Adenovirus-Encoding Virus-Associated RNAs Suppress HDGF Gene Expression to Support Efficient Viral Replication

Abstract

Non-coding small RNAs are involved in many physiological responses including viral life cycles. Adenovirus-encoding small RNAs, known as virus-associated RNAs (VA RNAs), are transcribed throughout the replication process in the host cells, and their transcript levels depend on the copy numbers of the viral genome. Therefore, VA RNAs are abundant in infected cells after genome replication, i.e. during the late phase of viral infection. Their function during the late phase is the inhibition of interferon-inducible protein kinase R (PKR) activity to prevent antiviral responses; recently, mivaRNAs, the microRNAs processed from VA RNAs, have been reported to inhibit cellular gene expression. Although VA RNA transcription starts during the early phase, little is known about its function. The reason may be because much smaller amount of VA RNAs are transcribed during the early phase than the late phase. In this study, we applied replication-deficient adenovirus vectors (AdVs) and novel AdVs lacking VA RNA genes to analyze the expression changes in cellular genes mediated by VA RNAs using microarray analysis. AdVs are suitable to examine the function of VA RNAs during the early phase, since they constitutively express VA RNAs but do not replicate except in 293 cells. We found that the expression level of hepatoma-derived growth factor (HDGF) significantly decreased in response to the VA RNAs under replication-deficient condition, and this suppression was also observed during the early phase under replication-competent conditions. The suppression was independent of mivaRNA-induced downregulation, suggesting that the function of VA RNAs during the early phase differs from that during the late phase. Notably, overexpression of HDGF inhibited AdV growth. This is the first report to show the function, in part, of VA RNAs during the early phase that may be contribute to efficient viral growth.

Adenovirus VA RNA: An essential pro-viral non-coding RNA

“…Mutations in these promoter regions reduce VA RNA transcription and limit virus replication in vivo (Ma and Mathews, 1996b). Accumulation of VA RNAs is a function of AdV genome copy number (Kondo et al, 2014) and in viruses which possess VA RNA I and VA RNA II , the RNAs compete for transcription by RNA Pol III (Fowlkes and Shenk, 1980). Though both VA RNAs are initially transcribed at similar levels, RNA Pol III becomes limiting following AdV genome replication, and VA RNA I outcompetes VA RNA II for transcription, resulting in the lower relative level of VA RNA II observed late in infection (Bhat and Thimmappaya, 1984).…”

“…In addition to binding and inhibiting PKR, VA RNA I interacts with the other innate immune system dsRNA-detecting proteins, RIG-I and OAS1 (Desai et al, 1995;Minamitani et al, 2011), as well as the host RNA interference (RNAi) machinery through the cellular endoribonuclease Dicer and Argonaute-2 (Ago-2) within the RNA-induced silencing complex (RISC) (Andersson et al, 2005;Xu et al, 2007). While most functions of VA RNA I are associated with its accumulation late in infection, recent work has revealed a novel role for VA RNA I early in infection as a repressor of Hepatoma-Derived Growth Factor (Kondo et al, 2014). Understanding the interactions of this RNA with host proteins during AdV infection will add to the growing body of knowledge of the multifaceted roles of non-coding RNAs (ncRNAs), improve our understanding of host-pathogen recognition, and promote effective development of AdV-based technologies.…”

Long Non-coding RNAs: Regulators of Viral Infection and the Interferon Antiviral Response

“…For example, PAN RNA (polyadenylated nuclear RNA) from KSHV interacts with several virus- and host-encoded factors, including IRF4. During the lytic phase of KSHV infection, the expression of PAN RNA reduces the expression of IFNα, IFNγ, and ISG RNaseL; sfRNAs (subgenomic flavivirus RNAs) from several viruses, including Japanese encephalitis virus (JEV), dengue virus, and West Nile Virus (WNV), may antagonize the antiviral response of IFN by inhibiting the IFN signaling, the expression of IFN-β or specific ISGs; adenovirus virus-associated RNA (VA) target the ISG PKR to regulate the expression of ISGs ( Rossetto and Pari, 2011 ; Schuessler et al, 2012 ; Chang et al, 2013 ; Bidet et al, 2014 ; Kondo et al, 2014 ). Interestingly, a chimeric lncRNA HBx-LINE1, which is generated by the integration of HBV into host cell genome, may attenuate the IFN antiviral response by inhibiting microRNA (miRNA)-122, a negative regulator of HBV replication which can be suppressed by IFN ( Qiu et al, 2010 ; Chen et al, 2011 ; Wang et al, 2012 ; Hao et al, 2013 ; Lau et al, 2014 ).…”

The role of microRNAs in respiratory viral infection: friend or foe?

“…Hepatoma‐derived growth factor inhibits adenovirus growth. However, the expression level of hepatoma‐derived growth factor significantly decreased in response to miVARNAs under replication‐deficient conditions, and this suppression was also observed during the early phase of viral infection under replication‐competent conditions . Adenovirus miVARNAs also target cellular genes involved in cell growth, gene expression and DNA repair.…”