Second to None: Plant Secondary siRNAs as Defensive Agents against Phytophthora
Authors: Michael J. Axtell
Journal: Cell Host & Microbe (2019)

The eukaryotic plant pathogen Phytophthora encodes conserved effector proteins to eliminate host secondary siRNAs. In this issue of Cell Host & Microbe, Hou et al., 2019Hou Y. Zhai Y. Feng L. Karimi H.Z. Rutter B.D. Zeng L. Choi D.S. Zhang B. Gu W. Chen X. et al.A Phytophthora effector suppresses trans-kingdom RNAi to promote disease susceptibility.Cell Host Microbe. 2019; 25 (this issue): 153-165Abstract Full Text Full Text PDF Scopus (115) Google Scholar report that reduction in secondary siRNA levels renders the host hypersusceptible to Phytophthora and plant secondary siRNAs likely serve as trans-species defensive molecules against pathogens. The eukaryotic plant pathogen Phytophthora encodes conserved effector proteins to eliminate host secondary siRNAs. In this issue of Cell Host & Microbe, Hou et al., 2019Hou Y. Zhai Y. Feng L. Karimi H.Z. Rutter B.D. Zeng L. Choi D.S. Zhang B. Gu W. Chen X. et al.A Phytophthora effector suppresses trans-kingdom RNAi to promote disease susceptibility.Cell Host Microbe. 2019; 25 (this issue): 153-165Abstract Full Text Full Text PDF Scopus (115) Google Scholar report that reduction in secondary siRNA levels renders the host hypersusceptible to Phytophthora and plant secondary siRNAs likely serve as trans-species defensive molecules against pathogens. Plants produce diverse small regulatory RNAs that play important roles in various biological processes. As a general rule, small RNAs act as specificity determinants that guide silencing complexes to target RNAs selected on the basis of complementarity (Axtell, 2013Axtell M.J. Classification and comparison of small RNAs from plants.Annu. Rev. Plant Biol. 2013; 64: 137-159Crossref PubMed Scopus (612) Google Scholar). Depending on the particular type of small RNA and associated silencing complex, this can lead to a combination of translational repression, RNA degradation, and/or reinforcement of repressive DNA and histone modifications at homologous DNA regions. Many plant small RNAs are homeostatic and control processes such as development, cell identity, nutrient acquisition, and suppression of transposons. Other plant small RNAs are induced upon viral infections and play anti-viral roles. A new article from Wenbo Ma and colleagues in this issue of Cell Host & Microbe extends this defensive paradigm of plant small RNAs to an important oomycete plant pathogen (Hou et al., 2019Hou Y. Zhai Y. Feng L. Karimi H.Z. Rutter B.D. Zeng L. Choi D.S. Zhang B. Gu W. Chen X. et al.A Phytophthora effector suppresses trans-kingdom RNAi to promote disease susceptibility.Cell Host Microbe. 2019; 25 (this issue): 153-165Abstract Full Text Full Text PDF Scopus (115) Google Scholar). Phytophthora spp. are oomycetes that cause serious diseases on a number of important crops. Perhaps most famously in the Western world, P. infestans was responsible for a devastating outbreak of potato blight in Ireland between 1845 and 1849 that contributed to a severe famine, social upheaval, and mass human migration. Phytophthora continues to plague agriculture around the world (Derevnina et al., 2016Derevnina L. Petre B. Kellner R. Dagdas Y.F. Sarowar M.N. Giannakopoulou A. De la Concepcion J.C. Chaparro-Garcia A. Pennington H.G. van West P. Kamoun S. Emerging oomycete threats to plants and animals.Philos. Trans. R. Soc. Lond. B Biol. Sci. 2016; 371: 20150459Crossref PubMed Scopus (79) Google Scholar). Like most cellular pathogens, Phytophthora delivers virulence effector proteins into the host cell, which serve to target and manipulate key host processes to the pathogen’s advantage. Previous work from Ma’s group described two effectors from Phytophthora sojae that decrease plant small RNA accumulation (Qiao et al., 2013Qiao Y. Liu L. Xiong Q. Flores C. Wong J. Shi J. Wang X. Liu X. Xiang Q. Jiang S. et al.Oomycete pathogens encode RNA silencing suppressors.Nat. Genet. 2013; 45: 330-333Crossref PubMed Scopus (184) Google Scholar). The existence of these effectors, termed Phytophthora suppressors of RNA silencing (PSR1 and PSR2), implied that host small RNAs might negatively impact Phytophthora. Importantly, the PSR2 effector is conserved in multiple species of Phytophthora, including P. infestans, and promotes Phytophthora growth in host plants engineered to express PSR2 (Xiong et al., 2014Xiong Q. Ye W. Choi D. Wong J. Qiao Y. Tao K. Wang Y. Ma W. Phytophthora suppressor of RNA silencing 2 is a conserved RxLR effector that promotes infection in soybean and Arabidopsis thaliana.Mol. Plant Microbe Interact. 2014; 27: 1379-1389Crossref PubMed Scopus (65) Google Scholar). In the new work, Hou et al., 2019Hou Y. Zhai Y. Feng L. Karimi H.Z. Rutter B.D. Zeng L. Choi D.S. Zhang B. Gu W. Chen X. et al.A Phytophthora effector suppresses trans-kingdom RNAi to promote disease susceptibility.Cell Host Microbe. 2019; 25 (this issue): 153-165Abstract Full Text Full Text PDF Scopus (115) Google Scholar conclusively identify the types of plant small RNAs affected by PSR2 and provide tantalizing clues to how those small RNAs might work against Phytophthora. By examining small RNA profiles of Arabidopsis plants expressing a PSR2 transgene, Hou et al. find that a specific type of small RNA, secondary small interfering RNAs (siRNAs), are reduced. Secondary siRNAs depend on an initial “trigger” small RNA to direct the cleavage of a target RNA (Fei et al., 2013Fei Q. Xia R. Meyers B.C. Phased, secondary, small interfering RNAs in posttranscriptional regulatory networks.Plant Cell. 2013; 25: 2400-2415Crossref PubMed Scopus (356) Google Scholar). The severed target RNA fragment is used as a template by an RNA-dependent RNA polymerase for the synthesis of double-stranded RNA (dsRNA), which is subsequently processed to make secondary siRNAs. The production of secondary siRNAs can be thought of as an amplification loop, with an initial small RNA targeting event giving rise to numerous subsidiary small RNAs with homology to the original target. Hou et al., 2019Hou Y. Zhai Y. Feng L. Karimi H.Z. Rutter B.D. Zeng L. Choi D.S. Zhang B. Gu W. Chen X. et al.A Phytophthora effector suppresses trans-kingdom RNAi to promote disease susceptibility.Cell Host Microbe. 2019; 25 (this issue): 153-165Abstract Full Text Full Text PDF Scopus (115) Google Scholar find that PSR2 specifically reduces accumulation of secondary siRNAs triggered by the microRNAs miR161 and miR173. miR173 targets long non-coding RNAs in the TAS1/TAS2 family, leading to TAS1/TAS2-derived secondary siRNAs. Both TAS1/TAS2 secondary siRNAs and miR161 target protein-coding mRNAs from the PPR family, spawning PPR-derived secondary siRNAs. Upon infection with a strain of P. capsici that lacks PSR2, levels of miR161 and its resultant PPR-derived secondary siRNAs increase; this increase is dependent upon known immune signal transduction cascades. Importantly, plants with reduced levels of miR161/miR173-dependent secondary siRNAs are hypersusceptible to P. capsici, while plants with increased levels of these secondary siRNAs show enhanced resistance. Hou et al., 2019Hou Y. Zhai Y. Feng L. Karimi H.Z. Rutter B.D. Zeng L. Choi D.S. Zhang B. Gu W. Chen X. et al.A Phytophthora effector suppresses trans-kingdom RNAi to promote disease susceptibility.Cell Host Microbe. 2019; 25 (this issue): 153-165Abstract Full Text Full Text PDF Scopus (115) Google Scholar hypothesize that PPR-derived secondary siRNAs are exported from host plants, enter Phytophthora, and silence Phytophthora mRNAs. Consistent with this hypothesis, a PPR-derived siRNA is found in extracellular vesicles (EVs). EVs are small, membrane-bound vesicles secreted by plant cells that contain anti-pathogen molecules (Rutter and Innes, 2017Rutter B.D. Innes R.W. Extracellular vesicles isolated from the leaf apoplast carry stress-response proteins.Plant Physiol. 2017; 173: 728-741Crossref PubMed Scopus (231) Google Scholar). Additionally, Hou et al. find that mRNA levels of a putative P. capsici mRNA target and a reporter gene respond to manipulation of secondary siRNA levels in the host. Thus, it is likely that host secondary siRNAs are exported to P. capsici in a trans-species manner to reduce pathogen fitness. Hou et al. also show that the mechanism of PSR2 action is to interfere with the host DRB4 protein, a known co-factor in secondary siRNA biogenesis. This work by Hou et al., 2019Hou Y. Zhai Y. Feng L. Karimi H.Z. Rutter B.D. Zeng L. Choi D.S. Zhang B. Gu W. Chen X. et al.A Phytophthora effector suppresses trans-kingdom RNAi to promote disease susceptibility.Cell Host Microbe. 2019; 25 (this issue): 153-165Abstract Full Text Full Text PDF Scopus (115) Google Scholar is an exciting step forward in understanding host responses to Phytophthora. It is crystal clear that the Phytophthora PSR2 effector interferes with secondary siRNA biogenesis, which would otherwise impact pathogen growth. The data for trans-species delivery of host secondary siRNAs to Phytophthora are compelling and are part of a growing theme of trans-species small RNA activity during plant-pathogen interactions. Intriguingly, related miR173-dependent secondary siRNAs from TAS1/TAS2 loci also appear to be delivered to the fungal plant pathogen Botrytis cinerea via EVs (Cai et al., 2018Cai Q. Qiao L. Wang M. He B. Lin F.-M. Palmquist J. Huang S.D. Jin H. Plants send small RNAs in extracellular vesicles to fungal pathogen to silence virulence genes.Science. 2018; 360: 1126-1129Crossref PubMed Scopus (446) Google Scholar). Secondary siRNAs from other protein-coding mRNAs are also induced as a result of trans-species delivery of microRNA from the parasitic plant Cuscuta campestris to its hosts (Shahid et al., 2018Shahid S. Kim G. Johnson N.R. Wafula E. Wang F. Coruh C. Bernal-Galeano V. Phifer T. dePamphilis C.W. Westwood J.H. Axtell M.J. MicroRNAs from the parasitic plant Cuscuta campestris target host messenger RNAs.Nature. 2018; 553: 82-85Crossref PubMed Scopus (190) Google Scholar). Thus, the trans-species small RNAs associated with diverse plant pathogens seem to consistently involve secondary siRNAs. The involvement of miR161- and miR173-dependent secondary siRNAs in Phytophthora resistance raises interesting evolutionary questions. In contrast to many miRNAs that are well conserved among diverse plants, neither miR161 nor miR173 is present outside of the Brassicaceae plant family, although PPR-derived secondary siRNAs are present in a wider range of plant species. The fact that PSR2 enhances virulence of P. sojae growth on soybean roots (Xiong et al., 2014Xiong Q. Ye W. Choi D. Wong J. Qiao Y. Tao K. Wang Y. Ma W. Phytophthora suppressor of RNA silencing 2 is a conserved RxLR effector that promotes infection in soybean and Arabidopsis thaliana.Mol. Plant Microbe Interact. 2014; 27: 1379-1389Crossref PubMed Scopus (65) Google Scholar) shows that suppression of secondary siRNAs pays dividends for Phytophthora even when the host is not a member of the Brassicaceae and thus lacks miR161 and miR173. The fact that secondary siRNAs spawned by the Arabidopsis miR161/miR173/TAS1/TAS2/PPR network also affect the distantly related fungal pathogen Botrytis (Cai et al., 2018Cai Q. Qiao L. Wang M. He B. Lin F.-M. Palmquist J. Huang S.D. Jin H. Plants send small RNAs in extracellular vesicles to fungal pathogen to silence virulence genes.Science. 2018; 360: 1126-1129Crossref PubMed Scopus (446) Google Scholar) further increases the mystery: how can the same set of secondary siRNAs affect gene expression in multiple, highly diverse pathogen transcriptomes? One intriguing idea discussed by Hou et al., 2019Hou Y. Zhai Y. Feng L. Karimi H.Z. Rutter B.D. Zeng L. Choi D.S. Zhang B. Gu W. Chen X. et al.A Phytophthora effector suppresses trans-kingdom RNAi to promote disease susceptibility.Cell Host Microbe. 2019; 25 (this issue): 153-165Abstract Full Text Full Text PDF Scopus (115) Google Scholar is that the host is employing a “shotgun” approach to trans-species secondary siRNA delivery. In this scenario, it is the production and delivery of a sequence-diverse set of small RNAs that matters. Perhaps, unlike classic microRNA-target relationships, there is no purifying selection on the sequence of these secondary siRNAs in order to maintain complementarity to any particular pathogen mRNA. When delivered to the pathogen, many siRNAs will fail to interact with any target mRNAs, but by chance some will hit important targets in the pathogen. Detailed study of the molecular evolution of these secondary siRNAs, and their potential targets within diverse pathogen transcriptomes, will illuminate this very interesting problem. In the meantime, it is clear that trans-species delivery of small RNAs between plant hosts and their pathogens is a widespread phenomenon. A Phytophthora Effector Suppresses Trans-Kingdom RNAi to Promote Disease SusceptibilityHou et al.Cell Host & MicrobeDecember 27, 2018In BriefThe role of plant RNAi in defense against eukaryotic pathogens is unclear. Hou et al. report that Arabidopsis produces a reservoir of secondary siRNAs that confer resistance against the notorious pathogen Phytophthora, likely through trans-kingdom gene silencing. However, a Phytophthora effector defeats this defense by specifically inhibiting secondary siRNA biogenesis. Full-Text PDF Open Archive