Protein Interaction Map of APOBEC3 Enzyme Family Reveals Deamination-Independent Role in Cellular Function

• Published in: Molecular & cellular proteomics Vol. 23; no. 5; p. 100755
• Main Authors: Jang, Gwendolyn M., Annan Sudarsan, Arun Kumar, Shayeganmehr, Arzhang, Prando Munhoz, Erika, Lao, Reanna, Gaba, Amit, Granadillo Rodríguez, Milaid, Love, Robin P., Polacco, Benjamin J., Zhou, Yuan, Krogan, Nevan J., Kaake, Robyn M., Chelico, Linda
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.05.2024; American Society for Biochemistry and Molecular Biology
• Subjects: Aminohydrolases - genetics; Aminohydrolases - metabolism; APOBEC Deaminases - metabolism; APOBEC-3G Deaminase - genetics; APOBEC-3G Deaminase - metabolism; APOBEC3; cancer; cMyc; Cytidine Deaminase - genetics; Cytidine Deaminase - metabolism; Cytosine Deaminase - metabolism; deaminase; Deamination; DNA; HEK293 Cells; Humans; Mass Spectrometry; Minor Histocompatibility Antigens - genetics; Minor Histocompatibility Antigens - metabolism; Protein Binding; Protein Interaction Maps; protein-protein interactions; restriction factor; RNA; RNA - metabolism; Spliceosomes - metabolism; APOBEC3; RNA; deaminase; restriction factor; PPI; protein-protein interactions; LC-MS/MS; A3; HIV; RNP; DNA; APOBEC; cancer; cMyc; AP-MS
• ISSN: 1535-9476; 1535-9484; 1535-9484
• DOI: 10.1016/j.mcpro.2024.100755

Human APOBEC3 enzymes are a family of single-stranded (ss)DNA and RNA cytidine deaminases that act as part of the intrinsic immunity against viruses and retroelements. These enzymes deaminate cytosine to form uracil which can functionally inactivate or cause degradation of viral or retroelement genomes. In addition, APOBEC3s have deamination-independent antiviral activity through protein and nucleic acid interactions. If expression levels are misregulated, some APOBEC3 enzymes can access the human genome leading to deamination and mutagenesis, contributing to cancer initiation and evolution. While APOBEC3 enzymes are known to interact with large ribonucleoprotein complexes, the function and RNA dependence are not entirely understood. To further understand their cellular roles, we determined by affinity purification mass spectrometry (AP-MS) the protein interaction network for the human APOBEC3 enzymes and mapped a diverse set of protein–protein and protein–RNA mediated interactions. Our analysis identified novel RNA-mediated interactions between APOBEC3C, APOBEC3H Haplotype I and II, and APOBEC3G with spliceosome proteins, and APOBEC3G and APOBEC3H Haplotype I with proteins involved in tRNA methylation and ncRNA export from the nucleus. In addition, we identified RNA-independent protein-protein interactions with APOBEC3B, APOBEC3D, and APOBEC3F and the prefoldin family of protein-folding chaperones. Interaction between prefoldin 5 (PFD5) and APOBEC3B disrupted the ability of PFD5 to induce degradation of the oncogene cMyc, implicating the APOBEC3B protein interaction network in cancer. Altogether, the results uncover novel functions and interactions of the APOBEC3 family and suggest they may have fundamental roles in cellular RNA biology, their protein–protein interactions are not redundant, and there are protein-protein interactions with tumor suppressors, suggesting a role in cancer biology. Data are available via ProteomeXchange with the identifier PXD044275. [Display omitted] •Determination of APOBEC3 family protein interaction network by mass spectrometry.•Differential analysis identifies APOBEC3 protein interactions mediated by RNA.•APOBEC3B/D/F stably interact with Prefoldin family proteins independent of RNA.•APOBEC3B interaction with PFD5 stabilizes cMyc in MCF7 cancer cells. We used affinity purification mass spectrometry to determine the RNA-dependent and -independent protein–protein interaction network of the APOBEC3 family of proteins that have antiviral and oncogenic functions. We discovered novel APOBEC3-specific and shared interactors that are RNA-dependent and -independent. Notably, there were stable interactions between prefoldin complex (PFD1-6) subunits and APOBEC3B, APOBEC3D, and APOBEC3F. Expression of APOBEC3B decreased PFD5 interaction with cMyc and increased cMyc steady-state levels, indicating a potential protein interaction-dependent contribution of APOBEC3B in cancer.