Gammaherpesviral Gene Expression and Virion Composition Are Broadly Controlled by Accelerated mRNA Degradation

Lytic gammaherpesvirus infection restricts host gene expression by promoting widespread degradation of cytoplasmic mRNA through the activity of the viral endonuclease SOX. Though generally assumed to be selective for cellular transcripts, the extent to which SOX impacts viral mRNA stability has remained unknown. We addressed this issue using the model murine gammaherpesvirus MHV68 and, unexpectedly, found that all stages of viral gene expression are controlled through mRNA degradation. Using both comprehensive RNA expression profiling and half-life studies we reveal that the levels of the majority of viral mRNAs but not noncoding RNAs are tempered by MHV68 SOX (muSOX) activity. The targeting of viral mRNA by muSOX is functionally significant, as it impacts intracellular viral protein abundance and progeny virion composition. In the absence of muSOX-imposed gene expression control the viral particles display increased cell surface binding and entry as well as enhanced immediate early gene expression. These phenotypes culminate in a viral replication defect in multiple cell types as well as in vivo, highlighting the importance of maintaining the appropriate balance of viral RNA during gammaherpesviral infection. This is the first example of a virus that fails to broadly discriminate between cellular and viral transcripts during host shutoff and instead uses the targeting of viral messages to fine-tune overall gene expression. Author Summary Many viruses restrict host gene expression during infection, presumably to provide a competitive expression advantage to viral transcripts. Not surprisingly, viruses that induce this host shutoff' phenotype therefore generally possess mechanisms to selectively spare viral genes. Gammaherpesviruses promote host shutoff by inducing widespread mRNA degradation, a process initiated by the viral SOX nuclease. However, the effect of SOX on viral mRNA during infection was unknown. Here, we reveal that during infection with the murine gammaherpesvirus MHV68, the majority of viral transcripts of all kinetic classes are broadly down regulated through the activity of the MHV68 SOX protein (muSOX). We further demonstrate that in the absence of muSOX-induced control of viral mRNA abundance, viral protein levels increase, thereby affecting the composition of progeny viral particles. Altered virion composition directly impacts early events such as entry and induction of lytic gene expression in subsequent rounds of replication. Furthermore, decreasing both virus and host gene expression via global mRNA degradation is critical for viral replication in a cell type specific manner both in vitro and in vivo. This is the first example of a eukaryotic virus whose host shutoff mechanism similarly tempers viral gene expression, and highlights the degree to which gammaherpesviral gene expression must be fine tuned to ensure replicative success.