Biology subjects

Olmo-Uceda, M. J.

Publications and source records attributed to Olmo-Uceda, M. J..

6 recordsLinked to original sources

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

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

Accumulation dynamics of defective genomes during experimental evolution of two betacoronaviruses

Virus-encoded replicases often generate aberrant RNA genomes, known as defective viral genomes (DVGs). When coinfected with a helper virus providing necessary proteins, DVGs can multiply and spread. While DVGs depend on the helper virus for propagation, they can disrupt infectious virus replication, impact immune responses, and affect viral persistence or evolution. Understanding the dynamics of DVGs alongside standard viral genomes during infection remains unclear. To address this, we conducted a long-term experimental evolution of two betacoronaviruses, the human coronavirus OC43 (HCoV-OC43) and the murine hepatitis virus (MHV), in cell culture at both high and low multiplicities of infection (MOI). We then performed RNA-seq at regular time intervals, reconstructed DVGs, and analyzed their accumulation dynamics. Our findings indicate that DVGs evolved to exhibit greater diversity and abundance, with deletions and insertions being the most common types. Notably, some high MOI deletions showed very limited temporary existence, while others became prevalent over time. We observed differences in DVG abundance between high and low MOI conditions in HCoV-OC43 samples. The size distribution of HCoV-OC43 genomes with deletions differed between high and low MOI passages. In low MOI lineages, short and long DVGs were most common, with an additional cluster in high MOI lineages which became more prevalent along evolutionary time. MHV also showed variations in DVG size distribution at different MOI conditions, though less pronounced compared to HCoV-OC43, suggesting a more random distribution of DVG sizes. We identified hotspot regions for deletions that evolved at high MOI, primarily within cistrons encoding structural and accessory proteins. In conclusion, our study illustrates the widespread formation of DVGs during betacoronavirus evolution, influenced by MOI and cell- and virus-specific factors.

evolutionary biology↗

bioRxiv2023

Story of an infection: viral dynamics and host responses in the Caenorhabditis elegans-Orsay virus pathosystem

Orsay virus (OrV) is the only known natural virus affecting Caenorhabditis elegans, with minimal impact on the worms fitness due to its robust innate immune response. This study aimed to understand the interactions between C. elegans and OrV by tracking the infections progression during larval development. Four distinct stages of infection were identified based on viral load, with a peak in capsid- encoding RNA2 coinciding with the first signs of viral egression. Transcriptomic analysis revealed temporal changes in gene expression and functions induced by the infection. A specific set of up- regulated genes remained active throughout the infection, and genes correlated and anticorrelated with virus accumulation were identified. Responses to OrV mirrored reactions to other biotic stressors, distinguishing between virus-specific responses and broader immune responses. Additionally, mutants of early response genes and defense-related processes showed altered viral load progression, uncovering new players in the antiviral defense response.

systems biology↗

bioRxiv2023

Phenotypic and genomic changes during Turnip mosaic virus adaptation to Arabidopsis thaliana mutants lacking epigenetic regulatory factors

In this study we investigated how RNA viral populations evolve, interact and adapt to epigenetically-controlled plant defense mechanisms. We have evolved five independent lineages of turnip mosaic virus (TuMV) in a set of Arabidopsis thaliana genotypes carrying mutations that influence important elements of two main epigenetic pathways. All evolved lineages showed adaptation to the lack of epigenetically-regulated responses through significant increases in infectivity, virulence and viral load although the magnitude of the improvements strongly depended on the plant genotype. In early passages, these traits evolved more rapidly, but the rate of evolution flattened out in later ones. Viral load was positively correlated with different measures of virulence, though the strength of the associations changed from the ancestral to the evolved viruses. High-throughput sequencing was used to evaluate the viral diversity of each lineage, as well as characterizing the nature of fixed mutations, evolutionary convergences and potential targets of TuMV adaptation. Within each lineage, we observed a net increase in genome-wide genetic diversity, with some instances where nonsynonymous alleles experienced a transient rise in abundance before being displaced by the ancestral allele. Viral VPg protein has been shown as a key player in the adaptation process, even though no obvious association between fixed alleles and host genotype was found. Layman SummaryEpigenetic factors influence the expression of defense genes in plants, allowing for phenotypic rapid responses to infections by pathogens. The role of epigenetics in shaping the coevolution between host and pathogens has received very little attention. Here, we explored how RNA viruses interact and adapt to plant defense mechanisms that are controlled by epigenetic factors. We conducted evolution experiments on turnip mosaic virus using Arabidopsis thaliana genotypes with mutations that affect epigenetic pathways. We found that all evolved viral lineages adapted to the alteration of epigenetically-regulated responses by becoming more infectious, virulent, and having a higher viral load. The improvements varied depending on the plant genotype. The study also found that viral load was positively correlated with virulence, but the associations changed from the original to the evolved viruses. We used high-throughput sequencing to evaluate viral diversity and found an increase in each evolving lineage. We found that virus adaptation primarily targeted viral VPg, despite no obvious association between fixed alleles and host genotype being found. Teaser TextDiscover how RNA viruses adapt and evolve to plant defense mechanisms controlled by epigenetic factors. This research found that epigenetic regulation of defense genes modulates viral evolution. Viral lineages became more infectious, virulent, and had a higher viral load. Find out more about the correlation between viral load and virulence, viral diversity, and the primary virus genomic target of adaptation.

evolutionary biology↗