Arabidopsis RNA–binding proteins interact with viral structural proteins and modify turnip yellows virus accumulation

As obligate intracellular parasites, viruses depend on host proteins and pathways for their multiplication. Among these host factors, specific nuclear proteins are involved in the life cycle of some cytoplasmic replicating RNA viruses, although their role in the viral cycle remains largely unknown. The polerovirus turnip yellows virus (TuYV) encodes a major coat protein (CP) and a 74 kDa protein known as the readthrough (RT) protein. The icosahedral viral capsid is composed of the CP and a minor component RT*, arising from a C-terminal cleavage of the full-length RT. In this study, we identified Arabidopsis (Arabidopsis thaliana) ALY family proteins as interacting partners of TuYV structural proteins using yeast 2-hybrid assays and co-immunoprecipitations in planta. ALY proteins are adaptor proteins of the THO-TREX-1 complex essential to the nuclear export of mature messenger RNAs (mRNAs). Although all 4 ALY proteins colocalized with the CP and the RT protein in the nucleus upon co-expression in agro-infiltrated Nicotiana benthamiana leaves, only the CP remained nuclear and colocalized with ALY proteins in TuYV-infected cells, suggesting that the CP is an essential partner of ALY proteins. Importantly, TuYV-infected A. thaliana 4xaly knock-out mutants showed a significant increase in viral accumulation, indicating that TuYV infection is affected by an unknown ALY-mediated antiviral defense mechanism or impairs the cellular mRNA export pathway to favor viral RNA translation. This finding underpins the crucial role played by nuclear factors in the life cycle of cytoplasmic RNA viruses.