A novel cold-inducible gene from Pak-choi (Brassica campestris ssp. chinensis), BcWRKY46, enhances the cold, salt and dehydration stress tolerance in transgenic tobacco

High-quality chromosome-level genomic insights into molecular adaptation to low-temperature stress in Madhuca longifolia in southern subtropical China

BACKGROUND

Madhuca longifolia, the energy-producing and medicinal tropical tree originally from southern India, faces difficulties in adapting to the low temperatures of late autumn and early winter in subtropical southern China, impacting its usability. Therefore, understanding the molecular mechanisms controlling the ability of this species to adapt to environmental challenges is essential for optimising horticulture efforts. Accordingly, this study aimed to elucidate the molecular responses of M. longifolia to low-temperature stress through genomic and transcriptomic analyses to inform strategies for its effective cultivation and utilisation in colder climates.

RESULTS

Herein, the high-quality reference genome and genomic assembly for M. longifolia are presented for the first time. Using Illumina sequencing, Hi-C technology, and PacBio HiFi sequencing, we assembled a chromosome-level genome approximately 737.92 Mb in size, investigated its genomic features, and conducted an evolutionary analysis of the genus Madhuca. Additionally, using transcriptome sequencing, we identified 17,941 differentially expressed genes related to low-temperature response. Through bioinformatics analysis of the WRKY gene family, 15 genes crucial for M. longifolia low-temperature resistance were identified.

CONCLUSIONS

This research not only lays the groundwork for the successful ecological adaptation and cultivation of M. longifolia in China's southern subtropical regions but also offers valuable insights for the genetic enhancement of cold tolerance in tropical species, contributing to their sustainable horticulture and broader industrial, medicinal, and agricultural use.

Less Frequently Used Growth Regulators in Plant Tissue Culture

Plant growth regulators are routinely added to in vitro culture media to foster the growth and differentiation of the cells, tissues, and organs. However, while the literature on usage of the more common auxins, cytokinins, gibberellins, abscisic acid, and ethylene is vast, other compounds that also have shown a growth-regulating activity have not been studied as frequently. Such substances are also capable of modulating the responses of plant cells and tissues in vitro by regulating their growth, differentiation, and regeneration competence, but also by enhancing their responses toward biotic and abiotic stress agents and improving the production of secondary metabolites of interest. This chapter will discuss the in vitro effects of several of such less frequently added plant growth regulators, including brassinosteroids (BRS), strigolactones (SLs), phytosulfokines (PSKs), methyl jasmonate, salicylic acid (SA), sodium nitroprusside (SNP), hydrogen sulfite, various plant growth retardants and inhibitors (e.g., ancymidol, uniconazole, flurprimidol, paclobutrazol), and polyamines.

The reference genome and abiotic stress responses of the model perennial grass Brachypodium sylvaticum

Perennial grasses are important forage crops and emerging biomass crops and have the potential to be more sustainable grain crops. However, most perennial grass crops are difficult experimental subjects due to their large size, difficult genetics, and/or their recalcitrance to transformation. Thus, a tractable model perennial grass could be used to rapidly make discoveries that can be translated to perennial grass crops. Brachypodium sylvaticum has the potential to serve as such a model because of its small size, rapid generation time, simple genetics, and transformability. Here, we provide a high-quality genome assembly and annotation for B. sylvaticum, an essential resource for a modern model system. In addition, we conducted transcriptomic studies under 4 abiotic stresses (water, heat, salt, and freezing). Our results indicate that crowns are more responsive to freezing than leaves which may help them overwinter. We observed extensive transcriptional responses with varying temporal dynamics to all abiotic stresses, including classic heat-responsive genes. These results can be used to form testable hypotheses about how perennial grasses respond to these stresses. Taken together, these results will allow B. sylvaticum to serve as a truly tractable perennial model system.

Advancements and prospects of CRISPR/Cas9 technologies for abiotic and biotic stresses in sugar beet

Sugar beet is a crop with high sucrose content, known for sugar production and recently being considered as an emerging raw material for bioethanol production. This crop is also utilized as cattle feed, mainly when animal green fodder is scarce. Bioethanol and hydrogen gas production from this crop is an essential source of clean energy. Environmental stresses (abiotic/biotic) severely affect the productivity of this crop. Over the past few decades, the molecular mechanisms of biotic and abiotic stress responses in sugar beet have been investigated using next-generation sequencing, gene editing/silencing, and over-expression approaches. This information can be efficiently utilized through CRISPR/Cas 9 technology to mitigate the effects of abiotic and biotic stresses in sugar beet cultivation. This review highlights the potential use of CRISPR/Cas 9 technology for abiotic and biotic stress management in sugar beet. Beet genes known to be involved in response to alkaline, cold, and heavy metal stresses can be precisely modified via CRISPR/Cas 9 technology for enhancing sugar beet's resilience to abiotic stresses with minimal off-target effects. Similarly, CRISPR/Cas 9 technology can help generate insect-resistant sugar beet varieties by targeting susceptibility-related genes, whereas incorporating Cry1Ab and Cry1C genes may provide defense against lepidopteron insects. Overall, CRISPR/Cas 9 technology may help enhance sugar beet's adaptability to challenging environments, ensuring sustainable, high-yield production.

Insights into the Transcriptomics of Crop Wild Relatives to Unravel the Salinity Stress Adaptive Mechanisms

The narrow genomic diversity of modern cultivars is a major bottleneck for enhancing the crop's salinity stress tolerance. The close relatives of modern cultivated plants, crop wild relatives (CWRs), can be a promising and sustainable resource to broaden the diversity of crops. Advances in transcriptomic technologies have revealed the untapped genetic diversity of CWRs that represents a practical gene pool for improving the plant's adaptability to salt stress. Thus, the present study emphasizes the transcriptomics of CWRs for salinity stress tolerance. In this review, the impacts of salt stress on the plant's physiological processes and development are overviewed, and the transcription factors (TFs) regulation of salinity stress tolerance is investigated. In addition to the molecular regulation, a brief discussion on the phytomorphological adaptation of plants under saline environments is provided. The study further highlights the availability and use of transcriptomic resources of CWR and their contribution to pangenome construction. Moreover, the utilization of CWRs' genetic resources in the molecular breeding of crops for salinity stress tolerance is explored. Several studies have shown that cytoplasmic components such as calcium and kinases, and ion transporter genes such as Salt Overly Sensitive 1 (SOS1) and High-affinity Potassium Transporters (HKTs) are involved in the signaling of salt stress, and in mediating the distribution of excess Na⁺ ions within the plant cells. Recent comparative analyses of transcriptomic profiling through RNA sequencing (RNA-Seq) between the crops and their wild relatives have unraveled several TFs, stress-responsive genes, and regulatory proteins for generating salinity stress tolerance. This review specifies that the use of CWRs transcriptomics in combination with modern breeding experimental approaches such as genomic editing, de novo domestication, and speed breeding can accelerate the CWRs utilization in the breeding programs for enhancing the crop's adaptability to saline conditions. The transcriptomic approaches optimize the crop genomes with the accumulation of favorable alleles that will be indispensable for designing salt-resilient crops.

Methyl jasmonate and salicylic acid as powerful elicitors for enhancing the production of secondary metabolites in medicinal plants: an updated review

Plant secondary metabolites are bioactive scaffolds that are crucial for plant survival in the environment and to maintain a defense mechanism from predators. These compounds are generally present in plants at a minimal level and interestingly, they are found to have a wide variety of therapeutic values for humans. Several medicinal plants are used for pharmaceutical purposes due to their affordability, fewer adverse effects, and vital role in traditional remedies. Owing to this reason, these plants are exploited at a high range worldwide and therefore many medicinal plants are on the threatened list. There is a need of the hour to tackle this major problem, one effective approach called elicitation can be used to enhance the level of existing and novel plant bioactive compounds using different types of elicitors namely biotic and abiotic. This process can be generally achieved by in vitro and in vivo experiments. The current comprehensive review provides an overview of biotic and abiotic elicitation strategies used in medicinal plants, as well as their effects on secondary metabolites enhancement. Further, this review mainly deals with the enhancement of biomass and biosynthesis of different bioactive compounds by methyl jasmonate (MeJA) and salicylic acid (SA) as elicitors of wide medicinal plants in in vitro by using different cultures. The present review was suggested as a significant groundwork for peers working with medicinal plants by applying elicitation strategies along with advanced biotechnological approaches.

Genome-Wide Identification and Expression Analysis of WRKY Transcription Factors in Siraitia siamensis

WRKY transcription factors, as the largest gene family in higher plants, play an important role in various biological processes including growth and development, regulation of secondary metabolites, and stress response. In this study, we performed genome-wide identification and analysis of WRKY transcription factors in S. siamensis. A total of 59 SsWRKY genes were identified that were distributed on all 14 chromosomes, and these were classified into three major groups based on phylogenetic relationships. Each of these groups had similar conserved motifs and gene structures. We compared all the S. siamensis SsWRKY genes with WRKY genes identified from three diverse plant species, and the results implied that segmental duplication and tandem duplication play an important roles in the evolution processes of the WRKY gene family. Promoter region analysis revealed that SsWRKY genes included many cis-acting elements related to plant growth and development, phytohormone response, and both abiotic and biotic stress. Expression profiles originating from the transcriptome database showed expression patterns of these SsWRKY genes in four different tissues and revealed that most genes are expressed in plant roots. Fifteen SsWRKY genes with low-temperature response motifs were surveyed for their gene expression under cold stress, showing that most genes displayed continuous up-regulation during cold treatment. Our study provides a foundation for further study on the function and regulatory mechanism of the SsWRKY gene family.

WRKY transcription factors (TFs): Molecular switches to regulate drought, temperature, and salinity stresses in plants

The WRKY transcription factor (TF) belongs to one of the major plant protein superfamilies. The WRKY TF gene family plays an important role in the regulation of transcriptional reprogramming associated with plant stress responses. Change in the expression patterns of WRKY genes or the modifications in their action; participate in the elaboration of numerous signaling pathways and regulatory networks. WRKY proteins contribute to plant growth, for example, gamete formation, seed germination, post-germination growth, stem elongation, root hair growth, leaf senescence, flowering time, and plant height. Moreover, they play a key role in many types of environmental signals, including drought, temperature, salinity, cold, and biotic stresses. This review summarizes the current progress made in unraveling the functions of numerous WRKY TFs under drought, salinity, temperature, and cold stresses as well as their role in plant growth and development.

WRKY41/WRKY46-miR396b-5p-TPR module mediates abscisic acid-induced cold tolerance of grafted cucumber seedlings

Grafting is one of the key agronomic measures to enhance the tolerance to environmental stresses in horticultural plants, but the specific molecular regulation mechanism in this tolerance largely remains unclear. Here, we found that cucumber grafted onto figleaf gourd rootstock increased cold tolerance through abscisic acid (ABA) activating WRKY41/WRKY46-miR396b-5p-TPR (tetratricopeptide repeat-like superfamily protein) module. Cucumber seedlings grafted onto figleaf gourd increased cold tolerance and induced the expression of miR396b-5p. Furthermore, overexpression of cucumber miR396b-5p in Arabidopsis improved cold tolerance. 5' RNA ligase-mediated rapid amplification of cDNA ends (5' RLM-RACE) and transient transformation experiments demonstrated that TPR was the target gene of miR396b-5p, while TPR overexpression plants were hypersensitive to cold stress. The yeast one-hybrid and dual-luciferase assays showed that both WRKY41 and WRKY46 bound to MIR396b-5p promoter to induce its expression. Furthermore, cold stress enhanced the content of ABA in the roots and leaves of figleaf gourd grafted cucumber seedlings. Exogenous application of ABA induced the expression of WRKY41 and WRKY46, and cold tolerance of grafted cucumber seedlings. However, figleaf gourd rootstock-induced cold tolerance was compromised when plants were pretreated with ABA biosynthesis inhibitor. Thus, ABA mediated figleaf gourd grafting-induced cold tolerance of cucumber seedlings through activating the WRKY41/WRKY46-miR396b-5p-TPR module.

OsWRKY115 on qCT7 links to cold tolerance in rice

qCT7, a novel QTL for increasing seedling cold tolerance in rice, was fine-mapped to a 70.9-kb region on chromosome 7, and key OsWRKY115 was identified in transgenic plants. Cold stress caused by underground cold-water irrigation seriously limits rice productivity. We systemically measured the cold-responsive traits of 2,570 F2 individuals derived from two widely cultivated rice cultivars, Kong-Yu-131 and Dong-Nong-422, to identify the major genomic regions associated with cold tolerance. A novel major QTL, qCT7, was mapped on chromosome 7 associated with the cold tolerance and survival, using whole-genome re-sequencing with bulked segregant analysis. Local QTL linkage analysis with F₂ and fine mapping with recombinant plant revealed a 70.9-kb core region on qCT7 encoding 13 protein-coding genes. Only the LOC_Os07g27670 expression level encoding the OsWRKY115 transcription factor on the locus was specifically induced by cold stress in the cold-tolerant cultivar. Moreover, haplotype analysis and the KASP8 marker indicated that OsWRKY115 was significantly associated with cold tolerance. Overexpression and knockout of OsWRKY115 significantly affected cold tolerance in seedlings. Our experiments identified OsWRKY115 as a novel regulatory gene associated with cold response in rice, and the Kong-Yu-131 allele with specific cold-induced expression may be an important molecular variant.

Analysis of Physiological and Transcriptomic Differences between a Premature Senescence Mutant (GSm) and Its Wild-Type in Common Wheat (Triticum aestivum L.)

Simple Summary

Early leaf senescence is an important agronomic trait that affects crop yield and quality. To understand the molecular mechanism of early leaf senescence, a wheat (Triticum aestivum L.) premature leaf senescence mutant (GSm) and its wild type were employed in this study. We compared the physiological characteristics and transcriptome of wheat leaves between the wild type (WT) and the mutant at two-time points. Physiological characteristics and differentially expressed gene (DEG) analysis revealed many genes and metabolic pathways that were closely related to senescence. These results will not only support further gene cloning and functional analysis of GSm, but also facilitate the study of leaf senescence in wheat.

Abstract

Premature leaf senescence has a profound influence on crop yield and quality. Here, a stable premature senescence mutant (GSm) was obtained from the common wheat (Triticum aestivum L.) cultivar Chang 6878 by mutagenesis with ethyl methanesulfonate. The differences between the GSm mutant and its wild-type (WT) were analyzed in terms of yield characteristics, photosynthetic fluorescence indices, and senescence-related physiological parameters. RNA sequencing was used to reveal gene expression differences between GSm and WT. The results showed that the yield of GSm was considerably lower than that of WT. The net photosynthetic rate, transpiration rate, maximum quantum yield, non-photochemical quenching coefficient, photosynthetic electron transport rate, soluble protein, peroxidase activity, and catalase activity all remarkably decreased in flag leaves of GSm, whereas malondialdehyde content distinctively increased compared with those of WT. The analysis of differentially expressed genes indicated blockade of chlorophyll and carotenoid biosynthesis, accelerated degradation of chlorophyll, and diminished photosynthetic capacity in mutant leaves; brassinolide might facilitate chlorophyll breakdown and consequently accelerate leaf senescence. NAC genes positively regulated the senescence process. Compared with NAC genes, expression of WRKY and MYB genes was induced earlier in the mutant possibly due to increased levels of reactive oxygen species and plant hormones (e.g., brassinolide, salicylic acid, and jasmonic acid), thereby accelerating leaf senescence. Furthermore, the antioxidant system played a role in minimizing oxidative damage in the mutant. These results provides novel insight into the molecular mechanisms of premature leaf senescence in crops.

De novo transcriptome analysis identifies key genes involved in dehydration stress response in kodo millet (Paspalum scrobiculatum L.)

Kodo millet (Paspalum scrobiculatum L.) is a small millet species known for its excellent nutritional and climate-resilient traits. To understand the genes and pathways underlying dehydration stress tolerance of kodo millet, the transcriptome of cultivar 'CO3' subjected to dehydration stress (0 h, 3 h, and 6 h) was sequenced. The study generated 239.1 million clean reads that identified 9201, 9814, and 2346 differentially expressed genes (DEGs) in 0 h vs. 3 h, 0 h vs. 6 h, and 3 h vs. 6 h libraries, respectively. The DEGs were found to be associated with vital molecular pathways, including hormone metabolism and signaling, antioxidant scavenging, photosynthesis, and cellular metabolism, and were validated using qRT-PCR. Also, a higher abundance of uncharacterized genes expressed during stress warrants further studies to characterize this class of genes to understand their role in dehydration stress response. Altogether, the study provides insights into the transcriptomic response of kodo millet during dehydration stress.

Genome-Wide Identification of WRKY Genes and Their Responses to Chilling Stress in Kandelia obovata

Background:Kandelia obovata, a dominant mangrove species, is widely distributed in tropical and subtropical areas. Low temperature is the major abiotic stress that seriously limits the survival and growth of mangroves. WRKY transcription factors (TFs) play vital roles in responses to biotic and abiotic stresses. However, genome-wide analysis of WRKY genes in K. obovata and their responses to chilling stress have not been reported.

Methods: Bioinformatic analysis was used to identify and characterize the K. obovata WRKY (KoWRKY) gene family, RNA-seq and qRT–PCR analyses were employed to screen KoWRKYs that respond to chilling stress.

Results: Sixty-four KoWRKYs were identified and they were unevenly distributed across all 18 K. obovata chromosomes. Many orthologous WRKY gene pairs were identified between Arabidopsis thaliana and K. obovata, showing high synteny between the two genomes. Segmental duplication events were found to be the major force driving the expansion for the KoWRKY gene family. Most of the KoWRKY genes contained several kinds of hormone- and stress-responsive cis-elements in their promoter. KoWRKY proteins belonged to three groups (I, II, III) according to their conserved WRKY domains and zinc-finger structure. Expression patterns derived from the RNA-seq and qRT–PCR analyses revealed that 9 KoWRKYs were significantly upregulated during chilling acclimation in the leaves. KEGG pathway enrichment analysis showed that the target genes of KoWRKYs were significantly involved in 11 pathways, and coexpression network analysis showed that 315 coexpressed pairs (KoWRKYs and mRNAs) were positively correlated.

Conclusion: Sixty-four KoWRKYs from the K. obovata genome were identified, 9 of which exhibited chilling stress-induced expression patterns. These genes represent candidates for future functional analysis of KoWRKYs involved in chilling stress related signaling pathways in K. obovata. Our results provide a basis for further analysis of KoWRKY genes to determine their functions and molecular mechanisms in K. obovata in response to chilling stress.

Salicylic Acid-Responsive Factor TcWRKY33 Positively Regulates Taxol Biosynthesis in Taxus chinensis in Direct and Indirect Ways

Taxol is a rare secondary metabolite that accumulates considerably in Taxus species under salicylic acid (SA) and methyl jasmonate treatment. However, the molecular mechanism of its accumulation remains unclear. We investigated TcWRKY33, a nuclear-localized group I WRKY transcription factor, as an SA-responsive regulator of taxol biosynthesis. Overexpression and RNA interference of TcWRKY33 confirmed that TcWRKY33 regulates the expression of most taxol biosynthesis genes, especially 10-deacetylbaccatin III-10-O-acetyltransferase (DBAT) and taxadiene synthase (TASY), which were considered as key enzymes in taxol biosynthesis. Transient overexpression of TcWRKY33 in Taxus chinensis leaves resulted in increased taxol and 10-deacetylbaccatin accumulation by 1.20 and 2.16 times compared with the control, respectively. Furthermore, TcWRKY33, DBAT, and TASY were confirmed to respond positively to SA signals. These results suggested that TcWRKY33 was the missing component of taxol biosynthesis that responds to SA. The sequence analysis identified two W-box motifs in the promoter of DBAT but not in the TASY. Yeast one-hybrid and dual-luciferase activity assays confirmed that TcWRKY33 can bind to the two W-boxes in the promoter of DBAT, upregulating its expression level. Hence, DBAT is a direct target of TcWRKY33. Furthermore, TcERF15, encoding a TASY activator, also contains two W-boxes in its promoter. Yeast one-hybrid and dual-luciferase activity assays further confirmed that TcWRKY33 can upregulate TASY expression through the activation of TcERF15. In summary, TcWRKY33 transmits SA signals and positively regulates taxol biosynthesis genes in two ways: directly and through the activation of other activators. Therefore, TcWRKY33 is an excellent candidate for genetically engineering regulation of taxol biosynthesis in Taxus plants.

Identification of the Group III WRKY Subfamily and the Functional Analysis of GhWRKY53 in Gossypium hirsutum L

WRKY transcription factors had multiple functions in plant secondary metabolism, leaf senescence, fruit ripening, adaptation to biotic and abiotic stress, and plant growth and development. However, knowledge of the group III WRKY subfamily in fiber development in upland cotton (Gossypium hirsutum L.) is largely absent. Previous studies have shown that there were 21 putative group III WRKY members in G. hirsutum L. These putative amino acid sequences from the III WRKY group were phylogenetically clustered into three clades. Multiple alignment, conservative motif analysis, and gene structure analysis showed that the members clustered together in the phylogenetic tree had similar motifs and gene structures. Expression pattern analysis revealed that variation in the expression levels of these genes in different tissues and fiber development stages. To better understand the functions of putative group III WRKY genes in G. hirsutum L., we selected the cotton fiber initiation-related gene GhWRKY53 for cloning and functional identification. The subcellular localization experiment of GhWRKY53 in Nicotiana tabacum leaves showed that it was located in the nucleus. The heterologous expression of GhWRKY53 in Arabidopsis thaliana could significantly increase the density of trichomes. Twelve proteins that interacted with GhWRKY53 were screened from the cotton fiber cDNA library by yeast two-hybrid experiment. This study findings lay a foundation for further research on the role of the GhWRKY53 during cotton fiber development and provide a new insight for further studying putative group III WRKY genes in G. hirsutum L. Our research results also provide vital information for the genetic mechanism of high-quality cotton fiber formation and essential genetic resources for cotton fiber quality improvement.

Ion homeostasis for salinity tolerance in plants: a molecular approach

Soil salinity is one of the major environmental stresses faced by the plants. Sodium chloride is the most important salt responsible for inducing salt stress by disrupting the osmotic potential. Due to various innate mechanisms, plants adapt to the sodic niche around them. Genes and transcription factors regulating ion transport and exclusion such as salt overly sensitive (SOS), Na⁺ /H⁺ exchangers (NHXs), high sodium affinity transporter (HKT) and plasma membrane protein (PMP) are activated during salinity stress and help in alleviating cells of ion toxicity. For salt tolerance in plants signal transduction and gene expression is regulated via transcription factors such as NAM (no apical meristem), ATAF (Arabidopsis transcription activation factor), CUC (cup-shaped cotyledon), Apetala 2/ethylene responsive factor (AP2/ERF), W-box binding factor (WRKY) and basic leucine zipper domain (bZIP). Cross-talk between all these transcription factors and genes aid in developing the tolerance mechanisms adopted by plants against salt stress. These genes and transcription factors regulate the movement of ions out of the cells by opening various membrane ion channels. Mutants or knockouts of all these genes are known to be less salt-tolerant compared to wild-types. Using novel molecular techniques such as analysis of genome, transcriptome, ionome and metabolome of a plant, can help in expanding the understanding of salt tolerance mechanism in plants. In this review, we discuss the genes responsible for imparting salt tolerance under salinity stress through transport dynamics of ion balance and need to integrate high-throughput molecular biology techniques to delineate the issue.

A transcriptomic view to wounding response in young Scots pine stems

We studied the stress response of five-year-old Scots pine xylem to mechanical wounding using RNA sequencing. In general, we observed a bimodal response in pine xylem after wounding. Transcripts associated with water deficit stress, defence, and cell wall modification were induced at the earliest time point of three hours; at the same time, growth-related processes were down-regulated. A second temporal wave was triggered either at the middle and/or at the late time points (one and four days). Secondary metabolism, such as stilbene and lignan biosynthesis started one day after wounding. Scots pine synthesises the stilbenes pinosylvin and its monomethyl ether both as constitutive and induced defence compounds. Stilbene biosynthesis is induced by wounding, pathogens and UV stress, but is also developmentally regulated when heartwood is formed. Comparison of wounding responses to heartwood formation shows that many induced processes (in addition to stilbene biosynthesis) are similar and relate to defence or desiccation stress, but often specific transcripts are up-regulated in the developmental and wounding induced contexts. Pine resin biosynthesis was not induced in response to wounding, at least not during the first four days.

Function and Mechanism of WRKY Transcription Factors in Abiotic Stress Responses of Plants

The WRKY gene family is a plant-specific transcription factor (TF) group, playing important roles in many different response pathways of diverse abiotic stresses (drought, saline, alkali, temperature, and ultraviolet radiation, and so forth). In recent years, many studies have explored the role and mechanism of WRKY family members from model plants to agricultural crops and other species. Abiotic stress adversely affects the growth and development of plants. Thus, a review of WRKY with stress responses is important to increase our understanding of abiotic stress responses in plants. Here, we summarize the structural characteristics and regulatory mechanism of WRKY transcription factors and their responses to abiotic stress. We also discuss current issues and future perspectives of WRKY transcription factor research.

Identification of tRFs and phasiRNAs in tomato (Solanum lycopersicum) and their responses to exogenous abscisic acid

BACKGROUND

The non-coding small RNA tRFs (tRNA-derived fragments) and phasiRNAs (plant-specific) exert important roles in plant growth, development and stress resistances. However, whether the tRFs and phasiRNAs respond to the plant important stress hormone abscisic acid (ABA) remain enigma.

RESULTS

Here, the RNA-sequencing was implemented to decipher the landscape of tRFs and phasiRNAs in tomato (Solanum lycopersicum) leaves and their responses when foliar spraying exogenous ABA after 24 h. In total, 733 tRFs and 137 phasiRNAs were detected. The tRFs were mainly derived from the tRNA^Ala transporting alanine, which tended to be cleaved at the 5^'terminal guanine site and D loop uracil site to produce tRF^Ala with length of 20 nt. Most of phasiRNAs originated from NBS-LRR resistance genes. Expression analysis revealed that 156 tRFs and 68 phasiRNAs expressed differentially, respectively. Generally, exogenous ABA mainly inhibited the expression of tRFs and phasiRNAs. Furthermore, integrating analysis of target gene prediction and transcriptome data presented that ABA significantly downregulated the abundance of phsaiRNAs associated with biological and abiotic resistances. Correspondingly, their target genes such as AP2/ERF, WRKY and NBS-LRR, STK and RLK, were mainly up-regulated.

CONCLUSIONS

Combined with the previous analysis of ABA-response miRNAs, it was speculated that ABA can improve the plant resistances to various stresses by regulating the expression and interaction of small RNAs (such as miRNAs, tRFs, phasiRNAs) and their target genes. This study enriches the plant tRFs and phasiRNAs, providing a vital basis for further investigating ABA response-tRFs and phasiRNAs and their functions in biotic and abiotic stresses.

Phylogenetic and Transcription Analysis of Hibiscus hamabo Sieb. et Zucc. WRKY Transcription Factors

WRKY transcription factors are known to play important roles in the regulation of various aspects of plant growth and development, including germination, stress resistance, and senescence. Nevertheless, there is little information about the WRKY genes in Hibiscus hamabo Sieb. et Zucc., an important semimangrove plant. In this study, HhWRKY genes in H. hamabo were identificated based on Illumina RNA-sequencing and isoform sequencing from salt-treated roots. Then phylogenetic analysis and conserved motif analysis of the WRKY family in H. hamabo and Arabidopsis thaliana were used to classify WRKY genes. Sixteen HhWRKY genes were selected from different groups to detect their expression patterns using real-time quantitative PCR in different organ (root, old leaf, tender leaf, receptacle, petal, or stamen) from 10-year-old H. hamabo plants grown in their natural environment and in seedlings with 8 to 10 true leaves challenged by phytohormone (salicylic acid, methyl jasmonate, or abscisic acid) and abiotic stress (drought, salt, or high temperature). As a result, the identified 78 HhWRKY genes were divided into two major groups and several subgroups based on their structural and phylogenetic features. Most transcripts of the selected 16 HhWRKY genes were more abundant in old than in tender leaves of H. hamabo. HhWRKY genes were regulated in reaction to abiotic stresses and phytohormone treatments and may participate in signaling networks to improve plant stress resistance. Some of HhWRKY genes behaved as would be predicted based on their homology with A. thaliana WRKY genes, but others showed divergent behavior. This systematic analysis lays the foundation for further identification of WRKY gene functions, with the aim of improving woody plants.

The WRKY transcription factor WRKY8 promotes resistance to pathogen infection and mediates drought and salt stress tolerance in Solanum lycopersicum

WRKY transcription factors play a key role in the tolerance of biotic and abiotic stresses across various crop species, but the function of some WRKY genes, particularly in tomato, remains unexplored. Here, we characterize the roles of a previously unstudied WRKY gene, SlWRKY8, in the resistance to pathogen infection and the tolerance to drought and salt stresses. Expression of SlWRKY8 was up-regulated upon Pseudomonas syringae pv. tomato DC3000 (Pst. DC3000), abiotic stresses such as drought, salt and cold, as well as ABA and SA treatments. The SlWRKY8 protein was localized to the nucleus with no transcription activation in yeast, but it could activate W-box-dependent transcription in plants. The overexpression of SlWRKY8 in tomato conferred a greater resistance to the pathogen Pst. DC3000 and resulted in the increased transcription levels of two pathogen-related genes SlPR1a1 and SlPR7. Moreover, transgenic plants displayed the alleviated wilting or chlorosis phenotype under drought and salt stresses, with higher levels of stress-induced osmotic substances like proline and higher transcript levels of the stress-responsive genes SlAREB, SlDREB2A and SlRD29. Stomatal aperature was smaller under drought stress in transgenic plants, maintaining higher water content in leaves compared with wild-type plants. The oxidative pressure, indicated by the concentration of hydrogen peroxide (H₂ O₂ ) and malondialdehyde (MDA), was also reduced in transgenic plants, where we also observed higher levels of antioxidant enzyme activities under stress. Overall, our results suggest that SlWRKY8 functions as a positive regulator in plant immunity against pathogen infection as well as in plant responses to drought and salt stresses.

Genome-wide identification, characterisation and functional evaluation of WRKY genes in the sweet potato wild ancestor Ipomoea trifida (H.B.K.) G. Don. under abiotic stresses

BACKGROUND

WRKY DNA-binding protein (WRKY) is a large gene family involved in plant responses and adaptation to salt, drought, cold and heat stresses. Sweet potato from the genus Ipomoea is a staple food crop, but the WRKY genes in Ipomoea species remain unknown to date. Hence, we carried out a genome-wide analysis of WRKYs in Ipomoea trifida (H.B.K.) G. Don., the wild ancestor of sweet potato.

RESULTS

A total of 83 WRKY genes encoding 96 proteins were identified in I. trifida, and their gene distribution, duplication, structure, phylogeny and expression patterns were studied. ItfWRKYs were distributed on 15 chromosomes of I. trifida. Gene duplication analysis showed that segmental duplication played an important role in the WRKY gene family expansion in I. trifida. Gene structure analysis showed that the intron-exon model of the ItfWRKY gene was highly conserved. Meanwhile, the ItfWRKYs were divided into five groups (I, IIa + IIb, IIc, IId + IIe and III) on the basis of the phylogenetic analysis on I. trifida and Arabidopsis thaliana WRKY proteins. In addition, gene expression profiles confirmed by quantitative polymerase chain reaction showed that ItfWRKYs were highly up-regulated or down-regulated under salt, drought, cold and heat stress conditions, implying that these genes play important roles in response and adaptation to abiotic stresses.

CONCLUSIONS

In summary, genome-wide identification, gene structure, phylogeny and expression analysis of WRKY gene in I. trifida provide basic information for further functional studies of ItfWRKYs and for the molecular breeding of sweet potato.

TaWRKY40 transcription factor positively regulate the expression of TaGAPC1 to enhance drought tolerance

BACKGROUNDS

Drought stress is one of the major factors that affects wheat yield. Glyceraldehyde-3-Phosphate dehydrogenase (GAPDH) is a multifunctional enzyme that plays the important role in abiotic stress and plant development. However, in wheat, limited information about drought-responsive GAPC genes has been reported, and the mechanism underlying the regulation of the GAPC protein is unknown.

RESULTS

In this study, we evaluated the potential role of GAPC1 in drought stress in wheat and Arabidopsis. We found that the overexpression of TaGAPC1 could enhance the tolerance to drought stress in transgenic Arabidopsis. Yeast one-hybrid library screening and EMSA showed that TaWRKY40 acts as a direct regulator of the TaGAPC1 gene. A dual luciferase reporter assay indicated that TaWRKY40 improved the TaGAPC1 promoter activity. The results of qRT-PCR in wheat protoplast cells with instantaneous overexpression of TaWRKY40 indicated that the expression level of TaGAPC1 induced by abiotic stress was upregulated by TaWRKY40. Moreover, TaGAPC1 promoted H2O2 detoxification in response to drought.

CONCLUSION

These results demonstrate that the inducible transcription factor TaWRKY40 could activate the transcription of the TaGAPC1 gene, thereby increasing the tolerance of plants to drought stress.

Identification, characterization and expression profiles of Fusarium udum stress-responsive WRKY transcription factors in Cajanus cajan under the influence of NaCl stress and Pseudomonas fluorescens OKC

The WRKY gene family has never been identified in pigeonpea (Cajanus cajan). Therefore, objective of the present study was to identify the WRKY gene family in pigeonpea and characterize the Fusarium udum stress-responsive WRKY genes under normal, NaCl-stressed and Pseudomonas fluorescens OKC (a plant growth-promoting bacterial strain) treated conditions. The aim was to characterize the Fusarium udum stress-responsive WRKY genes under some commonly occurring field conditions. We identified 97 genes in the WRKY family of pigeonpea, using computational prediction method. The gene family was then classified into three groups through phylogenetic analysis of the homologous genes from the representative plant species. Among the 97 identified WRKY genes 35 were further classified as pathogen stress responsive genes. Functional validation of the 35 WRKY genes was done through generating transcriptional profiles of the genes from root tissues of pigeonpea plants under the influence of P. fluorescens OKC after 24 h of stress application (biotic: Fusarium udum, abiotic: NaCl). The entire experiment was conducted in two pigeonpea cultivars Asha (resistant to F. udum) and Bahar (susceptible to F. udum) and the results were concluded on the basis of transcriptional regulation of the WRKY genes in both the pigeonpea cultivars. The results revealed that among the 35 tentatively identified biotic stress responsive CcWRKY genes, 26 were highly F. udum responsive, 17 were better NaCl responsive compared to F. udum and 11 were dual responsive to both F. udum and NaCl. Application of OKC was able to enhance transcript accumulation of the individual CcWRKY genes to both the stresses when applied individually but not in combined challenge of the two stresses. The results thus indicated that CcWRKY genes play a vital role in the defense signaling against F. udum and some of the F. udum responsive CcWRKYs (at least 11 in pigeonpea) are also responsive to abiotic stresses such as NaCl. Further, plant beneficial microbes such as P. fluorescens OKC also help pegionpea to defend itself against the two stresses (F. udum and NaCl) through enhanced expression of the stress responsive CcWRKY genes when the stresses are applied individually.

Genome-wide Analysis of the WRKY Gene Family and its Response to Abiotic Stress in Buckwheat (Fagopyrum Tataricum)

The WRKY gene family is an ancient plant transcription factor (TF) family with a vital role in plant growth and development, especially in response to biotic and abiotic stresses. Although many researchers have studied WRKY TFs in numerous plant species, little is known of them in Tartary buckwheat (Fagopyrum tataricum). Based on the recently reported genome sequence of Tartary buckwheat, we identified 78 FtWRKY proteins that could be classified into three major groups. All 77 WRKY genes were distributed unevenly across all eight chromosomes. Exon-intron analysis and motif composition prediction revealed the complexity and diversity of FtWRKYs, indicating that WRKY TFs may be of significance in plant growth regulation and stress response. Two separate pairs of tandem duplication genes were found, but no segmental duplications were identified. Overall, most orthologous gene-pairs between Tartary and common buckwheat evolved under strong purifying selection. qRT-PCR was used to analyze differences in expression among four FtWRKYs (FtWRKY6, 74, 31, and 7) under salt, drought, cold, and heat treatments. The results revealed that all four proteins are related to abiotic stress responses, although they exhibited various expression patterns. In particular, the relative expression levels of FtWRKY6, 74, and 31 were significantly upregulated under salt stress, while the highest expression of FtWRKY7 was observed from heat treatment. This study provides comprehensive insights into the WRKY gene family in Tartary buckwheat, and can support the screening of additional candidate genes for further functional characterization of WRKYs under various stresses.

Can WRKY transcription factors help plants to overcome environmental challenges?

WRKY transcription factors (TFs) are responsible for the regulation of genes responsive to many plant growth and developmental cues, as well as to biotic and abiotic stresses. The modulation of gene expression by WRKY proteins primarily occurs by DNA binding at specific cis-regulatory elements, the W-box elements, which are short sequences located in the promoter region of certain genes. In addition, their action can occur through interaction with other TFs and the cellular transcription machinery. The current genome sequences available reveal a relatively large number of WRKY genes, reaching hundreds of copies. Recently, functional genomics studies in model plants have enabled the identification of function and mechanism of action of several WRKY TFs in plants. This review addresses the more recent studies in plants regarding the function of WRKY TFs in both model and crop plants for coping with environmental challenges, including a wide variety of abiotic and biotic stresses.

The Maize WRKY Transcription Factor ZmWRKY40 Confers Drought Resistance in Transgenic Arabidopsis

Abiotic stresses restrict the growth and yield of crops. Plants have developed a number of regulatory mechanisms to respond to these stresses. WRKY transcription factors (TFs) are plant-specific transcription factors that play essential roles in multiple plant processes, including abiotic stress response. At present, little information regarding drought-related WRKY genes in maize is available. In this study, we identified a WRKY transcription factor gene from maize, named ZmWRKY40. ZmWRKY40 is a member of WRKY group II, localized in the nucleus of mesophyll protoplasts. Several stress-related transcriptional regulatory elements existed in the promoter region of ZmWRKY40. ZmWRKY40 was induced by drought, high salinity, high temperature, and abscisic acid (ABA). ZmWRKY40 could rapidly respond to drought with peak levels (more than 10-fold) at 1 h after treatment. Overexpression of ZmWRKY40 improved drought tolerance in transgenic Arabidopsis by regulating stress-related genes, and the reactive oxygen species (ROS) content in transgenic lines was reduced by enhancing the activities of peroxide dismutase (POD) and catalase (CAT) under drought stress. According to the results, the present study may provide a candidate gene involved in the drought stress response and a theoretical basis to understand the mechanisms of ZmWRKY40 in response to abiotic stresses in maize.

Chrysanthemum DgWRKY2 Gene Enhances Tolerance to Salt Stress in Transgenic Chrysanthemum

WRKY transcription factors (TFs) play a vital part in coping with different stresses. In this study, DgWRKY2 was isolated from Dendranthema grandiflorum. The gene encodes a 325 amino acid protein, belonging to the group II WRKY family, and contains one typical WRKY domain (WRKYGQK) and a zinc finger motif (C-X4-5-C-X22-23-H-X1-H). Overexpression of DgWRKY2 in chrysanthemum enhanced tolerance to high-salt stress compared to the wild type (WT). In addition, the activities of antioxidant enzymes (superoxide dismutase (SOD), peroxidase (POD), catalase (CAT)), proline content, soluble sugar content, soluble protein content, and chlorophyll content of transgenic chrysanthemum, as well as the survival rate of the transgenic lines, were on average higher than that of the WT. On the contrary, hydrogen peroxide (H₂O₂), superoxide anion (O₂-), and malondialdehyde (MDA) accumulation decreased compared to WT. Expression of the stress-related genes DgCAT, DgAPX, DgZnSOD, DgP5CS, DgDREB1A, and DgDREB2A was increased in the DgWRKY2 transgenic chrysanthemum compared with their expression in the WT. In conclusion, our results indicate that DgWRKY2 confers salt tolerance to transgenic chrysanthemum by enhancing antioxidant and osmotic adjustment. Therefore, this study suggests that DgWRKY2 could be used as a reserve gene for salt-tolerant plant breeding.

The grapevine VvWRKY2 gene enhances salt and osmotic stress tolerance in transgenic Nicotiana tabacum

Our study aims to assess the implication of WRKY transcription factor in the molecular mechanisms of grapevine adaptation to salt and water stresses. In this respect, a full-length VvWRKY2 cDNA, isolated from a Vitis vinifera grape berry cDNA library, was constitutively over-expressed in Nicotiana tabacum seedlings. Our results showed that transgenic tobacco plants exhibited higher seed germination rates and better growth, under both salt and osmotic stress treatments, when compared to wild type plants. Furthermore, our analyses demonstrated that, under stress conditions, transgenic plants accumulated more osmolytes, such as soluble sugars and free proline, while no changes were observed regarding electrolyte leakage, H₂O₂, and malondialdehyde contents. The improvement of osmotic adjustment may be an important mechanism underlying the role of VvWRKY2 in promoting tolerance and adaptation to abiotic stresses. Principal component analysis of our results highlighted a clear partition of plant response to stress. On the other hand, we observed a significant adaptation behaviour response for transgenic lines under stress. Taken together, all our findings suggest that over-expression of VvWRKY2 gene has a compelling role in abiotic stress tolerance and, therefore, would provide a useful strategy to promote abiotic stress tolerance in grape via molecular-assisted breeding and/or new biotechnology tools.

Overexpression of the alfalfa WRKY11 gene enhances salt tolerance in soybean

The WRKY transcription factors play an important role in the regulation of transcriptional reprogramming associated with plant abiotic stress responses. In this study, the WRKY transcription factor MsWRKY11, containing the plant-specific WRKY zinc finger DNA-binding motif, was isolated from alfalfa. The MsWRKY11 gene was detected in all plant tissues (root, stem, leaf, flower, and fruit), with high expression in root and leaf tissues. MsWRKY11 was upregulated in response to a variety of abiotic stresses, including salinity, alkalinity, cold, abscisic acid, and drought. Overexpression of MsWRKY11 in soybean enhanced the salt tolerance at the seedling stage. Transgenic soybean had a better salt-tolerant phenotype, and the hypocotyls were significantly longer than those of wild-type seeds after salt treatment. Furthermore, MsWRKY11 overexpression increased the contents of chlorophyll, proline, soluble sugar, superoxide dismutase, and catalase, but reduced the relative electrical conductivity and the contents of malonaldehyde, H2O2, and O2-. Plant height, pods per plant, seeds per plant, and 100-seed weight of transgenic MsWRKY11 soybean were higher than those of wild-type soybean, especially OX2. Results of the salt experiment showed that MsWRKY11 is involved in salt stress responses, and its overexpression improves salt tolerance in soybean.

WRKY transcription factors in plant responses to stresses

The WRKY gene family is among the largest families of transcription factors (TFs) in higher plants. By regulating the plant hormone signal transduction pathway, these TFs play critical roles in some plant processes in response to biotic and abiotic stress. Various bodies of research have demonstrated the important biological functions of WRKY TFs in plant response to different kinds of biotic and abiotic stresses and working mechanisms. However, very little summarization has been done to review their research progress. Not just important TFs function in plant response to biotic and abiotic stresses, WRKY also participates in carbohydrate synthesis, senescence, development, and secondary metabolites synthesis. WRKY proteins can bind to W-box (TGACC (A/T)) in the promoter of its target genes and activate or repress the expression of downstream genes to regulate their stress response. Moreover, WRKY proteins can interact with other TFs to regulate plant defensive responses. In the present review, we focus on the structural characteristics of WRKY TFs and the research progress on their functions in plant responses to a variety of stresses.

Genome-Wide Identification and Analysis of Genes, Conserved between japonica and indica Rice Cultivars, that Respond to Low-Temperature Stress at the Vegetative Growth Stage

Cold stress is very detrimental to crop production. However, only a few genes in rice have been identified with known functions related to cold tolerance. To meet this agronomic challenge more effectively, researchers must take global approaches to select useful candidate genes and find the major regulatory factors. We used five Gene expression omnibus series data series of Affymetrix array data, produced with cold stress-treated samples from the NCBI Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/), and identified 502 cold-inducible genes common to both japonica and indica rice cultivars. From them, we confirmed that the expression of two randomly chosen genes was increased by cold stress in planta. In addition, overexpression of OsWRKY71 enhanced cold tolerance in 'Dongjin,' the tested japonica cultivar. Comparisons between japonica and indica rice, based on calculations of plant survival rates and chlorophyll fluorescence, confirmed that the japonica rice was more cold-tolerant. Gene Ontology enrichment analysis indicate that the 'L-phenylalanine catabolic process,' within the Biological Process category, was the most highly overrepresented under cold-stress conditions, implying its significance in that response in rice. MapMan analysis classified 'Major Metabolic' processes and 'Regulatory Gene Modules' as two other major determinants of the cold-stress response and suggested several key cis-regulatory elements. Based on these results, we proposed a model that includes a pathway for cold stress-responsive signaling. Results from our functional analysis of the main signal transduction and transcription regulation factors identified in that pathway will provide insight into novel regulatory metabolism(s), as well as a foundation by which we can develop crop plants with enhanced cold tolerance.

The Cotton WRKY Gene GhWRKY41 Positively Regulates Salt and Drought Stress Tolerance in Transgenic Nicotiana benthamiana

WRKY transcription factors constitute a very large family of proteins in plants and participate in modulating plant biological processes, such as growth, development and stress responses. However, the exact roles of WRKY proteins are unclear, particularly in non-model plants. In this study, Gossypium hirsutum WRKY41 (GhWRKY41) was isolated and transformed into Nicotiana benthamiana. Our results showed that overexpression of GhWRKY41 enhanced the drought and salt stress tolerance of transgenic Nicotiana benthamiana. The transgenic plants exhibited lower malondialdehyde content and higher antioxidant enzyme activity, and the expression of antioxidant genes was upregulated in transgenic plants exposed to osmotic stress. A β-glucuronidase (GUS) staining assay showed that GhWRKY41 was highly expressed in the stomata when plants were exposed to osmotic stress, and plants overexpressing GhWRKY41 exhibited enhanced stomatal closure when they were exposed to osmotic stress. Taken together, our findings demonstrate that GhWRKY41 may enhance plant tolerance to stress by functioning as a positive regulator of stoma closure and by regulating reactive oxygen species (ROS) scavenging and the expression of antioxidant genes.

Overexpression of GhWRKY27a reduces tolerance to drought stress and resistance to Rhizoctonia solani infection in transgenic Nicotiana benthamiana

WRKY proteins constitute transcriptional regulators involved in various biological processes, especially in coping with diverse biotic and abiotic stresses. However, in contrast to other well-characterized WRKY groups, the functions of group III WRKY transcription factors are poorly understood in the economically important crop cotton (Gossypium hirsutum). In this study, a group III WRKY gene from cotton, GhWRKY27a, was isolated and characterized. Our data indicated that GhWRKY27a localized to the nucleus and that GhWRKY27a expression could be strongly induced by abiotic stresses, pathogen infection, and multiple defense-related signaling molecules. Virus-induced gene silencing (VIGS) of GhWRKY27a enhanced tolerance to drought stress in cotton. In contrast, GhWRKY27a overexpression in Nicotiana benthamiana markedly reduced plant tolerance to drought stress, as determined through physiological analyses of leaf water loss, survival rates, and the stomatal aperture. This susceptibility was coupled with reduced stomatal closure in response to abscisic acid and decreased expression of stress-related genes. In addition, GhWRKY27a-overexpressing plants exhibited reduced resistance to Rhizoctonia solani infection, mainly demonstrated by the transgenic lines exhibiting more severe disease symptoms, accompanied by attenuated expression of defense-related genes in N. benthamiana. Taken together, these findings indicated that GhWRKY27a functions in negative responses to drought tolerance and in resistance to R. solani infection.

Isolation of a WRKY30 gene from Muscadinia rotundifolia (Michx) and validation of its function under biotic and abiotic stresses

WRKY transcription factors (TFs) play important roles in many plant processes, including responses to biotic and abiotic stresses. In the present study, Muscadinia rotundifolia MrWRKY30 dramatically accumulated in grapevine leaves in response to inoculation of Plasmopara viticola, a pathogen causing grapevine downy mildew disease. Similar responses were also found on grapevines treated with exogenous SA/JA/ET. Ectopic expression of MrWRKY30 in Arabidopsis thaliana "COL0" enhanced its resistance to downy mildew pathogen Peronospora parasitica. Pathogenesis-related (PR) genes, including AtPR1, AtPR4, AtPR5, and AtPDF1.2, were significantly upregulated in transgenic A. thaliana after P. parasitica inoculation. In the mean time, two critical genes in SA and JA signaling pathways, AtEDS5 and AtJAR1, were abundantly expressed as well, indicating that MrWRKY30 may enhance disease resistance of A. thaliana through SA and JA defense system. The transgenic A. thaliana plants also enhanced tolerance to cold stress accompanied with upregulation of AtCBF1, AtCBF3, AtICE1, and AtCOR47. MrWRKY30 might protect A. thaliana from cold damage by activating the AtCBF-mediated signaling pathway to induce the downstream AtCOR47 gene. Interestingly, the transgenic seedlings had a negative effect on salt tolerance. Reverse transcription PCR (RT-PCR) analysis revealed that antioxidant enzyme genes AtAPX (ascorbate peroxidase), AtCAT (catalase), and AtGST (glutathione-S-transferase) were suppressed in transgenic plants, which may lead to reactive oxygen species (ROS)-mediated sensitivity to salt stress.

WRKY proteins: signaling and regulation of expression during abiotic stress responses

WRKY proteins are emerging players in plant signaling and have been thoroughly reported to play important roles in plants under biotic stress like pathogen attack. However, recent advances in this field do reveal the enormous significance of these proteins in eliciting responses induced by abiotic stresses. WRKY proteins act as major transcription factors, either as positive or negative regulators. Specific WRKY factors which help in the expression of a cluster of stress-responsive genes are being targeted and genetically modified to induce improved abiotic stress tolerance in plants. The knowledge regarding the signaling cascade leading to the activation of the WRKY proteins, their interaction with other proteins of the signaling pathway, and the downstream genes activated by them are altogether vital for justified targeting of the WRKY genes. WRKY proteins have also been considered to generate tolerance against multiple abiotic stresses with possible roles in mediating a cross talk between abiotic and biotic stress responses. In this review, we have reckoned the diverse signaling pattern and biological functions of WRKY proteins throughout the plant kingdom along with the growing prospects in this field of research.

Genome-wide analysis of the R2R3-MYB transcription factor genes in Chinese cabbage (Brassica rapa ssp. pekinensis) reveals their stress and hormone responsive patterns

Background

The MYB superfamily is one of the most abundant transcription factor (TF) families in plants. MYB proteins include highly conserved N-terminal MYB repeats (1R, R2R3, 3R, and atypical) and various C-terminal sequences that confer extensive functions. However, the functions of most MYB genes are unknown, and have been little studied in Chinese cabbage.

Results

Here, we analyzed 256 (55.2% of total MYBs) R2R3-MYB genes from Chinese cabbage (Brassica rapa ssp. pekinensis) and anchored them onto the 10 chromosomes and three subgenomes. The R2R3-, 3R- and atypical MYB proteins in Chinese cabbage formed 45 subgroups based on domain similarity and phylogenetic topology. Organization and syntenic analysis revealed the genomic distribution and collinear relationships of the R2R3-BrMYBs. Synonymous nucleotide substitution (Ka/Ks) analysis showed that the Chinese cabbage MYB DNA-binding domain is under strong purifying selection. Moreover, RNA-seq data revealed tissue-specific and distinct R2R3-BrMYB expression profiles, and quantitative real-time PCR (qPCR) analysis in leaves showed stress responsive expression and crosstalk with ABA-auxin signaling cascades.

Conclusions

In this study, we identified the largest MYB gene family in plants to date. Our results indicate that members of this superfamily may be involved in plant development, stress responses and leaf senescence, highlighting their functional diversity.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1216-y) contains supplementary material, which is available to authorized users.

Expression of TaWRKY44, a wheat WRKY gene, in transgenic tobacco confers multiple abiotic stress tolerances

The WRKY transcription factors have been reported to be involved in various plant physiological and biochemical processes. In this study, we successfully assembled 10 unigenes from expressed sequence tags (ESTs) of wheat and designated them as TaWRKY44-TaWRKY53, respectively. Among these genes, a subgroup I gene, TaWRKY44, was found to be upregulated by treatments with PEG6000, NaCl, 4°C, abscisic acid (ABA), H2O2 and gibberellin (GA). The TaWRKY44-GFP fusion protein was localized to the nucleus of onion epidermal cells, and TaWRKY44 was able to bind to the core DNA sequences of TTGACC and TTAACC in yeast. The N-terminal of TaWRKY44 showed transcriptional activation activity. Expression of TaWRKY44 in tobacco plants conferred drought and salt tolerance and transgenic tobacco exhibited a higher survival rate, relative water content (RWC), soluble sugar, proline and superoxide dismutase (SOD) content, as well as higher activities of catalase (CAT) and peroxidase (POD), but less ion leakage (IL), lower contents of malondialdehyde (MDA), and H2O2. In addition, expression of TaWRKY44 also increased the seed germination rate in the transgenic lines under osmotic stress conditions while exhibiting a lower H2O2 content and higher SOD, CAT, and POD activities. Expression of TaWRKY44 upregulated the expression of some reactive oxygen species (ROS)-related genes and stress-responsive genes in tobacco under osmotic stresses. These data demonstrate that TaWRKY44 may act as a positive regulator in drought/salt/osmotic stress responses by either efficient ROS elimination through direct or indirect activation of the cellular antioxidant systems or activation of stress-associated gene expression.

Identification and expression analysis of WRKY family genes under biotic and abiotic stresses in Brassica rapa

WRKY proteins constitute one of the largest transcription factor families in higher plants, and they are involved in multiple biological processes such as plant development, metabolism, and responses to biotic and abiotic stresses. Genes of this family have been well documented in response to many abiotic and biotic stresses in many plant species, but not yet against Pectobacterium carotovorum subsp. carotovorum and Fusarium oxysporum f.sp. conglutinans in any of the plants. Moreover, potentiality of a specific gene may vary depending on stress conditions and genotypes. To identify stress resistance-related potential WRKY genes of Brassica rapa, we analyzed their expressions against above-mentioned pathogens and cold, salt, and drought stresses in B. rapa. Stress resistance-related functions of all Brassica rapa WRKY (BrWRKY) genes were firstly analyzed through homology study with existing biotic and abiotic stress resistance-related WRKY genes of other plant species and found a high degree of homology. We then identified all BrWRKY genes in a Br135K microarray dataset, which was created by applying low-temperature stresses to two contrasting Chinese cabbage doubled haploid (DH) lines, Chiifu and Kenshin, and selected 41 BrWRKY genes with high and differential transcript abundance levels. These selected genes were further investigated under cold, salt, and drought stresses as well as after infection with P. carotovorum subsp. carotovorum and F. oxysporum f.sp. conglutinans in B. rapa. The selected genes showed an organ-specific expression, and 22 BrWRKY genes were differentially expressed in Chiifu compared to Kenshin under cold and drought stresses. Six BrWRKY genes were more responsive in Kenshin compared to Chiffu under salt stress. In addition, eight BrWRKY genes showed differential expression after P. carotovorum subsp. carotovorum infection and five genes after F. oxysporum f.sp. conglutinans infection in B. rapa. Thus, the differentially expressed BrWRKY genes might be potential resources for molecular breeding of Brassica crops against abiotic and biotic stresses and several genes, which showed differential expressions commonly in response to several stresses, might be useful for multiple stress resistance. These findings would also be helpful in resolving the complex regulatory mechanism of WRKY genes in stress resistance and for this further functional genomics study of these potential genes in different Brassica crops is essential.

Genome-wide identification of WRKY family genes and their response to cold stress in Vitis vinifera

BACKGROUND

WRKY transcription factors are one of the largest families of transcriptional regulators in plants. WRKY genes are not only found to play significant roles in biotic and abiotic stress response, but also regulate growth and development. Grapevine (Vitis vinifera) production is largely limited by stressful climate conditions such as cold stress and the role of WRKY genes in the survival of grapevine under these conditions remains unknown.

RESULTS

We identified a total of 59 VvWRKYs from the V. vinifera genome, belonging to four subgroups according to conserved WRKY domains and zinc-finger structure. The majority of VvWRKYs were expressed in more than one tissue among the 7 tissues examined which included young leaves, mature leaves, tendril, stem apex, root, young fruits and ripe fruits. Publicly available microarray data suggested that a subset of VvWRKYs was activated in response to diverse stresses. Quantitative real-time PCR (qRT-PCR) results demonstrated that the expression levels of 36 VvWRKYs are changed following cold exposure. Comparative analysis was performed on data from publicly available microarray experiments, previous global transcriptome analysis studies, and qRT-PCR. We identified 15 VvWRKYs in at least two of these databases which may relate to cold stress. Among them, the transcription of three genes can be induced by exogenous ABA application, suggesting that they can be involved in an ABA-dependent signaling pathway in response to cold stress.

CONCLUSIONS

We identified 59 VvWRKYs from the V. vinifera genome and 15 of them showed cold stress-induced expression patterns. These genes represented candidate genes for future functional analysis of VvWRKYs involved in the low temperature-related signal pathways in grape.

Characterization and co-expression analysis of WRKY orthologs involved in responses to multiple abiotic stresses in Pak-choi (Brassica campestris ssp. chinensis)

BACKGROUND

The WRKY transcription factor is an important member of the stress-related transcription factors, which mediate diverse abiotic stresses in many plants. However, up until now, the number of WRKY members, and the regulatory mechanisms involved in abiotic stress responses in Pak-choi (Brassica campestris ssp. chinensis), remained unknown.

RESULTS

We isolated and identified 56 full-length WRKY cDNAs from a Pak-choi stress-induced cDNA library. The 56 putative BcWRKY proteins were divided into three groups based on structural and phylogenetic analyses. A subcellular localization prediction indicated that the putative BcWRKY proteins were enriched in the nuclear region. Experiments involving BcWRKY25 and BcWRKY40 confirmed the prediction. A total of 22 BcWRKYs were differentially expressed in response to at least one stress condition (abscisic acid, cold, salinity, heat, or osmosis) tested on Pak-choi leaves, and a co-expression analysis indicated stress-inducible BcWRKYs co-regulated multiple abiotic stresses. BcWRKY33, BcWRKY40, BcWRKY53, and BcWRKY70 acted as key regulators and played dominant roles within co-regulatory networks of stress-inducible BcWRKYs.

CONCLUSIONS

We first isolated and characterized the 56 stress-inducible WRKY transcription factor family members. A total of 22 stress-inducible BcWRKYs found in leaves can co-regulate multiple environmental stresses by integrating the potential mutual interactions of WRKYs in Pak-choi. This information will be valuable when exploring the molecular mechanisms of WRKYs in response to abiotic stresses in plants.

Overexpression of a chrysanthemum transcription factor gene, DgWRKY3, in tobacco enhances tolerance to salt stress

WRKY transcription factor genes (TFs) play important roles in response to various abiotic stresses. However, the roles of the chrysanthemum WRKY genes in abiotic stress response remain obscure. In this study, we functionally characterized a novel WRKY gene, DgWRKY3, from chrysanthemum (Dendranthema grandiflorum). Its expression in the chrysanthemum was up-regulated by salinity or dehydration stress, but not by abscisic acid (ABA). The DgWRKY3-overexpression tobacco plants increase salt tolerance compared with wild-type (WT) tobacco plants. The increased levels of proline were observed in transgenic plants compared to WT plants under salt stress. In addition, the DgWRKY3 transgenic plants reduced accumulation of malondialdehyde (MDA) and hydrogen peroxide (H2O2) compared with WT plants, accompanied by higher activities of antioxidant enzymes including superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX) and the greater accumulation of antioxidants including ascorbate (AsA) and glutathione (GSH) under salt stress. Moreover, the DgWRKY3 transgenic plants enhanced the expression of stress-related genes involved in osmotic adjustment and membrane protection (NtP5CS, NtLEA5, and NtERD10D) and oxidative stress response (NtSOD, NtPOD, NtCAT, and NtAPX) under salt stress. However, no significant difference in the expression of stress-related genes (NtP5CS, NtLEA5, NtERD10D, NtSOD, NtPOD, NtCAT, and NtAPX) was found between the DgWRKY3-overexpression and WT tobacco plants under normal conditions, despite the fact that the constitutive promoter was used to drive DgWRKY3. These findings suggest that DgWRKY3 functions as a positive regulator to mediate tolerance of plants to salt stress.

A wheat WRKY transcription factor TaWRKY10 confers tolerance to multiple abiotic stresses in transgenic tobacco

WRKY transcription factors are reported to be involved in defense regulation, stress response and plant growth and development. However, the precise role of WRKY transcription factors in abiotic stress tolerance is not completely understood, especially in crops. In this study, we identified and cloned 10 WRKY genes from genome of wheat (Triticum aestivum L.). TaWRKY10, a gene induced by multiple stresses, was selected for further investigation. TaWRKY10 was upregulated by treatment with polyethylene glycol, NaCl, cold and H2O2. Result of Southern blot indicates that the wheat genome contains three copies of TaWRKY10. The TaWRKY10 protein is localized in the nucleus and functions as a transcriptional activator. Overexpression of TaWRKY10 in tobacco (Nicotiana tabacum L.) resulted in enhanced drought and salt stress tolerance, mainly demonstrated by the transgenic plants exhibiting of increased germination rate, root length, survival rate, and relative water content under these stress conditions. Further investigation showed that transgenic plants also retained higher proline and soluble sugar contents, and lower reactive oxygen species and malonaldehyde contents. Moreover, overexpression of the TaWRKY10 regulated the expression of a series of stress related genes. Taken together, our results indicate that TaWRKY10 functions as a positive factor under drought and salt stresses by regulating the osmotic balance, ROS scavenging and transcription of stress related genes.