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Revista mexicana de fitopatología
versión On-line ISSN 2007-8080versión impresa ISSN 0185-3309
Rev. mex. fitopatol vol.34 no.3 Texcoco sep. 2016
https://doi.org/10.18781/r.mex.fit.1606-8
Revision Articles
Mechanisms, applications, and perspectives of antiviral RNA silencing in plants
1Department of Plant Pathology, Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583 USA.
2Universidad Autónoma Chapingo, México, CP 56230.
3Department of Biology, Kuztown University of Pennsylvania, Kuztown, PA 19530 USA.
Viral diseases of plants cause important economic losses due to reduction in crop quality and quantity to the point of threatening food security in some countries. Given the reduced availability of natural sources, genetic resistance to viruses has been successfully engineered for some plant-virus combinations. A sound understanding of the basic mechanisms governing plant-virus interactions, including antiviral RNA silencing, is the foundation to design better management strategies and biotechnological approaches to engineer and implement antiviral resistance in plants. In this review, we present current molecular models to explain antiviral RNA silencing and its application in basic plant research, biotechnology and genetic engineering.
Key words: Plant viruses; gene silencing; antiviral defense; transgenic plants; genetic engineering of virus resistance
Las enfermedades virales en plantas causan pérdidas económicas importantes al reducir la calidad y rendimiento de los cultivos, lo que amenaza la seguridad alimentaria en algunos países. Dada la escasez de recursos naturales, plantas con resistencia genética a virus han sido desarrolladas con éxito por ingeniería genética. Un buen entendimiento de los mecanismos básicos que controlan las interacciones entre virus y plantas, incluido el silenciamiento génico de virus por ácido ribonucleico (ARN) de interferencia, es necesario para diseñar mejores estrategias de manejo y métodos biotecnológicos que servirán para desarrollar e implementar resistencia antiviral en plantas. En esta revisión, presentamos modelos moleculares vigentes para explicar el silenciamiento génico de virus por ARN de interferencia y sus aplicaciones en biotecnología e ingeniería genética de plantas.
Palabras clave: Virus de plantas; silenciamiento génico; ARN de interferencia; defensa antiviral; plantas transgénicas; ingeniería genética de resistencia a virus
RNA silencing is a sequence-specific gene inactivation system mediated by small interfering RNAs (siRNA) guiding endonucleolytic cleavage or translational repression of mRNAs, or by preventing transcription (Cuperus et al., 2010). RNA silencing has essential roles in development, stress response, and genome expression and maintenance (Ding and Voinnet, 2007). The roles and mechanistic activities of RNA silencing are highly conserved in eukaryotes. In plants, nematodes, and insects, RNA silencing is an essential component of antiviral immunity (Ding and Voinnet, 2007).
Plants naturally use RNA silencing to regulate gene expression in a temporal and tissue-specific manner (Chitwood et al., 2009). Virus-infected plants deploy antiviral RNA silencing to prevent, restrict, and clear virus infections (Garcia-Ruiz et al., 2010; Garcia-Ruiz et al., 2015; Ma et al., 2015). In plant-virus interactions, the outcome of disease or resistance is largely dependent on the balance between antiviral RNA silencing versus virus evasion or active suppression of antiviral defense (Garcia-Ruiz et al., 2010; Garcia-Ruiz et al., 2015; Ma et al., 2015). Endogenous and antiviral RNA silencing have conserved and overlapping pathways. Most of the genes that participate in endogenous RNA silencing are also part of antiviral RNA silencing (Ding and Voinnet, 2007).
In eukaryotes, including plants, RNA silencing regulates gene expression at the transcriptional or post-transcriptional levels (Figure 1). Transcriptional gene silencing inhibits transcription, resulting in a reduction of mRNA, by methylating DNA in chromosomes, plasmids or viral minichromosomes (Raja et al., 2008; Ceniceros-Ojeda et al., 2016). Transcriptional gene silencing is directed by siRNAs guiding enzymatic DNA methylation (Ding and Voinnet, 2007). Post-transcriptional gene silencing is the nucleolytic cleavage and degradation or translational repression of mRNA (Cuperus et al., 2010) (Figure 1). All viruses use RNA to express their genes, replicate, or both. That RNA is potentially perceived by the cell and activates antiviral defense responses, including RNA silencing (Ivanov et al., 2014). Transcriptional and post-transcriptional gene silencing has been demonstrated for DNA viruses, RNA viruses, viroids and satellite RNAs (Table 1).
Figure 1. Flow of genetic information and gene silencing in plants. RNA-induced silencing complexes are formed between effector proteins and small interfering RNAs (siRNAs) derived from non-coding transcripts. Gene silencing is a block in the flow of genetic information by preventing transcription or by inducing degradation or translational repression of protein-coding RNAs directed by endogenous siRNAs. Virus-infected plants accumulate virus-induced siRNAs and virus-derived siRNAs.
Table 1. Core genetic determinants of antiviral silencing for representative plant-pathogen combinations.
Pathogens. African cassava mosaic virus (ACMV), Cabbage leaf curl virus (CaLCuV), Cauliflower mosaic virus (CaMV), Cucumber mosaic virus Y satellite RNA (Y-sat), Grapevine fleck virus (GFkV), Grapevine Red Globe associated virus (GRGV), Grapevine rupestris stem-pitting associated virus (GRSPaV), Grapevine yellow speckle viroid 1 (GYSVd), Hop stunt viroid (HSVd), Maize chlorotic mottle virus (MCMV), Oryza sativa endornavirus (OsEV), Papaya mosaic virus (PapMV), Papaya ring spot virus (PRSV), Potato spindle tuber viroid (PSTVd), Rice dwarf virus (RDV), Rice stripe virus (RSV), Sugarcane mosaic virus (SCMV), Tomato spotted wilt virus (TSWV), Turnip crinkle virus (TCV), Turnip mosaic virus (TuMV).
Hosts. Arabidopsis (Arabidopsis thaliana), Cassava (Manihot esculenta), Grapevine (Vitis vinifera), Maize (Zea mays), N. b. (Nicotiana benthamiana), Papaya (Carica papaya), Rice (Oryza sativa), Tomato (Solanum lycopersicum).
Size and polarity. Size (nt) of the most abundant virus-derived siRNAs based on next generation sequencing, northern blotting, or both. Profile of virus-derived siRNAs determined by next generation sequencing. (+): siRNAs of positive polarity are more abundant than antisense. (-): siRNAs of negative polarity are more abundant than sense. (+/-): siRNAs of positive and negative polarity are equally abundant.
Viral infection of plants occurs in two phases. After entering the cell, viruses replicate and subsequently move to other cells and systemically through the vascular system to distal plant tissues and organs (Ivanov et al., 2014). RNA silencing directed against viral RNA (antiviral RNA silencing) restricts virus replication and movement (Garcia-Ruiz et al., 2015). Antiviral defense through RNA silencing is dependent on sensing and targeting viral RNA both; in the initially infected cells and in cells away from the initial site of infection (Ding and Voinnet, 2007).
Viruses modify the cellular environment to support their replication and spread (Ivanov et al., 2014) using mechanisms that include subversion, transcriptional reprograming and both RNA silencing induction and suppression (Ding and Voinnet, 2007; Garcia-Ruiz et al., 2015). Suppression of RNA silencing is essential for viruses to replicate, establish infection and move both cell-to-cell and systemically (Garcia-Ruiz et al., 2015). A better understanding of the basic mechanism of endogenous and antiviral RNA silencing and silencing suppression is important to explain several phenomena of interest to plant pathologists, such as virus resistance, virus movement, host range, tissue-specific distribution of virus, viral synergism, genetic determinants of virus resistance, and genetic engineering of plant-virus resistance.
Roles of RNA silencing
In eukaryotes, a wide range of biological processes are regulated through silencing mechanisms, including development, organ formation, and stress responses (Chitwood et al., 2009). For example, in plants, the abaxial-adaxial leaf polarity is regulated by siRNA gradients moving between cells (Chitwood et al., 2009). ARGONAUTE (AGO) proteins are the catylitic component of RNA silencing. In association with siRNA, AGO proteins slice target RNA (Carbonell et al., 2012; Cuperus et al., 2010; Cuperus et al., 2011). AGO7 and AGO10 are expressed specifically in the adaxial leaf primordial and in vascular tissues. AGO7 restricts activity of micro RNA390 (miR390) and directs a gradient of transacting small interfering RNAs from the adaxial to the abaxial side of developing leaves (Chitwood et al., 2009). The antiviral role of RNA silencing has been demonstrated in many plant species (Table 1), and regulatory siRNAs are also involved in plant-bacterial and plant-fungal interactions (Weiberg et al., 2014).
Non-coding and small RNAS in plants
Plant genomes encode two kinds of non-coding RNAs (Figure 1): long non-coding RNAs (lncRNA) and small regulatory RNAs also called small interfering RNAs (siRNAs). LncRNAs are formed by sense or antisense transcription, from introns or intergenic regions, are longer than 200 nucleotides (nt) and have been implicated in regulation of tissue differentiation, reproductive development, stress response, vernalization, flowering time, and plant immunity (Shafiq et al., 2016). Plant siRNAs range in size from 21 to 24 nt and are naturally expressed as part of the mechanisms of temporal and spatial gene regulation. Other siRNAs are produced in response to biotic (viral, bacterial or fungal infections) or abiotic stress (salt, water, heat or cold) (Axtell, 2013). Single stranded RNAs (ssRNA) that form a hairpin structure are precursors to hairpin small RNAs: microRNAs (miRNAs) and other siRNAs. Double stranded RNAs (dsRNA) are the precursors to heterochromatic siRNAs and secondary siRNAs such as trans-acting siRNAs and natural antisense transcript-derived siRNAs (Cuperus et al., 2010). A comprehensive review on this subject is provided by (Axtell, 2013).
MicroRNAs. MicroRNAs have critical roles in organ and tissue development of eukaryotes (Cuperus et al., 2011). Plant miRNAs usually measure 21 nt and are formed by endonuclease Dicer-Like I (DCL1) protein from Pol II-dependent transcripts (Cuperus et al., 2011). In Arabidopsis most miRNAs associate with AGO1, and a small number associate with AGO2 or AGO10 (Cuperus et al., 2010; Cuperus et al., 2011) to collectively target at least 250 transcripts. High complementarity between the miRNA and the target site guides transcript RNA endonucleolytic cleavage by AGO proteins and degradation or translational repression (Carbonell et al., 2012). MicroRNAs involved in plant development are highly conserved (Cuperus et al., 2011).
Trans-acting small interfering RNAs (tasiRNA). TasiRNAs function like miRNAs to repress target transcripts (Cuperus et al., 2010). During tasiRNA biogenesis, specific miRNAs in association with specific AGOs facilitate cleavage of tasiRNA primary transcripts, and recruit cellular RNAdependent RNA polymerase 6 (RDR6) and/or associated factors to the processed RNA precursor to dsRNA synthesis. Importantly, only a small subset of miRNA, most of which associate with AGO1, enable RDR6 recruitment. RDR6 recruitment by AGO1-miRNA complexes requires 22 nt long miRNAs, or 21 nt asymmetric duplexes (Cuperus et al., 2010).
Long siRNAs (lsiRNAs). LsiRNAs are induced by bacterial infection or some stress conditions. They are 30 to 40 nucleotides long. Several R genes involved in resistance to bacteria and fungi are regulated by lsiRNAs (Padmanabhan et al., 2009).
Virus-activated siRNAs. Infection of Arabidopsis thaliana with Cucumber mosaic virus (CMV) or Turnip mosaic virus (TuMV) induces the biogenesis of endogenous siRNAs from approximately 1,000 A. thaliana genes, by a mechanism dependent on RNA-dependent RNA polymerase 1 (RDR1). These siRNAs associate with AGO1 and AGO2 and are predicted to modulate host responses to virus infection (Cao et al., 2014).
Virus-derived siRNAs. Infected plants accumulate virus-derived siRNAs that are generally 21 to 24 nt long and are made by Dicer-Like (DCL) proteins. The most abundant size classes are 21 and 22 nt, and are made by DCL4 and DCL2, respectively (Deleris et al., 2006) (Table 1). Virus-derived siRNAs mediate antiviral defense by inducing transcriptional and post-transcriptional gene silencing of viruses (Brosseau and Moffett, 2015; Ceniceros-Ojeda et al., 2016).
Antiviral RNA silencing pathways
Antiviral RNA silencing is non-cell autonomous, initiates at the single cell level and spreads cellto-cell and long distance through plasmodesmata and the plant vascular system (Ding and Voinnet, 2007; Molnar et al., 2010). The pathway consists of four parts: Initiation, targeting, amplification, and systemic spread (Figure 2). After sensing viral RNA, siRNAs derived from viral dsRNA are made by DCL proteins (Deleris et al., 2006). In the targeting phase, virus-derived siRNAs associate with ARGONAUTE (AGO) proteins to form RNA-induced silencing complexes (RISC) and are predicted to target viral ssRNA for endonucleolytic cleavage or translational repression (Brosseau and Moffett, 2015). Initial recognition of viral RNA is necessary but not sufficient to restrict plant virus infection (Garcia-Ruiz et al., 2010). Restriction of plant virus infection requires silencing amplification by cellular RNA-dependent RNA polymerases (RDRs) (Garcia-Ruiz et al., 2010). After movin out of the infected cell, in recipient cells, endogenous RDRs make viral dsRNA to amplify the silencing response and establish an antiviral state (Figure 2). This amplification contributes to the specificity and strength of antiviral RNA silencing and is mediated by RDR1 and RDR6 to form secondary virus-derived siRNAs (Table 1). DNA viruses express their genes through mRNA. Silencing is activated at the post-transcriptional level, resulting in the formation of siRNAs that guide targeting of viral RNA. Furthermore, virusderived siRNAs in association of AGO and RDR proteins guide methylation of viral DNA, resulting in transcriptional gene silencing which prevents virus replication and movement (Raja et al., 2008; Buchmann et al., 2009; Ceniceros-Ojeda et al., 2016).
Figure 2. Antiviral RNA silencing pathway and basic components in plants. Dicer-like (DCL) proteins cut viral dsRNA to form primary virus-derived siRNAs that associate with ARGONAUTE (AGO) proteins and guide targeting of viral RNA. Slicing of viral RNA triggers amplification of antiviral RNA silencing resulting in the formation of viral dsRNA by cellular RNA-dependent RNA polymerases (RDR) and processed by DCL to form secondary-virus-derived siRNAs. Silencing amplification triggers methylation of viral DNA establishing transcriptional silencing. Virus-derived siRNA move cellto-cell and systemically to establish a state of antiviral immunity away from the initial infection site.
Virus-derived siRNA profiles
For a growing number of plant-virus combinations virus-derived siRNA populations have been profiled by next generation sequencing (Table 1). Three kinds of profiles have been described: sense and antisense strand equally represented (ambisense), and biased towards the sense or antisense polarity. For some plant positivestrand RNA viruses, virus-derived siRNAs of sense polarity are more abundant than antisense and there are fragments of the viral genome that accumulate more virus-derived siRNAs than others (Table 1). This pattern suggests that positive-strand viral RNA sequences, or structures, are recognized by DCL proteins. For most plant-virus combinations, infected plants accumulate virus-derived siRNAs from the entire viral genome in nearly equal amounts for both polarities (Table 1). Interestingly, mutant plants lacking silencing amplification proteins RDR1 or RDR6 accumulate reduced amounts of virus-derived siRNAs, implicating cellular RDRs in their biogenesis (Garcia-Ruiz et al., 2010).
Triggers of antiviral RNA silencing
The nature of the viral RNA that is recognized by the cell and triggers the antiviral response has not been determined. Based on several genetic analyses (Table 1), sources of viral substrates for DCL are cellular RDR-independent and cellular RDR-dependent (Figure 2). Viral dsRNA formed during silencing amplification is RDR-dependent. Self-complementary sequences in viral genomic RNA, viral replication intermediates, and products of overlapping or bidirectional transcription are cellular RDR-independent (Ding and Voinnet, 2007). It is widely assumed, that these RNA populations trigger the antiviral RNA silencing response and DLC proteins form primary virus-derived siRNAs (Ding and Voinnet, 2007). Alternatively, or in addition, viral RNA could be recognized by translational repressors arrested and routed to DCL processing or directed to cellular RDR-dependent dsRNA synthesis (Luo and Chen, 2007). A surveillance mechanism could also be formed by AGO proteins loaded with endogenous siRNAs with complementarity to viral RNA to trigger the antiviral RNA silencing pathway as described for artificial micro RNAs targeting viral RNA (Niu et al., 2006).
Small RNAS direct antiviral immunity
Virus-derived siRNAs associate with AGO proteins and are the specificity determinant guiding translational repression or cleavage of viral RNA with sequence complementarity to the siRNA (Schuck et al., 2013). In a variation of the pathway targeting DNA viruses, silencing complexes formed by virus-derived siRNAs and AGO4 direct methylation of viral DNA to prevent transcription (Raja et al., 2008). The end result is the establishment of a virus resistant state that inhibits virus replication and movement. Several phenomena in plant-virus interactions involve gene silencing such as cross protection, symptom recovery, synergism, and non-host resistance.
Cross protection occurs when infection by a mild virus strain prevents subsequent infection by a second virus of the same or closely related species (Kung et al., 2014). Although not all cross-protection cases are explained, according to the antiviral RNA silencing model, siRNAs-derived from the mild virus strain directs targeting of viruses with sequence similarity, thus creating a state of immunity (Kung et al., 2014). Symptom recovery has been described for several plant-virus combinations. Infected plants accumulate high virus titers and develop visible symptoms. However, the upper leaves of those plants contain low virus titters and do not develop symptoms. Virus-derived siRNAs formed in the lower part of the plant move systemically to the meristem to direct viral RNA targeting and prevent virus invasion of the meristem. Leaves formed after that harbor virus-derived siRNAs that mediate virus downregulation (Ma et al., 2015).
Viral synergism occurs when co-infection by two viruses results in disease with more severe symptoms than single virus infection (Xia et al., 2016). Most documented cases of viral synergism involve viruses in the Potyvirus genus and depend on silencing suppressors HC-Pro or P1 (Chavez-Calvillo et al., 2016; Xia et al., 2016). Potyviral HC-Pro binds both endogenous and virus-derived siRNAs (Garcia-Ruiz et al., 2015). Based on the silencing model (Figure 2), potyviral RNA silencing suppressors bind siRNAs derived from co-infecting viruses, preventing targeting of viral RNA and resulting in severe symptoms and higher accumulation of the non-potyvirus (Xia et al., 2016).
Several mechanisms explain non-host resistance, such as antiviral RNA silencing, host genetic determinants of viral RNA translation, replication or movement (Ivanov et al., 2014). Viral RNA targeting by endogenous siRNAs or virus activated siRNAs supports non-host resistance (Ding and Voinnet, 2007).
Suppression of RNA silencing by viruses
In order to replicate and move cell-to-cell and systemically, plant viruses must protect themselves from antiviral defense responses. At least two mechanisms have been described: evasion and suppression of RNA silencing. Positive-strand RNA viruses replicate in membrane bound compartments that sequester replication intermediates. Negative-strand RNA viruses and dsRNA viruses replicate in the nucleus or in enveloped vesicles. These structures might prevent access to viral dsRNA by the RNA silencing machinery (Laliberte and Sanfacon, 2010).
Most plant and some insect viruses encode silencing suppressors that inactivate RNA silencing by multiple mechanisms such as inhibition of siRNA biogenesis, sequestration of virus-derived siRNAs, triggering degradation of AGO or DCL proteins, and blocking RNA silencing amplification (Table 2). Virus-encoded silencing suppressors also bind cellular miRNAs and other siRNAs. Similarly effects on AGO, DCL, RDR and their accessory proteins affects biogenesis and activity of cellular miRNAs and siRNAs (Chapman et al., 2004). Gene silencing regulates plant development. Thus, perturbation of silencing pathways leads to changes in host gene expression and is, at least in part, responsible for symptom development (Chapman et al., 2004). Because antiviral silencing results in methylation of DNA virus minichromosomes, geminiviruses encode suppressor proteins that interfere with DNA methylation (Table 2).
Tabla 2. Representative virus-encoded gene silencing suppressors.
Viruses. Beet curly top virus (BCTV), Beet yellows virus (BYV), Cauliflower mosaic virus (CaMV), Cucumber mosaic virus (CMV), Rice dwarf phytoreovirus (RDV), Rice yellow mottle virus (RYMV), Tomato bushy stunt virus (TBSV), Tomato golden mosaic virus (TGMV), Tomato ringspot virus (ToRSV), Turnip crinkle virus (TCV).
Genetic engineering of virus resistance
For some plant-virus combinations, sources of natural genetic resistance have been identified and introduced by breeding into commercial cultivars. However, for most plant-virus combinations, natural genetic resistance has not been identified (Mehta et al., 2013; Cruz et al., 2014). Several RNA silencing-based approaches have been used to engineer virus resistance in plants using transgenes that express dsRNA, single stranded sense or antisense RNA, artificial miRNA (amiRNAs), or tasiRNAs (Figure 3 and Table 3). Sequences derived from the virus are integrated into DNA cassettes under control of constitutive or tissue-specific promoter. The transcript forms dsRNA processed into siRNAs that program targeting of viral RNA, creating a state of immunity.
These plants display a phenotype that varies from immunity to tolerance. The most targeted areas are the viral coat protein, the viral RNA-dependent RNA polymerase, silencing suppressor, or the geminiviral replication initiation site (Table 3).
Figure 3. Genetic engineering of antiviral immunity in plants by RNA silencing or DNA editing. A. Production of immunizing antiviral siRNAs is triggered by transgenes of viral origin forming dsRNA processed by Dicer-like proteins (DCL). B. Design of antiviral resistance against DNA viruses using the CRISPR/Cas9 system. Cas9 protein associates with the guide RNA (20 to 24 nt) to specifically cut DNA targets, preventing DNA replication.
Table 3. Representative virus resistant plants developed by RNA silencing or genome editing approaches.
Viruses. Bean golden mosaic virus (BGMV), Cassava brown streak virus (CBSV), Cucumber mosaic virus (CMV), Papaya ring spot virus (PRSV), Plum pox virus (PPV), Rice grassy stunt Virus (RGSV), Tobacco etch virus (TEV), Tobacco mosaic virus (TMV), Tomato leaf curl New Delhi virus (ToLCNDV), Tomato ringspot virus (ToRV), Turnip mosaic virus (TuMV), Turnip yellow mosaic virus (TuYMV), Watermelon mosaic virus (WMV), Wheat streak mosaic virus (WSMV), Zucchini yellow mosaic virus (ZYMV).
Cotton leaf curl disease complex: Cotton leaf curl Alabad virus (CLCuAlV), Cotton leaf curl Bangalore virus (CLCuBaV), Cotton leaf curl Kokhran virus (CLCuKoV), CLCuKoV-Bu(Burewala strain), Cotton leaf curl Multan virus (CLCuMuV) and Cotton leaf curl Rajasthan virus (CLCuRaV).
Hosts. Arabidopsis (Arabidopsis thaliana), Cassava (Manihot esculenta), common bean (Phaseolus vulgaris), Cotton (Gossypium hirsutum), Papaya (Carica papaya), Plum (Prunus spp), Rice (Oryza sativa), Squash (Cucurbita pepo), Tobacco (Nicotiana tabacum), Tomato (Solanum lycopersicum), Wheat (Triticum aestivum L.).
Target gene. Name of the viral or host genes (*) targeted for silencing or genome editing.
Clustered regularly interspaced short palindromic repeats (CRISPR) are segments of bacterial DNA containing short repetitions separated by a spacer sequence. CRISPR are bacteriophage virus, or plasmid DNA, integrated into the bacterial genome, and are processed by Cas nucleases into small RNA guides. Nuclease Cas9 associates with guide RNAs and specifically cuts DNA with sequence complementarity to the guide RNA. Interestingly, this specific RNA-guided DNA-nuclese provides antiviral immunity in bacteria (Horvath and Barrangou, 2010). This system has been adapted to design the most powerful genome editing tool available today with endless applications in functional genomics of eukaryotes, including humans, insects, nematodes, fungi, and plants (Ali et al., 2015). The CRISPER/Cas9 system has recently been used to design antiviral resistance against geminiviruses (Table 4) and will be part of current efforts to identify or validate plant susceptibility genes, leading to genetic engineering of antiviral resistance without transgenes.
Future challenges
Research efforts are currently focused on the identification of additional genetic components, identification and characterization of silencing suppressor proteins, and RNAs. Basic mechanisms expected to be elucidated in the near future include initial sensing of viral RNA by the cell, genetic determinants and mechanism of silencing amplification, downregulation of viral RNA by cleavage or translational repression, and the roles of virus-derived siRNAs in transcriptional reprograming of infected cells. A challenge for plant pathologists is to translate basic knowledge into practical applications.
Acknowledgments
Research in the Garcia-Ruiz laboratory is supported by an NIH grant (RO1GM120108).
REFERENCES
Abel PP, Nelson RS., De B, Hoffmann, N, Rogers SG, Fraley, RT and Beachy RN. 1986. Delay of disease development in transgenic plants that express the tobacco mosaic virus coat protein gene. Science 232, 738-743. PMID: 3457472 [ Links ]
Akbergenov R, Si-Ammour A, Blevins T, Amin I, Kutter C, Vanderschuren H, Zhang P, Gruissem W, Meins F Jr, Hohn T and Pooggin MM. 2006. Molecular characterization of geminivirus-derived small RNAs in different plant species. Nucleic Acids Res 34, 462-471. DOI: 10.1093/nar/gkj447 [ Links ]
Ali Z, Abulfaraj A, Idris A, Ali S, Tashkandi M and Mahfouz MM. 2015. CRISPR/Cas9-mediated viral interference in plants. Genome Biol 16, 238. DOI: 10.1186/s13059-015-0799-6 [ Links ]
Axtell, MJ. 2013. Classification and comparison of small RNAs from plants. Annu Rev Plant Biol 64, 137-159. DOI: 10.1146/annurev-arplant-050312-120043 [ Links ]
Azevedo J, Garcia D, Pontier D, Ohnesorge, S, Yu A, Garcia S, Braun L, Bergdoll M, Hakimi MA, Lagrange T and Voinnet O. 2010. Argonaute quenching and global changes in Dicer homeostasis caused by a pathogen-encoded GW repeat protein. Genes Dev 24, 904-915. DOI: 10.1101/gad.1908710 [ Links ]
Blevins T, Rajeswaran R, Aregger M, Borah BK, Schepetilnikov M, Baerlocher L, Farinelli L, Meins F Jr, Hohn T and Pooggin MM. 2011. Massive production of small RNAs from a non-coding region of Cauliflower mosaic virus in plant defense and viral counter-defense. Nucleic Acids Res 39, 5003-5014. DOI: 10.1093/nar/gkr119 [ Links ]
Blevins T, Rajeswaran R, Shivaprasad PV, Beknazariants D, Si-Ammour A, Park HS, Vazquez F, Robertson D, Meins F Jr, Hohn T and Pooggin MM. 2006. Four plant Dicers mediate viral small RNA biogenesis and DNA virus induced silencing. Nucleic Acids Res 34, 6233-6246. DOI: 10.1093/nar/gkl886 [ Links ]
Bonfim K, Faria JC, Nogueira EO, Mendes EA and Aragao FJ. 2007. RNAi-mediated resistance to Bean golden mosaic virus in genetically engineered common bean (Phaseolus vulgaris). Mol Plant Microbe Interact 20, 717-726. DOI: 10.1094/MPMI-20-6-0717 [ Links ]
Brosseau C and Moffett P. 2015. Functional and Genetic Analysis Identify a Role for Arabidopsis ARGONAUTE5 in Antiviral RNA Silencing. Plant Cell 27, 1742-1754. DOI: 10.1105/tpc.15.00264 [ Links ]
Buchmann RC, Asad S, Wolf JN, Mohannath G and Bisaro DM. 2009. Geminivirus AL2 and L2 proteins suppress transcriptional gene silencing and cause genome-wide reductions in cytosine methylation. J Virol 83, 5005-5013. DOI: 10.1128/JVI.01771-08 [ Links ]
Cao M, Du P, Wang X, Yu YQ, Qiu YH, Li W, Gal-On A, Zhou C, Li Y and Ding SW. 2014. Virus infection triggers widespread silencing of host genes by a distinct class of endogenous siRNAs in Arabidopsis. Proc Natl Acad Sci U S A 111, 14613-14618. DOI: 10.1073/pnas.1407131111 [ Links ]
Carbonell A, Fahlgren N, Garcia-Ruiz H, Gilbert KB, Montgomery TA, Nguyen T, Cuperus JT and Carrington JC. 2012. Functional analysis of three Arabidopsis ARGONAUTES using slicer-defective mutants. The Plant cell 24, 3613-3629. DOI: 10.1105/tpc.112.099945 [ Links ]
Ceniceros-Ojeda EA, Rodriguez-Negrete EA and Rivera-Bustamante RF. 2016. Two Populations of Viral Minichromosomes Are Present in a Geminivirus-Infected Plant Showing Symptom Remission (Recovery). J Virol 90, 3828-3838. DOI: 10.1128/JVI.02385-15 [ Links ]
Chapman EJ, Prokhnevsky AI, Gopinath K, Dolja VV and Carrington JC. 2004. Viral RNA silencing suppressors inhibit the microRNA pathway at an intermediate step. Genes Dev 18, 1179-1186. DOI: 10.1101/gad.1201204 [ Links ]
Chavez-Calvillo G, Contreras-Paredes CA, Mora-Macias J, Noa-Carrazana JC, Serrano-Rubio AA, Dinkova TD, Carrillo-Tripp M and Silva-Rosales L. 2016. Antagonism or synergism between papaya ringspot virus and papaya mosaic virus in Carica papaya is determined by their order of infection. Virology 489, 179-191. DOI: 10.1016/j.virol.2015.11.026 [ Links ]
Chitwood DH, Nogueira FT, Howell MD, Montgomery TA, Carrington, JC and Timmermans MC. 2009. Pattern formation via small RNA mobility. Genes Dev 23, 549-554. DOI: 10.1101/gad.1770009 [ Links ]
Cruz LF, Rupp JLS, Trick HN and Fellers JP. 2014. Stable resistance to Wheat streak mosaic virus in wheat mediated by RNAi. In Vitro Cellular & Developmental Biology-Plant 50, 665-672. DOI: 10.1007/s11627-014-9634-0 [ Links ]
Cuperus JT, Fahlgren N and Carrington JC. 2011. Evolution and functional diversification of MIRNA genes. The Plant cell 23, 431-442. DOI: 10.1105/tpc.110.082784 [ Links ]
Cuperus JT, Carbonell A, Fahlgren N, Garcia-Ruiz H, Burke RT, Takeda A, Sullivan CM, Gilbert SD, Montgomery TA and Carrington JC. 2010. Unique functionality of 22-nt miRNAs in triggering RDR6-dependent siRNA biogenesis from target transcripts in Arabidopsis. Nature structural & molecular biology 17, 997-1003. DOI: 10.1038/nsmb.1866 [ Links ]
Deleris A, Gallego-Bartolome J, Bao J, Kasschau KD, Carrington JC and Voinnet O. 2006. Hierarchical action and inhibition of plant Dicer-like proteins in antiviral defense. Science 313, 68-71. DOI: 10.1126/science.1128214 [ Links ]
Di Nicola-Negri E, Tavazza M, Salandri L and Ilardi V. 2010. Silencing of Plum pox virus 5’UTR/P1 sequence confers resistance to a wide range of PPV strains. Plant cell reports 29, 1435-1444. DOI: 10.1007/s00299-010-0933-6 [ Links ]
Ding SW and Voinnet O. 2007. Antiviral immunity directed by small RNAs. Cell 130, 413-426. DOI: 10.1016/j.cell.2007.07.039 [ Links ]
Fitch MM, Manshardt RM, Gonsalves D and Slightom JL. 1993. Transgenic papaya plants from Agrobacteriummediated transformation of somatic embryos. Plant cell reports 12, 245-249. DOI: 10.1007/BF00237128 [ Links ]
Fuchs M and Gonsalves D. 1995. Resistance of Transgenic Hybrid Squash Zw-20 Expressing the Coat Protein Genes of Zucchini Yellow Mosaic-Virus and Watermelon Mosaic-Virus-2 to Mixed Infections by Both Potyviruses. Bio-Technology 13, 1466-1473. DOI: 10.1038/nbt1295-1466 [ Links ]
Garcia-Ruiz H, Takeda A, Chapman EJ, Sullivan CM, Fahlgren N, Brempelis KJ and Carrington JC. 2010. Arabidopsis RNA-dependent RNA polymerases and dicer-like proteins in antiviral defense and small interfering RNA biogenesis during Turnip Mosaic Virus infection. Plant Cell 22, 481-496. DOI: 10.1105/tpc.109.073056 [ Links ]
Garcia-Ruiz H, Carbonell A, Hoyer JS, Fahlgren N, Gilbert KB, Takeda A, Giampetruzzi A, Garcia Ruiz, MT, McGinn MG, Lowery N, Martinez Baladejo MT and Carrington JC. 2015. Roles and Programming of Arabidopsis ARGONAUTE Proteins during Turnip Mosaic Virus Infection. PLoS Pathog 11, e1004755. DOI: 10.1371/journal.ppat.1004755 [ Links ]
Hong W, Qian D, Sun R, Jiang L, Wang Y, Wei C, Zhang Z and Li Y. 2015. OsRDR6 plays role in host defense against double-stranded RNA virus, Rice Dwarf Phytoreovirus. Sci Rep 5, 11324. DOI: 10.1038/srep11324 [ Links ]
Horvath P and Barrangou R. 2010. CRISPR/Cas, the immune system of bacteria and archaea. Science 327, 167-170. DOI: 10.1126/science.1179555 [ Links ]
Iqbal Z, Sattar MN and Shafiq M. 2016. CRISPR/Cas9: A Tool to Circumscribe Cotton Leaf Curl Disease. Frontiers in plant science 7, 475. DOI: 10.3389/fpls.2016.00475 [ Links ]
Ivanov KI, Eskelin K, Lohmus A and Makinen K. 2014. Molecular and cellular mechanisms underlying potyvirus infection. J Gen Virol 95, 1415-1429. DOI: 10.1099/vir.0.064220-0 [ Links ]
Karran RA and Sanfacon H. 2014. Tomato ringspot virus coat protein binds to ARGONAUTE 1 and suppresses the translation repression of a reporter gene. Mol Plant Microbe Interact 27, 933-943. DOI: 10.1094/MPMI-04-14-0099-R [ Links ]
Kung YJ, Lin PC, Yeh SD, Hong SF, Chua NH, Liu LY, Lin CP, Huang YH, Wu HW, Chen CC and Lin SS. 2014. Genetic analyses of the FRNK motif function of Turnip mosaic virus uncover multiple and potentially interactive pathways of cross-protection. Mol Plant Microbe Interact 27, 944-955. DOI: 10.1094/MPMI-04-14-0116-R [ Links ]
Lacombe S, Bangratz M, Vignols F and Brugidou C. 2010. The rice yellow mottle virus P1 protein exhibits dual functions to suppress and activate gene silencing. Plant J 61, 371-382. DOI: 10.1111/j.1365-313X.2009.04062.x [ Links ]
Laliberte JF and Sanfacon H. 2010. Cellular remodeling during plant virus infection. Annu Rev Phytopathol 48, 69-91. DOI: 10.1146/annurev-phyto-073009-114239 [ Links ]
Lindbo JA, Silva-Rosales L, Proebsting WM and Dougherty WG. 1993. Induction of a Highly Specific Antiviral State in Transgenic Plants: Implications for Regulation of Gene Expression and Virus Resistance. Plant Cell 5, 1749-1759. DOI: 10.1105/tpc.5.12.1749 [ Links ]
Luo Z and Chen Z. 2007. Improperly terminated, unpolyadenylated mRNA of sense transgenes is targeted by RDR6-mediated RNA silencing in Arabidopsis. Plant Cell 19, 943-958. DOI: 10.1105/tpc.106.045724 [ Links ]
Ma X, Nicole MC, Meteignier LV, Hong N, Wang G and Moffett P. 2015. Different roles for RNA silencing and RNA processing components in virus recovery and virus-induced gene silencing in plants. Journal of experimental botany 66, 919-932. DOI: 10.1093/jxb/eru447 [ Links ]
Mehta R, Radhakrishnan T, Kumar A, Yadav R, Dobaria JR, Thirumalaisamy PP, Jain RK and Chigurupati P. 2013. Coat protein-mediated transgenic resistance of peanut (Arachis hypogaea L.) to peanut stem necrosis disease through Agrobacterium-mediated genetic transformation. Indian J Virol 24, 205-213. DOI: 10.1007/s13337-013-0157-9 [ Links ]
Merai Z, Kerenyi Z, Kertesz S, Magna M, Lakatos L and Silhavy D. 2006. Double-stranded RNA binding may be a general plant RNA viral strategy to suppress RNA silencing. J Virol 80, 5747-5756. DOI: 10.1128/JVI.01963-05 [ Links ]
Minoia S, Carbonell A, Di Serio F, Gisel A, Carrington JC, Navarro B and Flores R. 2014. Specific argonautes selectively bind small RNAs derived from potato spindle tuber viroid and attenuate viroid accumulation in vivo. J Virol 88, 11933-11945. DOI: 10.1128/JVI.01404-14 [ Links ]
Mitter N, Koundal V, Williams S and Pappu H. 2013. Differential expression of tomato spotted wilt virus-derived viral small RNAs in infected commercial and experimental host plants. PLoS One 8, e76276. DOI: 10.1371/journal.pone.0076276 [ Links ]
Molnar A, Melnyk CW, Bassett A, Hardcastle TJ, Dunn R and Baulcombe, D.C. 2010. Small silencing RNAs in plants are mobile and direct epigenetic modification in recipient cells. Science 328, 872-875. DOI: 10.1126/science.1187959 [ Links ]
Navarro B, Pantaleo V, Gisel A, Moxon S, Dalmay T, Bisztray G, Di Serio F and Burgyan J. 2009. Deep sequencing of viroid-derived small RNAs from grapevine provides new insights on the role of RNA silencing in plant-viroid interaction. PLoS One 4, e7686. DOI: 10.1371/journal.pone.0007686 [ Links ]
Niu QW, Lin SS, Reyes JL, Chen KC, Wu HW, Yeh SD and Chua NH. 2006. Expression of artificial microRNAs in transgenic Arabidopsis thaliana confers virus resistance. Nat Biotechnol 24, 1420-1428. DOI: 10.1038/nbt1255 [ Links ]
Padmanabhan C, Zhang X and Jin H. 2009. Host small RNAs are big contributors to plant innate immunity. Curr Opin Plant Biol 12, 465-472. DOI: 10.1016/j.pbi.2009.06.005 [ Links ]
Pantaleo V, Saldarelli P, Miozzi L, Giampetruzzi A, Gisel A, Moxon S, Dalmay T, Bisztray G and Burgyan J. 2010. Deep sequencing analysis of viral short RNAs from an infected Pinot Noir grapevine. Virology 408, 49-56. DOI: 10.1016/j.virol.2010.09.001 [ Links ]
Pyott DE, Sheehan E and Molnar A. 2016. Engineering of CRISPR/Cas9-mediated potyvirus resistance in transgene-free Arabidopsis plants. Mol Plant Pathol. DOI: 10.1111/mpp.12417 [ Links ]
Qu F, Ye X and Morris, TJ. 2008. Arabidopsis DRB4, AGO1, AGO7, and RDR6 participate in a DCL4-initiated antiviral RNA silencing pathway negatively regulated by DCL1. Proc Natl Acad Sci U S A 105, 14732-14737. DOI: 10.1073/pnas.0805760105 [ Links ]
Raja P, Sanville BC, Buchmann RC and Bisaro, DM. 2008. Viral genome methylation as an epigenetic defense against geminiviruses. J Virol 82, 8997-9007. DOI: 10.1128/JVI.00719-08 [ Links ]
Ren B, Guo Y, Gao F, Zhou P, Wu F, Meng Z, Wei C and Li Y. 2010. Multiple functions of Rice dwarf phytoreovirus Pns10 in suppressing systemic RNA silencing. J Virol 84, 12914-12923. DOI: 10.1128/JVI.00864-10 [ Links ]
Schuck J, Gursinsky T, Pantaleo V, Burgyan J and Behrens SE. 2013. AGO/RISC-mediated antiviral RNA silencing in a plant in vitro system. Nucleic Acids Res 41, 5090-5103. DOI: 10.1093/nar/gkt193 [ Links ]
Shafiq S, Li J and Sun Q. 2016. Functions of plants long non-coding RNAs. Biochim Biophys Acta 1859, 155-162. DOI: 10.1016/j.bbagrm.2015.06.009 [ Links ]
Shimizu T, Ogamino T, Hiraguri A, Nakazono-Nagaoka E, Uehara-Ichiki T, Nakajima M, Akutsu K, Omura T and Sasaya T. 2013. Strong resistance against Rice grassy stunt virus is induced in transgenic rice plants expressing double-stranded RNA of the viral genes for nucleocapsid or movement proteins as targets for RNA interference. Phytopathology 103, 513-519. DOI: 10.1094/PHYTO-07-12-0165-R [ Links ]
Shimura H, Pantaleo V, Ishihara T, Myojo N, Inaba J, Sueda K, Burgyan J and Masuta C. 2011. A viral satellite RNA induces yellow symptoms on tobacco by targeting a gene involved in chlorophyll biosynthesis using the RNA silencing machinery. PLoS pathogens 7, e1002021. DOI: 10.1371/journal.ppat.1002021 [ Links ]
Singh A, Taneja J, Dasgupta I and Mukherjee SK. 2015. Development of plants resistant to tomato geminiviruses using artificial trans-acting small interfering RNA. Mol Plant Pathol 16, 724-734. DOI: 10.1111/mpp.12229 [ Links ]
Urayama S, Moriyama H, Aoki N, Nakazawa Y, Okada R, Kiyota E, Miki D, Shimamoto K and Fukuhara T. 2010. Knock-down of OsDCL2 in rice negatively affects maintenance of the endogenous dsRNA virus, Oryza sativa endornavirus. Plant Cell Physiol 51, 58-67. DOI: 10.1093/pcp/pcp167 [ Links ]
Wagaba H, Patil BL, Mukasa S, Alicai T, Fauquet CM and Taylor NJ. 2016. Artificial microRNA-derived resistance to Cassava brown streak disease. J Virol Methods 231, 38-43. DOI: 10.1016/j.jviromet.2016.02.004 [ Links ]
Wang X, Kohalmi SE, Svircev A, Wang A, Sanfacon H and Tian L. 2013. Silencing of the host factor eIF(iso)4E gene confers plum pox virus resistance in plum. PLoS One 8, e50627. DOI: 10.1371/journal.pone.0050627 [ Links ]
Weiberg A, Wang M, Bellinger M and Jin H. 2014. Small RNAs: a new paradigm in plant-microbe interactions. Annu Rev Phytopathol 52, 495-516. DOI: 10.1146/annu-rev-phyto-102313-045933 [ Links ]
Wu J, Yang Z, Wang Y, Zheng L, Ye R, Ji Y, Zhao S, Ji S, Liu R, Xu L, Zheng H, Zhou Y, Zhang X, Cao X, Xie L, Wu Z, Qi Y and Li Y. 2015. Viral-inducible Argonaute18 confers broad-spectrum virus resistance in rice by sequestering a host microRNA. Elife 4. DOI: 10.7554/eLife.05733 [ Links ]
Xia Z, Zhao Z, Chen L, Li M, Zhou T, Deng C, Zhou Q and Fan Z. 2016. Synergistic infection of two viruses MCMV and SCMV increases the accumulations of both MCMV and MCMV-derived siRNAs in maize. Sci Rep 6, 20520. DOI: 10.1038/srep20520 [ Links ]
Yepes LM, Fuchs M, Slightom JL and Gonsalves D. 1996. Sense and antisense coat protein gene constructs confer high levels of resistance to tomato ringspot nepovirus in transgenic Nicotiana species. Phytopathology 86, 417-424. DOI: 10.1094/Phyto-86-417 [ Links ]
Zhang X, Yuan YR, Pei Y, Lin SS, Tuschl T, Patel DJ and Chua NH. 2006. Cucumber mosaic virus-encoded 2b suppressor inhibits Arabidopsis Argonaute1 cleavage activity to counter plant defense. Genes Dev 20, 3255-3268. DOI: 10.1101/gad.1495506. [ Links ]
Received: June 30, 2016; Accepted: September 01, 2016
Este es un artículo publicado en acceso abierto bajo una licencia Creative Commons
