Nuclease escape elements protect messenger RNA against cleavage by multiple viral endonucleases

Abstract

During lytic Kaposi’s sarcoma-associated herpesvirus (KSHV) infection, the viral endonu- clease SOX promotes widespread degradation of cytoplasmic messenger RNA (mRNA). However, select mRNAs, including the transcript encoding interleukin-6 (IL-6), escape SOX-induced cleavage. IL-6 escape is mediated through a 3’ UTR RNA regulatory element that overrides the SOX targeting mechanism. Here, we reveal that this protective RNA element functions to broadly restrict cleavage by a range of homologous and non-homologous viral endonucleases. However, it does not impede cleavage by cellular endonucleases. The IL-6 protective sequence may be representative of a larger class of nuclease escape elements, as we identified a similar protective element in the GADD45B mRNA. The IL-6 and GADD45B-derived elements display similarities in their sequence, putative structure, and several associated RNA binding proteins. However, the overall composition of their ribonucleoprotein complexes appears distinct, leading to differences in the breadth of nucleases restricted. These findings highlight how RNA elements can selectively control transcript abundance in the background of widespread virus-induced mRNA degradation.

C19ORF66 Broadly Escapes Virus-Induced Endonuclease Cleavage and Restricts Kaposi’s Sarcoma-Associated Herpesvirus

“…This protective RNA element was termed SRE (for SOX resistance element), but we recently showed that the SRE is also effective against a broad range of viral endonucleases. Perhaps more surprisingly, the SRE is unable to restrict endonucleolytic cleavage originating from a cellular endonuclease, making it the first identified virus-specific RNase escape element (19). We showed that this broad-acting RNA element is not characterized by a defined sequence motif (19), rendering it difficult to identify new escaping transcripts by traditional sequence search.…”

“…Perhaps more surprisingly, the SRE is unable to restrict endonucleolytic cleavage originating from a cellular endonuclease, making it the first identified virus-specific RNase escape element (19). We showed that this broad-acting RNA element is not characterized by a defined sequence motif (19), rendering it difficult to identify new escaping transcripts by traditional sequence search. Consequently, the host versus viral endonuclease dichotomy is the only defining characteristic of this novel type of RNA element.…”

“…SOX is conserved throughout the herpesvirus family, but only gammaherpesviral SOX homologs display RNase activity in cells (8)(9)(10), and studies indicate that SOX activity is important for the in vivo viral life cycle (11,12). Although SOX targets a degenerate RNA motif present on most mRNAs (13)(14)(15), multiple studies have shown that some transcripts robustly escape SOX-induced decay (16)(17)(18)(19)(20)(21). Studying these "escapees" in aggregate is complicated, however, by the fact that multiple mechanisms can promote apparent escape.…”

“…These include the lack of a targeting motif, indirect transcriptional effects, and active evasion of ribonucleolytic cleavage (16,(20)(21)(22)(23)(24). The latter phenotype, termed "dominant escape," is particularly notable, as it involves a specific RNA element whose presence in the 3= untranslated region (UTR) of an mRNA protects against SOX cleavage, regardless of whether the RNA contains a targeting motif (19)(20)(21). This protective RNA element was termed SRE (for SOX resistance element), but we recently showed that the SRE is also effective against a broad range of viral endonucleases.…”

“…Little is currently known about these types of RNA elements, how widespread they may be in the genome, and how they may contribute to the overall viral-host arms race for the control of resources. To date, only two SRE-bearing dominant escapees are known: the host interleukin-6 (IL-6) (18,20,21) and the growth arrest and DNA damage-inducible 45 beta (GADD45B) (19) transcripts. Both the IL-6 and GADD45B SREs were mapped to their 3= UTRs and were shown to protect against an array of viral-but not host-RNases.…”