabacum) system was employed to investigate the possible role of SikCOR413PM1 in cold and drought tolerance. Analyses of growth, germination and survival rates, relative water content, malondialdehyde content, relative electrolyte leakage, and maximal photochemical efficiency of photosystem II showed that transgenic tobacco plants expressing SikCOR413PM1 were more tolerant to cold and drought stresses than WT plants. SikCOR413PM1 overexpression was also accompanied by constitutive activation of NtDREB1 and NtDREB3, two cold-responsive transcription factor genes, and NtERD10A and NtERD10B, two cold-induced genes. The expression levels of downstream transcription factor genes NtDREB3, NtERD10C, NtERD10D, and NtLEA5 were also induced in SikCOR413PM1-expressing transgenic plants under drought conditions. Our results suggest that the overexpression of SikCOR413PM1 induces changes in tobacco plants, and facilitates enhanced tolerance to cold and drought stresses.

Conformational selection of the intrinsically disordered plant stress protein COR15A in response to solution osmolarity - an X-ray and light scattering study

The plant stress protein COR15A stabilizes chloroplast membranes during freezing. COR15A is an intrinsically disordered protein (IDP) in aqueous solution, but acquires an α-helical structure during dehydration or the increase of solution osmolarity. We have used small- and wide-angle X-ray scattering (SAXS/WAXS) combined with static and dynamic light scattering (SLS/DLS) to investigate the structural and hydrodynamic properties of COR15A in response to increasing solution osmolarity. Coarse-grained ensemble modelling allowed a structure-based interpretation of the SAXS data. Our results demonstrate that COR15A behaves as a biomacromolecule with polymer-like properties which strongly depend on solution osmolarity. Biomacromolecular self-assembly occurring at high solvent osmolarity is initiated by the occurrence of two specific structural subpopulations of the COR15A monomer. The osmolarity dependent structural selection mechanism is an elegant way for conformational regulation and assembly of COR15A. It highlights the importance of the polymer-like properties of IDPs for their associated biological function.

Deacclimation after cold acclimation-a crucial, but widely neglected part of plant winter survival

Temperate and boreal plants show natural low temperature acclimation during autumn. This cold acclimation process results in increased freezing tolerance. Global climate change is leading to increasing spring and autumn temperatures that can trigger deacclimation and loss of freezing tolerance, making plants susceptible to both late-autumn and late-spring freezing events. In particular, spring frosts can have devastating effects on whole ecosystems and can significantly reduce the yield of crop plants. Although the timing and speed of deacclimation are clearly of crucial importance for plant winter survival, the molecular basis of this process is still largely unknown. The regulation of deacclimation is, however, not only related to freezing tolerance, but also to the termination of dormancy, and the initiation of growth and development. In this paper, we provide an overview of what is known about deacclimation in both woody and herbaceous plants. We use publicly available transcriptome data to identify a core set of deacclimation-related genes in Arabidopsis thaliana that highlight physiological determinants of deacclimation, and suggest important directions for future research in this area.

Protecting Enzymes from Stress-Induced Inactivation

The pharmaceutical and chemical industries depend on additives to protect enzymes and other proteins against stresses that accompany their manufacture, transport, and storage. Common stresses include vacuum-drying, freeze-thawing, and freeze-drying. The additives include sugars, compatible osmolytes, amino acids, synthetic polymers, and both globular and disordered proteins. Scores of studies have been published on protection, but the data have never been analyzed systematically. To spur efforts to understand the sources of protection and ultimately develop more effective formulations, we review ideas about the mechanisms of protection, survey the literature searching for patterns of protection, and then compare the ideas to the data.

Mechanisms underlying the enhanced biomass and abiotic stress tolerance phenotype of an Arabidopsis MIOX over-expresser

Myo-inositol oxygenase (MIOX) is the first enzyme in the inositol route to ascorbate (L-ascorbic acid, AsA, vitamin C). We have previously shown that Arabidopsis plants constitutively expressing MIOX have elevated foliar AsA content and displayed enhanced growth rate, biomass accumulation, and increased tolerance to multiple abiotic stresses. In this work, we used a combination of transcriptomics, chromatography, microscopy, and physiological measurements to gain a deeper understanding of the underlying mechanisms mediating the phenotype of the AtMIOX4 line. Transcriptomic analysis revealed increased expression of genes involved in auxin synthesis, hydrolysis, transport, and metabolism, which are supported by elevated auxin levels both in vitro and in vivo, and confirmed by assays demonstrating their effect on epidermal cell elongation in the AtMIOX4 over-expressers. Additionally, we detected up-regulation of transcripts involved in photosynthesis and this was validated by increased efficiency of the photosystem II and proton motive force. We also found increased expression of amylase leading to higher intracellular glucose levels. Multiple gene families conferring plants tolerance/expressed in response to cold, water limitation, and heat stresses were found to be elevated in the AtMIOX4 line. Interestingly, the high AsA plants also displayed up-regulation of transcripts and hormones involved in defense including jasmonates, defensin, glucosinolates, and transcription factors that are known to be important for biotic stress tolerance. These results overall indicate that elevated levels of auxin and glucose, and enhanced photosynthetic efficiency in combination with up-regulation of abiotic stresses response genes underly the higher growth rate and abiotic stresses tolerance phenotype of the AtMIOX4 over-expressers.

Structural properties and cellular expression of AfrLEA6, a group 6 late embryogenesis abundant protein from embryos of Artemia franciscana

Late embryogenesis abundant (LEA) proteins are intrinsically disordered proteins (IDPs) commonly found in anhydrobiotic organisms and are frequently correlated with desiccation tolerance. Herein we report new findings on AfrLEA6, a novel group 6 LEA protein from embryos of Artemia franciscana. Assessment of secondary structure in aqueous and dried states with circular dichroism (CD) reveals 89% random coil in the aqueous state, thus supporting classification of AfrLEA6 as an IDP. Removal of water from the protein by drying or exposure to trifluoroethanol (a chemical de-solvating agent) promotes a large gain in secondary structure of AfrLEA6, predominated by α-helix and exhibiting minimal β-sheet structure. We evaluated the impact of physiological concentrations (up to 400 mM) of the disaccharide trehalose on the folding of LEA proteins in solution. CD spectra for AfrLEA2, AfrLEA3m, and AfrLEA6 are unaffected by this organic solute noted for its ability to drive protein folding. AfrLEA6 exhibits its highest concentration in vivo during embryonic diapause, drops acutely at diapause termination, and then declines during development to undetectable values at the larval stage. Maximum cellular titer of AfrLEA6 was 10-fold lower than for AfrLEA2 or AfrLEA3, both group 3 LEA proteins. Acute termination of diapause with H2O2 (a far more effective terminator than desiccation in this Great Salt Lake, UT, population) fostered a rapid 38% decrease in AfrLEA6 content of embryos. While the ultimate mechanism of diapause termination is unknown, disruption of key macromolecules could initiate physiological signaling events necessary for resumption of development and metabolism.

LcFIN2, a novel chloroplast protein gene from sheepgrass, enhances tolerance to low temperature in Arabidopsis and rice

Adverse environmental stresses affect plant growth and crop yields. Sheepgrass (Leymus chinensis (Trin.) Tzvel), an important forage grass that is widely distributed in the east of Eurasia steppe, has high tolerance to extreme low temperature. Many genes that respond to cold stress were identified in sheepgrass by RNA-sequencing, but more detailed studies are needed to dissect the function of those genes. Here, we found that LcFIN2, a sheepgrass freezing-induced protein 2, encoded a chloroplast-targeted protein. Expression of LcFIN2 was upregulated by freezing, chilling, NaCl and abscisic acid (ABA) treatments. Overexpression of LcFIN2 enhanced the survival rate of transgenic Arabidopsis after freezing stress. Importantly, heterologous expression of LcFIN2 in rice exhibited not only higher survival rate but also accumulated various soluble substances and reduced membrane damage in rice under chilling stress. Furthermore, the chlorophyll content, the quantum photochemistry efficiency of photosystem II (ΦPSII), the non-photochemical quenching (NPQ), the net photosynthesis rate (Pn) and the expression of some chloroplast ribosomal-related and photosynthesis-related genes were higher in the transgenic rice under chilling stress. These findings suggested that the LcFIN2 gene could potentially be used to improve low-temperature tolerance in crops.

Smut infection of perennial hosts: the genome and the transcriptome of the Brassicaceae smut fungus Thecaphora thlaspeos reveal functionally conserved and novel effectors

Biotrophic fungal plant pathogens can balance their virulence and form intricate relationships with their hosts. Sometimes, this leads to systemic host colonization over long time scales without macroscopic symptoms. However, how plant-pathogenic endophytes manage to establish their sustained systemic infection remains largely unknown. Here, we present a genomic and transcriptomic analysis of Thecaphora thlaspeos. This relative of the well studied grass smut Ustilago maydis is the only smut fungus adapted to Brassicaceae hosts. Its ability to overwinter with perennial hosts and its systemic plant infection including roots are unique characteristics among smut fungi. The T. thlaspeos genome was assembled to the chromosome level. It is a typical smut genome in terms of size and genome characteristics. In silico prediction of candidate effector genes revealed common smut effector proteins and unique members. For three candidates, we have functionally demonstrated effector activity. One of these, TtTue1, suggests a potential link to cold acclimation. On the plant side, we found evidence for a typical immune response as it is present in other infection systems, despite the absence of any macroscopic symptoms during infection. Our findings suggest that T. thlaspeos distinctly balances its virulence during biotrophic growth ultimately allowing for long-lived infection of its perennial hosts.

Preferential adsorption to air-water interfaces: a novel cryoprotective mechanism for LEA proteins

Late embryogenesis abundant (LEA) proteins comprise a diverse family whose members play a key role in abiotic stress tolerance. As intrinsically disordered proteins, LEA proteins are highly hydrophilic and inherently stress tolerant. They have been shown to stabilise multiple client proteins under a variety of stresses, but current hypotheses do not fully explain how such broad range stabilisation is achieved. Here, using neutron reflection and surface tension experiments, we examine in detail the mechanism by which model LEA proteins, AavLEA1 and ERD10, protect the enzyme citrate synthase (CS) from aggregation during freeze–thaw. We find that a major contributing factor to CS aggregation is the formation of air bubbles during the freeze–thaw process. This greatly increases the air–water interfacial area, which is known to be detrimental to folded protein stability. Both model LEA proteins preferentially adsorb to this interface and compete with CS, thereby reducing surface-induced aggregation. This novel surface activity provides a general mechanism by which diverse members of the LEA protein family might function to provide aggregation protection that is not specific to the client protein.