Stealing the Show: KSHV Hijacks Host RNA Regulatory Pathways to Promote Infection

Abstract

Kaposi's sarcoma-associated herpesvirus (KSHV) induces life-long infections and has evolved many ways to exert extensive control over its host's transcriptional and post-transcriptional machinery to gain better access to resources and dampened immune sensing. The hallmark of this takeover is how KSHV reshapes RNA fate both to control expression of its own gene but also that of its host. From the nucleus to the cytoplasm, control of RNA expression, localization, and decay is a process that is carefully tuned by a multitude of factors and that can adapt or react to rapid changes in the environment. Intriguingly, it appears that KSHV has found ways to co-opt each of these pathways for its own benefit. Here we provide a comprehensive review of recent work in this area and in particular recent advances on the post-transcriptional modifications front. Overall, this review highlights the myriad of ways KSHV uses to control RNA fate and gathers novel insights gained from the past decade of research at the interface of RNA biology and the field of KSHV research.

Keywords: G4s; KSHV; RNA regulation; SOX; circRNA; m6A; miRNA.

Figure 1

Kaposi’s sarcoma-associated herpesvirus (KSHV) manipulation of nuclear RNA regulation. (A) During lytic reactivation, KSHV transcripts are preferentially m⁶A modified over host RNAs, co-opting host m⁶a readers and writers to direct viral mRNA post-transcriptional regulation, splice patterns, and nuclear export. (B) Back-splicing of viral RNAs leads to the production of viral circular RNAs (circRNAs). Viral circRNAs could act as microRNA (miRNA) sponges to enhance translation of their linear counterparts and potentially encode novel viral peptides with as-yet to be defined functions. Several circRNAs are also packaged into KSHV virions, which points to a potential immunomodulatory role during primary infection. (C) G-quadruplexes are RNA secondary structures found within guanine rich regions of pre-mRNA formed by a unique hydrogen bond stacking interaction. A G4 structure within the LANA mRNA regulates hnRNPA1-facilitated transcript export. It also binds LANA protein in a negative feedback loop that finely tunes the amount of LANA transcripts within the cytoplasmic RNA pool. G4 regulation of LANA mRNA balances the amount of LANA being produced during KSHV latency, aiding in latency maintenance. (D) The lytic early gene, ORF57, binds to KSHV early and delayed early transcripts in complex with ALYREF and ARS2, protecting them from targeting by the 3′ PAPα/γ-mediated RNA decay (PPD) and Cap-Binding Complex/ARS2-mediated (CBC/ARS2) nuclear decay pathways. Late KSHV mRNAs when produced prematurely are targeted for PPD-based decay by cellular MTR4 contributing to temporal viral gene regulation. PPD-targeting of these mRNA, when no longer necessary, is subverted as nuclear speckles fuse with viral replication compartments, which allows nuclear RNAi-defective 2 (NRDE2) to restrict the interaction of MTR4 with late transcripts.

Figure 2

KSHV manipulation of cytoplasmic RNA regulation. (A) G4s found within cytoplasmic LANA transcripts, when stabilized, inhibit LANA translation, which in turn reduces LANA-triggered antigenic presentation aiding in immune evasion during KSHV latency. (B). The fate of m⁶a modified viral transcripts in the cytoplasm is modulated by m⁶a readers. These readers, including YTHDF2 (YTH N6-Methyladenosine RNA Binding Protein 2), orchestrate silencing and/or degradation of modified mRNAs by driving their localization to cytoplasmic RNA granules such as P-bodies or recruitment of host exonucleases. Co-opting of this m⁶a machinery allows KSHV an unprecedented level of control over temporal viral gene expression. (C) KSHV encodes a large repertoire of viral miRNA. Taking advantage of the cellular miRNA silencing complex (RISC), viral miRNAs regulate translation of viral and host transcripts in trans by redirecting their localization to RNA granules for homeostasis or immediately triggering RNA decay. As a form of cis-regulation of a viral transcript, KSHV also co-opts cellular miRNA biogenesis machinery, namely DROSHA, to restrict the over-production of KapB during latency, which contributes to cell survival during latency and temporal regulation of KapB. (D) To swiftly seize control of the cell during lytic reactivation, KSHV encodes a viral endonuclease, SOX, which triggers a global RNA decay event. SOX selectively cleaves host and viral transcripts that bear conserved SOX recognition sites, rending transcripts susceptible to decay by cellular exonucleases. This massive degradation event releases host resources such as the translation machinery and RNA-binding proteins for reallocation to viral gene expression.