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

Comparative transcriptomic profiles of Paulownia catalpifolia under different degrees of chilling stress during the seedling stage

BACKGROUND

Paulownia, an ecologically and economically valuable plant species native to China, is notable for its excellent timber quality and strong adaptability. Among them, Paulownia catalpifolia displays the ability to survive in cold climate, a trait associated with northern China. Yet, the molecular information for its cold-tolerance has not been explored. This study was to investigate the changes in physiological indices and transcript levels of P. catalpifolia following cold exposure, which could provide evidence for revealing whether there were differences in the genetic basis of inducing physiological perturbations between moderate low temperature (MLT) and extreme low temperature (ELT).

RESULTS

The detection of physiological indices under diverse degrees of chilling stress showed similar patterns of alteration. Enhanced accumulation of osmoregulatory substances, such as soluble sugar and soluble protein, were more conducive under ELT compared to MLT in P. catalpifolia. Moreover, we observed leaf wilting symptoms distinctly after exposure to ELT for 48 h, while this effect was not obvious after MLT exposure for 48 h. Comparative transcriptomic analysis between MLT and ELT demonstrated 13,688 differentially expressed genes (DEGs), most of them appeared after 12 h and 48 h of treatment. GO and KEGG analyses elucidated prominent enrichment in aromatic-L-amino-acid decarboxylase activity term and carbohydrate metabolism pathways. Therefore, it was speculated that the DEGs involved in the above processes might be related to the difference in the contents of soluble protein and soluble sugar between MLT and ELT. Time series clustering analyses further highlighted several key genes engaged in the 'Glycosyltransferases', 'Galactose metabolism' and 'Starch and sucrose metabolism' pathways as well as the 'tyrosine decarboxylase activity' term. For instance, cellulose synthase-like A (CLSA2/9), raffinose synthase (RafS2), β-amylase (BAM1) and tyrosine/DOPA decarboxylase (TYDC1/2/5) genes, diverging in their expression trends between MLT and ELT, might significantly affect the soluble sugar and soluble protein abundance within P. catalpifolia.

CONCLUSION

Between MLT and ELT treatments, partial overlaps in response pathways of P. catalpifolia were identified, while several genes regulating the accumulation of osmotic adjustment substances had disparate expression patterns. These findings could provide a novel physiological and molecular perspective for P. catalpifolia to adapt to complex low temperature habitats.

Functions of Basic Helix-Loop-Helix (bHLH) Proteins in the Regulation of Plant Responses to Cold, Drought, Salt, and Iron Deficiency: A Comprehensive Review

Abiotic stresses including cold, drought, salt, and iron deficiency severely impair plant development, crop productivity, and geographic distribution. Several bodies of research have shed light on the pleiotropic functions of BASIC HELIX-LOOP-HELIX (bHLH) proteins in plant responses to these abiotic stresses. In this review, we mention the regulatory roles of bHLH TFs in response to stresses such as cold, drought, salt resistance, and iron deficiency, as well as in enhancing grain yield in plants, especially crops. The bHLH proteins bind to E/G-box motifs in the target promoter and interact with various other factors to form a complex regulatory network. Through this network, they cooperatively activate or repress the transcription of downstream genes, thereby regulating various stress responses. Finally, we present some perspectives for future research focusing on the molecular mechanisms that integrate and coordinate these abiotic stresses. Understanding these molecular mechanisms is crucial for the development of stress-tolerant crops.

FUL homologous gene CmFL1 is involved in regulating flowering time and floret numbers in Chrysanthemum morifolium

Flowering time and floret numbers are important ornamental characteristics of chrysanthemums that control their adaptability and inflorescence morphology, respectively. The FRUITFULL (FUL) gene plays a key role in inducing flowering and inflorescence meristem development. In this study, we isolated a homolog of the MADS-box gene FUL, CmFUL-Like 1 (CmFL1), from chrysanthemum inflorescence buds. Quantitative RT-PCR and in situ analyses showed that CmFL1 was strongly expressed in young inflorescence buds. Overexpression of CmFL1 caused early flowering while co-suppression expression of CmFL1 increased the number of florets. Furthermore, the floral promoting factors CmSOC1, CmFDL1, and CmLFY were up-regulated in the shoot tips of transgenic plants. In addition, RNA-seq analysis of the transgenic plants suggested that certain differentially expressed genes (DEGs)-such as MADS-box, homeobox family, and ethylene pathway genes-may be involved in the inflorescence meristem development. GO pathway enrichment analysis showed that the differentially transcribed genes enriched the representation of the carbohydrate metabolic pathway, which is critical for flower development. Overall, our findings revealed the conserved function of CmFL1 in controlling flowering time along with a novel function in regulating the number of florets.

Effects of differentially expressed microRNAs induced by rootstocks and silicon on improving chilling tolerance of cucumber seedlings (Cucumis sativus L.)

BACKGROUND

Rootstocks can improve the chilling tolerance of grafted cucumbers, but their effectiveness varies. Rootstocks with strong de-blooming capacity may result in lower chilling tolerance of grafted cucumbers compared to those with weak de-blooming capacity, while also reducing the silicon absorption. However, it remains unclear whether this reduction in chilling tolerance is due to differences in rootstock genotypes or the reduction in silicon absorption.

RESULTS

The chilling tolerance of cucumber seedlings was improved by using rootstocks and silicon nutrition. Rootstocks had a more significant effect than silicon nutrition, and the weak de-blooming rootstock 'Yunnan figleaf gourd' was superior to the strong de-blooming rootstock 'Huangchenggen No. 2'. Compared to self-rooted cucumber, twelve miRNAs were regulated by two rootstocks, including seven identical miRNAs (novel-mir23, novel-mir26, novel-mir30, novel-mir37, novel-mir46, miR395a and miR398a-3p) and five different miRNAs (novel-mir32, novel-mir38, novel-mir65, novel-mir78 and miR397a). Notably, four of these miRNAs (novel-mir38, novel-mir65, novel-mir78 and miR397a) were only identified in 'Yunnan figleaf gourd'-grafted cucumbers. Furthermore, six miRNAs (miR168a-5p, miR390a-5p, novel-mir26, novel-mir55, novel-mir67 and novel-mir70) were found to be responsive to exogenous silicon. Target gene prediction for 20 miRNAs resulted in 520 genes. Functional analysis of these target genes showed that 'Yunnan figleaf gourd' improves the chilling tolerance of cucumber by regulating laccase synthesis and sulfate metabolism, while 'Huangchenggen No. 2' and exogenous silicon reduced chilling stress damage to cucumber by regulating ROS scavenging and protein protection, respectively.

CONCLUSION

Among the identified miRNAs, novel-mir46 and miR398a-3p were found in cucumbers in response to chilling stress and two types of rootstocks. However, no identical miRNAs were identified in response to chilling stress and silicon. In addition, the differential expression of novel-mir38, novel-mir65, novel-mir78 and miR397a may be one of the important reasons for the differences in chilling tolerance of grafted cucumbers caused by two types of rootstocks.

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

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

Isolation and preliminary functional analysis of FvICE1, involved in cold and drought tolerance in Fragaria vesca through overexpression and CRISPR/Cas9 technologies

Cold and drought stresses are serious problems of strawberry cultivation in temperate and subtropical regions. In the molecular regulation system of cold and drought stresses, ICE transcription factors (TFs) are crucial. In this research, the FvICE1 was isolated from Fragaria vesca 'Hawaii 4', a bioinformatics analysis was conducted, overexpression vector and CRISPR/cas9 vector were constructed. The results showed that FvICE1 was a member of the bHLH TF family, with a length of 1608 bp, encoding 535 amino acids, and its molecular formula was C₂₅₀₄H₃₉₈₇N₇₄₅O₈₁₁S₂₂. By observing the fusion protein 35S-FvICE1-GFP, it was found that FvICE1 was a nuclear protein. The qRT-PCR results demonstrated that FvICE1 was significantly upregulated in different tissues of Fragaria vesca after cold, drought, salt and heat treatments. The wild type (WT) strawberry was selected as the control group, FvICE1-overexpression strawberries showed high tolerance to cold and drought treatments at the phenotypic and physiological levels. On the contrary, fvice1 mutant strawberries obtained by CRISPR/cas9 editing technology had lower tolerance to cold and drought treatments. Moreover, the expression of FvCBF1, FvCBF2, FvCBF3, FvCOR413, FvRD22 and FvKIN1 was positively regulated in the FvICE1-overexpression strawberries and inhibited in fvice1 mutant strawberries. Overall, the current results suggested that FvICE1 functioned as a positively regulator of cold and drought resistances.

Potato Stu-miR398b-3p Negatively Regulates Cu/Zn-SOD Response to Drought Tolerance

One of the main impacts of drought stress on plants is an excessive buildup of reactive oxygen species (ROS). A large number of ·OH, highly toxic to cells, will be produced if too much ROS is not quickly cleared. At the heart of antioxidant enzymes is superoxide dismutase (SOD), which is the first antioxidant enzyme to function in the active oxygen scavenging system. To shield cells from oxidative injury, SOD dismutation superoxide anion free radicals generate hydrogen peroxide and molecule oxygen. Cu/Zn SOD is a kind of SOD antioxidant enzyme that is mostly found in higher plants' cytoplasm and chloroplasts. Other studies have demonstrated the significance of the miR398s family of miRNAs in the response of plants to environmental stress. The cleavage location of potato stu-miR398b-3p on Cu/Zn SOD mRNA was verified using RLM-5'RACE. Using the potato variety 'Desiree', the stu-miR398b-3p overexpression mutant was created, and transgenic lines were raised. SOD activity in transgenic lines was discovered to be decreased during drought stress, although other antioxidant enzyme activities were mostly unaltered. Transgenic plants will wilt more quickly than wild-type plants without irrigation. Additionally, this demonstrates that the response of Cu/Zn SOD to drought stress is adversely regulated by potato stu-miR398b-3p.

MicroRNA398: A Master Regulator of Plant Development and Stress Responses

MicroRNAs (miRNAs) play crucial roles in plant development and stress responses, and a growing number of studies suggest that miRNAs are promising targets for crop improvement because they participate in the regulation of diverse, important agronomic traits. MicroRNA398 (miR398) is a conserved miRNA in plants and has been shown to control multiple stress responses and plant growth in a variety of species. There are many studies on the stress response and developmental regulation of miR398. To systematically understand its function, it is necessary to summarize the evolution and functional roles of miR398 and its target genes. In this review, we analyze the evolution of miR398 in plants and outline its involvement in abiotic and biotic stress responses, in growth and development and in model and non-model plants. We summarize recent functional analyses, highlighting the role of miR398 as a master regulator that coordinates growth and diverse responses to environmental factors. We also discuss the potential for fine-tuning miR398 to achieve the goal of simultaneously improving plant growth and stress tolerance.

Reference gene selection for quantitative RT-PCR in Miscanthus sacchariflorus under abiotic stress conditions

BACKGROUND

Reference genes are necessary for quantitative real-time PCR (qRT-PCR) analysis and their stability can directly influence the accuracy of gene expression result. Miscanthus sacchariflorus, a perennial C4 grass that serves as promising biofuel plant for temperate climates, has not been explored for the identification of stable reference genes yet.

MATERIALS AND METHODS

Nine potential reference genes (ACT, EF1a, FBOX, GAPDH, PP2A, SAND, TIP41, TUB and UBC) of M. sacchariflorus under different abiotic (salinity, drought and cadmium) stresses, as well as in two tissues (roots and leaves) were evaluated. The expression stability of these genes were analyzed by four commonly used software programs (geNorm, NormFinder, BestKeeper, ΔCt method and RefFinder).

RESULTS

Our results found that FBOX and SAND are the most stable genes among all tested samples. FBOX and EF1a are suitable for gene expression normalization of cadmium-treated samples and salinity-treated leaves. FBOX and PP2A are appropriate reference genes for salt-stressed roots and PEG-treated leaves. The traditional reference gene ACT and GAPDH exhibited the most variable pattern, which would not be recommended for qRT-PCR analysis under different abiotic stresses. Furthermore, the expression levels of PIP2, NHX1 and MT2a under drought, salt and cadmium treatment were detected with above reference genes.

CONCLUSIONS

This work identified the appropriate reference genes for qRT-PCR in M. sacchariflorus and FBOX was recommended to be effective internal control for gene expression normalization in M. sacchariflorus in response to different abiotic stresses.

Saussurea involucrata (Snow Lotus) ICE1 and ICE2 Orthologues Involved in Regulating Cold Stress Tolerance in Transgenic Arabidopsis

As with other environmental stresses, cold stress limits plant growth, geographical distribution, and agricultural productivity. CBF/DREB (CRT-binding factors/DRE-binding proteins) regulate tolerance to cold/freezing stress across plant species. ICE (inducer of CBF expression) is regarded as the upstream inducer of CBF expression and plays a crucial role as a main regulator of cold acclimation. Snow lotus (Saussurea involucrata) is a well-known traditional Chinese herb. This herb is known to have greater tolerance to cold/freezing stress compared to other plants. According to transcriptome datasets, two putative ICE homologous genes, SiICE1 and SiICE2, were identified in snow lotus. The predicted SiICE1 cDNA contains an ORF of 1506 bp, encoding a protein of 501 amino acids, whereas SiICE2 cDNA has an ORF of 1482 bp, coding for a protein of 493 amino acids. Sequence alignment and structure analysis show SiICE1 and SiICE2 possess a S-rich motif at the N-terminal region, while the conserved ZIP-bHLH domain and ACT domain are at the C-terminus. Both SiICE1 and SiICE2 transcripts were cold-inducible. Subcellular localization and yeast one-hybrid assays revealed that SiICE1 and SiICE2 are transcriptional regulators. Overexpression of SiICE1 (35S::SiICE1) and SiICE2 (35S::SiICE2) in transgenic Arabidopsis increased the cold tolerance. In addition, the expression patterns of downstream stress-related genes, CBF1, CBF2, CBF3, COR15A, COR47, and KIN1, were up-regulated when compared to the wild type. These results thus provide evidence that SiICE1 and SiICE2 function in cold acclimation and this cold/freezing tolerance may be regulated through a CBF-controlling pathway.

Transcriptome and Metabolome Analyses of the Flowers and Leaves of Chrysanthemum dichrum

Chrysanthemum dichrum is an important wild species in the family Asteraceae. However, because of a lack of genetic information, there has been relatively little research conducted on the molecular mechanisms in C. dichrum. There is no report describing the transcriptome and metabolome of C. dichrum flowers and leaves at different developmental stages. In this study, high-throughput sequencing and RNA-seq analyses were used to investigate the transcriptome of C. dichrum leaves, flower buds, and blooming flowers. Additionally, these three tissues also underwent a metabolomics analysis. A total of 447,313,764 clean reads were assembled into 77,683 unigenes, with an average length of 839 bp. Of the 44,204 annotated unigenes, 42,189, 28,531, 23,420, and 17,599 were annotated using the Nr, Swiss-Prot, KOG, and KEGG databases, respectively. Furthermore, 31,848 differentially expressed genes (DEGs) were detected between the leaves and flower buds, whereas 23,197 DEGs were detected between the leaves and blooming flowers, and 11,240 DEGs were detected between the flower buds and blooming flowers. Finally, a quantitative real-time Polymerase Chain Reaction (qRT-PCR) assay was conducted to validate the identified DEGs. The metabolome data revealed several abundant metabolites in C. dichrum leaves, flower buds, and blooming flowers, including raffinose, 1-kestose, asparagine, glutamine, and other medicinal compounds. The expression patterns of significant DEGs revealed by the transcriptome analysis as well as the data for the differentially abundant metabolites in three C. dichrum tissues provide important genetic and metabolic information relevant for future investigations of the molecular mechanisms in C. dichrum. Moreover, the results of this study may be useful for the molecular breeding, development, and application of C. dichrum resources.

The role of VvMYBA2r and VvMYBA2w alleles of the MYBA2 locus in the regulation of anthocyanin biosynthesis for molecular breeding of grape (Vitis spp.) skin coloration

In grape, MYBA1 and MYBA2 at the colour locus are the major genetic determinants of grape skin colour, and the mutation of two functional genes (VvMYBA1 and VvMYBA2) from these loci leads to white skin colour. This study aimed to elucidate the regulation of grape berry coloration by isolating and characterizing VvMYBA2w and VvMYBA2r alleles. The overexpression of VvMYBA2r up-regulated the expression of anthocyanin biosynthetic genes and resulted in higher anthocyanin accumulation in transgenic tobacco than wild-type (WT) plants, especially in flowers. However, the ectopic expression of VvMYBA2w inactivated the expression of anthocyanin biosynthetic genes and could not cause obvious phenotypic modulation in transgenic tobacco. Unlike in VvMYBA2r, CA dinucleotide deletion shortened the C-terminal transactivation region and disrupted the transcriptional activation activity of VvMYBA2w. The results indicated that VvMYBA2r positively regulated anthocyanin biosynthesis by forming the VvMYBA2r-VvMYCA1-VvWDR1 complex, and VvWDR1 enhanced anthocyanin accumulation by interacting with the VvMYBA2r-VvMYCA1 complex; however, R⁴⁴ L substitution abolished the interaction of VvMYBA2w with VvMYCA1. Meanwhile, both R⁴⁴ L substitution and CA dinucleotide deletion seriously affected the efficacy of VvMYBA2w to regulate anthocyanin biosynthesis, and the two non-synonymous mutations were additive in their effects. Investigation of the colour density and MYB haplotypes of 213 grape germplasms revealed that dark-skinned varieties tended to contain HapC-N and HapE2, whereas red-skinned varieties contained high frequencies of HapB and HapC-Rs. Regarding ploidy, the higher the number of functional alleles present in a variety, the darker was the skin colour. In summary, this study provides insight into the roles of VvMYBA2r and VvMYBA2w alleles and lays the foundation for the molecular breeding of grape varieties with different skin colour.

Ectopic expression of GmHP08 enhances resistance of transgenic Arabidopsis toward drought stress

Ectopic expression of Glycine max two-component system member GmHP08 in Arabidopsis enhanced drought tolerance of transgenic plants, possibly via ABA-dependent pathways. Phosphorelay by two-component system (TCS) is a signal transduction mechanism which has been evolutionarily conserved in both prokaryotic and eukaryotic organisms. Previous studies have provided lines of evidence on the involvement of TCS genes in plant perception and responses to environmental stimuli. In this research, drought-associated functions of GmHP08, a TCS member from soybean (Glycine max L.), were investigated via its ectopic expression in Arabidopsis system. Results from the drought survival assay showed that GmHP08-transgenic plants exhibited higher survival rates compared with their wild-type (WT) counterparts, indicating better drought resistance of the former group. Analyses revealed that the transgenic plants outperformed the WT in various regards, i.e. capability of water retention, prevention of hydrogen peroxide accumulation and enhancement of antioxidant enzymatic activities under water-deficit conditions. Additionally, the expression of stress-marker genes, especially antioxidant enzyme-encoding genes, in the transgenic plants were found greater than that of the WT plants. In contrary, the expression of SAG13 gene, one of the senescence-associated genes, and of several abscisic acid (ABA)-related genes was repressed. Data from this study also revealed that the ectopic expression lines at germination and early seedling development stages were hypersensitive to exogenous ABA treatment. Taken together, our results demonstrated that GmHP08 could play an important role in mediating plant response to drought, possibly via an ABA-dependent manner.

BrrICE1.1 is associated with putrescine synthesis through regulation of the arginine decarboxylase gene in freezing tolerance of turnip (Brassica rapa var. rapa)

BACKGROUND

In the agricultural areas of Qinghai-Tibet Plateau, temperature varies widely from day to night during the growing season, which makes the extreme temperature become one of the limiting factors of crop yield. Turnip (Brassica rapa var. rapa) is a traditional crop of Tibet grown in the Tibet Plateau, but its molecular and metabolic mechanisms of freezing tolerance are unclear.

RESULTS

Here, based on the changes in transcriptional and metabolic levels of Tibetan turnip under freezing treatment, the expression of the arginine decarboxylase gene BrrADC2.2 exhibited an accumulative pattern in accordance with putrescine content. Moreover, we demonstrated that BrrICE1.1 (Inducer of CBF Expression 1) could directly bind to the BrrADC2.2 promoter, activating BrrADC2.2 to promote the accumulation of putrescine, which was verified by RNAi and overexpression analyses for both BrrADC2.2 and BrrICE1.1 using transgenic hair root. The function of putrescine in turnip was further analyzed by exogenous application putrescine and its inhibitor DL-α-(Difluoromethyl) arginine (DFMA) under freezing tolerance. In addition, the BrrICE1.1 was found to be involved in the ICE1-CBF pathway to increase the freezing stress of turnip.

CONCLUSIONS

BrrICE1.1 could bind the promoter of BrrADC2.2 or CBFs to participate in freezing tolerance of turnip by transcriptomics and targeted metabolomics analyses. This study revealed the regulatory network of the freezing tolerance process in turnip and increased our understanding of the plateau crops response to extreme environments in Tibet.

Overexpression of Arabidopsis ICE1 enhances yield and multiple abiotic stress tolerance in indica rice

ICE1 (Inducer of CBF Expression 1), a MYC-type bHLH transcription factor, is a regulator of cold tolerance in Arabidopsis. Indica rice, which occupies the major rice cultivated area, is highly sensitive to cold stress. Hence in this study, Arabidopsis ICE1 (AtICE1) was overexpressed in indica rice to analyze its role in reproductive stage cold and other abiotic stress tolerance to indica rice. AtICE1 was overexpressed by using stress inducible AtRD29A promoter in mega rice cv. MTU1010. Under cold stress conditions, AtICE1 overexpression lines showed lower accumulation of MDA and H2O2, higher membrane stability, and thus higher seedling survival rate than the WT plants. Expression levels of OsDREB1A, OsMYB3R2, and OsTPP1 were significantly higher in transgenics as compared with WT under cold stress conditions. AtICE1 transgenic rice plants produced 44-60% higher grain yield as compared with WT plants under control conditions in three independent experiments. Of the three AtICE1 overexpression lines, two lines produced significantly higher grain yield as compared with WT plants after recovery from cold, salt and drought stresses. AtICE1 overexpression lines showed significantly higher stomatal density and conductance under non-stress conditions. qRT-PCR analysis showed that expression levels of stomatal pathway genes viz., OsSPCH1, OsSPCH2, OsSCR1, OsSCRM1, OsSCRM2 and OsMUTE were significantly higher in AtICE1 transgenics as compared with WT plants. The components of water use viz., stomatal conductance, photosynthesis, and instantaneous WUE were higher in transgenics as compared with WT plants. The results showed that AtICE1 confers multiple stress tolerance to indica rice, and the role of ICE1 in stress tolerance and stomatal development is conserved across species.

An eggplant SmICE1a gene encoding MYC-type ICE1-like transcription factor enhances freezing tolerance in transgenic Arabidopsis thaliana

Low temperature is a crucial environmental factor affecting the quality and production of eggplant. Therefore, it is necessary to explore the molecular mechanisms of low temperature response. We isolated an ICE (inducer of CBF expression) gene from Solanum melongena, named SmICE1a. We then analysed structure, transcriptional activity and expression patterns of SmICE1a. Moreover, we also expressed SmICE1a in Arabidopsis thaliana. Bioinformatics and expression analysis showed that SmICE1a has a typical S-rich motif, ZIP region, bHLH and ACT-like domain. The gene SmICE1a had transcriptional activity in yeast and was localized to the nucleus following transient expression in tobacco leaves, which suggests that SmICE1a is a transcription factor. A dual-LUC assay revealed that SmICE1a can enhance expression of SmCBF. Overexpression of SmICE1a in Arabidopsis increased freezing tolerance and caused multiple biochemical changes: transgenic lines have higher proline content and lower electrolyte leakage and malondialdehyde than the wild type in cold conditions. The expression of AtCBF and their target genes, AtCOR15A, AtCOR47, AtKIN1 and AtRD29A, were up-regulated in SmICE1a-overexpressing plants under low temperatures. Based on these results, we suggest that SmICE1a plays an important role in cold response, which may help to understand the cold response mechanism in eggplant and could be used to enhance cold tolerance of eggplant in future.

Cyclophilin AtROC1S58F confers Arabidopsis cold tolerance by modulating jasmonic acid signaling and antioxidant metabolism

Cyclophilins (CYPs), a class of proteins with a conserved peptidyl-prolyl cis-trans isomerase domain, are widely involved in the regulation of plant growth and development, as well as in the response to abiotic stresses including cold. In our previous study, we identified an Arabidopsis gain-of-function mutant ROC1S58F with enhanced cold-tolerance and enhanced expression of jasmonic acid (JA) and oxidative stress responsive genes. Here, we show the underlying molecular mechanisms for the improved cold tolerance observed in the ROC1S58F mutant. Compared to the WT, the ROC1S58F mutant showed an increased survival rates and a reduced level of electrolyte leakage and endogenous JA content under the freezing treatment. Correspondingly, the JA biosynthesis genes (AtAOC1 and AtOPR3) and signaling genes (AtJAZ5, AtJAZ10 and AtMYB15) are down-regulated in the ROC1S58F mutant compared with the WT. Moreover, both the transcripts and activities of the ROS-scavenging enzymes (SOD/POD/MDHAR) increased in cold-stressed ROC1S58F mutant, which might mitigate the ROS-induced oxidative stress and contribute to the mutant freezing tolerance. Taken together, our findings indicate that AtROC1S58F confers Arabidopsis freezing tolerance by modulating JA signaling and antioxidant metabolism jointly. This research thus provides a molecular mechanism for AtROC1S58F-conferred freezing resistance in Arabidopsis and offers guidance for crop breeding towards an improved cold tolerance.

Chrysanthemum (Chrysanthemum morifolium) CmICE2 conferred freezing tolerance in Arabidopsis

Genes of the ICE (Inducer of CBF Expression) family play a key role in cold and freezing stresses response via the CBF regulatory pathway. In this work, we identified the ICE family gene, CmICE2, from Chrysanthemum morifolium 'Jinba'. CmICE2 encodes a 451-amino acid protein with a conserved nuclear localization domain, a bHLH domain and ACT domain. CmICE2 is expressed in abundance in leaves and flowers, and the expression of CmICE2 is induced by freezing and drought stresses. CmICE2 localized to the nucleus, and has transcriptional activity in yeast cells. After a 24-hour 4 °C acclimation, Arabidopsis plants overexpressing CmICE2 were more tolerant to freezing stress (-9 °C for 6 h) than the Col-0. When exposed to -9 °C for 6 h, the expression levels of genes such as AtCBF1, AtCBF2, AtCBF4, AtCOR 6.6A, AtCOR 414 and AtKIN1 were up-regulated significantly in CmICE2 overexpression plant lines compared to wild type. The proline contents, activities of superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) were also increased in plants overexpressing CmICE2. In summary, CmICE2 confers to plant response to freezing stress.

The Soybean GmNAC019 Transcription Factor Mediates Drought Tolerance in Arabidopsis in an Abscisic Acid-Dependent Manner

Being master regulators of gene expression, transcription factors (TFs) play important roles in determining plant growth, development and reproduction. To date, many TFs have been shown to positively mediate plant responses to environmental stresses. In the current study, the biological functions of a stress-responsive NAC [NAM (No Apical Meristem), ATAF1/2 (Arabidopsis Transcription Activation Factor1/2), CUC2 (Cup-shaped Cotyledon2)]-TF encoding gene isolated from soybean (GmNAC019) in relation to plant drought tolerance and abscisic acid (ABA) responses were investigated. By using a heterologous transgenic system, we revealed that transgenic Arabidopsis plants constitutively expressing the GmNAC019 gene exhibited higher survival rates in a soil-drying assay, which was associated with lower water loss rate in detached leaves, lower cellular hydrogen peroxide content and stronger antioxidant defense under water-stressed conditions. Additionally, the exogenous treatment of transgenic plants with ABA showed their hypersensitivity to this phytohormone, exhibiting lower rates of seed germination and green cotyledons. Taken together, these findings demonstrated that GmNAC019 functions as a positive regulator of ABA-mediated plant response to drought, and thus, it has potential utility for improving plant tolerance through molecular biotechnology.

Zoysia japonica MYC type transcription factor ZjICE1 regulates cold tolerance in transgenic Arabidopsis

ICE1 (Inducer of CBF Expression 1) is a regulator of cold-induced transcriptome, which plays an important role in plant cold response pathway. To enhance the cold tolerance of Zoysia japonica, one of the warm-season turfgrasses, it is helpful to understand the cold response mechanism in Zoysia japonica. We identified stress-responsive ZjICE1 from Zoysia japonica and characterized its function in cold stress. Our results showed that ZjICE1 shared the typical feature of ICE homolog proteins belonging to a nucleic protein. Transactivation activity assay revealed that ZjICE1 bound to the MYC cis-element in the ZjDREB1's promotor. The ZjICE1 overexpressed transgenic Arabidopsis showed enhanced tolerance to cold stress with an increases in SOD, POD, and free proline content and reduction in MDA content. They also induced the transcripts abundance of cold-responsive genes (CBF1, CBF2, CBF3, COR47A, KIN1, and RD29A) after cold treatment. These results suggest that ZjICE1 is a positive regulator in Zoysia japonica plant during cold stress and can be a useful gene for the molecular breeding program to develop the cold tolerant zoysiagrass. Furthermore, the ZjICE1 also conferred resistance to salt and drought stresses, providing the better understanding of the basic helix-loop-helix (bHLH) gene family in abiotic stress responses.

An isoform of the plastid RNA polymerase-associated protein FSD3 negatively regulates chloroplast development

BACKGROUND

Plastid-encoded RNA polymerase (PEP) plays an essential role in chloroplast development by governing the expression of genes involved in photosynthesis. At least 12 PEP-associated proteins (PAPs), including FSD3/PAP4, regulate PEP activity and chloroplast development by modulating formation of the PEP complex.

RESULTS

In this study, we identified FSD3S, a splicing variant of FSD3; the FSD3 and FSD3S transcripts encode proteins with identical N-termini, but different C-termini. Characterization of FSD3 and FSD3S proteins showed that the C-terminal region of FSD3S contains a transmembrane domain, which promotes FSD3S localization to the chloroplast membrane but not to nucleoids, in contrast to FSD3, which localizes to the chloroplast nucleoid. We also found that overexpression of FSD3S negatively affects photosynthetic activity and chloroplast development by reducing expression of genes involved in photosynthesis. In addition, FSD3S failed to complement the chloroplast developmental defects in the fsd3 mutant.

CONCLUSION

These results suggest FSD3 and FSD3S, with their distinct localization patterns, have different functions in chloroplast development, and FSD3S negatively regulates expression of PEP-dependent chloroplast genes, and development of chloroplasts.

Genome-wide investigation of superoxide dismutase (SOD) gene family and their regulatory miRNAs reveal the involvement in abiotic stress and hormone response in tea plant (Camellia sinensis)

Superoxide dismutases (SODs), as a family of metalloenzymes related to the removal of reactive oxygen species (ROS), have not previously been investigated at genome-wide level in tea plant. In this study, 10 CsSOD genes were identified in tea plant genome, including 7 Cu/Zn-SODs (CSDs), 2 Fe-SODs (FSDs) and one Mn-SOD (MSD), and phylogenetically classified in three subgroups, respectively. Physico-chemical characteristic, conserved motifs and potential protein interaction analyses about CsSOD proteins were carried out. Exon-intron structures and codon usage bias about CsSOD genes were also examined. Exon-intron structures analysis revealed that different CsSOD genes contained various number of introns. On the basis of the prediction of regulatory miRNAs of CsSODs, a modification 5’ RNA ligase-mediated (RLM)-RACE was performed and validated that csn-miR398a-3p-1 directly cleaves CsCSD4. By prediction of cis-acting elements, the expression patterns of 10 CsSOD genes and their regulatory miRNAs were detected under cold, drought, exogenous methyl jasmonate (MeJA) and gibberellin (GA₃) treatments. The results showed that most of CsSODs except for CsFSD2 were induced under cold stress and CsCSDs may play primary roles under drought stress; exogenous GA₃ and MeJA could also stimulated/inhibited distinct CsSODs at different stages. In addition, we found that csn-miR398a-3p-1 negatively regulated the expression of CsCSD4 may be a crucial regulatory mechanism under cold stress. This study provides a certain basis for the studies about stress resistance in tea plants, even provide insight into comprehending the classification, evolution, diverse functions and influencing factors of expression patterns for CsSOD genes.

The Heterologous Expression of a Chrysanthemum nankingense TCP Transcription Factor Blocks Cell Division in Yeast and Arabidopsis thaliana

Both the presence of, and the important contribution to growth and development made by TCP transcription factors, have been established in various plant species. Here, a TCP4 homolog isolated from Chrysanthemum nankingense was shown to be more strongly transcribed in the diploid than in the autotetraploid form of the species. CnTCP4 was shown to encode a member of the class II TCP family and to be transcribed most strongly in the leaf and ligulate flowers. Its transcription was found to be substantially inhibited by spraying the plant with the synthetic cytokinin 6-benzylaminopurine. The transient expression of CnTCP4 in onion epidermal cells showed that its product localized to the nucleus, and a yeast one hybrid assay suggested that its product had transcriptional activation ability. The constitutive expression of CnTCP4 in fission yeast suppressed cell proliferation, inducing the formation of longer and a higher frequency of multinuclated cells. Its constitutive expression in Arabidopsis thaliana reduced the size of the leaves. The presence of the transgene altered the transcription of a number of cell division-related genes. A yeast one hybrid assay identified a second TCP gene (CnTCP2) able to interact with the CnTCP4 promoter. A transient expression experiment in Nicotiana benthamiana leaves showed that CnTCP2 was able to activate the CnTCP4 promoter. Like CnTCP4, CnTCP2 was shown to encode a member of the class II TCP family, to be transcribed most strongly in the leaf and ligulate flowers, and to be suppressed by exogenous 6-benzylaminopurine treatment. The CnTCP2 protein also localized to the nucleus, but had no transcriptional activation ability. Its constitutive expression in A. thaliana had similar phenotypic consequences to those induced by CnTCP4.

Characterization and Cloning of Grape Circular RNAs Identified the Cold Resistance-Related Vv-circATS1

Circular RNAs (circRNAs) are widely distributed and play essential roles in a series of developmental processes, although none have been identified or characterized in grapevines (Vitis vinifera). In this study, we characterized the function of grape circRNA and uncovered thousands of putative back-splicing sites by global transcriptome analysis. Our results indicated that several reported circRNA prediction algorithms should be used simultaneously to obtain comprehensive and reliable circRNA predictions in plants. Furthermore, the length of introns flanking grape circRNAs was closely related to exon circularization. Although the longer introns flanking grape circRNAs appeared to circularize more efficiently, a 20- to 50-nt region seemed large enough to drive grape circRNA biogenesis. In addition, the endogenous introns flanking circularized exon(s) in conjunction with reverse complementary sequences could support the accurate and efficient circularization of various exons in grape, which constitutes a new tool for exploring the functional consequences caused by circRNA expression. Finally, we identified 475 differentially expressed circRNAs in grape leaves under cold stress. Overexpression of Vv-circATS1, a circRNA derived from glycerol-3-P acyltransferase, improved cold tolerance in Arabidopsis (Arabidopsis thaliana), while the linear RNA derived from the same sequence cannot. These results indicate the functional difference between circRNA and linear RNA, and provide new insight into plant abiotic stress resistance.

Conserved Cu-MicroRNAs in Arabidopsis thaliana Function in Copper Economy under Deficiency

Copper (Cu) is a micronutrient for plants. Three small RNAs, which are up-regulated by Cu deficiency and target transcripts for Cu proteins, are among the most conserved microRNAs in plants. It was hypothesized that these Cu-microRNAs help save Cu for the most essential Cu-proteins under deficiency. Testing this hypothesis has been a challenge due to the redundancy of the Cu microRNAs and the properties of the regulatory circuits that control Cu homeostasis. In order to investigate the role of Cu-microRNAs in Cu homeostasis during vegetative growth, we used a tandem target mimicry strategy to simultaneously inhibit the function of three conserved Cu-microRNAs in Arabidopsis thaliana. When compared to wild-type, transgenic lines that express the tandem target mimicry construct showed reduced Cu-microRNA accumulation and increased accumulation of transcripts that encode Cu proteins. As a result, these mimicry lines showed impaired photosynthesis and growth compared to wild type on low Cu, which could be ascribed to a defect in accumulation of plastocyanin, a Cu-containing photosynthetic electron carrier, which is itself not a Cu-microRNA target. These data provide experimental support for a Cu economy model where the Cu-microRNAs together function to allow maturation of essential Cu proteins under impending deficiency.

Two ICE isoforms showing differential transcriptional regulation by cold and hormones participate in Brassica juncea cold stress signaling

C-repeat binding factor (CBF) dependent cold stress signaling cascade is well studied in the model plant arabidopsis but is relatively lesser studied in the crop plants. In the present study, two novel isoforms of an upstream regulator of CBF, Inducer of CBF expression (ICE), BjICE46 (1314 bp, accession number HQ446510) and BjICE53 (1494 bp, accession number HQ857208) were isolated from Brassica juncea seedlings. Genomic clones of both the isoforms (accession numbers HQ433510 and JX571043) showed three introns, out of which one intron was spanning the bHLH (basic helix-loop-helix) domain. Interestingly, the constitutive expression of BjICE53 was 21 fold higher than BjICE46. Real time quantitative expression (RT-qPCR) showed BjICE53 to be cold induced but non-responsive to phytohormones. Interestingly, BjICE46 was salinity stress induced and showed upregulation with methyl jasmonate (MeJa) and abscisic acid (ABA). This was supported by the presence of ABA, MeJa and defense related cis- acting regulatory elements in the promoter region of BjICE46. The downstream transcription factor BjCBF (645 bp) was also isolated. The promoter region of BjCBF showed three E-boxes, the binding site for ICE. BjCBF was expressed and purified from E. coli and binding of purified BjCBF with the DRE/CRT elements (present in the promoter of cold responsive genes) was EMSA confirmed. Overall, this study shows that ICE-CBF pathway is conserved in Brassica juncea along with the differential regulation of the ICE isoforms indicating cross-talk between cold and defense signaling.

Transcriptome-wide identification of miRNA targets and a TAS3-homologous gene in Populus by degradome sequencing

BACKGROUND

Degradome sequencing has been applied to identify miRNA-directed mRNA cleavage and understand the biological function of miRNAs and their target genes in plants defense to stress. miRNAs involved in the response to cold stress have been identified in Populus, however, there are few reports about the validated targets of miRNAs in Populus under cold stress.

OBJECTIVES

The primary objective of this investigation was to globally identify and validate the targets of the miRNAs and regulatory components in Populus under cold stress.

METHODS

Populus plantlets grown in vitro were treated with cold (4 °C for 8 h) and total RNA was extracted using Trizol reagent. Approximately 200 µg total RNA was used for the construction of the degradome library, and degradome sequencing was conducted on an Illumina HiSeq 2000. The sequences were mapped to Populus genome using SOAP 2.0 and then were collected for degradome analysis. Additionally, trans-acting siRNA sequences from transacting siRNA gene 3 sequences and mature miRNAs cleaved from precursor miRNAs of Populus were analyzed. 5' RNA ligase-mediated-RACE (5'-RACE) were further conducted.

RESULTS

80 genes were experimentally determined to be the target of 51 unique miRNAs, including three down-regulated miRNAs (pto-miR156k, pto-miR169i-m, and pto-miR394a-5p/b-5p) and two up-regulated miRNAs (pto-miR167a-d and pto-miR167f/g). The specificity and diversity of cleavage sites of miRNA targets were validated through 5'-RACE experiment and the results were similar with that of degradome sequencing, further supporting the empirical cleavage of miRNAs on targets in vivo in Populus. Interestingly, the TAS-homologous gene pto-TAS3 (EF146176.1) was identified and 11 potential ta-siRNAs [D1(+)-D11(+)] and their possible biogenesis sites within the pto-TAS3 transcript sequence were predicted in Populus. In addition, the biosynthesis of miRNA from precursor miRNA (pre-miRNA) was also validated through the detection of a total of 17 pre-miRNAs.

CONCLUSION

Our investigation expands the application of degradome sequencing for evaluating miRNA regulatory elements and evidence of the miRNA synthesis process, and provides empirical evidence of bona fide cleavage of target genes by miRNAs in Populus, which might be used for the research of miRNA-mediated regulation mechanism and molecular improvement of resistance to cold stress.

The Constitutive Expression of a Chrysanthemum ERF Transcription Factor Influences Flowering Time in Arabidopsis thaliana

AP2/ERF transcription factors (TFs) represent valuable targets for the genetic manipulation of crop plants, as they participate in the control of metabolism, growth and development, as well as in the plants' response to environmental stimuli. Here, an ERF TF encoded by the chrysanthemum (Chrysanthemum morifolium) genome, designated CmERF110, was cloned and functionally characterized. The predicted CmERF110 polypeptide included a conserved DNA-binding AP2/ERF domain. A transient expression experiment revealed that the protein was deposited in the nucleus, and a transactivation experiment in yeast suggested that it had no transcriptional activity. The gene was transcribed in the chrysanthemum root, stem and leaf, with its transcript level following a circadian rhythm under both long and short days. The effect of constitutively expressing the gene in Arabidopsis thaliana was to accelerate flowering. Transcriptional profiling implied that its effect on floral initiation operated through the photoperiod pathway.

Integration of small RNAs and transcriptome sequencing uncovers a complex regulatory network during vernalization and heading stages of orchardgrass (Dactylis glomerata L.)

BACKGROUND

Flowering is a critical reproductive process in higher plants. Timing of optimal flowering depends upon the coordination among seasonal environmental cues. For cool season grasses, such as Dactylis glomerata, vernalization induced by low temperature provides competence to initiate flowering after prolonged cold. We combined analyses of the transcriptome and microRNAs (miRNAs) to generate a comprehensive resource for regulatory miRNAs and their target circuits during vernalization and heading stages.

RESULTS

A total of 3,846 differentially expressed genes (DEGs) and 69 differentially expressed miRNAs were identified across five flowering stages. The expression of miR395, miR530, miR167, miR396, miR528, novel_42, novel_72, novel_107, and novel_123 demonstrated significant variations during vernalization. These miRNA targeted genes were involved in phytohormones, transmembrane transport, and plant morphogenesis in response to vernalization. The expression patterns of DEGs related to plant hormones, stress responses, energy metabolism, and signal transduction changed significantly in the transition from vegetative to reproductive phases.

CONCLUSIONS

Five hub genes, c136110_g1 (BRI1), c131375_g1 (BZR1), c133350_g1 (VRN1), c139830_g1 (VIN3), and c125792_g2 (FT), might play central roles in vernalization response. Our comprehensive analyses have provided a useful platform for investigating consecutive transcriptional and post-transcriptional regulation of critical phases in D. glomerata and provided insights into the genetic engineering of flowering-control in cereal crops.

De novo sequencing, assembly, and analysis of Iris lactea var. chinensis roots' transcriptome in response to salt stress

As a halophyte, Iris lactea var. chinensis (I. lactea var. chinensis) is widely distributed and has good drought and heavy metal resistance. Moreover, it is an excellent ornamental plant. I. lactea var. chinensis has extensive application prospects owing to the global impacts of salinization. To better understand its molecular mechanism involved in salt resistance, the de novo sequencing, assembly, and analysis of I. lactea var. chinensis roots' transcriptome in response to salt-stress conditions was performed. On average, 74.17% of the clean reads were mapped to unigenes. A total of 121,093 unigenes were constructed and 56,398 (46.57%) were annotated. Among these, 13,522 differentially expressed genes (DEGs) were identified between salt-treated and control samples Compared to the transcriptional level of control, 7037 DEGs were up-regulated and 6539 down-regulated. In addition, 129 up-regulated and 1609 down-regulated genes were simultaneously detected in all three pairwise comparisons between control and salt-stressed libraries. At least 247 and 250 DEGs encoding transcription factors and transporter proteins were identified. Meanwhile, 130 DEGs regarding reactive oxygen species (ROS) scavenging system were also summarized. Based on real-time quantitative RT-PCR, we verified the changes in the expression patterns of 10 unigenes. Our study identified potential salt-responsive candidate genes and increased the understanding of halophyte responses to salinity stress.

Gene Regulation and Signal Transduction in the ICE-CBF-COR Signaling Pathway during Cold Stress in Plants

Low temperature is an abiotic stress that adversely affects the growth and production of plants. Resistance and adaptation of plants to cold stress is dependent upon the activation of molecular networks and pathways involved in signal transduction and the regulation of cold-stress related genes. Because it has numerous and complex genes, regulation factors, and pathways, research on the ICE-CBF-COR signaling pathway is the most studied and detailed, which is thought to be rather important for cold resistance of plants. In this review, we focus on the function of each member, interrelation among members, and the influence of manipulators and repressors in the ICE-CBF-COR pathway. In addition, regulation and signal transduction concerning plant hormones, circadian clock, and light are discussed. The studies presented provide a detailed picture of the ICE-CBF-COR pathway.

A novel Zea mays ssp. mexicana L. MYC-type ICE-like transcription factor gene ZmmICE1, enhances freezing tolerance in transgenic Arabidopsis thaliana

The annual Zea mays ssp. mexicana L., a member of the teosinte group, is a close wild relative of maize and thus can be effectively used in maize improvement. In this study, an ICE-like gene, ZmmICE1, was isolated from a cDNA library of RNA-Seq from cold-treated seedling tissues of Zea mays ssp. mexicana L. The deduced protein of ZmmICE1 contains a highly conserved basic helix-loop-helix (bHLH) domain and C-terminal region of ICE-like proteins. The ZmmICE1 protein localizes to the nucleus and shows sumoylation when expressed in an Escherichia coli reconstitution system. In addition, yeast one hybrid assays indicated that ZmmICE1 has transactivation activities. Moreover, ectopic expression of ZmmICE1 in the Arabidopsis ice1-2 mutant increased freezing tolerance. The ZmmICE1 overexpressed plants showed lower electrolyte leakage (EL), reduced contents of malondialdehyde (MDA). The expression of downstream cold related genes of Arabidopsis C-repeat-binding factors (AtCBF1, AtCBF2 and AtCBF3), cold-responsive genes (AtCOR15A and AtCOR47), kinesin-1 member gene (AtKIN1) and responsive to desiccation gene (AtRD29A) was significantly induced when compared with wild type under low temperature treatment. Taken together, these results indicated that ZmmICE1 is the homolog of Arabidopsis inducer of CBF expression genes (AtICE1/2) and plays an important role in the regulation of freezing stress response.

Stress-responsive gene RsICE1 from Raphanus sativus increases cold tolerance in rice

The ICE1 transcription factor plays a critical role in plant cold tolerance via triggering CBF/DREB1 cold-regulated signal networks. In this work, a novel MYC-type ICE1-like gene, RsICE1, was isolated from radish (Raphanus sativus L.), and its function in cold tolerance was characterized in rice. The RsICE1 gene was expressed constitutively with higher transcriptional levels in the roots and stems of radish seedlings. The NaCl, cold, and ABA treatments could significantly upregulate RsICE1 expression levels, but dehydration stress had a weak effect on its expression. Ectopic expression of the RsICE1 gene in rice conferred enhanced tolerance to low-temperature stress grounded on a higher survival rate, higher accumulation of soluble sugars and free proline content, a decline in electrolyte leakage and MDA levels, and higher chlorophyll levels relative to control plants. OsDREBL and OsTPP1, downstream cold-regulated genes, were remarkably upregulated at transcription levels in rice overexpressing RsICE1 under low-temperature stress, which indicated that RsICE1 was involved in CBF/DREB1 cold-regulated signal networks. Overall, the above data showed that RsICE1 played an active role in improving rice cold tolerance, most likely resulting from the upregulation of OsDREBL and OsTPP1 expression levels by interacting with the RsICE1 gene under low-temperature stress.

The copper microRNAs

1030 I. 1030 II. 1030 III. 1031 IV. 1031 V. 1032 VI. 1033 VII. 1034 VIII. 1034 1034 References 1034 SUMMARY: Copper (Cu) microRNAs are upregulated by Cu deficiency and mediate the post-transcriptional downregulation of transcripts that encode Cu proteins, suggesting a role directly related to Cu. However, expression and phenotypic analyses of copper microRNA mutants and over-expressors have suggested roles mainly in tolerance to abiotic stresses. To reconcile available data, a model is proposed which emphasizes the mobile nature of copper microRNA molecules in the regulation of Cu homeostasis. It is proposed that the Cu-microRNA regulatory circuits are further co-opted by plants to regulate both beneficial and pathogenic interactions with microbes. Further exploration of Cu-microRNA functions that account for the cell-to-cell mobility should give novel insight into plant microbe interactions and the integration of micronutrition and development.

Identification and differential regulation of microRNAs in response to methyl jasmonate treatment in Lycoris aurea by deep sequencing

Background

Lycoris aurea is a medicine-valuable and ornamental herb widely distributed in China. Former studied have showed that methyl jasmonate (MJ) treatment could increase the content of glanthamine-a worldwide medicine for symptomatic treatment of Alzheimer’s disease in genus Lycoris plants. To explore the possible role of miRNAs in the regulation of jasmonic acid signaling pathway and uncover their potential correlations, we investigated the expression profiles of small RNAs (sRNAs) and their targets in Lycoris aurea, with MJ treatment by using next-generation deep sequencing.

Results

A total of 365 miRNAs were identified, comprising 342 known miRNAs (representing 60 miRNA families) and 23 novel miRNAs. Among them, 143 known and 11 novel miRNAs were expressed differently under MJ treatment. Quantitative real-time PCR of eight selected miRNAs validated the expression pattern of these loci in response to MJ treatment. In addition, degradome sequencing analysis showed that 32 target genes were validated to be targeted by the 49 miRNAs, respectively. Gene function and pathway analyses showed that these targets such as auxin response factors (ARFs), squamosa promoter-binding like (SPL) proteins, basic helix-loop-helix (bHLH) proteins, and ubiquitin-conjugating enzyme E2 are involved in different plant processes, indicating miRNAs mediated regulation might play important roles in L. aurea response to MJ treatment. Furthermore, several L. aurea miRNAs associated with their target genes that might be involved in Amaryllidaceae alkloids biosynthehsis were also analyzed.

Conclusions

A number of miRNAs with diverse expression patterns, and complex relationships between expression of miRNAs and targets were identified. This study represents the first transcriptome-based analysis of miRNAs in Lycoris and will contribute to understanding the potential roles of miRNAs involved in regulation of MJ response.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2645-y) contains supplementary material, which is available to authorized users.

Identification and characterization of a novel NAC-like gene in chrysanthemum (Dendranthema lavandulifolium)

KEY MESSAGE

A NAC -like gene named DlNAC1 was identified in chrysanthemum and characterized; it may be involved in regulation of response to abiotic stressors, especially in tolerance to drought and salinity. NAC transcription factors in plants play crucial roles in tolerance to abiotic stressors, and overexpression of the NAC gene in Arabidopsis has been demonstrated to lead to improved drought tolerance. Functions of the NAC genes in chrysanthemum, however, remain poorly understood. In this study, a NAC-like gene named DlNAC1 was identified in chrysanthemum (Dendranthema lavandulifolium) and characterized. Phylogenetic analysis indicated that DlNAC1 contains a typical NAC domain and belongs to the ONAC022 subgroup. According to the subcellular localization and yeast one-hybrid assay, the DlNAC1 protein is localized to nuclei and has a transcription activation ability. Moreover, quantitative real-time PCR analyses showed that DlNAC1 was induced by low-temperature, high-salinity, and drought conditions (separately), but not by abscisic acid (ABA) and heat shock. In these experiments, the downstream genes of NAC transcription factors were found to be up-regulated, including stress-responsive genes KIN1 and AMY1. To further explore the effects of DlNAC1 in response to abiotic stressors, DlNAC1 was overexpressed in tobacco, and these transgenic plants showed significantly enhanced tolerance to drought and salinity. This study suggests that in chrysanthemum, the DlNAC1 gene is involved in regulation of the response to abiotic stressors, especially in tolerance to drought and salinity.

Functional Identification and Characterization of Genes Cloned from Halophyte Seashore Paspalum Conferring Salinity and Cadmium Tolerance

Salinity-affected and heavy metal-contaminated soils limit the growth of glycophytic plants. Identifying genes responsible for superior tolerance to salinity and heavy metals in halophytes has great potential for use in developing salinity- and Cd-tolerant glycophytes. The objective of this study was to identify salinity- and Cd-tolerance related genes in seashore paspalum (Paspalum vaginatum), a halophytic perennial grass species, using yeast cDNA expression library screening method. Based on the Gateway-compatible vector system, a high-quality entry library was constructed, which contained 9.9 × 10(6) clones with an average inserted fragment length of 1.48 kb representing a 100% full-length rate. The yeast expression libraries were screened in a salinity-sensitive and a Cd-sensitive yeast mutant. The screening yielded 32 salinity-tolerant clones harboring 18 salinity-tolerance genes and 20 Cd-tolerant clones, including five Cd-tolerance genes. qPCR analysis confirmed that most of the 18 salinity-tolerance and five Cd-tolerance genes were up-regulated at the transcript level in response to salinity or Cd stress in seashore paspalum. Functional analysis indicated that salinity-tolerance genes from seashore paspalum could be involved mainly in photosynthetic metabolism, antioxidant systems, protein modification, iron transport, vesicle traffic, and phospholipid biosynthesis. Cd-tolerance genes could be associated with regulating pathways that are involved in phytochelatin synthesis, HSFA4-related stress protection, CYP450 complex, and sugar metabolism. The 18 salinity-tolerance genes and five Cd-tolerance genes could be potentially used as candidate genes for genetic modification of glycophytic grass species to improve salinity and Cd tolerance and for further analysis of molecular mechanisms regulating salinity and Cd tolerance.

Chrysanthemum transcription factor CmLBD1 direct lateral root formation in Arabidopsis thaliana

The plant-specific LATERAL ORGAN BOUNDARIES DOMAIN (LBD) genes are important regulators of growth and development. Here, a chrysanthemum class I LBD transcription factor gene, designated CmLBD1, was isolated and its function verified. CmLBD1 was transcribed in both the root and stem, but not in the leaf. The gene responded to auxin and was shown to participate in the process of adventitious root primordium formation. Its heterologous expression in Arabidopsis thaliana increased the number of lateral roots formed. When provided with exogenous auxin, lateral root emergence was promoted. CmLBD1 expression also favored callus formation from A. thaliana root explants in the absence of exogenously supplied phytohormones. In planta, CmLBD1 probably acts as a positive regulator of the response to auxin fluctuations and connects auxin signaling with lateral root formation.

Overexpression of a bHLH1 Transcription Factor of Pyrus ussuriensis Confers Enhanced Cold Tolerance and Increases Expression of Stress-Responsive Genes

The basic helix-loop-helix (bHLH) transcription factors are involved in arrays of physiological and biochemical processes. However, knowledge concerning the functions of bHLHs in cold tolerance remains poorly understood. In this study, a PubHLH1 gene isolated from Pyrus ussuriensis was characterized for its function in cold tolerance. PubHLH1 was upregulated by cold, salt, and dehydration, with the greatest induction under cold conditions. PubHLH1 had the transactivational activity and localized in the nucleus. Ectopic expression of PubHLH1 in transgenic tobacco conferred enhanced tolerance to cold stress. The transgenic lines had higher survival rates, higher chlorophyll, higher proline contents, lower electrolyte leakages and MDA when compared with wild type (WT). In addition, transcript levels of eight genes associated with ROS scavenging, regulation, and stress defense were higher in the transgenic plants relative to the WT under the chilling stress. Taken together, these results demonstrated that PubHLH1 played a key role in cold tolerance and, at least in part, contributed to activation of stress-responsive genes.

ICE1 of Pyrus ussuriensis functions in cold tolerance by enhancing PuDREBa transcriptional levels through interacting with PuHHP1

ICE1 transcription factor plays an important role in plant cold stress via regulating the expression of stress-responsive genes. In this study, a PuICE1 gene isolated from Pyrus ussuriensis was characterized for its function in cold tolerance. The expression levels of the PuICE1 were induced by cold, dehydration and salt, with the greatest induction under cold conditions. PuICE1 was localized in the nucleus and could bind specifically to the MYC element in the PuDREBa promoter. The PuICE1 fused to the GAL4 DNA-binding domain to have transcriptional activation activity. Ectopic expression of the PuICE1 in tomato conferred enhanced tolerance to cold stress at cold temperatures, less electrolyte leakage, less MDA content, higher chlorophyll content, higher survival rate, higher proline content, higher activities of enzymes. In additon, steady-state mRNA levels of six stress-responsive genes coding for either functional or regulatory genes were induced to higher levels in the transgenic lines by cold stress. Yeast two-hybrid, transient assay, split luciferase complementation and BiFC assays all revealed that PuHHP1 protein can physically interact with PuICE1. Taken together, these results demonstrated that PuICE1 plays a positive role in cold tolerance, which may be due to enhancement of PuDREBa transcriptional levels through interacting with the PuHHP1.

ICE1 of Pyrus ussuriensis functions in cold tolerance by enhancing PuDREBa transcriptional levels through interacting with PuHHP1

ICE1 transcription factor plays an important role in plant cold stress via regulating the expression of stress-responsive genes. In this study, a PuICE1 gene isolated from Pyrus ussuriensis was characterized for its function in cold tolerance. The expression levels of the PuICE1 were induced by cold, dehydration and salt, with the greatest induction under cold conditions. PuICE1 was localized in the nucleus and could bind specifically to the MYC element in the PuDREBa promoter. The PuICE1 fused to the GAL4 DNA-binding domain to have transcriptional activation activity. Ectopic expression of the PuICE1 in tomato conferred enhanced tolerance to cold stress at cold temperatures, less electrolyte leakage, less MDA content, higher chlorophyll content, higher survival rate, higher proline content, higher activities of enzymes. In additon, steady-state mRNA levels of six stress-responsive genes coding for either functional or regulatory genes were induced to higher levels in the transgenic lines by cold stress. Yeast two-hybrid, transient assay, split luciferase complementation and BiFC assays all revealed that PuHHP1 protein can physically interact with PuICE1. Taken together, these results demonstrated that PuICE1 plays a positive role in cold tolerance, which may be due to enhancement of PuDREBa transcriptional levels through interacting with the PuHHP1.

Selection and validation of reference genes for target gene analysis with quantitative RT-PCR in leaves and roots of bermudagrass under four different abiotic stresses

Quantitative real-time reverse transcriptase polymerase chain reaction (qRT-PCR) is an effective method for quantifying expression levels of target genes. The accuracy of qRT-PCR results is largely dependent on the selection of stable reference genes. The stability of reference gene expression may vary with plant species and environmental conditions. The objective of this study was to select stable reference genes for qRT-PCR analysis of target genes in different organs under different abiotic stresses for a perennial grass species, bermudagrass (Cynodon dactylon). The stability of eight potential reference genes (TUB, ACT, GAPDH, EF1α, TIP41, PP2A, CACS and UPL7) was evaluated under four different abiotic stresses (salt, drought, cold and heat) and in leaves and roots of bermudagrass. Four programs (geNorm, NormFinder, BestKeeper and RefFinder) were employed to evaluate the stability of reference gene expression and to identify the most stable reference genes for bermudagrass. Eight potential reference genes exhibited differential expression stability in leaves and roots under salt, drought, cold and heat stress. The expression levels of PP2A and CACS were stable in roots and leaves under salt stress, in leaves under drought stress and in roots exposed to cold and heat stress. EF1α and TIP41 expression was stable in roots of drought-stressed plants. UPL7, TUB and GAPDH were stably expressed in leaves under cold stress. Expression levels of PP2A and TIP41 were stable in leaves under heat stress. The use of the reference genes identified as internal controls for examination of gene expression patterns and quantification of expression levels of target genes will enable accurate qRT-PCR analysis in bermudagrass.

The over-expression of a chrysanthemum WRKY transcription factor enhances aphid resistance

Members of the large WRKY transcription factor family are responsible for the regulation of plant growth, development and the stress response. Here, five WRKY members were isolated from chrysanthemum. They each contained a single WRKY domain and a C2H2 zinc finger motif, so were classified into group II. Transient expression experiments demonstrated that all five were expressed in the nucleus, although CmWRKY42 was also expressed in the cytoplasm. When expressed heterologously in yeast, the products of CmWRKY22 and CmWRKY48 exhibited transactivation activity, while those of CmWRKY21, CmWRKY40 and CmWRKY42 did not. The transcription of the five CmWRKY genes was profiled when the plants were challenged with a variety of abiotic and biotic stress agents, as well as being treated with various phytohormones. CmWRKY21 proved to be markedly induced by salinity stress, and suppressed by high temperature exposure; CmWRKY22 was induced by high temperature exposure; CmWRKY40 was highly induced by salinity stress, and treatment with either abscisic acid (ABA) or methyl jasmonate (MeJA); CmWRKY42 was up-regulated by salinity stress, low temperature, ABA and MeJA treatment and aphid infestation; CmWRKY48 was induced by drought stress, ABA and MeJA treatment and aphid infestation. The function of CmWRKY48 was further investigated by over-expressing it transgenically. The constitutive expression of this transcription factor inhibited the aphids' population growth capacity, suggesting that it may represent an important component of the plant's defense machinery against aphids.

Heterologous expression of the halophyte Zoysia matrella H⁺-pyrophosphatase gene improved salt tolerance in Arabidopsis thaliana

A number of vacuolar H(+)-pyrophosphatase (VP) family genes play important roles in plant growth under salt stress condition. Despite their biological importance in plant salt-stress regulation, there is no report about VP in the halophytic turfgrass Zoysia matrella. Here, we isolated ZmVP1, a type I VP homologues gene encoding 768 amino acids by using the degenerated PCR and RACE PCR methods from Zoysia matrella. The expression level of ZmVP1 was significantly induced by salinity, drought and cold, but not by heat. ZmVP1 can restore the salt-tolerant ability of a salt-sensitive yeast strain. Overexpression of ZmVP1 in Arabidopsis thaliana resulted in more vigorous growth under salt stress. Moreover, the transgenic Arabidopsis accumulated more Na(+) and K(+) in the leaves compared to that of wild type plants under salt stress, had higher activities of V-ATPase and V-PPase, and showed higher relative gene expression levels of 5 stress-related genes (AtNHX1, AtLEA, AtP5CS, AtMn-SOD, AtAPX1). These results demonstrated that ZmVP1 from Z. matrella was a functional tonoplast H(+)-pyrophosphatase contributing to salt tolerance potentially through regulating the Na(+) compartment in vacuole, K(+) assimilation, osmotic regulation and antioxidant response.

ICE1 of Poncirus trifoliata functions in cold tolerance by modulating polyamine levels through interacting with arginine decarboxylase

ICE1 (Inducer of CBF Expression 1) encodes a MYC-like basic helix-loop-helix transcription factor that acts as a central regulator of cold response. In this study, we elucidated the function and underlying mechanisms of PtrICE1 from trifoliate orange [Poncirus trifoliata (L.) Raf.]. PtrICE1 was upregulated by cold, dehydration, and salt, with the greatest induction under cold conditions. PtrICE1 was localized in the nucleus and could bind to a MYC-recognizing sequence. Ectopic expression of PtrICE1 in tobacco and lemon conferred enhanced tolerance to cold stresses at either chilling or freezing temperatures. Yeast two-hybrid screening revealed that 21 proteins belonged to the PtrICE1 interactome, in which PtADC (arginine decarboxylase) was confirmed as a bona fide protein interacting with PtrICE1. Transcript levels of ADC genes in the transgenic lines were slightly elevated under normal growth condition but substantially increased under cold conditions, consistent with changes in free polyamine levels. By contrast, accumulation of the reactive oxygen species, H2O2 and O2 (-), was appreciably alleviated in the transgenic lines under cold stress. Higher activities of antioxidant enzymes, such as superoxide dismutase and catalase, were detected in the transgenic lines under cold conditions. Taken together, these results demonstrated that PtrICE1 plays a positive role in cold tolerance, which may be due to modulation of polyamine levels through interacting with the ADC gene.

Systematic mining of salt-tolerant genes in halophyte-Zoysia matrella through cDNA expression library screening

Though a large number of salt-tolerant genes were identified from Glycophyte in previous study, genes involved in salt-tolerance of halophyte were scarcely studied. In this report, an important halophyte turfgrass, Zoysia matrella, was used for systematic excavation of salt-tolerant genes using full-length cDNA expression library in yeast. Adopting the Gateway-compatible vector system, a high quality entry library was constructed, containing 3 × 10(6) clones with an average inserted fragments length of 1.64 kb representing a 100% full-length rate. The yeast expression library was screened in a salt-sensitive yeast mutant. The screening yielded dozens of salt-tolerant clones harboring 16 candidate salt-tolerant genes. Under salt-stress condition, these 16 genes exhibited different transcription levels. According to the results, we concluded that the salt-tolerance of Z. matrella might result from known genes involved in ion regulation, osmotic adjustment, as well as unknown pathway associated with protein folding and modification, RNA metabolism, and mitochondrial membrane translocase, etc. In addition, these results shall provide new insight for the future researches with respect to salt-tolerance.

Identification and validation of reference genes for quantification of target gene expression with quantitative real-time PCR for tall fescue under four abiotic stresses

Tall fescue (Festuca arundinacea Schreb.) is widely utilized as a major forage and turfgrass species in the temperate regions of the world and is a valuable plant material for studying molecular mechanisms of grass stress tolerance due to its superior drought and heat tolerance among cool-season species. Selection of suitable reference genes for quantification of target gene expression is important for the discovery of molecular mechanisms underlying improved growth traits and stress tolerance. The stability of nine potential reference genes (ACT, TUB, EF1a, GAPDH, SAND, CACS, F-box, PEPKR1 and TIP41) was evaluated using four programs, GeNorm, NormFinder, BestKeeper, and RefFinder. The combinations of SAND and TUB or TIP41 and TUB were most stably expressed in salt-treated roots or leaves. The combinations of GAPDH with TIP41 or TUB were stable in roots and leaves under drought stress. TIP41 and PEPKR1 exhibited stable expression in cold-treated roots, and the combination of F-box, TIP41 and TUB was also stable in cold-treated leaves. CACS and TUB were the two most stable reference genes in heat-stressed roots. TIP41 combined with TUB and ACT was stably expressed in heat-stressed leaves. Finally, quantitative real-time polymerase chain reaction (qRT-PCR) assays of the target gene FaWRKY1 using the identified most stable reference genes confirmed the reliability of selected reference genes. The selection of suitable reference genes in tall fescue will allow for more accurate identification of stress-tolerance genes and molecular mechanisms conferring stress tolerance in this stress-tolerant species.

Isolation and characterization of six AP2/ERF transcription factor genes in Chrysanthemum nankingense

The AP2/ERF family of plant transcription factors (TFs) regulate a variety of developmental and physiological processes. Here, we report the isolation of six AP2/ERF TF family genes from Chrysanthemum nankingense. On the basis of sequence similarity, one of these belonged to the Ethylene Responsive Factor (ERF) subfamily and the other five to the Dehydration Responsive Element Binding protein (DREB) subfamily. A transient expression experiment showed that all six AP2/ERF proteins localized to the nucleus. A yeast-one hybrid assay demonstrated that CnDREB1-1, 1-2 and 1-3 all function as transactivators, while CnERF1, CnDREB3-1 and 3-2 have no transcriptional activation ability. The transcription response of the six TFs in response to wounding, salinity and low temperature stress and treatment with abscisic acid (ABA), salicylic acid (SA) and jasmonic acid (JA) showed that CnERF1 was up-regulated by wounding and low temperature stress but suppressed by salinity stress. The transcription of CnDREB1-1, 1-2 and 1-3 was down-regulated by ABA and JA to varying degrees. CnDREB3-1 and 3-2 was moderately increased or decreased by wounding and SA treatment, suppressed by salinity stress and JA treatment, and enhanced by low temperature stress and ABA treatment.