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Plant Perceptions of Extracellular DNA and RNA

2016; Elsevier BV; Volume: 9; Issue: 7 Linguagem: Inglês

10.1016/j.molp.2016.05.014

1674-2052

Abhayprasad Bhat, Choong‐Min Ryu,

Plant Virus Research Studies

Plants and microbes interact in a myriad of ways in terrestrial ecosystems, which span from molecular to open-field scales. The basis of such communications among and within species is of intense interest among the plant–biotic interactions research community. While we think of DNA as the code that provides the genetic information of all organisms, recent discoveries on the functions of fragmented extracellular DNA (eDNA) have opened up a new arena in our understanding of biotic interactions (Mazzoleni et al., 2015aMazzoleni S. Bonanomi G. Incerti G. Chiusano M.L. Termolino P. Mingo A. Senatore M. Giannino F. Cartenì F. Rietkerk M. et al.Inhibitory and toxic effects of extracellular self-DNA in litter: a mechanism for negative plant-soil feedbacks?.New Phytol. 2015; 205: 1195-1210Google Scholar). In particular, plant perceptions of eDNA and extracellular RNA (eRNA) have embarked on a new journey in the fields of molecular pattern recognition and plant immune response (Lee et al., 2015Lee B. Park Y.-S. Lee S. Song G.C. Ryu C.-M. Bacterial RNAs activate innate immunity in Arabidopsis.New Phytol. 2015; 12: 785-797Google Scholar, Mazzoleni et al., 2015aMazzoleni S. Bonanomi G. Incerti G. Chiusano M.L. Termolino P. Mingo A. Senatore M. Giannino F. Cartenì F. Rietkerk M. et al.Inhibitory and toxic effects of extracellular self-DNA in litter: a mechanism for negative plant-soil feedbacks?.New Phytol. 2015; 205: 1195-1210Google Scholar, Mazzoleni et al., 2015bMazzoleni S. Carteni F. Bonanomi G. Senatore M. Termolino P. Giannino F. Incerti G. Rietkerk M. Lanzotti V. Chiusano M.L. Inhibitory effects of extracellular self-DNA: a general biological process?.New Phytol. 2015; 206: 127-132Google Scholar). Such genetic materials in plant–microbe interactions play a provocative role in self- and non-self-recognition and induction of innate immunity in plants. eDNA and eRNA from bacteria are a strong trigger of biofilm formation, affecting colonization of the plant surface and a novel microbe-associated molecular pattern (MAMP), respectively (Panstruga, 2016Panstruga R. Bacterial RNA—a new MAMP on the block?.New Phytol. 2016; 209: 458-460Google Scholar). These findings suggest the intersection of disciplines, bringing to light new and interesting insight into the ways in which organisms interact and communicate in their natural environment. The dynamic nature of communication between plants and microbes has profound implications on terrestrial ecosystems and confers selective benefits to plant fitness. Plants invariably deploy membrane-bound cell-surface proteins called pattern-recognition receptors (PRRs) to perceive biomolecular signatures of microbes known as MAMPs or pathogen-associated molecular patterns (PAMPs). Upon recognition, PRRs trigger signal transduction cascades that ultimately enhance plant innate immunity, termed PAMP-triggered immunity (PTI). A wide range of MAMPs has been reported that are recognized by an equally diverse number of PRRs. In fact, genome analysis of Arabidopsis thaliana has revealed that the number of putative PRRs is much higher in plants than in mammals. MAMPs such as fungal chitins are recognized by chitin elicitor receptor kinase 1 (CERK1) and Lysm-RLP chitin elicitor-binding protein (CEBiP), while flagellins and elongation factor thermo-unstable (EF-Tu) are detected by flagellin-sensitive-2 (FLS2) and EF-Tu receptor (EFR), respectively (Zipfel, 2014Zipfel C. Plant pattern-recognition receptors.Trends Immunol. 2014; 35: 345-351Google Scholar). Similarly, damage-associated molecular patterns (DAMPs) that originate from necrotrophic fungi such as peptidoglycans, SCLEROTINIA CULTURE FILTRATE ELICITOR 1 (SCFE1), oligosaccharides, and PHYTOSULFOKINE-ALPHA (PSK-alpha) and plant peptide-containing sulfated tyrosine 1 (PSY1) are recognized by RLP RESPONSIVENESS TO BOTRYTIS POLYGALACTURONASES 1 (RBPG1), RECEPTOR-LIKE PROTEIN30 (RLP30), wall-associated kinase 1 (WAK1), and phytosulfokine receptor 1 (PSKR1), respectively. Nevertheless, cognate receptors of oligosaccharides such as beta-glucans, chitosans, fucans, and many other relatively new MAMPS such as extracellular purine nucleotides, eDNAs, and eRNAs are yet to be identified (Lee et al., 2015Lee B. Park Y.-S. Lee S. Song G.C. Ryu C.-M. Bacterial RNAs activate innate immunity in Arabidopsis.New Phytol. 2015; 12: 785-797Google Scholar, Mazzoleni et al., 2015bMazzoleni S. Carteni F. Bonanomi G. Senatore M. Termolino P. Giannino F. Incerti G. Rietkerk M. Lanzotti V. Chiusano M.L. Inhibitory effects of extracellular self-DNA: a general biological process?.New Phytol. 2015; 206: 127-132Google Scholar). Upon perception of MAMPs, PRRs can elicit the plant immune response directly or indirectly by activating reactive oxygen species-, mitogen-activated protein kinase (MAPK)-, salicylic acid-, and jasmonic acid (JA)-related genes and by callose deposition. DNA encodes heritable genetic information that is unique to an individual or a species. Hence, it is conceivable that DNA and RNA can be perceived as molecular markers of an individual. In mammalian systems, heterologous nucleic acids such as DNA and RNA, which are released from tissue damage, act as DAMPs, while microbial DNA and RNA act as MAMPs/PAMPs. Both DAMPs and MAMPs are recognized by endosomal membrane-bound receptors known as Toll-like receptors (TLRs) and by non-self-RNA receptor helicases known as retinoic acid-inducible protein 1-like receptors (RIG-1 like receptors) that are localized in the cytoplasmic milieu (Wagner and Bauer, 2006Wagner H. Bauer S. All is not Toll: new pathways in DNA recognition.J. Exp. Med. 2006; 203: 265-268Google Scholar, Heil and Land, 2014Heil M. Land W.G. Danger signals—damaged-self recognition across the tree of life.Front Plant Sci. 2014; 5: 578Google Scholar). TLRs such as TLR7 and TLR8 recognize single-strand RNA (ssRNA) from bacterial infections, while TLR7 also recognizes self-ssRNA (Wagner and Bauer, 2006Wagner H. Bauer S. All is not Toll: new pathways in DNA recognition.J. Exp. Med. 2006; 203: 265-268Google Scholar, Heil and Land, 2014Heil M. Land W.G. Danger signals—damaged-self recognition across the tree of life.Front Plant Sci. 2014; 5: 578Google Scholar). How does TLR7 differentiate between self- and non-self-RNA to prevent abnormal activation of immune cells? A well-organized compartmentalization should be sufficient for an effective safety mechanism. It is speculated that rapid degradation of self-RNA by host-derived RNases prevents them from reaching the endolysosomes and causing damage (Heil and Land, 2014Heil M. Land W.G. Danger signals—damaged-self recognition across the tree of life.Front Plant Sci. 2014; 5: 578Google Scholar). On the contrary, endosome-specific expression of TLRs allows selective detection of extracellular nucleic acids such as capsid-coated viral genome that are protected from host RNases and effectively initiate innate immune response (Wagner and Bauer, 2006Wagner H. Bauer S. All is not Toll: new pathways in DNA recognition.J. Exp. Med. 2006; 203: 265-268Google Scholar). Alternatively, differences in the frequency of CpGs and methylation patterns between self- and non-self-RNA may render TLR7 non-stimulatory to self-RNA. In one such instance, TLR9 detects pathogen-borne unmethylated ssDNA, which ultimately leads to production of proinflammatory cytokines (Wagner and Bauer, 2006Wagner H. Bauer S. All is not Toll: new pathways in DNA recognition.J. Exp. Med. 2006; 203: 265-268Google Scholar). In addition, evidence suggests that chemical modifications such as pseudouridylation, and 5′-triphosphate and differences in sequence length can be the key determinants in discriminating self from non-self nucleic acid double-stranded RNA (dsRNA) (Heil and Land, 2014Heil M. Land W.G. Danger signals—damaged-self recognition across the tree of life.Front Plant Sci. 2014; 5: 578Google Scholar). Interestingly, comprehensive sequence analysis of 450 plant RNA viruses revealed that CpG dinucleotides are under-represented in most cases, wherein CpG was more repressed in dicot-infecting viruses than in monocot-infecting viruses (Cheng et al., 2014Cheng X. Virk N. Wang H. Chapter 19—Impact of the host on plant virus evolution.in: Gaur R.K. Thomas Hohn P.S. Plant Virus–Host Interaction. Academic Press, Boston (MA)2014: 359-371Google Scholar). Thus, CpG-negating selective pressure operates across all plant RNA viruses, which hints at a potential RNA receptor that is yet to be discovered. Remarkably, recent reports highlighted the active yet differential perception of eDNA and eRNA in plants (Lee et al., 2015Lee B. Park Y.-S. Lee S. Song G.C. Ryu C.-M. Bacterial RNAs activate innate immunity in Arabidopsis.New Phytol. 2015; 12: 785-797Google Scholar, Mazzoleni et al., 2015bMazzoleni S. Carteni F. Bonanomi G. Senatore M. Termolino P. Giannino F. Incerti G. Rietkerk M. Lanzotti V. Chiusano M.L. Inhibitory effects of extracellular self-DNA: a general biological process?.New Phytol. 2015; 206: 127-132Google Scholar, Niehl et al., 2016Niehl A. Wyrsch I. Boller T. Heinlein M. Double-stranded RNAs induce a pattern-triggered immune signaling pathway in plants.New Phytol. 2016; 4: 1-12Google Scholar). Exogenous application of purified self-genomic DNA inhibited growth in a concentration-dependent manner (Mazzoleni et al., 2015aMazzoleni S. Bonanomi G. Incerti G. Chiusano M.L. Termolino P. Mingo A. Senatore M. Giannino F. Cartenì F. Rietkerk M. et al.Inhibitory and toxic effects of extracellular self-DNA in litter: a mechanism for negative plant-soil feedbacks?.New Phytol. 2015; 205: 1195-1210Google Scholar). Interestingly, genomic DNA from taxonomically distant species (heterologous DNA) did not inhibit plant growth, suggesting a potential role of eDNA in plant–soil negative feedback operating in nature. Litter autotoxicity and eDNA-mediated plant growth inhibition experiments invited multiple explanations and questions due to their profound implications in plant research (Duran-Flores and Heil, 2015Duran-Flores D. Heil M. Growth inhibition by self-DNA: a phenomenon and its multiple explanations.New Phytol. 2015; 207: 482-485Google Scholar, Panstruga, 2016Panstruga R. Bacterial RNA—a new MAMP on the block?.New Phytol. 2016; 209: 458-460Google Scholar). Furthermore, organisms representing a wide taxonomic range (bacteria, protozoa, algae, fungi, plants, and insects) display growth inhibition when purified self-genomic DNA is applied exogenously (Mazzoleni et al., 2015bMazzoleni S. Carteni F. Bonanomi G. Senatore M. Termolino P. Giannino F. Incerti G. Rietkerk M. Lanzotti V. Chiusano M.L. Inhibitory effects of extracellular self-DNA: a general biological process?.New Phytol. 2015; 206: 127-132Google Scholar). In conjunction with rapid advancement in this area of research, Lee et al., 2015Lee B. Park Y.-S. Lee S. Song G.C. Ryu C.-M. Bacterial RNAs activate innate immunity in Arabidopsis.New Phytol. 2015; 12: 785-797Google Scholar uncovered a new role of eRNA as a PAMP/MAMP in plants. They observed that plant leaf infiltration of total RNA isolated from a phytopathogenic bacterium (Pseudomonas syringae pv. tomato DC3000) notably elevated the plant innate immune response, leading to reduced infection of this bacterium in systemic leaves. Intact RNA molecules seem to be essential for such a robust innate immune response because sheared and RNase-pre-treated bacterial RNA failed to inhibit phytopathogen growth. In addition, exogenous RNA treatment caused the generation of superoxide anions, activation of MAPK, defense gene expression, and callose deposition. As a representative major constituent of total RNA, the authors used a random portion of 16s ribosomal RNA (rRNA) for in vitro synthesis. Interestingly, a more recent study showed that a 746-bp dsRNA induced typical PTI response in Arabidopsis leaf disks that resulted in MPK6, MPK3 activation, ethylene production, and seedling growth inhibition (Niehl et al., 2016Niehl A. Wyrsch I. Boller T. Heinlein M. Double-stranded RNAs induce a pattern-triggered immune signaling pathway in plants.New Phytol. 2016; 4: 1-12Google Scholar). The results show that in vitro synthesized dsRNA did not act through antiviral dicer-like (DCL) proteins but in a SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE 1 (SERK1)-dependent fashion. The possibility of 16s rRNA being a MAMP cannot be excluded (Lee et al., 2015Lee B. Park Y.-S. Lee S. Song G.C. Ryu C.-M. Bacterial RNAs activate innate immunity in Arabidopsis.New Phytol. 2015; 12: 785-797Google Scholar). In mice, TLR13 recognizes bacterial 23s rRNA, leading to the activation of innate immune responses (Panstruga, 2016Panstruga R. Bacterial RNA—a new MAMP on the block?.New Phytol. 2016; 209: 458-460Google Scholar). The bacterial rRNA folded into complex three-dimensional shapes with robust secondary structures that are conserved at the species level may hold a differentiating factor. These unique secondary structures of rRNA possess sequence conspecificity that defines species differentiation. Thus, it is very tempting to speculate that so-called PRRs may be able to recognize and discriminate species-specific 16s rRNA (Figure 1). Ethylene production and Oilseed rape mosaic virus accumulation was greatly reduced in dsRNA-treated serk1 mutant, leading to impairment in PTI response in Arabidopsis (Niehl et al., 2016Niehl A. Wyrsch I. Boller T. Heinlein M. Double-stranded RNAs induce a pattern-triggered immune signaling pathway in plants.New Phytol. 2016; 4: 1-12Google Scholar). Based on the cumulative data, the authors suggested membrane-bound SERK1 as a potential dsRNA receptor, which is analogous to Figure 1A. Transcriptome analysis of bacterial RNA-treated plants revealed high expression of ribonuclease (RNS)-1 among others (Lee et al., 2015Lee B. Park Y.-S. Lee S. Song G.C. Ryu C.-M. Bacterial RNAs activate innate immunity in Arabidopsis.New Phytol. 2015; 12: 785-797Google Scholar) (Figure 1). RNS-1 belongs to the ubiquitous T(2) family of RNS that are secretory in nature and typically expressed as a response to wounding in A. thaliana independent of the JA, oligogalacturonide, and abscisic acid pathways. During infection, plants deploy defense proteins known as pathogen-related (PR) proteins, most of which are transported to an extracellular niche, while some are localized in vacuoles. Certain PR proteins such as GaPR10 and Vpr10.1 display RNase and DNase activities in vitro and have a putative ATP-binding domain (Xu et al., 2014Xu T.F. Zhao X.C. Jiao Y.T. Wei J.Y. Wang L. Xu Y. A pathogenesis related protein, VpPR-10.1, from Vitis pseudoreticulata: an insight of its mode of antifungal activity.PLoS One. 2014; 9: e95102Google Scholar). Such PR proteins with canonical RNase activity are potential eDNA and eRNA receptors. Furthermore, plants express ribosome-inactivating proteins (RIPs) with antifungal activity. RIPs target ribosomes by exhibiting N-glycosidase activity, thereby removing a single adenine from rRNA, and translation is thus inhibited (Duran-Flores and Heil, 2015Duran-Flores D. Heil M. Growth inhibition by self-DNA: a phenomenon and its multiple explanations.New Phytol. 2015; 207: 482-485Google Scholar). Alternatively, passive internalization of extracellular nucleic acids cannot be ruled out (Figure 1). In metazoans and mammalian systems, extracellular foreign nucleic acids are internalized by endosomal compartments that bear specific TLRs for recognition (Wagner and Bauer, 2006Wagner H. Bauer S. All is not Toll: new pathways in DNA recognition.J. Exp. Med. 2006; 203: 265-268Google Scholar). Global transcriptome and proteome analysis and high-throughput analysis such as RNA sequencing may hold the key to elucidating receptor-mediated recognition of eDNA and eRNA moieties. The molecular mechanism underlying growth inhibition by eDNA and plant innate immune stimulation by eRNA is uncharacterized and requires further investigation. Uptake of fragmented free DNA or RNA by living cells can block mRNA translation in a manner similar to RNA interference (Figure 1) or can cause genome instability (Mazzoleni et al., 2015bMazzoleni S. Carteni F. Bonanomi G. Senatore M. Termolino P. Giannino F. Incerti G. Rietkerk M. Lanzotti V. Chiusano M.L. Inhibitory effects of extracellular self-DNA: a general biological process?.New Phytol. 2015; 206: 127-132Google Scholar). The selective inhibitory effect of fragmented DNA formulations is conceptualized for drug and antibiotic applications (Mazzoleni et al., 2015bMazzoleni S. Carteni F. Bonanomi G. Senatore M. Termolino P. Giannino F. Incerti G. Rietkerk M. Lanzotti V. Chiusano M.L. Inhibitory effects of extracellular self-DNA: a general biological process?.New Phytol. 2015; 206: 127-132Google Scholar). Determining the minimal regulatory region required for immune stimulation of rRNA is important for practical applications. For example, spray application of eRNA or eDNA can be potentially utilized to stimulate plant immune response in a dose-dependent manner. Alternatively, the optimized combination of eDNA and eRNA can be useful for weed control, eliciting induced systemic resistance and improving plant fitness. In addition, the unprecedented phenomenon of litter autotoxicity mediated by extracellular self-DNA opened a new scenario in ecology that contributes as a novel plant–soil negative feedback mechanism in a species-specific manner (Van der Putten et al., 2013Van der Putten W.H. Bardgett R.D. Bever J.D. Bezemer T.M. Casper B.B. Fukami T. Kardol P. Klironomos J.N. Kulmatiski A. Schweitzer J.A. et al.Plant-soil feedbacks: the past, the present and future challenges.J. Ecol. 2013; 101: 265-276Google Scholar, Mazzoleni et al., 2015aMazzoleni S. Bonanomi G. Incerti G. Chiusano M.L. Termolino P. Mingo A. Senatore M. Giannino F. Cartenì F. Rietkerk M. et al.Inhibitory and toxic effects of extracellular self-DNA in litter: a mechanism for negative plant-soil feedbacks?.New Phytol. 2015; 205: 1195-1210Google Scholar). Nonetheless, these recent discoveries have elucidated yet new functions of nucleic acids, which are the pillars of the central dogma of life. Financial support was obtained from BioNano Health-Guard Research Center funded by the Ministry of Science, ICT & Future Planning (MSIP) as Global Frontier Project (Grant No. H-GUARD_2013M3A6B2078952), the Next-Generation BioGreen 21 Program (SSAC grant #PJ009524), Rural Development Administration, South Korea, and the KRIBB initiative program, South Korea.