Structural basis for sequence-specific DNA recognition by an Arabidopsis WRKY transcription factor

Unravelling the role of WRKY transcription factors in leaf senescence: Genetic and molecular insights

BACKGROUND

Leaf senescence (LS), the final phase in leaf development, is an important and precisely regulated process crucial for plant well-being and the redistribution of nutrients. It is intricately controlled by various regulatory factors, including WRKY transcription factors (TFs). WRKYs are one of the most significant plant TF families, and several of them are differentially regulated and important during LS. Recent research has enhanced our understanding of the structural and functional characteristics of WRKY TFs, providing insights into their regulatory roles.

AIM OF REVIEW

This review aims to elucidate the genetic and molecular mechanisms underlying the intricate regulatory networks associated with LS by investigating the role of WRKY TFs. We seek to highlight the importance of WRKY-mediated signaling pathways in understanding LS, plant evolution, and response to varying environmental conditions.

KEY SCIENTIFIC CONCEPTS OF REVIEW

WRKY TFs exhibit specific DNA-binding activity at the N-terminus and dynamic interactions of the intrinsically disordered domain at the C-terminus with various proteins. These WRKY TFs not only control the activity of other WRKYs, but also interact with either WRKYs or other TFs, thereby fine- tuning the expression of target genes. By unraveling the complex interactions and regulatory mechanisms of WRKY TFs, this review broadens our knowledge of the genetic and molecular basis of LS. Understanding WRKY-mediated signalling pathways provides crucial insights into specific aspects of plant development, such as stress-induced senescence, and offers potential strategies for improving crop resilience to environmental stresses like drought and pathogen attacks. By targeting these pathways, it may be possible to enhance specific productivity traits, such as increased yield stability under adverse conditions, thereby contributing to more reliable agricultural outputs.

Structural basis for the regulation of plant transcription factor WRKY33 by the VQ protein SIB1

The WRKY transcription factors play essential roles in a variety of plant signaling pathways associated with biotic and abiotic stress response. The transcriptional activity of many WRKY members are regulated by a class of intrinsically disordered VQ proteins. While it is known that VQ proteins interact with the WRKY DNA-binding domains (DBDs), also termed as the WRKY domains, structural information regarding VQ-WRKY interaction is lacking and the regulation mechanism remains unknown. Herein we report a solution NMR study of the interaction between Arabidopsis WRKY33 and its regulatory VQ protein partner SIB1. We uncover a SIB1 minimal sequence neccessary for forming a stable complex with WRKY33 DBD, which comprises not only the consensus "FxxhVQxhTG" VQ motif but also its preceding region. We demonstrate that the βN-strand and the extended βN-β1 loop of WRKY33 DBD form the SIB1 docking site, and build a structural model of the complex based on the NMR paramagnetic relaxation enhancement and mutagenesis data. Based on this model, we further identify a cluster of positively-charged residues in the N-terminal region of SIB1 to be essential for the formation of a SIB1-WRKY33-DNA ternary complex. These results provide a framework for the mechanism of SIB1-enhanced WRKY33 transcriptional activity.

Review: Structural-functional relationship of WRKY transcription factors: Unfolding the role of WRKY in plants

WRKY as the name suggests, are the transcription factors (TFs) that contain the signature WRKY domains, hence named after it. Since their discovery in 1994, they have been well studied in plants with exploration of approximately 74 WRKY genes in the model plant, Arabidopsis alone. However, the study of these transcription factors (TFs) is not just limited to model plant now. They have been studied widely in crop plants as well, because of their tremendous contribution in stress as well as in growth and development. Here, in this review, we describe the story of WRKY TFs from their identification to their origin, the binding mechanisms, structure and their contribution in regulating plant development and stress physiology. High throughput transcriptomics-based data also opened a doorway to understand the comprehensive and detailed functioning of WRKY TFs in plants. Indeed, the detailed functional role of each and every WRKY member in regulating the gene expression is required to pave the path to develop holistic understanding of their role in stress physiology and developmental processes in plants.

Genomic characterization of WRKY transcription factors related to secoiridoid biosynthesis in Gentiana macrophylla

Gentiana macrophylla is one of Chinese herbal medicines in which 4 kinds of iridoids or secoiridoids, such as loganic acid, sweroside, swertiamarin, and gentiopicroside, are identified as the dominant medicinal secondary metabolites. WRKY, as a large family of transcription factors (TFs), plays an important role in the synthesis of secondary metabolites in plants. Therefore, WRKY genes involved in the biosynthesis of secoiridoids in G. macrophylla were systematically studied. First, a comprehensive genome-wide analysis was performed, and 42 GmWRKY genes were identified, which were unevenly distributed in 12 chromosomes. Accordingly, gene structure, collinearity, sequence alignment, phylogenetic, conserved motif and promoter analyses were performed, and the GmWRKY proteins were divided into three subfamilies based on phylogenetic and multiple sequence alignment analyses. Moreover, the enzyme-encoding genes of the secoiridoid biosynthesis pathway and their promoters were then analysed, and the contents of the four secoiridoids were determined in different tissues. Accordingly, correlation analysis was performed using Pearson's correlation coefficient to construct WRKY gene-enzyme-encoding genes and WRKY gene-metabolite networks. Meanwhile, G. macrophylla seedlings were treated with methyl jasmonate (MeJA) to detect the dynamic change trend of GmWRKYs, biosynthetic genes, and medicinal ingredient accumulation. Thus, a total of 12 GmWRKYs were identified to be involved in the biosynthesis of secoiridoids, of which 8 (GmWRKY1, 6, 12, 17, 33, 34, 38 and 39) were found to regulate the synthesis of gentiopicroside, and 4 (GmWRKY7, 14, 26 and 41) were found to regulate the synthesis of loganic acid. Taken together, this study systematically identified WRKY transcription factors related to the biosynthesis of secoiridoids in G. macrophylla, which could be used as a cue for further investigation of WRKY gene functions in secondary metabolite accumulation.

Multifaceted roles of WRKY transcription factors in abiotic stress and flavonoid biosynthesis

Increasing biotic and abiotic stresses are seriously impeding the growth and yield of staple crops and threatening global food security. As one of the largest classes of regulators in vascular plants, WRKY transcription factors play critical roles governing flavonoid biosynthesis during stress responses. By binding major W-box cis-elements (TGACCA/T) in target promoters, WRKYs modulate diverse signaling pathways. In this review, we optimized existing WRKY phylogenetic trees by incorporating additional plant species with WRKY proteins implicated in stress tolerance and flavonoid regulation. Based on the improved frameworks and documented results, we aim to deduce unifying themes of distinct WRKY subfamilies governing specific stress responses and flavonoid metabolism. These analyses will generate experimentally testable hypotheses regarding the putative functions of uncharacterized WRKY homologs in tuning flavonoid accumulation to enhance stress resilience.

KaScape: a sequencing-based method for global characterization of protein‒DNA binding affinity

It is difficult to exhaustively screen all possible DNA binding sequences for a given transcription factor (TF). Here, we developed the KaScape method, in which TFs bind to all possible DNA sequences in the same DNA pool where DNA sequences are prepared by randomized oligo synthesis and the random length can be adjusted to a length such as 4, 5, 6, or 7. After separating bound from unbound double-stranded DNAs (dsDNAs), their sequences are determined by next-generation sequencing. To demonstrate the relative binding affinities of all possible DNA sequences determined by KaScape, we developed three-dimensional KaScape viewing software based on a K-mer graph. We applied KaScape to 12 plant TF family AtWRKY proteins and found that all AtWRKY proteins bound to the core sequence GAC with similar profiles. KaScape can detect not only binding sequences consistent with the consensus W-box "TTGAC(C/T)" but also other sequences with weak affinity. KaScape provides a high-throughput, easy-to-operate, sensitive, and exhaustive method for quantitatively characterizing the relative binding strength of a TF with all possible binding sequences, allowing us to comprehensively characterize the specificity and affinity landscape of transcription factors, particularly for moderate- and low-affinity binding sites.

Binding of stress-responsive OsWRKY proteins through WRKYGQK heptapeptide residue with the promoter region of two rice blast disease resistance genes Pi2 and Pi54 is important for development of blast resistance

Molecular docking was done to investigate the interactions between five differentially expressed rice WRKY proteins when challenged with the rice blast disease caused by Magnaporthe oryzae and drought stresses applied either individually or overlapped, with the promoter region of two blast resistance genes (Pi2 and Pi54). Molecular docking was performed using the HDOCK server. Initially, the homology models for each of the five rice WRKY proteins were prepared using I-TASSER server, and then the secondary structure as well as the DNA-binding pockets were predicted using PSIPRED and BindUP servers, respectively. The molecular docking study revealed a differential binding pattern of the rice WRKYs with the two blast resistance genes. The WRKY proteins (OsWRKY88 and OsWRKY102), whose transcript levels decrease when drought and blast stresses are overlapped, interact with the two resistance genes mostly involving the residues of the zinc finger structure. On the other hand, the WRKY proteins (OsWRKY53-1 and OsWRKY113), whose transcript levels did not reduce significantly when challenged by drought and blast overlapped condition compared to individual treatment of blast, interact mostly involving the residues of the conserved WRKYGQK heptapeptide sequence. Interestingly, the protein OsWRKY74 whose transcript levels are unaffected in both individual and overlapped stresses, interacts with both the blast resistance genes involving few residues of both WRKYGQK heptapeptide and the zinc finger structure. The findings thus indicate that the interaction of OsWRKY proteins involving the conserved WRKYGQK heptapeptide sequence with the blast resistance genes Pi2 and Pi54 is important to mitigate the blast challenge in rice even during overlapping challenges of drought.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03711-y.

Genome-Wide Identification and Analysis of the WRKY Gene Family in Asparagus officinalis

In recent years, the related research of the WRKY gene family has been gradually promoted, which is mainly reflected in the aspects of environmental stress and hormone response. However, to make the study of the WRKY gene family more complete, we also need to focus on the whole-genome analysis and identification of the family. In previous studies, the whole WRKY gene family of Arabidopsis, legumes and other plants has been thoroughly studied. However, since the publication of Asparagus officinalis genome-wide data, there has never been an analysis of the whole WRKY gene family. To understand more broadly the function of the WRKY gene family, the whole genome and salt stress transcriptome data of asparagus were used for comprehensive analysis in this study, including WRKY gene family identification, phylogenetic tree construction, analysis of conserved mods and gene domains, extraction of cis-acting elements, intron/exon analysis, species collinearity analysis, and WRKY expression analysis under salt stress. The results showed that a total of 70 genes were selected and randomly distributed on 10 chromosomes and one undefined chromosome. According to the functional classification of Arabidopsis thaliana, the WRKY family of asparagus was divided into 11 subgroups (C1-C9, U1, U2). It is worth considering that the distribution rules of gene-conserved motifs, gene domains and introns/exons in the same subfamily are similar, which suggests that genes in the same subfamily may regulate similar physiological processes. In this study, 11 cis-acting elements of WRKY family were selected, among which auxin, gibberellin, abscisic acid, salicylic acid and other hormone-regulated induction elements were involved. In addition, environmental stress (such as drought stress and low-temperature response) also accounted for a large proportion. Interestingly, we analyzed a total of two tandem duplicate genes and 13 segmental duplication genes, suggesting that this is related to the amplification of the WRKY gene family. Transcriptome data analysis showed that WRKY family genes could regulate plant growth and development by up-regulating and down-regulating gene expression under salt stress. Volcanic maps showed that 3 and 15 AoWRKY genes were significantly up-regulated or down-regulated in NI&NI+S and AMF&AMF+S, respectively. These results provide a new way to analyze the evolution and function of the WRKY gene family, and can provide a reference for the production and research of asparagus.

Rice WRKY13 TF protein binds to motifs in the promoter region to regulate downstream disease resistance-related genes

In plants, pathogen resistance is brought about by the binding of certain transcription factor (TF) proteins to the cis-elements of certain target genes. These cis-elements are present upstream in the motif of the promoters of each gene. This ensures the binding of a specific TF to a specific promoter, therefore regulating the expression of that gene. Therefore, the study of each promoter sequence of all the rice genes would help identify the target genes of a specific TF. Rice 1 kb upstream promoter sequences of 55,986 annotated genes were analyzed using the Perl program algorithm to detect WRKY13 binding motifs (bm). The resulting genes were grouped using Gene Ontology and gene set enrichment analysis. A gene with more than 4 TF bm in their promoter was selected. Ten genes reported to have a role in rice disease resistance were selected for further analysis. Cis-acting regulatory element analysis was carried out to find the cis-elements and confirm the presence of the corresponding motifs in the promoter sequences of these genes. The 3D structure of WRKY13 TF and the corresponding ten genes were built, and the interacting residues were determined. The binding capacity of WRKY13 to the promoter of these selected genes was analyzed using docking studies. WRKY13 was considered for docking analysis based on the prior reports of autoregulation. Molecular dynamic simulations provided more details regarding the interactions. Expression data revealed the expression of the genes that helped provide the mechanism of interaction. Further co-expression network helped to characterize the interaction of these selected disease resistance-related genes with the WRKY13 TF protein. This study suggests downstream target genes that are regulated by the WRKY13 TF. The molecular mechanism involving the gene network regulated by WRKY13 TF in disease resistance against rice fungal pathogens is explored.

Structural basis of DNA binding by the NAC transcription factor ORE1, a master regulator of plant senescence

Plants use sophisticated mechanisms of gene expression to control senescence in response to environmental stress or aging. ORE1 (Arabidopsis thaliana NAC092) is a master regulator of senescence that belongs to the plant-specific NAC transcription factor protein family. ORE1 has been reported to bind to multiple DNA targets to orchestrate leaf senescence, yet the mechanistic basis for recognition of the cognate gene sequence remains unclear. Here, we report the crystal structure of the ORE1-NAC domain alone and its DNA-binding form. The structure of DNA-bound ORE1-NAC revealed the molecular basis for nucleobase recognition and phosphate backbone interactions. We show that local versatility in the DNA-binding site, in combination with domain flexibility of the ORE-NAC homodimer, is crucial for the maintenance of binding to intrinsically flexible DNA. Our results provide a platform for understanding other plant-specific NAC protein-DNA interactions as well as insight into the structural basis of NAC regulators in plants of agronomic and scientific importance.

The Role of Plant Transcription Factors in the Fight against Plant Viruses

Plants are vulnerable to the challenges of unstable environments and pathogen infections due to their immobility. Among various stress conditions, viral infection is a major threat that causes significant crop loss. In response to viral infection, plants undergo complex molecular and physiological changes, which trigger defense and morphogenic pathways. Transcription factors (TFs), and their interactions with cofactors and cis-regulatory genomic elements, are essential for plant defense mechanisms. The transcriptional regulation by TFs is crucial in establishing plant defense and associated activities during viral infections. Therefore, identifying and characterizing the critical genes involved in the responses of plants against virus stress is essential for the development of transgenic plants that exhibit enhanced tolerance or resistance. This article reviews the current understanding of the transcriptional control of plant defenses, with a special focus on NAC, MYB, WRKY, bZIP, and AP2/ERF TFs. The review provides an update on the latest advances in understanding how plant TFs regulate defense genes expression during viral infection.

Single-cytosine methylation at W-boxes repels binding of WRKY transcription factors through steric hindrance

DNA methylation is an epigenetic mark that fine-tunes gene expression, notably by negatively or positively regulating transcription factor (TF)-DNA binding. In plants, DNA methylation has primarily been shown to inhibit TF-DNA binding. However, little is known about the underlying mechanisms. Here, we show that DNA methylation decreases the binding of several Arabidopsis (Arabidopsis thaliana) WRKY TFs to their genomic regions and their binding sites in vitro. We also provide evidence that DNA methylation at a single cytosine located in a functional core W-box motif repels DNA binding of AtWRKY40 in vitro. Using structural modelling, we further demonstrate that this cytosine interacts through van der Waals contacts with the conserved tyrosine of WRKY-DNA binding domains. Importantly, our model predicts steric hindrance when a 5-methyl group is present on this specific cytosine, thereby likely preventing tight binding of WRKY-DNA binding domains. Finally, because the WRKY motif and the residues involved in DNA contacts are conserved across Arabidopsis and rice (Oryza sativa) WRKY TFs, we propose that this methylation-dependent WRKY-DNA binding inhibitory mechanism could be widespread across plant species.

Solution structure of the DNA binding domain of Arabidopsis transcription factor WRKY11

The Arabidopsis WRKY11 (AtWRKY11) protein is an important transcription factor involved in plant response to biotic and abiotic stresses. Its DNA-binding domain specifically binds to gene promoter regions harboring the W-box consensus motif. Herein we report the high-resolution structure of the AtWRKY11 DNA-binding domain (DBD) determined by solution NMR spectroscopy. The results show that AtWRKY11-DBD adopts an all-β fold comprising five β-strands packed in an antiparallel topology, stabilized by a zinc-finger motif. Structural comparison reveals that the long β₁-β₂ loop shows the highest structural variation from other available WRKY domain structures. Moreover, this loop was further found to contribute to the binding between AtWRKY11-DBD and W-box DNA. Our current study provides atomic-level structural basis for further understanding the structure-function relationship of plant WRKY proteins.

Overexpression of ClWRKY48 from Cunninghamia lanceolata improves Arabidopsis phosphate uptake

Our findings suggested that ClWRKY48 promoted the expression level of Arabidopsis phosphate transporter genes, enhanced phosphate uptake, and delayed the transition from the vegetative stage to the reproductive phase in Arabidopsis. Phosphorus (P) is an essential mineral for plants that influences their growth and development. ClWRKY48, one of the most highly expressed genes in the leaf, was identified by RT-PCR from Chinese fir [Cunninghamia lanceolata (Lamb.) Hook] (C. lanceolata). Furthermore, when treating C. lanceolata with increasing phosphate (Pi) concentration, the expression level of ClWRKY48 rose in leaves, the trends followed the increasing phosphate concentration treatment. ClWRKY48 is a transcription factor in C. lanceolata, according to the results of a yeast one hybridization experiment. Based on subcellular localization studies, ClWRKY48 is a nuclear-localized protein. Under Pi deficiency conditions, the phosphorus concentration of ClWRKY48 overexpressing Arabidopsis increased by 43.2-51.1% compared to the wild-type. Moreover, under Pi limiting conditions, the phosphate transporter genes AtPHT1;1 (Arabidopsis Phosphate transporter 1;1), AtPHT1;4, and AtPHO1 (Arabidopsis PHOSPHATE 1) were expressed 2.1-2.5, 2.2-2.7, and 6.7-7.3-fold greater than the wild-type in ClWRKY48 transgenic Arabidopsis, respectively. Under Pi-sufficient conditions, the phosphorus concentration and phosphate transporter genes of ClWRKY48 overexpression in Arabidopsis are not significantly different from the wild type. These findings indicated that ClWRKY48 increased phosphate absorption in transgenic Arabidopsis. Furthermore, compared to the wild type, the ClWRKY48 transgenic Arabidopsis not only had a delayed flowering time characteristic but also had lower expression of flowering-related genes AtFT (FLOWERING LOCUS T), AtFUL (FRUITFUL), and AtTSF (TWIN SISTER OF FT). Our findings show that ClWRKY48 enhances phosphate absorption and slows the transition from the vegetative to the reproductive stage in ClWRKY48 transgenic Arabidopsis.

Genome-Wide Analysis of WRKY Gene Family and Negative Regulation of GhWRKY25 and GhWRKY33 Reveal Their Role in Whitefly and Drought Stress Tolerance in Cotton

The WRKY transcription factor family is marked by its significant responsiveness to both biotic and abiotic plant stresses. In the present study, the WRKY family of Gossypium hirsutum has been identified and classified into three groups based on the number of conserved WRKY domains and the type of zinc finger motif. This classification is further validated by conserved domain and phylogenetic analysis. Two members of the WRKY family, WRKY25 and WRKY33, have been targeted through VIGS in G. hirsutum. VIGS-infiltrated plants were evaluated under drought stress and whitefly infestation. It was observed that GhWRKY33-downregulated plants showed a decrease in whitefly egg and nymph population, and GhWRKY33 was found to be a strong negative regulator of whitefly and drought stress, while GhWRKY25 was found to be a moderate negative regulator of whitefly and drought stress. As the targeted genes are transcription factors influencing the expression of other genes, the relative expression of other stress-responsive genes, namely MPK6, WRKY40, HSP, ERF1, and JAZ1, was also analyzed through qRT-PCR. It was found elevated in GhWRKY33-downregulated plants, while GhWRKY25-downregulated plants through VIGS showed the elevated expression of ERF1 and WRKY40, a slightly increased expression of HSP, and a lower expression level of MPK6. Overall, this study provides an important insight into the WRKY TF family and the role of two WRKY TFs in G. hirsutum under drought stress and whitefly infestation. The findings will help to develop crops resilient to drought and whitefly stress.

A systematical genome-wide analysis and screening of WRKY transcription factor family engaged in abiotic stress response in sweetpotato

BACKGROUND

WRKY transcription factors play pivotal roles in regulating plant multiple abiotic stress tolerance, however, a genome-wide systematical analysis of WRKY genes in sweetpotato is still missing.

RESULTS

Herein, 84 putative IbWRKYs with WRKY element sequence variants were identified in sweetpotato reference genomes. Fragment duplications, rather than tandem duplications, were shown to play prominent roles in IbWRKY gene expansion. The collinearity analysis between IbWRKYs and the related orthologs from other plants further depicted evolutionary insights into IbWRKYs. Phylogenetic relationships displayed that IbWRKYs were divided into three main groups (I, II and III), with the support of the characteristics of exon-intron structures and conserved protein motifs. The IbWRKY genes, mainly from the group Ib, displayed remarkable and diverse expression profiles under multiple abiotic stress (NaCl, PEG6000, cold and heat) and hormone (ABA, ACC, JA and SA) treatments, which were determined by RNA-seq and qRT-PCR assays, suggesting their potential roles in mediating particular stress responses. Moreover, IbWRKY58L could interact with IbWRKY82 as revealed by yeast two-hybrid based on the protein interaction network screening. And abiotic stress-remarkably induced IbWRKY21L and IbWRKY51 were shown to be localized in the nucleus and had no transactivation activities.

CONCLUSION

These results provide valuable insights into sweetpotato IbWRKYs and will lay a foundation for further exploring functions and possible regulatory mechanisms of IbWRKYs in abiotic stress tolerance.

Genome-Wide Identification of the Hypericum perforatum WRKY Gene Family Implicates HpWRKY85 in Drought Resistance

WRKY, named for its special heptapeptide conserved sequence WRKYGOK, is one of the largest transcription factor families in plants and is widely involved in plant responses to biotic, abiotic, and hormonal stresses, especially the important regulatory function in response to drought stress. However, there is no complete comprehensive analysis of this family in H. perforatum, which is one of the most extensively studied plants and is probably the best-known herbal medicine on the market today, serving as an antidepressant, neuroprotective, an antineuralgic, and an antiviral. Here, we identified 86 HpWRKY genes according to the whole genome database of H. perforatum, and classified them into three groups through phylogenetic analysis. Gene structure, conserved domain, motif, cis-elements, gene ontology, and expression profiling were performed. Furthermore, it was found that HpWRKY85, a homologous gene of AtWRKY75, showed obvious responses to drought treatment. Subcellular localization analysis indicated that this protein was localized in the nucleus by the Arabidopsis protoplasts transient transfection. Meanwhile, HpWRKY85-overexpressing Arabidopsis plants showed a stronger ability of root growth and scavenging endogenous reactive oxygen species. The results provide a reference for further understanding the role of HpWRKY85 in the molecular mechanism of drought resistance of H. perforatum.

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.

New aspects of DNA recognition by group II WRKY transcription factor revealed by structural and functional study of AtWRKY18 DNA binding domain

WRKY transcription factors (TFs) constitute one of the largest families of plant TFs. Based on the organization of domains and motifs, WRKY TFs are divided into three Groups (I-III). The WRKY subgroup IIa includes three representatives in A. thaliana, AtWRKY18, AtWRKY40, and AtWRKY60, that participate in biotic and abiotic stress responses. Here we present crystal structures of the DNA binding domain (DBD) of AtWRKY18 alone and in the complex with a DNA duplex containing the WRKY-recognition sequence, W-box. Subgroup IIa WRKY TFs are known to form homo and heterodimers. Our data suggest that the dimerization interface of the full-length AtWRKY18 involves contacts between the DBD subunits. DNA binding experiments and structural analysis point out novel aspects of DNA recognition by WRKY TFs. In particular, AtWRKY18-DBD preferentially binds an overlapping tandem of W-boxes accompanied by a quasi-W-box motif. The binding of DNA deforms the B-type double helix, which suggests that the DNA fragment must be prone to form a specific structure. This can explain why despite the short W-box consensus, WRKY TFs can precisely control gene expression. Finally, this first experimental structure of a Group II WRKY TF allowed us to compare Group I-III representatives.

Insight into the Phylogeny and Binding Ability of WRKY Transcription Factors

WRKY transcription factors (TFs), which make up one of the largest families of TFs in the plant kingdom, are key players in modulating gene expression relating to embryogenesis, senescence, pathogen resistance, and abiotic stress responses. However, the phylogeny and grouping of WRKY TFs and how their binding ability is affected by the flanking regions of W-box sequences remain unclear. In this study, we reconstructed the phylogeny of WRKY across the plant kingdom and characterized the DNA-binding profile of Arabidopsis thaliana WRKY (WRKY54) based on its W-box recognition sequence. We found that WRKY TFs could be separated into five clades, and that the functional zinc-finger motif at the C-terminal of WRKY appeared after several nucleotide substitutions had occurred at the 3′-end of the zinc-finger region in chlorophytes. In addition, we found that W-box flanking regions affect the binding ability of WRKY54 based on the results of a fluorescence-based electrophoretic mobility shift assay (fEMSA) and quartz crystal microbalance (QCM) analysis. The great abundance of WRKY TFs in plants implicates their involvement in diverse molecular regulatory networks, and the flanking regions of W-box sequences may contribute to their molecular recognition mechanism. This phylogeny and our findings on the molecular recognition mechanism of WRKY TFs should be helpful for further research in this area.

The small GTPase NtRHO1 negatively regulates tobacco defense response to tobacco mosaic virus by interacting with NtWRKY50

Small GTPases play critical roles in the regulation of plant growth and development. However, the mechanism of action of small GTPases in plant response to virus infection remains largely unknown. Here, the gene encoding a Rho-type GTPase, NtRHO1, was identified as one of the genes up-regulated after tobacco mosaic virus (TMV) infection. Subcellular localization of NtRHO1 showed that it was located in the cytoplasm, plasma membrane, and nucleus. Transient overexpression of NtRHO1 in Nicotiana benthamiana accelerated TMV reproduction and led to the production of reactive oxygen species. By contrast, silencing of NtRHO1 reduced the sensitivity of N. benthamiana to TMV-GFP. Further exploration revealed a direct interaction between NtRHO1 and NtWRKY50, a positive regulator of the N. benthamiana response to virus infection. Yeast one-hybrid and electrophoretic mobility shift assays showed that this regulation was related to the capacity of NtWRKY50 to bind to the WK-box of the PR1 promoter, which was weakened by the interaction between NtRHO1 and NtWRKY50. Thus, our results indicate that the small GTPase NtRHO1 plays a negative role in tobacco response to TMV infection by interacting with transcription factor NtWRKY50, resulting in reduced plant immunity.

Perception of structurally distinct effectors by the integrated WRKY domain of a plant immune receptor

Plants use intracellular nucleotide-binding domain (NBD) and leucine-rich repeat (LRR)-containing immune receptors (NLRs) to detect pathogen-derived effector proteins. The Arabidopsis NLR pair RRS1-R/RPS4 confers disease resistance to different bacterial pathogens by perceiving the structurally distinct effectors AvrRps4 from Pseudomonas syringae pv. pisi and PopP2 from Ralstonia solanacearum via an integrated WRKY domain in RRS1-R. How the WRKY domain of RRS1 (RRS1WRKY) perceives distinct classes of effector to initiate an immune response is unknown. Here, we report the crystal structure of the in planta processed C-terminal domain of AvrRps4 (AvrRps4C) in complex with RRS1WRKY Perception of AvrRps4C by RRS1WRKY is mediated by the β2-β3 segment of RRS1WRKY that binds an electronegative patch on the surface of AvrRps4C Structure-based mutations that disrupt AvrRps4C-RRS1WRKY interactions in vitro compromise RRS1/RPS4-dependent immune responses. We also show that AvrRps4C can associate with the WRKY domain of the related but distinct RRS1B/RPS4B NLR pair, and the DNA-binding domain of AtWRKY41, with similar binding affinities and how effector binding interferes with WRKY-W-box DNA interactions. This work demonstrates how integrated domains in plant NLRs can directly bind structurally distinct effectors to initiate immunity.

Transcription Factors in Alkaloid Engineering

Plants produce a large variety of low-molecular-weight and specialized secondary compounds. Among them, nitrogen-containing alkaloids are the most biologically active and are often used in the pharmaceutical industry. Although alkaloid chemistry has been intensively investigated, characterization of alkaloid biosynthesis, including biosynthetic enzyme genes and their regulation, especially the transcription factors involved, has been relatively delayed, since only a limited number of plant species produce these specific types of alkaloids in a tissue/cell-specific or developmental-specific manner. Recent advances in molecular biology technologies, such as RNA sequencing, co-expression analysis of transcripts and metabolites, and functional characterization of genes using recombinant technology and cutting-edge technology for metabolite identification, have enabled a more detailed characterization of alkaloid pathways. Thus, transcriptional regulation of alkaloid biosynthesis by transcription factors, such as basic helix-loop-helix (bHLH), APETALA2/ethylene-responsive factor (AP2/ERF), and WRKY, is well elucidated. In addition, jasmonate signaling, an important cue in alkaloid biosynthesis, and its cascade, interaction of transcription factors, and post-transcriptional regulation are also characterized and show cell/tissue-specific or developmental regulation. Furthermore, current sequencing technology provides more information on the genome structure of alkaloid-producing plants with large and complex genomes, for genome-wide characterization. Based on the latest information, we discuss the application of transcription factors in alkaloid engineering.

WRKY Transcription Factor Response to High-Temperature Stress

Plant growth and development are closely related to the environment, and high-temperature stress is an important environmental factor that affects these processes. WRKY transcription factors (TFs) play important roles in plant responses to high-temperature stress. WRKY TFs can bind to the W-box cis-acting elements of target gene promoters, thereby regulating the expression of multiple types of target genes and participating in multiple signaling pathways in plants. A number of studies have shown the important biological functions and working mechanisms of WRKY TFs in plant responses to high temperature. However, there are few reviews that summarize the research progress on this topic. To fully understand the role of WRKY TFs in the response to high temperature, this paper reviews the structure and regulatory mechanism of WRKY TFs, as well as the related signaling pathways that regulate plant growth under high-temperature stress, which have been described in recent years, and this paper provides references for the further exploration of the molecular mechanisms underlying plant tolerance to high temperature.

Genome-Wide Profiling of WRKY Genes Involved in Benzylisoquinoline Alkaloid Biosynthesis in California Poppy (Eschscholzia californica)

Transcription factors of the WRKY family play pivotal roles in plant defense responses, including the biosynthesis of specialized metabolites. Based on the previous findings of WRKY proteins regulating benzylisoquinoline alkaloid (BIA) biosynthesis, such as CjWRKY1-a regulator of berberine biosynthesis in Coptis japonica-and PsWRKY1-a regulator of morphine biosynthesis in Papaver somniferum-we performed genome-wide characterization of the WRKY gene family in Eschscholzia californica (California poppy), which produces various BIAs. Fifty WRKY genes were identified by homology search and classified into three groups based on phylogenetic, gene structure, and conserved motif analyses. RNA sequencing showed that several EcWRKY genes transiently responded to methyl jasmonate, a known alkaloid inducer, and the expression patterns of these EcWRKY genes were rather similar to those of BIA biosynthetic enzyme genes. Furthermore, tissue expression profiling suggested the involvement of a few subgroup IIc EcWRKYs in the regulation of BIA biosynthesis. Transactivation analysis using luciferase reporter genes harboring the promoters of biosynthetic enzyme genes indicated little activity of subgroup IIc EcWRKYs, suggesting that the transcriptional network of BIA biosynthesis constitutes multiple members. Finally, we investigated the coexpression patterns of EcWRKYs with some transporter genes and discussed the diversified functions of WRKY genes based on a previous finding that CjWRKY1 overexpression in California poppy cells enhanced BIA secretion into the medium.

Evolutionarily conserved hierarchical gene regulatory networks for plant salt stress response

Plant cells constantly alter their gene expression profiles to respond to environmental fluctuations. These continuous adjustments are regulated by multi-hierarchical networks of transcription factors. To understand how such gene regulatory networks (GRNs) have stabilized evolutionarily while allowing for species-specific responses, we compare the GRNs underlying salt response in the early-diverging and late-diverging plants Marchantia polymorpha and Arabidopsis thaliana. Salt-responsive GRNs, constructed on the basis of the temporal transcriptional patterns in the two species, share common trans-regulators but exhibit an evolutionary divergence in cis-regulatory sequences and in the overall network sizes. In both species, WRKY-family transcription factors and their feedback loops serve as central nodes in salt-responsive GRNs. The divergent cis-regulatory sequences of WRKY-target genes are probably associated with the expansion in network size, linking salt stress to tissue-specific developmental and physiological responses. The WRKY modules and highly linked WRKY feedback loops have been preserved widely in other plants, including rice, while keeping their binding-motif sequences mutable. Together, the conserved trans-regulators and the quickly evolving cis-regulatory sequences allow salt-responsive GRNs to adapt over a long evolutionary timescale while maintaining some consistent regulatory structure. This strategy may benefit plants as they adapt to changing environments.

A conserved double-W box in the promoter of CaWRKY40 mediates autoregulation during response to pathogen attack and heat stress in pepper

CaWRKY40 was previously found to be transcriptionally up-regulated by Ralstonia solanacearum inoculation (RSI) or heat stress (HS), but the underlying mechanism remains unknown. Herein, we report that a double-W box-element (DWE) in the promoter of CaWRKY40 is critical for these responses. The upstream W box unit WI of this composite element is crucial for preferential binding by CaWRKY40 and responsiveness to RSI or HS. DWE-driven CaWRKY40 can be transcriptionally and nonspecifically regulated by itself and by CaWRKY58 and CaWRKY27. The DWE was also found in the promoters of CaWRKY40 orthologs, including AtWRKY40, VvWRKY40, GmWRKY40, CplWRKY40, SaWRKY40, SpWRKY40, NtWRKY40, and NaWRKY40. DWE^AtWRKY40 was analogous to DWE^CaWRKY40 by responding to RSI or HS and AtWRKY40 expression. These data suggest that a conserved response of plants to pathogen infection or HS is probably mediated by binding of the DWE by WRKY40.

Structural basis of dimerization and dual W-box DNA recognition by rice WRKY domain

In rice, the critical regulator of the salicylic acid signalling pathway is OsWRKY45, a transcription factor (TF) of the WRKY TF family that functions by binding to the W-box of gene promoters, but the structural basis of OsWRKY45/W-box DNA recognition is unknown. Here, we show the crystal structure of the DNA binding domain of OsWRKY45 (OsWRKY45–DBD, i.e. the WRKY and zinc finger domain) in complex with a W-box DNA. Surprisingly, two OsWRKY45–DBD molecules exchange β4-β5 strands to form a dimer. The domain swapping occurs at the hinge region between the β3 and β4 strands, and is bridged and stabilized by zinc ion via coordinating residues from different chains. The dimer contains two identical DNA binding domains that interact with the major groove of W-box DNA. In addition to hydrophobic and direct hydrogen bonds, water mediated hydrogen bonds are also involved in base-specific interaction between protein and DNA. Finally, we discussed the cause and consequence of domain swapping of OsWRKY45–DBD, and based on our work and that of previous studies present a detailed mechanism of W-box recognition by WRKY TFs. This work reveals a novel dimerization and DNA-binding mode of WRKY TFs, and an intricate picture of the WRKY/W-box DNA recognition.

Understanding the Effect of Structural Diversity in WRKY Transcription Factors on DNA Binding Efficiency through Molecular Dynamics Simulation

A precise understanding of the molecular mechanism involved in stress conditions has great importance for crop improvement. Biomolecules, such as WRKY proteins, which are the largest transcription factor family that is widely distributed in higher plants, plays a significant role in plant defense response against various biotic and abiotic stressors. In the present study, an extensive homology-based three-dimensional model construction and subsequent interaction study of WRKY DNA-binding domain (DBD) in CcWRKY1 (Type I), CcWRKY51 (Type II), and CcWRKY70 (Type III) belonging to pigeonpea, a highly tolerant crop species, was performed. Evaluation of the generated protein models was done to check their reliability and accuracy based on the quantitative and qualitative parameters. The final model was subjected to investigate the comparative binding analysis of different types of WRKY–DBD with DNA-W-box (a cis-acting element) by protein–DNA docking and molecular dynamics (MD) simulation. The DNA binding specificity with WRKY variants was scrutinized through protein–DNA interaction using the HADDOCK server. The stability, as well as conformational changes of protein–DNA complex, was investigated through molecular dynamics (MD) simulations for 100 ns using GROMACS. Additionally, the comparative stability and dynamic behavior of each residue of the WRKY–DBD type were analyzed in terms of root mean square deviation (RMSD), root mean square fluctuation (RMSF)values of the backbone atoms for each frame taking the minimized structure as a reference. The details of DNA binding activity of three different types of WRKY–DBD provided here will be helpful to better understand the regulation of WRKY gene family members in plants.

A strong NF-κB p65 responsive cis-regulatory sequence from Arabidopsis thaliana interacts with WRKY40

Transcription factors from mammals and plants, which play a role in innate immunity, interact with the same microbe-associated molecular pattern (MAMP)-responsive sequences from Arabidopsis thaliana. The interaction of mouse NF-κB p65 with MAMP-responsive sequences containing the core motif GACTTT of the WT-box was investigated. This revealed one sequence, derived from the promoter of the A. thaliana gene At1g76960, a gene with unknown function, to activate NF-κB p65 dependent reporter gene expression in plant cells very strongly. A bioinformatic analysis predicts three putative NF-κB p65 binding sites in this sequence and all three sites are required for reporter gene activation and binding. The sequence is one of the weakest MAMP-responsive sequences previously isolated, but the introduction of a GCC-box increases its MAMP responsivity in combination with upstream WT-box sequences. Although a bioinformatic analysis of the unmutated cis-sequence only predicts NF-κB p65 binding, A. thaliana WRKY40 was selected in a yeast one-hybrid screen. WRKY40, which is a transcriptional repressor, requires the sequence TTTTCTA for direct binding. This sequence is similar to the WK-box TTTTCCAC, previously shown to interact with tobacco NtWRKY12. In summary, this work supports the similarity in binding site recognition between NF-κB and WRKY factors.

ChiIV3 Acts as a Novel Target of WRKY40 to Mediate Pepper Immunity Against Ralstonia solanacearum Infection

ChiIV3, a chitinase of pepper (Capsicum annuum), stimulates cell death in pepper plants. However, there are only scarce reports on its role in resistance against bacterial wilt disease such as that caused by Ralstonia solanacearum and their transcriptional regulation. In this study, the silencing of ChiIV3 in pepper plants significantly reduced the resistance to R. solanacearum. The transcript of ChiIV3 was induced by R. solanacearum inoculation (RSI) as well as exogenous application of methyl jasmonate and abscisic acid. The bioinformatics analysis revealed that the ChiIV3 promoter consists of multiple stress-related cis elements, including six W-boxes and one MYB1AT. With the 5' deletion assay in the ChiIV3 promoter, the W4-box located from -640 to -635 bp was identified as the cis element that is required for the response to RSI. In addition, the W4-box element was shown to be essential for the binding of the ChiIV3 promoter by the WRKY40 transcription factor, which is known to positively regulate the defense response to R. solanacearum. Site-directed mutagenesis in the W4-box sequence impaired the binding of WRKY40 to the ChiIV3 promoter. Subsequently, the transcription of ChiIV3 decreased in WRKY40-silenced pepper plants. These results demonstrated that the expression of the defense gene ChiIV3 is controlled through multiple modes of regulation, and WRKY40 directly binds to the W4-box element of the ChiIV3 promoter region for its transcriptional regulation.

Transcription factors involved in basal immunity in mammals and plants interact with the same MAMP-responsive cis-sequence from Arabidopsis thaliana

WRKY and NF-κB transcription factors, involved in innate immunity in plants and mammals, interact with the same cis-sequence. Novel microbe-associated molecular pattern (MAMP)-responsive cis-sequences, designated type II WT-boxes, are required for flg22-responsive gene expression in Arabidopsis thaliana protoplasts. While type I WT-boxes like TGACTTTT and CGACTTTT interact with WRKY transcription factors (TFs), the question remained which TFs bind to the type II WT-boxes GGACTTTC, GGACTTTT, and GGACTTTG. Surprisingly, a bioinformatic analysis predicts mouse (Mus musculus) NF-κB p65 as a TF interacting with type II WT-boxes. NF-κB p65, like WRKY factors in plants, plays a role in innate immunity in mammals. Therefore, the interaction of NF-κB p65 with type II WT-boxes was tested experimentally. NF-κB p65 requires the WT-boxes GGACTTTC, GGACTTTT, and GGACTTTG for activating reporter gene expression in plant cells. NF-κB p65 directly binds to WT-box containing synthetic promoters in vitro and requires the WT-box for binding. Earlier studies indicate that the sequence GGACTTTC is also required for WRKY26 mediated reporter gene activation. Here it is shown that WRKY26, like NF-κB p65, binds to the sequence GGACTTTC. Consistent with other recent studies, type II WT boxes are WRKY binding sites and the distinction between type I and type II no longer applies.

Physical interaction between nuclear accumulated CC-NB-ARC-LRR protein and WRKY64 promotes EDS1 dependent Fusarium wilt resistance in chickpea

Fusarium wilt is one of the most serious diseases affecting chickpea (Cicer arietinum L.). Here, we identified a putative Resistance Gene Analog (CaRGA) from chickpea, encoding a coiled-coil (CC) nucleotide-binding oligomerization domain (NB-ARC) containing leucine-rich repeat (LRR) protein (CC-NLR protein) that confers resistance against Fusarium oxysporum f. sp. ciceri race1 (Foc1). Over-expression and silencing of CaRGA in chickpea resulted in enhanced resistance and hyper-susceptibility, respectively against Foc1. Furthermore, defense response to Foc1 depends on CC-NLR interaction with WRKY64 transcription factor. CaRGA mediated wilt resistance largely compromised when WRKY64 was silenced. We also determined in planta intramolecular interactions and self-association of chickpea CC-NLR protein. The study shows CC domain suppressing auto-activation of the full-length CC-NLR protein in the absence of pathogen through self-inhibitory intramolecular interaction with NB-ARC domain, which is attenuated by self-interactions to LRR domain. Chickpea CC-NLR protein forms homocomplexes and then interacts with WRKY64. CC-NLR protein further phosphorylates WRKY64 thereby, ubiquitination and proteasome mediated degradation are protected. Phosphorylated WRKY64 with increased stability binds to EDS1 promoter and stimulates its transcription that induces in planta ectopic cell-death. The detailed analysis of CC-NLR and WRKY interactions provide a better understanding of the immune regulation by NLR proteins under biotic stresses.

Deciphering genome-wide WRKY gene family of Triticum aestivum L. and their functional role in response to Abiotic stress

WRKY transcription factors (TFs) act in regulating plant growth and development as well as in response to different stress. Some earlier studies done by individual researchers reported different wheat WRKY TFs. Although, the recently released wheat genome has opened an avenue to investigate wheat WRKYs (TaWRKY) TFs. Prime objective of this study to performed genome-wide classifications of TaWRKYs and their functional annotation. The classification of 107 individual identified characterized sequences of TaWRKY (IICS-TaWRKY) and 160 uncharacterized draft sequences of TaWRKY (UDS-TaWRKY), along with their gene structures and motifs analysis was performed. Along with comparative sequence analysis and microarray analysis was performed to mimic out TaWRKYs functions in response to different abiotic stresses, accompanied by in-vitro validation. The comparative phylogenetic analysis and estimation of Ka/Ks ratio with Triticum urartu, illustrate group based clasifications of TaWRKYs and evolutionary divergences. Furthermore, motif-based and protein-DNA interaction analysis of TaWRKYs helps to identify, their putative function in target DNA recognition sites. Subsequently, results of microarray and comparative sequence analysis provides the evidence of TaWRKYs involved in heat and/or drought stress. Further, in-vitro results validates that TaWRKY014, TaWRKY090 are found to participate in response of drought stress, whereas TaWRKY008, TaWRKY122, and WRKY45 are involved in response of heat and drought stress. These findings can be utilized in developing novel heat and drought-tolerant wheat cultivars using marker-assisted breeding and transgenic development.

CaWRKY22 Acts as a Positive Regulator in Pepper Response to RalstoniaSolanacearum by Constituting Networks with CaWRKY6, CaWRKY27, CaWRKY40, and CaWRKY58

The WRKY web, which is comprised of a subset of WRKY transcription factors (TFs), plays a crucial role in the regulation of plant immunity, however, the mode of organization and operation of this network remains obscure, especially in non-model plants such as pepper (Capsicum annuum). Herein, CaWRKY22, a member of a subgroup of IIe WRKY proteins from pepper, was functionally characterized in pepper immunity against Ralstonia Solanacearum. CaWRKY22 was found to target the nuclei, and its transcript level was significantly upregulated by Ralstonia Solanacearum inoculation (RSI) and exogenously applied salicylic acid (SA), Methyl jasmonate (MeJA), or ethephon (ETH). Loss-of-function CaWRKY22, caused by virus-induced gene silencing (VIGS), enhanced pepper’s susceptibility to RSI. In addition, the silencing of CaWRKY22 perturbed the hypersensitive response (HR)-like cell death elicited by RSI and downregulated defense-related genes including CaPO2, CaPR4, CaACC, CaBPR1, CaDEF1, CaHIR1, and CaWRKY40. CaWRKY22 was found to directly bind to the promoters of CaPR1, CaDEF1, and CaWRKY40 by chromatin immuno-precipitation (ChIP) analysis. Contrastingly, transient overexpression of CaWRKY22 in pepper leaves triggered significant HR-like cell death and upregulated the tested immunity associated maker genes. Moreover, the transient overexpression of CaWRKY22 upregulated the expression of CaWRKY6 and CaWRKY27 while it downregulated of the expression of CaWRKY58. Conversely, the transient overexpression of CaWRKY6, CaWRKY27, and CaWRKY40 upregulated the expression of CaWRKY22, while transient overexpression of CaWRKY58 downregulated the transcript levels of CaWRKY22. These data collectively recommend the role of CaWRKY22 as a positive regulator of pepper immunity against R. Solanacearum, which is regulated by signaling synergistically mediated by SA, jasmonic acid (JA), and ethylene (ET), integrating into WRKY networks with WRKY TFs including CaWRKY6, CaWRKY27, CaWRKY40, and CaWRKY58.

Structural and functional dissection of differentially expressed tomato WRKY transcripts in host defense response against the vascular wilt pathogen (Fusarium oxysporum f. sp. lycopersici)

The WRKY transcription factors have indispensable role in plant growth, development and defense responses. The differential expression of WRKY genes following the stress conditions has been well demonstrated. We investigated the temporal and tissue-specific (root and leaf tissues) differential expression of plant defense-related WRKY genes, following the infection of Fusarium oxysporum f. sp. lycopersici (Fol) in tomato. The genome-wide computational analysis revealed that during the Fol infection in tomato, 16 different members of WRKY gene superfamily were found to be involved, of which only three WRKYs (SolyWRKY4, SolyWRKY33, and SolyWRKY37) were shown to have clear-cut differential gene expression. The quantitative real time PCR (qRT-PCR) studies revealed different gene expression profile changes in tomato root and leaf tissues. In root tissues, infected with Fol, an increased expression for SolyWRKY33 (2.76 fold) followed by SolyWRKY37 (1.93 fold) gene was found at 24 hrs which further increased at 48 hrs (5.0 fold). In contrast, the leaf tissues, the expression was more pronounced at an earlier stage of infection (24 hrs). However, in both cases, we found repression of SolyWRKY4 gene, which further decreased at an increased time interval. The biochemical defense programming against Fol pathogenesis was characterized by the highest accumulation of H₂O₂ (at 48 hrs) and enhanced lignification. The functional diversity across the characterized WRKYs was explored through motif scanning using MEME suite, and the WRKYs specific gene regulation was assessed through the DNA protein docking studies The functional WRKY domain modeled had β sheets like topology with coil and turns. The DNA-protein interaction results revealed the importance of core residues (Tyr, Arg, and Lys) in a feasible WRKY-W-box DNA interaction. The protein interaction network analysis revealed that the SolyWRKY33 could interact with other proteins, such as mitogen-activated protein kinase 5 (MAPK), sigma factor binding protein1 (SIB1) and with other WRKY members including WRKY70, WRKY1, and WRKY40, to respond various biotic and abiotic stresses. The STRING results were further validated through Predicted Tomato Interactome Resource (PTIR) database. The CELLO2GO web server revealed the functional gene ontology annotation and protein subcellular localization, which predicted that SolyWRKY33 is involved in amelioration of biological stress (39.3%) and other metabolic processes (39.3%). The protein (SolyWRKY33) most probably located inside the nucleus (91.3%) with having transcription factor binding activity. We conclude that the defense response following the Fol challenge was accompanied by differential expression of the SolyWRKY4(↓), SolyWRKY33(↑) and SolyWRKY37(↑) transcripts. The biochemical changes are occupied by elicitation of H₂O₂ generation and accumulation and enhanced lignified tissues.

Arabidopsis WRKY50 and TGA Transcription Factors Synergistically Activate Expression of PR1

Arabidopsis PR1 is a salicylic acid (SA) inducible marker gene for systemic acquired resistance (SAR). However, the regulation of PR1 in plants is poorly understood. In this study, we showed that AtWRKY50 transcription factor binds to two promoter elements of PR1 via its DNA binding domain. Interestingly, the DNA-binding sites for AtWRKY50 deviate significantly from the consensus WRKY binding W-box. The binding sites are located in close proximity to the binding sites for TGA transcription factors. Transactivation experiments in Arabidopsis protoplasts derived from wild type, npr1-1 and tga256 mutant plants indicated that AtWRKY50 alone was able to induce expression of a PR1::β-glucuronidase (GUS) reporter gene, independent of TGAs or NPR1. However, co-expression of TGA2 or TGA5 with AtWRKY50 synergistically enhanced expression to high levels. Yeast-2-hybrid assays and bimolecular fluorescence complementation (BiFC) experiments revealed that AtWRKY50 could interact with TGA2 and TGA5. Using electrophoretic mobility shift assays (EMSA) it was established that AtWRKY50 and TGA2 or TGA5 simultaneously bind to the PR1 promoter. Taken together, these results support a role of AtWRKY50 in SA-induced expression of PR1. Highlights: AtWRKY50 specifically binds to LS10 region of PR1 promoter and interacts with TGAs to synergistically activate PR1 expression.

A Genome-Wide Identification of the WRKY Family Genes and a Survey of Potential WRKY Target Genes in Dendrobium officinale

The WRKY family, one of the largest families of transcription factors, plays important roles in the regulation of various biological processes, including growth, development and stress responses in plants. In the present study, 63 DoWRKY genes were identified from the Dendrobium officinale genome. These were classified into groups I, II, III and a non-group, each with 14, 28, 10 and 11 members, respectively. ABA-responsive, sulfur-responsive and low temperature-responsive elements were identified in the 1-k upstream regulatory region of DoWRKY genes. Subsequently, the expression of the 63 DoWRKY genes under cold stress was assessed, and the expression profiles of a large number of these genes were regulated by low temperature in roots and stems. To further understand the regulatory mechanism of DoWRKY genes in biological processes, potential WRKY target genes were investigated. Among them, most stress-related genes contained multiple W-box elements in their promoters. In addition, the genes involved in polysaccharide synthesis and hydrolysis contained W-box elements in their 1-k upstream regulatory regions, suggesting that DoWRKY genes may play a role in polysaccharide metabolism. These results provide a basis for investigating the function of WRKY genes and help to understand the downstream regulation network in plants within the Orchidaceae.

Zn(2+) -induced Ca(2+) release via ryanodine receptors triggers calcineurin-dependent redistribution of cortical neuronal Kv2.1 K(+) channels

KEY POINTS

Increases in intracellular Zn(2+) concentrations are an early, necessary signal for the modulation of Kv2.1 K(+) channel localization and physiological function. Intracellular Zn(2+) -mediated Kv2.1 channel modulation is dependent on calcineurin, a Ca(2+) -activated phosphatase. We show that intracellular Zn(2+) induces a significant increase in ryanodine receptor-dependent cytosolic Ca(2+) transients, which leads to a calcineurin-dependent redistribution of Kv2.1 channels from pre-existing membrane clusters to diffuse localization. As such, the link between Zn(2+) and Ca(2+) signalling in this Kv2.1 modulatory pathway is established. We observe that a sublethal ischaemic preconditioning insult also leads to Kv2.1 redistribution in a ryanodine receptor-dependent fashion. We suggest that Zn(2+) may be an early and ubiquitous signalling molecule mediating Ca(2+) release from the cortical endoplasmic reticulum via ryanodine receptor activation.

ABSTRACT

Sublethal injurious stimuli in neurons induce transient increases in free intracellular Zn(2+) that are associated with regulating adaptive responses to subsequent lethal injury, including alterations in the function and localization of the delayed-rectifier potassium channel, Kv2.1. However, the link between intracellular Zn(2+) signalling and the observed changes in Kv2.1 remain undefined. In the present study, utilizing exogenous Zn(2+) treatment, along with a selective Zn(2+) ionophore, we show that transient elevations in intracellular Zn(2+) concentrations are sufficient to induce calcineurin-dependent Kv2.1 channel dispersal in rat cortical neurons in vitro, which is accompanied by a relatively small but significant hyperpolarizing shift in the voltage-gated activation kinetics of the channel. Critically, using a molecularly encoded calcium sensor, we found that the calcineurin-dependent changes in Kv2.1 probably occur as a result of Zn(2+) -induced cytosolic Ca(2+) release via activation of neuronal ryanodine receptors. Finally, we couple this mechanism with an established model for in vitro ischaemic preconditioning and show that Kv2.1 channel modulation in this process is also ryanodine receptor-sensitive. Our results strongly suggest that intracellular Zn(2+) -initiated signalling may represent an early and possibly widespread component of Ca(2+) -dependent processes in neurons.

Structural modelling and molecular dynamics of a multi-stress responsive WRKY TF-DNA complex towards elucidating its role in stress signalling mechanisms in chickpea

Chickpea is a premier food legume crop with high nutritional quality and attains prime importance in the current era of 795 million people being undernourished worldwide. Chickpea production encounters setbacks due to various stresses and understanding the role of key transcription factors (TFs) involved in multiple stresses becomes inevitable. We have recently identified a multi-stress responsive WRKY TF in chickpea. The present study was conducted to predict the structure of WRKY TF to identify the DNA-interacting residues and decipher DNA-protein interactions. Comparative modelling approach produced 3D model of the WRKY TF with good stereochemistry, local/global quality and further revealed W19, R20, K21, and Y22 motifs within a vicinity of 5 Å to the DNA amongst R18, G23, Q24, K25, Y36, Y37, R38 and K47 and these positions were equivalent to the 2LEX WRKY domain of Arabidopsis. Molecular simulations analysis of reference protein -PDB ID 2LEX, along with Car-WRKY TF modelled structure with the DNA coordinates derived from PDB ID 2LEX and docked using HADDOCK were executed. Root Mean Square (RMS) Deviation and RMS Fluctuation values yielded consistently stable trajectories over 50 ns simulation. Strengthening the obtained results, neither radius of gyration, distance and total energy showed any signs of DNA-WRKY complex falling apart nor any significant dissociation event over 50 ns run. Therefore, the study provides first insights into the structural properties of multi-stress responsive WRKY TF-DNA complex in chickpea, enabling genome wide identification of TF binding sites and thereby deciphers their gene regulatory networks.

Mechanism of host substrate acetylation by a YopJ family effector

The Yersinia outer protein J (YopJ) family of bacterial effectors depends on a novel acetyltransferase domain to acetylate signalling proteins from plant and animal hosts. However, the underlying mechanism is unclear. Here, we report the crystal structures of PopP2, a YopJ effector produced by the plant pathogen Ralstonia solanacearum, in complex with inositol hexaphosphate (InsP₆), acetyl-coenzyme A (AcCoA) and/or substrate Resistance to Ralstonia solanacearum 1 (RRS1-R)_WRKY. PopP2 recognizes the WRKYGQK motif of RRS1-R_WRKY to position a targeted lysine in the active site for acetylation. Importantly, the PopP2-RRS1-R_WRKY association is allosterically regulated by InsP₆ binding, suggesting a previously unidentified role of the eukaryote-specific cofactor in substrate interaction. Furthermore, we provide evidence for the reaction intermediate of PopP2-mediated acetylation, an acetyl-cysteine covalent adduct, lending direct support to the 'ping-pong'-like catalytic mechanism proposed for YopJ effectors. Our study provides critical mechanistic insights into the virulence activity of YopJ class of acetyltransferases.

Structural and Functional Insights into WRKY3 and WRKY4 Transcription Factors to Unravel the WRKY-DNA (W-Box) Complex Interaction in Tomato (Solanum lycopersicum L.). A Computational Approach

The WRKY transcription factors (TFs), play crucial role in plant defense response against various abiotic and biotic stresses. The role of WRKY3 and WRKY4 genes in plant defense response against necrotrophic pathogens is well-reported. However, their functional annotation in tomato is largely unknown. In the present work, we have characterized the structural and functional attributes of the two identified tomato WRKY transcription factors, WRKY3 (SlWRKY3), and WRKY4 (SlWRKY4) using computational approaches. Arabidopsis WRKY3 (AtWRKY3: NP_178433) and WRKY4 (AtWRKY4: NP_172849) protein sequences were retrieved from TAIR database and protein BLAST was done for finding their sequential homologs in tomato. Sequence alignment, phylogenetic classification, and motif composition analysis revealed the remarkable sequential variation between, these two WRKYs. The tomato WRKY3 and WRKY4 clusters with Solanum pennellii showing the monophyletic origin and evolution from their wild homolog. The functional domain region responsible for sequence specific DNA-binding occupied in both proteins were modeled [using AtWRKY4 (PDB ID:1WJ2) and AtWRKY1 (PDBID:2AYD) as template protein structures] through homology modeling using Discovery Studio 3.0. The generated models were further evaluated for their accuracy and reliability based on qualitative and quantitative parameters. The modeled proteins were found to satisfy all the crucial energy parameters and showed acceptable Ramachandran statistics when compared to the experimentally resolved NMR solution structures and/or X-Ray diffracted crystal structures (templates). The superimposition of the functional WRKY domains from SlWRKY3 and SlWRKY4 revealed remarkable structural similarity. The sequence specific DNA binding for two WRKYs was explored through DNA-protein interaction using Hex Docking server. The interaction studies found that SlWRKY4 binds with the W-box DNA through WRKYGQK with Tyr⁴⁰⁸, Arg⁴⁰⁹, and Lys⁴¹⁹ with the initial flanking sequences also get involved in binding. In contrast, the SlWRKY3 made interaction with RKYGQK along with the residues from zinc finger motifs. Protein-protein interactions studies were done using STRING version 10.0 to explore all the possible protein partners involved in associative functional interaction networks. The Gene ontology enrichment analysis revealed the functional dimension and characterized the identified WRKYs based on their functional annotation.

The Solanum lycopersicum WRKY3 Transcription Factor SlWRKY3 Is Involved in Salt Stress Tolerance in Tomato

Salinity threatens productivity of economically important crops such as tomato (Solanum lycopersicum L.). WRKY transcription factors appear, from a growing body of knowledge, as important regulators of abiotic stresses tolerance. Tomato SlWRKY3 is a nuclear protein binding to the consensus CGTTGACC/T W box. SlWRKY3 is preferentially expressed in aged organs, and is rapidly induced by NaCl, KCl, and drought. In addition, SlWRKY3 responds to salicylic acid, and 35S::SlWRKY3 tomatoes showed under salt treatment reduced contents of salicylic acid. In tomato, overexpression of SlWRKY3 impacted multiple aspects of salinity tolerance. Indeed, salinized (125 mM NaCl, 20 days) 35S::SlWRKY3 tomato plants displayed reduced oxidative stress and proline contents compared to WT. Physiological parameters related to plant growth (shoot and root biomass) and photosynthesis (stomatal conductance and chlorophyll a content) were retained in transgenic plants, together with lower Na⁺ contents in leaves, and higher accumulation of K⁺ and Ca²⁺. Microarray analysis confirmed that many stress-related genes were already up-regulated in transgenic tomatoes under optimal conditions of growth, including genes coding for antioxidant enzymes, ion and water transporters, or plant defense proteins. Together, these results indicate that SlWRKY3 is an important regulator of salinity tolerance in tomato.

The role of ZmWRKY4 in regulating maize antioxidant defense under cadmium stress

WRKY transcription factors act as positive regulators in abiotic stress responses by activation of the cellular antioxidant systems. However, there are few reports on the response of WRKY genes to cadmium (Cd) stress. In this study, the role of maize ZmWRKY4 in regulating antioxidant enzymes in Cd stress was investigated. The results indicated that Cd induced up-regulation of the expression and the activities of ZmWRKY4 and superoxide dismutase (SOD) and ascorbate peroxidase (APX). Transient expression and RNA interference (RNAi) silencing of ZmWRKY4 in maize mesophyll protoplasts further revealed that ZmWRKY4 was required for the abscisic acid (ABA)-induced increase in expression and activity of SOD and APX. Overexpression of ZmWRKY4 in protoplasts upregulated the expression and the activities of antioxidant enzymes, whereas ABA induced increases in the expression and the activities of antioxidant enzymes were blocked by the RNAi silencing of ZmWRKY4. Bioinformatic analysis indicated that ZmSOD4 and ZmcAPX both harbored two W-boxes, binding motif for WRKY transcription factors, in their promoter region. Intriguingly, ZmWRKY4 belongs to group I WRKYs with two WRKY domains. Moreover, the synchronized expression patterns indicate that ZmWRKY4 might play a critical role in either regulating the ZmSOD4 and ZmcAPX expression or cooperating with them in response to stress and phytohormone.