The DNA deaminase APOBEC3B interacts with the cell-cycle protein CDK4 and disrupts CDK4-mediated nuclear import of Cyclin D1

Abstract

Edited by Charles E. Samuel Apolipoprotein B mRNA editing enzyme catalytic subunitlike protein 3B (APOBEC3B or A3B), as other APOBEC3 members, is a single-stranded (ss)DNA cytosine deaminase with antiviral activity. A3B is also overexpressed in multiple tumor types, such as carcinomas of the bladder, cervix, lung, head/neck, and breast. A3B generates both dispersed and clustered C-toT and C-to-G mutations in intrinsically preferred trinucleotide motifs (TCA/TCG/TCT). A3B-catalyzed mutations are likely to promote tumor evolution and cancer progression and, as such, are associated with poor clinical outcomes. However, little is known about cellular processes that regulate A3B. Here, we used a proteomics approach involving affinity purification coupled to MS with human 293T cells to identify cellular proteins that interact with A3B. This approach revealed a specific interaction with cyclin-dependent kinase 4 (CDK4). We validated and mapped this interaction by co-immunoprecipitation experiments. Functional studies and immunofluorescence microscopy experiments in multiple cell lines revealed that A3B is not a substrate for CDK4-Cyclin D1 phosphorylation nor is its deaminase activity modulated. Instead, we found that A3B is capable of disrupting the CDK4-dependent nuclear import of Cyclin D1. We propose that this interaction may favor a more potent antiviral response and simultaneously facilitate cancer mutagenesis.

HPV‐16/18 E6‐induced APOBEC3B expression associates with proliferation of cervical cancer cells and hypomethylation of Cyclin D1

“…Interestingly, C→T transitions have been suggested to be caused by APOBEC3B in multiple human cancers 59 . One Recent report found that APOBEC3B is capable of disrupting the CDK4‐dependent nuclear import of Cyclin D1 60 . We found that APOBEC3B affects the expression of the downstream Cyclin D1 through hypomethylation of the CCND1 promoter in cervical cancer.…”

DHX9 interacts with APOBEC3B and attenuates the anti-HBV effect of APOBEC3B

“…Therefore, it is important to identify host factors that potentially interact with and regulate the function of A3B. Recently, hnRNP A3 and CDK4 have been suggested to interact with A3B [25,26]; however, whether these factors affect the anti-HBV function of A3B is unclear. In this research, we employed a proteomic approach to identify and comprehensively compare host factors that potentially interact with A3B in the presence of HBV, and we identified eight distinct PPI networks, including mRNA metabolism, protein folding and viral process (Figure 1).…”

R-loop homeostasis and cancer mutagenesis promoted by the DNA cytosine deaminase APOBEC3B

“…These proteins were abundant in all 6 A3B-SF data sets and, importantly, absent in GFP-SF or empty vector datasets. Only CDK4, which regulates A3B localization during the cell cycle 54 , and hnRNPUL1, which tethered to Cas9 is capable of targeting A3B for base editing 55 , had been reported previously. However, literature analyses revealed that 60% of these A3B interactors had been found independently in S9.6 AP-MS experiments 53 (Fig.…”

“…These proteins were abundant in all 6 A3B-SF data sets and, importantly, absent in GFP-SF or empty vector datasets. Only CDK4, which regulates A3B localization during the cell cycle 54 , and hnRNPUL1, which tethered to Cas9 is capable of targeting A3B for base editing 55 , 151…”