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

Abstract

During lytic Kaposi's sarcoma-associated herpesvirus (KSHV) infection, the viral endonuclease 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.

Virus infection-induced host mRNA degradation and potential application of live cell imaging

“…Recently, Mendez et al demonstrated that SOX cleaves its target mRNA without other factors by in vitro cleavage assay [22]. Moreover, Muller et al revealed that some mRNAs that 'overrided' SOX were also degraded, suggesting multiple viral endonucleases' existence [23]. BGLF5 in EpsteineBarr virus (EBV) plays a role in processing non-linear or branched viral DNA intermediates in order to promote the production of mature packaged unitlength linear progeny viral DNA molecules [24], serves as an endoribonuclease of host mRNA after infection [25].…”

C19ORF66 broadly escapes viral-induced endonuclease cleavage and restricts Kaposi’s Sarcoma Associated Herpesvirus (KSHV)

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

“…This protective RNA element was termed SRE (for S OX R esistance E lement), 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 viral-specific ribonuclease 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 viral-specific ribonuclease 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 vs. viral endonuclease dichotomy to only defining characteristic of this novel type of RNA element.…”

“…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’UTR and were shown to protect against an array of viral – but not host – RNAses.…”