Viral fitness predicts the magnitude and direction of perturbations in the infected host transcriptome

Héctor Cervera; Silvia Ambrós; Guillermo P. Bernet; Guillermo Rodrigo; Santiago F. Elena

In essence, there are genes that are significantly altered (up or down) upon infection irrespective of the ability of the virus to replicate, genes whose expression correlates with this ability (positively or negatively), and genes that remain unaltered. Nevertheless, this picture of virus-plant interaction may be biased by the limited number of viral genotypes analyzed in this work. Three out of six genotypes correspond to HC-Pro mutants. As a multifunctional protein, it is not surprising that different fitness levels can be reached by introducing mutations in different . CC-BY-NC-ND 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/206789 doi: bioRxiv preprint functional domains. But, certainly, more mutants should be analyzed in future work to provide a comprehensive picture, avoiding the bias towards certain virus proteins. In addition, we here focused on the transcription regulation, but other networks exist in the cell (e.g., metabolism, protein-protein interactions, …), all them interlinked. To provide an insight on these other networks, we constructed the interactome (Fig. 8B) of HC-Pro with the host proteins known to interact with this virus protein 40 . We then contextualized our gene expression data over multiple TEV infections. Many of the cellular functions in which HC-Pro participate (protein degradation, translation, redox processes, and cation signaling) are not regulated transcriptionally upon infection (or regulated marginally). Presumably, the virus exploits these processes in its own benefit (mainly to enhance replication and movement within a cell), and the normal expression of the corresponding genes is sufficient for such subversion. By contrast, RNA silencing and methylation are functions involved in defense against pathogens that are quantitatively regulated, as a sort of control strategy exerted by the plant, as long as they are needed, that is, according to viral fitness.