The ability to regulate RNA stability has the potential to impact gene expression on a global scale, but is also critical for fine-tuning cellular responses to specific stimuli as well as eliminating flawed and potentially deleterious transcripts. Lytic gammaherpesvirus infection promotes widespread destruction of messenger RNAs (mRNAs), a phenotype driven primarily by the viral SOX protein. By probing how SOX and other functionally related viral proteins drive messenger RNA degradation, we hope to reveal novel interplay between viruses and host gene regulatory pathways, as well as identify cellular factors with capacity to broadly influence message stability.
Using both a directed siRNA-based knockdown screen of known host RNases as well as mapping studies to identify RNA degradation intermediates, we found that SOX-induced RNA degradation occurs as a two-step process (Covarrubias & Gaglia et al., 2011, PLoS Path 7(10):e1002339). In the first step, SOX makes a sequence-dependent endonucleolytic (internal) cut. This type of cleavage yields unprotected RNA termini, leading to rapid degradation of the RNA body by the cellular 5’-3’ exonuclease Xrn1. We are currently exploring what RNA features direct SOX targeting, as well as whether additional cellular factors contribute to SOX-triggered global mRNA degradation.
The use of a primary endonucleolytic cleavage presumably enables the virus to bypass the highly regulated and rate-limiting steps of deadenylation and decapping, which normally precede degradation of the RNA body in cells. Additionally, it allows the virus to make use of host RNases to clear the bulk of the mRNAs. Interestingly, this endonuclease and Xrn1-coordinated mechanism of RNA degradation strongly resembles that used by host quality control pathways such as nonsense-mediated decay, though by encoding its own endonuclease KSHV is able to target mRNAs in a global manner.