Root-specific role for Nicotiana benthamiana RDR6 in the inhibition of Chinese wheat mosaic virus accumulation at higher temperatures

TaWRKY50-TaSARK7 module-mediated cysteine-rich protein phosphorylation suppresses the programmed cell death response to Chinese wheat mosaic virus infection

WRKY transcription factors are widely involved in plant responses to biotic and abiotic stresses. However, there is currently a limited understanding of the regulation of viral infection by WRKY transcription factors in wheat (Triticum aestivum). The WRKY transcription factor TaWRKY50 in group IIb wheat exhibited a significant response to Chinese wheat mosaic virus infection. TaWRKY50 is localized in the nucleus and is an activating transcription factor. Interestingly, we found that silencing TaWRKY50 induces cell death following inoculation with CWMV. The protein kinase TaSAPK7 is specific to plants, whereas NbSRK is a closely related kinase with high homology to TaSAPK7. The transcriptional activities of both TaSAPK7 and NbSRK can be enhanced by TaWRKY50 binding to their promoters. CRP is an RNA silencing suppressor. Furthermore, TaWRKY50 may regulate CWMV infection by regulating the expression of TaSAPK7 and NbSRK to increase CRP phosphorylation and reduce the amount of programmed cell death (PCD).

A novel ilarvirus protein CP-RT is expressed via stop codon readthrough and suppresses RDR6-dependent RNA silencing

Ilarviruses are a relatively understudied but important group of plant RNA viruses that includes a number of crop pathogens. Their genomes comprise three RNA segments encoding two replicase subunits, movement protein, coat protein (CP), and (in some ilarvirus subgroups) a protein that suppresses RNA silencing. Here we report that, in many ilarviruses, RNA3 encodes an additional protein (termed CP-RT) as a result of ribosomal readthrough of the CP stop codon into a short downstream readthrough (RT) ORF. Using asparagus virus 2 as a model, we find that CP-RT is expressed in planta where it functions as a weak suppressor of RNA silencing. CP-RT expression is essential for persistent systemic infection in leaves and shoot apical meristem. CP-RT function is dependent on a putative zinc-finger motif within RT. Replacing the asparagus virus 2 RT with the RT of an ilarvirus from a different subgroup restored the ability to establish persistent infection. These findings open up a new avenue for research on ilarvirus silencing suppression, persistent meristem invasion and vertical transmission.

TaTHI2 interacts with Ca2+-dependent protein kinase TaCPK5 to suppress virus infection by regulating ROS accumulation

Thiamine (vitamin B1) biosynthesis involves key enzymes known as thiazole moieties (THI1/THI2), which have been shown to participate in plant responses to abiotic stress. However, the role of THI1/THI2 in plant immunity remains unclear. In this study, we cloned TaTHI2 from wheat and investigated its function in Chinese wheat mosaic virus (CWMV) infection. Overexpression of TaTHI2 (TaTHI2-OE) inhibited CWMV infection, while TaTHI2 silencing enhanced viral infection in wheat. Interestingly, the membrane-localized TaTHI2 protein was increased during CWMV infection. TaTHI2 also interacted with the Ca2+-dependent protein kinase 5 (TaCPK5), which is localized in the plasma membrane, and promoted reactive oxygen species (ROS) production by repressing TaCPK5-mediated activity of the catalase protein TaCAT1. CWMV CP disrupted the interaction between TaTHI2 and TaCAT1, reducing ROS accumulation and facilitating viral infection. Additionally, transgenic plants overexpressing TaTHI2 showed increased seed number per ear and 1000-kernel weight compared to control plants. Our findings reveal a novel function of TaTHI2 in plant immunity and suggest its potential as a valuable gene for balancing disease resistance and wheat yield. Furthermore, the disruption of the TaTHI2-mediated plant immune pathway by CWMV CP provides further evidence for the evolutionary arms race between plants and viruses.

Auxin as an architect of the pectin matrix

Auxin is a versatile plant growth regulator that triggers multiple signalling pathways at different spatial and temporal resolutions. A plant cell is surrounded by the cell wall, a complex and dynamic network of polysaccharides. The cell wall needs to be rigid to provide mechanical support and protection and highly flexible to allow cell growth and shape acquisition. The modification of the pectin components, among other processes, is a mechanism by which auxin activity alters the mechanical properties of the cell wall. Auxin signalling precisely controls the transcriptional output of several genes encoding pectin remodelling enzymes, their local activity, pectin deposition, and modulation in different developmental contexts. This review examines the mechanism of auxin activity in regulating pectin chemistry at organ, cellular, and subcellular levels across diverse plant species. Moreover, we ask questions that remain to be addressed to fully understand the interplay between auxin and pectin in plant growth and development.

The P1 protein of wheat yellow mosaic virus exerts RNA silencing suppression activity to facilitate virus infection in wheat plants

Wheat yellow mosaic virus (WYMV) causes severe wheat viral disease in Asia. However, the viral suppressor of RNA silencing (VSR) encoded by WYMV has not been identified. Here, the P1 protein encoded by WYMV RNA2 was shown to suppress RNA silencing in Nicotiana benthamiana. Mutagenesis assays revealed that the alanine substitution mutant G175A of P1 abolished VSR activity and mutant Y10A VSR activity remained only in younger leaves. P1, but not G175A, interacted with gene silencing-related protein, N. benthamiana calmodulin-like protein (NbCaM), and calmodulin-binding transcription activator 3 (NbCAMTA3), and Y10A interacted with NbCAMTA3 only. Competitive Bimolecular fluorescence complementation and co-immunoprecipitation assays showed that the ability of P1 disturbing the interaction between NbCaM and NbCAMTA3 was stronger than Y10A, Y10A was stronger than G175A. In vitro transcript inoculation of infectious WYMV clones further demonstrated that VSR-defective mutants G175A and Y10A reduced WYMV infection in wheat (Triticum aestivum L.), G175A had a more significant effect on virus accumulation in upper leaves of wheat than Y10A. Moreover, RNA silencing, temperature, and autophagy have significant effects on the accumulation of P1 in N. benthamiana. Taken together, WYMV P1 acts as VSR by interfering with calmodulin-associated antiviral RNAi defense to facilitate virus infection in wheat, which has provided clear insights into the function of P1 in the process of WYMV infection.

Genome-Wide Identification and Analysis of the ABCF Gene Family in Triticum aestivum

The ATP-binding cassette (ABC) superfamily of proteins is a group of evolutionarily conserved proteins. The ABCF subfamily is involved in ribosomal synthesis, antibiotic resistance, and transcriptional regulation. However, few studies have investigated the role of ABCF in wheat (Triticum aestivum) immunity. Here, we identified 18 TaABCFs and classified them into four categories based on their domain characteristics. Functional similarity between Arabidopsis and wheat ABCF genes was predicted using phylogenetic analysis. A comprehensive genome-wide analysis of gene structure, protein motifs, chromosomal location, and cis-acting elements was also performed. Tissue-specific analysis and expression profiling under temperature, hormonal, and viral stresses were performed using real-time quantitative reverse transcription polymerase chain reaction after randomly selecting one gene from each group. The results revealed that all TaABCF genes had the highest expression at 25 °C and responded to methyl jasmonate induction. Notably, TaABCF2 was highly expressed in all tissues except the roots, and silencing it significantly increased the accumulation of Chinese wheat mosaic virus or wheat yellow mosaic virus in wheat leaves. These results indicated that TaABCF may function in response to viral infection, laying the foundation for further studies on the mechanisms of this protein family in plant defence.

Development of an efficient expression system with large cargo capacity for interrogation of gene function in bamboo based on bamboo mosaic virus

Bamboo is one of the fastest growing plants among monocotyledonous species and is grown extensively in subtropical regions. Although bamboo has high economic value and produces much biomass quickly, gene functional research is hindered by the low efficiency of genetic transformation in this species. We therefore explored the potential of a bamboo mosaic virus (BaMV)-mediated expression system to investigate genotype-phenotype associations. We determined that the sites between the triple gene block proteins (TGBps) and the coat protein (CP) of BaMV are the most efficient insertion sites for the expression of exogenous genes in both monopodial and sympodial bamboo species. Moreover, we validated this system by individually overexpressing the two endogenous genes ACE1 and DEC1, which resulted in the promotion and suppression of internode elongation, respectively. In particular, this system was able to drive the expression of three 2A-linked betalain biosynthesis genes (more than 4 kb in length) to produce betalain, indicating that it has high cargo capacity and may provide the prerequisite basis for the development of a DNA-free bamboo genome editing platform in the future. Since BaMV can infect multiple bamboo species, we anticipate that the system described in this study will greatly contribute to gene function research and further promote the molecular breeding of bamboo.

Genome-wide identification and analysis of wheat LRR-RLK family genes following Chinese wheat mosaic virus infection

BACKGROUND

As the largest plant receptor-like protein kinase (RLK) superfamily, the 21 leucine-rich repeat receptor-like kinases (LRR-RLKs) family are involved in plant 22 growth, development, and stress responses. However, the functions of LRR-RLKs in 23 wheat immunity remain unknown.

RESULTS

In the current study, 929 LRR-RLKs were identified in Triticum aestivum 25 genome database using the BLAST and hidden Markov models (HMM) approach and 26 divided into 14 clades. Chromosomal localization and synteny analysis revealed that 27 TaLRR-RLKs were randomly distributed on all chromosomes with 921 collinear 28 events. Through the cis-acting elements analysis, we observed that TaLRR-RLKs 29 participated in hormone response, light response, development, metabolism, and 30 response to environmental stress. The transcript level of 14 random selected 31 TaLRR-RLKs from each subfamily was regulated by plant hormone treatment and 32 Chinese wheat mosaic virus (CWMV) infection. The function of TaLRR-RLKs in 33 wheat resistance to CWMV infection was further investigated by virus-induced gene 34 silencing assay. Additionally, the accumulation of MeJA response genes, as well as 35 CWMV RNA were not changed in the TaLRR-RLK silencing plants under MeJA 36 treatment.

CONCLUSIONS

Our results demonstrated that TaLRR-RLKs play an important role in 38 wheat resistance to viral infection via hormone signals and lay the groundwork for the 39 functional study of TaLRR-RLKs in wheat.

Coat protein of Chinese wheat mosaic virus upregulates and interacts with cytosolic glyceraldehyde-3-phosphate dehydrogenase, a negative regulator of plant autophagy, to promote virus infection

Autophagy is an intracellular degradation mechanism involved in antiviral defense, but the strategies employed by plant viruses to counteract autophagy-related defense remain unknown for the majority of the viruses. Herein, we describe how the Chinese wheat mosaic virus (CWMV, genus Furovirus) interferes with autophagy and enhances its infection in Nicotiana benthamiana. Yeast two-hybrid screening and in vivo/in vitro assays revealed that the 19 kDa coat protein (CP19K) of CWMV interacts with cytosolic glyceraldehyde-3-phosphate dehydrogenases (GAPCs), negative regulators of autophagy, which bind autophagy-related protein 3 (ATG3), a key factor in autophagy. CP19K also directly interacts with ATG3, possibly leading to the formation of a CP19K-GAPC-ATG3 complex. CP19K-GAPC interaction appeared to intensify CP19K-ATG3 binding. Moreover, CP19K expression upregulated GAPC gene transcripts and reduced autophagic activities. Accordingly, the silencing of GAPC genes in transgenic N. benthamiana reduced CWMV accumulation, whereas CP19K overexpression enhanced it. Overall, our results suggest that CWMV CP19K interferes with autophagy through the promotion and utilization of the GAPC role as a negative regulator of autophagy.

Phosphorylated viral protein evades plant immunity through interfering the function of RNA-binding protein

Successful pathogen infection in plant depends on a proper interaction between the invading pathogen and its host. Post-translational modification (PTM) plays critical role(s) in plant-pathogen interaction. However, how PTM of viral protein regulates plant immunity remains poorly understood. Here, we found that S162 and S165 of Chinese wheat mosaic virus (CWMV) cysteine-rich protein (CRP) are phosphorylated by SAPK7 and play key roles in CWMV infection. Furthermore, the phosphorylation-mimic mutant of CRP (CRP^S162/165D) but not the non-phosphorylatable mutant of CRP (CRP^S162/165A) interacts with RNA-binding protein UBP1-associated protein 2C (TaUBA2C). Silencing of TaUBA2C expression in wheat plants enhanced CWMV infection. In contrast, overexpression of TaUBA2C in wheat plants inhibited CWMV infection. TaUBA2C inhibits CWMV infection through recruiting the pre-mRNA of TaNPR1, TaPR1 and TaRBOHD to induce cell death and H₂O₂ production. This effect can be supressed by CRP^S162/165D through changing TaUBA2C chromatin-bound status and attenuating it’s the RNA- or DNA-binding activities. Taken together, our findings provide new knowledge on how CRP phosphorylation affects CWMV infection as well as the arms race between virus and wheat plants.

Chinese wheat mosaic virus (CWMV) causes a damaging disease in cereal plants. However, CWMV interacts with host factors to facilitate virus infection is not clear yet. Here, we found that S162 and S165 of CWMV cysteine-rich protein (CRP) are phosphorylated by SAPK7 in vivo and in vitro. Mutational analyses have indicated that these two phosphorylation sites of CRP (CRP^S162/165D) promoting CWMV infection in plants, due to the supressed cell death and H₂O₂ production. Further investigations found the CRP^S162/165D can interact with TaUBA2C, while the non-phosphorylatable mutant of CRP (CRP^S162/165A) does not. Futhermore, we have determined that CRP^S162/165D and TaUBA2C interaction inhibited the formation of TaUBA2C speckles in nucleus to attenuate its RNA- and DNA-binding activity. We also showed that TaUBA2C recruit the pre-mRNA of TaNPR1, TaPR1 and TaRBOHD to up-regulated these genes expressions and then induce cell death and H₂O₂ production in plant. This effect can be supressed by the expression of CRP^S162/165D, in a dose-dependent manner. Taken together, our discovery may provide a new sight for the arms race between virus and its host plants.

Binding between elongation factor 1A and the 3'-UTR of Chinese wheat mosaic virus is crucial for virus infection

The Chinese wheat mosaic virus (CWMV) genome consists of two positive-strand RNAs that are required for CWMV replication and translation. The eukaryotic translation elongation factor (eEF1A) is crucial for the elongation of protein translation in eukaryotes. Here, we show that silencing eEF1A expression in Nicotiana benthamiana plants by performing virus-induced gene silencing can greatly reduce the accumulation of CWMV genomic RNAs, whereas overexpression of eEF1A in plants increases the accumulation of CWMV genomic RNAs. In vivo and in vitro assays showed that eEF1A does not interact with CWMV RNA-dependent RNA polymerase. Electrophoretic mobility shift assays revealed that eEF1A can specifically bind to the 3'-untranslated region (UTR) of CWMV genomic RNAs. By performing mutational analyses, we determined that the conserved region in the 3'-UTR of CWMV genomic RNAs is necessary for CWMV replication and translation, and that the sixth stem-loop (SL-6) in the 3'-UTR of CWMV genomic RNAs plays a key role in CWMV infection. We conclude that eEF1A is an essential host factor for CWMV infection. This finding should help us to develop new strategies for managing CWMV infections in host plants.

Temperature modulates virus-induced transcriptional gene silencing via secondary small RNAs

Virus-induced gene silencing (VIGS) can be harnessed to sequence-specifically degrade host transcripts and induce heritable epigenetic modifications referred to as virus-induced post-transcriptional gene silencing (ViPTGS) and virus-induced transcriptional gene silencing (ViTGS), respectively. Both ViPTGS and ViTGS enable manipulation of endogenous gene expression without the need for transgenesis. Although VIGS has been widely used in many plant species, it is not always uniform or highly efficient. The efficiency of VIGS is affected by developmental, physiological and environmental factors. Here, we use recombinant Tobacco rattle viruses (TRV) to study the effect of temperature on ViPTGS and ViTGS using GFP as a reporter gene of silencing in N. benthamiana 16c plants. We found that unlike ViPTGS, ViTGS was impaired at high temperature. Using a novel mismatch-small interfering RNA (siRNA) tool, which precisely distinguishes virus-derived (primary) from target-generated (secondary) siRNAs, we demonstrated that the lack of secondary siRNA production/amplification was responsible for inefficient ViTGS at 29°C. Moreover, inefficient ViTGS at 29°C inhibited the transmission of epigenetic gene silencing to the subsequent generations. Our finding contributes to understanding the impact of environmental conditions on primary and secondary siRNA production and may pave the way to design/optimize ViTGS for transgene-free crop improvement.

Trigger and Suppression of Antiviral Defenses by Grapevine Pinot Gris Virus (GPGV): Novel Insights into Virus-Host Interaction

Grapevine Pinot gris virus (GPGV) is an emerging trichovirus that has been putatively associated with a novel grapevine disease known as grapevine leaf mottling and deformation (GLMD). Yet the role of GPGV in GLMD disease is poorly understood, since it has been detected both in symptomatic and symptomless grapevines. We exploited a recently constructed GPGV infectious clone (pRI::GPGV-vir) to induce an antiviral response in Nicotiana benthamiana plants. In silico prediction of virus-derived small interfering RNAs and gene expression analyses revealed the involvement of DCL4, AGO5, and RDR6 genes during GPGV infection, suggesting the activation of the posttranscriptional gene-silencing (PTGS) pathway as a plant antiviral defense. PTGS suppression assays in transgenic N. benthamiana 16c plants revealed the ability of the GPGV coat protein to suppress RNA silencing. This work provides novel insights on the interaction between GPGV and its host, revealing the ability of the virus to trigger and suppress antiviral RNA silencing.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Comprehensive Proteomic Analysis of Lysine Acetylation in Nicotiana benthamiana After Sensing CWMV Infection

Protein lysine acetylation (Kac) is an important post-translational modification mechanism in eukaryotes that is involved in cellular regulation. To investigate the role of Kac in virus-infected plants, we characterized the lysine acetylome of Nicotiana benthamiana plants with or without a Chinese wheat mosaic virus (CWMV) infection. We identified 4,803 acetylated lysine sites on 1,964 proteins. A comparison of the acetylation levels of the CWMV-infected group with those of the uninfected group revealed that 747 sites were upregulated on 422 proteins, including chloroplast localization proteins and histone H3, and 150 sites were downregulated on 102 proteins. Nineteen conserved motifs were extracted and 51 percent of the acetylated proteins located on chloroplast. Nineteen Kac sites were located on histone proteins, including 10 Kac sites on histone 3. Bioinformatics analysis results indicated that lysine acetylation occurs on a large number of proteins involved in biological processes, especially photosynthesis. Furthermore, we found that the acetylation level of chloroplast proteins, histone 3 and some metabolic pathway-related proteins were significantly higher in CWMV-infected plants than in uninfected plants. In summary, our results reveal the regulatory roles of Kac in response to CWMV infection.

RNA silencing machinery contributes to inability of BSBV to establish infection in Nicotiana benthamiana: evidence from characterization of agroinfectious clones of Beet soil-borne virus

Beet soil-borne virus (BSBV) is a sugar beet pomovirus frequently associated with Beet necrotic yellow veins virus, the causal agent of the rhizomania disease. BSBV has been detected in most of the major beet-growing regions worldwide, yet its impact on this crop remains unclear. With the aim to understand the life cycle of this virus and clarify its putative pathogenicity, agroinfectious clones have been engineered for each segment of its tripartite genome. The biological properties of these clones were then studied on different plant species. Local infection was obtained on agroinfiltrated leaves of Beta macrocarpa. On leaves of Nicotiana benthamiana, similar results were obtained, but only when heterologous viral suppressors of RNA silencing were co-expressed or in a transgenic line down regulated for both dicer-like protein 2 and 4. On sugar beet, local infection following agroinoculation was obtained on cotyledons, but not on other tested plant parts. Nevertheless, leaf symptoms were observed on this host via sap inoculation. Likewise, roots were efficiently mechanically infected, highlighting low frequency of root necrosis and constriction, and enabling the demonstration of transmission by the vector Polymyxa betae. Altogether, the entire viral cycle was reproduced, validating the constructed agroclones as efficient inoculation tools, paving the way for further studies on BSBV and its related pathosystem.

Comparative proteomic analysis of Nicotiana benthamiana plants under Chinese wheat mosaic virus infection

BACKGROUND

Chinese wheat mosaic virus (CWMV) is a severe threat to winter wheat and is transmitted by Polymyxa graminis. The mechanisms of interactions between CWMV and plants are poorly understood. In this study, a comparative proteomics analysis based on nanoliquid chromatography mass spectrometry (MS)/MS was conducted to characterize proteomic changes in plants responding to CWMV infection.

RESULTS

In total, 2751 host proteins were identified, 1496 of which were quantified and 146 up-regulated and 244 down-regulated proteins were identified as differentially expressed proteins (DEPs). Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that DEPs were most strongly associated with photosynthesis antenna proteins, MAPK signaling plant and glyoxylate and dicarboxylate metabolism pathways. Subcellular localization analysis predicted that more than half of the DEPs were localized in the chloroplast, an organelle indispensable for abscisic acid (ABA) synthesis. Our results suggest that CWMV infection interrupts normal chloroplast functions and decreases ABA concentrations in Nicotiana benthamiana. Further analysis showed that the ABA pathway was suppressed during CWMV infection and that ABA treatment induced plant hosts defenses against CWMV.

CONCLUSIONS

We identified several candidate proteins expressed during CWMV infection, and the ABA pathway was strongly associated with responses to CWMV infection in N. benthamiana.

Genome-wide identification of the histone acetyltransferase gene family in Triticum aestivum

Background

Histone acetylation is a ubiquitous and reversible post-translational modification in eukaryotes and prokaryotes that is co-regulated by histone acetyltransferase (HAT) and histone deacetylase (HDAC). HAT activity is important for the modification of chromatin structure in eukaryotic cells, affecting gene transcription and thereby playing a crucial regulatory role in plant development. Comprehensive analyses of HAT genes have been performed in Arabidopsis thaliana, Oryza sativa, barley, grapes, tomato, litchi and Zea mays, but comparable identification and analyses have not been conducted in wheat (Triticum aestivum).

Results

In this study, 31 TaHATs were identified and divided into six groups with conserved gene structures and motif compositions. Phylogenetic analysis was performed to predict functional similarities between Arabidopsis thaliana, Oryza sativa and Triticum aestivum HAT genes. The TaHATs appeared to be regulated by cis-acting elements such as LTR and TC-rich repeats. The qRT–PCR analysis showed that the TaHATs were differentially expressed in multiple tissues. The TaHATs in expression also responded to temperature changes, and were all significantly upregulated after being infected by barley streak mosaic virus (BSMV), Chinese wheat mosaic virus (CWMV) and wheat yellow mosaic virus (WYMV).

Conclusions

These results suggest that TaHATs may have specific roles in the response to viral infection and provide a basis for further study of TaHAT functions in T. aestivum plant immunity.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-020-07348-6.

Effect of RNA silencing suppression activity of chrysanthemum virus B p12 protein on small RNA species

Chrysanthemum virus B encodes a multifunctional p12 protein that acts as a transcriptional activator in the nucleus and as a suppressor of RNA silencing in the cytoplasm. Here, we investigated the impact of p12 on accumulation of major classes of small RNAs (sRNAs). The results show dramatic changes in the sRNA profiles characterised by an overall reduction in sRNA accumulation, changes in the pattern of size distribution of canonical siRNAs and in the ratio between sense and antisense strands, lower abundance of siRNAs with a U residue at the 5'-terminus, and changes in the expression of certain miRNAs, most of which were downregulated.

Molecular characterization of virus-derived small RNAs in Nicotiana benthamiana plants infected with tobacco curly shoot virus and its β satellite

Tobacco curly shoot virus (TbCSV) is a monopartite DNA virus of the genus Begomovirus, which causes leaf curl symptoms in tobacco and tomato. The β satellite of TbCSV (TbCSB induces more severe symptoms and enhanced virus accumulation when co-infects the host plants with TbCSV. Small interfering RNAs derived from virus(vsiRNAs) induce disease symptoms and promote virus invasion by target and guide the degradation of host transcripts The vsiRNAs derived from TbCSV and TbCSV + TbCSB remained to be explored to elucidate the molecular mechanism of symptoms development in plants. In the present work, two libraries of small RNA from TbCSV-infected and TbCSV + TbCSB-infected N. benthamiana plants were constructed and the vsiRNAs in both samples shared the same characteristics. The size of the vsiRNAs ranged from 18 to 30 nucleotides (nt), with most of them being 21 or 22 nt, which accounted for 29.11% and 23.22% in TbCSV plants and 29.39% and 21.82% in TbCSV + TbCSV plants, respectively. The vsiRNAs with A/U bias at the first site were abundant in both the TbCSV-treated and TbCSV + TbCSB-treated plants. It is discovered that the vsiRNAs continuously, but heterogeneously, distributed through bothe the TbCSV and TbCSB sequences. And the distribution profiles were similar in both the treatments such as mainly in the overlapping region of the AC2/AC3 coding sequences. The host transcripts targeted by vsiRNAs were predicted, and the targeted genes were found to be involved in varied biological processes. It is indicated that the presence of TbCSB does not significantly affect the production of vsiRNAs from TbCSV in plants, the distribution hotsopt of TbCSV vsiRNAs could be useful in designing effective targets for TbCSV resistance exploiting RNA interference.

RNA Interference: A Natural Immune System of Plants to Counteract Biotic Stressors

During plant-pathogen interactions, plants have to defend the living transposable elements from pathogens. In response to such elements, plants activate a variety of defense mechanisms to counteract the aggressiveness of biotic stressors. RNA interference (RNAi) is a key biological process in plants to inhibit gene expression both transcriptionally and post-transcriptionally, using three different groups of proteins to resist the virulence of pathogens. However, pathogens trigger an anti-silencing mechanism through the expression of suppressors to block host RNAi. The disruption of the silencing mechanism is a virulence strategy of pathogens to promote infection in the invaded hosts. In this review, we summarize the RNA silencing pathway, anti-silencing suppressors, and counter-defenses of plants to viral, fungal, and bacterial pathogens.

The resistance of sour orange to Citrus tristeza virus is mediated by both the salicylic acid and RNA silencing defence pathways

Citrus tristeza virus (CTV) induces in the field the decline and death of citrus varieties grafted on sour orange (SO) rootstock, which has forced the use of alternative decline-tolerant rootstocks in affected countries, despite the highly desirable agronomic features of the SO rootstock. Declining citrus plants display phloem necrosis below the bud union. In addition, SO is minimally susceptible to CTV compared with other citrus varieties, suggesting partial resistance of SO to CTV. Here, by silencing different citrus genes with a Citrus leaf blotch virus-based vector, we have examined the implication of the RNA silencing and salicylic acid (SA) defence pathways in the resistance of SO to CTV. Silencing of the genes RDR1, NPR1 and DCL2/DCL4, associated with these defence pathways, enhanced virus spread and accumulation in SO plants in comparison with non-silenced controls, whereas silencing of the genes NPR3/NPR4, associated with the hypersensitive response, produced a slight decrease in CTV accumulation and reduced stunting of SO grafted on CTV-infected rough lemon plants. We also found that the CTV RNA silencing suppressors p20 and p23 also suppress the SA signalling defence, with the suppressor activity being higher in the most virulent isolates.

Differential Characteristics of Viral siRNAs between Leaves and Roots of Wheat Plants Naturally Infected with Wheat Yellow Mosaic Virus, a Soil-Borne Virus

RNA silencing is an important innate antiviral defense in plants. Soil-borne plant viruses naturally infect roots via soil-inhabiting vectors, but it is unclear how antiviral RNA silencing responds to virus infection in this particular tissue. In this study, viral small interfering RNA (siRNA) profiles from leaves and roots of wheat plants naturally infected with a soil-borne virus, wheat yellow mosaic virus (WYMV, genus Bymovirus), were analyzed by deep sequencing. WYMV siRNAs were much more abundant in roots than leaves, which was positively correlated with the accumulation of viral RNA. WYMV siRNAs in leaves and roots were predominantly 21- and 22-nt long and equally derived from the positive- and negative-strands of the viral genome. WYMV siRNAs from leaves and roots differed in distribution pattern along the viral genome. Interestingly, compared to siRNAs from leaves (and most other reports), those from roots obviously had a lower A/U bias at the 5'-terminal nucleotide. Moreover, the expression of Dicer-like genes upon WYMV infection were differently regulated between leaves and roots. Our data suggest that RNA silencing in roots may operate differently than in leaves against soil-borne virus invasion.

A furoviral replicase recruits host HSP70 to membranes for viral RNA replication

Many host factors have been identified to be involved in viral infection. However, although furoviruses cause important diseases of cereals worldwide, no host factors have yet been identified that interact with furoviral genes or participate in the viral infection cycle. In this study, both TaHSP70 and NbHSP70 were up-regulated in Chinese wheat mosaic furovirus (CWMV)-infected plants. Their overexpression and inhibition were correlated with the accumulation of viral genomic RNAs, suggesting that the HSP70 genes could be necessary for CWMV infection. The subcellular distributions of TaHSP70 and NbHSP70 were significantly affected by CWMV infection or by infiltration of RNA1 alone. Further assays showed that the viral replicase encoded by CWMV RNA1 interacts with both TaHSP70 and NbHSP70 in vivo and vitro and that its region aa167-333 was responsible for the interaction. Subcellular assays showed that the viral replicase could recruit both TaHSP70 and NbHSP70 from the cytoplasm or nucleus to the granular aggregations or inclusion-like structures on the intracellular membrane system, suggesting that both HSP70s may be recruited into the viral replication complex (VRC) to promote furoviral replication. This is the first host factor identified to be involved in furoviral infection, which extends the list and functional scope of HSP70 chaperones.

Characterization of virus-derived small interfering RNAs in Apple stem grooving virus-infected in vitro-cultured Pyrus pyrifolia shoot tips in response to high temperature treatment

Background

Heat treatment (known as thermotherapy) together with in vitro culture of shoot meristem tips is a commonly used technology to obtain virus-free germplasm for the effective control of virus diseases in fruit trees. RNA silencing as an antiviral defense mechanism has been implicated in this process. To understand if high temperature-mediated acceleration of the host antiviral gene silencing system in the meristem tip facilitates virus-derived small interfering RNAs (vsiRNA) accumulation to reduce the viral RNA titer in the fruit tree meristem tip cells, we used the Apple stem grooving virus (ASGV)–Pyrus pyrifolia pathosystem to explore the possible roles of vsiRNA in thermotherapy.

Results

At first we determined the full-length genome sequence of the ASGV-Js2 isolate and then profiled vsiRNAs in the meristem tip of in vitro-grown pear (cv. ‘Jinshui no. 2’) shoots infected by ASGV-Js2 and cultured at 24 and 37 °C. A total of 7,495 and 7,949 small RNA reads were obtained from the tips of pear shoots cultured at 24 and 37 °C, respectively. Mapping of the vsiRNAs to the ASGV-Js2 genome revealed that they were unevenly distributed along the ASGV-Js2 genome, and that 21- and 22-nt vsiRNAs preferentially accumulated at both temperatures. The 5′-terminal nucleotides of ASGV-specific siRNAs in the tips cultured under different temperatures had a similar distribution pattern, and the nucleotide U was the most frequent. RT-qPCR analyses suggested that viral genome accumulation was drastically compromised at 37 °C compared to 24 °C, which was accompanied with the elevated levels of vsiRNAs at 37 °C. As plant Dicer-like proteins (DCLs), Argonaute proteins (AGOs), and RNA-dependent RNA polymerases (RDRs) are implicated in vsiRNA biogenesis, we also cloned the partial sequences of PpDCL2,4, PpAGO1,2,4 and PpRDR1 genes, and found their expression levels were up-regulated in the ASGV-infected pear shoots at 37 °C.

Conclusions

Collectively, these results showed that upon high temperature treatment, the ASGV-infected meristem shoot tips up-regulated the expression of key genes in the RNA silencing pathway, induced the biogenesis of vsiRNAs and inhibited viral RNA accumulation. This study represents the first report on the characterization of the vsiRNA population in pear plants infected by ASGV-Js2, in response to high temperature treatment.

Electronic supplementary material

The online version of this article (doi:10.1186/s12985-016-0625-0) contains supplementary material, which is available to authorized users.

Interplays between Soil-Borne Plant Viruses and RNA Silencing-Mediated Antiviral Defense in Roots

Although the majority of plant viruses are transmitted by arthropod vectors and invade the host plants through the aerial parts, there is a considerable number of plant viruses that infect roots via soil-inhabiting vectors such as plasmodiophorids, chytrids, and nematodes. These soil-borne viruses belong to diverse families, and many of them cause serious diseases in major crop plants. Thus, roots are important organs for the life cycle of many viruses. Compared to shoots, roots have a distinct metabolism and particular physiological characteristics due to the differences in development, cell composition, gene expression patterns, and surrounding environmental conditions. RNA silencing is an important innate defense mechanism to combat virus infection in plants, but the specific information on the activities and molecular mechanism of RNA silencing-mediated viral defense in root tissue is still limited. In this review, we summarize and discuss the current knowledge regarding RNA silencing aspects of the interactions between soil-borne viruses and host plants. Overall, research evidence suggests that soil-borne viruses have evolved to adapt to the distinct mechanism of antiviral RNA silencing in roots.

Functional identification of two minor capsid proteins from Chinese wheat mosaic virus using its infectious full-length cDNA clones

Full-length cDNA clones of Chinese wheat mosaic virus (CWMV) RNA1 and RNA2 were produced from single reverse transcription PCR reactions and transcripts were shown to be infectious in both wheat and Nicotiana benthamiana. An efficient and reliable agro-infiltration method was then developed for reverse genetic assays in N. benthamiana. Inoculation of infectious cDNA clones resulted in obvious chlorotic symptoms, and CWMV viral genomic RNAs, capsid protein (CP)-related proteins, and typical rod-shaped particles were detectable on the inoculated and upper leaves, similar to those of WT virus. The optimal temperature for virus multiplication was 12 °C, but the optimum for systematic infection in plants was 17 °C. Mutant clones that abolished the N- or C-terminal extensions of the major CP did not inhibit systemic infection or the formation of rod-shaped particles but sometimes modified the symptoms in inoculated plants. These results suggest that the two minor CP-related proteins of CWMV are dispensable for viral infection, replication, systemic movement and virion assembly in plants.

Two amino acids near the N-terminus of Cucumber mosaic virus 2b play critical roles in the suppression of RNA silencing and viral infectivity

Cucumber mosaic virus (CMV) 2b suppresses RNA silencing primarily through the binding of double-stranded RNA (dsRNA) of varying sizes. However, the biologically active form of 2b remains elusive. Here, we demonstrate that the single and double alanine substitution mutants in the N-terminal 15th leucine and 18th methionine of CMV 2b exhibit drastically attenuated virulence in wild-type plants, but are efficiently rescued in mutant plants defective in RNA-dependent RNA polymerase 6 (RDR6) and Dicer-like 4 (DCL4). Moreover, the transgenic plants of 2b, but not 2blm (L15A/M18A), rescue the high infectivity of CMV-Δ2b through the suppression of antiviral silencing. L15A, M18A or both weaken 2b suppressor activity on local and systemic transgene silencing. In contrast with the high affinity of 2b to short and long dsRNAs, 2blm is significantly compromised in 21-bp duplex small interfering RNA (siRNA) binding ability, but maintains a strong affinity for long dsRNAs. In cross-linking assays, 2b can form dimers, tetramers and oligomers after treatment with glutaraldehyde, whereas 2blm only forms dimers, rather than tetramers and oligomers, in vitro. Together, these findings suggest that L15 and M18 of CMV 2b are required for high affinity to ds-siRNAs and oligomerization activity, which are essential for the suppression activity of 2b on antiviral silencing.

Differential contributions of plant Dicer-like proteins to antiviral defences against potato virus X in leaves and roots

Members of the plant Dicer-like (DCL) protein family are the critical components of the RNA-silencing pathway that mediates innate antiviral defence. The distinct antiviral role of each individual DCL protein has been established with mostly based on observations of aerial parts of plants. Thus, although the roots are closely associated with the life cycle of many plant viruses, little is known about the antiviral activities of DCL proteins in roots. We observed that antiviral silencing strongly inhibits potato virus X (PVX) replication in roots of some susceptible Solanaceae species. Silencing of the DCL4 homolog in Nicotiana benthamiana partially elevated PVX replication levels in roots. In Arabidopsis thaliana, which was originally considered a non-host plant of PVX, high levels of PVX accumulation in inoculated leaves were achieved by inactivation of DCL4, while in the upper leaves and roots, it required the additional inactivation of DCL2. In transgenic A. thaliana carrying the PVX amplicon with a green fluorescent protein (GFP) gene insertion in the chromosome (AMP243 line), absence of DCL4 enabled high levels of PVX-GFP accumulation in various aerial organs but not in the roots, suggesting that DCL4 is critical for intracellular antiviral silencing in shoots but not in roots, where it can be functionally compensated by other DCL proteins. Together, the high level of functional redundancies among DCL proteins may contribute to the potent antiviral activities against PVX replication in roots.

Genetic and epigenetic control of plant heat responses

Plants have evolved sophisticated genetic and epigenetic regulatory systems to respond quickly to unfavorable environmental conditions such as heat, cold, drought, and pathogen infections. In particular, heat greatly affects plant growth and development, immunity and circadian rhythm, and poses a serious threat to the global food supply. According to temperatures exposing, heat can be usually classified as warm ambient temperature (about 22-27°C), high temperature (27-30°C) and extremely high temperature (37-42°C, also known as heat stress) for the model plant Arabidopsis thaliana. The genetic mechanisms of plant responses to heat have been well studied, mainly focusing on elevated ambient temperature-mediated morphological acclimation and acceleration of flowering, modulation of circadian clock and plant immunity by high temperatures, and thermotolerance to heat stress. Recently, great progress has been achieved on epigenetic regulation of heat responses, including DNA methylation, histone modifications, histone variants, ATP-dependent chromatin remodeling, histone chaperones, small RNAs, long non-coding RNAs and other undefined epigenetic mechanisms. These epigenetic modifications regulate the expression of heat-responsive genes and function to prevent heat-related damages. This review focuses on recent progresses regarding the genetic and epigenetic control of heat responses in plants, and pays more attention to the role of the major epigenetic mechanisms in plant heat responses. Further research perspectives are also discussed.