Biology subjects

Elena, S. F.

Publications and source records attributed to Elena, S. F..

At least 19 recordsLinked to original sources

bioRxiv2026

Hidden Players: Latent Viruses Can Modulate Plant Disease Outcomes in Coinfection Contexts

Latent viruses are ubiquitous components of plant viromes and are likely the rule rather than the exception in natural host populations. Yet, despite their prevalence, little is known about how they influence the outcome of infections by acute viruses. Here, we used a factorial design to test the effects of two latent secoviruses, apple latent spherical virus (ALSV) and Arabidopsis latent virus 1 (ArLV1), on infections by the acute viruses tobacco rattle virus (TRV) and turnip mosaic virus (TuMV). Coinfections were evaluated across eight Arabidopsis thaliana genotypes, including wild-type and mutants impaired in RNA silencing, DNA methylation and hormone-signaling pathways. Latent-virus effects on both viral accumulation and disease severity were highly dependent on the combination of host and viral genotypes. Hormonal pathways played a prominent role in mediating these interactions, with recurrent responses involving jasmonic acid, salicylic acid and ethylene signaling. ALSV generally attenuated disease severity and acute-virus accumulation, whereas ArLV1 produced both antagonistic and synergistic outcomes depending on host background. Notably, ArLV1 coinfection increased TuMV-induced disease severity in some genotype, an effect never observed with ALSV. These results demonstrate that latent viruses can substantially modify disease expression and viral fitness and highlight the need to account for the pre-existing virome when predicting plant disease outcomes, viral emergence, and epidemiological dynamics.

pathology↗

bioRxiv2026

The hidden diversity: Replication-strand asymmetry shapes short-term nucleotide and structural variation in an RNA virus

Orsay virus (OrV), a positive-sense RNA virus infecting Caenorhabditis elegans, establishes latent infections with minimal impact on host fitness. Using strand-specific RNA-seq across twelve time points spanning larval development, we characterized OrV replication dynamics and short-term evolutionary patterns. Viral accumulation followed four distinct phases and exhibited strong strand asymmetry, consistent with a predominance of the stamping-machine replication mechanism. Diversity analyses revealed that negative-strand genomes harbor more mutations than positive strands, with hotspots concentrated in the replicase C-terminal tail and structural protein regions. Many negative-strand variants failed to propagate to positive strands, suggesting within-cell constraints or purifying selection at the RNA level. We also report the first evidence of non-standard viral genomes in OrV, dominated by deletions in RNA2, including a recurrent large deletion that may function as a subgenomic RNA encoding a shorter version of the {delta} protein. These findings highlight replication asymmetry, strand-specific mutational filtering, and pervasive non-standard genomes as key features shaping OrV evolution during a primary infection.

evolutionary biology↗

bioRxiv2026

Native virion structure reveals stochastic genome assortment underlying dose-dependent Orsay virus infection

Orsay virus (OrV), infecting Caenorhabditis elegans, is a valuable model for studying host-virus interactions, yet its bipartite RNA genome packaging and assembly mechanisms remain unclear. To investigate these mechanisms, we combine infection assays, single-molecule imaging, and cryo-electron microscopy. We find that the two RNA segments accumulate asymmetrically, and that productive infection depends on coinfection by multiple particles. We therefore asked whether unequal segment availability generates heterogeneous virions. Cryo-EM analysis of OrV, including symmetric and asymmetric reconstructions to 2.5 [A] resolution, unveils uniform internal density, excluding large populations of empty or semi-empty particles. We show the genome forms a semi-ordered network contacting the electropositive capsid interior through sequence-independent interactions with the N-terminus and penton region. We also resolve the capsid-8 linker, identifying the penton as a likely site coordinating capsid assembly. Together, we propose a model in which stochastic genome assortment emerges during assembly modulated by segment-specific replication dynamics.

microbiology↗

bioRxiv2026

Simulated microgravity alters short-term evolutionary trajectories of Orsay virus in Caenorhabdidits elegans

BackgroundEnvironmental conditions shape the evolutionary trajectories of RNA viruses, yet little is known about how complex physical stressors such as microgravity influence host-virus interactions and viral evolution. Here, we investigated the short-term evolutionary consequences of simulated microgravity on the Caenorhabditis elegans - Orsay virus (OrV) system. MethodsOrV was subjected to six serial passages in hosts acclimated to low-shear modeled microgravity, with parallel evolution under standard-gravity. Evolutionary outcomes were evaluated using virulence, transmission, and replication traits, all measured under standard-gravity conditions. ResultsViral load fluctuated across passages in both environments, with lower mean accumulation in microgravity-evolved lineages. After evolution, we detected no significant changes in virulence. Transmission increased in standard-gravity lineages but not in microgravity-evolved ones, while viral replication decreased in all lineages, with a stronger decline in those evolved under microgravity. However, the magnitude of phenotypic changes was generally modest. DiscussionThese results indicate that evolution under microgravity can alter viral phenotypic trajectories over short timescales. However, because all traits were assayed under standard-gravity conditions, we cannot directly assess local adaptation to microgravity, and the observed differences may reflect environment-specific trade-offs rather than reduced fitness per se. Furthermore, the limited number of passages and the modest magnitude of phenotypic change suggest that evolutionary responses may still be in an early stage. ConclusionOverall, our findings provide initial evidence that simulated microgravity can influence the evolutionary dynamics of an RNA virus, while highlighting the need for reciprocal fitness assays and longer-term experiments to fully characterize adaptation to altered gravitational environments.

evolutionary biology↗

bioRxiv2026

Species-specific barriers constrict Orsay virus host range across the Caenorhabditis genus

Predicting the host range and spillover potential of RNA viruses requires understanding how ecological, immunological, and evolutionary factors jointly shape viral life cycles across related hosts. Here we integrate population-level viral load dynamics, single-animal heterogeneity, tissue-level progression, transmission competence, and evolutionary sustainability to map the eco evolutionary barriers that Orsay virus encounters across six Caenorhabditis species. We show that host species identity determines the timing and completeness of the viral life cycle, producing species specific combinations of susceptibility, replication kinetics, RNA2 to RNA1 stoichiometric balance, virion egress, and onward transmission. These phenotypes correspond to distinct host competence phenotypes, ranging from permissive (Caenorhabditis elegans) to restrictive or evolutionarily dead end host species. Alternative host species disrupt viral life cycle synchrony through delayed replication, truncated cycles, or failure to produce lumen localized virus, thereby reducing transmission and preventing viral adaptation upon serial passage. Our results demonstrate how temporal mismatches between viral replication and host physiology create a series of eco evolutionary barriers to emergence, offering a mechanistic framework for predicting viral host range.

evolutionary biology↗

bioRxiv2026

Evolution of virulence of a plant RNA virus in age-diverse host populations

Natural host populations are intrinsically age-structured, and developmental stages differ in susceptibility and within-host dynamics, meaning age compositions can impose distinct selective pressure on pathogens. However, how host age structure shapes viral evolution remains largely untested. We experimentally evolved turnip mosaic virus (TuMV) for five passages in Arabidopsis thaliana populations spanning seven demographic regimes (from juvenile-dominated to mature-dominated cohorts). We quantified disease progression, symptom severity and viral load, cross-inoculated evolved lineages across host stages to build quantitative infection matrices, and performed whole-population sequencing at passages 1 and 5 to infer selection coefficients and test for parallelism. Disease traits changed strongly with passage, demography, and their interaction. Disease progression evolved faster in older host populations, whereas severity showed no detectable dependence on median age, implying demographic reweighting of virulence components. Viral load increased through passages and positively correlated with severity, linking within-host fitness to symptoms. Cross-assays revealed a non-nested but modular infection network: juvenile-evolved lineages specialized on pre-bolting plants, whereas lineages from intermediate/older demographies were more stage-generalist. Genomically, both parallel and demography-specific solutions emerged, with a dense cluster of recurrent changes in VPg and several synonymous variants showing consistent or sign-flipping selection across demographies. In conclusion, host age structure is a primary ecological driver of virulence evolution, determining whether viruses evolve faster disease timing versus stronger severity, and whether they specialize or generalize across host stages. These results integrate phenotypes with genome-level responses and suggest that manipulating crop age pyramids could steer virus evolution toward less damaging outcomes.

evolutionary biology↗

bioRxiv2025

Cosmic silence and viral noise: transcriptomic crosstalk in Caenorhabditis elegans under simulated space conditions

Spaceflight environments pose unique physiological challenges due to altered gravity and radia-tion exposure. To investigate how these abiotic stressors interact with viral infection, we analyzed the transcriptomic response of Caenorhabditis elegans acclimated to simulated microgravity ({micro}G) and below-background muon radiation flux (BBR), upon infection with Orsay virus (OrV). Using RNA-seq, we characterized gene expression profiles across single and combined stress condi-tions. Both {micro}G and BBR elicited distinct stress responses, including modulation of oxidative stress, lipid metabolism, and immune pathways. OrV infection alone induced robust transcrip-tional changes, but its impact was significantly attenuated when combined with either abiotic stress, suggesting antagonistic interactions. Notably, proviral genes such as drl-1, fat-7 and hipr-1 were downregulated under BBR and {micro}G, potentially impairing viral replication. Gene ontology analyses revealed enrichment in immune effectors, RNA metabolism, and proteostasis-related pathways, particularly under BBR. Viral load and RNA2/RNA1 ratios were reduced in both stress conditions, indicating a shift in viral replication dynamics. Moreover, genomic diversity and de-fective viral genome formation were differentially affected, with increased genetic diversity and structural variation under stress. These findings suggest that acclimation to off-Earth conditions primes the host for a dampened response to an acute viral infection, potentially through resource reallocation and transcriptional attenuation. This study provides transcriptomic insight into viral infection under space-relevant conditions, highlighting complex stress interactions and their im-plications for host-pathogen dynamics in extraterrestrial environments.

microbiology↗

bioRxiv2025

Multiple origins, one function: evolutionary pathways of HSP70 proteins in viruses

Heat shock proteins 70 (HSP70) are highly conserved molecular chaperones found across all domains of life, where they play essential roles in cellular stress responses. While HSP70 homologs have been previously identified in closteroviruses (ssRNA viruses), their broader presence and evolutionary history in viruses remain poorly understood. In this study, we conducted a comprehensive search of viral protein databases and identified HSP70 homologs in viruses beyond ssRNA, including dsDNA viruses from the classes Megaviricetes and Caudoviricetes. These viral HSP70s exhibit diverse gene organizations, copy numbers, and structural features. Notably, HSP70s from Megaviricetes showed up to three gene copies per genome and distinct structural motifs, while those from closteroviruses displayed higher sequence and structural diversity, suggesting faster evolutionary rates. Structural and phylogenetic analyses revealed two major clusters of viral HSP70s, with dsDNA virus HSP70s closely resembling those of their protist hosts, supporting the hypothesis of horizontal gene transfer. In contrast, ssRNA virus HSP70s formed a distinct, highly divergent group. Our findings suggest multiple independent acquisitions of HSP70 genes by viruses and provide new insights into their evolutionary trajectories and potential functional adaptations.

evolutionary biology↗

bioRxiv2025

The interplay between Caenorhabditis elegans larval development and Orsay virus infection

Caenorhabditis elegans development can be altered by its interactions with pathogens, such as bacteria1,2 or fungi3. However, the impact of viral infections on the nematodes development remains largely unexplored, and conversely, whether molting periods affect viral replication is unknown. Studying infections with Orsay virus (OrV), the only known natural C. elegans virus4, we investigated the role of molting on virus replication dynamics and the impact of OrV infection on C. elegans larval development. We found that OrV replicates during C. elegans molting periods. Indeed, nematodes inoculated near molt initiation exhibited higher OrV viral loads and the virus infected more intestinal cells. Moreover, nematodes inoculated right after hatching accelerated the start of the first molt and lengthened the second larval stage, effectively resynchronizing normal developmental timing. Overall, our work enhances understanding of OrV dynamics in C. elegans and elucidates the interplay between viral infection and nematode development. HIGHLIGHTSO_LIrsay virus replication peaks during molting periods, with larvae acquiring virus later in the first larval stage producing higher viral loads and more widespread intestinal infection than larvae acquiring it right after hatching. C_LIO_LIinfection alters the expression of key developmental regulators, particularly those with oscillatory profiles synchronized with molting cycles (such as let-7, lin-42 and nhr-23). C_LIO_LInematodes display temporal plasticity in development: accelerating the first molt while extending the second larval stage, ultimately resynchronizing their developmental timeline. C_LIO_LIis a bidirectional interaction between Orsay virus infection and C. elegans development: molting appears to transiently weaken antiviral defenses, while host development adapts to infection through temporal plasticity. C_LI

microbiology↗

bioRxiv2025

Host replacement dynamics shape virulence and genome evolution in a plant RNA virus

We have investigated how the dynamics of host replacement affect the evolution of a plant RNA virus. Specifically, we have examined how sudden vs. gradual transitions from more susceptible to less susceptible Arabidopsis thaliana genotypes influence turnip mosaic virus virulence and population genomic diversity. Our results show that the evolution of virulence and the complexity of the mutant swarm is linked to both the type of host succession and the genetic basis of the host resistance. Faster changes in virulence are observed after sudden transitions, with an evolutionary trend towards more severe symptoms that appear later during infection. Gradual transitions resulted in greater population mutational load and higher genetic polymorphism compared to sudden transitions. In contrast, beneficial mutations associated with sudden transitions had stronger fitness effects than those linked to gradual transitions. This research highlights the importance of considering the rate of environmental changes in virus evolution and provides insights into predicting how viruses adapt and evolve in temporally changing environments, with implications for agriculture and public health.

evolutionary biology↗

bioRxiv2024

Genetic shifts in viral populations: how sudden vs gradual changes in host species composition affect the stability and dynamics of genetic variability in viral populations

Sudden and gradual changes in host species composition --transitioning from more permissive to less permissive hosts-- have been shown to influence viral fitness, virulence, and rates of molecular evolution. In this study, we analyzed the roles of stochasticity and selection using previously published time-series data from evolving populations of Sindbis virus under different rates of host replacement. First, an approximate Markov model within the Wright-Fisher diffusion framework revealed a reduction in effective population size by approximately half in scenarios involving sudden host changes. These scenarios were also associated with fewer and generally weaker beneficial mutations. Second, genetic distance analysis between populations at consecutive time points indicated that populations undergoing gradual host changes evolved steadily until the original host was no longer present. Distances to the ancestral sequence in these cases exhibited occasional leapfrog phenomena, where the rise of certain haplotypes is not predictable based solely on their relatedness to previously dominant ones. In contrast, populations exposed to sudden host changes displayed less stable compositions and diverged from the ancestral sequence at a more constant rate. Third, we observed that allele frequencies distribution followed a power law consistent with Taylors law. Both treatments exhibited high levels of allele aggregation with significant fluctuations, where neutral, beneficial, and deleterious alleles could be distinguished by their general behavior and their position on Taylors plot. Finally, we found evidence that the host replacement regime influences the temporal distribution of mutations across the genome.

evolutionary biology↗

bioRxiv2024

Chronic infection of Caenorhabditis elegans by Orsay virus induces age-dependent immunity and superinfection exclusion

Orsay virus (OrV) is a natural pathogen of C. elegans, which mounts an antiviral response upon infection and enables the investigation of the mechanisms governing infection and immunity. Here, we focus on two of these features, namely the effect of life-long infections and superinfection dynamics. By following the course of an infection throughout the lifespan of a synchronous wild-type population, we describe several viral load peaks followed by sharp decreases in viral load, suggesting that the infection is chronic and that animals manage to suppress viral replication successfully throughout most of their lives. Moreover, we show that animals that have been previously exposed to the virus are able to control viral replication upon a subsequent inoculation, indicative of superinfection exclusion. Primary infections produced transcriptomic and small RNA alterations, whose extent was highly dependent on the developmental stage of the worm at the time of infection and the time until sampling. Superinfection, in turn, had little impact on the overall transcriptome, but showed a misregulation of piRNAs, rRNAs, and tsRNAs. Superinfection exclusion was robust throughout larval development and adulthood, providing protection against various OrV isolates. However, the protective effect of the initial infection diminished over time, suggesting different mechanisms of action and ultimately favoring the primary infecting virus. This phenomenon was dependent on a functional RNA interference pathway.

genomics↗

bioRxiv2024

Microgravity and low muon radiation affect viral pathogenesis and physiology in Caenorhabditis elegans

Environmental conditions fundamentally shape host-pathogen interactions, yet how multiple extreme abiotic stressors combine to influence infection outcomes remains poorly understood. Organisms evolved under specific gravitational and radiation regimes; deviations from these conditions --whether in extreme terrestrial environments or beyond Earth-- may alter immune function and pathogen replication. In this study, we investigated the effects of reduced gravity and lowered muon flux on Orsay virus infection in the nematode Caenorhabditis elegans. We employed a fully factorial experimental design, examining how each factor, alone and in combination, influences physiological traits and viral load. While below-background radiation radically affected viral accumulation dynamics, reduced gravity had a minor effect. Both factors significantly impacted reproduction and morphology, with some effects magnified by viral infection. These results reveal how even partial modifications of Earth-like gravity and radiation levels can alter pathogen-host interactions. By integrating experimental observations with mathematical modeling, we show that these environmental stressors primarily affect prezygotic reproductive processes and modulate viral replication through distinct and sometimes antagonistic mechanisms. Although this work does not encompass the full complexity of space environments, where cosmic radiation includes high-energy protons and heavy ions, it provides insight into how adjustable models of reduced gravity and radiation can advance our understanding of biological adaptation beyond standard terrestrial conditions. IMPORTANCEUnderstanding how extreme environmental conditions affect host-pathogen interactions is critical both for safeguarding biological systems during spaceflight and for exploring fundamental principles of stress biology. This study demonstrates that reduced gravity and diminished muon radiation flux can significantly alter viral infection dynamics and host physiology in Caenorhabditis elegans. By integrating experimental data with mathematical modeling, we reveal that these abiotic stresses impact prezygotic reproductive processes and modulate viral replication in distinct and sometimes antagonistic ways. Our findings suggest that even partial deviations from Earth-like conditions can reshape infection outcomes and developmental trajectories, highlighting the need for deeper mechanistic insights into biological adaptation beyond terrestrial norms. These results have implications for space biosciences, evolutionary virology, radiation hormesis theory, and the design of countermeasures to preserve organismal health in extreme or non-terrestrial habitats.

microbiology↗

bioRxiv2024

Quantifying defective and wild-type viruses from high-throughput RNA sequencing

Defective viral genomes (DVGs) are variants of the wild-type (wt) virus that lack the ability to complete an infectious cycle independently. However, in the presence of their parental (helper) wt virus, DVGs can interfere with the replication, encapsidation, and spread of functional genomes, acting as a significant selective force in viral evolution. DVGs also affect the hosts immune responses and are linked to chronic infections and milder symptoms. Thus, identifying and characterizing DVGs is crucial for understanding infection prognosis. Quantifying DVGs is challenging due to their inability to sustain themselves, which makes it difficult to distinguish them from the helper virus, especially using high-throughput RNA sequencing (RNA-seq). Accurate quantification is essential for understanding their interactions with their helper virus. We present a method to simultaneously estimate the abundances of DVGs and wt genomes within a sample by identifying genomic regions with significant deviations from the expected sequencing depth. Our approach involves reconstructing the depth profile through a linear system of equations, which provides an estimate of the number of wt and DVG genomes of each type. Until now, in silico methods have only estimated the DVG-to-wt ratio for localized genomic regions. This is the first method that simultaneously estimates the proportions of wt and DVGs across RNA sequencing of the whole genome. Availability and implementationThe MO_SCPLOWATLABC_SCPLOW code and the synthetic datasets are freely available at https://github.com/jmusan/wtDVGquantific.

bioinformatics↗

bioRxiv2024

Transcriptomic Insights into the Epigenetic Modulation of Turnip Mosaic Virus Evolution in Arabidopsis thaliana

Plant-virus interaction models propose that a viruss ability to infect a host genotype depends on the compatibility between virulence and resistance genes. Recently, we conducted an evolution experiment in which lineages of turnip mosaic virus (TuMV) were passaged in Arabidopsis thaliana genotypes carrying mutations in components of the DNA methylation and the histone demethylation epigenetic pathways. All evolved lineages increased infectivity, virulence and viral load in a host genotype-dependent manner. To better understand the underlying reasons for these evolved relationships, we delved into the transcriptomic responses of mutant and WT plant genotypes in mock conditions and infected with either the ancestral or evolved viruses. Such a comparison allowed us to classify every gene into nine basic expression profiles. Regarding the targets of viral adaptation, our analyses allowed the identification of common viral targets as well as host genotype-specific genes and categories of biological processes. As expected, immune response-related genes were found to be altered upon infection. However, we also noticed the pervasive over-representation of other functional groups, suggesting that viral adaptation was not solely driven by the level of expression of plant resistance genes. In addition, a significant association between the presence of transposable elements within or upstream the differentially expressed genes was observed. Finally, integration of transcriptomic data into a virus-host protein-protein interaction network highlighted the most impactful interactions. These findings shed extra light on the complex dynamics between plants and viruses, indicating that viral infectivity depends on various factors beyond just the plants resistance genes.

evolutionary biology↗

bioRxiv2024

System and transcript dynamics of cells infected with severe acute respiratory syndrome virus 2 (SARS-CoV-2)

Statistical laws arise in many complex systems and can be explored to gain insights into their structure and behavior. Here, we investigate the dynamics of cells infected with severe acute respiratory syndrome virus 2 (SARS-CoV-2) at the system and individual gene levels; and demonstrate that the statistical frameworks used here are robust in spite of the technical noise associated with single-cell RNA sequencing (scRNA-seq) data. A biphasic fit to Taylors power law was observed, and it is likely associated with the larger sampling noise inherent to the measure of less expressed genes. The type of the distribution of the system, as assessed by Taylors parameters, varies along the course of infection in a cell type-dependent manner, but also sampling noise had a significant influence on Taylors parameters. At the individual gene level, we found that genes that displayed signals of punctual rank stability and/or long-range dependence behavior, as measured by Hurst exponents, were associated with translation, cellular respiration, apoptosis, protein-folding, virus processes, and immune response. Author summaryViruses replicate within susceptible cells by exploiting the cellular machinery. Consequently, cells initiate defenses against the virus and signal other cells, notably immune cells. This ongoing battle prompts significant alterations in the cells gene expression patterns throughout the infection process. In this study, we apply statistical principles from complex systems theory to analyze gene expression data from individual cells infected with SARS-CoV-2. Our research aims to elucidate how viral infection impacts cells at both systemic and individual gene levels. Our primary findings are twofold: (i) the virus influences the distribution of gene transcripts over the course of infection, varying depending on cell type. (ii) As the infection progresses, numerous genes associated with critical cellular functions and immunity exhibit signs of punctual instability and/or autocorrelation, indicating their response to viral infection at various stages of the process.

systems biology↗

bioRxiv2024

Experimental evolution of an RNA virus in Caenorhabditis elegans

The discovery of Orsay virus (OrV), the first virus infecting wild populations of Caenorhabditis elegans, has boosted studies of viral immunity pathways in this nematode. Considering the many advantages that C. elegans offers for fundamental research in host-pathogen interactions, this pathosystem has high potential to become a model system for experimental virus evolution studies. However, the evolutionary constraints operating in this pathosystem have barely been explored. Here we describe for the first time an evolution experiment of two different OrV strains in C. elegans. After 10 serial passages of evolution, we report slight changes in infectivity and non-synonymous mutations fixed in the evolved viral populations. In addition, we observed numerous minor variants emerging in the viral population. These minor variants were not randomly distributed along the genome but concentrated in polymorphic genomic regions. Overall, our work established the grounds for future experimental virus evolution studies using Caenorhabditis nematodes. HIGHLIGHTSO_LICaenorhabditis elegans-Orsay virus is a convenient pathosystem to study virus evolution. C_LIO_LIThe approach used to test the viral strains may interfere with the infection phenotypes observed. C_LIO_LIThere may be specific genomic hotspots regions of nucleotide diversity important for the evolution of Orsay virus. C_LIO_LIThe substitution rate observed for Orsay virus was low, suggesting that the two strains studied might be already well adapted to laboratory conditions. C_LI

evolutionary biology↗

bioRxiv2024

Adaptation of turnip mosaic virus to Arabidopsis thaliana involves rewiring of VPg - host proteome interactions

The outcome of a viral infection depends on a complex interplay between the host physiology and the virus, mediated through numerous protein-protein interactions. In a previous study we used high-throughput yeast two-hybrid (HT-Y2H) to identify proteins in Arabidopsis thaliana that bind to the proteins encoded by the turnip mosaic virus (TuMV) genome. Furthermore, after experimental evolution of TuMV lineages in plants with mutations in defense-related or proviral genes, most mutations observed in the evolved viruses affected the VPg cistron. Among these mutations, D113G was a convergent mutation selected in many lineages across different plant genotypes. In contrast, mutation R118H specifically emerged in the jin1 mutant with affected jasmonate signaling. Using the HT-Y2H system, we analyzed the impact of these two mutations on VPgs interaction with plant proteins. Interestingly, both mutations severely compromised the interaction of VPg with the translation initiation factor eIF(iso)4E, a crucial interactor for potyvirus infection. Moreover, mutation D113G, but not R118H, adversely affected the interaction with RHD1, a zinc-finger homeodomain transcription factor involved in regulating DNA demethylation. Our results suggest that RHD1 enhances plant tolerance to TuMV infection.

evolutionary biology↗