Diverse Functions of Small RNAs in Different Plant-Pathogen Communications

Abstract

RNA silencing is a conserved mechanism that utilizes small RNAs (sRNAs) to direct the regulation of gene expression at the transcriptional or post-transcriptional level. Plants utilizing RNA silencing machinery to defend pathogen infection was first identified in plant-virus interaction and later was observed in distinct plant-pathogen interactions. RNA silencing is not only responsible for suppressing RNA accumulation and movement of virus and viroid, but also facilitates plant immune responses against bacterial, oomycete, and fungal infection. Interestingly, even the same plant sRNA can perform different roles when encounters with different pathogens. On the other side, pathogens counteract by generating sRNAs that directly regulate pathogen gene expression to increase virulence or target host genes to facilitate pathogen infection. Here, we summarize the current knowledge of the characterization and biogenesis of host- and pathogen-derived sRNAs, as well as the different RNA silencing machineries that plants utilize to defend against different pathogens. The functions of these sRNAs in defense and counter-defense and their mechanisms for regulation during different plant-pathogen interactions are also discussed.

Keywords: RNA silencing; pathogen virulence; plant immunity; plant–pathogen interaction; small RNA.

FIGURE 1

Role of sRNAs in plant-bacteria interaction. (A) Plant sRNAs defend bacteria attack by fine-tuning plant hormone and disease resistance activity. Upon the infection, plants detect PAMPs and modulate the accumulation of miRNA and siRNA. miRNAs, such as miR393, miR160, and miR167, regulate disease resistance by fine-tuning plant hormone networks, while other miRNAs regulate the activation of R protein (miR482/miR472) or the slicing of genes inhibiting plant immunity (miR398/miR773). miR393b*, the pairing strand of miR393, increases plant immunity by promoting the exocytosis of antimicrobial protein. siRNAs, including siRNAATGB2 and AtlsiRNA-1, are induced by bacteria effectors and enhance ETI by silencing genes that negatively regulate plant disease resistance. (B) Bacteria non-coding sRNAs (ncRNAs) regulate bacteria gene expression to improve virulence. Through imperfect base-pairing of short regions (10- to 25-nt), bacteria ncRNAs bind to target mRNAs and guide the suppression of genes or proteins that are involved in virulence. ncRNAs can regulate bacteria virulence by inhibiting proteins that trigger host defense (BLP) or affecting the expression of effectors (AvrRpt2). Bacteria effectors translocate into host plant cell and inhibit the regulation of plant sRNA (bottom). The AvrPtoB effector specifically represses the accumulation of miR393 at the transcriptional level, while AvrPto reduces the processing of miR393.

FIGURE 2

Role of sRNAs in plant-fungi/oomycete interaction. (A) Plant sRNAs regulate PTI and ETI in response to fungi or oomycete infection. The infection of fungi (left) and oomycete (right) alters the accumulation of miRNAs, by which changes the expression of genes contribute to plant resistance. Fungi elicitorsor fungi infections triggers the accumulation of some sRNAs, such as miR7695, miR168, miR823 and siRNA415, while miR528, miR1879, miR9863, and miR482 are down-regulated to improve plant resistance. The accumulations of miR403 and miR396 are down-regulated upon oomycete infection. (B) Schematic representation of the function of fungi/oomycete sRNAs in pathogen virulence. sRNAs encoded by fungi and oomycetes are usually generated from TE region, effector coding region, and other regions. These sRNA can be either DCL-dependent or DCL-independent and are involved in the regulation of pathogen development and virulence. In particular, sRNA regulate the expression of effectors, which further influence the accumulation of host miRNA and siRNA. sRNAs generated from Avr3a region of oomycete can transgenerationally change the pathogen virulence. The PSR1 and PSR2 effectors of oomycete are secreted into plant cells and alter host RNA silencing machineries as RNA silencing suppressor to decrease host immunity. On the other hand, fungi sRNAs, Bc-sRNAs, translocate into host cell and utilize plant RNA silencing component to reduce the expression of host immune genes and facilitate fungi infection.

FIGURE 3

Role of sRNAs in plant-virus interaction. RNA silencing inside plant cells can be divided into two parts: (A) Plant generate vsiRNAs, targeting on virus genome directly to defend viral infection. The generation of vsiRNA are slightly different for RNA virus or DNA virus. For RNA virus, the structure region of virus genome, dsRNA replicative intermediate forms of ssRNA viruses, and the dsRNA genomes of dsRNA viruses can be processed by DCL proteins (right). The vsiRNAs of DNA virus, on the other hand, can be processed from the structured region of the transcript and the overlapping region of the bi-direction transcription (left). In both cases, RDR1 and RDR6 are involved in the generation of secondary vsiRNA (shown in blank dash line). After generation, vsiRNAs are loaded into different AGOs and perform the silencing of virus genome. vsiRNAs target on RNA virus to slice the genomic RNA, while perform DNA methylation on the genome of DNA virus. Whether vsiRNA targets on the transcription of DNA virus remains unknown (blue dash line). (B) The counter-defense of virus to plant RNA silencing machinery. As plant generates vsiRNA to silence virus genome, viruses encode suppressors, such as 2b, Hc-Pro, P19, AL2/AC2, P38, and etc., as a counter-defense (left above). The effect of suppressor on RNA silencing include the interfere of DCL slicing, the blocking of methylation, the binding of vsiRNsA, the preventing of RISC assembly, and etc. vsiRNAs encoded by TMV, CMV, CaMV, and RSV can also target the host genes to decrease plant defense. In addition, plant viruses are often accompanied with a variety of subviral RNA/DNAs. These satellite RNA/DNAs affect virus pathogenicity by generating satRNA-derived siRNAs (satsiRNAs). CMV Y satellite (Y-sat) produces a 22-nt satsiRNA that targets Chll, a key gene involved in chlorophyll synthesis, resulting in bright yellow symptom. sat-siR-12, another satsiRNA can loaded into AGO1/3/5 and regulate CMV transcripts accumulation with the function of RDR6. As counter defense, CMV encodes VSR 2b to inhibit the function of AGOs (right above). TCV is often accompanied with a single strand satellite RNA (satC) that is composed of the 3′ end of TCV helper virus (left bottom). Because of the sequence similarity of satsiRNA and the 3′ end of TCV helper virus, the presence of satC-siRNA represses the accumulation of TCV genomic RNA. At the same time, TCV genomic RNA and the CP protein assemble to a virion. CP is a VSR encode by TCV. The down-regulation of TCV transcripts by satC-siRNAs result in the increase of free CP protein, which subsequently suppresses the accumulation of satC-siRNAs (shown in dash line). DNA ß satellites are circular ssDNA that associate with many monopartit begomoviruses. The ßC1 protein encoded by DNAß satellite is a VSR that suppresses TGS by the interaction with SAHH, and PTGS through the interaction with rgs-CaM (right bottom).

FIGURE 4

Role of sRNAs in plant-viroid interaction. (A) The biogenesis of vdsiRNAs in plant and the possible function of vdsiRNA in plant defense to viroid. PSTVd is mainly found in nucleolus, and its vdsiRNAs predominately map to the positive strand of the left and right terminal regions. It is most likely that PSTVd-vdsiRNAs are generated from the hairpin or stem-loop structure of plus-strand of PSTV transcripts. The secondary structure of PSTVd transcripts are targeted by DCL protein and sliced into vdsiRNA. Another possible source of vdsiRNA are the accidental association of (+) and (-) strand replication, which are further target by DCL protein. On the other hand, PLMVd, viroid that replicate in the chloroplast, generate vdsiRNAs from both polarities. The stem-loop structures of PLMVd are processed by DCL protein to generate vdsiRNAs. Furthermore, some research indicate that vdsiRNAs can be amplified through the activity of RDRs. After generation, vdsiRNA may be loaded into plant AGO proteins and target viroid RNAs. (B) The function of vdsiRNAs in producing viroid symptom. Some of the viroid symptom maybe caused by vdsiRNAs that target host genes. vdsiRNA generated by PSTVd can target on various plant genes including soluble inorganic pyrophosphatase (siPPase) gene, callose synthase genes CalS11-like and CalS12-like, and LeExp2 gene, while PLMVd vdsiRNA has been reported to target HSP90 and trigger signal transduction that eventually leads to viroid disease symptoms. TPMVd vdsiRNA has also been shown to slice the SolWD40 gene. In addition, HSVd vdsiRNAs are involved in TGS by inducing DNA methylation of the promoter region of rRNA genes.