Biology subjects

Santiago F. Elena

Publications and source records attributed to Santiago F. Elena.

6 recordsLinked to original sources

bioRxiv2016

2b or not 2b: Experimental evolution of functional exogenous sequences in a plant RNA virus

Horizontal gene transfer (HGT) is pervasive in viruses, and thought to be a key mechanism in their evolution. On the other hand, strong selective constraints against increasing genome size are an impediment for HGT, rapidly purging horizontally transferred sequences and thereby potentially hindering evolutionary innovation. Here we explore experimentally the evolutionary fate of viruses with simulated HGT events, using the plant RNA virus Tobacco etch virus (TEV), by separately introducing two functional, exogenous sequences to its genome. One of the events simulates the acquisition of a new function though HGT of a conserved AlkB domain, responsible for the repair of alkylation or methylation damage in many organisms. The other event simulates the acquisition of a sequence that duplicates an existing function, through HGT of the 2b RNA silencing suppressor from Cucumber mosaic virus (CMV). We then evolved these two viruses, tracked the maintenance of the horizontally transferred sequences over time, and for the final virus populations, sequenced their genome and measured viral fitness. We found that the AlkB domain was rapidly purged from the TEV genome, restoring fitness to wild-type levels. Conversely, the 2b gene was stably maintained and did not have a major impact on viral fitness. Moreover, we found that 2b is functional in TEV, as it provides a replicative advantage when the RNA silencing suppression domain of HC-Pro is mutated. These observations suggest a potentially interesting role for HGT of short functional sequences in ameliorating evolutionary constraints on viruses, through the duplication of functions.

Evolutionary Biology↗

bioRxiv2016

Molecular and biological characterization of an isolate of Tomato mottle mosaic virus (ToMMV) infecting tomato and other experimental hosts in a greenhouse in Valencia, Spain

Tomato is known to be a natural and experimental reservoir host for many plant viruses. In the last few years a new tobamovirus species, Tomato mottle mosaic virus (ToMMV), has been described infecting tomato and pepper plants in several countries worldwide. Upon observation of symptoms in tomato plants growing in a greenhouse in Valencia, Spain, we aimed to ascertain the etiology of the disease. Using standard molecular techniques, we first detected a positive sense single-stranded RNA virus as the probable causal agent. Next, we amplified, cloned and sequenced a ~3 kb fragment of its RNA genome which allowed us to identify the virus as a new ToMMV isolate. Through extensive assays on distinct plant species, we validated Kochs postulates and investigated the host range of the ToMMV isolate. Several plant species were locally and/or systemically infected by the virus, some of which had not been previously reported as ToMMV hosts despite they are commonly used in research greenhouses. Finally, two reliable molecular diagnostic techniques were developed and used to assess the presence of ToMMV in different plants species. We discuss the possibility that, given the high sequence homology between ToMMV and Tomato mosaic virus, the former may have been mistakenly diagnosed as the latter by serological methods.

Microbiology↗

bioRxiv2016

Predicting the stability of homologous gene duplications in a plant RNA virus

One of the striking features of many eukaryotes is the apparent amount of redundancy in coding and non-coding elements of their genomes. Despite the possible evolutionary advantages, there are fewer examples of redundant sequences in viral genomes, particularly those with RNA genomes. The low prevalence of gene duplication in RNA viruses most likely reflects the strong selective constraints against increasing genome size. Here we investigated the stability of genetically redundant sequences and how adaptive evolution proceeds to remove them. We generated plant RNA viruses with potentially beneficial gene duplications, measured their fitness and performed experimental evolution, hereby exploring their genomic stability and evolutionary potential. We found that all gene duplication events resulted in a loss of viability or significant reductions in fitness. Moreover, upon evolving the viable viruses and analyzing their genomes, we always observed the deletion of the duplicated gene copy and maintenance of the ancestral copy. Interestingly, there were clear differences in the deletion dynamics of the duplicated gene associated with the passage duration, the size of the gene and the position for duplication. Based on the experimental data, we developed a mathematical model to characterize the stability of genetically redundant sequences, and showed that the fitness of viruses with duplications is not enough information to predict genomic stability as a recombination rate dependent on the genetic context - the duplicated gene and its position - is also required. Our results therefore demonstrate experimentally the deleterious nature of gene duplications in RNA viruses, and we identify factors that constrain the maintenance of duplicated genes.

Evolutionary Biology↗

bioRxiv2016

High virulence does not necessarily impede viral adaptation to a new host: A case study using a plant RNA virus

BackgroundWhen between-host selection pressures predominate, theory suggests that high virulence could hinder between-host transmission of microparasites, and that virulence therefore will evolve to lower levels that optimize between-host transmission. Highly virulent microparasites could also curtail host development, thereby limiting both the host resources available to them and their own within-host effective population size. High virulence might therefore curtail the mutation supply rate and increase the strength with which genetic drift acts on microparasite populations, thereby limiting the potential to adapt to the host and ultimately perhaps the ability to evolve lower virulence. As a first exploration of this hypothesis, we evolved Tobacco etch virus carrying an eGFP fluorescent marker in two semi-permissive host species, Nicotiana benthamiana and Datura stramonium, for which it has a large difference in virulence. We compared the results to those previously obtained in the typical host, Nicotiana tabacum, where we have shown that carriage of eGFP has a high fitness cost and its loss serves as a real-time indicator of adaptation.\n\nResultsAfter over half a year of evolution, we sequenced the genomes of the evolved lineages and measured their fitness. During the evolution experiment, marker loss leading to viable virus variants was only observed in one lineage of the host for which the virus has low virulence, D. stramonium. This result was consistent with the observation that there was a fitness cost of eGFP in this host, while surprisingly no fitness cost was observed in the host for which the virus has high virulence, N. benthamiana. Furthermore, in both hosts we observed few lineages with increases in viral fitness, and host-specific convergent evolution at the genomic level was only found in N. benthamiana.\n\nConclusionsThe results of this study do not lend support to the hypothesis that high virulence impedes microparasites evolution. Rather, they exemplify that jumps between host species can be game changers for evolutionary dynamics. When considering the evolution of genome architecture, host species jumps might play a very important role, by allowing evolutionary intermediates to be competitive.

Evolutionary Biology↗

bioRxiv2014

The rugged adaptive landscape of an emerging plant RNA virus

RNA viruses are the main source of emerging infectious diseases owed to the evolutionary potential bestowed by their fast replication, large population sizes and high mutation and recombination rates. However, an equally important parameter, which is usually neglected, is the topography of the fitness landscape, that is, how many fitness maxima exist and how well connected they are, which determines the number of accessible evolutionary pathways. To address this question, we have reconstructed the fitness landscape describing the adaptation of Tobacco etch potyvirus to its new host, Arabidopsis thaliana. Fitness was measured for most of the genotypes in the landscape, showing the existence of peaks and holes. We found prevailing epistatic effects between mutations, with cases of reciprocal sign epistasis being common at latter stages. Therefore, results suggest that the landscape was rugged and holey, with several local fitness peaks and a very limited number of potential neutral paths. The viral genotype fixed at the end of the evolutionary process was not on the global fitness optima but stuck into a suboptimal peak.

Evolutionary Biology↗

bioRxiv2014

A putative antiviral role of plant cytidine deaminases

A mechanism of innate antiviral immunity operating against viruses infecting mammalian cells has been described during the last decade. Host cytidine deaminases (e.g., APOBEC3 proteins) edit viral genomes giving raise to hypermutated nonfunctional viruses; consequently, viral fitness is reduced through lethal mutagenesis. By contrast, sub-lethal hypermutagenesis may contribute to virus evolvability by increasing population diversity. To prevent genome editing, some viruses have evolved proteins that mediate APOBEC3 degradation. The model plant Arabidopsis thaliana encodes for nine cytidine deaminases (AtCDAs), raising the question of whether deamination is an antiviral mechanism in plants as well. Here we tested the effects of AtCDAs expression on the pararetrovirus Cauliflower mosaic virus (CaMV). We show that A. thaliana AtCDA1 gene product exerts a mutagenic activity, which indeed generates a negative correlation between the level of AtCDA1 expression and CaMV accumulation in the plant, suggesting that deamination may also work as an antiviral mechanism in plants.

Microbiology↗