ILF2 enhances the DNA cytosine deaminase activity of tumor mutator APOBEC3B in multiple myeloma cells

Abstract

DNA cytosine deaminase APOBEC3B (A3B) is an endogenous source of mutations in many human cancers, including multiple myeloma. A3B proteins form catalytically inactive high molecular mass (HMM) complexes in nuclei, however, the regulatory mechanisms of A3B deaminase activity in HMM complexes are still unclear. Here, we performed mass spectrometry analysis of A3B-interacting proteins from nuclear extracts of myeloma cell lines and identified 30 putative interacting proteins. These proteins are involved in RNA metabolism, including RNA binding, mRNA splicing, translation, and regulation of gene expression. Except for SAFB, these proteins interact with A3B in an RNA-dependent manner. Most of these interacting proteins are detected in A3B HMM complexes by density gradient sedimentation assays. We focused on two interacting proteins, ILF2 and SAFB. We found that overexpressed ILF2 enhanced the deaminase activity of A3B by 30%, while SAFB did not. Additionally, siRNA-mediated knockdown of ILF2 suppressed A3B deaminase activity by 30% in HEK293T cell lysates. Based on these findings, we conclude that ILF2 can interact with A3B and enhance its deaminase activity in HMM complexes.

Protein interaction map of APOBEC3 enzyme family reveals deamination-independent role in cellular function

“…If a protein had more than one BP and one CC, the term with a larger population was selected to represent it in the network ( Table S8 ). Several PPIs captured in this network have been described in previous studies, or have been reported in interaction databases ( Table S8 ) (51, 52, 58, 70, 71), though we capture a number of novel interactors as well. The most interconnected A3 interacting proteins were RNA binding proteins including proteins involved in splicing, ribonucleoprotein complexes (RNP), and RNA modification.…”

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

“…If a protein had more than one BP and one CC, the term with a larger population was selected to represent it in the network ( Supplemental Table S8 ). Several PPIs captured in this network have been described in previous studies, or have been reported in interaction databases ( Supplemental Table S8 ) ( 51 , 52 , 58 , 70 , 71 ), although we capture a number of novel interactors as well. The most interconnected A3 interacting proteins were RNA binding proteins including proteins involved in splicing, ribonucleoprotein complexes (RNP), and RNA modification.…”

APOBEC3B drives PKR-mediated translation shutdown and protects stress granules in response to viral infection

“…We did not detect any interaction between A3B and G3BP1, verifying that A3B immunoprecipitation did not precipitate the full SG structures. It is worth noting that PABPC1, DDX3, SAF-A, and MATR3 have been also identified in several published proteomic data sets of A3B pulldown from different cell lines 61,75,76 . Finally, we monitored the localization of these five A3B-interacting proteins after SeV infection via immunofluorescence.…”