Vitis CBF1 and Vitis CBF4 differ in their effect on Arabidopsis abiotic stress tolerance, development and gene expression

VvJAZ13 Positively Regulates Cold Tolerance in Arabidopsis and Grape

Cold stress adversely impacts grape growth, development, and yield. Therefore, improving the cold tolerance of grape is an urgent task of grape breeding. The Jasmonic acid (JA) pathway responsive gene JAZ plays a key role in plant response to cold stress. However, the role of JAZ in response to low temperatures in grape is unclear. In this study, VvJAZ13 was cloned from the 'Pinot Noir' (Vitis vinefera cv. 'Pinot Noir') grape, and the potential interacting protein of VvJAZ13 was screened by yeast two-hybrid (Y2H). The function of VvJAZ13 under low temperature stress was verified by genetic transformation. Subcellular localization showed that the gene was mainly expressed in cytoplasm and the nucleus. Y2H indicated that VvF-box, VvTIFY5A, VvTIFY9, Vvbch1, and VvAGD13 may be potential interacting proteins of VvJAZ13. The results of transient transformation of grape leaves showed that VvJAZ13 improved photosynthetic capacity and reduced cell damage by increasing maximum photosynthetic efficiency of photosystem II (Fv/Fm), reducing relative electrolyte leakage (REL) and malondialdehyde (MDA), and increasing proline content in overexpressed lines (OEs), which played an active role in cold resistance. Through the overexpression of VvJAZ13 in Arabidopsis thaliana and grape calli, the results showed that compared with wild type (WT), transgenic lines had higher antioxidant enzyme activity and proline content, lower REL, MDA, and hydrogen peroxide (H2O2) content, and an improved ability of scavenging reactive oxygen species. In addition, the expression levels of CBF1-2 and ICE1 genes related to cold response were up-regulated in transgenic lines. To sum up, VvJAZ13 is actively involved in the cold tolerance of Arabidopsis and grape, and has the potential to be a candidate gene for improving plant cold tolerance.

A novel R2R3-MYB transcription factor PbMYB1L of Pyrus bretschneideri regulates cold tolerance and anthocyanin accumulation

KEY MESSAGE

PbMYB1L enhances the cold tolerance and anthocyanin accumulation of transgenic Arabidopsis by regulating the expression of genes related to the cold-responsive genes pathway and anthocyanin synthesis pathway. MYB transcription factors (TFs) have been demonstrated to play diverse roles in plant growth and development. In the present study, we identified a novel R2R3-MYB transcription factor, PbMYB1L, from the peel of 'Red Zaosu' pear (Pyrus bretschneideri), which was induced by cold stress and acted as a positive regulator in anthocyanin biosynthesis. Notably, the transgenic Arabidopsis lines exhibited enhanced tolerance to cold stress. Compared to the Arabidopsis wild-type plants, the transgenic lines displayed longer primary roots and reduced reactive oxygen species (ROS) levels including O2-, hydrogen peroxide (H2O2), and malondialdehyde (MDA). Furthermore, significant upregulation of key cold-responsive genes AtCBF1, AtCBF2, AtCBF3, AtCBF4, and AtKIN1 was observed in the transgenic plants under cold stress conditions compared to wild type. Arabidopsis plants overexpressing PbMYB1L had significant anthocyanin accumulation in leaves after cold treatment with quantitative results indicating higher expression of anthocyanin structural genes compared to wild type. These findings suggest that PbMYB1L not only plays a vital role in conferring cold tolerance but also acts as a crucial regulator of anthocyanin biosynthesis.

Genome-wide identification and expression analysis of the CBF transcription factor family in Lolium perenne under abiotic stress

C-repeat binding factor (CBF) subfamily genes encoding transcriptional activators are members of the AP2/ERF superfamily. CBFs play important roles in plant tolerance to abiotic stress. In this study, we identified and analyzed the structure, phylogeny, conserved motifs, and expression profiles of 12 CBFs of the grass species Lolium perenne cultured under abiotic stress. The identified LpCBFs were grouped into three phylogenetic clades according to their protein structures and motif organizations. LpCBF expression was differentially induced by cold, heat, water deficit, salinity, and abscisic acid, among which cold treatment induced LpCBF gene expression significantly. Furthermore, association network analysis indicated that different proteins, including certain stress-related proteins, potentially interact with LpCBFs. Altogether, these findings will enhance our understanding of LpCBFs protein structure and function in the regulation of L. perenne stress responses. Our results will provide valuable information for further functional research of LpCBF proteins in L. perenne stress resistance.

Genome-Wide Identification of the CBF Gene Family and ICE Transcription Factors in Walnuts and Expression Profiles under Cold Conditions

Cold stress impacts woody tree growth and perennial production, especially when the temperature rapidly changes in late spring. To address this issue, we conducted the genome-wide identification of two important transcription factors (TFs), CBF (C-repeat binding factors) and ICE (inducers of CBF expression), in three walnut (Juglans) genomes. Although the CBF and ICE gene families have been identified in many crops, very little systematic analysis of these genes has been carried out in J. regia and J. sigillata. In this study, we identified a total of 16 CBF and 12 ICE genes in three Juglans genomes using bioinformatics analysis. Both CBF and ICE had conserved domains, motifs, and gene structures, which suggests that these two TFs were evolutionarily conserved. Most ICE genes are located at both ends of the chromosomes. The promoter cis-regulatory elements of CBF and ICE genes are largely involved in light and phytohormone responses. Based on 36 RNA sequencing of leaves from four walnut cultivars ('Zijing', 'Lvling', 'Hongren', and 'Liao1') under three temperature conditions (8 °C, 22 °C, and 5 °C) conditions in late spring, we found that the ICE genes were expressed more highly than CBFs. Both CBF and ICE proteins interacted with cold-related proteins, and many putative miRNAs had interactions with these two TFs. These results determined that CBF1 and ICE1 play important roles in the tolerance of walnut leaves to rapid temperature changes. Our results provide a useful resource on the function of the CBF and ICE genes related to cold tolerance in walnuts.

Involvement of CBF in the fine-tuning of litchi flowering time and cold and drought stresses

Litchi (Litchi chinensis) is an economically important fruit tree in southern China and is widely cultivated in subtropical regions. However, irregular flowering attributed to inadequate floral induction leads to a seriously fluctuating bearing. Litchi floral initiation is largely determined by cold temperatures, whereas the underlying molecular mechanisms have yet to be identified. In this study, we identified four CRT/DRE BINDING FACTORS (CBF) homologs in litchi, of which LcCBF1, LcCBF2 and LcCBF3 showed a decrease in response to the floral inductive cold. A similar expression pattern was observed for the MOTHER OF FT AND TFL1 homolog (LcMFT) in litchi. Furthermore, both LcCBF2 and LcCBF3 were found to bind to the promoter of LcMFT to activate its expression, as indicated by the analysis of yeast-one-hybrid (Y1H), electrophoretic mobility shift assays (EMSA), and dual luciferase complementation assays. Ectopic overexpression of LcCBF2 and LcCBF3 in Arabidopsis caused delayed flowering and increased freezing and drought tolerance, whereas overexpression of LcMFT in Arabidopsis had no significant effect on flowering time. Taken together, we identified LcCBF2 and LcCBF3 as upstream activators of LcMFT and proposed the contribution of the cold-responsive CBF to the fine-tuning of flowering time.

Transcription Factor VvDREB2A from Vitis vinifera Improves Cold Tolerance

Low temperatures restrict the growth of the grapevine industry. The DREB transcription factors are involved in the abiotic stress response. Here, we isolated the VvDREB2A gene from Vitis vinifera cultivar 'Zuoyouhong' tissue culture seedlings. The full-length VvDREB2A cDNA was 1068 bp, encoding 355 amino acids, which contained an AP2 conserved domain belonging to the AP2 family. Using transient expression in leaves of tobacco, VvDREB2A was localized to the nucleus, and it potentiated transcriptional activity in yeasts. Expression analysis revealed that VvDREB2A was expressed in various grapevine tissues, with the highest expression in leaves. VvDREB2A was induced by cold and the stress-signaling molecules H₂S, nitric oxide, and abscisic acid. Furthermore, VvDREB2A-overexpressing Arabidopsis was generated to analyze its function. Under cold stress, the Arabidopsis overexpressing lines exhibited better growth and higher survival rates than the wild type. The content of oxygen free radicals, hydrogen peroxide, and malondialdehyde decreased, and antioxidant enzyme activities were enhanced. The content of raffinose family oligosaccharides (RFO) also increased in the VvDREB2A-overexpressing lines. Moreover, the expression of cold stress-related genes (COR15A, COR27, COR6.6, and RD29A) was also enhanced. Taken together, as a transcription factor, VvDREB2A improves plants resistance to cold stress by scavenging reactive oxygen species, increasing the RFO amount, and inducing cold stress-related gene expression levels.

Advances in understanding cold tolerance in grapevine

Grapevine (Vitis ssp.) is a deciduous perennial fruit crop, and the canes and buds of grapevine should withstand low temperatures annually during winter. However, the widely cultivated Vitis vinifera is cold-sensitive and cannot survive the severe winter in regions with extremely low temperatures, such as viticulture regions in northern China. By contrast, a few wild Vitis species like V. amurensis and V. riparia exhibit excellent freezing tolerance. However, the mechanisms underlying grapevine cold tolerance remain largely unknown. In recent years, much progress has been made in elucidating the mechanisms, owing to the advances in sequencing and molecular biotechnology. Assembly of grapevine genomes together with resequencing and transcriptome data enable researchers to conduct genomic and transcriptomic analyses in various grapevine genotypes and populations to explore genetic variations involved in cold tolerance. In addition, a number of pivotal genes have been identified and functionally characterized. In this review, we summarize recent major advances in physiological and molecular analyses of cold tolerance in grapevine and put forward questions in this field. We also discuss the strategies for improving the tolerance of grapevine to cold stress. Understanding grapevine cold tolerance will facilitate the development of grapevines for adaption to global climate change.

RAP2.6 enhanced salt stress tolerance by reducing Na+ accumulation and stabilizing the electron transport in Arabidopsis thaliana

The transcription factors of the AP2/ERF family are involved in plant growth and development and responses to biotic and abiotic stresses. Here, we found RAP2.6, a transcription factor which belongs to the ERF subfamily, was responsive to salt stress in Arabidopsis. Under salt stress conditions, rap2.6 mutant seedlings were the sensitivity deficiency to salt stress which was reflected in higher germination rate and longer root length compared to the wild type. Also, the expressions of salt-related gene including SOS1, SOS2, SOS3, NHX1, NHX3, NHX5 and HKT1 in rap2.6 mutant seedlings were lower than the wild type under salt stress. rap2.6 mutant adult lacked salt stress tolerance based on the results of the phenotype, survival rates and ion leakage. Compared to wild type, rap2.6 mutant adult accumulated more Na⁺ in leaves and roots while the salt-related gene expressions were lower. In addition, the photosynthetic electron transport and PSII energy distribution in rap2.6 mutant plant leaves had been more seriously affected under salt stress conditions compared to the wild type. In summary, this study identified essential roles of RAP2.6 in regulating salt stress tolerance in Arabidopsis.

StLTO1, a lumen thiol oxidoreductase in Solanum tuberosum L., enhances the cold resistance of potato plants

Cold stress reduces plant photosynthesis and increases the accumulation of reactive oxygen species (ROS) in plants, thereby dramatically affecting plant growth, crop productivity and quality. Here, we report that lumen thiol oxidoreductase 1 (StLTO1), a vitamin K epoxide reductase (VKOR)-like protein in the thylakoid membrane of Solanum tuberosum L., enhances the cold tolerance of potato plants. Under normal conditions, overexpression of StLTO1 in plants promoted plant growth. In addition, potato plants overexpressing StLTO1 displayed enhanced photosynthetic capacity and increased capacity for scavenging ROS compared to StLTO1 knockdown and wild-type potato plants under cold conditions. Overexpression of StLTO1 in potato plants also improved cold-regulated (COR) gene expression after cold stress. Our results suggest that StLTO1 acts as a positive regulator of cold resistance in potato plants.

ScCBF1 plays a stronger role in cold, salt and drought tolerance than StCBF1 in potato (Solanum tuberosum)

Solanum tuberosum (St) and Solanum commersonii (Sc) are two potato varieties with different freezing tolerance. Among them, St is a freezing-sensitive variety and. Sc is a cold-resistant wild potato. CBF/DREB family members mainly function in response to freezing stress. In order to explore the different roles of St C-Repeat Binding Factor1 (StCBF1) and Sc C-Repeat Binding Factor1 (ScCBF1) in potato plants (Solanum tuberosum) under stress conditions, two kinds of potato lines were obtained with ScCBF1 and StCBF1 overexpressing respectively. Phenotypes analysis showed that both overexpressing ScCBF1 and StCBF1 caused smaller leaves, and reduced tuber yield. While the limited phenotypes of StCBF1 lines were more severe than that of ScCBF lines. After freezing treatment, StCBF1 over expression plants grown better than WT plants and worse than ScCBF1 over expression plants. Specifically, compared with wild-type lines, overexpressing ScCBF1 could up-regulate fatty acid desaturase genes, key enzyme of Calvin cycle genes, and antioxidant enzyme genes. Both ScCBF1 and StCBF1 lines showed higher PSII activity, thus maintaining a higher photosynthetic rate under cold stress. In addition, we also found that overexpression ScCBF1 and StCBF1 could also enhance the drought and salt tolerance in potato. In summary, ScCBF1 plays a stronger role in cold, salt, and drought tolerance than StCBF1 in potato (Solanum tuberosum).

Sprayed biodegradable liquid film improved the freezing tolerance of cv. Cabernet Sauvignon by up-regulating soluble protein and carbohydrate levels and alleviating oxidative damage

Most cultivars of Vitis vinifera L. are very sensitive to cold. As an exogenous protectant, Biodegradable Liquid Film (BLF) is considered to protect winegrapes from low temperatures and dry winds for safe overwintering. This study aimed to reveal the physiological and biochemical mechanisms of BLF regulating the freezing tolerance of wine grapes. Groups of ten-year-old vines (Cabernet Sauvignon) were sprayed with BLF in November 2020 and 2021, or left untreated as a control treatment, and field plant mortality after overwintering were investigated. Branch samples were collected monthly for determination of biochemical indicators. Dormant two-year-old cuttings (Cabernet Sauvignon) were also used for the determination of relative expression levels of key genes. The results showed that the application of BLF reduced the branch semi-lethal temperature in January and February samples compared with control, and reduced the mortality of above-ground parts, branches and buds. The physiological status of shoots was greatly affected by the climatic conditions of the year, but BLF treatment increased the levels of soluble protein and soluble sugar, and also decreased the content of superoxide anion and malondialdehyde at most sampling times. Correlation analysis showed that the differences in freezing tolerance between BLF and no treated overwintering(CK) vines were mainly related to peroxidase activity, soluble sugar, reducing sugar and starch content. Low temperature stress activated the over expression of ICE1, CBF1, and CBF3, especially for 12h. BLF treatment significantly increased the expression levels of CBF1 and CBF3 under low temperature stress. Overall, these results demonstrate that BLF treatment protects vines from freezing damage by upregulating osmo-regulatory substances and alleviating oxidative damage.

Plasma membrane proteomic changes of Arabidopsis DRP1E during cold acclimation in association with the enhancement of freezing tolerance

The freezing tolerance of plants that live in cold regions increases after exposure to low temperature, a process termed cold acclimation (CA). During CA, restructuring of the plasma membrane (PM) is important to enhance freezing tolerance. We have previously shown that the function of DYNAMIN-RELATED PROTEIN 1 E (DRP1E), which regulates endocytosis by pinching vesicles from the PM, is associated with the enhancement of freezing tolerance during CA in Arabidopsis. DRP1E is predicted to play a role in reconstituting the PM composition during CA. In this study, to test the validity of this hypothesis, we studied the changes in PM proteome patterns induced by drp1e mutation. In a detailed physiological analysis, after 3 days of CA, only young leaves showed significantly less increase in freezing tolerance in the mutant than in the wild type (WT). Using nano-liquid chromatography-tandem mass spectrometry, 496 PM proteins were identified. Among these proteins, 81 or 71 proteins were specifically altered in the WT or the mutant, respectively, in response to CA. Principal component analysis showed that the proteomic pattern differed between the WT and the mutant upon cold acclimation (CA), suggesting that DRP1E contributes to reconstruction of the PM during CA. Cluster analysis revealed that proteins that were significantly increased in the mutant after CA were biased toward glycosylphosphatidylinositol-anchored proteins, such as fasciclin-like arabinogalactan proteins. Thus, a primary target of DRP1E-associated PM reconstruction during CA is considered to be glycosylphosphatidylinositol-anchored proteins, which may be removed from the PM by DRP1E in young leaves after 3 days of CA.

The cold-stress responsive gene DREB1A involved in low-temperature tolerance in Xinjiang wild walnut

Background

Low-temperatures have the potential to be a serious problem for plants and can negatively affect the normal growth and development of walnuts. DREB1/CBF (Dehydration Responsive Element Binding Protein 1/C-repeat Binding Factor), one of the most direct transcription factors in response to low-temperature stress, may improve the resistance of plants to low-temperatures by regulating their functional genes. However, few studies have been conducted in walnut. The Xinjiang wild walnut is a rare wild plant found in China, with a large number of excellent trait genes, and is hardier than cultivated walnuts in Xinjiang.

Methods

In this work, we identified all of the DREB1 members from the walnut genome and analyzed their expression levels in different tissues and during low-temperature stress on the Xinjiang wild walnut. The JfDREB1A gene of the Xinjiang wild walnut was cloned and transformed into Arabidopsis thaliana for functional verification.

Results

There were five DREB1 transcription factors in the walnut genome. Among them, the relative expression level of the DREB1A gene was significantly higher than other members in the different tissues (root, stem, leaf) and was immediately un-regulated under low-temperature stress. The overexpression of the JfDREB1A gene increased the survival rates of transgenic Arabidopsis lines, mainly through maintaining the stability of cell membrane, decreasing the electrical conductivity and increasing the activities of antioxidant enzymes including superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT). Additionally, the expression levels of cold-inducible genes like AtKIN1, AtERD10, AtRD29A, AtCOR15A and AtCOR47, were significantly increased. These results showed that the JfDREB1A gene may play an important role in the response to cold stress of the Xinjiang wild walnut. This study contributes to our understanding of the molecular mechanism of the Xinjiang wild walnut's response to low-temperature stress and will be beneficial for developing walnut cultivars with improved cold resistance.

StATL2-like could affect growth and cold tolerance of plant by interacting with StCBFs

Our results confirmed that StATL2-like could interact with StCBFs and regulate plant growth. Meanwhile, StATL2-like acted as a negative regulator on low-temperature tolerance in plants. As important transcription factors for resisting many kinds of stresses, C-repeat-binding factors (CBF) play a key role in plant low-temperature tolerance by increasing COR genes expressions. Here, we report that StATL2-like, a RING-H2 E3 ubiquitin in Solanum tuberosum L., interacted with StCBF1 and StCBF4, respectively. AtATL2 is a highly homologous gene of StATL2-like in Arabidopsis thaliana. Under normal conditions, atl2 Arabidopsis mutant showed a growth inhibition phenotype while overexpressed StATL2-like in wild type Arabidopsis and atl2 mutant promoted plant growth. Besides, atl2 mutant had better low-temperature tolerance compared with wild type and StATL2-like transgenic lines which demonstrated that StATL2-like acted as a negatively regulator on low-temperature tolerance in plant. Moreover, atl2 mutant improved the scavenging capacity of reactive oxygen species (ROS) and alleviate the damage of photosynthetic system II (PSII) compared with StATL2-like transgenic lines under cold conditions. These results suggested a new component in CBF-dependent pathway to regulate plant growth and response to low-temperature stress in potato plants.

Comprehensive analysis of cucumber C-repeat/dehydration-responsive element binding factor family genes and their potential roles in cold tolerance of cucumber

BACKGROUND

Cold stress is one of the main abiotic stresses limiting cucumber (Cucumis sativus L.) growth and production. C-repeat binding factor/Dehydration responsive element-binding 1 protein (CBF/DREB1), containing conserved APETALA2 (AP2) DNA binding domains and two characteristic sequences, are key signaling genes that can be rapidly induced and play vital roles in plant response to low temperature. However, the CBF family has not been systematically elucidated in cucumber, and the expression pattern of this family genes under cold stress remains unclear.

RESULTS

In this study, three CsCBF family genes were identified in cucumber genome and their protein conserved domain, protein physicochemical properties, gene structure and phylogenetic analysis were further comprehensively analyzed. Subcellular localization showed that all three CsCBFs were localized in the nucleus. Cis-element analysis of the promoters indicated that CsCBFs might be involved in plant hormone response and abiotic stress response. Expression analysis showed that the three CsCBFs could be significantly induced by cold stress, salt and ABA. The overexpression of CsCBFs in cucumber seedlings enhanced the tolerance to cold stress, and importantly, the transcript levels of CsCOR genes were significantly upregulated in 35S:CsCBFs transgenic plants after cold stress treatment. Biochemical analyses ascertained that CsCBFs directly activated CsCOR genes expression by binding to its promoter, thereby enhancing plant resistance to cold stress.

CONCLUSION

This study provided a foundation for further research on the function of CsCBF genes in cold stress resistance and elucidating its mechanism.

Genetic Mechanisms of Cold Signaling in Wheat (Triticum aestivum L.)

Cold stress is a major environmental factor affecting the growth, development, and productivity of various crop species. With the current trajectory of global climate change, low temperatures are becoming more frequent and can significantly decrease crop yield. Wheat (Triticum aestivum L.) is the first domesticated crop and is the most popular cereal crop in the world. Because of a lack of systematic research on cold signaling pathways and gene regulatory networks, the underlying molecular mechanisms of cold signal transduction in wheat are poorly understood. This study reviews recent progress in wheat, including the ICE-CBF-COR signaling pathway under cold stress and the effects of cold stress on hormonal pathways, reactive oxygen species (ROS), and epigenetic processes and elements. This review also highlights possible strategies for improving cold tolerance in wheat.

Cellular Protein Trafficking: A New Player in Low-Temperature Response Pathway

Unlike animals, plants are unable to escape unfavorable conditions, such as extremities of temperature. Among abiotic variables, the temperature is notableas it affects plants from the molecular to the organismal level. Because of global warming, understanding temperature effects on plants is salient today and should be focused not only on rising temperature but also greater variability in temperature that is now besetting the world's natural and agricultural ecosystems. Among the temperature stresses, low-temperature stress is one of the major stresses that limits crop productivity worldwide. Over the years, although substantial progress has been made in understanding low-temperature response mechanisms in plants, the research is more focused on aerial parts of the plants rather than on the root or whole plant, and more efforts have been made in identifying and testing the major regulators of this pathway preferably in the model organism rather than in crop plants. For the low-temperature stress response mechanism, ICE-CBF regulatory pathway turned out to be the solely established pathway, and historically most of the low-temperature research is focused on this single pathway instead of exploring other alternative regulators. In this review, we tried to take an in-depth look at our current understanding of low temperature-mediated plant growth response mechanism and present the recent advancement in cell biological studies that have opened a new horizon for finding promising and potential alternative regulators of the cold stress response pathway.

Characterization of Chromatin Accessibility and Gene Expression upon Cold Stress Reveals that the RAV1 Transcription Factor Functions in Cold Response in Vitis Amurensis

Cold tolerance is regulated by a variety of transcription factors (TFs) and their target genes. Except for the well-characterized C-repeat binding factors (CBFs)-dependent transcriptional cascade, the mechanisms of cold tolerance mediated by other transcriptional regulatory networks are still largely unknown. Here, we used the assay for transposase-accessible chromatin with sequencing (ATAC-seq) and RNA-seq to identify cold responsive TFs in Vitis amurensis, a grape species with high cold hardiness. Nine TFs, including CBF4, RAV1 and ERF104, were identified after cold treatment. Weighted gene co-expression network analysis (WGCNA) and gene ontology (GO) analysis revealed that these TFs may regulate cold response through different pathways. As a prime candidate TF, overexpression of VaRAV1 in grape cells improved its cold tolerance. The transgenic cells exhibited low electrolyte leakage and malondialdehyde content and high peroxidase activity. Moreover, the TF gene TCP8 and a gene involving in homogalacturonan biosynthesis were found to be regulated by VaRAV1, suggesting that the contribution of VaRAV1 to cold tolerance may be achieved by enhancing the stability of cell membrane and regulating the expression of target genes involved in plant cell wall composition. Our work provides novel insights into plant response to cold stress and demonstrates the utility of ATAC-seq and RNA-seq for the rapid identification of TFs in response to cold stress in grapevine. VaRAV1 may play an important role in adaption to cold stress.

Cold induced genes (CIGs) regulate flower development and dormancy in Prunus avium L

The flower buds continue to develop during the whole winter in tree fruit species, which is affected by environmental factors and hormones. However, little is known about the molecular mechanism of flower development during dormancy phase of sweet cherry in response to light, temperature and ABA. Therefore, we identified two cold induced gene (CIG) PavCIG1 and PavCIG2 from sweet cherry, which were closely to PpCBF and PyDREB from Prunus persica and Prunus yedoensis by using phylogenetic analysis, suggesting conserved functions with these evolutionarily closer DREB subfamily genes. Subcellular localization analysis indicated that, PavCIG1 and PavCIG2 were both localized in the nucleus. The seasonal expression levels of PavCIG1 and PavCIG2 were higher at the stage of endodormancy in winter, and induced by low temperature. Ectopic expression of PavCIG1 and PavCIG2 resulted in a delayed flowering in Arabidopsis. Furthermore, PavCIG2 increased light-responsive gene PavHY5 transcriptional activity by binding to its promoter, meanwhile, PavHY5-mediated positive feedback regulated PavCIG2. Moreover, ABA-responsive protein PavABI5-like could also increase transcriptional activity of PavCIG and PavCIG2. In addition, PavCIG and PavCIG2 target gene PavCAL-like was involved in floral initiation, demonstrated by ectopic expression in Arabidopsis. These findings provide evidences to better understand the molecular mechanism of CIG-mediated flower development and dormancy in fruit species, including sweet cherry.

Genome-wide survey and identification of AP2/ERF genes involved in shoot and leaf development in Liriodendron chinense

BACKGROUND

Liriodendron chinense is a distinctive ornamental tree species due to its unique leaves and tulip-like flowers. The discovery of genes involved in leaf development and morphogenesis is critical for uncovering the underlying genetic basis of these traits. Genes in the AP2/ERF family are recognized as plant-specific transcription factors that contribute to plant growth, hormone-induced development, ethylene response factors, and stress responses.

RESULTS

In this study, we identified 104 putative AP2/ERF genes in the recently released L. chinense genome and transcriptome database. In addition, all 104 genes were grouped into four subfamilies, the AP2, ERF, RAV, and Soloist subfamilies. This classification was further supported by the results of gene structure and conserved motif analyses. Intriguingly, after application of a series test of cluster analysis, three AP2 genes, LcERF 94, LcERF 96, and LcERF 98, were identified as tissue-specific in buds based on the expression profiles of various tissues. These results were further validated via RT-qPCR assays and were highly consistent with the STC analysis. We further investigated the dynamic changes of immature leaves by dissecting fresh shoots into seven discontinuous periods, which were empirically identified as shoot apical meristem (SAM), leaf primordia and tender leaf developmental stages according to the anatomic structure. Subsequently, these three candidates were highly expressed in SAM and leaf primordia but rarely in tender leaves, indicating that they were mainly involved in early leaf development and morphogenesis. Moreover, these three genes displayed nuclear subcellular localizations through the transient transformation of tobacco epidermal cells.

CONCLUSIONS

Overall, we identified 104 AP2/ERF family members at the genome-wide level and discerned three candidate genes that might participate in the development and morphogenesis of the leaf primordium in L. chinense.

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.

Overexpressing Jatropha curcas CBF2 in Nicotiana benthamiana improved plant tolerance to drought stress

Jatropha curcas is an important bioenergy oil plant, and often planted on barren land to save the area of arable land. It is significant to improve the adaptability of J. curcas to various abiotic stresses. In the present study, we transferred a J. curcas gene, encoding a CBF2 transcription factor, into Nicotiana benthamiana. Under drought treatment, the JcCBF2 transgenic lines showed improved survival rate, leaf water retention and active oxygen scavenging capacity, but reduced photosynthesis and transpiration rate, suggesting that JcCBF2 played an important role in improving plant drought tolerance. Overexpressing JcCBF2 decreased leaf area and increased leaf thickness. To explore the possible mechanisms for the change of leaf anatomical structure, the leaves of wild-type and overexpression lines under drought stress were RNA sequenced. Genes involved in the plant hormones signal transduction were found to be enriched. Cytokinin and indole-3-acetic acid were the major plant hormones whose abundance increased. Quantitative RT-PCR analysis showed expression of NbMYB21, NbMYB86 and NbMYB44 and both abscisic acid (ABA) and jasmonic acid (JA) related genes in the overexpression lines were increased under drought stress. These results indicated that JcCBF2 was able to positively regulate plant drought response by changing the leaf anatomical structure and possibly through JA and ABA signalling pathways. Our work may help us to understand the drought tolerant mechanism.

Recent advances in biotechnological studies on wild grapevines as valuable resistance sources for smart viticulture

Cultivated grapevines, Vitis vinifera subsp. sativa, are thought to have been domesticated from wild populations of Vitis vinifera subsp. sylvestris in Central Asia. V. vinifera subsp. sativa is one of the most economically important fruit crops worldwide. Since cultivated grapevines are susceptible to multiple biotic and abiotic soil factors, they also need to be grafted on resistant rootstocks that are mostly developed though hybridization between American wild grapevine species (V. berlandieri, V. riparia, and V. rupestris). Therefore, wild grapevine species are essential genetic materials for viticulture to face biotic and abiotic stresses in both cultivar and rootstock parts. Actually, viticulture faces several environmental constraints that are further intensified by climate change. Recently, several reports on biotic and abiotic stresses-response in wild grapevines revealed accessions tolerant to different constraints. The emergence of advanced techniques such as omics technologies, marker-assisted selection (MAS), and functional analysis tools allowed a more detailed characterization of resistance mechanisms in these wild grapevines and suggest a number of species (V. rotundifolia, V. rupestris, V. riparia, V. berlandieri and V. amurensis) have untapped potential for new resistance traits including disease resistance loci and key tolerance genes. The present review reports on the importance of different biotechnological tools in exploring and examining wild grapevines tolerance mechanisms that can be employed to promote elite cultivated grapevines under climate change conditions.

The SWI/SNF ATP-Dependent Chromatin Remodeling Complex in Arabidopsis Responds to Environmental Changes in Temperature-Dependent Manner

SWI/SNF ATP-dependent chromatin remodeling complexes (CRCs) play important roles in the regulation of transcription, cell cycle, DNA replication, repair, and hormone signaling in eukaryotes. The core of SWI/SNF CRCs composed of a SWI2/SNF2 type ATPase, a SNF5 and two of SWI3 subunits is sufficient for execution of nucleosome remodeling in vitro. The Arabidopsis genome encodes four SWI2/SNF2 ATPases, four SWI3, a single SNF5 and two SWP73 subunits. Genes of the core SWI/SNF components have critical but not fully overlapping roles during plant growth, embryogenesis, and sporophyte development. Here we show that the Arabidopsis swi3c mutant exhibits a phenotypic reversion when grown at lower temperature resulting in partial restoration of its embryo, root development and fertility defects. Our data indicates that the swi3c mutation alters the expression of several genes engaged in low temperature responses. The location of SWI3C-containing SWI/SNF CRCs on the ICE1, MYB15 and CBF1 target genes depends on the temperature conditions, and the swi3c mutation thus also influences the transcription of several cold-responsive (COR) genes. These findings, together with genetic analysis of swi3c/ice1 double mutant and enhanced freezing tolerance of swi3c plants illustrate that SWI/SNF CRCs contribute to fine-tuning of plant growth responses to different temperature regimes.

Ectopic expression of Medicago truncatula homeodomain finger protein, MtPHD6, enhances drought tolerance in Arabidopsis

BACKGROUND

The plant homeodomain (PHD) finger is a Cys4HisCys3-type zinc finger which promotes protein-protein interactions and binds to the cis-acting elements in the promoter regions of target genes. In Medicago truncatula, five PHD homologues with full-length sequence were identified. However, the detailed function of PHD genes was not fully addressed.

RESULTS

In this study, we characterized the function of MtPHD6 during plant responses to drought stress. MtPHD6 was highly induced by drought stress. Ectopic expression of MtPHD6 in Arabidopsis enhanced tolerance to osmotic and drought stresses. MtPHD6 transgenic plants exhibited decreased water loss rate, MDA and ROS contents, and increased leaf water content and antioxidant enzyme activities under drought condition. Global transcriptomic analysis revealed that MtPHD6 reprogramed transcriptional networks in transgenic plants. Expression levels of ABA receptor PYR/PYLs, ZINC FINGER, AP2/EREBP and WRKY transcription factors were mainly up-regulated after transformation of MtPHD6. Interaction network analysis showed that ZINC FINGER, AP2/EREBP and WRKY interacted with each other and downstream stress induced proteins.

CONCLUSIONS

We proposed that ZINC FINGER, AP2/EREBP and WRKY transcription factors were activated through ABA dependent and independent pathways to increase drought tolerance of MtPHD6 transgenic plants.

Phylogenetic, Molecular, and Functional Characterization of PpyCBF Proteins in Asian Pears (Pyrus pyrifolia)

C-repeat binding factor/dehydration-responsive element (CBF/DRE) transcription factors (TFs) participate in a variety of adaptive mechanisms, and are involved in molecular signaling and abiotic stress tolerance in plants. In pear (Pyrus pyrifolia) and other rosaceous crops, the independent evolution of CBF subfamily members requires investigation to understand the possible divergent functions of these proteins. In this study, phylogenetic analysis divided six PpyCBFs from the Asian pear genome into three clades/subtypes, and collinearity and phylogenetic analyses suggested that PpyCBF3 was the mother CBF. All PpyCBFs were found to be highly expressed in response to low temperature, salt, drought, and abscisic acid (ABA) as well as bud endodormancy, similar to PpyCORs (PpyCOR47, PpyCOR15A, PpyRD29A, and PpyKIN). Transcript levels of clade II PpyCBFs during low temperature and ABA treatments were higher than those of clades I and III. Ectopic expression of PpyCBF2 and PpyCBF3 in Arabidopsis enhanced its tolerance against abiotic stresses, especially to low temperature in the first case and salt and drought stresses in the latter, and resulted in lower reactive oxygen species (ROS) and antioxidant gene activities compared with the wild type. The increased expression of endogenous ABA-dependent and -independent genes during normal conditions in PpyCBF2- and PpyCBF3-overexpressing Arabidopsis lines suggested that PpyCBFs were involved in both ABA-dependent and -independent pathways. All PpyCBFs, especially the mother CBF, had high transactivation activities with 6XCCGAC binding elements. Luciferase and Y1H assays revealed the existence of phylogenetically and promoter-dependent conserved CBF-COR cascades in the pear. The presence of a previously identified CCGA binding site, combined with the results of mutagenesis of the CGACA binding site of the PpyCOR15A promoter, indicated that CGA was a core binding element of PpyCBFs. In conclusion, PpyCBF TFs might operate redundantly via both ABA-dependent and -independent pathways, and are strongly linked to abiotic stress signaling and responses in the Asian pear.

Abscisic acid (ABA) and low temperatures synergistically increase the expression of CBF/DREB1 transcription factors and cold-hardiness in grapevine dormant buds

BACKGROUND AND AIMS

It has been reported that low temperatures (LTs) and the plant hormone abscisic acid (ABA) induce the expression of CBF/DREB1 transcription factors in vegetative tissues and seedlings of Vitis vinifera and Vitis riparia and that foliar applications of ABA to V. vinifera increase the freezing tolerance or cold-hardiness of dormant buds. However, the combined effect of ABA and LTs on the expression of CBF/DREB1 transcription factors and on the acquisition of freezing tolerance in dormant grapevine buds has not been investigated. The objective of this study was to analyse the combined effect of ABA and LT treatments on the expression of CBF/DREB transcription factors and the acquisition of freezing tolerance.

METHODS

In vitro experiments with single-bud cuttings of grapevines were used to analyse the effect of ABA, ABA + LT and LT on the expression of CBF/DREB transcription factors, dehydrin and antioxidant genes, the acquisition of freezing tolerance and the endogenous content of ABA. Gene expression analysis was performed by quantitative real-time PCR and freezing tolerance was determined by measuring the low-temperature exotherm by differential thermal analysis. ABA levels were determined by gas chromatography coupled to an electron capture detector.

KEY RESULTS

The LT treatment and exogenous application of ABA to grapevine dormant buds increased the expression of the CBF/DREB1 transcription factors VvCBF2, VvCBF3, VvCBF4 and VvCBF6. The joint application of LT and ABA produced a huge increase in the expression of these transcription factors, which was greater than the sum of the increases produced by them individually, which indicates the existence of a synergistic effect between ABA and LT on the activation of these transcription factors. This synergic effect was also observed on the increase in bud cold-hardiness and on the expression of antioxidant and dehydrin genes.

CONCLUSIONS

The synergy between ABA and LT on the expression of CBF/DREB1 transcription factors VvCBF2, VvCBF3, VvCBF4 and VvCBF6 plays a key role in cold acclimatization of grapevine buds. The results highlight the importance of the combination of stimuli in the improvement of genetic and physiological responses and help us to understand the adaption of plants to complex environments.

Expression, purification and molecular characterization of a novel transcription factor KcCBF3 from Kandelia candel

Kandelia candel, a major species of mangrove in the tropical and subtropical area, is susceptible to low temperature in winter. K. candel was introduced into Zhejiang Province (the northern margin of South China) several decades ago, and suffered from low temperature causing growth retardation, in server cases, even death. To explore the molecular mechanisms of cold acclimation in K. candel, a novel C-repeat binding factor gene KcCBF3 (Genbank accession no. KF111715) of 729 bp open reading frame (ORF) encoding a protein of 242 amino acid residues was isolated, expressed, purified and characterized. Multiple sequence alignment analysis revealed that KcCBF3 contained a highly conserved AP2/EREBP DNA-binding domain which consisting of 79 amino acid residues, as well as two CBF signature sequences. Phylogenetic analysis indicated that KcCBF3 belonged to the A-1 subgroup of DREB subfamily based on the classification of AP2/EREBP transcription factors in Arabidopsis. Semi-quantitative RT-PCR showed that KcCBF3 transcripts were highly accumulated in roots and leaves, and could be induced by low temperature. Electrophoresis mobility shift assay (EMSA) demonstrated KcCBF3 could bind to the core sequence (CCGAC) of cis-acting element C-repeat (CRT)/dehydration-responsive element (DRE) in vitro. These results implied that KcCBF3 might participate in the adaptation of K. candel to low-temperature stress by binding to CRT/DRE element.

Ectopic expression of StCBF1and ScCBF1 have different functions in response to freezing and drought stresses in Arabidopsis

Solanum tuberosum potato species constitute the bulk of economically and agronomically important potato production. However, S. tuberosum is a drought- and frost-sensitive species that is incapable of acclimating to the cold. Solanum commersonii is a tuber-bearing wild potato species that exhibits greater frost and drought resistance than S. tuberosum. CBF/DREB (C-REPET BINDING FACTOR/DROUGHT RESPONSE ELEMENT BINGING FACTOR) transcription factors play important roles in response to a variety of abiotic stresses, such as cold, drought and salt stresses. To explore different functions between S. tuberosum CBF1 (StCBF1) and S. commersonii CBF1 (ScCBF1), Arabidopsis was transformed with the ScCBF1 and StCBF1 genes driven by a constitutive CaMV35S promoter. Our results reveal that the ScCBF1 transgenic lines are much more tolerant to freezing and drought than the StCBF1 transgenic lines. The development of transgenic plants was altered, resulting in dwarf phenotype with delayed flowering and thicker and additional rosette leaves. The expression levels of several COR (COLD-RESPONSIVE) genes and development-related genes, including genes that inhibited plant growth (GA2ox7, RGL3) and delayed flowering (FLC) were higher in transgenic plants. These results suggest that these two potato CBF1 play important roles in the plant response to abiotic stress and can influence plant growth and development, and ScCBF1 plays a more pronounced function than StCBF1.

Identification of genes from the ICE-CBF-COR pathway under cold stress in Aegilops-Triticum composite group and the evolution analysis with those from Triticeae

Adverse environmental conditions limit various aspects of plant growth, productivity, and ecological distribution. To get more insights into the signaling pathways under low temperature, we identified 10 C-repeat binding factors (CBFs), 9 inducer of CBF expression (ICEs) and 10 cold-responsive (CORs) genes from Aegilops-Triticum composite group under cold stress. Conserved amino acids analysis revealed that all CBF, ICE, COR contained specific and typical functional domains. Phylogenetic analysis of CBF proteins from Triticeae showed that these CBF homologs were divided into 11 groups. CBFs from Triticum were found in every group, which shows that these CBFs generated prior to the divergence of the subfamilies of Triticeae. The evolutionary relationship among the ICE and COR proteins in Poaceae were divided into four groups with high multispecies specificity, respectively. Moreover, expression analysis revealed that mRNA accumulation was altered by cold treatment and the genes of three types involved in the ICE-CBF-COR signaling pathway were induced by cold stress. Together, the results make CBF, ICE, COR genes family in Triticeae more abundant, and provide a starting point for future studies on transcriptional regulatory network for improvement of chilling tolerance in crop.

Crosstalk of PmCBFs and PmDAMs Based on the Changes of Phytohormones under Seasonal Cold Stress in the Stem of Prunus mume

Plants facing the seasonal variations always need a growth restraining mechanism when temperatures turn down. C-repeat binding factor (CBF) genes work essentially in the cold perception. Despite lots of researches on CBFs, the multiple crosstalk is still interesting on their interaction with hormones and dormancy-associated MADS (DAM) genes in the growth and dormancy control. Therefore, this study highlights roles of PmCBFs in cold-induced dormancy from different orgens. And a sense-response relationship between PmCBFs and PmDAMs is exhibited in this process, jointly regulated by six PmCBFs and PmDAM4-6. Meantime, GA3 and ABA showed negative and positive correlation with PmCBFs expression levels, respectively. We also find a high correlation between IAA and PmDAM1-3. Finally, we display the interaction mode of PmCBFs and PmDAMs, especially PmCBF1-PmDAM1. These results can disclose another view of molecular mechanism in plant growth between cold-response pathway and dormancy regulation together with genes and hormones.

Deciphering the Role of CBF/DREB Transcription Factors and Dehydrins in Maintaining the Quality of Table Grapes cv. Autumn Royal Treated with High CO2 Levels and Stored at 0°C

C-repeat/dehydration-responsive element binding factors (CBF/DREB) are transcription factors which play a role in improving plant cold stress resistance and recognize the DRE/CRT element in the promoter of a set of cold regulated genes. Dehydrins (DHNs) are proteins that accumulate in plants in response to cold stress, which present, in some cases, CBF/DREB recognition sequences in their promoters and are activated by members of this transcription factor family. The application of a 3-day gaseous treatment with 20 kPa CO2 at 0°C to table grapes cv. Autumn Royal maintained the quality of the bunches during postharvest storage at 0°C, reducing weight loss and rachis browning. In order to determine the role of CBF/DREB genes in the beneficial effect of the gaseous treatment by regulating DHNs, we have analyzed the gene expression pattern of three VviDREBA1s (VviDREBA1-1, VviDREBA1-6, and VviDREBA1-7) as well as three VviDHNs (VviDHN1a, VviDHN2, and VviDHN4), in both alternative splicing forms. Results showed that the differences in VviDREBA1s expression were tissue and atmosphere composition dependent, although the application of high levels of CO2 caused a greater increase of VviDREBA1-1 in the skin, VviDREBA1-6 in the pulp and VviDREBA1-7 in the skin and pulp. Likewise, the application of high levels of CO2 regulated the retention of introns in the transcripts of the dehydrins studied in the different tissues analyzed. The DHNs promoter analysis showed that VviDHN2 presented the cis-acting DRE and CRT elements, whereas VviDHN1a presented only the DRE motif. Our electrophoretic mobility shift assays (EMSA) showed that VviDREBA1-1 was the only transcription factor that had in vitro binding capacity to the CRT element of the VviDHN2 promoter region, indicating that the transcriptional regulation of VviDHN1a and VviDHN4 would be carried out by activating other independent routes of these transcription factors. Our results suggest that the application of high CO2 levels to maintain table grape quality during storage at 0°C, leads to an activation of CBF/DREBs transcription factors. Among these factors, VviDREBA1-1 seems to participate in the transcriptional activation of VviDHN2 via CRT binding, with the unspliced form of this DHN being activated by high CO2 levels in all the tissues analyzed.

Special trends in CBF and DREB2 groups in Eucalyptus gunnii vs Eucalyptus grandis suggest that CBF are master players in the trade-off between growth and stress resistance

Annotation of the Eucalyptus grandis genome showed a large amplification of the dehydration-responsive element binding 1/C-repeat binding factor (DREB1/CBF) group without recent DREB2 gene duplication compared with other plant species. The present annotation of the CBF and DREB2 genes from a draft of the Eucalyptus gunnii genome sequence reveals at least one additional CBF copy in the E. gunnii genome compared with E. grandis, suggesting that this group is still evolving, unlike the DREB2 group. This study aims to investigate the redundancy/neo- or sub-functionalization of the duplicates and the relative involvement of the two groups in abiotic stress responses in both E. grandis and E. gunnii (lower growth but higher cold resistance). A comprehensive transcriptional analysis using high-throughput quantitative real-time polymerase chain reaction (qRT-PCR) was performed on leaves, stems and roots from the two Eucalyptus species after cold, heat or drought treatment. A large CBF cluster accounted for most of the cold response in all the organs, whereas heat and drought responses mainly involved a small CBF cluster and the DREB2 genes. In addition, CBF putative target genes, known to be involved in plant tolerance and development, were found to be cold-regulated. The higher transcript amounts of both the CBF and target genes in the cold tolerant E. gunnii contrasted with the higher CBF induction rates in the fast growing E. grandis. Altogether, the present results, in agreement with previous data about Eucalyptus transgenic lines over-expressing CBF, suggest that these factors, which promote both stress protection and growth limitation, participate in the trade-off between growth and resistance in this woody species.

Arabidopsis CBF3 and DELLAs positively regulate each other in response to low temperature

The C-repeat binding factor (CBF) is crucial for regulation of cold response in higher plants. In Arabidopsis, the mechanism of CBF3-caused growth retardation is still unclear. Our present work shows that CBF3 shares the similar repression of bioactive gibberellin (GA) as well as upregulation of DELLA proteins with CBF1 and -2. Genetic analysis reveals that DELLAs play an essential role in growth reduction mediated by CBF1, -2, -3 genes. The in vivo and in vitro evidences demonstrate that GA2-oxidase 7 gene is a novel CBF3 regulon. Meanwhile, DELLAs contribute to cold induction of CBF1, -2, -3 genes through interaction with jasmonate (JA) signaling. We conclude that CBF3 promotes DELLAs accumulation through repressing GA biosynthesis and DELLAs positively regulate CBF3 involving JA signaling. CBFs and DELLAs collaborate to retard plant growth in response to low temperature.

Overexpression of Muscadinia rotundifolia CBF2 gene enhances biotic and abiotic stress tolerance in Arabidopsis

C-repeat-binding factor dehydration-responsive element-binding factor 1C (CBF2/DREB1C) gene encodes a small family of transcriptional activator that has been described as playing an important role in freezing tolerance and cold acclimation of plants. We here report that CBF2 gene also plays an important role in the early response to the pathogen infection of grapevine downy mildew disease. The expression level of CBF2 increased dramatically and reached a peak at 7 h after infection in immune grapevine Muscadinia rotundifolia 'Noble', which was much faster than moderate resistant Vitis amurensis 'PI1288' and susceptible Vitis vinifera 'Cabernet Sauvignon'. Muscadinia rotundifolia MrCBF2 exhibited amino acid domains characteristic of Vitis CBF2 proteins with unique features including rich serine repeats and slight differences in NLS, DSAWRL, and AP2 domains. The MrCBF2 gene was introduced to Arabidopsis 'COL0' which are susceptible to downy mildew pathogen. The transgenic lines showed an increased resistance to downy mildew disease and more accumulation of SA as well as higher expression of pathogenesis-related (PR) genes (AtPR1, AtPR4, and AtPR5) as a consequence of MrCBF2 overexpression. Besides, constitutive expression of MrCBF2 enhanced phytohormone abscisic acid (ABA)-independent drought tolerance of transgenic plants. Freezing tolerance of transgenic lines was also enhanced accompanied with an increase in the expression of the cold-regulated genes AtCOR, AtCOR15A, AtKIN1, AtRD29A, and AtSuSy. In addition, the development of MrCBF2-overexpressing plants was seen to be altered and resulted in growth retardation, dwarfism, late flowering, and prone rosette leaves, which may be because of an increase in the gene expression of partial DELLA proteins and DDF1.

Functional and Structural Characterization of a Receptor-Like Kinase Involved in Germination and Cell Expansion in Arabidopsis

Leucine-rich repeat receptor-like kinases (LRR-RLKs) are widespread in different plant species and play important roles in growth and development. Germination inhibition is vital for the completion of seed maturation and cell expansion is a fundamental cellular process driving plant growth. Here, we report genetic and structural characterizations of a functionally uncharacterized LRR-RLK, named GRACE (Germination Repression and Cell Expansion receptor-like kinase). Overexpression of GRACE in Arabidopsis exhibited delayed germination, enlarged cotyledons, rosette leaves and stubbier petioles. Conversely, these phenotypes were reversed in the T-DNA insertion knock-down mutant grace-1 plants. A crystal structure of the extracellular domain of GRACE (GRACE-LRR) determined at the resolution of 3.0 Å revealed that GRACE-LRR assumed a right-handed super-helical structure with an island domain (ID). Structural comparison showed that structure of the ID in GRACE-LRR is strikingly different from those observed in other LRR-RLKs. This structural observation implies that GRACE might perceive a new ligand for signaling. Collectively, our data support roles of GRACE in repressing seed germination and promoting cell expansion of Arabidopsis, presumably by perception of unknown ligand(s).

Photosynthetic acclimation, vernalization, crop productivity and 'the grand design of photosynthesis'

Daniel Arnon first proposed the notion of a 'grand design of photosynthesis' in 1982 to illustrate the central role of photosynthesis as the primary energy transformer for all life on Earth. However, we suggest that this concept can be extended to the broad impact of photosynthesis not only in global energy transformation but also in the regulation of plant growth, development, survival and crop productivity through chloroplast redox signalling. We compare and contrast the role of chloroplast redox imbalance, measured as excitation pressure, in governing acclimation to abiotic stress and phenotypic plasticity. Although all photoautrophs sense excessive excitation energy through changes in excitation pressure, the response to this chloroplast redox signal is species dependent. Due to a limited capacity to adjust metabolic sinks, cyanobacteria and green algae induce photoprotective mechanisms which dissipate excess excitation energy at a cost of decreased photosynthetic performance. In contrast, terrestrial, cold tolerant plants such as wheat enhance metabolic sink capacity which leads to enhanced photosynthetic performance and biomass accumulation with minimal dependence on photoprotection. We suggest that the family of nuclear C-repeat binding transcription factors (CBFs) associated with the frost resistance locus, FR2, contiguous with the vernalization locus,VRN1, and mapped to chromosome 5A of wheat, may be critical components that link leaf chloroplast redox regulation to enhanced photosynthetic performance, the accumulation of growth-active gibberellins and the dwarf phenotype during cold acclimation prior to the vegetative to reproductive transition controlled by vernalization in winter cereals. Further genetic, molecular and biochemical research to confirm these links and to elucidate the molecular mechanism by which chloroplast redox modulation of CBF expression leads to enhanced photosynthetic performance is required. Because of the superior abiotic stress tolerance of cold tolerant winter wheat and seed yields that historically exceed those of spring wheat by 30-40%, we discuss the potential to exploit winter cereals for the maintenance or perhaps even the enhancement of cereal productivity under future climate change scenarios that will be required to feed a growing human population.

Breadfruit (Artocarpus altilis) gibberellin 2-oxidase genes in stem elongation and abiotic stress response

Breadfruit (Artocarpus altilis) is a traditional staple tree crop in the Oceania. Susceptibility to windstorm damage is a primary constraint on breadfruit cultivation. Significant tree loss due to intense tropical windstorm in the past decades has driven a widespread interest in developing breadfruit with dwarf stature. Gibberellin (GA) is one of the most important determinants of plant height. GA 2-oxidase is a key enzyme regulating the flux of GA through deactivating biologically active GAs in plants. As a first step toward understanding the molecular mechanism of growth regulation in the species, we isolated a cohort of four full-length GA2-oxidase cDNAs, AaGA2ox1- AaGA2ox4 from breadfruit. Sequence analysis indicated the deduced proteins encoded by these AaGA2oxs clustered together under the C19 GA2ox group. Transcripts of AaGA2ox1, AaGA2ox2 and AaGA2ox3 were detected in all plant organs, but exhibited highest level in source leaves and stems. In contrast, transcript of AaGA2ox4 was predominantly expressed in roots and flowers, and displayed very low expression in leaves and stems. AaGA2ox1, AaGA2ox2 and AaGA2ox3, but not AaGA2ox4 were subjected to GA feedback regulation where application of exogenous GA3 or gibberellin biosynthesis inhibitor, paclobutrazol was shown to manipulate the first internode elongation of breadfruit. Treatments of drought or high salinity increased the expression of AaGA2ox1, AaGA2ox2 and AaGA2ox4. But AaGA2ox3 was down-regulated under salt stress. The function of AaGA2oxs is discussed with particular reference to their role in stem elongation and involvement in abiotic stress response in breadfruit.

Comparison of CBF1, CBF2, CBF3 and CBF4 expression in some grapevine cultivars and species under cold stress

Grapevine, an important horticultural crop in the world, is moderately tolerant to cold conditions and is subjected to the cold injuries at different regions. So studies on different aspects of tolerance mechanism to unexpected cold of late spring as well as winter freezing seems necessary about this vine. For this reason, study on genes responsible for acquiring cold tolerance is very important. Transcription factors are among regulatory proteins that are responsible for cold acclimation. In this research work, expression levels of CBF1, CBF2, CBF3, and CBF4 transcription factors were studied on two cvs of Vitis vinifera ("Khalili-Danedar" and "Shahroodi") as well as one Vitis riparia at different times after treating at 4 °C. Results showed that two vinifera cultivars, "Khalili-Danedar" and "Shahroodi", had similar trend for each transcription factor. Gene expression increased at the beginning of cold stress and then decreased. Expression of these TF started some minutes (CBF1) after cold treatment and continued for several hours (CBF2), even till the tenth day (CBF4). All together V. riparia which is endemic to the cold regions behaved stronger and showed higher expression for all studied transcription factors. Among two V. vinifera cultivars, "Khalili-Danedar" showed significantly higher expression compared with "Shahroodi". The comparison of expression levels of these four transcription factors revealed that the least and the greatest expressions were recorded for CBF1 and CBF3 respectively, and two CBF2 and CBF4 had approximately the same expression levels.

Characterization and expression analysis of a gene encoding CBF/DREB1 transcription factor from mangrove Aegiceras corniculatum

Several transcription factors play important roles in survival of plants under cold, drought and salt stresses by serving as master regulator of sets of downstream stress-responsive genes. A gene encoding CBF/DREB1 transcription factor (C-repeat binding factor/dehydration responsive element-binding factor 1) was isolated from mangrove Aegiceras corniculatum and designated AcCBF1. The full-length cDNA of AcCBF1 was 896 bp containing 618 bp ORF encoding a protein of 205 amino acids. Multiple sequence analysis showed that the corresponding protein had 100 % identity to AmCBF1 (KC776908) from mangrove Avicennia marina, and contains an AP2/ERE DNA-binding domain and two CBF signature sequences. Expression analyses based on quantitative real-time PCR revealed that the AcCBF1 gene was expressed in all tissues of A. corniculatum under normal condition with the highest expression level detected in leaves. When exposed to abiotic stresses, AcCBF1 gene showed different expression patterns in different tissues. Generally, AcCBF1 gene could be rapidly and strongly induced by cold and drought, while slightly induced by abscisic acid and salinity. Furthermore, light could positively regulate the cold-induction level of AcCBF1. These results suggest that the AcCBF1 may be playing important role in the signaling pathway of cold stress and also involved in the cross-talk among abiotic stresses. Further studies focusing on the promotors and downstream stress-responsive genes of AcCBF1 will help to better understand the regulatory mechanisms of mangrove A. corniculatum under abiotic stresses.

Association genetics and expression patterns of a CBF4 homolog in Populus under abiotic stress

New strategies for prevention and treatment of abiotic stress require an improved understanding of stress responses. Here, we examined response differences of a C-repeat binding factor gene (PsCBF4) between five species in the genus Populus. We also used a candidate gene-based approach to identify single nucleotide polymorphisms (SNPs) within PsCBF4 that were associated with physiological and biochemical traits in a natural population (528 unrelated individuals) of Populus simonii. We first isolated a 1,044-bp PsCBF4 cDNA encoding a polypeptide of 256 amino acids. Expression profiling revealed that CBF4 is differentially expressed under cold, heat, drought, and salt conditions among five Populus species. Cold stress is the most significant interspecific difference, and PsCBF4 transcript levels ranged from 6.5 to 379.5 times higher than in unstressed controls. A natural population of P. simonii showed high nucleotide diversity (π T = 0.00880, θ w = 0.01192) and low linkage disequilibrium (r (2) ≥ 0.1, within 700 bp) across PsCBF4. Association analysis showed that nine SNPs (false discovery rate Q < 0.10) and two haplotypes (Q < 0.10) were significantly associated with six physiological and biochemical traits, with each marker explaining 3.36-6.12 % of the phenotypic variance in the corresponding trait. Transcript analysis further detected significant differences among genotypic classes for all significant SNPs. Identification of these significant associations will help reveal the molecular bases of physiological and biochemical differences and provide a starting point for marker-assisted selection for traits involved in stress tolerance in P. simonii.

Overexpression of AtDREB1D transcription factor improves drought tolerance in soybean

Drought is one of the major abiotic stresses that affect productivity in soybean (Glycine max L.) Several genes induced by drought stress include functional genes and regulatory transcription factors. The Arabidopsis thaliana DREB1D transcription factor driven by the constitutive and ABA-inducible promoters was introduced into soybean through Agrobacterium tumefaciens-mediated gene transfer. Several transgenic lines were generated and molecular analysis was performed to confirm transgene integration. Transgenic plants with an ABA-inducible promoter showed a 1.5- to two-fold increase of transgene expression under severe stress conditions. Under well-watered conditions, transgenic plants with constitutive and ABA-inducible promoters showed reduced total leaf area and shoot biomass compared to non-transgenic plants. No significant differences in root length or root biomass were observed between transgenic and non-transgenic plants under non-stress conditions. When subjected to gradual water deficit, transgenic plants maintained higher relative water content because the transgenic lines used water more slowly as a result of reduced total leaf area. This caused them to wilt slower than non-transgenic plants. Transgenic plants showed differential drought tolerance responses with a significantly higher survival rate compared to non-transgenic plants when subjected to comparable severe water-deficit conditions. Moreover, the transgenic plants also showed improved drought tolerance by maintaining 17-24 % greater leaf cell membrane stability compared to non-transgenic plants. The results demonstrate the feasibility of engineering soybean for enhanced drought tolerance by expressing stress-responsive genes.

Increased drought tolerance through the suppression of ESKMO1 gene and overexpression of CBF-related genes in Arabidopsis

Improved drought tolerance is always a highly desired trait for agricultural plants. Significantly increased drought tolerance in Arabidopsis thaliana (Columbia-0) has been achieved in our work through the suppression of ESKMO1 (ESK1) gene expression with small-interfering RNA (siRNA) and overexpression of CBF genes with constitutive gene expression. ESK1 has been identified as a gene linked to normal development of the plant vascular system, which is assumed directly related to plant drought response. By using siRNA that specifically targets ESK1, the gene expression has been reduced and drought tolerance of the plant has been enhanced dramatically in the work. However, the plant response to external abscisic acid application has not been changed. ICE1, CBF1, and CBF3 are genes involved in a well-characterized plant stress response pathway, overexpression of them in the plant has demonstrated capable to increase drought tolerance. By overexpression of these genes combining together with suppression of ESK1 gene, the significant increase of plant drought tolerance has been achieved in comparison to single gene manipulation, although the effect is not in an additive way. Accompanying the increase of drought tolerance via suppression of ESK1 gene expression, the negative effect has been observed in seeds yield of transgenic plants in normal watering conditions comparing with wide type plant.

Cold response in Phalaenopsis aphrodite and characterization of PaCBF1 and PaICE1

Phalaenopsis is a winter-blooming orchid genus commonly cultivated in tropical Asian countries. Because orchids are one of the most economically important flower crops in Taiwan, it is crucial to understand their response to cold and other abiotic stresses. The present study focused on gene regulation of P. aphrodite in response to abiotic stress, mainly cold. Our results demonstrate that P. aphrodite is sensitive to low temperatures, especially in its reproductive stage. We found that after exposure to 4°C, plants in the vegetative stage maintained better membrane integrity and photosynthetic capacity than in the flowering stage. At the molecular level, C-repeat binding factor1 (PaCBF1) and its putative target gene dehydrin1 (PaDHN1) mRNAs were induced by cold, whereas inducer of CBF expression1 (PaICE1) mRNA was constitutively expressed. PaICE1 transactivated MYC motifs in the PaCBF1 promoter, indicating that up-regulation of PaCBF1 may be mediated by the binding of PaICE1 to MYC motifs. Overexpression of PaCBF1 in transgenic Arabidopsis induced AtCOR6.6 and RD29a without cold stimulus and maintained better membrane integrity after cold stress. Herein, we present evidence that cold induction of PaCBF1 transcripts in P. aphrodite may be transactivated by PaICE1 and consequently protect plants from cold damage through up-regulation of cold-regulated (COR) genes, such as DHN. To our knowledge, this study is the first report of the isolation and characterization of CBF, DHN and ICE genes in the Orchidaceae family.

ExpressionData - A public resource of high quality curated datasets representing gene expression across anatomy, development and experimental conditions

Reference datasets are often used to compare, interpret or validate experimental data and analytical methods. In the field of gene expression, several reference datasets have been published. Typically, they consist of individual baseline or spike-in experiments carried out in a single laboratory and representing a particular set of conditions. Here, we describe a new type of standardized datasets representative for the spatial and temporal dimensions of gene expression. They result from integrating expression data from a large number of globally normalized and quality controlled public experiments. Expression data is aggregated by anatomical part or stage of development to yield a representative transcriptome for each category. For example, we created a genome-wide expression dataset representing the FDA tissue panel across 35 tissue types. The proposed datasets were created for human and several model organisms and are publicly available at http://www.expressiondata.org.

The grapevine basic helix-loop-helix (bHLH) transcription factor positively modulates CBF-pathway and confers tolerance to cold-stress in Arabidopsis

Basic helix-loop-helix (bHLH)-type transcription factors play diverse roles in plant physiological response and stress-adaptive regulation network. Here, we identified one grapevine bHLH transcription factor from a cold-tolerant accession 'Heilongjiang seedling' of Chinese wild Vitis amurensis (VabHLH1) as a transcriptional activator involved in cold stress. We also compared with its counterpart from a cold-sensitive Vitis vinifera cv. Cabernet Sauvignon (VvbHLH1). These two putative proteins are characterized by the presence of the identically conserved regions of 54 amino acid residues of bHLH signature domain, and shared 99.1% amino acid identity, whereas several stress-related cis-regulatory elements located in both promoter regions differed in types and positions. Expressions of two bHLHs in grapevine leaves were induced by cold stress, but evidently differ between two grapevine genotypes upon cold exposure. Two grapevine bHLH proteins were exclusively localized to the nucleus and exhibited strong transcriptional activation activities in yeast cells. Overexpression of either VabHLH1 or VvbHLH1 transcription factor did not affect the growth and development of transgenic Arabidopsis plants, but enhanced tolerance to cold stress. The improved tolerance in VabHLH1- or VvbHLH1-overexpressing Arabidopsis plants is associated with multiple physiological and biochemical changes that occurred during the time-course cold stress. These most common changes include the evaluated levels of proline, decreased amounts of malondialdehyde and reduced membrane injury as reflected by electrolyte leakage. VabHLH1 and VvbHLH1 displayed overlapping, but not identical, roles in activating the corresponding CBF cold signaling pathway, especially in regulating the expression of CBF3 and RD29A. Our findings demonstrated that two grapevine bHLHs act as positive regulators of the cold stress response, modulating the level of COR gene expression, which in turn confer tolerance to cold stress.

Newly developed quantitative transactivation system shows difference in activation by Vitis CBF transcription factors on DRE/CRT elements

BACKGROUND

Agroinfiltration-based transactivation systems can determine if a protein functions as a transcription factor, and via which promoter element. However, this activation is not always a yes or no proposition. Normalization for variation in plasmid delivery into plant cells, sample collection and protein extraction is desired to allow for a quantitative comparison between transcription factors or promoter elements.

RESULTS

We developed new effector and reporter plasmids which carry additional reporter genes, as well as a procedure to assay all three reporter enzymes from a single extract. The applicability of these plasmids was demonstrated with the analysis of CBF transcription factors and their target promoter sequence, DRE/CRT. Changes in the core DRE/CRT sequence abolished activation by Vitis CBF1 or Vitis CBF4, whereas changes in the surrounding sequence lowered activation by Vitis CBF1 but much less so for Vitis CBF4. The system also detected a reduction in activation due to one amino acid change in Vitis CBF1.

CONCLUSIONS

The newly developed effector and reporter plasmids improve the ability to quantitatively compare the activation on two different promoter elements by the same transcription factor, or between two different transcription factors on the same promoter element. The quantitative difference in activation by VrCBF1 and VrCBF4 on various DRE/CRT elements support the hypothesis that these transcription factors have unique roles in the cold acclimation process.

Ambient temperature enhanced freezing tolerance of Chrysanthemum dichrum CdICE1 Arabidopsis via miR398

Background

ICE (Inducer of CBF Expression) family genes play an important role in the regulation of cold tolerance pathways. In an earlier study, we isolated the gene CdICE1 from Chrysanthemum dichrum and demonstrated that freezing tolerance was enhanced by CdICE1 overexpression. Therefore, we sought to determine the mechanism by which ICE1 family genes participate in freezing tolerance.

Results

Using EMSA (Electrophoretic Mobility Shift Assay) and yeast one-hybrid assays, we confirmed that CdICE1 binds specifically to the MYC element in the CdDREBa promoter and activates transcription. In addition, overexpression of CdICE1 enhanced Arabidopsis freezing tolerance after transition from 23°C to 4°C or 16°C. We found that after acclimation to 4°C, CdICE1, like Arabidopsis AtICE1, promoted expression of CBFs (CRT/DRE Binding Factor) and their genes downstream involved in freezing tolerance, including COR15a (Cold-Regulated 15a), COR6.6, and RD29a (Responsive to Dessication 29a). Interestingly, we observed that CdICE1-overexpressing plants experienced significant reduction in miR398. In addition, its target genes CSD1 (Copper/zinc Superoxide Dismutase 1) and CSD2 showed inducible expression under acclimation at 16°C, indicating that the miR398-CSD pathway was involved in the induction of freezing tolerance.

Conclusions

Our data indicate that CdICE1-mediated freezing tolerance occurs via different pathways, involving either CBF or miR398, under acclimation at two different temperatures.

Bioengineering for salinity tolerance in plants: state of the art

Genetic engineering of plants for abiotic stress tolerance is a challenging task because of its multifarious nature. Comprehensive studies for developing abiotic stress tolerance are in progress, involving genes from different pathways including osmolyte synthesis, ion homeostasis, antioxidative pathways, and regulatory genes. In the last decade, several attempts have been made to substantiate the role of "single-function" gene(s) as well as transcription factor(s) for abiotic stress tolerance. Since, the abiotic stress tolerance is multigenic in nature, therefore, the recent trend is shifting towards genetic transformation of multiple genes or transcription factors. A large number of crop plants are being engineered by abiotic stress tolerant genes and have shown the stress tolerance mostly at laboratory level. This review presents a mechanistic view of different pathways and emphasizes the function of different genes in conferring salt tolerance by genetic engineering approach. It also highlights the details of successes achieved in developing salt tolerance in plants thus far.

Characterization and expression analysis of three CBF/DREB1 transcriptional factor genes from mangrove Avicennia marina

Three CBF/DREB1 (C-repeat binding factor/dehydration responsive element-binding factor 1) homologues were isolated from mangrove Avicennia marina and designated AmCBF1, 2 and 3. Multiple sequence analysis showed that the three deduced proteins all contain an AP2 DNA-binding domain and two CBF signature sequences. According to the phylogenetic analysis, these proteins belong to the A-1 subgroup of the DREB subfamily. Expression analyses based on quantitative real-time PCR revealed that the AmCBF2 displayed relatively high expression under normal conditions, with the highest level in stems, while both AmCBF1 and 3 were weakly expressed without stress. The three genes also showed different responses to various environmental stimuli. The AmCBF2 was inducible by cold, drought, high salinity, heavy metals, as well as abscisic acid (ABA), and exhibited much stronger induction by cold, drought, Pb(2+) or Zn(2+) than by NaCl, ABA or Cd(2+). In contrast, both AmCBF1 and AmCBF3 displayed insignificant changes under these stimuli. These results indicate that the three AmCBF genes play different roles in A. marina and the AmCBF2 might be involved in the signaling pathway of cold, drought and heavy metal stress response.