Molecular pathways of WRKY genes in regulating plant salinity tolerance

Salinity is a natural and anthropogenic process that plants overcome using various responses. Salinity imposes a two-phase effect, simplified into the initial osmotic challenges and subsequent salinity-specific ion toxicities from continual exposure to sodium and chloride ions. Plant responses to salinity encompass a complex gene network involving osmotic balance, ion transport, antioxidant response, and hormone signaling pathways typically mediated by transcription factors. One particular transcription factor mega family, WRKY, is a principal regulator of salinity responses. Here, we categorize a collection of known salinity-responding WRKYs and summarize their molecular pathways. WRKYs collectively play a part in regulating osmotic balance, ion transport response, antioxidant response, and hormone signaling pathways in plants. Particular attention is given to the hormone signaling pathway to illuminate the relationship between WRKYs and abscisic acid signaling. Observed trends among WRKYs are highlighted, including group II WRKYs as major regulators of the salinity response. We recommend renaming existing WRKYs and adopting a naming system to a standardized format based on protein structure

Hypersensitive Response-Like Reaction Is Associated with Hybrid Necrosis in Interspecific Crosses between Tetraploid Wheat and Aegilops tauschii Coss

BACKGROUND: Hybrid speciation is classified into homoploid and polyploid based on ploidy level. Common wheat is an allohexaploid species that originated from a naturally occurring interploidy cross between tetraploid wheat and diploid wild wheat Aegilops tauschii Coss. Aegilops tauschii provides wide naturally occurring genetic variation. Sometimes its triploid hybrids with tetraploid wheat show the following four types of hybrid growth abnormalities: types II and III hybrid necrosis, hybrid chlorosis, and severe growth abortion. The growth abnormalities in the triploid hybrids could act as postzygotic hybridization barriers to prevent formation of hexaploid wheat. METHODOLOGY/PRINCIPAL FINDINGS: Here, we report on the geographical and phylogenetic distribution of Ae. tauschii accessions inducing the hybrid growth abnormalities and showed that they are widely distributed across growth habitats in Ae. tauschii. Molecular and cytological characterization of the type III necrosis phenotype was performed. The hybrid abnormality causing accessions were widely distributed across growth habitats in Ae. tauschii. Transcriptome analysis showed that a number of defense-related genes such as pathogenesis-related genes were highly up-regulated in the type III necrosis lines. Transmission electron microscope observation revealed that cell death occurred accompanied by generation of reactive oxygen species in leaves undergoing type III necrosis. The reduction of photosynthetic activity occurred prior to the appearance of necrotic symptoms on the leaves exhibiting hybrid necrosis. CONCLUSIONS/SIGNIFICANCE: Taking these results together strongly suggests that an autoimmune response might be triggered by intergenomic incompatibility between the tetraploid wheat and Ae. tauschii genomes in type III necrosis, and that genetically programmed cell death could be regarded as a hypersensitive response-like cell death similar to that observed in Arabidopsis intraspecific and Nicotiana interspecific hybrids. Only Ae. tauschii accessions without such inhibiting factors could be candidates for the D-genome donor for the present hexaploid wheat

A Transcriptional Regulatory Network of \u3cem\u3eRsv3\u3c/em\u3e-Mediated Extreme Resistance against \u3cem\u3eSoybean Mosaic Virus\u3c/em\u3e

Resistance genes are an effective means for disease control in plants. They predominantly function by inducing a hypersensitive reaction, which results in localized cell death restricting pathogen spread. Some resistance genes elicit an atypical response, termed extreme resistance, where resistance is not associated with a hypersensitive reaction and its standard defense responses. Unlike hypersensitive reaction, the molecular regulatory mechanism(s) underlying extreme resistance is largely unexplored. One of the few known, naturally occurring, instances of extreme resistance is resistance derived from the soybean Rsv3 gene, which confers resistance against the most virulent Soybean mosaic virus strains. To discern the regulatory mechanism underlying Rsv3-mediated extreme resistance, we generated a gene regulatory network using transcriptomic data from time course comparisons of Soybean mosaic virus-G7-inoculated resistant (L29, Rsv3-genotype) and susceptible (Williams82, rsv3-genotype) soybean cultivars. Our results show Rsv3 begins mounting a defense by 6 hpi via a complex phytohormone network, where abscisic acid, cytokinin, jasmonic acid, and salicylic acid pathways are suppressed. We identified putative regulatory interactions between transcription factors and genes in phytohormone regulatory pathways, which is consistent with the demonstrated involvement of these pathways in Rsv3-mediated resistance. One such transcription factor identified as a putative transcriptional regulator was MYC2 encoded by Glyma.07G051500. Known as a master regulator of abscisic acid and jasmonic acid signaling, MYC2 specifically recognizes the G-box motif (“CACGTG”), which was significantly enriched in our data among differentially expressed genes implicated in abscisic acid- and jasmonic acid-related activities. This suggests an important role for Glyma.07G051500 in abscisic acid- and jasmonic acid-derived defense signaling in Rsv3. Resultantly, the findings from our network offer insights into genes and biological pathways underlying the molecular defense mechanism of Rsv3-mediated extreme resistance against Soybean mosaic virus. The computational pipeline used to reconstruct the gene regulatory network in this study is freely available at https://github.com/LiLabAtVT/rsv3-network

Transcriptomic profiling of the extremophile eutrema salsugineum response to environmental stressors

Plants are sessile organisms that are constantly exposed to a variety of abiotic and biotic environmental stresses. Some plants are known to be more tolerant to those environmental stressors than others; those are the extremophilic plants. Studying the stress response pathways in such plants is extremely important in developing transgenic crop plants with enhanced tolerance to environmental stresses. Eutrema salsugineum is an extremophilic plant that is known to be resistant to many abiotic stress factors such as drought, cold, salt, and nitrogen deficiency. Experiments were carried out in KAUST by exposing the extremophilic plant to heat stress and exogenous ABA stress. RNA sequencing was done in order to get the transcriptome profile of the plant in response to the stresses. De novo transcriptome assembly was done followed by transcript abundance quantification and normalization using Kallisto. Differential expression analaysis was done to identify the differentially expressed transcripts in response to the different treatments in the shoot and root using the R bioconductor package EdgeR. The transcripts were annotated using EggNOG. The protein coding transcripts were identified by aligning them to the nr protein database using tblastx. Functional analysis of the DE transcripts to get the enriched terms was carried out using DAVID. Trinity de novo assembly produced 49857 genes and 134493 transcripts. Out of the 134493 transcripts, 114692 (85.28%) transcripts had tblastx hits (protein coding). Thus, 19801 potentially non coding or novel transcripts have been identified. A large variety of proteins were found to be differentially expressed depending on the pair-wise comparison. The genes were mainly involved in plant heat and ABA stress, ROS signaling pathway, ROS scavenging, secondary metabolite production, and lipid transfer. Further investigation of the role of secondary metabolites such as flavonoids, and nitrogen and sulfur containing compounds in the abiotic stress response of E. salsugineum is needed since it appears to be a major mechanism used by the plant. The results of this research offer a wide variety of stress related protein in E.salsugineum. Investigation of the over-expression of some of these genes in stress sensitive plants will help in further understanding their functions and mechanisms of action

A novel activator-type ERF of Thinopyrum intermedium, TiERF1, positively regulates defence responses

Thinopyrum intermedium is resistant to many different pathogens. To understand the roles of ethylene response factors (ERFs) in defence responses, the first member of the ERF family in T. intermedium, TiERF1, was characterized and functionally analysed in this study. The TiERF1 gene encodes a putative protein of 292 amino acids, belonging to the B3 subgroup of the ERF transcription factor family. Biochemical assays demonstrated that the TiERF1 protein is capable of binding to the GCC box, a cis-element present in the promoters of pathogenesis-related (PR) genes, and possessing transactivation activity, as well as localizing to the nucleus. The transcript of TiERF1 in T. intermedium is rapidly induced by infection with Rhizoctonia cerealis, Fusarium graminearum, or Blumeria graminis, and ethylene, jasmonic acid, and salicylic acid treatments. More importantly, the ectopic expression of TiERF1 in tobacco activated the transcript of the PR genes of tobacco with a GCC box cis-element, and ACO and ACS genes key to ethylene synthesis, and in turn improved the resistance level to Alternaria alternata and tobacco mosaic virus, as well as causing some phenotypic changes associated with ethylene response in the transgenic tobacco plants. Taken together, TiERF1 protein as an ERF transcription activator positively regulates defence responses via the activation of some defence-related genes

Disease Resistance in Wheat and Its Relatives

Plants have evolved a complex defense system against pests and pathogens utilizing many types of receptors, signaling factors, and defense compounds to detect pathogen presence and respond effectively. Since many pathogens have evolved immunesuppressing effectors used to reduce plant resistance, plants have evolved a family of receptors that detect pathogenic effectors as a result of an evolutionary arms race. These receptors contain Nucleotide-Binding Site and Leucine-Rich Repeat domains and are called NBS-LRR or NLR proteins. Many grasses possess huge genomes with hundreds of NLR-encoding genes, often found in clusters at the extra-pericentromeric regions of chromosomes, where unequal crossing over causes tandem duplication and a mechanism for resistance (R) gene diversification. R genes also possess domains associated with signaling factors that either serve as baits for pathogen effectors or as active signaling components to initiate defense responses. The objectives of this dissertation project were to: 1) identify R genes in wheat and some of its relatives; 2) assess how they may have evolved in grasses with available genomes, such as wheat, barley, foxtail millet, and rice; 3) investigate integrated domains found in wheat NLRs; and 4) assess differences in gene expression between tan spot resistant and susceptible wheat when exposed to Pyrenophora tritici-repentis (Ptr), a pathogen that uses wheat R gene Tsn1 as a susceptibility gene to facilitate infection. Genomic data was analyzed by the construction of Hidden Markov Model profiles and sequence annotation using programs such as InterProScan and MEME (Multiple Expectation maximization for Motif Elicitation). R genes were used to construct phylogenetic trees, chromosomal maps, exon-intron diagrams, and syntenic maps. The interaction between wheat and Ptr was investigated through a greenhouse experiment, where resistant and susceptible wheat was inoculated with Ptr spores or directly infiltrated with the Ptr ToxA protein. Genome-wide identification of R genes revealed that Hordeum vulgare, Setaria italica, Aegilops tauschii, and Triticum aestivum had 175, 202, 402, and 802 NLRs with N-terminal Coiled-Coil domains (CNLs), respectively. In each species studied, R genes formed clusters, many containing highly similar genes, providing evidence of tandem duplication. CNLs in wheat and wheat relatives formed an expansion of the CNL-C clade that showed evidence of purifying selection. R gene sequences necessary for effector detection diversified, while domains necessary for signaling remained conserved. Wheat NLRs contained integrated domains (IDs) associated with kinase, transcription factor, and other signaling mechanisms. Wheat NLR-ID genes encoded multiple transcripts, indicating that wheat is able to include or exclude IDs through alternative splicing. Greenhouse experiments revealed several groups of genes that differed in expression between tan spot resistant and susceptible cultivars. Wheat resistant to Ptr showed increased expression of genes associated with resistance: chitinases, signaling factors (i.e. transcription factors and kinases), resistance receptors, and enzymes associated with phytoalexin production. These results all showed that resistance in wheat and its relatives relies on a complex network of factors, and that NLRs have diversified to be a variable family of components that initiate defense responses when triggered by pathogenic effectors

Genome-wide identification and transcriptional profiling of small heat shock protein gene family under diverse abiotic stress conditions in Sorghum bicolor (L.)

The small heat shock proteins (sHsps/Hsp20s) are the molecular chaperones that maintain proper folding, trafficking and disaggregation of proteins under diverse abiotic stress conditions. In the present investigation, a genome-wide scan revealed the presence of a total of 47 sHsps in Sorghum bicolor (SbsHsps), distributed across 10 subfamilies, the major subfamily being P (plastid) group with 17 genes. Chromosomes 1 and 3 appear as the hot spot regions for SbsHsps, and majority of them were found acidic, hydrophilic, unstable and intron less. Interestingly, promoter analysis indicated that they are associated with both biotic and abiotic stresses, as well as plant development. Sorghum sHsps exhibited 15 paralogous and 20 orthologous duplications. Expression analysis of 15 genes selected from different subfamilies showed high transcript levels in roots and leaves implying that they are likely to participate in the developmental processes. SbsHsp genes were highly induced by diverse abiotic stresses inferring their critical role in mediating the environmental stress responses. Gene expression data revealed that SbsHsp-02 is a candidate gene expressed in all the tissues under varied stress conditions tested. Our results contribute to the understanding of the complexity of SbsHsp genes and help to analyse them further for functional validation

Stress signaling convergence and nutrient crosstalk determine zinc-mediated amelioration against cadmium toxicity in rice

Consumption of rice (Oryza sativa L.) is one of the major pathways for heavy metal bioaccumulation in humans over time. Understanding the molecular responses of rice to heavy metal contamination in agriculture is useful for eco-toxicological assessment of cadmium (Cd) and its interaction with zinc (Zn). In certain crops, the impacts of Cd stress or Zn nutrition on the biophysical chemistry and gene expression have been widely investigated, but their molecular interactions at transcriptomic level, particularly in rice roots, are still elusive. Here, hydroponic investigations were carried out with two rice genotypes (Yinni-801 and Heizhan-43), varying in Cd contents in plant tissues to determine their transcriptomic responses upon Cd15 (15 µM) and Cd15+Zn50 (50 µM) treatments. High throughput RNA-sequencing analysis confirmed that 496 and 2407 DEGs were significantly affected by Cd15 and Cd15+Zn50, respectively, among which 1016 DEGs were commonly induced in both genotypes. Multitude of DEGs fell under the category of protein kinases, such as calmodulin (CaM) and calcineurin B-like protein-interacting protein kinases (CBL), indicating a dynamic shift in hormonal signal transduction and Ca2+ involvement with the onset of treatments. Both genotypes expressed a mutual regulation of transcription factors (TFs) such as WRKY, MYB, NAM, AP2, bHLH and ZFP families under both treatments, whereas genes econding ABC transporters (ABCs), high affinity K+ transporters (HAKs) and Glutathione-S-transferases (GSTs), were highly up-regulated under Cd15+Zn50 in both genotypes. Zinc addition triggered more signaling cascades and detoxification related genes in regulation of immunity along with the suppression of Cd-induced DEGs and restriction of Cd uptake. Conclusively, the effective integration of breeding techniques with candidate genes identified in this study as well as economically and technologically viable methods, such as Zn nutrient management, could pave the way for selecting cultivars with promising agronomic qualities and reduced Cd for sustainable rice production

Wheat Domestication Accelerated Evolution and Triggered Positive Selection in the β-Xylosidase Enzyme of Mycosphaerella graminicola

Plant cell wall degrading enzymes (PCWDEs) of plant pathogens are receiving increasing interest for their potential to trigger plant defense reactions. In an antagonistic co-evolutionary arms race between host and pathogen, PCWDEs could be under strong selection. Here, we tested the hypothesis that PCWDEs in the fungal wheat pathogen Mycosphaerella graminicola have been positively selected by analyzing ratios of non-synonymous and synonymous nucleotide changes in the genes encoding these enzymes. Analyses of five PCWDEs demonstrated that one (β-xylosidase) has been under strong positive selection and experienced an accelerated rate of evolution. In contrast, PCWDEs in the closest relatives of M. graminicola collected from wild grasses did not show evidence for selection or deviation from a molecular clock. Since the genealogical divergence of M. graminicola from these latter species coincided with the onset of agriculture, we hypothesize that the recent domestication of the host plant and/or agricultural practices triggered positive selection in β-xylosidase and that this enzyme played a key role in the emergence of a host-specialized pathogen