Extracellular Self-DNA (esDNA), but Not Heterologous Plant or Insect DNA (etDNA), Induces Plasma Membrane Depolarization and Calcium Signaling in Lima Bean (Phaseolus lunatus) and Maize (Zea mays)

Viral Recognition and Evasion in Plants

Viruses, causal agents of devastating diseases in plants, are obligate intracellular pathogens composed of a nucleic acid genome and a limited number of viral proteins. The diversity of plant viruses, their diminutive molecular nature, and their symplastic localization pose challenges to understanding the interplay between these pathogens and their hosts in the currently accepted framework of plant innate immunity. It is clear, nevertheless, that plants can recognize the presence of a virus and activate antiviral immune responses, although our knowledge of the breadth of invasion signals and the underpinning sensing events is far from complete. Below, I discuss some of the demonstrated or hypothesized mechanisms enabling viral recognition in plants, the step preceding the onset of antiviral immunity, as well as the strategies viruses have evolved to evade or suppress their detection.

Extracellular Self-DNA Effects on Yeast Cell Cycle and Transcriptome during Batch Growth

The cell cycle and the transcriptome dynamics of yeast exposed to extracellular self-DNA during an aerobic batch culture on glucose have been investigated using cytofluorimetric and RNA-seq analyses. In parallel, the same study was conducted on yeast cells growing in the presence of (heterologous) nonself-DNA. The self-DNA treatment determined a reduction in the growth rate and a major elongation of the diauxic lag phase, as well as a significant delay in the achievement of the stationary phase. This was associated with significant changes in the cell cycle dynamics, with slower exit from the G0 phase, followed by an increased level of cell percentage in the S phase, during the cultivation. Comparatively, the exposure to heterologous DNA did not affect the growth curve and the cell cycle dynamics. The transcriptomic analysis showed that self-DNA exposure produced a generalized downregulation of transmembrane transport and an upregulation of genes associated with sulfur compounds and the pentose phosphate pathway. Instead, in the case of the nonself treatment, a clear response to nutrient deprivation was detected. Overall, the presented findings represent further insights into the complex functional mechanisms of self-DNA inhibition.

Damage-Associated Molecular Patterns and Systemic Signaling

Cellular damage inflicted by wounding, pathogen infection, and herbivory releases a variety of host-derived metabolites, degraded structural components, and peptides into the extracellular space that act as alarm signals when perceived by adjacent cells. These so-called damage-associated molecular patterns (DAMPs) function through plasma membrane localized pattern recognition receptors to regulate wound and immune responses. In plants, DAMPs act as elicitors themselves, often inducing immune outputs such as calcium influx, reactive oxygen species generation, defense gene expression, and phytohormone signaling. Consequently, DAMP perception results in a priming effect that enhances resistance against subsequent pathogen infections. Alongside their established function in local tissues, recent evidence supports a critical role of DAMP signaling in generation and/or amplification of mobile signals that induce systemic immune priming. Here, we summarize the identity, signaling, and synergy of proposed and established plant DAMPs, with a focus on those with published roles in systemic signaling.

Extracellular Self- and Non-Self DNA Involved in Damage Recognition in the Mistletoe Parasitism of Mesquite Trees

Psittacanthus calyculatus parasitizes mesquite trees through a specialized structure called a haustorium, which, in the intrusive process, can cause cellular damage in the host tree and release DAMPs, such as ATP, sugars, RNA, and DNA. These are highly conserved molecules that primarily function as signals that trigger and activate the defense responses. In the present study, we generate extracellular DNA (exDNA) from mesquite (P. laevigata) tree leaves (self-exDNA) and P. calyculatus (non-self exDNA) mistletoe as DAMP sources to examine mesquite trees' capacity to identify specific self or non-self exDNA. We determined that mesquite trees perceive self- and non-self exDNA with the synthesis of O2•-, H2O2, flavonoids, ROS-enzymes system, MAPKs activation, spatial concentrations of JA, SA, ABA, and CKs, and auxins. Our data indicate that self and non-self exDNA application differs in oxidative burst, JA signaling, MAPK gene expression, and scavenger systems. This is the first study to examine the molecular biochemistry effects in a host tree using exDNA sources derived from a mistletoe.

Self-DNA Inhibition in Drosophila melanogaster Development: Metabolomic Evidence of the Molecular Determinants

We investigated the effects of dietary delivered self-DNA in the model insect Drosophila melanogaster. Self-DNA administration resulted in low but significant lethality in Drosophila larvae and considerably extended the fly developmental time. This was characterized by the abnormal persistence of the larvae in the L2 and L3 stages, which largely accounted for the average 72 h delay observed in pupariation, as compared to controls. In addition, self-DNA exposure affected adult reproduction by markedly reducing both female fecundity and fertility, further demonstrating its impact on Drosophila developmental processes. The effects on the metabolites of D. melanogaster larvae after exposure to self-DNA were studied by NMR, LC-MS, and molecular networking. The results showed that self-DNA feeding reduces the amounts of all metabolites, particularly amino acids and N-acyl amino acids, which are known to act as lipid signal mediators. An increasing amount of phloroglucinol was found after self-DNA exposure and correlated to developmental delay and egg-laying suppression. Pidolate, a known intermediate in the γ-glutamyl cycle, also increased after exposure to self-DNA and correlated to the block of insect oogenesis.

Metabolic Responses of the Microalga Neochloris oleoabundans to Extracellular Self- and Nonself-DNA

Stressed organisms identify intracellular molecules released from damaged cells due to trauma or pathogen infection as components of the innate immune response. These molecules called DAMPs (Damage-Associated Molecular Patterns) are extracellular ATP, sugars, and extracellular DNA, among others. Animals and plants can recognize their own DNA applied externally (self-exDNA) as a DAMP with a high degree of specificity. However, little is known about the microalgae responses to damage when exposed to DAMPs and specifically to self-exDNAs. Here we compared the response of the oilseed microalgae Neochloris oleoabundans to self-exDNA, with the stress responses elicited by nonself-exDNA, methyl jasmonate (MeJA) and sodium bicarbonate (NaHCO3). We analyzed the peroxidase enzyme activity related to the production of reactive oxygen species (ROS), as well as the production of polyphenols, lipids, triacylglycerols, and phytohormones. After 5 min of addition, self-exDNA induced peroxidase enzyme activity higher than the other elicitors. Polyphenols and lipids were increased by self-exDNA at 48 and 24 h, respectively. Triacylglycerols were increased with all elicitors from addition and up to 48 h, except with nonself-exDNA. Regarding phytohormones, self-exDNA and MeJA increased gibberellic acid, isopentenyladenine, and benzylaminopurine at 24 h. Results show that Neochloris oleoabundans have self-exDNA specific responses.

ATM and ATR, two central players of the DNA damage response, are involved in the induction of systemic acquired resistance by extracellular DNA, but not the plant wound response

Background

The plant immune response to DNA is highly self/nonself-specific. Self-DNA triggered stronger responses by early immune signals such as H2O2 formation than nonself-DNA from closely related plant species. Plants lack known DNA receptors. Therefore, we aimed to investigate whether a differential sensing of self-versus nonself DNA fragments as damage- versus pathogen-associated molecular patterns (DAMPs/PAMPs) or an activation of the DNA-damage response (DDR) represents the more promising framework to understand this phenomenon.

Results

We treated Arabidopsis thaliana Col-0 plants with sonicated self-DNA from other individuals of the same ecotype, nonself-DNA from another A. thaliana ecotype, or nonself-DNA from broccoli. We observed a highly self/nonself-DNA-specific induction of H2O2 formation and of jasmonic acid (JA, the hormone controlling the wound response to chewing herbivores) and salicylic acid (SA, the hormone controlling systemic acquired resistance, SAR, to biotrophic pathogens). Mutant lines lacking Ataxia Telangiectasia Mutated (ATM) or ATM AND RAD3-RELATED (ATR) - the two DDR master kinases - retained the differential induction of JA in response to DNA treatments but completely failed to induce H2O2 or SA. Moreover, we observed H2O2 formation in response to in situ-damaged self-DNA from plants that had been treated with bleomycin or SA or infected with virulent bacteria Pseudomonas syringae pv. tomato DC3000 or pv. glycinea carrying effector avrRpt2, but not to DNA from H2O2-treated plants or challenged with non-virulent P. syringae pv. glycinea lacking avrRpt2.

Conclusion

We conclude that both ATM and ATR are required for the complete activation of the plant immune response to extracellular DNA whereas an as-yet unknown mechanism allows for the self/nonself-differential activation of the JA-dependent wound response.

Self-DNA Early Exposure in Cultivated and Weedy Setaria Triggers ROS Degradation Signaling Pathways and Root Growth Inhibition

The accumulation of fragmented extracellular DNA reduces conspecific seed germination and plantlet growth in a concentration-dependent manner. This self-DNA inhibition was repeatedly reported, but the underlying mechanisms are not fully clarified. We investigated the species-specificity of self-DNA inhibition in cultivated vs. weed congeneric species (respectively, Setaria italica and S. pumila) and carried out a targeted real-time qPCR analysis under the hypothesis that self-DNA elicits molecular pathways that are responsive to abiotic stressors. The results of a cross-factorial experiment on root elongation of seedlings exposed to self-DNA, congeneric DNA, and heterospecific DNA from Brassica napus and Salmon salar confirmed a significantly higher inhibition by self-DNA as compared to non-self-treatments, with the latter showing a magnitude of the effect consistent with the phylogenetic distance between the DNA source and the target species. Targeted gene expression analysis highlighted an early activation of genes involved in ROS degradation and management (FSD2, ALDH22A1, CSD3, MPK17), as well as deactivation of scaffolding molecules acting as negative regulators of stress signaling pathways (WD40-155). While being the first exploration of early response to self-DNA inhibition at molecular level on C4 model plants, our study highlights the need for further investigation of the relationships between DNA exposure and stress signaling pathways by discussing potential applications for species-specific weed control in agriculture.

Osmoelectric siphon models for signal and water dispersal in wounded plants

When attacked by herbivores, plants produce electrical signals which can activate the synthesis of the defense mediator jasmonate. These wound-induced membrane potential changes can occur in response to elicitors that are released from damaged plant cells. We list plant-derived elicitors of membrane depolarization. These compounds include the amino acid l-glutamate (Glu), a potential ligand for GLUTAMATE RECEPTOR-LIKE (GLR) proteins that play roles in herbivore-activated electrical signaling. How are membrane depolarization elicitors dispersed in wounded plants? In analogy with widespread turgor-driven cell and organ movements, we propose osmoelectric siphon mechanisms for elicitor transport. These mechanisms are based on membrane depolarization leading to cell water shedding into the apoplast followed by membrane repolarization and water uptake. We discuss two related mechanisms likely to occur in response to small wounds and large wounds that trigger leaf-to-leaf electrical signal propagation. To reduce jasmonate pathway activation, a feeding insect must cut through tissues cleanly. If their mandibles become worn, the herbivore is converted into a robust plant defense activator. Our models may therefore help to explain why numerous plants produce abrasives which can blunt herbivore mouthparts. Finally, if verified, the models we propose may be generalizable for cell to cell transport of water and pathogen-derived regulators.

The small brown planthopper (Laodelphax striatellus) as a vector of the rice stripe virus

The small brown planthopper, Laodelphax striatellus, is a destructive pest insect found in rice fields. L. striatellus not only directly feeds on the phloem sap of rice but also transmits various viruses, such as rice stripe virus (RSV) and rice black-streaked dwarf virus, resulting in serious loss of rice production. RSV is a rice-infecting virus that is found mainly in Korea, China, and Japan. To develop novel strategies to control L. striatellus and L. striatellus-transmitted viruses, various studies have been conducted, based on vector biology, interactions between vectors and pathogens, and omics, including transcriptomics, proteomics, and metabolomics. In this review, we discuss the roles of saliva proteins during phloem sap-sucking and virus transmission, the diversity and role of the microbial community in L. striatellus, the profile and molecular mechanisms of insecticide resistance, classification of L. striatellus-transmitted RSV, its host range and symptoms, its genome composition and roles of virus-derived proteins, its distribution, interactions with L. striatellus, and resistance and control, to suggest future directions for integrated pest management to control L. striatellus and L. striatellus-transmitted viruses.

Metabolomics and molecular networking analyses in Arabidopsis thaliana show that extracellular self-DNA affects nucleoside/nucleotide cycles with accumulation of cAMP, cGMP and N6-methyl-AMP

Extracellular DNA (exDNA) widely occurs in the environment due to release by either cell lysis or active secretion. The role of exDNA in plant-soil interactions has been investigated and inhibitory effects on the growth of conspecific individuals by their self-DNA have been reported. Transcriptome analysis in the model plant Arabidopsis thaliana showed a clear recognition by the plant roots of self- and nonself-exDNA, with inhibition occurring only after exposure to the former. In this study, an untargeted metabolomics approach was used to assess at molecular level the plant reactions to exDNA exposure. Thus, the effects on the metabolites profile of A. thaliana after exposure to self- and nonself-exDNA from plants and fish, were studied by NMR, LC-MS, chemometrics and molecular networking analyses. Results show that self-DNA significantly induces the accumulation of RNA constituents (nucleobases, ribonucleosides, dinucleotide and trinucleotide oligomers). Interestingly, AMP and GMP are found along with their cyclic analogues cAMP and cGMP, and in form of cyclic dimers (c-di-AMP and c-di-GMP). Also methylated adenosine monophosphate (m6AMP) and the dimeric dinucleotide N-methyladenylyl-(3'→5') cytidine (m6ApC) increased only in the self-DNA treatment. Such striking evidence of self-DNA effects highlights a major role of exDNA in plant sensing of its environment.

Calcium Signaling in Plant-Insect Interactions

In plant-insect interactions, calcium (Ca²⁺) variations are among the earliest events associated with the plant perception of biotic stress. Upon herbivory, Ca²⁺ waves travel long distances to transmit and convert the local signal to a systemic defense program. Reactive oxygen species (ROS), Ca²⁺ and electrical signaling are interlinked to form a network supporting rapid signal transmission, whereas the Ca²⁺ message is decoded and relayed by Ca²⁺-binding proteins (including calmodulin, Ca²⁺-dependent protein kinases, annexins and calcineurin B-like proteins). Monitoring the generation of Ca²⁺ signals at the whole plant or cell level and their long-distance propagation during biotic interactions requires innovative imaging techniques based on sensitive sensors and using genetically encoded indicators. This review summarizes the recent advances in Ca²⁺ signaling upon herbivory and reviews the most recent Ca²⁺ imaging techniques and methods.

Field evidence for litter and self-DNA inhibitory effects on Alnus glutinosa roots

Litter decomposition releases nutrients beneficial to plants but also induces phytotoxicity. Phytotoxicity can result from either labile allelopathic compounds or species specific and caused by conspecific DNA. Aquatic plants in flowing water generally do not suffer phytotoxicity because litter is regularly removed. In stagnant water or in litter packs an impact on root functionality can occur. So far, studies on water plant roots have been carried out in laboratory and never in field conditions. The effect of conspecific vs heterospecific litter and purified DNA were assessed on aquatic roots of the riparian woody species Alnus glutinosa L. using a novel method, using closed and open plastic tubes fixed to single roots in the field with closed tubes analogous to stagnant water. Four fresh and four decomposed litter types were used and analysed on extractable C, cellulose, lignin, N content and using ¹³ C-CPMAS NMR spectroscopy. Inhibitory effects were observed with fresh litter in closed systems, with a positive correlation with extractable C and negative with lignin and lignin : N ratio. Alnus self-DNA, but not heterologous one, caused acute toxic effects in the closed system. Our results demonstrate the first field-based evidence for self-DNA inhibition as causal factor of negative feedback between plants and substrate.

Extracellular self-RNA: A danger elicitor in pepper induces immunity against bacterial and viral pathogens in the field

Plants and animals serve as hosts for microbes. To protect themselves from microbe-induced damage, plants and animals need to differentiate self-molecules/signals from non-self, microbe-derived molecules. Damage-associated molecular patterns (DAMPs) are danger signals released from the damaged host tissue or present on the surface of stressed cells. Although a self-extracellular DNA has previously been shown to act as a DAMP in different plant species, the existence of a self-extracellular RNA (eRNA) as a danger signal in plants remains unknown. Here, we firstly evaluated the ability of a pepper self-eRNA to activate immunity against viral and bacterial pathogens under field conditions. Pepper leaves pre-infiltrated with self-eRNA exhibited reduced titer of the naturally occurring Tomato spotted wilt virus and diminished symptoms of Xanthomonas axonopodis pv. vesicatoria infection through eliciting defense priming of abscisic acid signaling. At the end of the growing season at 90 days after transplanting, pepper plants treated with self- and non-self-eRNAs showed no difference in fruit yield. Taken together, our discovery demonstrated that self-eRNA can successfully activate plant systemic immunity without any growth penalty, indicating its potential as a novel disease management agent against a broad range of pathogenic microbes.

The simultaneous perception of self- and non-self-danger signals potentiates plant innate immunity responses

The simultaneous perception of endogenous and exogenous danger signals potentiates PAMP-triggered immunity in tomato and other downstream defence responses depending on the origin of the signal. Abstract Plant cells perceive a pathogen invasion by recognising endogenous or exogenous extracellular signals such as Damage-Associated Molecular Patterns (DAMPs) or Pathogen-Associated Molecular Patterns (PAMPs). In particular, DAMPs are intracellular molecules or cell wall fragments passive or actively released to the apoplast, whose extracellular recognition by intact cells triggers specific immune signalling, the so-called DAMP-triggered immunity. The extracellular recognition of DAMPs and PAMPs leads to a very similar intracellular signalling, and this similarity has generated a biological need to know why plants perceive molecules with such different origins and with overlapped innate immunity responses. Here, we report that the simultaneous perception of DAMPs and a PAMP strengthens early and late plant defence responses. To this aim, we studied classical PTI responses such as the generation of ROS and MAPK phosphorylation, but we also monitored the biosynthesis of phytocytokines and performed a non-targeted metabolomic analysis. We demonstrate that co-application of the bacterial peptide flagellin with the DAMPs cyclic AMP or cellobiose amplifies PAMP-triggered immunity responses. Both co-applications enhanced the synthesis of phytocytokines, but only simultaneous treatments with cAMP strengthened the flagellin-dependent metabolomic responses. In addition, cAMP and cellobiose treatments induced resistance against the hemibiotrophic bacteria Pseudomonas syringae pv. tomato DC3000. Overall, these results indicate that the complex mixture of DAMPs and PAMPs carries specific information that potentiates plant defence responses. However, downstream responses seem more specific depending on the composition of the mixture.

Effects of Extracellular Self- and Nonself-DNA on the Freshwater Microalga Chlamydomonas reinhardtii and on the Marine Microalga Nannochloropsis gaditana

The role of extracellular DNA (exDNA) in soil and aquatic environments was mainly discussed in terms of source of mineral nutrients and of genetic material for horizontal gene transfer. Recently, the self-exDNA (conspecific) has been shown to have an inhibitory effect on the growth of that organism, while the same was not evident for nonself-exDNA (non conspecific). The inhibitory effect of self-exDNA was proposed as a universal phenomenon, although evidence is mainly reported for terrestrial species. The current study showed the inhibitory effect of self-exDNA also on photosynthetic aquatic microorganisms. We showed that self-exDNA inhibits the growth of the microalgae Chlamydomonas reinhardtii and Nannochloropsis gaditana, a freshwater and a marine species, respectively. In addition, the study also revealed the phenotypic effects post self-exDNA treatments. Indeed, Chlamydomonas showed the formation of peculiar heteromorphic aggregates of palmelloid cells embedded in an extracellular matrix, favored by the presence of DNA in the environment, that is not revealed after exposure to nonself-exDNA. The differential effect of self and nonself-exDNA on both microalgae, accompanied by the inhibitory growth effect of self-exDNA are the first pieces of evidence provided for species from aquatic environments.

Self-DNA Exposure Induces Developmental Defects and Germline DNA Damage Response in Caenorhabditis elegans

All organisms, from bacteria to mammals, sense and respond to foreign nucleic acids to fight infections in order to survive and preserve genome integrity across generations. The innate immune system is an evolutionarily conserved defence strategy. Complex organisms have developed various cellular processes to respond to and recognise not only infections, i.e., pathogen-associated molecular patterns (PAMPs), but also to sense injury and tissue dysfunctions, i.e., damage-associated molecular patterns (DAMPs). Mis-localized self-DNA can be sensed as DAMP by specific DNA-sensing pathways, and self-DNA chronic exposure can be detrimental to the organisms. Here, we investigate the effects of dietary delivered self-DNA in the nematode Caenorhabditis elegans. The hermaphrodite worms were fed on Escherichia coli genomic libraries: a C. elegans library (self) and a legume (Medicago truncatula) library (non-self). We show that the self-library diet affects embryogenesis, larval development and gametogenesis. DNA damage and activation of p53/CEP-1-dependent apoptosis occur in gonadal germ cells. Studies of self-DNA exposure in this model organism were not pursued up to now. The genetic tractability of C. elegans will help to identify the basic molecular pathways involved in such mechanisms. The specificity of the adverse effects associated with a self-DNA enriched diet suggests applications in biological pest control approaches.

Extracellular DNA as an elicitor of broad-spectrum resistance in Arabidopsis thaliana

Like in mammals, the plant immune system has evolved to perceive damage. Damaged-associated molecular patterns (DAMPs) are endogenous signals generated in wounded or infected tissue after pathogen or insect attack. Although extracellular DNA (eDNA) is a DAMP signal that induces immune responses, plant responses after eDNA perception remain largely unknown. Here, we report that signaling defenses but not direct defense responses are induced after eDNA applications enhancing broad-range plant protection. A screening of defense signaling and hormone biosynthesis marker genes revealed that OXI1, CML37 and MPK3 are relevant eDNA-Induced Resistance markers (eDNA-IR). Additionally, we observed that eDNA from several Arabidopsis ecotypes and other phylogenetically distant plants such as citrus, bean and, more surprisingly, a monocotyledonous plant such as maize upregulates eDNA-IR marker genes. Using 3,3'-Diaminobenzidine (DAB) and aniline blue staining methods, we observed that H₂O₂ but not callose was strongly accumulated following self-eDNA treatments. Finally, eDNA resulted in effective induced resistance in Arabidopsis against the pathogens Hyaloperonospora arabidopsidis, Pseudomonas syringae, and Botrytis cinerea and against aphid infestation, reducing the number of nymphs and moving forms. Hence, the unspecificity of DNA origin and the wide range of insects to which eDNA can protect opens many questions about the mechanisms behind eDNA-IR.

Extracellular DNA: Insight of a Signal Molecule in Crop Protection

Simple Summary

Agriculture systems use multiple chemical treatments to prevent pests and diseases, and to fertilize plants and eliminate weeds around the crop. These practices are less accepted by the consumers each day, mostly because of the associated environmental, health, and ecological impact; thus, new sustainable green technologies are being developed to replace the use of chemical products. Among green technologies for agriculture practices, the use of plant elicitors represents an alternative with great potential, and extracellular DNA has shown beneficial effects on important production traits such as defence mechanisms, plant growth and development, and secondary metabolites production that results in yield increment and better-quality food. In this review, we reunite experimental evidence of the natural effect that extracellular DNA has on plants. We also aim to contribute a step closer to the agricultural application of extracellular DNA. Additionally, we suggest that extracellular DNA can have a biostimulant effect on plants, and can be applied as a highly sustainable treatment contributing to the circular economy of primary production.

Abstract

Agricultural systems face several challenges in terms of meeting everyday-growing quantities and qualities of food requirements. However, the ecological and social trade-offs for increasing agricultural production are high, therefore, more sustainable agricultural practices are desired. Researchers are currently working on diverse sustainable techniques based mostly on natural mechanisms that plants have developed along with their evolution. Here, we discuss the potential agricultural application of extracellular DNA (eDNA), its multiple functioning mechanisms in plant metabolism, the importance of hormetic curves establishment, and as a challenge: the technical limitations of the industrial scale for this technology. We highlight the more viable natural mechanisms in which eDNA affects plant metabolism, acting as a damage/microbe-associated molecular pattern (DAMP, MAMP) or as a general plant biostimulant. Finally, we suggest a whole sustainable system, where DNA is extracted from organic sources by a simple methodology to fulfill the molecular characteristics needed to be applied in crop production systems, allowing the reduction in, or perhaps the total removal of, chemical pesticides, fertilizers, and insecticides application.

Damage-Associated Molecular Patterns (DAMPs) in Plant Innate Immunity: Applying the Danger Model and Evolutionary Perspectives

Danger signals trigger immune responses upon perception by a complex surveillance system. Such signals can originate from the infectious nonself or the damaged self, the latter termed damage-associated molecular patterns (DAMPs). Here, we apply Matzinger's danger model to plant innate immunity to discuss the adaptive advantages of DAMPs and their integration into preexisting signaling pathways. Constitutive DAMPs (cDAMPs), e.g., extracellular ATP, histones, and self-DNA, fulfill primary, conserved functions and adopt a signaling role only when cellular damage causes their fragmentation or localization to aberrant compartments. By contrast, immunomodulatory peptides (also known as phytocytokines) exclusively function as signals and, upon damage, are activated as inducible DAMPs (iDAMPs). Dynamic coevolutionary processes between the signals and their emerging receptors and shared co-receptors have likely linked danger recognition to preexisting, conserved downstream pathways.

Arabidopsis thaliana Response to Extracellular DNA: Self Versus Nonself Exposure

The inhibitory effect of extracellular DNA (exDNA) on the growth of conspecific individuals was demonstrated in different kingdoms. In plants, the inhibition has been observed on root growth and seed germination, demonstrating its role in plant-soil negative feedback. Several hypotheses have been proposed to explain the early response to exDNA and the inhibitory effect of conspecific exDNA. We here contribute with a whole-plant transcriptome profiling in the model species Arabidopsis thaliana exposed to extracellular self- (conspecific) and nonself- (heterologous) DNA. The results highlight that cells distinguish self- from nonself-DNA. Moreover, confocal microscopy analyses reveal that nonself-DNA enters root tissues and cells, while self-DNA remains outside. Specifically, exposure to self-DNA limits cell permeability, affecting chloroplast functioning and reactive oxygen species (ROS) production, eventually causing cell cycle arrest, consistently with macroscopic observations of root apex necrosis, increased root hair density and leaf chlorosis. In contrast, nonself-DNA enters the cells triggering the activation of a hypersensitive response and evolving into systemic acquired resistance. Complex and different cascades of events emerge from exposure to extracellular self- or nonself-DNA and are discussed in the context of Damage- and Pathogen-Associated Molecular Patterns (DAMP and PAMP, respectively) responses.

Understanding In Vitro Tissue Culture-Induced Variation Phenomenon in Microspore System

In vitro tissue culture plant regeneration is a complicated process that requires stressful conditions affecting the cell functioning at multiple levels, including signaling pathways, transcriptome functioning, the interaction between cellular organelles (retro-, anterograde), compounds methylation, biochemical cycles, and DNA mutations. Unfortunately, the network linking all these aspects is not well understood, and the available knowledge is not systemized. Moreover, some aspects of the phenomenon are poorly studied. The present review attempts to present a broad range of aspects involved in the tissue culture-induced variation and hopefully would stimulate further investigations allowing a better understanding of the phenomenon and the cell functioning.

Exposure to (Z)-11-hexadecenal [(Z)-11-16:Ald] increases Brassica nigra susceptibility to subsequent herbivory

It is well established that plants emit, detect and respond to volatile organic compounds; however, knowledge on the ability of plants to detect and respond to volatiles emitted by non-plant organisms is limited. Recent studies indicated that plants detect insect-emitted volatiles that induce defence responses; however, the mechanisms underlying this detection and defence priming is unknown. Therefore, we explored if exposure to a main component of Plutella xylostella female sex pheromone namely (Z)-11-hexadecenal [(Z)-11-16:Ald] induced detectable early and late stage defence-related plant responses in Brassica nigra. Exposure to biologically relevant levels of vapourised (Z)-11-16:Ald released from a loaded septum induced a change in volatile emissions of receiver plants after herbivore attack and increased the leaf area consumed by P. xylostella larvae. Further experiments examining the effects of the (Z)-11-16:Ald on several stages of plant defence-related responses showed that exposure to 100 ppm of (Z)-11-16:Ald in liquid state induced depolarisation of the transmembrane potential (Vm), an increase in cytosolic calcium concentration [Ca²⁺]_cyt, production of H₂O₂ and an increase in expression of reactive oxygen species (ROS)-mediated genes and ROS-scavenging enzyme activity. The results suggest that exposure to volatile (Z)-11-16:Ald increases the susceptibility of B. nigra to subsequent herbivory. This unexpected finding, suggest alternative ecological effects of detecting insect pheromone to those reported earlier. Experiments conducted in vitro showed that high doses of (Z)-11-16:Ald induced defence-related responses, but further experiments should assess how specific the response is to this particular aldehyde.

Green pesticide: Tapping to the promising roles of plant secreted small RNAs and responses towards extracellular DNA

The diverse roles of non-coding RNA and DNA in cross-species communication is yet to be revealed. Once thought to only involve intra-specifically in regulating gene expression, the evidence that these genetic materials can also modulate gene expression between species that belong to different kingdoms is accumulating. Plants send small RNAs to the pathogen or parasite when they are being attacked, targeting essential mRNAs for infection or parasitism of the hosts. However, the same survival mechanism is also deployed by the pathogen or parasite to destabilize plant immune responses. In plants, it is suggested that exposure to extracellular self-DNA impedes growth, while to extracellular non-self-DNA induces the modulation of reactive oxygen species, expression of resistance related genes, epigenetic mechanism, or suppression of disease severity. Exploring the potential of secreted RNA and extracellular DNA as a green pesticide could be a promising alternative if we are to provide food for the future global population without further damaging the environment. Hence, some studies on plant secreted RNA and responses towards extracellular DNA are discussed in this review. The precise mode of action of entry and the following cascade of signaling once the plant cell is exposed to secreted RNA or extracellular DNA could be an interesting topic for future research.

Making Sense of the Way Plants Sense Herbivores

Plants are constantly threatened by herbivore attacks and must devise survival strategies. Some plants sense and respond to elicitors including specific molecules secreted by herbivores and molecules that are innate to plants. Elicitors activate diverse arrays of plant defense mechanisms that confer resistance to the predator. Recent new insights into the cellular pathways by which plants sense elicitors and elicit defense responses against herbivores are opening doors to a myriad of agricultural applications. This review focuses on the machinery of herbivory-sensing and on cellular and systemic/airborne signaling via elicitors, exemplified by the model case of interactions between Arabidopsis hosts and moths of the genus Spodoptera.

Effect of Fragmented DNA From Plant Pathogens on the Protection Against Wilt and Root Rot of Capsicum annuum L. Plants

Chili pepper (Capsicum annuum L.) production is affected by wilt and root rot, the most devastating disease caused by the pathogen complex of oomycete Phytophthora capsici Leon and the fungi Fusarium oxysporum Schlecht and Rhizoctonia solani Kühn, infecting roots, stems, leaves, and fruits. Fungicides are currently inefficient against this disease and have a high environmental impact. The use of elicitors is a sustainable alternative for inducing resistance to wilting and root rot. DNA fragments of an organism's own origin (conspecific or self-DNA) have shown the ability to inhibit growth and activate defense mechanisms in some plant species. In this investigation, the effect of the fragmented DNA mixture of Phytophthora capsici L., Fusarium oxysporum S., and Rhizoctonia solani K. on the protection against wilt and root rot of Capsicum annuum L. plants was evaluated. Changes in plant performance, phenolics, and flavonoids contents, as well as gene expression involved in the production of defense metabolites after the fragmented and unfragmented DNA mixture in three concentrations (20, 60, and 100 μg mL^-1) in chili peppers, were studied. The results obtained showed a decrease in plant height in 60 and 100 μg mL^-1 concentrations in absence of pathogens. Moreover, the treatment with fragmented DNA 100 μg mL^-1 showed significant increase in the content of phenolic compounds and total flavonoids as well as gene expression associated to plant defense in comparison with control plants. Interestingly, foliar application of DNA fragments of the pathogen complex to a concentration of 100 μg mL^-1 caused a 40% decrease in the mortality of infected plants with the pathogens at 30 days post-inoculation compared with control plants inoculated with the pathogen complex but not sprayed with DNA fragments. These results suggested a perspective for application of fragmented DNA of these pathogens at the agricultural level in crop protection strategies to cope with wilt and root rot in Capsicum.

Roots drive oligogalacturonide-induced systemic immunity in tomato

Oligogalacturonides (OGs) are fragments of pectin released from the plant cell wall during insect or pathogen attack. They can be perceived by the plant as damage signals, triggering local and systemic defence responses. Here, we analyse the dynamics of local and systemic responses to OG perception in tomato roots or shoots, exploring their impact across the plant and their relevance in pathogen resistance. Targeted and untargeted metabolomics and gene expression analysis in plants treated with purified OGs revealed that local responses were transient, while distal responses were stronger and more sustained. Remarkably, changes were more conspicuous in roots, even upon foliar application of the OGs. The treatments differentially activated the synthesis of defence-related hormones and secondary metabolites including flavonoids, alkaloids and lignans, some of them exclusively synthetized in roots. Finally, the biological relevance of the systemic defence responses activated upon OG perception was confirmed, as the treatment induced systemic resistance to Botrytis cinerea. Overall, this study shows the differential regulation of tomato defences upon OGs perception in roots and shoots and reveals the key role of roots in the coordination of the plant responses to damage sensing.

Extracellular Fragmented Self-DNA Is Involved in Plant Responses to Biotic Stress

A growing body of evidence indicates that extracellular fragmented self-DNA (eDNA), by acting as a signaling molecule, triggers inhibitory effects on conspecific plants and functions as a damage-associated molecular pattern (DAMP). To evaluate early and late events in DAMP-dependent responses to eDNA, we extracted, fragmented, and applied the tomato (Solanum lycopersicum) eDNA to tomato leaves. Non-sonicated, intact self-DNA (intact DNA) was used as control. Early event analyses included the evaluation of plasma transmembrane potentials (Vm), cytosolic calcium variations (Ca²⁺ _{cy t}), the activity and subcellular localization of both voltage-gated and ligand-gated rectified K⁺ channels, and the reactive oxygen species (ROS) subcellular localization and quantification. Late events included RNA-Seq transcriptomic analysis and qPCR validation of gene expression of tomato leaves exposed to tomato eDNA. Application of eDNA induced a concentration-dependent Vm depolarization which was correlated to an increase in (Ca²⁺)_cyt; this event was associated to the opening of K⁺ channels, with particular action on ligand-gated rectified K⁺ channels. Both eDNA-dependent (Ca²⁺)_cyt and K⁺ increases were correlated to ROS production. In contrast, application of intact DNA produced no effects. The plant response to eDNA was the modulation of the expression of genes involved in plant-biotic interactions including pathogenesis-related proteins (PRPs), calcium-dependent protein kinases (CPK1), heat shock transcription factors (Hsf), heat shock proteins (Hsp), receptor-like kinases (RLKs), and ethylene-responsive factors (ERFs). Several genes involved in calcium signaling, ROS scavenging and ion homeostasis were also modulated by application of eDNA. Shared elements among the transcriptional response to eDNA and to biotic stress indicate that eDNA might be a common DAMP that triggers plant responses to pathogens and herbivores, particularly to those that intensive plant cell disruption or cell death. Our results suggest the intriguing hypothesis that some of the plant reactions to pathogens and herbivores might be due to DNA degradation, especially when associated to the plant cell disruption. Fragmented DNA would then become an important and powerful elicitor able to trigger early and late responses to biotic stress.

Breaking Bad News: Dynamic Molecular Mechanisms of Wound Response in Plants

Recognition and repair of damaged tissue are an integral part of life. The failure of cells and tissues to appropriately respond to damage can lead to severe dysfunction and disease. Therefore, it is essential that we understand the molecular pathways of wound recognition and response. In this review, we aim to provide a broad overview of the molecular mechanisms underlying the fate of damaged cells and damage recognition in plants. Damaged cells release the so-called damage associated molecular patterns to warn the surrounding tissue. Local signaling through calcium (Ca2+), reactive oxygen species (ROS), and hormones, such as jasmonic acid, activates defense gene expression and local reinforcement of cell walls to seal off the wound and prevent evaporation and pathogen colonization. Depending on the severity of damage, Ca2+, ROS, and electrical signals can also spread throughout the plant to elicit a systemic defense response. Special emphasis is placed on the spatiotemporal dimension in order to obtain a mechanistic understanding of wound signaling in plants.

Single-stranded oligodeoxynucleotides induce plant defence in Arabidopsis thaliana

BACKGROUND AND AIMS

Single-stranded DNA oligodeoxynucleotides (ssODNs) have been shown to elicit immune responses in mammals. In plants, RNA and genomic DNA can activate immunity, although the exact mechanism through which they are sensed is not clear. The aim of this work was to study the possible effect of ssODNs on plant immunity.

KEY RESULTS

The ssODNs IMT504 and 2006 increased protection against the pathogens Pseudomonas syringae pv. tomato DC3000 and Botrytis cinerea but not against tobacco mosaic virus-Cg when infiltrated in Arabidopsis thaliana. In addition, ssODNs inhibited root growth and promoted stomatal closure in a concentration-dependent manner, with half-maximal effective concentrations between 0.79 and 2.06 µm. Promotion of stomatal closure by ssODNs was reduced by DNase I treatment. It was also diminished by the NADPH oxidase inhibitor diphenyleneiodonium and by coronatine, a bacterial toxin that inhibits NADPH oxidase-dependent reactive oxygen species (ROS) synthesis in guard cells. In addition it was found that ssODN-mediated stomatal closure was impaired in bak1-5, bak1-5/bkk1, mpk3 and npr1-3 mutants. ssODNs also induced early expression of MPK3, WRKY33, PROPEP1 and FRK1 genes involved in plant defence, an effect that was reduced in bak1-5 and bak1-5/bkk1 mutants.

CONCLUSIONS

ssODNs are capable of inducing protection against pathogens through the activation of defence genes and promotion of stomatal closure through a mechanism similar to that of other elicitors of plant immunity, which involves the BAK1 co-receptor, and ROS synthesis.

Perception of Damaged Self in Plants

Plants use specific receptor proteins on the cell surface to detect host-derived danger signals released in response to attacks by pathogens or herbivores and activate immune responses against them.

The Role of DNA in the Extracellular Environment: A Focus on NETs, RETs and Biofilms

The capacity to actively release genetic material into the extracellular environment has been reported for bacteria, archaea, fungi, and in general, for microbial communities, but it is also described in the context of multicellular organisms, animals and plants. This material is often present in matrices that locate outside the cells. Extracellular matrices have important roles in defense response and disease in microbes, animal and plants cells, appearing as barrier against pathogen invasion or for their recognition. Specifically, neutrophils extracellular traps (NETs) in animals and root extracellular traps (RETs) in plants, are recognized to be important players in immunity. A growing amount of evidence revealed that the extracellular DNA, in these contexts, plays an active role in the defense action. Moreover, the protective role of extracellular DNA against antimicrobials and mechanical stress also appears to be confirmed in bacterial biofilms. In parallel, recent efforts highlighted different roles of self (homologous) and non-self (heterologous) extracellular DNA, paving the way to discussions on its role as a "Damage-associated molecular pattern" (DAMP). We here provide an evolutionary overview on extracellular DNA in extracellular matrices like RETs, NETs, and microbial biofilms, discussing on its roles and inferring on possible novel functionalities.

Salivary DNase II from Laodelphax striatellus acts as an effector that suppresses plant defence

Extracellular DNA, released by damaged plant cells, acts as a damage-associated molecular pattern (DAMP). We demonstrated previously that the small brown planthopper (Laodelphax striatellus, SBPH) secreted DNase II when feeding on artificial diets. However, the function of DNase II in insect feeding remained elusive. The influences of DNase II on SBPHs and rice plants were investigated by suppressing expression of DNase II or by application of heterogeneously expressed DNase II. We demonstrated that DNase II is mainly expressed in the salivary gland and is responsible for DNA-degrading activity of saliva. Knocking down the expression of DNase II resulted in decreased performance of SBPH reared on rice plants. The dsDNase II-treated SBPH did not influenced jasmonic acid (JA), salicylic acid (SA), ethylene (ET) pathways, but elicited a higher level of H2 O2 and callose accumulation. Application of heterogeneously expressed DNase II in DNase II-deficient saliva slightly reduced the wound-induced defence response. We propose a DNase II-based invading model for SBPH feeding on host plants, and provide a potential target for pest management.

Damage-Associated Molecular Pattern-Triggered Immunity in Plants

As a universal process in multicellular organisms, including animals and plants, cells usually emit danger signals when suffering from attacks of microbes and herbivores, or physical damage. These signals, termed as damage-associated molecular patterns (DAMPs), mainly include cell wall or extracellular protein fragments, peptides, nucleotides, and amino acids. Once exposed on cell surfaces, DAMPs are detected by plasma membrane-localized receptors of surrounding cells to regulate immune responses against the invading organisms and promote damage repair. DAMPs may also act as long-distance mobile signals to mediate systemic wounding responses. Generation, release, and perception of DAMPs, and signaling events downstream of DAMP perception are all rigorously modulated by plants. These processes integrate together to determine intricate mechanisms of DAMP-triggered immunity in plants. In this review, we present an extensive overview on our current understanding of DAMPs in plant immune system.

Nucleic Acid Sensing in Mammals and Plants: Facts and Caveats

The accumulation of nucleic acids in aberrant compartments is a signal of danger: fragments of cytosolic or extracellular self-DNA indicate cellular dysfunctions or disruption, whereas cytosolic fragments of nonself-DNA or RNA indicate infections. Therefore, nucleic acids trigger immunity in mammals and plants. In mammals, endosomal Toll-like receptors (TLRs) sense single-stranded (ss) or double-stranded (ds) RNA or CpG-rich DNA, whereas various cytosolic receptors sense dsDNA. Although a self/nonself discrimination could favor targeted immune responses, no sequence-specific sensing of nucleic acids has been reported for mammals. Specific immune responses to extracellular self-DNA versus DNA from related species were recently reported for plants, but the underlying mechanism remains unknown. The subcellular localization of mammalian receptors can favor self/nonself discrimination based on the localization of DNA fragments. However, autoantibodies and diverse damage-associated molecular patterns (DAMPs) shuttle DNA through membranes, and most of the mammalian receptors share downstream signaling elements such as stimulator of interferon genes (STING) and the master transcription regulators, nuclear factor (NF)-κB, and interferon regulatory factor 3 (IRF3). The resulting type I interferon (IFN) response stimulates innate immunity against multiple threats-from infection to physical injury or endogenous DNA damage-all of which lead to the accumulation of eDNA or cytoplasmatic dsDNA. Therefore, no or only low selective pressures might have favored a strict self/nonself discrimination in nucleic acid sensing. We conclude that the discrimination between self- and nonself-DNA is likely to be less strict-and less important-than assumed originally.

Extracellular DAMPs in Plants and Mammals: Immunity, Tissue Damage and Repair

Innate immune receptors, well known mediators of response to non-self-molecules and inflammation, also act as mediators of immunity triggered by 'damage-associated molecular patterns' (DAMPs). Pathogen-associated molecular patterns (PAMPs) cause inflammation in mammals and a rapid immune response in plants, while DAMPs trigger more complex responses, including immunity, tissue maintenance and repair. DAMPs, their receptors and downstream transduction mechanisms are often conserved within a kingdom or, due to convergent evolution, are similar across the kingdoms of life. Herein, we describe the dynamics and functionality of specific extracellular DAMP classes and their receptors in immunity, inflammation and repair of tissue damage in plants and mammals.

Exogenous fragmented DNA acts as a damage-associated molecular pattern (DAMP) inducing changes in CpG DNA methylation and defence-related responses in Lactuca sativa

Damage-associated molecular patterns (DAMPs) have been studied recently to understand plant self-nonself recognition in response to attack by biotic and abiotic stresses. Extracellular DNA has emerged as a possible DAMP. As a DAMP DNA seems to function depending on the phylogenetic scale and has been tested in a few plant species. This study aimed to evaluate the possible role of self DNA (sDNA) as a DAMP by analysing changes in CpG DNA methylation and defence-related responses in lettuce (Lactuca sativa L.) as a model plant. sDNA and nonself DNA (nsDNA) from Capsicum chinense Murray (both species belong to the same clade, Asterids) stimulated aberrant seed germination and root growth in lettuce seedlings. Similar resultswere obtained with nsDNA obtained from Acaciella angustissima (Mill.) Britton & Rose plants (belonging to the clade Rosids I), although at significantly higher concentrations. Moreover, in most cases, this behaviour was correlated with hypomethylation of CpG DNA as well as defence responses measured as altered gene expression associated with oxidative burst and production of secondary metabolites (phenylpropanoids) related to coping with stress conditions. Our results suggested that extracellular and fragmented DNA has a role as a DAMP depending on phylogenetic closeness in plants as lettuce, inducing epigenetic, genetic and biochemical changes within the plant. The importance of our results is that, for the first time, they demonstrate that sDNA acts as a DAMP in plants, changing CpG DNA methylation levels as well as increasing the production of secondary metabolites associated with defence responses to stress.

Extracellular self-DNA as a damage-associated molecular pattern (DAMP) that triggers self-specific immunity induction in plants

Mammals sense self or non-self extracellular or extranuclear DNA fragments (hereinafter collectively termed eDNA) as indicators of injury or infection and respond with immunity. We hypothesised that eDNA acts as a damage-associated molecular pattern (DAMP) also in plants and that it contributes to self versus non-self discrimination. Treating plants and suspension-cultured cells of common bean (Phaseolus vulgaris) with fragmented self eDNA (obtained from other plants of the same species) induced early, immunity-related signalling responses such as H₂O₂ generation and MAPK activation, decreased the infection by a bacterial pathogen (Pseudomonas syringae) and increased an indirect defence to herbivores (extrafloral nectar secretion). By contrast, non-self DNA (obtained from lima bean, Phaseolus lunatus, and Acacia farnesiana) had significantly lower or no detectable effects. Only fragments below a size of 700 bp were active, and treating the eDNA preparation DNAse abolished its inducing effects, whereas treatment with RNAse or proteinase had no detectable effect. These findings indicate that DNA fragments, rather than small RNAs, single nucleotides or proteins, accounted for the observed effects. We suggest that eDNA functions a DAMP in plants and that plants discriminate self from non-self at a species-specific level. The immune systems of plants and mammals share multiple central elements, but further work will be required to understand the mechanisms and the selective benefits of an immunity response that is triggered by eDNA in a species-specific manner.

DNA Damage and Chromatin Conformation Changes Confer Nonhost Resistance: A Hypothesis Based on Effects of Anti-cancer Agents on Plant Defense Responses

Over the last decades, medical research has utilized DNA altering procedures in cancer treatments with the objective of killing cells or suppressing cell proliferation. Simultaneous research related to enhancing disease resistance in plants reported that alterations in DNA can enhance defense responses. These two opposite perspectives have in common their effects on the center for gene transcription, the nuclear chromatin. A review of selected research from both anticancer- and plant defense-related research provides examples of some specific DNA altering actions: DNA helical distortion, DNA intercalation, DNA base substitution, DNA single cleavage by DNases, DNA alkylation/methylation, and DNA binding/exclusion. The actions of the pertinent agents are compared, and their proposed modes of action are described in this study. Many of the DNA specific agents affecting resistance responses in plants, e.g., the model system using pea endocarp tissue, are indeed anticancer agents. The tumor cell death or growth suppression in cancer cells following high level treatments may be accompanied with chromatin distortions. Likewise, in plants, DNA-specific agents activate enhanced expression of many genes including defense genes, probably due to the chromatin alterations resulting from the agents. Here, we propose a hypothesis that DNA damage and chromatin structural changes are central mechanisms in initiating defense gene transcription during the nonhost resistance response in plants.