Uncovering the Mechanisms: The Role of Biotrophic Fungi in Activating or Suppressing Plant Defense Responses

This paper discusses the mechanisms by which fungi manipulate plant physiology and suppress plant defense responses by producing effectors that can target various host proteins. Effector-triggered immunity and effector-triggered susceptibility are pivotal elements in the complex molecular dialogue underlying plant-pathogen interactions. Pathogen-produced effector molecules possess the ability to mimic pathogen-associated molecular patterns or hinder the binding of pattern recognition receptors. Effectors can directly target nucleotide-binding domain, leucine-rich repeat receptors, or manipulate downstream signaling components to suppress plant defense. Interactions between these effectors and receptor-like kinases in host plants are critical in this process. Biotrophic fungi adeptly exploit the signaling networks of key plant hormones, including salicylic acid, jasmonic acid, abscisic acid, and ethylene, to establish a compatible interaction with their plant hosts. Overall, the paper highlights the importance of understanding the complex interplay between plant defense mechanisms and fungal effectors to develop effective strategies for plant disease management.

A transition from enemies to allies: how viruses improve drought resilience in plants

Global crop production is severely affected by environmental factors such as drought, salinity, cold, flood etc. Among these stresses, drought is one of the major abiotic stresses reducing crop productivity. It is expected that drought conditions will further increase because of the increasing global temperature. In general, viruses are seen as a pathogen affecting the crop productivity. However, several researches are showing that viruses can induce drought tolerance in plants. This review explores the mechanisms underlying the interplay between viral infections and the drought response mechanisms in plants. We tried to address the molecular pathways and physiological changes induced by viruses that confer drought tolerance, including alterations in hormone signaling, antioxidant defenses, scavenging the reactive oxygen species, role of RNA silencing and miRNA pathway, change in the expression of several genes including heat shock proteins, cellulose synthase etc. Furthermore, we discuss various viruses implicated in providing drought tolerance and examine the range of plant species exhibiting this phenomenon. By applying current knowledge and identifying gaps in understanding, this review aims to provide valuable insights into the complex dynamics of virus-induced drought tolerance in plants, paving the way for future research directions and practical applications in sustainable agriculture.

Lipo-chitooligosaccharide and thuricin 17 act as plant growth promoters and alleviate drought stress in Arabidopsis thaliana

Lipo-chito-oligosaccharide (LCO-from Bradyrhizobium japonicum) and thuricin 17 (Th17-from Bacillus thuringiensis) are bacterial signal compounds from the rhizosphere of soybean that have been shown to enhance plant growth in a range of legumes and non-legumes. In this study, an attempt to quantify phytohormones involved in the initial hours after exposure of Arabidopsis thaliana to these compounds was conducted using UPLC-ESI-MS/MS. A petri-plate assay was conducted to screen for drought stress tolerance to PEG 8000 infusion and plant growth was studied 21-days post-stress. Arabidopsis thaliana plants grown in trays with drought stress imposed by water withhold were used for free proline determination, elemental analysis, and untargeted proteomics using LC-MS/MS studies. At 24 h post-exposure to the signal compounds under optimal growth conditions, Arabidopsis thaliana rosettes varied in their responses to the two signals. While LCO-treated rosettes showed a decrease in total IAA, cytokinins, gibberellins, and jasmonic acid, increases in ABA and SA was very clear. Th17-treated rosettes, on the other hand, showed an increase in IAA and SA. Both treatments resulted in decreased JA levels. Under severe drought stress imposed by PEG 8000 infusion, LCO and Th17 treatments were found to significantly increase fresh and dry weight over drought-stressed control plates, indicating that the presence of the signaling compounds decreased the negative effects experienced by the plants. Free proline content increased in LCO- and Th17-treated plants after water-withhold drought stress. Elemental analysis showed a significant increase in carbon percentage at the lower concentration of Th17. Untargeted proteomics revealed changes in the levels of drought-specific ribosomal proteins, glutathione S-transferase, late embryogenesis proteins, vegetative storage proteins 1 and 2, thaumatin-like proteins, and those related to chloroplast and carbon metabolism. The roles of some of these significantly affected proteins detected under drought stress are discussed.

The evolutionary and molecular features of the broad-host-range plant pathogen Sclerotinia sclerotiorum

Sclerotinia sclerotiorum is a pathogenic fungus that infects hundreds of plant species, including many of the world's most important crops. Key features of S. sclerotiorum include its extraordinary host range, preference for dicotyledonous plants, relatively slow evolution, and production of protein effectors that are active in multiple host species. Plant resistance to this pathogen is highly complex, typically involving numerous polymorphisms with infinitesimally small effects, which makes resistance breeding a major challenge. Due to its economic significance, S. sclerotiorum has been subjected to a large amount of molecular and evolutionary research. In this updated pathogen profile, we review the evolutionary and molecular features of S. sclerotiorum and discuss avenues for future research into this important species.

Enhanced volatile emissions and anti-herbivore functions mediated by the synergism between jasmonic acid and salicylic acid pathways in tea plants

The interaction between jasmonic acid (JA) and salicylic acid (SA) pathways, which affects plant stress resistance, is mainly considered to be antagonistic. Using an established theoretical model, we investigated how tea plant (Camellia sinensis) volatiles induced by exogenous elicitors of the JA and SA pathways are affected by the sequence of elicitor application, elicitor identity, and the applied concentrations. We also examined the effects of the volatiles mediated by the JA-SA synergistic interaction on the behaviors of a tea leaf-chewing herbivore (Ectropis grisescens) and its parasitic wasp (Apanteles sp.). The JA and SA pathway interactions were almost always reciprocally synergistic when the two pathways were elicited at different times, except at high JA elicitor concentrations. However, the JA pathway antagonized the SA pathway when they were elicited simultaneously. The elicitor identity affected the degree of JA-SA interaction. The volatiles induced by the JA pathway in the JA-SA reciprocal synergism treatments included up to 11 additional compounds and the total amount of volatiles was up to 7.9-fold higher. Similarly, the amount of emitted volatiles induced by the SA pathway in the reciprocal synergism treatments increased by up to 4.2-fold. Compared with the volatiles induced by either pathway, the enriched volatiles induced by the JA-SA reciprocal synergism similarly repelled E. grisescens, but attracted Apanteles sp. more strongly. Thus, non-simultaneous activation is important for optimizing the JA-SA reciprocal synergism. This reciprocal synergism enables plants to induce multifarious responses, leading to increased biotic stress resistance.

The Effects of Exogenous Salicylic Acid on Endogenous Phytohormone Status in Hordeum vulgare L. under Salt Stress

Acclimation to salt stress in plants is regulated by complex signaling pathways involving endogenous phytohormones. The signaling role of salicylic acid (SA) in regulating crosstalk between endogenous plant growth regulators' levels was investigated in barley (Hordeum vulgare L. 'Ince'; 2n = 14) leaves and roots under salt stress. Salinity (150 and 300 mM NaCl) markedly reduced leaf relative water content (RWC), growth parameters, and leaf water potential (LWP), but increased proline levels in both vegetative organs. Exogenous SA treatment did not significantly affect salt-induced negative effects on RWC, LWP, and growth parameters but increased the leaf proline content of plants under 150 mM salt stress by 23.1%, suggesting that SA enhances the accumulation of proline, which acts as a compatible solute that helps preserve the leaf's water status under salt stress. Changes in endogenous phytohormone levels were also investigated to identify agents that may be involved in responses to increased salinity and exogenous SA. Salt stress strongly affected endogenous cytokinin (CK) levels in both vegetative organs, increasing the concentrations of CK free bases, ribosides, and nucleotides. Indole-3-acetic acid (IAA, auxin) levels were largely unaffected by salinity alone, especially in barley leaves, but SA strongly increased IAA levels in leaves at high salt concentration and suppressed salinity-induced reductions in IAA levels in roots. Salt stress also significantly increased abscisic acid (ABA) and ethylene levels; the magnitude of this increase was reduced by treatment with exogenous SA. Both salinity and SA treatment reduced jasmonic acid (JA) levels at 300 mM NaCl but had little effect at 150 mM NaCl, especially in leaves. These results indicate that under high salinity, SA has antagonistic effects on levels of ABA, JA, ethylene, and most CKs, as well as basic morphological and physiological parameters, but has a synergistic effect on IAA, which was well exhibited by principal component analysis (PCA).

Transcriptomic Landscape of Herbivore Oviposition in Arabidopsis: A Systematic Review

Herbivore oviposition produces all sorts of responses in plants, involving wide and complex genetic rearrangements. Many transcriptomic studies have been performed to understand this interaction, producing a bulk of transcriptomic data. However, the use of many transcriptomic techniques across the years, the lack of comparable transcriptomic context at the time of publication, and the use of outdated databases are limitations to understand this biological process. The current analysis intends to retrieve oviposition studies and process them with up-to-date techniques and updated databases. To reduce heterogeneities, the same processing techniques were applied, and Arabidopsis was selected to avoid divergencies on plant taxa stress response strategies. By doing so, we intended to understand the major mechanisms and regulatory processes linked to oviposition response. Differentially expressed gene (DEG) identification and co-expression network-based analyses were the main tools to achieve this goal. Two microarray studies and three RNA-seq analyses passed the screening criteria. The collected data pertained to the lepidopteran Pieris brassicae and the mite Tetranychus urticae, and covered a timeline from 3 to 144 h. Among the 18, 221 DEGs found, 15, 406 were exclusive of P. brassicae (72 h) and 801 were exclusive for the rest of the experiments. Excluding P. brassicae (72 h), shared genes on the rest of the experiments were twice the unique genes, indicating common response mechanisms were predominant. Enrichment analyses indicated that shared processes were circumscribed to earlier time points, and after 24 h, the divergences escalated. The response was characterized by patterns of time-dependent waves of unique processes. P. brassicae oviposition induced a rich response that shared functions across time points, while T. urticae eggs triggered less but more diverse time-dependent functions. The main processes altered were associated with hormonal cascades [e.g., salicilic acid (SA) and jasmonic acid (JA)], defense [reactive oxygen species (ROS) and glucosinolates], cell wall rearrangements, abiotic stress responses, and energy metabolism. Key gene drivers of the identified processes were also identified and presented. The current results enrich and clarify the information regarding the molecular behavior of the plant in response to oviposition by herbivores. This information is valuable for multiple stress response engineering tools, among other applications.

Transcriptomics Analysis of Wheat Tassel Response to Tilletia laevis Kühn, Which Causes Common Bunt of Wheat

Tilletia laevis Kühn [synonym T. foetida (Wallr.) Liro] can lead to a wheat common bunt, which is one of the most serious diseases affecting kernels, a serious reduction in grain yield, and losses can reach up to 80% in favorable environments. To understand how wheat tassels respond to T. laevis, based on an RNA-Seq technology, we analyzed a host transcript accumulation on healthy wheat tassels and on tassels infected by the pathogen. Our results showed that 7,767 out of 15,658 genes were upregulated and 7,891 out of 15,658 genes were downregulated in wheat tassels. Subsequent gene ontology (GO) showed that differentially expressed genes (DEGs) are predominantly involved in biological processes, cellular components, and molecular functions. Additionally, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that 20 pathways were expressed significantly during the infection of wheat with T. laevis, while biosynthesis of amino acids, carbon metabolism, and starch and sucrose metabolism pathways were more highly expressed. Our findings also demonstrated that genes involved in defense mechanisms and myeloblastosis (MYB) transcription factor families were mostly upregulated, and the RNA-seq results were validated by quantitative real-time polymerase chain reaction (qRT-PCR). This is the first report on transcriptomics analysis of wheat tassels in response to T. laevis, which will contribute to understanding the interaction of T. laevis and wheat, and may provide higher efficiency control strategies, including developing new methods to increase the resistance of wheat crops to T. laevis-caused wheat common bunt.

Function and Mechanism of Jasmonic Acid in Plant Responses to Abiotic and Biotic Stresses

As sessile organisms, plants must tolerate various environmental stresses. Plant hormones play vital roles in plant responses to biotic and abiotic stresses. Among these hormones, jasmonic acid (JA) and its precursors and derivatives (jasmonates, JAs) play important roles in the mediation of plant responses and defenses to biotic and abiotic stresses and have received extensive research attention. Although some reviews of JAs are available, this review focuses on JAs in the regulation of plant stress responses, as well as JA synthesis, metabolism, and signaling pathways. We summarize recent progress in clarifying the functions and mechanisms of JAs in plant responses to abiotic stresses (drought, cold, salt, heat, and heavy metal toxicity) and biotic stresses (pathogen, insect, and herbivore). Meanwhile, the crosstalk of JA with various other plant hormones regulates the balance between plant growth and defense. Therefore, we review the crosstalk of JAs with other phytohormones, including auxin, gibberellic acid, salicylic acid, brassinosteroid, ethylene, and abscisic acid. Finally, we discuss current issues and future opportunities in research into JAs in plant stress responses.

Stress-Related Changes in the Expression and Activity of Plant Carbonic Anhydrases

The data on stress-related changes in the expression and activity of plant carbonic anhydrases (CAs) suggest that they are generally upregulated at moderate stress severity. This indicates probable involvement of CAs in adaptation to drought, high salinity, heat, high light, C_i deficit, and excess bicarbonate. The changes in CA levels under cold stress are less studied and generally represented by the downregulation of CAs excepting βCA2. Excess Cd²⁺ and deficit of Zn²⁺ specifically reduce CA activity and reduce its synthesis. Probable roles of βCAs in stress adaptation include stomatal closure, ROS scavenging and partial compensation for decreased mesophyll CO₂ conductance. βCAs play contrasting roles in pathogen responses, interacting with phytohormone signaling networks. Their role can be either negative or positive, probably depending on the host-pathogen system, pathogen initial titer, and levels of ·NO and ROS. It is still not clear why CAs are suppressed under severe stress levels. It should be noted, that the role of βCAs in the facilitation of CO₂ diffusion and their involvement in redox signaling or ROS detoxication are potentially antagonistic, as they are inactivated by oxidation or nitrosylation. Interestingly, some chloroplastic βCAs may be relocated to the cytoplasm under stress conditions, but the physiological meaning of this effect remains to be studied.

Identification and validation of new reference genes for accurate quantitative reverse transcriptase-PCR normalization in the Antarctic plant Colobanthus quitensis under abiotic stress conditions

The Antarctic ecotype of Colobanthus quitensis is a vascular plant highly adapted to the harsh environmental conditions of Maritime Antarctica which is now facing with the rapid local warming experienced in the Antarctic Peninsula during the last decades. Thus, the identification of the molecular mechanisms leading to the adaptation to this warming trend is a new target for modern cell physiology. The selection of suitable reference genes for quantification of key stress-responsive genes through quantitative Reverse Transcriptase-Polymerase Chain Reaction (qRT-PCR) is important to ensure accurate and reliable results. In this study, we evaluated the expression stability of eleven candidate genes in C. quitensis under different abiotic stress conditions using geNorm and RefFinder tools. The statistical analysis showed that the appropriate reference genes varied depending on the experimental conditions, even if EF1α and PP2Acs ranked as the most stable reference genes when all stress conditions were considered. To further validate the stability of the selected reference genes, the expression patterns of C. quitensis catalase gene (CqCAT) was analyzed. The reference genes validated in this study will be useful for improving the accuracy of qRT-PCR analysis for gene expression studies of the Antarctic ecotype of C. quitensis and could be extended to other ecotypes adapted to low temperatures.

Proteomic Analysis of MeJa-Induced Defense Responses in Rice against Wounding

The role of jasmonates in defense priming has been widely recognized. Priming is a physiological process by which a plant exposed to low doses of biotic or abiotic elicitors activates faster and/or stronger defense responses when subsequently challenged by a stress. In this work, we investigated the impact of MeJA-induced defense responses to mechanical wounding in rice (Oryza sativa). The proteome reprogramming of plants treated with MeJA, wounding or MeJA+wounding has been in-depth analyzed by using a combination of high throughput profiling techniques and bioinformatics tools. Gene Ontology analysis identified protein classes as defense/immunity proteins, hydrolases and oxidoreductases differentially enriched by the three treatments, although with different amplitude. Remarkably, proteins involved in photosynthesis or oxidative stress were significantly affected upon wounding in MeJA-primed plants. Although these identified proteins had been previously shown to play a role in defense responses, our study revealed that they are specifically associated with MeJA-priming. Additionally, we also showed that at the phenotypic level MeJA protects plants from oxidative stress and photosynthetic damage induced by wounding. Taken together, our results add novel insight into the molecular actors and physiological mechanisms orchestrated by MeJA in enhancing rice plants defenses after wounding.

Downregulation of Nuclear Protein H2B Induces Salicylic Acid Mediated Defense Against PVX Infection in Nicotiana benthamiana

Histone H2B protein is not only structurally important for chromosomal DNA packaging but is also involved in the regulation of gene expression, including the immune response of plants against pathogens. In this study, we show that the potato virus X (PVX) infection resulted in the reduced expression of H2B at both the mRNA and protein level in Nicotiana benthamiana. Tobacco rattle virus (TRV)-based virus-induced gene silencing (VIGS) was then used to down-regulate the expression of H2B in N. benthamiana and tests showed that the titre of TRV was similar in these plants to that in control treated plants. When these H2B-silenced plants were inoculated with PVX, the virus spread more slowly through the plant and there was a lower titre of PVX compared to non-silenced plants. Abnormal leaf development and stem necrosis were observed in the H2B-silenced plants, which were alleviated in H2B-silenced NahG transgenic plants suggesting the involvement of salicylic acid (SA) in the production of these symptoms. Indeed, quantitative reverse transcription (qRT)-PCR and liquid chromatography tandem mass spectroscopy (LC-MS) results showed that endogenous SA is increased in H2B-silenced N. benthamiana. Thus, downregulation of H2B induced the accumulation of endogenous SA, which was correlated with stem necrosis and a decreased accumulation of PVX in N. benthamiana.

Unraveling the Initial Plant Hormone Signaling, Metabolic Mechanisms and Plant Defense Triggering the Endomycorrhizal Symbiosis Behavior

Arbuscular mycorrhizal (AM) fungi establish probably one of the oldest mutualistic relationships with the roots of most plants on earth. The wide distribution of these fungi in almost all soil ecotypes and the broad range of host plant species demonstrate their strong plasticity to cope with various environmental conditions. AM fungi elaborate fine-tuned molecular interactions with plants that determine their spread within root cortical tissues. Interactions with endomycorrhizal fungi can bring various benefits to plants, such as improved nutritional status, higher photosynthesis, protection against biotic and abiotic stresses based on regulation of many physiological processes which participate in promoting plant performances. In turn, host plants provide a specific habitat as physical support and a favorable metabolic frame, allowing uptake and assimilation of compounds required for the life cycle completion of these obligate biotrophic fungi. The search for formal and direct evidences of fungal energetic needs raised strong motivated projects since decades, but the impossibility to produce AM fungi under axenic conditions remains a deep enigma and still feeds numerous debates. Here, we review and discuss the initial favorable and non-favorable metabolic plant context that may fate the mycorrhizal behavior, with a focus on hormone interplays and their links with mitochondrial respiration, carbon partitioning and plant defense system, structured according to the action of phosphorus as a main limiting factor for mycorrhizal symbiosis. Then, we provide with models and discuss their significances to propose metabolic targets that could allow to develop innovations for the production and application of AM fungal inocula.

Hydrogen Peroxide: Its Role in Plant Biology and Crosstalk with Signalling Networks

Hydrogen peroxide (H₂O₂) is steadily gaining more attention in the field of molecular biology research. It is a major REDOX (reduction⁻oxidation reaction) metabolite and at high concentrations induces oxidative damage to biomolecules, which can culminate in cell death. However, at concentrations in the low nanomolar range, H₂O₂ acts as a signalling molecule and in many aspects, resembles phytohormones. Though its signalling network in plants is much less well characterized than are those of its counterparts in yeast or mammals, accumulating evidence indicates that the role of H₂O₂-mediated signalling in plant cells is possibly even more indispensable. In this review, we summarize hydrogen peroxide metabolism in plants, the sources and sinks of this compound and its transport via peroxiporins. We outline H₂O₂ perception, its direct and indirect effects and known targets in the transcriptional machinery. We focus on the role of H₂O₂ in plant growth and development and discuss the crosstalk between it and phytohormones. In addition to a literature review, we performed a meta-analysis of available transcriptomics data which provided further evidence for crosstalk between H₂O₂ and light, nutrient signalling, temperature stress, drought stress and hormonal pathways.

Evolution of heat-shock protein expression underlying adaptive responses to environmental stress

Heat-shock proteins (Hsps) and their cognates are primary mitigators of cell stress. With increasingly severe impacts of climate change and other human modifications of the biosphere, the ability of the heat-shock system to affect evolutionary fitness in environments outside the laboratory and to evolve in response is topic of growing importance. Since the last major reviews, several advances have occurred. First, demonstrations of the heat-shock response outside the laboratory now include many additional taxa and environments. Many of these demonstrations are only correlative, however. More importantly, technical advances in "omic" quantification of nucleic acids and proteins, genomewide association analysis, and manipulation of genes and their expression have enabled the field to move beyond correlation. Several consequent advances are already evident: The pathway from heat-shock gene expression to stress tolerance in nature can be extremely complex, mediated through multiple biological processes and systems, and even multiple species. The underlying genes are more numerous, diverse and variable than previously appreciated, especially with respect to their regulatory variation and epigenetic changes. The impacts and limitations (e.g., due to trade-offs) of natural selection on these genes have become more obvious and better established. At last, as evolutionary capacitors, Hsps may have distinctive impacts on the evolution of other genes and ecological consequences.

Verticillium dahliae-Arabidopsis Interaction Causes Changes in Gene Expression Profiles and Jasmonate Levels on Different Time Scales

Verticillium dahliae is a soil-borne vascular pathogen that causes severe wilt symptoms in a wide range of plants. Co-culture of the fungus with Arabidopsis roots for 24 h induces many changes in the gene expression profiles of both partners, even before defense-related phytohormone levels are induced in the plant. Both partners reprogram sugar and amino acid metabolism, activate genes for signal perception and transduction, and induce defense- and stress-responsive genes. Furthermore, analysis of Arabidopsis expression profiles suggests a redirection from growth to defense. After 3 weeks, severe disease symptoms can be detected for wild-type plants while mutants impaired in jasmonate synthesis and perception perform much better. Thus, plant jasmonates have an important influence on the interaction, which is already visible at the mRNA level before hormone changes occur. The plant and fungal genes that rapidly respond to the presence of the partner might be crucial for early recognition steps and the future development of the interaction. Thus they are potential targets for the control of V. dahliae-induced wilt diseases.

Involvement of the def-1 Mutation in the Response of Tomato Plants to Arbuscular Mycorrhizal Symbiosis Under Well-Watered and Drought Conditions

Jasmonic acid (JA) and arbuscular mycorrhizal (AM) symbioses are known to protect plants against abiotic and biotic stresses, but are also involved in the regulation of root hydraulic conductance (L). The objective of this experiment was to elucidate the role of JA in the water relations and hormonal regulation of AM plants under drought by using tomato plants defective in the synthesis of JA (def-1). Our results showed that JA is involved in the uptake and transport of water through its effect on both physiological parameters (stomatal conductance and L) and molecular parameters, mainly by controlling the expression and abundance of aquaporins. We observed that def-1 plants increased the expression of seven plant aquaporin genes under well-watered conditions in the absence of AM fungus, which partly explain the increment of L by this mutation under well-watered conditions. In addition, the effects of the AM symbiosis on plants were modified by the def-1 mutation, with the expression of some aquaporins and plant hormone concentration being disturbed. On the other hand, methyl salicylate (MeSA) content was increased in non-mycorrhizal def-1 plants, suggesting that MeSA and JA can act together in the regulation of L. In a complementary experiment, it was found that exogenous MeSA increased L, confirming our hypothesis. Likewise, we confirmed that JA, ABA and SA are hormones involved in plant mechanisms to cope with stressful situations, their concentrations being controlled by the AM symbiosis. In conclusion, under well-watered conditions, the def-1 mutation mimics the effects of AM symbiosis, but under drought conditions the def-1 mutation changed the effects of the AM symbiosis on plants.

Mutation in Rice Abscisic Acid2 Results in Cell Death, Enhanced Disease-Resistance, Altered Seed Dormancy and Development

Lesion mimic mutants display spontaneous cell death, and thus are valuable for understanding the molecular mechanism of cell death and disease resistance. Although a lot of such mutants have been characterized in rice, the relationship between lesion formation and abscisic acid (ABA) synthesis pathway is not reported. In the present study, we identified a rice mutant, lesion mimic mutant 9150 (lmm9150), exhibiting spontaneous cell death, pre-harvest sprouting, enhanced growth, and resistance to rice bacterial and blast diseases. Cell death in the mutant was accompanied with excessive accumulation of H₂O₂. Enhanced disease resistance was associated with cell death and upregulation of defense-related genes. Map-based cloning identified a G-to-A point mutation resulting in a D-to-N substitution at the amino acid position 110 of OsABA2 (LOC_Os03g59610) in lmm9150. Knock-out of OsABA2 through CRISPR/Cas9 led to phenotypes similar to those of lmm9150. Consistent with the function of OsABA2 in ABA biosynthesis, ABA level in the lmm9150 mutant was significantly reduced. Moreover, exogenous application of ABA could rescue all the mutant phenotypes of lmm9150. Taken together, our data linked ABA deficiency to cell death and provided insight into the role of ABA in rice disease resistance.

Assessing the Role of ETHYLENE RESPONSE FACTOR Transcriptional Repressors in Salicylic Acid-Mediated Suppression of Jasmonic Acid-Responsive Genes

Salicylic acid (SA) and jasmonic acid (JA) cross-communicate in the plant immune signaling network to finely regulate induced defenses. In Arabidopsis, SA antagonizes many JA-responsive genes, partly by targeting the ETHYLENE RESPONSE FACTOR (ERF)-type transcriptional activator ORA59. Members of the ERF transcription factor family typically bind to GCC-box motifs in the promoters of JA- and ethylene-responsive genes, thereby positively or negatively regulating their expression. The GCC-box motif is sufficient for SA-mediated suppression of JA-responsive gene expression. Here, we investigated whether SA-induced ERF-type transcriptional repressors, which may compete with JA-induced ERF-type activators for binding at the GCC-box, play a role in SA/JA antagonism. We selected ERFs that are transcriptionally induced by SA and/or possess an EAR transcriptional repressor motif. Several of the 16 ERFs tested suppressed JA-dependent gene expression, as revealed by enhanced JA-induced PDF1.2 or VSP2 expression levels in the corresponding erf mutants, while others were involved in activation of these genes. However, SA could antagonize JA-induced PDF1.2 or VSP2 in all erf mutants, suggesting that the tested ERF transcriptional repressors are not required for SA/JA cross-talk. Moreover, a mutant in the co-repressor TOPLESS, that showed reduction in repression of JA signaling, still displayed SA-mediated antagonism of PDF1.2 and VSP2. Collectively, these results suggest that SA-regulated ERF transcriptional repressors are not essential for antagonism of JA-responsive gene expression by SA. We further show that de novo SA-induced protein synthesis is required for suppression of JA-induced PDF1.2, pointing to SA-stimulated production of an as yet unknown protein that suppresses JA-induced transcription.

Transcriptomics Analysis of Apple Leaves in Response to Alternaria alternata Apple Pathotype Infection

Alternaria blotch disease of apple (Malus × domestica Borkh.), caused by the apple pathotype of Alternaria alternata, is one of the most serious fungal diseases to affect apples. To develop an understanding of how apples respond to A. alternata apple pathotype (AAAP) infection, we examined the host transcript accumulation over the period between 0 and 72 h post AAAP inoculation. Large-scale gene expression analysis was conducted of the compatible interaction between "Starking Delicious" apple cultivar and AAAP using RNA-Seq and digital gene expression (DGE) profiling methods. Our results show that a total of 9080 differentially expressed genes (DEGs) were detected (>two-fold and FDR < 0.001) by RNA-Seq. During the early phase of infection, 12 h post inoculation (HPI), AAAP exhibited limited fungal development and little change in the transcript accumulation status (950 DEGs). During the intermediate phase of infection, the period between 18 and 36 HPI, increased fungal development, active infection, and increased transcript accumulation were detected (4111 and 3838 DEGs detected at each time point, respectively). The majority of DEGs were detected by 72 HPI, suggesting that this is an important time point in the response of apples' AAAP infection. Subsequent gene ontology (GO) and pathway enrichment analyses showed that DEGs are predominately involved in biological processes and metabolic pathways; results showed that almost gene associated with photosynthesis, oxidation-reduction were down-regulated, while transcription factors (i.e., WRKY, MYB, NAC, and Hsf) and DEGs involved in cell wall modification, defense signaling, the synthesis of defense-related metabolites, including pathogenesis-related (PRs) genes and phenylpropanoid/cyanoamino acid /flavonoid biosynthesis, were activated during this process. Our study also suggested that the cell wall defensive vulnerability and the down-regulation of most PRs and HSP70s in "Starking Delicious" following AAAP infection might interpret its susceptible to AAAP.

Reverse Genetics and High Throughput Sequencing Methodologies for Plant Functional Genomics

In the post-genomic era, increasingly sophisticated genetic tools are being developed with the long-term goal of understanding how the coordinated activity of genes gives rise to a complex organism. With the advent of the next generation sequencing associated with effective computational approaches, wide variety of plant species have been fully sequenced giving a wealth of data sequence information on structure and organization of plant genomes. Since thousands of gene sequences are already known, recently developed functional genomics approaches provide powerful tools to analyze plant gene functions through various gene manipulation technologies. Integration of different omics platforms along with gene annotation and computational analysis may elucidate a complete view in a system biology level. Extensive investigations on reverse genetics methodologies were deployed for assigning biological function to a specific gene or gene product. We provide here an updated overview of these high throughout strategies highlighting recent advances in the knowledge of functional genomics in plants.

Analysis of salicylic acid-dependent pathways in Arabidopsis thaliana following infection with Plasmodiophora brassicae and the influence of salicylic acid on disease

Salicylic acid (SA) biosynthesis, the expression of SA-related genes and the effect of SA on the Arabidopsis-Plasmodiophora brassicae interaction were examined. Biochemical analyses revealed that, in P. brassicae-infected Arabidopsis, the majority of SA is synthesized from chorismate. Real-time monitored expression of a gene for isochorismate synthase was induced on infection. SA can be modified after accumulation, either by methylation, improving its mobility, or by glycosylation, as one possible reaction for inactivation. Quantitative reverse transcription-polymerase chain reaction (qPCR) confirmed the induction of an SA methyltransferase gene, whereas SA glucosyltransferase expression was not changed after infection. Col-0 wild-type (wt) did not provide a visible phenotypic resistance response, whereas the Arabidopsis mutant dnd1, which constitutively activates the immune system, showed reduced gall scores. As dnd1 showed control of the pathogen, exogenous SA was applied to Arabidopsis in order to test whether it could suppress clubroot. In wt, sid2 (SA biosynthesis), NahG (SA-deficient) and npr1 (SA signalling-impaired) mutants, SA treatment did not alter the gall score, but positively affected the shoot weight. This suggests that SA alone is not sufficient for Arabidopsis resistance against P. brassicae. Semi-quantitative PCR revealed that wt, cpr1, dnd1 and sid2 showed elevated PR-1 expression on P. brassicae and SA + P. brassicae inoculation at 2 and 3 weeks post-inoculation (wpi), whereas NahG and npr1 showed no expression. This work contributes to the understanding of SA involvement in the Arabidopsis-P. brassicae interaction.

Arbuscular mycorrhizal symbiosis and methyl jasmonate avoid the inhibition of root hydraulic conductivity caused by drought

Hormonal regulation and symbiotic relationships provide benefits for plants to overcome stress conditions. The aim of this study was to elucidate the effects of exogenous methyl jasmonate (MeJA) application on root hydraulic conductivity (L) of Phaseolus vulgaris plants which established arbuscular mycorrhizal (AM) symbiosis under two water regimes (well-watered and drought conditions). The variation in endogenous contents of several hormones (MeJA, JA, abscisic acid (ABA), indol-3-acetic acid (IAA), salicylic acid (SA)) and the changes in aquaporin gene expression, protein abundance and phosphorylation state were analyzed. AM symbiosis decreased L under well-watered conditions, which was partially reverted by the MeJA treatment, apparently by a drop in root IAA contents. Also, AM symbiosis and MeJA prevented inhibition of L under drought conditions, most probably by a reduction in root SA contents. Additionally, the gene expression of two fungal aquaporins was upregulated under drought conditions, independently of the MeJA treatment. Plant aquaporin gene expression could not explain the behaviour of L. Conversely, evidence was found for the control of L by phosphorylation of aquaporins. Hence, MeJA addition modified the response of L to both AM symbiosis and drought, presumably by regulating the root contents of IAA and SA and the phosphorylation state of aquaporins.

Trait Specific Expression Profiling of Salt Stress Responsive Genes in Diverse Rice Genotypes as Determined by Modified Significance Analysis of Microarrays

Stress responsive gene expression is commonly profiled in a comparative manner involving different stress conditions or genotypes with contrasting reputation of tolerance/resistance. In contrast, this research exploited a wide natural variation in terms of taxonomy, origin and salt sensitivity in eight genotypes of rice to identify the trait specific patterns of gene expression under salt stress. Genome wide transcptomic responses were interrogated by the weighted continuous morpho-physiological trait responses using modified Significance Analysis of Microarrays. More number of genes was found to be differentially expressed under salt stressed compared to that of under unstressed conditions. Higher numbers of genes were observed to be differentially expressed for the traits shoot Na(+)/K(+), shoot Na(+), root K(+), biomass and shoot Cl(-), respectively. The results identified around 60 genes to be involved in Na(+), K(+), and anion homeostasis, transport, and transmembrane activity under stressed conditions. Gene Ontology (GO) enrichment analysis identified 1.36% (578 genes) of the entire transcriptome to be involved in the major molecular functions such as signal transduction (>150 genes), transcription factor (81 genes), and translation factor activity (62 genes) etc., under salt stress. Chromosomal mapping of the genes suggests that majority of the genes are located on chromosomes 1, 2, 3, 6, and 7. The gene network analysis showed that the transcription factors and translation initiation factors formed the major gene networks and are mostly active in nucleus, cytoplasm and mitochondria whereas the membrane and vesicle bound proteins formed a secondary network active in plasma membrane and vacuoles. The novel genes and the genes with unknown functions thus identified provide picture of a synergistic salinity response representing the potentially fundamental mechanisms that are active in the wide natural genetic background of rice and will be of greater use once their roles are functionally verified.

Role of the proteome in phytohormonal signaling

Phytohormones are orchestrators of plant growth and development. A lot of time and effort has been invested in attempting to comprehend their complex signaling pathways but despite success in elucidating some key components, molecular mechanisms in the transduction pathways are far from being resolved. The last decade has seen a boom in the analysis of phytohormone-responsive proteins. Abscisic acid, auxin, brassinosteroids, cytokinin, ethylene, gibberellins, nitric oxide, oxylipins, strigolactones, salicylic acid--all have been analyzed to various degrees. For this review, we collected data from proteome-wide analyses resulting in a list of over 2000 annotated proteins from Arabidopsis proteomics and nearly 500 manually filtered protein families merged from all the data available from different species. We present the currently accepted model of phytohormone signaling, highlight the contributions made by proteomic-based research and describe the key nodes in phytohormone signaling networks, as revealed by proteome analysis. These include ubiquitination and proteasome mediated degradation, calcium ion signaling, redox homeostasis, and phosphoproteome dynamics. Finally, we discuss potential pitfalls and future perspectives in the field. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.

Exploring Jasmonates in the Hormonal Network of Drought and Salinity Responses

Present and future food security is a critical issue compounded by the consequences of climate change on agriculture. Stress perception and signal transduction in plants causes changes in gene or protein expression which lead to metabolic and physiological responses. Phytohormones play a central role in the integration of different upstream signals into different adaptive outputs such as changes in the activity of ion-channels, protein modifications, protein degradation, and gene expression. Phytohormone biosynthesis and signaling, and recently also phytohormone crosstalk have been investigated intensively, but the function of jasmonates under abiotic stress is still only partially understood. Although most aspects of jasmonate biosynthesis, crosstalk and signal transduction appear to be similar for biotic and abiotic stress, novel aspects have emerged that seem to be unique for the abiotic stress response. Here, we review the knowledge on the role of jasmonates under drought and salinity. The crosstalk of jasmonate biosynthesis and signal transduction pathways with those of abscisic acid (ABA) is particularly taken into account due to the well-established, central role of ABA under abiotic stress. Likewise, the accumulating evidence of crosstalk of jasmonate signaling with other phytohormones is considered as important element of an integrated phytohormonal response. Finally, protein post-translational modification, which can also occur without de novo transcription, is treated with respect to its implications for phytohormone biosynthesis, signaling and crosstalk. To breed climate-resilient crop varieties, integrated understanding of the molecular processes is required to modulate and tailor particular nodes of the network to positively affect stress tolerance.

Over-Expression of Rice CBS Domain Containing Protein, OsCBSX3, Confers Rice Resistance to Magnaporthe oryzae Inoculation

Cystathionine β-synthase (CBS) domain containing proteins (CDCPs) constitute a big family in plants and some members in this family have been implicated in a variety of biological processes, but the precise functions and the underlying mechanism of the majority of this family in plant immunity remain to be elucidated. In the present study, a CBS domain containing protein gene, OsCBSX3, is functionally characterized in rice resistance against Magnaporthe oryzae (M. oryzae). By quantitative real-time PCR, transcripts of OsCBSX3 are up-regulated significantly by inoculation of M. oryzae and the exogenously applied salicylic acid (SA) and methyl jasmonate (MeJA). OsCBSX3 is exclusively localized to the plasma membrane by transient expression of OsCBSX3 fused to green fluorescent protein (GFP) through approach of Agrobacterium infiltration in Nicotiana benthamiana leaves. The plants of homozygous T3 transgenic rice lines of over-expressing OsCBSX3 exhibit significant enhanced resistance to M. oryzae inoculation, manifested by decreased disease symptoms, and inhibition of pathogen growth detected in DNA. Consistently, the over-expression of OsCBSX3 enhances the transcript levels of immunity associated marker genes including PR1a, PR1b, PR5, AOS2, PAL, NH1, and OsWRKY13 in plants inoculated with M. oryzae. These results suggest that OsCBSX3 acts as a positive regulator in resistance of rice to M. oryzae regulated by SA and JA-mediated signaling pathways synergistically.

Identifying the potential extracellular electron transfer pathways from a c-type cytochrome network

Extracellular electron transfer (EET) is the key feature of some bacteria, such as Geobacter sulfurreducens and Shewanella oneidensis. Via EET processes, these bacteria can grow on electrode surfaces and make current output of microbial fuel cells. c-Type cytochromes can be used as carriers to transfer electrons, which play an important role in EET processes. Typically, from the inner (cytoplasmic) membrane through the periplasm to the outer membrane, they could form EET pathways. Recent studies suggest that a group of c-type cytochromes could form a network which extended the well-known EET pathways. We obtained the protein interaction information for all 41 c-type cytochromes in Shewanella oneidensis MR-1, constructed a large-scale protein interaction network, and studied its structural characteristics and functional significance. Centrality analysis has identified the top 10 key proteins of the network, and 7 of them are associated with electricity production in the bacteria, which suggests that the ability of Shewanella oneidensis MR-1 to produce electricity might be derived from the unique structure of the c-type cytochrome network. By modularity analysis, we obtained 5 modules from the network. The subcellular localization study has shown that the proteins in these modules all have diversiform cellular compartments, which reflects their potential to form EET pathways. In particular, combination of protein subcellular localization and operon analysis, the well-known and new candidate EET pathways are obtained from the Mtr-like module, indicating that potential EET pathways could be obtained from such a c-type cytochrome network.

Interactions between the jasmonic and salicylic acid pathway modulate the plant metabolome and affect herbivores of different feeding types

The phytohormones jasmonic acid (JA) and salicylic acid (SA) mediate induced plant defences and the corresponding pathways interact in a complex manner as has been shown on the transcript and proteine level. Downstream, metabolic changes are important for plant-herbivore interactions. This study investigated metabolic changes in leaf tissue and phloem exudates of Plantago lanceolata after single and combined JA and SA applications as well as consequences on chewing-biting (Heliothis virescens) and piercing-sucking (Myzus persicae) herbivores. Targeted metabolite profiling and untargeted metabolic fingerprinting uncovered different categories of plant metabolites, which were influenced in a specific manner, indicating points of divergence, convergence, positive crosstalk and pronounced mutual antagonism between the signaling pathways. Phytohormone-specific decreases of primary metabolite pool sizes in the phloem exudates may indicate shifts in sink-source relations, resource allocation, nutrient uptake or photosynthesis. Survival of both herbivore species was significantly reduced by JA and SA treatments. However, the combined application of JA and SA attenuated the negative effects at least against H. virescens suggesting that mutual antagonism between the JA and SA pathway may be responsible. Pathway interactions provide a great regulatory potential for the plant that allows triggering of appropriate defences when attacked by different antagonist species.

Priming of protein expression in the defence response of Zantedeschia aethiopica to Pectobacterium carotovorum

The defence response of Zantedeschia aethiopica, a natural rhizomatous host of the soft rot bacterium Pectobacterium carotovorum, was studied following the activation of common induced resistance pathways—systemic acquired resistance and induced systemic resistance. Proteomic tools were used, together with in vitro quantification and in situ localization of selected oxidizing enzymes. In total, 527 proteins were analysed by label-free mass spectrometry (MS) and annotated against the National Center for Biotechnology Information (NCBI) nonredundant (nr) protein database of rice (Oryza sativa). Of these, the fore most differentially expressed group comprised 215 proteins that were primed following application of methyl jasmonate (MJ) and subsequent infection with the pathogen. Sixty-five proteins were down-regulated following MJ treatments. The application of benzothiadiazole (BTH) increased the expression of 23 proteins; however, subsequent infection with the pathogen repressed their expression and did not induce priming. The sorting of primed proteins by Gene Ontology protein function category revealed that the primed proteins included nucleic acid-binding proteins, cofactor-binding proteins, ion-binding proteins, transferases, hydrolases and oxidoreductases. In line with the highlighted involvement of oxidoreductases in the defence response, we determined their activities, priming pattern and localization in planta. Increased activities were confined to the area surrounding the pathogen penetration site, associating these enzymes with the induced systemic resistance afforded by the jasmonic acid signalling pathway. The results presented here demonstrate the concerted priming of protein expression following MJ treatment, making it a prominent part of the defence response of Z. aethiopica to P. carotovorum.

A liquid chromatography/electrospray ionisation tandem mass spectrometry method for the simultaneous quantification of salicylic, jasmonic and abscisic acids in Coffea arabica leaves

BACKGROUND

Plants have developed an efficient system of recognition that induces a complex network of signalling molecules such as salicylic acid (SA), jasmonic acid (JA) and abscisic acid (ABA) in case of a pathogenic infection. The use of specific and sensitive methods is mandatory for the analysis of compounds in these complex samples.

RESULTS

In this study a liquid chromatography/electrospray ionisation tandem mass spectrometry method was developed and validated for the simultaneous quantification of SA, JA and ABA in Coffea arabica (L.) leaves in order to understand the role of these phytohormones in the signalling network involved in the coffee defence response against Hemileia vastatrix. The results showed that the method was specific, linear (r ≥ 0.99) in the range 0.125-1.00 µg mL⁻¹ for JA and ABA and 0.125-5.00 µg mL⁻¹ for SA, and precise (relative standard deviation ≤11%), and the limit of detection (0.010 µg g⁻¹ fresh weight) was adequate for quantifying these phytohormones in this type of matrix.

CONCLUSION

In comparison with healthy leaves, those infected with H. vastatrix (resistance reaction) displayed an increase in SA level 24 h after inoculation, suggesting the involvement of an SA-dependent pathway in coffee resistance.