Suppression of immediate-early viral gene expression by herpesvirus-coded microRNAs: Implications for latency

Abstract

A quantitative algorithm was developed and applied to predict target genes of microRNAs encoded by herpesviruses. Although there is almost no conservation among microRNAs of different herpesvirus subfamilies, a common pattern of regulation emerged. The algorithm predicts that herpes simplex virus 1, human cytomegalovirus, Epstein-Barr virus, and Kaposi's sarcoma-associated herpesvirus all employ microRNAs to suppress expression of their own genes, including their immediate-early genes. In the case of human cytomegalovirus, a virus-coded microRNA, miR-112-1, was predicted to target the viral immediate-early protein 1 mRNA. To test this prediction, mutant viruses were generated that were unable to express the microRNA, or encoded an immediate-early 1 mRNA lacking its target site. Analysis of RNA and protein within infected cells demonstrated that miR-UL112-1 inhibits expression of the major immediate-early protein. We propose that herpesviruses use microRNA-mediated suppression of immediate-early genes as part of their strategy to enter and maintain latency.miRNAs ͉ reactivation ͉ immune evasion M icroRNAs (miRNAs) are 20-23-nucleotide RNA molecules that bind to mRNA targets, generally within their 3Ј untranslated region (3Ј UTR), and interfere with their translation (1, 2). Viruses have co-evolved with cellular miRNAs and many encode their own miRNAs (3). Every herpesvirus genome that has been examined has been found to encode multiple miRNAs, including Epstein-Barr virus (EBV) (4 -6), human cytomegalovirus (HCMV) (4, 7, 8), herpes simplex virus 1 (HSV-1) (9, 10), and Kaposi's sarcoma-associated herpesvirus (KSHV) (4,6,11,12). These miRNAs can potentially function during lytic replication and latency. Lytic replication proceeds in a coordinated three-phase cascade: immediate-early (IE), early and late. IE products prepare the cell for infection and propagate the cascade. Early gene products support replication of viral DNA, and DNA replication is, in turn, a prerequisite for full activation of the late genes that encode the structural proteins of the virus. During latency, the virus is quiescent. A limited subset of the viral genome is expressed, but, importantly, the virus has the potential to reactivate and reenter the lytic cycle. Although the molecular mechanisms of reactivation are not understood, it is widely assumed that the lytic cascade is reinitiated with the expression of IE genes. Ectopic expression of a single IE protein has been shown to reactivate HSV-1 (13, 14), EBV (15), or KSHV (16,17) in cell culture models of latency.Whereas none or only a few protein-coding genes are expressed, multiple miRNAs are transcribed during latency. The HSV-1 miR-LAT lies within one of the latency associated transcripts (LATs), the only viral RNAs known to be expressed in latency. EBV and KSHV miRNAs also are expressed during latent infection. Because they are nonimmunogenic, miRNAs should be optimal agents for suppression of anti-viral responses and to modify behaviors of latently infected cells, and recent reports ...

How does cytomegalovirus factor into diseases of aging and vaccine responses, and by what mechanisms?

“…This miR inhibits the translation of the CMV's trans-activator IE72, which impacts on active infection and might favor maintenance of latency (Murphy et al 2008). This miR also targets cellular mechanisms involved in IL-32-mediated TNF-α release, which may also affect the establishment and maintenance of viral latency and persistence (Huang et al 2013).…”

The immunology of human cytomegalovirus latency: could latent infection be cleared by novel immunotherapeutic strategies?

“…50 During lytic infection, HCMV expresses approximately 24 miRNAs derived from 13 pre-miRNAs which have been shown to target both viral and cellular RNAs. Viral targets include IE72 as well as a number of viral genes involved in DNA synthesis and it has been suggested that these targets might play some role in latency establishment and reactivation, [51][52][53] although, as yet, there is no direct evidence for this. Cellular targets of HCMV-encoded miRNAs include gene products with functions relating to control of cell cycle, secretory cellular pathways and, of particular interest, immune evasion.…”

MicroRNAs in the regulation of TLR and RIG-I pathways

“…69 For instance, miR-UL112 is encoded by HCMV and targets transcriptional factor IE1, which controls the expression of many viral genes and is vital for viral replication at the onset of infection. [114][115][116] HCMV miR-US4-1 specifically downregulates ERAP1, which participates in trimming MHC class I-presented peptide precursors to mature epitopes. 117 Accordingly, the trimming of HCMV-derived peptides is inhibited, leading to decreased susceptibility of infected cells to HCMV-specific cytotoxic T lymphocytes, thus helping identify a previously unknown viral miRNA-based cytotoxic T lymphocyte-evasion mechanism.…”