Determinants of Persistent Patterns of Pepino Mosaic Virus Mixed Infections

Characterization of Two Aggressive PepMV Isolates Useful in Breeding Programs

Pepino mosaic virus (PepMV) causes significant economic losses in tomato crops worldwide. Since its first detection infecting tomato in 1999, aggressive PepMV variants have emerged. This study aimed to characterize two aggressive PepMV isolates, PepMV-H30 and PepMV-KLP2. Both isolates were identified in South-Eastern Spain infecting tomato plants, which showed severe symptoms, including bright yellow mosaics. Full-length infectious clones were generated, and phylogenetic relationships were inferred using their nucleotide sequences and another 35 full-length sequences from isolates representing the five known PepMV strains. Our analysis revealed that PepMV-H30 and PepMV-KLP2 belong to the EU and CH2 strains, respectively. Amino acid sequence comparisons between these and mild isolates identified 8 and 15 amino acid substitutions for PepMV-H30 and PepMV-KLP2, respectively, potentially involved in severe symptom induction. None of the substitutions identified in PepMV-H30 have previously been described as symptom determinants. The E236K substitution, originally present in the PepMV-H30 CP, was introduced into a mild PepMV-EU isolate, resulting in a virus that causes symptoms similar to those induced by the parental PepMV-H30 in Nicotiana benthamiana plants. In silico analyses revealed that this residue is located at the C-terminus of the CP and is solvent-accessible, suggesting its potential involvement in CP-host protein interactions. We also examined the subcellular localization of PepGFPm2E236K in comparison to that of PepGFPm2, focusing on chloroplast affection, but no differences were observed in the GFP subcellular distribution between the two viruses in epidermal cells of N. benthamiana plants. Due to the easily visible symptoms that PepMV-H30 and PepMV-KLP2 induce, these isolates represent valuable tools in programs designed to breed resistance to PepMV in tomato.

A subset of highly responsive transcription factors upon tomato infection by pepino mosaic virus

Plants have evolved well-tuned surveillance systems, including complex defence mechanisms, to constrain pathogens. TFs are master regulators of host molecular responses against plant pathogens. While PepMV constitutes a major threat to the global tomato production, there is still a lack of information on the key TFs that regulate host responses to this virus. A combinatorial research approach was applied relying on tomato transcriptome analysis, RT-qPCR validation, phylogenetic classification, comparative analysis of structural features, cis-regulatory element mining and in silico co-expression analysis to identify a set of 11 highly responsive TFs involved in the regulation of host responses to PepMV. An endemic PepMV isolate, generating typical mosaic symptoms, modified expression of ca. 3.3% of tomato genes, resulting in 1,120 DEGs. Functional classification of 502 upregulated DEGs revealed that photosynthesis, carbon fixation and gene silencing were widely affected, whereas 618 downregulated genes had an impact mainly on plant defence and carotenoid biosynthesis. Strikingly, all 11 highly responsive TFs carried abiotic stress response cis-regulatory elements, whereas five of them were better aligned with rice than with Arabidopsis gene homologues, suggesting that plant responses against viruses may predate divergence into monocots and dicots. Interestingly, tomato C2H2 family TFs, ZAT1-like and ZF2, may have distinct roles in plant defence due to opposite response patterns, similar to their Arabidopsis ZAT10 and ZAT12 homologues. These highly responsive TFs provide a basis to study in-depth molecular responses of the tomato-PepMV pathosystem, providing a perspective to better comprehend viral infections.

Plant Virus Adaptation to New Hosts: A Multi-scale Approach

Viruses are studied at each level of biological complexity: from within-cells to ecosystems. The same basic evolutionary forces and principles operate at each level: mutation and recombination, selection, genetic drift, migration, and adaptive trade-offs. Great efforts have been put into understanding each level in great detail, hoping to predict the dynamics of viral population, prevent virus emergence, and manage their spread and virulence. Unfortunately, we are still far from this. To achieve these ambitious goals, we advocate for an integrative perspective of virus evolution. Focusing in plant viruses, we illustrate the pervasiveness of the above-mentioned principles. Beginning at the within-cell level, we describe replication modes, infection bottlenecks, and cellular contagion rates. Next, we move up to the colonization of distal tissues, discussing the fundamental role of random events. Then, we jump beyond the individual host and discuss the link between transmission mode and virulence. Finally, at the community level, we discuss properties of virus-plant infection networks. To close this review we propose the multilayer network theory, in which elements at different layers are connected and submit to their own dynamics that feed across layers, resulting in new emerging properties, as a way to integrate information from the different levels.

Transcriptome analyses unveiled differential regulation of AGO and DCL genes by pepino mosaic virus strains

Pepino mosaic virus (PepMV) is a single-stranded (ss), positive-sense (+) RNA potexvirus that affects tomato crops worldwide. We have described an in planta antagonistic interaction between PepMV isolates of two strains in which the EU isolate represses the accumulation of the CH2 isolate during mixed infections. Reports describing transcriptomic responses to mixed infections are scant. We carried out transcriptomic analyses of tomato plants singly and mixed-infected with two PepMV isolates of both strains. Comparison of the transcriptomes of singly infected plants showed that deeper transcriptomic alterations occurred at early infection times, and also that each of the viral strains modulated the host transcriptome differentially. Mixed infections caused transcriptomic alterations similar to those for the sum of single infections at early infection times, but clearly differing at later times postinfection. We next tested the hypothesis that PepMV-EU, in either single or mixed infections, deregulates host gene expression differentially so that virus accumulation of both strains gets repressed. That seemed to be the case for the genes AGO1a, DCL2d, AGO2a, and DCL2b, which are involved in the antiviral silencing pathway and were upregulated by PepMV-EU but not by PepMV-CH2 at early times postinfection. The pattern of AGO2a expression was validated by reverse transcription-quantitative PCR in tomato and Nicotiana benthamiana plants. Using an N. benthamiana ago2 mutant line, we showed that AGO2 indeed plays an important role in the antiviral defence against PepMV, but it is not the primary determinant of the outcome of the antagonistic interaction between the two PepMV strains.