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

Diverting host cell resources and reprograming the metabolic machinery to support RNA metabolism and ATP production is a general strategy both of plant 56 and animal viruses 57, 58 . TEV achieves this reprogramming by altering the expression of a series of genes in its own benefit. The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/206789 doi: bioRxiv preprint For example, we found the expression of genes involved in actin cytoskeleton organization such as ADF4 and PFN3 to be negatively correlated with TEV fitness. The profilin PNF3 is a actinbinding protein and ADF4 participates in the depolymerization of actin filaments that results from microbial-associated molecular patterns being recognized by the corresponding patternrecognition receptors 59 . Therefore, by downregulating this function, longer and more stable actin filaments are produced that virions use to move around the cell from the ER-associated replication factories to plasmodesmata. Other example is the repression observed for the UBP1B gene, a negative regulator of potyvirus translation, that would allow for a more optimal virus accumulation 60 . Genes involved in nonsense-mediated decay (NMD) defenses 61 , such as the ATP-dependent RNA helicase UPF1, also show reduction in levels of expression. Other group of proteins that show alteration during viral infection are those involved in protein degradation, via ubiquitination and downstream into the proteasome pathway (e.g., ubiquitin-protein ligase 1, UPL1; ubiquitin-conjugating enzyme 2, UBC2; ubiquitin E2 variant 1B, MMZ2; EIN3-binding F box protein 1, EBF) or via autophagy (e.g., the ATP-driven chaperone CDC48C and the plant autophagy adaptor NBR1). Moreover, TEV activates in a fitness-dependent manner the expression of genes RH8, an RNA helicase, and PCaP1, a membrane-associated cation-binding protein, also required by potyviruses for cell-to-cell movement 62 (Fig. 8A) , and of a diversity of transcription factors including global (e.g., GRA2, GTE8), sequence-specific (e.g., SACL1 and SPL12), GATA/NAC family members (e.g., GATA1, NAC083, NAC029), bZIP G-box finding factors (e.g., GBF1 and BZIP63), and involved in homeotic gene expression (e.g., AGL20 and homeobox-1). We also found genes related to genome integrity, (e.g., the cohesins SYN2 and SMC3, and the chromatin protein SPT2), DNA replication and nucleosome assembly, alternative splicing (e.g., SF1, an homolog nuclear splicing factor), chromatin transition (e.g., SPT16, an histone chaperone involved in transcription elongation from RNApolII promoters and regulation of chromatin transitions; or the histone acetyltransferase HAC1, a coactivator of gene transcription with a major role in controlling flowering time and also essential for resistance to bacterial infections), DNA replication and cell division (e.g., the mitotic cohesin RAD21 and the cyclin-dependent protein kinase CYCH1). However, not all host factors recruited by the virus present alterations in their expressions. According to our data, the translation initiation factor eIF4E, known to be exploited by TEV for its own translation 63 , was found to be unperturbed (Fig. 8A ) whilst eIF3A and eIF4G expression positively correlated with TEV fitness.