In silico based screening of WRKY genes for identifying functional genes regulated by WRKY under salt stress

Genome-wide identification and expression analysis of the WRKY gene family in Rhododendron henanense subsp. lingbaoense

Background

This work explored the characteristics of the WRKY transcription factor family in Rhododendron henanense subsp. lingbaoense (Rhl) and the expression patterns of these genes under abiotic stress by conducting bioinformatics and expression analyses.

Methods

RhlWRKY genes were identified from a gene library of Rhl. Various aspects of these genes were analyzed, including genetic structures, conserved sequences, physicochemical properties, cis-acting elements, and chromosomal location. RNA-seq was employed to analyze gene expression in five different tissues of Rhl: roots, stems, leaves, flowers, and hypocotyls. Additionally, qRT-PCR was used to detect changes in the expression of five RhlWRKY genes under abiotic stress.

Result

A total of 65 RhlWRKY genes were identified and categorized into three subfamilies based on their structural characteristics: Groups I, II, and III. Group II was further divided into five subtribes, with shared similar genetic structures and conserved motifs among members of the same subtribe. The physicochemical properties of these proteins varied, but the proteins are generally predicted to be hydrophilic. Most proteins are predicted to be in the cell nucleus, and distributed across 12 chromosomes. A total of 84 cis-acting elements were discovered, with many related to responses to biotic stress. Among the identified RhlWRKY genes, there were eight tandem duplicates and 97 segmental duplicates. The majority of duplicate gene pairs exhibited Ka/Ks values <1, indicating purification under environmental pressure. GO annotation analysis indicated that WRKY genes regulate biological processes and participate in a variety of molecular functions. Transcriptome data revealed varying expression levels of 66.15% of WRKY family genes in all five tissue types (roots, stems, leaves, flowers, and hypocotyls). Five RhlWRKY genes were selected for further characterization and there were changes in expression levels for these genes in response to various stresses.

Conclusion

The analysis identified 65 RhlWRKY genes, among which the expression of WRKY_42 and WRKY_17 were mainly modulated by the drought and MeJA, and WRKY_19 was regulated by the low-temperature and high-salinity conditions. This insight into the potential functions of certain genes contributes to understanding the growth regulatory capabilities of Rhl.

Insights into Salinity Tolerance in Wheat

Salt stress has a detrimental impact on food crop production, with its severity escalating due to both natural and man-made factors. As one of the most important food crops, wheat is susceptible to salt stress, resulting in abnormal plant growth and reduced yields; therefore, damage from salt stress should be of great concern. Additionally, the utilization of land in coastal areas warrants increased attention, given diminishing supplies of fresh water and arable land, and the escalating demand for wheat. A comprehensive understanding of the physiological and molecular changes in wheat under salt stress can offer insights into mitigating the adverse effects of salt stress on wheat. In this review, we summarized the genes and molecular mechanisms involved in ion transport, signal transduction, and enzyme and hormone regulation, in response to salt stress based on the physiological processes in wheat. Then, we surveyed the latest progress in improving the salt tolerance of wheat through breeding, exogenous applications, and microbial pathways. Breeding efficiency can be improved through a combination of gene editing and multiple omics techniques, which is the fundamental strategy for dealing with salt stress. Possible challenges and prospects in this process were also discussed.

Genome and Transcriptome Analysis of the Torreya grandis WRKY Gene Family during Seed Development

Torreya grandis, an economically significant evergreen tree species exclusive to subtropical China, is highly valued for its seeds. However, the seed development process of T. grandis remains relatively unexplored. Given the pivotal role WRKY transcription factors (TFs) play in coordinating diverse cellular and biological activities, as well as crucial signaling pathways essential for plant growth and development, and the lack of comprehensive investigation into their specific functions in T. grandis, our study investigated its genome and successfully isolated 78 WRKY genes and categorized them into three distinct clades. A conserved motif analysis unveiled the presence of the characteristic WRKY domain in each identified TgWRKY protein. The examination of gene structures revealed variable numbers of introns (ranging from zero to eight) and exons (ranging from one to nine) among TgWRKY genes. A chromosomal distribution analysis demonstrated the presence of TgWRKY across eight chromosomes in T. grandis. Tissue-specific expression profiling unveiled distinctive patterns of these 78 TgWRKY genes across various tissues. Remarkably, a co-expression analysis integrating RNA-seq data and morphological assessments pinpointed the pronounced expression of TgWRKY25 during the developmental stages of T. grandis seeds. Moreover, a KEGG enrichment analysis, focusing on genes correlated with TgWRKY25 expression, suggested its potential involvement in processes such as protein processing in the endoplasmic reticulum, starch, and sucrose metabolism, thereby modulating seed development in T. grandis. These findings not only underscore the pivotal role of WRKY genes in T. grandis seed development but also pave the way for innovative breeding strategies.

Plant salinity stress, sensing, and its mitigation through WRKY

Salinity or salt stress has deleterious effects on plant growth and development. It imposes osmotic, ionic, and secondary stresses, including oxidative stress on the plants and is responsible for the reduction of overall crop productivity and therefore challenges global food security. Plants respond to salinity, by triggering homoeostatic mechanisms that counter salt-triggered disturbances in the physiology and biochemistry of plants. This involves the activation of many signaling components such as SOS pathway, ABA pathway, and ROS and osmotic stress signaling. These biochemical responses are accompanied by transcriptional modulation of stress-responsive genes, which is mostly mediated by salt-induced transcription factor (TF) activity. Among the TFs, the multifaceted significance of WRKY proteins has been realized in many diverse avenues of plants' life including regulation of plant stress response. Therefore, in this review, we aimed to highlight the significance of salinity in a global perspective, the mechanism of salt sensing in plants, and the contribution of WRKYs in the modulation of plants' response to salinity stress. This review will be a substantial tool to investigate this problem in different perspectives, targeting WRKY and offering directions to better manage salinity stress in the field to ensure food security.

Genome-Wide Analysis of MYB Transcription Factors in the Wheat Genome and Their Roles in Salt Stress Response

Large and rapidly increasing areas of salt-affected soils are posing major challenges for the agricultural sector. Most fields used for the important food crop Triticum aestivum (wheat) are expected to be salt-affected within 50 years. To counter the associated problems, it is essential to understand the molecular mechanisms involved in salt stress responses and tolerance, thereby enabling their exploitation in the development of salt-tolerant varieties. The myeloblastosis (MYB) family of transcription factors are key regulators of responses to both biotic and abiotic stress, including salt stress. Thus, we used the Chinese spring wheat genome assembled by the International Wheat Genome Sequencing Consortium to identify putative MYB proteins (719 in total). Protein families (PFAM) analysis of the MYB sequences identified 28 combinations of 16 domains in the encoded proteins. The most common consisted of MYB_DNA-binding and MYB-DNA-bind_6 domains, and five highly conserved tryptophans were located in the aligned MYB protein sequence. Interestingly, we found and characterized a novel 5R-MYB group in the wheat genome. In silico studies showed that MYB transcription factors MYB3, MYB4, MYB13 and MYB59 are involved in salt stress responses. qPCR analysis confirmed upregulation of the expression of all these MYBs in both roots and shoots of the wheat variety BARI Gom-25 (except MYB4, which was downregulated in roots) under salt stress. Moreover, we identified nine target genes involved in salt stress that are regulated by the four MYB proteins, most of which have cellular locations and are involved in catalytic and binding activities associated with various cellular and metabolic processes.

MSALigMap-A Tool for Mapping Active-Site Amino Acids in PDB Structures onto Known and Novel Unannotated Homologous Sequences with Similar Function

MSALigMap (Multiple Sequence Alignment Ligand Mapping) is a tool for mapping active-site amino-acid residues that bind selected ligands on to target protein sequences of interest. Users can also provide novel sequences (unavailable in public databases) for analysis. MSALigMap is written in Python. There are several tools and servers available for comparing and mapping active-site amino-acid residues among protein structures. However, there has not previously been a tool for mapping ligand binding amino-acid residues onto protein sequences of interest. Using MSALigMap, users can compare multiple protein sequences, such as those from different organisms or clinical strains, with sequences of proteins with crystal structures in PDB that are bound with the ligand/drug and DNA of interest. This allows users to easily map the binding residues and to predict the consequences of different mutations observed in the binding site. The MSALigMap server can be accessed at https://albiorix.bioenv.gu.se/MSALigMap/HomePage.py.

Improved Salinity Tolerance-Associated Variables Observed in EMS Mutagenized Wheat Lines

Salinity tolerance-associated phenotypes of 35 EMS mutagenized wheat lines originating from BARI Gom-25 were compared. Vegetative growth was measured using non-destructive image-based phenotyping. Five different NaCl concentrations (0 to 160 mM) were applied to plants 19 days after planting (DAP 19), and plants were imaged daily until DAP 38. Plant growth, water use, leaf Na⁺, K⁺ and Cl⁻ content, and thousand kernel weight (TKW) were measured, and six lines were selected for further analysis. In saline conditions, leaf Na⁺, K^+, and Cl⁻ content variation on a dry weight basis within these six lines were ~9.3, 1.4, and 2.4-fold, respectively. Relative to BARI Gom-25, two (OA6, OA62) lines had greater K⁺ accumulation, three (OA6, OA10, OA62) had 50–75% lower Na⁺:K⁺ ratios, and OA62 had ~30% greater water-use index (WUI). OA23 had ~2.2-fold greater leaf Na⁺ and maintained TKW relative to BARI Gom-25. Two lines (OA25, OA52) had greater TKW than BARI Gom-25 when grown in 120 mM NaCl but similar Na⁺:K⁺, WUI, and biomass accumulation. OA6 had relatively high TKW, high leaf K^+, and WUI, and low leaf Na⁺ and Cl⁻. Phenotypic variation revealed differing associations between the parameters measured in the lines. Future identification of the genetic basis of these differences, and crossing of lines with phenotypes of interest, is expected to enable the assessment of which combinations of parameters deliver the greatest improvement in salinity tolerance.

Genome-Wide Identification and Characterization of the WRKY Gene Family in Scutellaria baicalensis Georgi under Diverse Abiotic Stress

The WRKY gene family is an important inducible regulatory factor in plants, which has been extensively studied in many model plants. It has progressively become the focus of investigation for the secondary metabolites of medicinal plants. Currently, there is no systematic analysis of the WRKY gene family in Scutellaria baicalensis Georgi. For this study, a systematic and comprehensive bioinformatics analysis of the WRKY gene family was conducted based on the genomic data of S. baicalensis. A total of 77 WRKY members were identified and 75 were mapped onto nine chromosomes, respectively. Their encoded WRKY proteins could be classified into three subfamilies: Group I, Group II (II-a, II-b, II-c, II-d, II-e), and Group III, based on the characteristics of the amino acid sequences of the WRKY domain and genetic structure. Syntenic analysis revealed that there were 35 pairs of repetitive fragments. Furthermore, the transcriptome data of roots, stems, leaves, and flowers showed that the spatial expression profiles of WRKYs were different. qRT-PCR analysis revealed that 11 stress-related WRKYs exhibited specific expression patterns under diverse treatments. In addition, sub cellular localization analysis indicated that SbWRKY26 and SbWRKY41 were localized in nucleus. This study is the first to report the identification and characterization of the WRKY gene family in S. baicalensis, which is valuable for the further exploration of the biological function of SbWRKYs. It also provides valuable bioinformatics data for S. baicalensis and provides a reference for assessing the medicinal properties of the genus.

Mutation of ZmWRKY86 confers enhanced salt stress tolerance in maize

As one of the largest families of transcription factors in plants, the WRKY proteins play crucial roles in plant growth and development, defense regulation and stress responses. In this research, ZmWRKY86 encoding a WRKY transcription factor was cloned from maize (Zea mays L.). ZmWRKY86 expression was up-regulated by salt stress. ZmWRKY86 is a nuclear protein and has no transcriptional activation ability in yeast. ZmWRKY86 can specifically bind to W-box (TTGACC), which was confirmed by electrophoretic mobility shift assay (EMSA) and dual-LUC experiments. As compared with control, the wrky86 mutants showed enhanced plant tolerance to salt stress with higher survival rate, catalase activity and K⁺ content, but lower malondialdehyde accumulation, relative electrical leakage level and Na⁺ content under salt-stress condition. Transcriptome and quantitative real-time PCR analyses indicated that the mutation of ZmWRKY86 led to significant changes in the expression of stress-related genes in maize. Further assays showed that ZmWRKY86 directly interacted with the promoter of two salt stress-related genes Zm00001d020840 and Zm00001d046813. In summary, we identified a WRKY transcription factor ZmWRKY86 that participates in salt stress regulation through controlling the expression of stress-related genes.

Wheat (Triticum aestivum L.) TaHMW1D Transcript Variants Are Highly Expressed in Response to Heat Stress and in Grains Located in Distal Part of the Spike

High-temperature stress during the grain filling stage has a deleterious effect on grain yield and end-use quality. Plants undergo various transcriptional events of protein complexity as defensive responses to various stressors. The "Keumgang" wheat cultivar was subjected to high-temperature stress for 6 and 10 days beginning 9 days after anthesis, then two-dimensional gel electrophoresis (2DE) and peptide analyses were performed. Spots showing decreased contents in stressed plants were shown to have strong similarities with a high-molecular glutenin gene, TraesCS1D02G317301 (TaHMW1D). QRT-PCR results confirmed that TaHMW1D was expressed in its full form and in the form of four different transcript variants. These events always occurred between repetitive regions at specific deletion sites (5'-CAA (Glutamine) GG/TG (Glycine) or (Valine)-3', 5'-GGG (Glycine) CAA (Glutamine) -3') in an exonic region. Heat stress led to a significant increase in the expression of the transcript variants. This was most evident in the distal parts of the spike. Considering the importance of high-molecular weight glutenin subunits of seed storage proteins, stressed plants might choose shorter polypeptides while retaining glutenin function, thus maintaining the expression of glutenin motifs and conserved sites.

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.

Transcriptome analysis provides insights into the mechanisms underlying wheat cultivar Shumai126 responding to stripe rust

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a destructive fungal disease of wheat globally. Breeding resistance cultivars is one of the most cost-effective methods to control Pst. Shumai126 (SM126), a high-yielding commercial wheat cultivar, showed strong stripe rust resistance for more than ten years. However, the molecular mechanisms and the responsive genes underlying the SM126 resistance to Pst have not been explored yet. In the present study, RNA-seq was used to analyze changes in the transcriptome at different time points of Pst infection in seedling leaves of SM126. In total, 520, 148 and 1439 differentially expressed genes (DEGs) were found to be up- or down-regulated after Pst infection at 1, 3, and 7 days post inoculation, respectively. The majority of DEGs exhibited transient expression patterns during Pst infection at different time points. GO and KEGG enrichment analysis revealed that many biological processes, such as photosynthesis, flavonoid biosynthesis, oxidative phosphorylation, MAPK signaling pathway, and phenylalanine metabolism are involved in SM126 response to Pst. Expression of genes involved in the plant-pathogen interaction pathway was detected and some key genes showed differential expression. DEGs encoded R proteins and transcription factors were also identified. Our study suggests the gene resources in SM126 related to stripe rust response could be valuable for understanding the mechanisms involved in stripe rust resistance and improvement of wheat resistance to Pst.

Genome-wide Identification of WRKY transcription factor family members in sorghum (Sorghum bicolor (L.) moench)

WRKY transcription factors regulate diverse biological processes in plants, including abiotic and biotic stress responses, and constitute one of the largest transcription factor families in higher plants. Although the past decade has seen significant progress towards identifying and functionally characterizing WRKY genes in diverse species, little is known about the WRKY family in sorghum (Sorghum bicolor (L.) moench). Here we report the comprehensive identification of 94 putative WRKY transcription factors (SbWRKYs). The SbWRKYs were divided into three groups (I, II, and III), with those in group II further classified into five subgroups (IIa–IIe), based on their conserved domains and zinc finger motif types. WRKYs from the model plant Arabidopsis (Arabidopsis thaliana) were used for the phylogenetic analysis of all SbWRKY genes. Motif analysis showed that all SbWRKYs contained either one or two WRKY domains and that SbWRKYs within the same group had similar motif compositions. SbWRKY genes were located on all 10 sorghum chromosomes, and some gene clusters and two tandem duplications were detected. SbWRKY gene structure analysis showed that they contained 0–7 introns, with most SbWRKY genes consisting of two introns and three exons. Gene ontology (GO) annotation functionally categorized SbWRKYs under cellular components, molecular functions and biological processes. A cis-element analysis showed that all SbWRKYs contain at least one stress response-related cis-element. We exploited publicly available microarray datasets to analyze the expression profiles of 78 SbWRKY genes at different growth stages and in different tissues. The induction of SbWRKYs by different abiotic stresses hinted at their potential involvement in stress responses. qRT-PCR analysis revealed different expression patterns for SbWRKYs during drought stress. Functionally characterized WRKY genes in Arabidopsis and other species will provide clues for the functional characterization of putative orthologs in sorghum. Thus, the present study delivers a solid foundation for future functional studies of SbWRKY genes and their roles in the response to critical stresses such as drought.