Differential Inhibition of Long Interspersed Element 1 by APOBEC3 Does Not Correlate with High-Molecular-Mass-Complex Formation or P-Body Association

Abstract

The human cytidine deaminase APOBEC3G (A3G) and other APOBEC3 proteins exhibit differential inhibitory activities against diverse endogenous retroelements and retroviruses, including Vif-deficient human immunodeficiency virus type 1. The potential inhibitory activity of human APOBEC proteins against long interspersed element 1 (LINE-1) has not been fully evaluated. Here, we demonstrate inhibition of LINE-1 by multiple human APOBEC3 cytidine deaminases, including previously unreported activity for A3DE and A3G. More ancient members of APOBEC, cytidine deaminases AID and APOBEC2, had no detectable activity against LINE-1. A3A, which did not form high-molecular-mass (HMM) complexes and interacted poorly with P bodies, was the most potent inhibitor of LINE-1. A3A specifically recognizes LINE-1 RNA but not the other cellular RNAs tested. However, in the presence of LINE-1, A3A became associated with HMM complexes containing LINE-1 RNA. The ability of A3A to recognize LINE-1 RNA required its catalytic domain and was important for its LINE-1 suppression. Although the mechanism of LINE-1 restriction did not seem to involve DNA editing, A3A inhibited the accumulation of nascent LINE-1 DNA, suggesting interference with LINE-1 reverse transcription and/or integration or intracellular movement of LINE-1 ribonucleoprotein. Thus, association with P bodies or cellular HMM complexes could not predict the potency of APOBEC3 anti-LINE-1 activities. The catalytic domain of APOBEC3 proteins may be important for proper folding and target factors such as RNA or protein interaction in addition to cytidine deamination.A3G and other APOBEC3 proteins (22) belong to a family of proteins that also includes activation-induced cytidine deaminase (AID), apolipoprotein B-editing catalytic subunit 1 (APOBEC1), and APOBEC2 (1,16,19,35,39,45). These proteins have cytidine deaminase activities that can modify RNA or DNA. A3G was the first APOBEC3 protein to be identified as a potent inhibitor of human immunodeficiency virus type 1 (HIV-1) in the absence of Vif (41). Subsequently, several other human APOBEC3 proteins, including APOBE C3A (A3A), APOBEC3B (A3B), APOBEC3C (A3C), APOB EC3DE (A3DE), and APOBEC3F (A3F), were identified as broad antiviral factors against HIV-1, simian immunodeficiency virus, murine leukemia virus, and various endogenous retroelements (3, 4, 11-14, 24, 26, 37, 40, 48, 49, 53) as well as hepatitis B virus (44).Like AID, which edits single-stranded immunoglobulin gene DNA, APOBEC3 proteins prefer minus-strand retroviral DNAs as targets (1,10,16,19,29,35,39,45,51). In the absence of Vif-induced A3G degradation in virus-producing cells, virion-packaged A3G induces C-to-U mutations in minus-strand viral DNA during reverse transcription (18,25,30,31,43,50,52). Both cytidine deamination-dependent and -independent antiviral functions of APOBEC3 proteins have been reported (2,8,17,20,28,33,36,44).The potential inhibitory activity of certain human APOBEC3 proteins against LINE-1 has been reported. A3A and A3B are potent inhibitors...

Endogenous APOBEC3A DNA Cytosine Deaminase Is Cytoplasmic and Nongenotoxic

“…Expression of A3A in HEK293 cells to lower levels than those observed in the CD14 ϩ cells, however, caused marked genotoxicity. We show that endogenous A3A in CD14 ϩ and THP-1 cells localized to the cytoplasm, in contrast to the cell-wide localization observed for exogenous A3A in a variety of heterologous cell types (3,13,14,16,21,(27)(28)(29)(30)(31)(32)(33)(34). We further reveal that nuclear localization is necessary for A3A-mediated genotoxicity.…”

“…Previous studies of A3A localization have shown that untagged protein in HeLa cells (27), GFP-tagged protein in HeLa (28 -30) and HEK293T cells (29), or HA-tagged protein in HeLa (13,14,31,32), HEK293 (3), HEK293T (21,33,34), and U20S cells (16) has a cell-wide localization. A3A was determined to enter the nucleus of HeLa cells by passive diffusion (29).…”

“…A3B is observed to be nuclear in the majority of tested cell lines, including HeLa (14,28,29,44,45) (26), whereas it is cell-wide in 293T (29,33) cells, which are believed to have an import defect (29). A3C is considered cell-wide in both HeLa (14,28,30) and 293T cells (31,33,34). A3D, A3F, and A3G are cytoplasmic in HeLa (14, 28, 30, 44, 45, 48 -51) (48,51), primary peripheral blood mononuclear cells (51), and primary T cells (48).…”

Stress out the LINEs

“…One example is the APOBEC family of proteins that are cytidine deaminase and inactivate viral or LINE-1 DNA by introducing lethal mutations. [19][20][21][22][23] An RNA helicase MOV10 inhibits retrotransposition of LINE-1 by CONTACT Chen Liang …”

“…One example is the APOBEC family of proteins that are cytidine deaminase and inactivate viral or LINE-1 DNA by introducing lethal mutations. [19][20][21][22][23] An RNA helicase MOV10 inhibits retrotransposition of LINE-1 by associating with LINE-1 RNP and diminishing LINE-1 RNA level. [24][25][26] A recent study by Goodier et al tested a panel of viral restriction factors and showed that many of them, including BST-2, ISG20, MAVS, Mx2 and ZAP, strongly reduce LINE-1 activity.…”