The C2 protein of tomato leaf curl Taiwan virus is a pathogenicity determinant that interferes with expression of host genes encoding chromomethylases

DNA methylation dynamics in response to abiotic and pathogen stress in plants

DNA methylation is a dynamic epigenetic mechanism that plays a significant role in gene expression and also maintains chromatin stability. The process is conserved in both plants and animals, and crucial for development and stress responses. Differential DNA methylation during adverse environmental conditions or pathogen attack facilitates the selective expression of defense-related genes. Both stress-induced DNA hypomethylation and hypermethylation play beneficial roles in activating the defense response. These DNA marks may be carried to the next generation making the progenies 'primed' for abiotic and biotic stress responses. Over the recent years, rapid advancements in the area of high throughput sequencing have enabled the detection of methylation status at genome levels in several plant species. Epigenotyping offers an alternative tool to plant breeders in addition to conventional markers for the selection of the desired offspring. In this review, we briefly discuss the mechanism of DNA methylation, recent understanding of DNA methylation-mediated gene regulation during abiotic and biotic stress responses, and stress memory in plants.

Combinatorial interactions between viral proteins expand the potential functional landscape of the tomato yellow leaf curl virus proteome

Viruses manipulate the cells they infect in order to replicate and spread. Due to strict size restrictions, viral genomes have reduced genetic space; how the action of the limited number of viral proteins results in the cell reprogramming observed during the infection is a long-standing question. Here, we explore the hypothesis that combinatorial interactions may expand the functional landscape of the viral proteome. We show that the proteins encoded by a plant-infecting DNA virus, the geminivirus tomato yellow leaf curl virus (TYLCV), physically associate with one another in an intricate network, as detected by a number of protein-protein interaction techniques. Importantly, our results indicate that intra-viral protein-protein interactions can modify the subcellular localization of the proteins involved. Using one particular pairwise interaction, that between the virus-encoded C2 and CP proteins, as proof-of-concept, we demonstrate that the combination of viral proteins leads to novel transcriptional effects on the host cell. Taken together, our results underscore the importance of studying viral protein function in the context of the infection. We propose a model in which viral proteins might have evolved to extensively interact with other elements within the viral proteome, enlarging the potential functional landscape available to the pathogen.

Viruses are obligate intracellular parasites that depend on the molecular machinery of their host cell to complete their life cycle. For this purpose, viruses co-opt host processes, modulating or redirecting them. Most viruses have small genomes, and hence limited coding capacity. During the viral invasion, virus-encoded proteins will be produced in large amounts and coexist in the infected cell, which enables physical or functional interactions among viral proteins, potentially expanding the virus-host functional interface by increasing the number of potential targets in the host cell and/or synergistically modulating the cellular environment. Examples of interactions between viral proteins have been recently documented for both animal and plant viruses; however, the hypothesis that viral proteins might have a combinatorial effect, which would lead to the acquisition of novel functions, lacks systematic experimental validation. Here, we use the geminivirus tomato yellow leaf curl virus (TYLCV), a plant-infecting virus with reduced proteome and causing devastating diseases in crops, to test the idea that combinatorial interactions between viral proteins exist and might underlie an expansion of the functional landscape of the viral proteome. Our results indicate that viral proteins prevalently interact with one another in the context of the infection, which can result in the acquisition of novel functions.

Disruption of tomato TGS machinery by ToLCNDV causes reprogramming of vascular tissue-specific TORNADO1 gene expression

Vascular development-related TRN1 transcription is suppressed by cytosine methylation in fully developed leaves of tomato. ToLCNDV infection disrupts methylation machinery and reactivates TRN1 expression - likely causing abnormal leaf growth pattern. Leaf curl disease of tomato caused by tomato leaf curl New Delhi virus (ToLCNDV) inflicts huge economical loss. Disease symptoms resemble leaf developmental defects including abnormal vein architecture. Leaf vein patterning-related TORNADO1 gene's (SlTRN1) transcript level is augmented in virus-infected leaves. To elucidate the molecular mechanism of the upregulation of SlTRN1 in vivo, we have deployed SlTRN1 promoter-reporter transgenic tomato plants and investigated the gene's dynamic expression pattern in leaf growth stages and infection. Expression of the gene was delimited in the vascular tissues and suppressed in fully developed leaves. WRKY16 transcription factor readily activated SlTRN1 promoter in varied sized leaves and upon virus infection, while silencing of WRKY16 gene resulted in dampened promoter activity. Methylation-sensitive PCR analyses confirmed the accumulation of CHH methylation at multiple locations in the SlTRN1 promoter in older leaves. However, ToLCNDV infection reverses the methylation status and restores expression level in the leaf vascular bundle. The virus dampens the level of key maintenance and de novo DNA methyltransferases SlDRM5, SlMET1, SlCMT2 with concomitant augmentation of two DNA demethylases, SlDML1 and SlDML2 levels in SlTRN1 promoter-reporter transgenics. Transient overexpression of SlDML2 mimics the virus-induced hypomethylation state of the SlTRN1 promoter in mature leaves, while silencing of SlDML2 lessens promoter activity. Furthermore, in line with the previous studies, we confirm the crucial role of viral suppressors of RNA silencing AC2 and AC4 proteins in promoting DNA demethylation and directing it to restore activated transcription of SlTRN1. Unusually elevated expression of SlTRN1 may negatively impact normal growth of leaves.

Insights into the multifunctional roles of geminivirus-encoded proteins in pathogenesis

Geminiviruses are a major threat to agriculture in tropical and subtropical regions of the world. Geminiviruses have small genome with limited coding capacity. Despite this limitation, these viruses have mastered hijacking the host cellular metabolism for their survival. To compensate for the small size of their genome, geminiviruses encode multifunctional proteins. In addition, geminiviruses associate themselves with satellite DNA molecules which also encode proteins that support the virus in establishing successful infection. Geminiviral proteins recruit multiple host factors, suppress the host defense, and manipulate host metabolism to establish infection. We have updated the knowledge accumulated about the proteins of geminiviruses and their satellites in the context of pathogenesis in a single review. We also discuss their interactions with host factors to provide a mechanistic understanding of the infection process.

The interplay of plant hormonal pathways and geminiviral proteins: partners in disease development

Viruses belonging to the family Geminiviridae infect plants and are responsible for a number of diseases of crops in the tropical and sub-tropical regions of the World. The innate immune response of the plant assists in its defense against such viral pathogens by the recognition of pathogen/microbe-associated molecular patterns through pattern-recognition receptors. Phytohormone signalling pathways play a vital role in plant defense responses against these devastating viruses. Geminiviruses, however, have developed counter-defense strategies that prevail over the above defense pathways. The proteins encoded by geminiviruses act as suppressors of plant immunity by interacting with the signalling components of several hormones. In this review we focus on the molecular interplay of phytohormone pathways and geminiviral infection and try to find interesting parallels with similar mechanisms known in other plant-infecting viruses and strengthen the argument that this interplay is necessary for disease development.

Epigenetic regulation of geminivirus pathogenesis: a case of relentless recalibration of defence responses in plants

Geminiviruses constitute one of the largest families of plant viruses and they infect many economically important crops. The proteins encoded by the single-stranded DNA genome of these viruses interact with a wide range of host proteins to cause global dysregulation of cellular processes and help establish infection in the host. Geminiviruses have evolved numerous mechanisms to exploit host epigenetic processes to ensure the replication and survival of the viral genome. Here, we review our current knowledge of diverse epigenetic processes that have been implicated in the regulation of geminivirus pathogenesis, including DNA methylation, histone post-transcriptional modification, chromatin remodelling, and nucleosome repositioning. In addition, we discuss the currently limited evidence of host epigenetic defence responses that are aimed at counteracting geminivirus infection, and the potential for exploiting these responses for the generation of resistance against geminiviruses in crop species.

A virus-encoded protein suppresses methylation of the viral genome through its interaction with AGO4 in the Cajal body

In plants, establishment of de novo DNA methylation is regulated by the RNA-directed DNA methylation (RdDM) pathway. RdDM machinery is known to concentrate in the Cajal body, but the biological significance of this localization has remained elusive. Here, we show that the antiviral methylation of the Tomato yellow leaf curl virus (TYLCV) genome requires the Cajal body in Nicotiana benthamiana cells. Methylation of the viral genome is countered by a virus-encoded protein, V2, which interacts with the central RdDM component AGO4, interfering with its binding to the viral DNA; Cajal body localization of the V2-AGO4 interaction is necessary for the viral protein to exert this function. Taken together, our results draw a long sought-after functional connection between RdDM, the Cajal body, and antiviral DNA methylation, paving the way for a deeper understanding of DNA methylation and antiviral defences in plants.

Molecular Characterization and Genomic Function of Grapevine Geminivirus A

A new grapevine geminivirus A (GGVA) isolate (named as GGVA-17YM1) and its associated defective genome (GGVA-D) were identified from a grapevine sample collected in Yuanmou, Yunnan Province, using sRNA high throughput sequencing and traditional Sanger sequencing. To explore the pathogenicity of GGVA and GGVA-D, infectious clones of GGVA-17YM1 and GGVA-D-17YM1 were constructed. Infection assays indicated that Nicotiana benthamiana plants inoculated with GGVA alone or a combination of GGVA and GGVA-D exhibited upward curled apical leaves and dwarfism. Southern blotting and quantitative real-time polymerase chain reaction analysis revealed that GGVA-D increased the accumulation level of GGVA DNA. Transient expression using a PVX-derived recombinant vector indicated that C2 and C4 encoded by GGVA are involved in symptom induction in N. benthamiana. Furthermore, the V2 protein inhibited local RNA silencing in co-infiltration assays in GFP transgenic N. benthamiana plants. Subsequently, full-length genome sequencing resulted in the identification of 11 different isolates of GGVA and 9 associated defective DNA molecules. Phylogenetic analysis based on whole genome sequences showed that all GGVA isolates, including our sequences, clustered into two distinct branches with no geographical grouping. Analyses of molecular variation indicated single nucleotide polymorphisms (SNPs) with more transitions (55.97%) than transversions (44.03%). Furthermore, the main variants for ORF C1, C3, or V1 were synonymous mutations, and non-synonymous mutations for ORF C2, C4, and V2. Genetic selection analysis indicated that negative selection acted on four ORFs (V1, C1, C2, and C3), while V2 and C4 were under positive selection. Our results contribute to the characterization of the genetic diversity of GGVA and provide insights into its pathogenicity.

Epigenetics in the plant-virus interaction

Plants have developed diverse molecular mechanisms to resist viruses. RNA silencing plays a dominant role in antiviral defense. Recent studies have correlated plant antiviral silencing to epigenetic modification in genomic DNA and protein by remodeling the expression levels of coding genes. The plant host methylation level is reprogrammed in response to viral challenge. Genomes of some viruses have been implicated in the epigenetic modification via small RNA-mediated transcriptional gene silencing and post-transcriptional gene silencing. These mechanisms can be primed prior to a virus attack through methylation changes for antiviral defense. This review highlights the findings concerning the methylation changes in plant-virus interactions and demonstrates a possible direction to improve the understanding of plant host methylation regulation in response to viral infection.

Silencing of NbCMT3s has Pleiotropic Effects on Development by Interfering with Autophagy-Related Genes in Nicotiana benthamiana

DNA methylation is a chromatin mark that has a crucial role in regulating gene expression. The chromomethylase (CMT) protein family is a plant-specific DNA methyltransferase that mediates growth and development. However, the roles of CMT3 in autophagy remain to be elucidated. Here, we identified the potential targets of CMT3 in Nicotiana benthamiana (NbCMT3) during developmental programs. Virus-induced gene silencing of NbCMT3/3-2 in N. benthamiana had pleiotropic effects on plant morphology, which indicates its indispensible role in development. Genome-wide transcriptome analysis of NbCMT3/3-2-silenced plants revealed interference with genes related to autophagy and ubiquitination. The expression of NbBeclin 1 and NbHRD1B was higher in NbCMT3/3-2-silenced than control plants. The formation of autophagosomes and starch degradation was disrupted in NbCMT3/3-2-silenced plants, which implies a perturbed autophagic processes. We further generated transgenic N. benthamiana plants carrying a chimeric promoter-reporter construct linking the NbBeclin 1 promoter region and β-glucuronidase (GUS) reporter (pNbBeclin::GUS). NbBeclin 1 promoter activity was significantly enhanced in NbCMT3/3-2-silenced plants. Thus, NbCMT3/3-2 silencing had pleiotropic effects on development by interfering with NbBeclin 1 expression and autophagy-related processes.