Combinatorial interactions between viral proteins expand the potential functional landscape of the tomato yellow leaf curl virus proteome

Viruses manipulate the cells they infect in order to replicate and spread. Due to strict size restrictions, viral genomes have reduced genetic space; how the action of the limited num- ber of viral proteins results in the cell reprogramming observed during the infection is a long- standing question. Here, we explore the hypothesis that combinatorial interactions may expand the functional landscape of the viral proteome. We show that the proteins encoded by a plant-infecting DNA virus, the geminivirus tomato yellow leaf curl virus (TYLCV), physi- cally associate with one another in an intricate network, as detected by a number of protein- protein interaction techniques. Importantly, our results indicate that intra-viral protein-protein interactions can modify the subcellular localization of the proteins involved. Using one partic- ular pairwise interaction, that between the virus-encoded C2 and CP proteins, as proof-of- concept, we demonstrate that the combination of viral proteins leads to novel transcriptional effects on the host cell. Taken together, our results underscore the importance of studying viral protein function in the context of the infection. We propose a model in which viral pro- teins might have evolved to extensively interact with other elements within the viral prote- ome, enlarging the potential functional landscape available to the pathogen Overall design: RNA-seq profiling of Nicotiana benthamiana leaves transiently expressing C2, CP and C2+CP TYLCV genes, and infected with TYLCV, TYLCV-C2 mutant and TYLCV-CP mutant