Vaccinia virus D10 has broad decapping activity that is regulated by mRNA splicing

Abstract

The mRNA 5’ cap structure serves both to protect transcripts from degradation and promote their translation. Cap removal is thus an integral component of mRNA turnover that is carried out by cellular decapping enzymes, whose activity is tightly regulated and coupled to other stages of the mRNA decay pathway. The poxvirus vaccinia virus (VACV) encodes its own decapping enzymes, D9 and D10, that act on cellular and viral mRNA, but may be regulated differently than their cellular counterparts. Here, we evaluated the targeting potential of these viral enzymes using RNA sequencing from cells infected with wild-type and decapping mutant versions of VACV as well as in uninfected cells expressing D10. We found that D9 and D10 target an overlapping subset of viral transcripts but that D10 plays a dominant role in depleting the vast majority of human transcripts, although not in an indiscriminate manner. Unexpectedly, the splicing architecture of a gene influences how robustly its corresponding transcript is targeted by D10, as transcripts derived from intronless genes are less susceptible to enzymatic decapping by D10. As all VACV genes are intronless, preferential decapping of transcripts from intron-containing genes provides an unanticipated mechanism for the virus to disproportionately deplete host transcripts and remodel the infected cell transcriptome.

A Poxvirus Decapping Enzyme Colocalizes with Mitochondria To Regulate RNA Metabolism and Translation and Promote Viral Replication

“…Consequently, mitochondrial colocalization is required for efficient VACV replication. Interestingly, one group of mRNAs that are preferentially targeted by D10 for degradation are those involved in oxidative phosphorylation, which was reported by Ly et al during the revision of this manuscript ( 46 ). As mRNA-encoded oxidative phosphorylation complex proteins are often translated by ribosomes associated with mitochondria ( 47 , 48 ), it further supports the close association of D10 with mitochondria.…”

Spatio-temporal analysis of Vaccinia virus infection and host response dynamics using single-cell transcriptomics and proteomics

“…We speculate that these factors are targeted for degradation by VV at protein level, despite their overexpression and escape of shutoff. Host shutoff escape may occur from a lesser affinity of the viral decapping enzyme D10 in transcripts containing few introns, a mechanism used for the escape of viral transcripts 98 . However, TENT4A gene contains 13 exons, which argues in favor of an upregulation as a consequence of gene overexpression.…”

Nonstructural protein 1 (nsp1) widespread RNA decay phenotype varies among Coronaviruses

“…Destabilization and degradation of host mRNA is a prevalent strategy employed by numerous viruses as a means of usurping the host gene expression machinery and to dampen the host immune responses [28][29][30][31][32][33][34][35][36]. Prior research has highlighted the ability of SARS1, SARS2, and MERS coronavirus protein nsp1 to disrupt host gene expression through two prominent methods: modulation of host gene expression through mRNA degradation as well as binding of the 40s ribosomal subunit and subsequent translational arrest [21,22,17].…”