Functional Upregulation of the DNA Cytosine Deaminase APOBEC3B by Polyomaviruses

Abstract

The APOBEC3 family of DNA cytosine deaminases has important roles in innate immunity and cancer. It is unclear how DNA tumor viruses regulate these enzymes and how these interactions, in turn, impact the integrity of both the viral and cellular genomes. Polyomavirus (PyVs) are small DNA pathogens that contain oncogenic potentials. In this study, we examined the effects of PyV infection on APOBEC3 expression and activity. We demonstrate that APOBEC3B is specifically upregulated by BK polyomavirus (BKPyV) infection in primary kidney cells and that the upregulated enzyme is active. We further show that the BKPyV large T antigen, as well as large T antigens from related polyomaviruses, is alone capable of upregulating APOBEC3B expression and activity. Furthermore, we assessed the impact of A3B on productive BKPyV infection and viral genome evolution. Although the specific knockdown of APOBEC3B has little short-term effect on productive BKPyV infection, our informatics analyses indicate that the preferred target sequences of APOBEC3B are depleted in BKPyV genomes and that this motif underrepresentation is enriched on the nontranscribed stand of the viral genome, which is also the lagging strand during viral DNA replication. Our results suggest that PyV infection upregulates APOBEC3B activity to influence virus sequence composition over longer evolutionary periods. These findings also imply that the increased activity of APOBEC3B may contribute to PyV-mediated tumorigenesis. IMPORTANCEPolyomaviruses (PyVs) are a group of emerging pathogens that can cause severe diseases, including cancers in immunosuppressed individuals. Here we describe the finding that PyV infection specifically induces the innate immune DNA cytosine deaminase APOBEC3B. The induced APOBEC3B enzyme is fully functional and therefore may exert mutational effects on both viral and host cell DNA. We provide bioinformatic evidence that, consistent with this idea, BK polyomavirus genomes are depleted of APOBEC3B-preferred target motifs and enriched for the corresponding predicted reaction products. These data imply that the interplay between PyV infection and APOBEC proteins may have significant impact on both viral evolution and virusinduced tumorigenesis. P olyomaviruses (PyVs) are a family of small nonenveloped viruses containing an ϳ5-kb circular double-stranded DNA genome. Most human PyVs establish a subclinical persistent infection in healthy individuals (1). These viruses can reactivate under various immunosuppression conditions and cause a variety of severe diseases, including cancers (2). Among them, BK polyomavirus (BKPyV) reactivation is a major concern in kidney and bone marrow transplant patients due to the possibility of development of polyomavirus-associated nephropathy and hemorrhagic cystitis, respectively (3). Recently, there have also been increasing reports demonstrating an association between BKPyV infection and the occurrence of renourinary tumors (4). JC polyomavirus (JCPyV) reactivation can lead to progressive multifocal leu...

Merkel Cell Polyomavirus Exhibits Dominant Control of the Tumor Genome and Transcriptome in Virus-Associated Merkel Cell Carcinoma

“…Considering this, it is unusual that there is no strong evidence of APOBEC3 family upregulation or activity in MCPyV-positive tumors. A recent study also demonstrated that another human polyomavirus, BK polyomavirus, is able to upregulate APOBEC3B in infections of primary renal tubule epithelial cells and that this is at least partially mediated by large T antigen expression (7). This same study also demonstrated that MCPyV large T antigen is able to upregulate APOBEC3B in this cell culture system.…”

“…The effects of this integration event and the constitutive expression of viral proteins on the host genome structure and somatic mutation profile of the tumor genome have not been studied in depth. Using in vitro models, it has been suggested that expression of full-length MCPyV large T antigen is able to disrupt the stability of the host genome and upregulate the mutagenic enzyme APOBEC3B (6, 7). Another small DNA tumor virus, human papillomavirus (HPV), also triggers the upregulation of the DNA cytosine deaminase APOBEC3B and is likely responsible for the majority of mutations observed in HPV-positive cervical, head and neck squamous cell, and bladder carcinomas (8–12).…”

APOBEC3B lysine residues are dispensable for DNA cytosine deamination, HIV-1 restriction, and nuclear localization

“…These results mirror prior studies on human A3G and A3F, where 20 and 19 lysines were simultaneously converted to arginine, and the K-less variants resisted Vif-mediated degradation (Albin et al, 2013; Dang et al, 2008; Shao et al, 2010). Since A3B may very well restrict the replication of other viruses, including HBV, HPV, and HTLV (Ahasan et al, 2015; Lucifora et al, 2014; Ooms et al, 2012; Starrett et al, 2016; Starrett et al, 2017; Verhalen et al, 2016; Vieira et al, 2014; Warren et al, 2015), it is likely that additional A3B counteraction strategies exist and that the functional K-free construct described here may be useful as a mechanistic probe. The K-free enzyme may also be useful for future studies investigating A3B cellular interactions.…”

“…First, although A3B does not appear to overtly restrict the replication of polyomaviruses and papillomaviruses, the preferred 5′-TC ssDNA target motifs of A3B are depleted from these viral genomes and the predicted 5′-TT product is enriched implying continual selective pressure (Ahasan et al, 2015; Starrett et al, 2016; Starrett et al, 2017; Verhalen et al, 2016; Vieira et al, 2014; Warren et al, 2015). Moreover, both of these small DNA viruses specifically upregulate A3B at the transcriptional level (Mori et al, 2017; Starrett et al, 2017; Verhalen et al, 2016; Vieira et al, 2014).…”

“…First, although A3B does not appear to overtly restrict the replication of polyomaviruses and papillomaviruses, the preferred 5′-TC ssDNA target motifs of A3B are depleted from these viral genomes and the predicted 5′-TT product is enriched implying continual selective pressure (Ahasan et al, 2015; Starrett et al, 2016; Starrett et al, 2017; Verhalen et al, 2016; Vieira et al, 2014; Warren et al, 2015). Moreover, both of these small DNA viruses specifically upregulate A3B at the transcriptional level (Mori et al, 2017; Starrett et al, 2017; Verhalen et al, 2016; Vieira et al, 2014). Second, A3B knockdown in liver-derived HepG2 cells results in elevated levels of HBV circular DNA replication intermediates suggesting A3B may have a role in suppressing virus replication (Lucifora et al, 2014), however this result has been debated (Chisari et al, 2014; Ding and Robek, 2014; Meier et al, 2017; Shlomai and Rice, 2014; Xia et al, 2014).…”