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

Abstract

9One striking characteristic of certain herpesviruses is their ability to induce rapid and 10 widespread RNA decay in order to gain access to host resources. This phenotype is induced by 11 viral endoribonucleases, including SOX in KSHV, muSOX in MHV68, BGLF5 in EBV and vhs in 12 HSV-1. Here, we performed comparative RNA-seq upon expression of these herpesviral 13 endonucleases in order to characterize their effect on the host transcriptome. Consistent with 14 previous reports, we found that approximately two thirds of transcripts are downregulated in 15 cells expressing any of these viral endonucleases. Among transcripts spared from degradation, 16we uncovered a cluster of transcripts that systematically escape degradation from all tested 17 endonucleases. Among these escapees, we identified C19ORF66 and reveal that like the 18 previously identified escapees, this transcript is protected from degradation by its 3'UTR. We 19 then show that C19ORF66, a known anti-viral protein, is a potent KSHV restriction factor, 20suggesting that its ability to escape viral cleavage may be an important component of the host 21 response to viral infection. Collectively, our comparative approach is a powerful tool to pinpoint 22 key regulators of the viral-host interplay and led us to uncover a novel KSHV regulator. 23 24 25 26 All rights reserved. No reuse allowed without permission.The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. . https://doi.org/10.1101/506410 doi: bioRxiv preprint characterized by a defined sequence motif (19) rendering it difficult to identify new escaping 48 transcripts by traditional sequence search. Consequently, the host vs. viral endonuclease 49 dichotomy to only defining characteristic of this novel type of RNA element. 50 All rights reserved. No reuse allowed without permission.

Fated for decay: RNA elements targeted by viral endonucleases

“…1F), where it was shown early on that while the vast majority of host transcripts are targeted for degradation, a portion of transcripts are only mildly affected by SOX-mediated degradation [64,65,67,68]. While most of these "escapees" likely simply lack the targeting features required for SOX cleavage, some select transcripts were found to resist SOX decay even in the presence of a robust SOX targeting element [20,25,64,65]. This type of dominant negative effect was shown to stem from a sequence that is confided to the escaping transcript 3 ′ UTR and was dubbed the SOX-resistant element (SRE) [25,64,65].…”

“…This type of dominant negative effect was shown to stem from a sequence that is confided to the escaping transcript 3 ′ UTR and was dubbed the SOX-resistant element (SRE) [25,64,65]. Strikingly, despite the limited sequence similarity between the known escaping mRNA, there seems to be a conserved structurally important stem-loop located within the SOX resistant elements [20,25]. This would suggest that from an evolutionary standpoint the structure of the SRE is conserved over sequence and could suggest that it serves as a platform to recruitment of trans-acting factors.…”

“…Viruses that express these mRNA-specific endonucleases include alphaand gammaherpesviruses, influenza A virus, SARS and MERS coronaviruses, vaccinia virus, and African swine fever virus [12][13][14][15][16][17][18][19]. The effect of these viral RNAses is extensive, as it is estimated that over two-thirds of the host transcriptome is impacted by viral-mediated decay [17,[20][21][22]. However, how the host reacts to this massive takeover, or how these viral endonucleases can target mRNA in such a widespread manner remains elusive and is still an active area of research.…”

“…In the past five years, studies of viral endonucleases and accelerated RNA decay have greatly enhanced our understanding of RNA regulation. In particular, recent studies have unveiled several RNA elements that confer susceptibility or resistance to endonuclease cleavage [20][21][22][23][24][25][26]. Many of these elements consist of RNA structural motifs and/or internal sequences that recruit RNA binding proteins.…”