Update on Exogenous Application of RNAi

Genetically Modified Organism-Free RNA Interference:Exogenous Application of RNA Molecules in Plants1[OPEN]

Athanasios Dalakouras,a,b,2,3 Michael Wassenegger,c Elena Dadami,a Ioannis Ganopoulos,b

Maria L. Pappas,d and Kalliope Papadopouloua

aUniversity of Thessaly, Department of Biochemistry and Biotechnology, 41500 Larissa, GreecebInstitute of Plant Breeding and Genetic Resources Hellenic Agricultural Organization (ELGO)-DEMETER,57001 Thessaloniki, GreececRLP AgroScience, Alplanta Institute for Plant Research, 67435 Neustadt an der Weinstrasse, GermanydDemocritus University of Thrace, Department of Agricultural Development, 68200 Orestiada, Greece

ORCID IDs: 0000-0002-4446-1808 (A.D.); 0000-0001-7967-5702 (I.G.); 0000-0003-4563-3023 (M.L.P.); 0000-0001-7731-1825 (K.P.).

Since its discovery more than 20 years ago, RNAinterference (RNAi) has been extensively used in cropprotection platforms. So far, RNAi approaches havebeen conventionally based on the use of transgenicplants expressing double-stranded RNAs (dsRNAs)against selected targets. However, the use of trans-genes and genetically modified organisms (GMOs)has raised considerable scientific and public concerns.Hence emerged the need for alternative approachesthat avoid the use of transgenes and resort instead todirect exogenous application of RNA molecules thathave the potential to trigger RNAi. Here, we highlightthe most important advances in this field, discussingthe various methods of RNA delivery in plants againstdiverse targets such as plant genes, viruses, viroids,fungi, insects, mites, and nematodes. In addition, weexamine the possible shortcomings of these methods,underline the critical parameters that have to be metfor a desired outcome, and explore feasible possibili-ties to increase their efficiency and applicability, evenagainst bacterial pathogens.

RNAi IN PLANTS

In plants, RNAi is triggered by dsRNA having var-iable sources of origin, ranging from viral replicationintermediates, transcription of inverted repeats, stress-induced overlapping antisense transcripts, and RNA-DIRECTED RNA POLYMERASE (RDR) transcription

of aberrant transcripts (Hamilton and Baulcombe,1999; Mette et al., 1999; Borsani et al., 2005; Luoand Chen, 2007). Once present in the plant cell,dsRNAs are processed by DICER-LIKE (DCL) en-donucleases into 21–24-nt short interfering RNAs(siRNAs; Fig. 1; Liu et al., 2009). The model plantArabidopsis (Arabidopsis thaliana) contains four DCLparalogs. DCL2, DCL3, and DCL4 generate the 22-,24-, and 21-nt siRNAs, respectively, whereas DCL1recognizes genome-encoded imperfect hairpin RNAsresulting in the biogenesis of 21-nt/22-nt micro RNAs(miRNAs; Bologna and Voinnet, 2014; Borges andMartienssen, 2015). Plant siRNAs and miRNAs, col-lectively termed “small RNAs” (sRNAs; Ruiz-Ferrerand Voinnet, 2009), exhibit 39 2-nt overhangs and be-come stabilized though 39 end methylation by HUA

ADVANCES

Exogenous application of RNA molecules (dsRNAs, siRNAs) in plants can trigger RNAi in a GMO-free manner. So far, exogenous application of RNA in plants has efficiently triggered RNAi of plant genes, viruses, viroids, fungi, insects and mites. Conjugating RNA molecules to nanoparticles and carrier peptides greatly enhances their resistance to nucleases and efficiency of delivery. Exogenously applied 22-nt siRNAs are the most potent inducers of local and systemic RNAi in plants. High pressure spraying allows the symplastic delivery of exogenous RNA whereas petiole absorption and/or trunk injection results in apoplastic delivery of the exogenous RNA.

1This work was supported by the European Union’s Horizon 2020Research and Innovation Programme (Marie Skłodowska-Curiegrant agreement no. 793186 RNASTIP to A.D. and K.P.).

2Author for contact: nasosdal@gmail.com.3Senior author.A.D. and K.P. conceived the idea and supervised the project; A.D.,

M.W., and E.D. wrote the sections on RNAi; A.D., E.D., and I.G.wrote the section on viruses and viroids; A.D. and K.P. wrote thesections on fungi and bacteria; A.D. and M.P. wrote the sections oninsects and mites.

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ENHANCER1 (Yu et al., 2005; Yang et al., 2006). Afterthis modification, and depending on its 59-terminalnucleotide, one of the two sRNA strands will be loadedonto an ARGONAUTE (AGO) protein (Kim, 2008). Ingeneral, 21-nt sRNAs with 59-U are loaded on AGO1and scan the cytoplasm for complementary tran-scripts for cleavage and degradation in a process termed“post-transcriptional gene silencing” (Hamilton andBaulcombe, 1999; Mi et al., 2008; Fig. 1). Twenty-two–nt sRNAs are also loaded on AGO1 but seem-ingly change AGO1 conformation and recruit RDR6to the 39 of the target, transcribing the target tran-script into dsRNA and thus generating additional(secondary) siRNAs in a mechanism coined “transi-tive silencing” (Dalmay et al., 2000; Chen et al., 2010;Fig. 1). Finally, 24-nt sRNAs with 59-A are incorpo-rated on AGO4, recognize cognate DNA or its nascenttranscript, and recruit DNA methyltransferases tomethylate the cytosine residues of both DNA strandsin a process termed “RNA-directed DNAmethylation”(RdDM; Wassenegger et al., 1994; Chan et al., 2004;Fig. 1). Importantly, RNAi is not cell-autonomous inplants. Thus, once generated in a single cell, siRNAs areable to move through plasmodesmata to 10–15 neigh-boring cells while RNA molecules of a yet unknownnature move through the vasculature system to distantparts of the plant, a phenomenon called “systemic si-lencing” (Voinnet and Baulcombe, 1997; Palauqui andVaucheret, 1998).

GMO-FREE RNAi IN PLANTS

In addition to mediating a broad range of devel-opmental events, RNAi has great potential againstinvading pests and pathogens (Eamens et al., 2008;Martínez de Alba et al., 2013). So far, conventional RNAiapplications have been largely based on the use of re-combinant viruses (virus-induced gene silencing), Agro-bacterium tumefaciens-mediated transiently expressedtransgenes, and stably transformed transgenic plantsthat enable the production of dsRNA molecules againstselected targets (host-induced gene silencing; Baulcombe,2004, 2015). In 2017, the transgenic maize (Zea mays)SmartStax Pro, engineered to express dsRNA againstcorn rootworm (Diabrotica virgifera virgifera), was ap-proved by the U.S. Environmental Protection Agency,the U.S. Food and Drug Administration, and the U.S.Department of Agriculture (https://www.epa.gov/newsreleases/epa-registers-innovative-tool-control-corn-rootworm). However, despite their demonstratedsuccess, RNAi-based transgenic crops have not beencommercialized as much as one might have expected.Transgenic plants and GMOs in general have met suchsevere criticism that their chances for widespread ap-proval are gloomy, at the least. According to some es-timates, it costs;140 million USD to bring a transgeniccrop to commercialization (Rosa et al., 2018), and evenwhen that happens, several anti-GMO responses fol-low. Taking these into consideration, and to tacklethis issue, new GMO-free RNAi approaches need to

Figure 1. DCL processing of exogenouslyapplied dsRNA in plants. DCL4 generates 21-nt siRNAs that are loaded onto AGO1 andtarget complementary transcripts for cleav-age. DCL2 generates 22-nt siRNAs that arealso loaded onto AGO1 and recruit RDR6 tothe target transcripts’ 39 ends for the genera-tion of secondary siRNAs. Finally, DCL3generates 24-nt siRNAs that are loaded ontoAGO4 and trigger de novo DNA methylationby hybridizing with nascent Pol V or Pol IItranscripts. Whether DCL1, which is mainlyinvolved in themiRNApathway, also processesexogenously applied dsRNA, is not clear.

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be developed that will enable the activation of RNAinot through the use of recombinant viruses or trans-genes but through the direct exogenous delivery ofRNA molecules (dsRNAs and/or sRNAs) in plants.In this article, only GMO-free RNAi strategies involv-ing exogenous application of RNAmolecules directlyin plants will be discussed; transgene-based host-induced gene silencing and virus-induced gene silenc-ing approaches have been extensively reviewed else-where and will not be discussed here (Eamens et al.,2008; Prins et al., 2008; Nowara et al., 2010; Koch andKogel, 2014; Baulcombe, 2015; Zotti and Smagghe,2015; Joga et al., 2016; Cai et al., 2018a; Rosa et al.,2018; Zotti et al., 2018; Qi et al., 2019).

APPLYING RNA MOLECULES IN PLANTS TOTARGET ENDOGENES AND TRANSGENES

The first report wherein exogenous RNA applica-tion into plants triggered RNAi of a plant gene wasdescribed in a 2011 Monsanto patent; Nicotiana ben-thamiana plants pretreated with the surfactant SilwetL-77 (Momentive; https://www.momentive.com/en-us/categories/super-spreaders/silwet-l-77/) andsprayed (2.5 bar) with in vitro-transcribed 685-bpdsRNA and/or chemically synthesized 21-nt sRNAstargeting the endogenous phytoene desaturase mRNAdisplayed extensive phytoene desaturaseRNAi (Sammonset al., 2011). (Note that because chemically synthesizedsRNA oligonucleotide duplexes are not the biologicaloutcome of DCL endonucleolytic processing and/orHUA ENHANCER1 methylation, they cannot be con-sidered bona fide siRNAs, and thus will be collectivelycalled hereafter as “sRNAs”). After this initial obser-vation, several others followed using diverse methodsof RNA application, succinctly mentioned below inchronological order. Hence, when Arabidopsis leaveswere infiltrated with 21-nt sRNAs fused to a positivelycharged carrier peptide that combined a copolymerof His and Lys, (KH)9 (18 amino acids), RNAi of theyellow fluorescent protein (YFP) transgene and thechalcone synthase endogene was recorded (Numataet al., 2014). Subsequent studies demonstrated thatRNA molecules can be absorbed by the roots anddisplay biological activity throughout the plant. SHOOTMERISTEMLESS (STM) is a class-I knotted-like homeo-domain protein expressed in the shoot apical meristemand required for shoot apical meristem formation,whereas WEREWOLF (WER) is an R2R3-type MyB-related transcription factor expressed in the root epi-dermal cells. When STM or WER dsRNA conjugatedto cationic fluorescent nanoparticle was applied toArabidopsis seedling roots for five consecutive days,expression of STM and WER was suppressed andresulted in phenotypic defects (Jiang et al., 2014).Moreover, when dsRNA targeting MOB1A and actinwas applied to Arabidopsis and rice (Oryza sativa)roots, respectively, RNAi of the corresponding genestook place and normal root growth was perturbed

(Li et al., 2015). These results suggest that irrigation-mediated RNA application is a possibility that needsto be further elaborated. In a subsequent study (Lauet al., 2014), instead of using in vitro-transcribed dsRNA,crude extracts of Escherichia coli HT115 (DE3; see “Ap-plying RNA Molecules in Plants Against Viruses”)expressing a 430-bp dsRNA targeting MYB1 weremechanically inoculated into the hybrid orchid (Den-drobium hybrida) flower buds (Lau et al., 2015). MYB1 isexpressed throughout flower bud development and isinvolved in the development of the conical cell shape ofthe epidermal cells of the flower labellum. Scanningelectron microscopy of the adaxial epidermal cellsrevealed that application of MYB1 dsRNA changed thephenotype of floral cells, an outcome of great interestfor floriculture biotechnology.

Plant cells contain a very tough cellulose-rich cellwall ranging from 0.1 mm to several micrometers inthickness, which poses a physical barrier to biomol-ecule delivery. To facilitate RNA delivery inside theplant cell, RNA molecules are usually conjugated tocarrier compounds, asmentioned above (Jiang et al., 2014;Numata et al., 2014). Recently, DNAnanostructures, suchas 3D tetrahedron, 1D hairpin tile, and 1D nanostring,were used to facilitate the delivery and biological actionof 21-nt GFP sRNAs in infiltratedN. benthamiana leaves(Zhang et al., 2019). Instead of remaining in the meso-phyllic apoplast, the nanostructure-conjugated sRNAsentered the symplast and silenced GFP expression.Interestingly, sRNAs tethered to 3D nanostructuresexhibited both mRNA degradation and translationalarrest of the GFP, whereas sRNAs attached to 1Dnanostructures led mainly to translational arrest, al-though the reasons underlying this observation werenot elucidated. It should be noted here that, althoughcarrier compounds greatly facilitate RNA delivery,they are also quite expensive and/or difficult to synthe-size. The use of carrier compounds seems to be dispens-able when plant cell walls are mechanically damaged.Indeed, RNAi of a GFP transgene was efficiently initiatedwhen 22-nt sRNAs or 720-bpdsRNAs (pure nucleic acids)were applied by high-pressure spraying (8 bar) or brush-mediated application on the leaf surface ofN. benthamianaand Arabidopsis, respectively (Dalakouras et al., 2016;Dubrovina et al., 2019).

TRANSITIVITY AND SYSTEMIC SILENCING

Although 21-nt sRNAs (miRNAs and siRNAs) me-diate RNA cleavage in plants, 22-nt sRNAs seeminglyrecruit RDR6 to the RNA target and are responsiblefor the amplification, transitive, and, likely, systemicspread of RNAi (Chen et al., 2010; Cuperus et al., 2010;McHale et al., 2013). Yet, it had been also suggestedthat recruitment of RDR6 to their target transcript ismediated not necessarily by 22-nt sRNAs, but by any-sized sRNA that contains an asymmetric bulge in itsduplex structure (Manavella et al., 2012). To investigatehow the sRNA size/structure affects the onset of local,

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transitive, and systemic RNAi in GFP-expressingN. benthamiana (Nb-GFP) plants, we applied, by high-pressure spraying, chemically synthesized 21-, 22-, and24-nt GFP sRNAs either as perfect duplexes or assiRNAs containing an asymmetric bulge (Dalakouraset al., 2016). Ultraviolet light examination of sprayedplants revealed that although all tested sRNAs trig-gered local RNAi to variable degrees, only 22-nt sRNAs(either as perfect duplexes or containing an asymmet-ric bulge) also triggered systemic silencing (Fig. 2, left).DCL2, responsible for the biogenesis of 22-nt siRNAs, isrequired for transitivity (Mlotshwa et al., 2008; Parentet al., 2015). Moreover, 22-nt miRNAs recruit RDR6 andtrigger transitivity (Chen et al., 2010; Cuperus et al.,2010; McHale et al., 2013). Thus, it is reasonable to as-sume that any sRNA (siRNA or miRNA or chemicallysynthesized oligonucleotide) having a size of 22 nt canrecruit RDR6 to its target and lead to the biogenesisof secondary siRNAs. Upon transitivity, the siRNApopulation surpasses a certain threshold required forthe onset of systemic silencing (Kalantidis et al., 2006,2008). Thus, transitivity is seemingly connected togeneration of systemic silencing signals in the sourcetissues. Yet, reception of systemic silencing in the sink

tissues requires RDR6 processing of the target (Schwachet al., 2005). A growing body of recent evidence hassuggested that in contrast to intron-containing genes,intronless genes are much more susceptible to RDR6processivity and thus transitivity and systemic silenc-ing (Christie and Carroll, 2011; Christie et al., 2011;Dadami et al., 2013, 2014). Taking these observationsinto consideration, the chances of systemic RNAi uponexogenous RNA application may significantly increasewhen then the trigger is 22-nt sRNA and the target geneis intronless (see “Outstanding Questions”).

SYMPLASTIC AND APOPLASTIC DELIVERY OF RNA

It needs to be noted here that depending on themethod of RNA application, the efficiency of RNAifluctuates. When chemically synthesized 22-nt sRNAswere applied in Nb-GFP upon high-pressure spraying,they triggered local and systemic RNAi; yet, whenthey were applied by petiole absorption, they failed todo so (Dalakouras et al., 2018). Confocal microscopyrevealed that the petiole-absorbed sRNA was trans-ported through the xylem and was restricted to the

Figure 2. Methods for RNA delivery to plants. Left, High-pressure spraying of chemically synthesized GFP sRNAs in Nb-GFPallows the delivery of sRNAs into the symplast and initiation of RNAi. Only the 22-nt GFP sRNAs, with or without an asymmetricbulge, are able to trigger efficient local (2 dpa) and systemic (20 dpa) RNAi (ultraviolet examination). Notably, targeting the budinstead of the leaf results inmore pronounced andwidespread RNAi.Middle, Petiole absorption of chemically synthesized sRNAsand in vitro-transcribed GFP hpRNAs results in the localization of applied RNAs in the apoplast and xylem (confocal microscopyof CY3-labeled RNAs). Thus, the applied 22-nt GFP sRNAs fail to induce RNAi in Nb-GFP (ultraviolet examination) whereas theapplied GFP hpRNA is not processed by DCLs into GFP siRNAs (northern blot analysis). Right, Trunk injection of in vitro-transcribed GFP hpRNA into apple and grapevine results in its localization in the apoplast and xylem. Thus, similar to petioleabsorption, no DCL processing takes place (northern blot analysis). Image adapted from Dalakouras et al. (2016, 2018).

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apoplast (Fig. 2, middle; Dalakouras et al., 2018). Simi-larly, a 499-nt GFP hairpin RNA (hpRNA) appliedthrough petiole absorption and/or trunk injection ingrapevine (Vitis vinifera) and apple (Malus domestica)trees was also confined to the xylem and apoplast,and no RNAi was observed (Fig. 2, middle and right).In summary, when the target of exogenously appliedRNA is an intracellular transcript such as plant mRNAor viral/viroid RNA (Fig. 3, left), then the high-pressuremethod ensures efficient RNA delivery into plant cellsleading to the onset of, at least, local RNAi. In contrast,RNA applied through petiole absorption and trunkinjection is retained in the xylem and apoplast anddoes not trigger RNAi. However, this is not necessarilya drawback. When dsRNAs are applied to plants withthe aim of targeting some insects or fungi (Fig. 3, right),it may be of advantage to deliver nonprocessed (byplant DCLs) dsRNAs. Should the plant-applied dsRNAsavoid plant DCL processing, they will be taken up in-tact by the insects or fungi and be processed therein bythe pathogen/pest DICER proteins; the resulting siR-NAs will conceivably exhibit greater biological activityagainst insect or fungal genes. To achieve this, recentapproaches rely on the expression of dsRNA transgenesin chloroplasts (Bally et al., 2016, 2018). Chloroplasts

lack DCLs and thus the chloroplast-expressed dsRNAsremain intact for pathogen/pest uptake. Our own ob-servations suggest that dsRNA application throughpetiole uptake and/or trunk injection could serve as aGMO-alternative to such transplastomic plants becausethey both maintain dsRNA intact.

THE ISSUE OF EPIGENETIC CHANGES

So far, all reports on exogenous applications of dsRNAsin plants aimed to trigger degradation of a given mRNA.However, once present in the plant cell, the applieddsRNAs may be processed not only by DCL4/DCL2into 21-/22-nt siRNAs but also by DCL3 into 24-ntsiRNAs, given the DCL colocalization (Pontes et al.,2013; Pumplin et al., 2016). Thus, besides mRNA deg-radation in the cytoplasm, the applied dsRNAsmay alsotrigger RdDM of the cognate coding region in the nu-cleus (Dubrovina et al., 2019; Dubrovina and Kiselev,2019). Thus, dsRNA-treated plants considered on theone hand GMO-free, could, on the other hand, beepigenetically modified. Moreover, exogenous appli-cation of dsRNA targeting a promoter sequence maytrigger not only RdDM but also histone modifications

Figure 3. Exogenous application of RNA molecules into plants against various targets, such as endogenous plant genes, viruses,insects, and fungi. In the first two cases, RNAi should take place inside the plant cell. Thus, themost suitable applicationmethod ishigh-pressure spraying, which allows symplastic RNA delivery. In contrast, in the cases of insects and fungi, RNAi takes placeinside the insect and fungal cells, which thus need to uptake intact dsRNA (unprocessed by the plant DCLs) to achieve efficientRNAi. Hence, in these cases, trunk injection, petiole absorption, and/or low-pressure spraying (wherein RNA stays on the leafsurface) are the most suitable methods, because these methods do not result in symplastic RNA delivery. Importantly, althoughtrunk injection and/or petiole absorption is the ideal method for xylem-feeding and/or chewing insects, the spraying methodwould be more suitable for phloem-feeding insects (e.g. aphids).

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that will eventually result in transcriptional gene si-lencing (Wassenegger, 2005). If RdDM takes place inthe dsRNA-treated plants, DOMAINS REARRANGEDMETHYLTRANSFERASE will mediate the de novomethylation of the cognate DNA sequence (promoter orcoding region) at any sequence context: CG, CHG, andCHH (Pélissier et al., 1999; Cao and Jacobsen, 2002;Aufsatz et al., 2004). In the progeny of treated plants, CGand, to a lesser extent, CHG methylation can be main-tained by METHYLTRANSFERASE1 and CHROMO-METHYLASE3, respectively (Lindroth et al., 2001;Aufsatz et al., 2004). Although CG/CHG methylationof a coding region does not seem to negatively affecttranscription in plants, CG/CHG methylation of pro-moter sequences reinforces the heterochromatic state,and thus, transcriptional gene silencing can be trans-generationally maintained (Wang et al., 2015; Wakasaet al., 2018). Whether such scenario holds remains to bevalidated (see “Outstanding Questions”).

APPLYING RNA MOLECULES IN PLANTSAGAINST VIRUSES

It has been suggested that RNAi in plants evolvedas an antiviral defense mechanism (Baulcombe, 2004).Indeed, most plant viruses contain single-strandedgenomes that replicate through dsRNA intermediates.The dsRNA is processed into virus-derived siRNAsresulting in degradation of any homologous RNA,including the single-stranded virus RNA genomes.To counter the host’s defense, viruses encode RNAsilencing suppressors, most of which sequester and/orinhibit the function of the siRNAs (Silhavy and Burgyán,2004, 2013). However, the cellular pre-existence ofdsRNAs/siRNAs designed to target the virus alreadybefore it manages to replicate and generate RNA si-lencing suppressors is a well-established antiviral cropprotection strategy. The GMO approach wherein trans-genic plants express dsRNAs against viral proteins hasbeen well documented with very satisfactory results(Prins et al., 2008; Khalid et al., 2017; Pooggin, 2017).Focusing here only on the nontransgenic approaches,Tenllado and coworkers were the first to demonstratethat exogenous application of dsRNA molecules inplants renders them resistant to viral infections. Whenpepper mild mottle virus, tobacco etch virus, and al-falfa mosaic virus were mechanically coinoculated inN. benthamiana leaves with in vitro-transcribed 977-bp,1,483-bp, and 1,124-bp dsRNAs targeting the peppermild mottle virus replicase, tobacco etch virus helpercomponent, and alfalfa mosaic virus RNA3, respec-tively, viral infections were attenuated (Tenllado andDíaz-Ruíz, 2001). The authors applied crude extractfrom E. coli HT115 (DE3) expressing the correspondingdsRNA fragments by lysing cell pellets with a Frenchpress and documented similar resistance phenotypes(Tenllado et al., 2003). Using bacterial expression sys-tems, dsRNA expression can easily be scaled-up andstill remain cost-effective. With an average dsRNA yield

of 4 mg/mL of bacterial culture, large fermenters wouldmost possibly meet the huge agricultural demands(Tenllado et al., 2004). Besides HT115 (DE3), alter-native strains such as M-JM109lacY have been usedwith equally satisfactory results. Mechanical inocula-tion of RNA extract from E. coli M-JM109lacY express-ing 480-bp dsRNA that target the tobacco mosaic virus(TMV) coat protein (CP) and RNA extract from E. coliHT115 (DE3) expressing 480-bp dsRNA targeting theTMV movement protein both resulted in viral resis-tance in tobacco (Nicotiana tabacum; Yin et al., 2009,2010). Recently, an alternative system for high-qualitylong dsRNA production was developed, based onPseudomonas syringae harboring components of thebacteriophage phi6, wherein dsRNA generation isbased not on DNA transcription but on RNA transcrip-tion by an RNA-dependent RNA polymerase (Niehlet al., 2018). Compared to E. coli-expressed dsRNA,whichmay result in relatively low yields of fully duplexeddsRNA, the P. syringae system seems advantageous be-cause the RNA-dependent RNA polymerase of phagephi6 converts single-stranded RNA templates intodsRNAwith high processivity using a de novo, primer-independent initiation mechanism.Using the aforementioned methods, viral resistance

has been achieved in a plethora of other cases as listedhere: in maize, upon spraying of crude extract fromE. coli HT115 (DE3) expressing dsRNA targeting thesugarcane mosaic virus CP (Gan et al., 2010); in papaya(Carica papaya), upon mechanical inoculation of crudeextract from E. coli M-JM109lacY expressing 279-bpdsRNA targeting the papaya ringspot virus CP (Shenet al., 2014); in pea (Pisum sativum), upon biolistic de-livery of in vitro-transcribed 500-bp dsRNA targetingthe pea seed-borne mosaic virus CP (Safarova et al.,2014); in orchid (Brassolaeliocattleya hybrida), upon me-chanical inoculation of crude extract from E. coliHT115(DE3) expressing dsRNA targeting the cymbidiummosaic virus CP (Lau et al., 2014); in tobacco, uponmechanical inoculation of in vitro-transcribed 237-bpdsRNA targeting the TMV p126 (Konakalla et al., 2016);in cucurbits, upon mechanical inoculation of in vitro-transcribed 588-bp dsRNA targeting the zucchini yel-low mosaic virus helper component proteinase (Kaldiset al., 2018); and in N. benthamiana, upon spraying ofRNA extracts from P. syringae LM2691 expressingdsRNAs targeting a 2,611-bp region of TMV replicaseand movement protein (Niehl et al., 2018).A major issue concerning the aforementioned

approaches is that dsRNA application offers a shortantiviral protection window (usually 5–10 d), becausedsRNA eventually is degraded. Thus, dsRNA wouldneed to be supplied afresh in frequent intervals forlifelong crop protection. To increase the dsRNA stabil-ity and thus prolong antiviral protection, Mitter andcoworkers bound dsRNA to layered double hydroxideclay nanosheets having an average particle size of80–300 nm (BioClay; Mitter et al., 2017). The dsRNAbound to BioClay was significantly protected fromnucleases, while the dsRNA/BioClay complex did

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not wash off, even after rigorous rinsing. On the leafsurface, atmospheric CO2 and moisture resulted ina gradual breakdown of BioClay into a biocompatibleresidue, releasing the dsRNA in the plant cell eitherby passive diffusion or active transport. A 330-bpdsRNA targeting the CMV CP and bound to BioClaycould be detected even 30 d post-application (dpa)and upon single application in tobacco resulted inCMV protection for at least 20 d (Mitter et al., 2017).Similar results were recently obtained, when spray-ing of 461-bp dsRNA bound to BioClay and target-ing the bean common mosaic virus CP, protectedN. benthamiana and cowpea (Vigna unguiculata) plantsagainst bean common mosaic virus infection (Worrallet al., 2019).

APPLYING RNA MOLECULES IN PLANTSAGAINST VIROIDS

Viroids are infectious single-stranded RNA path-ogens that, unlike viruses, are nonencapsidated andnoncoding but, similar to viruses, trigger the hostRNAi mechanism (Tabler and Tsagris, 2004; Tsagriset al., 2008; Flores et al., 2014, 2017). Single-strandedcircular RNA viroids exhibit significant intramolec-ular folding and resemble dsRNA molecules andas such are processed by plant DCLs into siRNAs.Initial reports suggested that viroids are resistant tosiRNA-mediated degradation due to their extensivesecondary structure (Itaya et al., 2007). Yet, subse-quent studies demonstrated that transgenic plantsexpressing viroid dsRNAswere viroid-resistant (Schwindet al., 2009). Hence, despite their secondary structure,and similar to viruses, viroids can most likely be tar-geted for sRNA-mediated degradation (Dalakouraset al., 2015; Flores et al., 2017). Returning to the non-transgenic approaches, to the best of our knowledgethere is only one study where exogenous RNA wasapplied in plants for antiviroid resistance, whereinCarbonell and coworkers applieddsRNA inplants againstboth nuclear-replicating Pospiviroidae and chloroplast-replicating Avsunviroidae members. In tomato (Solanumlycopersicum), gynura (Gynura aurantiaca), and chrysan-themum (Dendranthema grandiflora), mechanical inocula-tion of in vitro-transcribed 353-, 364-, and 399-bpdsRNA targeting regions of Potato spindle tuber viroid,Citrus exocortis viroid, and Chrysanthemum chloroticmottle viroid, respectively, resulted in significant inhi-bition of infection, at least for up to 30 dpa (Carbonellet al., 2008). Interestingly, the effect was temperature-dependent, reminiscent of previous reports on thetemperature-dependency of the general RNAi mecha-nism in plants (Kalantidis et al., 2002; Szittya et al.,2003). Taking these observations into consideration,exogenous application of RNA in plants for any ap-plications should be performed in a temperature re-gime of 20oC to 30oC, since the efficiency of the RNAimachinery is compromised outside this temperaturewindow.

APPLYING RNAi MOLECULES IN PLANTSAGAINST FUNGI

With the notable exceptions of Saccharomyces cerevisiaeand Ustilago maydis, most fungi, like the rest of eu-karyotes, contain several DICER and AGO genes andthus display active RNAi mechanisms. Transgenicplants expressing dsRNAs against fungal genes is avery promising antifungal approach (Koch and Kogel,2014; Baulcombe, 2015) but will not be addressed here.Koch and coworkers demonstrated that sprayingof barley (Hordeum vulgare) with in vitro-transcribed791-bp dsRNA simultaneously targeting three Fusariumgraminearum ergosterol biosynthesis genes (CYP51A,CYP51B, and CYP51C) strongly inhibited fungal growth(Koch et al., 2016). Interestingly, the sprayed dsRNAwaspoorly processed in barley into siRNAs, and the effect onfungal growth was due to the uptaken dsRNA ratherthan the barley-produced siRNAs, because upon dsRNAspraying no RNAi was observed in a dcl1 F. graminearummutant. Spraying of in vitro-produced siRNAs alsoinhibited fungal growth but to lesser extent than dsRNAdid. Surprisingly, dsRNA seemed to be more mobilethroughout the barley than the smaller siRNAs, butthe reasons underlying this phenomenon are unclear.It is also unclear how the dsRNA that first reached theapoplast was transported to the symplast (Koch et al.,2016). In another study, foliar application in Brassicanapus of in vitro-transcribed dsRNA targeting variousfungal genes conferred plant protection against Sclerotiniasclerotium and Botrytis cinerea (McLoughlin et al., 2018).More recently, spraying of in vitro-transcribed dsRNAtargeting the myosine5 of Fusarium asiaticum in woundedwheat (Triticum aestivum) coleoptiles resulted in reducedfungal virulence (Song et al., 2018). Yet, the RNAi effectlasted for only 9 h, unless the dsRNA was continuouslysupplied. Interestingly, despite the presence of RDRgenesin F. asiaticum, sRNA deep sequencing revealed thatno secondary siRNAs were generated, suggesting thatfungal myosine5 mRNA could not be processed byRDR (Song et al., 2018). Thus, in contrast to plantswhere RNAi is maintained through an RDR-mediatedself-amplification loop, this is likely not happeningin fungi.

Recent advances from the Hailing Jin laboratoryhave broadened our knowledge of the mechanisticdetails of RNA transport phenomena between plantsand fungi. Hence, it was discovered that the aggres-sive fungal pathogen B. cinerea is able not only todeliver siRNAs into host plant cells to suppress hostimmunity genes, but also uptake exogenously applieddsRNAs and siRNAs that inhibit its growth, provid-ing a typical case of bidirectional trans-kingdom RNAi(Weiberg et al., 2013; Wang et al., 2016). More specifi-cally, when in vitro-transcribed dsRNA or siRNAstargeting the Bc-DCL1 and Bc-DCL2 genes were ap-plied on the surface of fruits (tomato [S. lycopersicum‘Roma’]; strawberry [Fragaria3 ananassa]; and fox grape[Vitis labrusca ‘Concord’]), vegetables (iceberg lettuce[Lactuca sativa]; and onion [Allium cepa]), and flowers

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(rose [Rosa hybrid]), they significantly inhibited graymold disease (Wang et al., 2016). These findings illus-trated that exogenous RNA application can be used tocontrol diseases in post-harvest fruits and vegetables.Whereas the movement of siRNAs through plasmo-desmata to neighboring cells and through the vasculaturesystem to distant parts of the plant is well established,it was unknown until recently how siRNAs/dsRNAstravel across the boundaries between organisms of dif-ferent taxonomic kingdom, e.g. from plants to fungiand/or vice versa. To investigate how RNA moleculesmove from plants into interacting fungal cells, HailingJin and coworkers demonstrated that Arabidopsissecretes exosome-like extracellular vesicles to deliverRNA molecules into B. cinerea (Cai et al., 2018b). Itis reasonable to assume that such observations reflecta more generalized mechanism of exosome involve-ment in trans-kingdom RNA transport, and if so, exo-somes are likely to be employed in the future in thedevelopment of antifungal RNA delivery methods.

APPLYING RNAi MOLECULES IN PLANTSAGAINST INSECTS

Triggering RNAi in insects upon exogenous appli-cation of dsRNA in plants is a challenging task. Sub-sequent to the uptake by chewing/sucking insects,the dsRNA must survive the salivary nucleases in themidgut and/or hemolymph, which threaten to quicklydegrade it. Next, the dsRNA must be taken up from theepithelial cells through either the endocytic pathwayor the transmembrane Sid-1 channel protein-mediatedpathway and processed by Dicer-2 into siRNAs, whichwill be loaded onto Ago-2 and trigger local RNAi(Fig. 3). To be efficiently established throughout theinsect, the RNAi molecules (dsRNAs or siRNAs) needto systemically spread to neighboring and to distantcells. In plants and the nematode Caenorhabditis elegans,systemic spread of RNAi is associated with RNAi am-plification by RDRs, proteins that are not present in in-sects. Yet, despite all these barriers, a proof-of-conceptarticle demonstrated that western corn rootworm in-gestion of vacuolar ATPase dsRNA through artificialdiet or upon feeding on dsRNA-expressing transgenicmaize plants resulted in significant larval mortality,suggesting that widespread RNAi in insects can beestablished. Indeed, coleopterans seem to exhibit sys-temic RNAi spread, although the enzymes involvedhave not been identified yet (Vélez and Fishilevich,2018).Induction of RNAi in insects through the use of

methods such as dsRNA injection, dsRNA-expressingtransgenic plants, dsRNA-containing artificial diet,or dsRNA-coating of leaf discs has been thoroughlyreviewed elsewhere (Zotti and Smagghe, 2015; Jogaet al., 2016; San Miguel and Scott, 2016; Bally et al.,2018; Vélez and Fishilevich, 2018; Zotti et al., 2018).Exogenous application of dsRNA directly in plantsagainst insects was first demonstrated by Hunter and

coworkers, who injected the trunk and/or drenchedthe roots of citrus and grapevine trees with dsRNAtargeting the Arg kinase of two psyllids (Diaphorina citriand Bactericera cockerelli) and the sharpshooterHomalodiscavitripennis. Interestingly, the introduced dsRNA wasdetected in 2.5-m tall 6-year–old Mexican limes (Citrusaurantifolia) even after 7 weeks post-single application(2-g dsRNA diluted in 15 L of water). After this proof-of-concept report, several others followed, exhibitingsignificant degrees of pest management upon exoge-nous application of in vitro-transcribed/synthesizedRNAs in plants: in Brassica oleracea, upon spraying of59-PEG 21-nt siRNAs targeting the diamondbackmothPlutella xylostella acetylcholine esterase genes AChE1and AChE2; in tomato, upon application of dsRNAtargeting the D. virgifera vacuolar ATPase (Ivashutaet al., 2015); in rice, upon root absorption of dsRNAtargeting the brown planthopper Nilaparyata lugensP450 (Li et al., 2015); in maize, upon root absorption ofdsRNA targeting the Ostrinia furnacalis KTI (Li et al.,2015); in potato (Solanum tuberosum), upon spraying ofdsRNA targeting the Colorado potato beetle Leptinosadecemlineata actin; in tomato, upon petiole uptake ofdsRNA targeting the tomato leafminer Tuta absolutavacuolar ATPase (Camargo et al., 2016), and upon rootabsorption of dsRNA targeting T. absoluta ryanodine,acetylcholinesterase, and nicotinic acetylcholine alpha6(Majidiani et al., 2019). In general, the orders Coleop-tera, Lepidoptera, and Hemiptera include key pests ofcrops. Coleopterans are the most susceptible to RNAi,whereas lepidopterans and hemipterans seem recalci-trant to RNAi, most likely because lepidopterans re-strict the uptaken dsRNA to endocytic compartments,and hemipterans inject nucleases into the plant tissuebefore feeding (Lomate and Bonning, 2016; Shuklaet al., 2016). Of note, and to improve dsRNA stability,uptake, and overall RNAi response, various insecticidaldsRNA formulations have been explored, such as lipo-somes, chitosan nanoparticles, cationic core-shell nano-particles, and guanylated polymers (Joga et al., 2016;Vélez and Fishilevich, 2018).

APPLYING RNA MOLECULES IN PLANTSAGAINST MITES

Mites belong to the subphylum Chelicerata, a sub-group in the phylumArthropoda to which insects alsobelong. Mite genomes encode for most known RNAienzymes, including two DICERs, seven AGOs, and,importantly, five RDRs (Grbic et al., 2011), suggestingthat amplification of RNAi and systemic RNAi spreadin mites may occur. Indeed, in the citrus red mitePanonychus citri, RNAi spread from the gut to moredistant tissues such as cuticle, hemolymph, and protho-racic glands (Li et al., 2017). Similar to insects, mites havebeen targeted for RNAi by various methods, such asfeeding on leaves floating on dsRNA solution, dsRNA-expressing transgenic plants, and dsRNA-containingartificial diet, as discussed elsewhere (Suzuki et al., 2017;

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Niu et al., 2018). To the best of our knowledge, the onlystudy wherein mites took up dsRNA that was exoge-nously applied in plants involved mechanical inocula-tion of tomato leaves with in vitro-transcribed dsRNA(targeting the otherwise irrelevant zucchini yellow mo-saic virus helper component proteinase) and the con-comitant detection by stem loop reverse transcriptionPCR of the corresponding siRNAs in the two-spottedspider mite Tetranychus urticae at 3 and 10 dpa (Gogoiet al., 2017). However, in that case it was not possibleto determine whether the mite absorbed the applieddsRNA or the plant-produced siRNAs. In addition,no conclusions could be drawn concerning the RNAiaction of the detected siRNAs, because the applieddsRNA had no mite target. In another study whereT. urticae was fed on Arabidopsis leaves coated within vitro-transcribed dsRNA targeting the vacuolarATPase, the mite exhibited visible dark body phe-notype but lethalitywas not observed (Suzuki et al., 2017).Interestingly, to identify the most suitable RNAi tar-get genes for mite mortality, two independent studiessuggested that coatamer I genes and genes involvedin the biosynthesis and action of juvenile hormoneand action of ecdysteroids were the best candidates(Kwon et al., 2016; Yoon et al., 2018) and should be thustaken into consideration for future RNA applications.

APPLYING RNA MOLECULES IN PLANTSAGAINST NEMATODES

RNAiwas discovered in themodel nematodeC. elegans(Fire et al., 1998). In agriculture, root-knot nematodescause significant crop losses in several plant speciesworldwide. Transgenic Arabidopsis expressing 16D10dsRNAagainstMeloidogyne incognita,Meloidogyne javanica,Meloidogyne arenaria, and Meloidogyne hapla exhibitedsignificant reductions in the number of nematode eggsper gram of root (Huang et al., 2006). So far, no reportson exogenous RNA application in plants against nema-todes are available. Arguably, the challenge here wouldbe to deliver RNAmolecules to the root tissues. Trunkinjection would deliver RNA mainly to the xylem(Dalakouras et al., 2018) and thus only to the upper/aerial part of the plant. Alternatively, RNAmoleculescan be directly absorbed by the roots (Jiang et al.,2014; Li et al., 2015). It is thus reasonable to assumethat RNA molecules conjugated to compounds thatwould protect them against degradation in the ag-gressive soil environment could be delivered throughirrigation as a nematode protection strategy.

PERSPECTIVES FOR BACTERIAL MANAGEMENT

Plant pathogenic bacteria may cause devastatingdiseases and huge crop losses. Although RNAi is absentin bacteria, similar RNA-based regulation mechanismsdo exist in which ;100-nt cis and trans antisense tran-scripts repress translation and lead to transcript decay(Good and Stach, 2011). Typically, antisense RNAs

(asRNAs) that are cis-encoded display high degreesof complementarity with the target mRNA, whereasasRNAs that are trans-encoded exhibit limited com-plementarity with the target mRNA and require Hfqchaperones to facilitate binding to the target mRNA.So far, exogenous application in plants of syntheticasRNAs designed to combat bacterial pathogens hasnot been tested. In contrast to dsRNAs applied in RNAiapproaches, asRNAs are single-stranded and thusmoresusceptible to plant nucleases. To tackle this problem,exogenously applied asRNAs based on peptide nucleicacids and/or phosphorothioate morpholino oligomerscould be used (Good and Stach, 2011). Yet, the biggestchallenge upon exogenous application of syntheticasRNAs would be the intracellular delivery acrossthe stringent bacterial cell barriers, because nucleo-base oligomers are too large for uptake by simplediffusion. To this end, conjugating the peptide nucleicacid or phosphorothioate morpholino oligomers to cellcationic entry peptides would greatly facilitate theirintracellular delivery (Mellbye et al., 2009). These beingsaid, exogenously applied antibacterial asRNAs couldbe used with considerable chances of success, particu-larly in the case of xylem-restricted bacteria such asXylella fastidiosa, Clavibacter xyli, and Pseudomonas syzygii,especially when taking into account that delivery of RNAwith robust methods, such as trunk injection or petioleabsorption, restricts the presence of the applied RNA tothe xylem (Dalakouras et al., 2018). Besides the afore-mentioned direct management of bacterial pathogensthrough exogenous application of synthetic asRNAs,indirect RNAi-based strategies could be applied. Forexample, although RNAi cannot be used directly againstX. fastidiosa, it can nevertheless be employed against itsxylem sap-feeding vectors, mainly sharpshooters and

OUTSTANDING QUESTIONS

Besides RNA degradation, do exogenously applied RNA molecules also trigger epigenetic modifications in plants?

In contrast to intron-containing genes, are intronless genes more susceptible to systemic RNAi upon exogenous application of RNAs in plants?

Is the efficiency of RNAi inside insects and fungi higher when they take up dsRNAs that did not undergo processing by plant DCLs?

Are bacteria susceptible to exogenously applied synthetic asRNAs?

Besides dsRNAs and siRNAs, could other RNA molecules, such as mRNAs, miRNA sponges and CRISPR components, be efficiently applied in plants?

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spittlebugs (Rosa et al., 2010; Overall and Rebek,2015). Trunk injected-dsRNAs designed to target es-sential insect mRNAs will remain unprocessed in thexylem of the woody plant, and provided that theyare taken up by the xylem-feeding insect, they willbe processed into siRNAs that that will lead toRNAi-mediated insect lethality, ideally minimizing thespread of the devastating pathogen (see “OutstandingQuestions”).

CONCLUDING REMARKS

For field-scale management of pests and pathogens,metric-ton levels of dsRNAswould be required. A roughestimation suggests 10 g of dsRNA per hectare, althoughthis amount may vary depending on the target sensitivityto RNAi and its capacity for systemic RNAi (Zotti et al.,2018). Conceivably, such huge needs could not be merelymet by in vitro dsRNA transcription systems, which ex-hibit aminimumcost of 100USDper 1 g of dsRNA.To thisend, several industrial companies enable low-cost (almost2 USD per 1 g of dsRNA), large-scale manufacturing ofdsRNA (Zotti et al., 2018). According to “RNAagri” pro-prietary technology (https://www.rnagri.com/), bacteriaand yeast are engineered to produce the desired dsRNAand a capsid protein that offers protection againstnucleases. As the bacteria multiply in the fermenta-tors, the dsRNA:protein complex is self-assembledand accumulates in huge quantities that can be iso-lated with conventional low-cost methods. The finalproduct is environmentally stable and ready-to-use.Field-scale trunk injection of such huge amounts ofdsRNAs could be performed by commercially availabletrunk drilling equipment such as the one developed by“Arborjet” (https://arborjet.com/arborjet-advantage/).Such advances have facilitated the development ofcommercial products that are soon to emerge in themarket, such as “BioDirect,” which is designed forinsect, virus, and weed control and which has alreadypassed the phase I or II of the research and developmentprocess (Zotti et al., 2018).In summary, exogenous application of RNAmolecules

with the potential to trigger RNAi is a very powerful toolin modern crop protection and improvement plat-forms, considering the political and public pressurefor sustainable solutions to current agricultural prob-lems. According to the the 40th Annual Meeting of TheToxicology Forum, the currently available evindencesuggests that the presence of RNAimolecules in humandiet pose no threat to humans (Sherman et al., 2015).Moreover, compared to conventional disease man-agement strategies, exogenous RNAi promises sig-nificantly lower off-target effects, because its activitycan be narrowed down to a window of a few nucleo-tides’ complementarity with its target. With the rapidlyaccumulating sequence datasets, nonconserved regionscan be selected as targets to exclude as much as pos-sible off-target effects. To the same end, applying uniquesRNAs, rather than long dsRNAs, which are processed

in a diverse population of siRNAs, would also greatlydecrease off-targets. Arguably, the lack of genome datafor any existing organisms near the site of exogenousRNA application undermines the proper ecological riskof RNAi technology in the agroecosystem. Nevertheless,the chance to silence nonintended targets is very low andfar beyond any other available crop protection strategyhas yet to offer. It cannot be excluded that certain path-ogens may display gene mutations rendering them re-sistant to RNAi sprays. In cases of monogenic resistance,alternating;200-bp regions of the target sequence couldtackle this issue, whereas for polygenic resistance cases,using chimeric RNAs or a mixture of different RNAscould offer a solution, underpinning the overall flex-ibility of the RNA-based approaches. Importantly,it was recently demonstrated that the RNAi efficiencyin plants can be enhanced by the addition of chemicalenhancers such as Sortin1, Isoxazolone and [5-(3,4-dichlorophenyl)furan-2-yl]-piperidine-1-ylmethanethione(Jay et al., 2019). In the near future, it is reasonable to as-sume that optimization of RNAproduction, delivery, andstability methods may pave the way for the exogenousapplication of diverse RNA molecules not necessarilytriggering only RNAi. Indicatively, such moleculescould include: capped and polyadenylated mRNAswhen accumulation of a protein is desired; miRNAdecoys/sponges for sequestering of a given miRNAand thus upregulating its endogenous target; andeven clustered regularly interspaced short palindromicrepeats components (CRISPR; CRISPR associated pro-tein 9 mRNA and single guide RNAs ) for the inductionof editing events in aGMO-freemanner (see “OutstandingQuestions”).Received May 13, 2019; accepted June 28, 2019; published July 8, 2019.

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