Chromatin modification acts as a memory for systemic acquired resistance in the plant stress response

Long-distance communication and signal amplification in systemic acquired resistance

Systemic acquired resistance (SAR) is an inducible defense mechanism in plants that confers enhanced resistance against a variety of pathogens. SAR is activated in the uninfected systemic (distal) organs in response to a prior (primary) infection elsewhere in the plant. SAR is associated with the activation of salicylic acid (SA) signaling and the priming of defense responses for robust activation in response to subsequent infections. The activation of SAR requires communication by the primary infected tissues with the distal organs. The vasculature functions as a conduit for the translocation of factors that facilitate long-distance intra-plant communication. In recent years, several metabolites putatively involved in long-distance signaling have been identified. These include the methyl ester of SA (MeSA), the abietane diterpenoid dehydroabietinal (DA), the dicarboxylic acid azelaic acid (AzA), and a glycerol-3-phosphate (G3P)-dependent factor. Long-distance signaling by some of these metabolites also requires the lipid-transfer protein DIR1 (DEFECTIVE IN INDUCED RESISTANCE 1). The relative contribution of these factors in long-distance signaling is likely influenced by environmental conditions, for example light. In the systemic leaves, the AGD2-LIKE DEFENSE RESPONSE PROTEIN1 (ALD1)-dependent production of the lysine catabolite pipecolic acid (Pip), FLAVIN-DEPENDENT MONOOXYGENASE1 (FMO1) signaling, as well as SA synthesis and downstream signaling are required for the activation of SAR. This review summarizes the involvement and interaction between long-distance SAR signals and details the recently discovered role of Pip in defense amplification and priming that allows plants to acquire immunity at the systemic level. Recent advances in SA signaling and perception are also highlighted.

Priming of the Arabidopsis pattern-triggered immunity response upon infection by necrotrophic Pectobacterium carotovorum bacteria

Boosted responsiveness of plant cells to stress at the onset of pathogen- or chemically induced resistance is called priming. The chemical β-aminobutyric acid (BABA) enhances Arabidopsis thaliana resistance to hemibiotrophic bacteria through the priming of the salicylic acid (SA) defence response. Whether BABA increases Arabidopsis resistance to the necrotrophic bacterium Pectobacterium carotovorum ssp. carotovorum (Pcc) is not clear. In this work, we show that treatment with BABA protects Arabidopsis against the soft-rot pathogen Pcc. BABA did not prime the expression of the jasmonate/ethylene-responsive gene PLANT DEFENSIN 1.2 (PDF1.2), the up-regulation of which is usually associated with resistance to necrotrophic pathogens. Expression of the SA marker gene PATHOGENESIS RELATED 1 (PR1) on Pcc infection was primed by BABA treatment, but SA-defective mutants demonstrated a wild-type level of BABA-induced resistance against Pcc. BABA primed the expression of the pattern-triggered immunity (PTI)-responsive genes FLG22-INDUCED RECEPTOR-LIKE KINASE 1 (FRK1), ARABIDOPSIS NON-RACE SPECIFIC DISEASE RESISTANCE GENE (NDR1)/HAIRPIN-INDUCED GENE (HIN1)-LIKE 10 (NHL10) and CYTOCHROME P450, FAMILY 81 (CYP81F2) after inoculation with Pcc or after treatment with purified bacterial microbe-associated molecular patterns, such as flg22 or elf26. PTI-mediated callose deposition was also potentiated in BABA-treated Arabidopsis, and BABA boosted Arabidopsis stomatal immunity to Pcc. BABA treatment primed the PTI response in the SA-defective mutants SA induction deficient 2-1 (sid2-1) and phytoalexin deficient 4-1 (pad4-1). In addition, BABA priming was associated with open chromatin configurations in the promoter region of PTI marker genes. Our data indicate that BABA primes the PTI response upon necrotrophic bacterial infection and suggest a role for the PTI response in BABA-induced resistance.

The proteome response of potato leaves to priming agents and S-nitrosoglutathione

The primed mobilization for more potent defense responses to subsequent stress has been shown for many plant species, but there is a growing need to identify reliable molecular markers for this unique phenomenon. In the present study a proteomic approach was used to screen similarities in protein abundance in leaves of primed potato (Solanum tuberosum L.) treated with four well-known inducers of plant resistance, i.e. β-aminobutyric acid (BABA), γ-aminobutyric acid (GABA), Laminarin and 2,6-dichloroisonicotinic acid (INA), respectively. Moreover, to gain insight into the importance of nitric oxide (NO) in primed protein accumulation the potato leaves were supplied by S-nitrosoglutathione (GSNO), as an NO donor. The comparative analysis, using two-dimensional electrophoresis and mass spectrometry, revealed that among 25 proteins accumulated specifically after BABA, GABA, INA and Laminarin treatments, 13 proteins were accumulated also in response to GSNO. Additionally, overlapping proteomic changes between BABA-primed and GSNO-treated leaves showed 5 protein spots absent in the proteome maps obtained in response to the other priming agents. The identified 18 proteins belonged, in most cases, to functional categories of primary metabolism. The selected proteins including three redox-regulated enzymes, i.e. glyceraldehyde 3-phosphate dehydrogenase, carbonic anhydrase, and fructose-bisphosphate aldolase, were discussed in relation to the plant defence responses. Taken together, the overlapping effects in the protein profiles obtained between priming agents, GSNO and cPTIO treatments provide insight indicating that the primed potato exhibits unique changes in the primary metabolism, associated with selective protein modification via NO.

Downy mildew resistance induced by Trichoderma harzianum T39 in susceptible grapevines partially mimics transcriptional changes of resistant genotypes

BACKGROUND

Downy mildew, caused by Plasmopara viticola, is one of the most severe diseases of grapevine and is commonly controlled by fungicide treatments. The beneficial microorganism Trichoderma harzianum T39 (T39) can induce resistance to downy mildew, although the molecular events associated with this process have not yet been elucidated in grapevine. A next generation RNA sequencing (RNA-Seq) approach was used to study global transcriptional changes associated with resistance induced by T39 in Vitis vinifera Pinot Noir leaves. The long-term aim was to develop strategies to optimize the use of this agent for downy mildew control.

RESULTS

More than 14.8 million paired-end reads were obtained for each biological replicate of T39-treated and control leaf samples collected before and 24 h after P. viticola inoculation. RNA-Seq analysis resulted in the identification of 7,024 differentially expressed genes, highlighting the complex transcriptional reprogramming of grapevine leaves during resistance induction and in response to pathogen inoculation. Our data show that T39 has a dual effect: it directly modulates genes related to the microbial recognition machinery, and it enhances the expression of defence-related processes after pathogen inoculation. Whereas several genes were commonly affected by P. viticola in control and T39-treated plants, opposing modulation of genes related to responses to stress and protein metabolism was found. T39-induced resistance partially inhibited some disease-related processes and specifically activated defence responses after P. viticola inoculation, causing a significant reduction of downy mildew symptoms.

CONCLUSIONS

The global transcriptional analysis revealed that defence processes known to be implicated in the reaction of resistant genotypes to downy mildew were partially activated by T39-induced resistance in susceptible grapevines. Genes identified in this work are an important source of markers for selecting novel resistance inducers and for the analysis of environmental conditions that might affect induced resistance mechanisms.

Epigenetics and crop improvement

There is considerable excitement about the potential for epigenetic information to contribute to heritable variation in many species. Our understanding of the molecular mechanisms of epigenetic inheritance is rapidly growing, and it is now possible to profile the epigenome at high resolution. Epigenetic information plays a role in developmental gene regulation, response to the environment, and in natural variation of gene expression levels. Because of these central roles, there is the potential for epigenetics to play a role in crop improvement strategies including the selection for favorable epigenetic states, creation of novel epialleles, and regulation of transgene expression. In this review we consider the potential, and the limitations, of epigenetic variation in crop improvement.

Nitric oxide-mediated stress imprint in potato as an effect of exposure to a priming agent

We investigated how potato exposed to a chemical agent could activate nitric oxide (NO)-dependent events facilitating more potent defense responses to a subsequent pathogen attack. Obtained data revealed that all applied inducers, i.e., β-aminobutyric acid (BABA), γ-aminobutyric acid (GABA), laminarin, or 2,6-dichloroisonicotinic acid (INA), were active stimuli in potentiating NO synthesis in the primed potato. It is assumed, for the mechanism proposed in this paper, that priming involves reversible S-nitrosylated protein (S-nitrosothiols [SNO]) storage as one of the short-term stress imprint components, apart from epigenetic changes sensitized by NO. Based on BABA- and GABA-induced events, it should be stated that a rise in NO generation and coding the NO message in SNO storage at a relatively low threshold together with histone H2B upregulation might create short-term imprint activation, facilitating acquisition of a competence to react faster after challenge inoculation. Laminarin elicited strong NO upregulation with an enhanced SNO pool-altered biochemical imprint in the form of less effective local recall, nevertheless being fully protective in distal responses against P. infestans. In turn, INA showed the most intensified NO generation and abundant formation of SNO, both after the inducer treatment and challenge inoculation abolishing potato resistance against the pathogen. Our results indicate, for the first time, that a precise control of synthesized NO in cooperation with reversible SNO storage and epigenetic modifications might play an important role in integrating and coordinating defense potato responses in the priming phenomenon.

Epigenetic responses to stress: triple defense?

Stressful conditions for plants can originate from numerous physical, chemical and biological factors, and plants have developed a plethora of survival strategies including developmental and morphological adaptations, specific signaling and defense pathways as well as innate and acquired immunity. While it has become clear in recent years that many stress responses involve epigenetic components, we are far from understanding the mechanisms and molecular interactions. Extending our knowledge is fundamental, not least for plant breeding and conservation biology. This review will highlight recent insights into epigenetic stress responses at the level of signaling, chromatin modification, and potentially heritable consequences.

SOS - too many signals for systemic acquired resistance?

Following pathogen infection, activation of systemic acquired resistance (SAR) in uninfected tissues requires transmission of a signal(s) from the infected tissue via the vasculature. Several candidates for this long-distance signal have been identified, including methyl salicylate (MeSA), an SFD1/GLY1-derived glycerol-3-phosphate (G3P)-dependent signal, the lipid-transfer protein DIR1, the dicarboxylic acid azelaic acid (AzA), the abietane diterpenoid dehydroabietinal (DA), jasmonic acid (JA), and the amino acid-derivative pipecolic acid (Pip). Some of these signals work cooperatively to activate SAR and/or regulate MeSA metabolism. However, Pip appears to activate SAR via an independent pathway that may impinge on these other signaling pathway(s) during de novo salicylic acid (SA) biosynthesis in the systemic tissue. Thus, a complex web of cross-interacting signals appears to activate SAR.

HDA19 is required for the repression of salicylic acid biosynthesis and salicylic acid-mediated defense responses in Arabidopsis

To cope with a lifetime of exposure to a variety of pathogens, plants have developed exquisite and refined defense mechanisms that vary depending on the type of attacking pathogen. Defense-associated transcriptional reprogramming is a central part of plant defense mechanisms. Chromatin modification has recently been shown to be another layer of regulation for plant defense mechanisms. Here, we show that the RPD3/HDA1-class histone deacetylase HDA19 is involved in the repression of salicylic acid (SA)-mediated defense responses in Arabidopsis. Loss of HDA19 activity increased SA content and increased the expression of a group of genes required for accumulation of SA as well as pathogenesis related (PR) genes, resulting in enhanced resistance to Pseudomonas syringae. We found that HDA19 directly associates with and deacetylates histones at the PR1 and PR2 promoters. Thus, our study shows that HDA19, by modifying chromatin to a repressive state, ensures low basal expression of defense genes, such as PR1, under unchallenged conditions, as well as their proper induction without overstimulation during defense responses to pathogen attacks. Thus, the role of HDA19 might be critical in preventing unnecessary activation and self-destructive overstimulation of defense responses, allowing successful growth and development.

The epigenetic machinery controlling transgenerational systemic acquired resistance

Progeny from diseased Arabidopsis shows enhanced resistance, which is associated with priming of defense genes. This transgenerational systemic acquired resistance (SAR) is effective against biotrophic pathogens, such as the downy mildew pathogen Hyaloperonospora arabidopsidis. In this study, we have examined mutants in RNA-directed DNA methylation (RdDM) for transgenerational SAR. Our analysis suggests that transgenerational SAR is regulated by the RdDM pathway and transmitted by hypomethylation at CpNpG sites.

Genome-Wide Characterization of ISR Induced in Arabidopsis thaliana by Trichoderma hamatum T382 Against Botrytis cinerea Infection

In this study, the molecular basis of the induced systemic resistance (ISR) in Arabidopsis thaliana by the biocontrol fungus Trichoderma hamatum T382 against the phytopathogen Botrytis cinerea B05-10 was unraveled by microarray analysis both before (ISR-prime) and after (ISR-boost) additional pathogen inoculation. The observed high numbers of differentially expressed genes allowed us to classify them according to the biological pathways in which they are involved. By focusing on pathways instead of genes, a holistic picture of the mechanisms underlying ISR emerged. In general, a close resemblance is observed between ISR-prime and systemic acquired resistance, the systemic defense response that is triggered in plants upon pathogen infection leading to increased resistance toward secondary infections. Treatment with T. hamatum T382 primes the plant (ISR-prime), resulting in an accelerated activation of the defense response against B. cinerea during ISR-boost and a subsequent moderation of the B. cinerea induced defense response. Microarray results were validated for representative genes by qRT-PCR. The involvement of various defense-related pathways was confirmed by phenotypic analysis of mutants affected in these pathways, thereby proving the validity of our approach. Combined with additional anthocyanin analysis data these results all point to the involvement of the phenylpropanoid pathway in T. hamatum T382-induced ISR.

Dissecting phosphite-induced priming in Arabidopsis infected with Hyaloperonospora arabidopsidis

Phosphite (Phi), a phloem-mobile oxyanion of phosphorous acid (H(3)PO(3)), protects plants against diseases caused by oomycetes. Its mode of action is unclear, as evidence indicates both direct antibiotic effects on pathogens as well as inhibition through enhanced plant defense responses, and its target(s) in the plants is unknown. Here, we demonstrate that the biotrophic oomycete Hyaloperonospora arabidopsidis (Hpa) exhibits an unusual biphasic dose-dependent response to Phi after inoculation of Arabidopsis (Arabidopsis thaliana), with characteristics of indirect activity at low doses (10 mm or less) and direct inhibition at high doses (50 mm or greater). The effect of low doses of Phi on Hpa infection was nullified in salicylic acid (SA)-defective plants (sid2-1, NahG) and in a mutant impaired in SA signaling (npr1-1). Compromised jasmonate (jar1-1) and ethylene (ein2-1) signaling or abscisic acid (aba1-5) biosynthesis, reactive oxygen generation (atrbohD), or accumulation of the phytoalexins camalexin (pad3-1) and scopoletin (f6'h1-1) did not affect Phi activity. Low doses of Phi primed the accumulation of SA and Pathogenesis-Related protein1 transcripts and mobilized two essential components of basal resistance, Enhanced Disease Susceptibility1 and Phytoalexin Deficient4, following pathogen challenge. Compared with inoculated, Phi-untreated plants, the gene expression, accumulation, and phosphorylation of the mitogen-activated protein kinase MPK4, a negative regulator of SA-dependent defenses, were reduced in plants treated with low doses of Phi. We propose that Phi negatively regulates MPK4, thus priming SA-dependent defense responses following Hpa infection.

Stress-induced chromatin changes: a critical view on their heritability

The investigation of stress responses has been a focus of plant research, breeding and biotechnology for a long time. Insight into stress perception, signaling and genetic determinants of resistance has recently been complemented by growing evidence for substantial stress-induced changes at the chromatin level. These affect specific sequences or occur genome-wide and are often correlated with transcriptional regulation. The majority of these changes only occur during stress exposure, and both expression and chromatin states typically revert to the pre-stress state shortly thereafter. Other changes result in the maintenance of new chromatin states and modified gene expression for a longer time after stress exposure, preparing an individual for developmental decisions or more effective defence. Beyond this, there are claims for stress-induced heritable chromatin modifications that are transmitted to progeny, thereby improving their characteristics. These effects resemble the concept of Lamarckian inheritance of acquired characters and represent a challenge to the uniqueness of DNA sequence-based inheritance. However, with the growing insight into epigenetic regulation and transmission of chromatin states, it is worth investigating these phenomena carefully. While genetic changes (mainly transposon mobility) in response to stress-induced interference with chromatin are well documented and heritable, in our view there is no unambiguous evidence for transmission of exclusively chromatin-controlled stress effects to progeny. We propose a set of criteria that should be applied to substantiate the data for stress-induced, chromatin-encoded new traits. Well-controlled stress treatments, thorough phenotyping and application of refined genome-wide epigenetic analysis tools should be helpful in moving from interesting observations towards robust evidence.

A fruitful chromatin harvest: meeting summary of the Second European Workshop on Plant Chromatin 2011 in Versailles, France

In September 2011, the Second European Workshop on Plant Chromatin took place in Versailles, France. The workshop covered a range of topics related to plant chromatin biology, including regulation of gene expression by Polycomb group proteins, chromatin dynamics, reconfiguration of epigenetic marks in response to various cues and chromatin assembly. Here, we summarize some of the highlights discussed during the meeting.

Multiple exposures to drought 'train' transcriptional responses in Arabidopsis

Pre-exposure to stress may alter plants' subsequent responses by producing faster and/or stronger reactions implying that plants exercise a form of 'stress memory'. The mechanisms of plants' stress memory responses are poorly understood leaving this fundamental biological question unanswered. Here we show that during recurring dehydration stresses Arabidopsis plants display transcriptional stress memory demonstrated by an increase in the rate of transcription and elevated transcript levels of a subset of the stress-response genes (trainable genes). During recovery (watered) states, trainable genes produce transcripts at basal (preinduced) levels, but remain associated with atypically high H3K4me3 and Ser5P polymerase II levels, indicating that RNA polymerase II is stalled. This is the first example of a stalled RNA polymerase II and its involvement in transcriptional memory in plants. These newly discovered phenomena might be a general feature of plant stress-response systems and could lead to novel approaches for increasing the flexibility of a plant's ability to respond to the environment.

Descendants of primed Arabidopsis plants exhibit resistance to biotic stress

An attack of plants by pathogens or treatment with certain resistance-inducing compounds can lead to the establishment of a unique primed state of defense. Primed plants show enhanced defense reactions upon further challenge with biotic or abiotic stress. Here, we report that the primed state in Arabidopsis (Arabidopsis thaliana) is still functional in the next generation without additional treatment. We compared the reactions of Arabidopsis plants that had been either primed with β-amino-butyric acid (BABA) or with an avirulent isolate of the bacteria Pseudomonas syringae pv tomato (PstavrRpt2). The descendants of primed plants showed a faster and higher accumulation of transcripts of defense-related genes in the salicylic acid signaling pathway and enhanced disease resistance upon challenge inoculation with a virulent isolate of P. syringae. In addition, the progeny of primed plants was also more resistant against the oomycete pathogen Hyaloperonospora arabidopsidis. When transgenerationally primed plants were subjected to an additional priming treatment, their descendants displayed an even stronger primed phenotype, suggesting that plants can inherit a sensitization for the priming phenomenon. Interestingly, this primed to be primed phenotype was much reduced in the Arabidopsis β-amino-butyric acid priming mutant ibs1 (induced BABA sterility1). Our results demonstrate that the primed state of plants is transferred to their progeny and confers improved protection from pathogen attack as compared to the descendants of unprimed plants.

Next-generation systemic acquired resistance

Systemic acquired resistance (SAR) is a plant immune response to pathogen attack. Recent evidence suggests that plant immunity involves regulation by chromatin remodeling and DNA methylation. We investigated whether SAR can be inherited epigenetically following disease pressure by Pseudomonas syringae pv tomato DC3000 (PstDC3000). Compared to progeny from control-treated Arabidopsis (Arabidopsis thaliana; C(1)), progeny from PstDC3000-inoculated Arabidopsis (P(1)) were primed to activate salicylic acid (SA)-inducible defense genes and were more resistant to the (hemi)biotrophic pathogens Hyaloperonospora arabidopsidis and PstDC3000. This transgenerational SAR was sustained over one stress-free generation, indicating an epigenetic basis of the phenomenon. Furthermore, P(1) progeny displayed reduced responsiveness of jasmonic acid (JA)-inducible genes and enhanced susceptibility to the necrotrophic fungus Alternaria brassicicola. This shift in SA- and JA-dependent gene responsiveness was not associated with changes in corresponding hormone levels. Instead, chromatin immunoprecipitation analyses revealed that SA-inducible promoters of PATHOGENESIS-RELATED GENE1, WRKY6, and WRKY53 in P(1) plants are enriched with acetylated histone H3 at lysine 9, a chromatin mark associated with a permissive state of transcription. Conversely, the JA-inducible promoter of PLANT DEFENSIN1.2 showed increased H3 triple methylation at lysine 27, a mark related to repressed gene transcription. P(1) progeny from the defense regulatory mutant non expressor of PR1 (npr1)-1 failed to develop transgenerational defense phenotypes, demonstrating a critical role for NPR1 in expression of transgenerational SAR. Furthermore, the drm1drm2cmt3 mutant that is affected in non-CpG DNA methylation mimicked the transgenerational SAR phenotype. Since PstDC3000 induces DNA hypomethylation in Arabidopsis, our results suggest that transgenerational SAR is transmitted by hypomethylated genes that direct priming of SA-dependent defenses in the following generations.

Plant communication: mediated by individual or blended VOCs?

Plants emit volatile organic compounds (VOCs) as a means to warn other plants of impending danger. Nearby plants exposed to the induced VOCs prepare their own defense weapons in response. Accumulated data supports this assertion, yet much of the evidence has been obtained in laboratories under artificial conditions where, for example, a single VOC might be applied at a concentration that plants do not actually experience in nature. Experiments conducted outdoors suggest that communication occurs only within a limited distance from the damaged plants. Thus, the question remains as to whether VOCs work as a single component or a specific blend, and at which concentrations VOCs elicit insect and pathogen defenses in undamaged plants. We discuss these issues based on available literature and our recent work, and propose future directions in this field.

Plant communication: mediated by individual or blended VOCs?

Plants emit volatile organic compounds (VOCs) as a means to warn other plants of impending danger. Nearby plants exposed to the induced VOCs prepare their own defense weapons in response. Accumulated data supports this assertion, yet much of the evidence has been obtained in laboratories under artificial conditions where, for example, a single VOC might be applied at a concentration that plants do not actually experience in nature. Experiments conducted outdoors suggest that communication occurs only within a limited distance from the damaged plants. Thus, the question remains as to whether VOCs work as a single component or a specific blend, and at which concentrations VOCs elicit insect and pathogen defenses in undamaged plants. We discuss these issues based on available literature and our recent work, and propose future directions in this field.

Treating seeds with activators of plant defence generates long-lasting priming of resistance to pests and pathogens

• Priming of defence is a strategy employed by plants exposed to stress to enhance resistance against future stress episodes with minimal associated costs on growth. Here, we test the hypothesis that application of priming agents to seeds can result in plants with primed defences. • We measured resistance to arthropod herbivores and disease in tomato (Solanum lycopersicum) plants grown from seed treated with jasmonic acid (JA) and/or β-aminobutryric acid (BABA). • Plants grown from JA-treated seed showed increased resistance against herbivory by spider mites, caterpillars and aphids, and against the necrotrophic fungal pathogen, Botrytis cinerea. BABA seed treatment provided primed defence against powdery mildew disease caused by the biotrophic fungal pathogen, Oidium neolycopersici. Priming responses were long-lasting, with significant increases in resistance sustained in plants grown from treated seed for at least 8 wk, and were associated with enhanced defence gene expression during pathogen attack. There was no significant antagonism between different forms of defence in plants grown from seeds treated with a combination of JA and BABA. • Long-term defence priming by seed treatments was not accompanied by reductions in growth, and may therefore be suitable for commercial exploitation.

Next-generation systemic acquired resistance

Systemic acquired resistance (SAR) is a plant immune response to pathogen attack. Recent evidence suggests that plant immunity involves regulation by chromatin remodeling and DNA methylation. We investigated whether SAR can be inherited epigenetically following disease pressure by Pseudomonas syringae pv tomato DC3000 (PstDC3000). Compared to progeny from control-treated Arabidopsis (Arabidopsis thaliana; C(1)), progeny from PstDC3000-inoculated Arabidopsis (P(1)) were primed to activate salicylic acid (SA)-inducible defense genes and were more resistant to the (hemi)biotrophic pathogens Hyaloperonospora arabidopsidis and PstDC3000. This transgenerational SAR was sustained over one stress-free generation, indicating an epigenetic basis of the phenomenon. Furthermore, P(1) progeny displayed reduced responsiveness of jasmonic acid (JA)-inducible genes and enhanced susceptibility to the necrotrophic fungus Alternaria brassicicola. This shift in SA- and JA-dependent gene responsiveness was not associated with changes in corresponding hormone levels. Instead, chromatin immunoprecipitation analyses revealed that SA-inducible promoters of PATHOGENESIS-RELATED GENE1, WRKY6, and WRKY53 in P(1) plants are enriched with acetylated histone H3 at lysine 9, a chromatin mark associated with a permissive state of transcription. Conversely, the JA-inducible promoter of PLANT DEFENSIN1.2 showed increased H3 triple methylation at lysine 27, a mark related to repressed gene transcription. P(1) progeny from the defense regulatory mutant non expressor of PR1 (npr1)-1 failed to develop transgenerational defense phenotypes, demonstrating a critical role for NPR1 in expression of transgenerational SAR. Furthermore, the drm1drm2cmt3 mutant that is affected in non-CpG DNA methylation mimicked the transgenerational SAR phenotype. Since PstDC3000 induces DNA hypomethylation in Arabidopsis, our results suggest that transgenerational SAR is transmitted by hypomethylated genes that direct priming of SA-dependent defenses in the following generations.

Descendants of primed Arabidopsis plants exhibit resistance to biotic stress

An attack of plants by pathogens or treatment with certain resistance-inducing compounds can lead to the establishment of a unique primed state of defense. Primed plants show enhanced defense reactions upon further challenge with biotic or abiotic stress. Here, we report that the primed state in Arabidopsis (Arabidopsis thaliana) is still functional in the next generation without additional treatment. We compared the reactions of Arabidopsis plants that had been either primed with β-amino-butyric acid (BABA) or with an avirulent isolate of the bacteria Pseudomonas syringae pv tomato (PstavrRpt2). The descendants of primed plants showed a faster and higher accumulation of transcripts of defense-related genes in the salicylic acid signaling pathway and enhanced disease resistance upon challenge inoculation with a virulent isolate of P. syringae. In addition, the progeny of primed plants was also more resistant against the oomycete pathogen Hyaloperonospora arabidopsidis. When transgenerationally primed plants were subjected to an additional priming treatment, their descendants displayed an even stronger primed phenotype, suggesting that plants can inherit a sensitization for the priming phenomenon. Interestingly, this primed to be primed phenotype was much reduced in the Arabidopsis β-amino-butyric acid priming mutant ibs1 (induced BABA sterility1). Our results demonstrate that the primed state of plants is transferred to their progeny and confers improved protection from pathogen attack as compared to the descendants of unprimed plants.

SlWRKY70 is required for Mi-1-mediated resistance to aphids and nematodes in tomato

Plant resistance (R) gene-mediated defense responses against biotic stresses include vast transcriptional reprogramming. In several plant-pathogen systems, members of the WRKY family of transcription factors have been demonstrated to act as both positive and negative regulators of plant defense transcriptional networks. To identify the possible roles of tomato (Solanum lycopersicum) WRKY transcription factors in defense mediated by the R gene Mi-1 against potato aphid, Macrosiphum euphorbiae, and root-knot nematode (RKN), Meloidogyne javanica, we used tobacco rattle virus (TRV)-based virus-induced gene silencing and transcriptionally suppressed SlWRKY70, a tomato ortholog of the Arabidopsis thaliana WRKY70 gene. Silencing SlWRKY70 attenuated Mi-1-mediated resistance against both potato aphid and RKN showing that SlWRKY70 is required for Mi-1 function. Furthermore, we found SlWRKY70 transcripts to be inducible in response to aphid infestation and RKN inoculation. Mi-1-mediated recognition of these pests modulates this transcriptional response. As previously described for AtWRKY70, we found SlWRKY70 transcript levels to be up-regulated by salicylic acid and suppressed by methyl jasmonate. This indicates that some aspects of WRKY70 regulation are conserved among distantly related eudicots.

Descendants of primed Arabidopsis plants exhibit resistance to biotic stress

An attack of plants by pathogens or treatment with certain resistance-inducing compounds can lead to the establishment of a unique primed state of defense. Primed plants show enhanced defense reactions upon further challenge with biotic or abiotic stress. Here, we report that the primed state in Arabidopsis (Arabidopsis thaliana) is still functional in the next generation without additional treatment. We compared the reactions of Arabidopsis plants that had been either primed with β-amino-butyric acid (BABA) or with an avirulent isolate of the bacteria Pseudomonas syringae pv tomato (PstavrRpt2). The descendants of primed plants showed a faster and higher accumulation of transcripts of defense-related genes in the salicylic acid signaling pathway and enhanced disease resistance upon challenge inoculation with a virulent isolate of P. syringae. In addition, the progeny of primed plants was also more resistant against the oomycete pathogen Hyaloperonospora arabidopsidis. When transgenerationally primed plants were subjected to an additional priming treatment, their descendants displayed an even stronger primed phenotype, suggesting that plants can inherit a sensitization for the priming phenomenon. Interestingly, this primed to be primed phenotype was much reduced in the Arabidopsis β-amino-butyric acid priming mutant ibs1 (induced BABA sterility1). Our results demonstrate that the primed state of plants is transferred to their progeny and confers improved protection from pathogen attack as compared to the descendants of unprimed plants.

How do plants achieve immunity? Defence without specialized immune cells

Vertebrates have evolved a sophisticated adaptive immune system that relies on an almost infinite diversity of antigen receptors that are clonally expressed by specialized immune cells that roam the circulatory system. These immune cells provide vertebrates with extraordinary antigen-specific immune capacity and memory, while minimizing self-reactivity. Plants, however, lack specialized mobile immune cells. Instead, every plant cell is thought to be capable of launching an effective immune response. So how do plants achieve specific, self-tolerant immunity and establish immune memory? Recent developments point towards a multilayered plant innate immune system comprised of self-surveillance, systemic signalling and chromosomal changes that together establish effective immunity.

Priming against environmental challenges and proteomics in plants: Update and agricultural perspectives

Priming is the cellular state in which the harmful effects of abiotic stress factors in plants are hindered by pre-exposure to a stimulus, thus resulting in greater survival. It is becoming increasingly evident that priming techniques (e.g., external application of natural or synthetic compounds in plants) can enhance the tolerance of crops to environmental stresses. Innovative systems biology approaches such as proteomics are currently recognized as essential tools to understand the molecular mechanisms underlying plant responses to environmental stimuli and priming phenomena. The few published proteomic studies on priming in the context of environmental stress identify key protein targets and signaling pathways which are being involved in the alleviation of negative effects of stress factors. Since priming is a very promising strategy in modern crop production management, further research is needed in order to establish the global picture of priming phenomena against environmental challenges as well as to characterize specific priming-related protein indicators in plants.

Sulfonamides identified as plant immune-priming compounds in high-throughput chemical screening increase disease resistance in Arabidopsis thaliana

Plant activators are agrochemicals that protect crops from diseases by activating the plant immune system. To isolate lead compounds for use as practical plant activators, we screened two different chemical libraries composed of various bioactive substances by using an established screening procedure that can selectively identify immune-priming compounds. We identified and characterized a group of sulfonamide compounds - sulfameter, sulfamethoxypyridazine, sulfabenzamide, and sulfachloropyridazine - among the various isolated candidate molecules. These sulfonamide compounds enhanced the avirulent Pseudomonas-induced cell death of Arabidopsis suspension cell cultures and increased disease resistance in Arabidopsis plants against both avirulent and virulent strains of the bacterium. These compounds did not prevent the growth of pathogenic bacteria in minimal liquid media at 200 μM. They also did not induce the expression of defense-related genes in Arabidopsis seedlings, at least not at 24 and 48 h after treatment, suggesting that they do not act as salicylic acid analogs. In addition, although sulfonamides are known to be folate biosynthesis inhibitors, the application of folate did not restore the potentiation effects of the sulfonamides on pathogen-induced cell death. Our data suggest that sulfonamides potentiate Arabidopsis disease resistance by their novel chemical properties.

Plant immunity to necrotrophs

Plants inhabit environments crowded with infectious microbes that pose constant threats to their survival. Necrotrophic pathogens are notorious for their aggressive and wide-ranging virulence strategies that promote host cell death and acquire nutrients for growth and reproduction from dead cells. This lifestyle constitutes the axis of their pathogenesis and virulence strategies and marks contrasting immune responses to biotrophic pathogens. The diversity of virulence strategies in necrotrophic species corresponds to multifaceted host immune response mechanisms. When effective, the plant immune system disarms the infectious necrotroph of its pathogenic arsenal or attenuates its effect, restricting further ingress and disease symptom development. Simply inherited resistance traits confer protection against host-specific necrotrophs (HSNs), whereas resistance to broad host-range necrotrophs (BHNs) is complex. Components of host genetic networks, as well as the molecular and cellular processes that mediate host immune responses to necrotrophs, are being identified. In this review, recent advances in our understanding of plant immune responses to necrotrophs and comparison with responses to biotrophic pathogens are summarized, highlighting common and contrasting mechanisms.

The RNA silencing enzyme RNA polymerase v is required for plant immunity

RNA-directed DNA methylation (RdDM) is an epigenetic control mechanism driven by small interfering RNAs (siRNAs) that influence gene function. In plants, little is known of the involvement of the RdDM pathway in regulating traits related to immune responses. In a genetic screen designed to reveal factors regulating immunity in Arabidopsis thaliana, we identified NRPD2 as the OVEREXPRESSOR OF CATIONIC PEROXIDASE 1 (OCP1). NRPD2 encodes the second largest subunit of the plant-specific RNA Polymerases IV and V (Pol IV and Pol V), which are crucial for the RdDM pathway. The ocp1 and nrpd2 mutants showed increases in disease susceptibility when confronted with the necrotrophic fungal pathogens Botrytis cinerea and Plectosphaerella cucumerina. Studies were extended to other mutants affected in different steps of the RdDM pathway, such as nrpd1, nrpe1, ago4, drd1, rdr2, and drm1drm2 mutants. Our results indicate that all the mutants studied, with the exception of nrpd1, phenocopy the nrpd2 mutants; and they suggest that, while Pol V complex is required for plant immunity, Pol IV appears dispensable. Moreover, Pol V defective mutants, but not Pol IV mutants, show enhanced disease resistance towards the bacterial pathogen Pseudomonas syringae DC3000. Interestingly, salicylic acid (SA)-mediated defenses effective against PsDC3000 are enhanced in Pol V defective mutants, whereas jasmonic acid (JA)-mediated defenses that protect against fungi are reduced. Chromatin immunoprecipitation analysis revealed that, through differential histone modifications, SA-related defense genes are poised for enhanced activation in Pol V defective mutants and provide clues for understanding the regulation of gene priming during defense. Our results highlight the importance of epigenetic control as an additional layer of complexity in the regulation of plant immunity and point towards multiple components of the RdDM pathway being involved in plant immunity based on genetic evidence, but whether this is a direct or indirect effect on disease-related genes is unclear.

EMSY-like genes are required for full RPP7-mediated race-specific immunity and basal defense in Arabidopsis

The Arabidopsis thaliana gene enhanced downy mildew 2 (EDM2) encodes a nuclear protein required for RPP7-mediated race-specific disease resistance against Hyaloperonospora arabidopsidis, proper floral transition and additional developmental processes. Transcript levels of the disease-resistance gene RPP7 are enhanced by EDM2 while those of the floral suppressor FLC are repressed by EDM2. By yeast two-hybrid screening for EDM2-interacting proteins, we identified AtEML1, a member of a small group of four Arabidopsis proteins containing an EMSY N-terminal domain, a central Agenet domain, and a C-terminal coiled-coil motif. Using T-DNA mutants combined with silencing by artificial microRNAs, we found AtEML1, AtEML2, and, likely, AtEML4 to contribute to RPP7-mediated immunity. Besides this, AtEML1 and AtEML2 participate in a second EDM2-dependent function and affect floral transition. Unlike EDM2, whose role in immunity appears to be limited to RPP7-mediated disease resistance, some AtEML members contribute to basal defense, an unspecific general defense mechanism. Domain architectures of EDM2 as well as AtEML proteins suggest roles of these proteins in the regulation of chromatin states. Thus, possible cooperation of AtEML members with EDM2 at the level of chromatin dynamics may link race-specific pathogen recognition to general defense mechanisms.

Prerequisites, performance and profits of transcriptional profiling the abiotic stress response

During the last decade, microarrays became a routine tool for the analysis of transcripts in the model plant Arabidopsis thaliana and the crop plant species rice, poplar or barley. The overwhelming amount of data generated by gene expression studies is a valuable resource for every scientist. Here, we summarize the most important findings about the abiotic stress responses in plants. Interestingly, conserved patterns of gene expression responses have been found that are common between different abiotic stresses or that are conserved between different plant species. However, the individual histories of each plant affect the inter-comparability between experiments already before the onset of the actual stress treatment. This review outlines multiple aspects of microarray technology and highlights some of the benefits, limitations and also pitfalls of the technique. This article is part of a Special Issue entitled: Plant gene regulation in response to abiotic stress.

Molecular aspects of defence priming

Plants can be primed for more rapid and robust activation of defence to biotic or abiotic stress. Priming follows perception of molecular patterns of microbes or plants, recognition of pathogen-derived effectors or colonisation by beneficial microbes. However the process can also be induced by treatment with some natural or synthetic compounds and wounding. The primed mobilization of defence is often associated with development of immunity and stress tolerance. Although the phenomenon has been known for decades, the molecular basis of priming is poorly understood. Here, I summarize recent progress made in unravelling molecular aspects of defence priming that is the accumulation of dormant mitogen-activated protein kinases, chromatin modifications and alterations of primary metabolism.

Detection of histone modifications in plant leaves

Chromatin structure is important for the regulation of gene expression in eukaryotes. In this process, chromatin remodeling, DNA methylation, and covalent modifications on the amino-terminal tails of histones H3 and H4 play essential roles(1-2). H3 and H4 histone modifications include methylation of lysine and arginine, acetylation of lysine, and phosphorylation of serine residues(1-2). These modifications are associated either with gene activation, repression, or a primed state of gene that supports more rapid and robust activation of expression after perception of appropriate signals (microbe-associated molecular patterns, light, hormones, etc.)(3-7). Here, we present a method for the reliable and sensitive detection of specific chromatin modifications on selected plant genes. The technique is based on the crosslinking of (modified) histones and DNA with formaldehyde(8,9), extraction and sonication of chromatin, chromatin immunoprecipitation (ChIP) with modification-specific antibodies(9,10), de-crosslinking of histone-DNA complexes, and gene-specific real-time quantitative PCR. The approach has proven useful for detecting specific histone modifications associated with C(4;) photosynthesis in maize(5,11) and systemic immunity in Arabidopsis(3).

Trained immunity: a memory for innate host defense

Immune responses in vertebrates are classically divided into innate and adaptive, with only the latter being able to build up immunological memory. However, although lacking adaptive immune responses, plants and invertebrates are protected against reinfection with pathogens, and invertebrates even display transplant rejection. In mammals, past "forgotten" studies demonstrate cross-protection between infections independently of T and B cells, and more recently memory properties for NK cells and macrophages, prototypical cells of innate immunity, have been described. We now posit that mammalian innate immunity also exhibits an immunological memory of past insults, for which we propose the term "trained immunity." Understanding trained immunity will revolutionize our view of host defense and immunological memory, and could lead to defining a new class of vaccines and immunotherapies.

Chromatin modifications and remodeling in plant abiotic stress responses

Sensing environmental changes and initiating a gene expression response are important for plants as sessile autotrophs. The ability of epigenetic status to alter rapidly and reversibly could be a key component to the flexibility of plant responses to the environment. The involvement of epigenetic mechanisms in the response to environmental cues and to different types of abiotic stresses has been documented. Different environmental stresses lead to altered methylation status of DNA as well as modifications of nucleosomal histones. Understanding how epigenetic mechanisms are involved in plant response to environmental stress is highly desirable, not just for a better understanding of molecular mechanisms of plant stress response but also for possible application in the genetic manipulation of plants. In this review, we highlight our current understanding of the epigenetic mechanisms of chromatin modifications and remodeling, with emphasis on the roles of specific modification enzymes and remodeling factors in plant abiotic stress responses. This article is part of a Special Issue entitled: Plant gene regulation in response to abiotic stress.