APOBEC3D

Summary

Gene Symbol: APOBEC3D
Description: apolipoprotein B mRNA editing enzyme catalytic subunit 3D
Alias: A3D, APOBEC3DE, APOBEC3E, ARP6, DNA dC->dU-editing enzyme APOBEC-3D, apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3D, apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3E pseudogene
Species: human
Products:     APOBEC3D

Top Publications

  1. Wedekind J, Dance G, Sowden M, Smith H. Messenger RNA editing in mammals: new members of the APOBEC family seeking roles in the family business. Trends Genet. 2003;19:207-16 pubmed
    ..In light of the hypothesis that these proteins might represent novel mRNA editing systems that could affect proteome diversity, we consider their structure, expression and relevance to biomedically significant processes or pathologies. ..
  2. Sawyer S, Emerman M, Malik H. Ancient adaptive evolution of the primate antiviral DNA-editing enzyme APOBEC3G. PLoS Biol. 2004;2:E275 pubmed
    ..Despite being only recently discovered, editing of RNA and DNA may thus represent an ancient form of host defense in primate genomes. ..
  3. Harris R, Liddament M. Retroviral restriction by APOBEC proteins. Nat Rev Immunol. 2004;4:868-77 pubmed
    ..This APOBEC abundance might help to tip the balance in favour of cellular defences. ..
  4. Zhang W, Chen G, Niewiadomska A, Xu R, Yu X. Distinct determinants in HIV-1 Vif and human APOBEC3 proteins are required for the suppression of diverse host anti-viral proteins. PLoS ONE. 2008;3:e3963 pubmed publisher
    ..Mapping these determinants may be useful for the design of novel anti-HIV inhibitors. ..
  5. Smith J, Pathak V. Identification of specific determinants of human APOBEC3F, APOBEC3C, and APOBEC3DE and African green monkey APOBEC3F that interact with HIV-1 Vif. J Virol. 2010;84:12599-608 pubmed publisher
  6. Hultquist J, Lengyel J, Refsland E, LaRue R, Lackey L, Brown W, et al. Human and rhesus APOBEC3D, APOBEC3F, APOBEC3G, and APOBEC3H demonstrate a conserved capacity to restrict Vif-deficient HIV-1. J Virol. 2011;85:11220-34 pubmed publisher
    ..In addition to APOBEC3G, we find that three other human APOBEC3 proteins, APOBEC3D, APOBEC3F, and APOBEC3H, are all potent HIV-1 restriction factors...
  7. Chen G, He Z, Wang T, Xu R, Yu X. A patch of positively charged amino acids surrounding the human immunodeficiency virus type 1 Vif SLVx4Yx9Y motif influences its interaction with APOBEC3G. J Virol. 2009;83:8674-82 pubmed publisher
    ..These structural motifs in HIV-1 Vif represent attractive targets for the development of lead inhibitors to combat HIV infection. ..
  8. Conticello S, Thomas C, Petersen Mahrt S, Neuberger M. Evolution of the AID/APOBEC family of polynucleotide (deoxy)cytidine deaminases. Mol Biol Evol. 2005;22:367-77 pubmed
  9. Goila Gaur R, Strebel K. HIV-1 Vif, APOBEC, and intrinsic immunity. Retrovirology. 2008;5:51 pubmed publisher

More Information

Publications64

  1. Jarmuz A, Chester A, Bayliss J, Gisbourne J, Dunham I, Scott J, et al. An anthropoid-specific locus of orphan C to U RNA-editing enzymes on chromosome 22. Genomics. 2002;79:285-96 pubmed
    ..Tissue-specific expression of these genes in a variety of cell lines, along with other evidence, suggests a role for these enzymes in growth or cell cycle control. ..
  2. Malim M. APOBEC proteins and intrinsic resistance to HIV-1 infection. Philos Trans R Soc Lond B Biol Sci. 2009;364:675-87 pubmed publisher
  3. Stenglein M, Harris R. APOBEC3B and APOBEC3F inhibit L1 retrotransposition by a DNA deamination-independent mechanism. J Biol Chem. 2006;281:16837-41 pubmed
    ..Expression of two related proteins, APOBEC3D or APOBEC3G, had little effect...
  4. Chiu Y, Greene W. The APOBEC3 cytidine deaminases: an innate defensive network opposing exogenous retroviruses and endogenous retroelements. Annu Rev Immunol. 2008;26:317-53 pubmed publisher
  5. Dang Y, Wang X, Esselman W, Zheng Y. Identification of APOBEC3DE as another antiretroviral factor from the human APOBEC family. J Virol. 2006;80:10522-33 pubmed
    ..These are APOBEC3A, APOBEC3B, APOBEC3C, APOBEC3DE, APOBEC3F, APOBEC3G, and APOBEC3H...
  6. Refsland E, Hultquist J, Harris R. Endogenous origins of HIV-1 G-to-A hypermutation and restriction in the nonpermissive T cell line CEM2n. PLoS Pathog. 2012;8:e1002800 pubmed publisher
    ..knockdown of other APOBEC3 genes in an APOBEC3F-null background revealed a significant contribution from APOBEC3D in promoting 5'GA-to-AA hypermutations...
  7. Stenglein M, Burns M, Li M, Lengyel J, Harris R. APOBEC3 proteins mediate the clearance of foreign DNA from human cells. Nat Struct Mol Biol. 2010;17:222-9 pubmed publisher
    ..The efficiency and fidelity of genetic engineering, gene therapy, and DNA vaccination are likely to be influenced by this anti-DNA defense system. ..
  8. Albin J, Harris R. Interactions of host APOBEC3 restriction factors with HIV-1 in vivo: implications for therapeutics. Expert Rev Mol Med. 2010;12:e4 pubmed publisher
    ..We also summarise, for the first time, current clinical data on the in vivo effects of APOBEC3 proteins, and survey strategies and progress towards developing therapeutics aimed at the APOBEC3-Vif axis. ..
  9. Chaipan C, Smith J, HU W, Pathak V. APOBEC3G restricts HIV-1 to a greater extent than APOBEC3F and APOBEC3DE in human primary CD4+ T cells and macrophages. J Virol. 2013;87:444-53 pubmed publisher
    ..We observed significant inhibition of HIV-1?vif produced in 293T cells in the presence of APOBEC3DE (A3DE), APOBEC3F (A3F), APOBEC3G (A3G), and APOBEC3H haplotype II (A3H HapII) but not APOBEC3B (A3B), APOBEC3C (..
  10. Bilal B, Azim M. Nematicidal activity of 'major royal jelly protein'-containing glycoproteins from Acacia honey. Exp Parasitol. 2018;192:52-59 pubmed publisher
    ..of gene transcripts involved in the citric acid cycle (mdh-1 and idhg-1) and cytoskeleton (act-1, act-2, and arp6)...
  11. Matume N, Tebit D, Gray L, Turner S, Rekosh D, Bessong P, et al. Characterization of APOBEC3 variation in a population of HIV-1 infected individuals in northern South Africa. BMC Med Genet. 2019;20:21 pubmed publisher
    ..The study showed significant polymorphisms in the APOBEC3D, 3F, 3G and 3H genes in our South African HIV1-infected cohort...
  12. Refsland E, Hultquist J, Luengas E, Ikeda T, Shaban N, Law E, et al. Natural polymorphisms in human APOBEC3H and HIV-1 Vif combine in primary T lymphocytes to affect viral G-to-A mutation levels and infectivity. PLoS Genet. 2014;10:e1004761 pubmed publisher
    ..HIV-1 with a Vif protein hypo-functional for APOBEC3H degradation, yet fully able to counteract APOBEC3D, APOBEC3F, and APOBEC3G, was susceptible to restriction and hypermutation in stable APOBEC3H expressing ..
  13. Nützmann H, Osbourn A. Regulation of metabolic gene clusters in Arabidopsis thaliana. New Phytol. 2015;205:503-10 pubmed publisher
    ..We show that the transcript levels of genes within two metabolic clusters are coordinately reduced in an arp6 and h2a.z background. We demonstrate that H2A...
  14. Kim E, Lorenzo Redondo R, Little S, Chung Y, Phalora P, Maljkovic Berry I, et al. Human APOBEC3 induced mutation of human immunodeficiency virus type-1 contributes to adaptation and evolution in natural infection. PLoS Pathog. 2014;10:e1004281 pubmed publisher
    ..in culture and highly parallel DNA sequencing, we defined trinucleotide contexts of the edited sites for APOBEC3D, APOBEC3F, APOBEC3G, and APOBEC3H...
  15. Xu M, Leichty A, Hu T, Poethig R. H2A.Z promotes the transcription of MIR156A and MIR156C in Arabidopsis by facilitating the deposition of H3K4me3. Development. 2018;145: pubmed publisher
    ..We found that mutations in components of the SWR1 complex (ARP6, SEF) and in genes encoding H2A...
  16. Anderson B, Harris R. Transcriptional regulation of APOBEC3 antiviral immunity through the CBF-β/RUNX axis. Sci Adv. 2015;1:e1500296 pubmed publisher
    ..The APOBEC3 family of DNA cytosine deaminases is an integral part of these defenses. For instance, APOBEC3D, APOBEC3F, APOBEC3G, and APOBEC3H would have the potential to destroy HIV-1 complementary DNA replication ..
  17. Pandey D, Chaudhary B. Domestication-driven Gossypium profilin 1 (GhPRF1) gene transduces early flowering phenotype in tobacco by spatial alteration of apical/floral-meristem related gene expression. BMC Plant Biol. 2016;16:112 pubmed publisher
    ..flowering regulators are spatially controlled by the Actin-Related Protein (ARP) genes, specifically ARP4 and ARP6 in proximate association with profilins...
  18. Aumeier C, Polinski E, Menzel D. Actin, actin-related proteins and profilin in diatoms: a comparative genomic analysis. Mar Genomics. 2015;23:133-42 pubmed publisher
    ..Among these are the highly conserved cytoplasmic Arp1 protein and the nuclear Arp4 as well as Arp6. Diatom genomes contain genes coding for two structurally different homologues of Arp4 that might serve specific ..
  19. Krisko J, Begum N, Baker C, Foster J, Garcia J. APOBEC3G and APOBEC3F Act in Concert To Extinguish HIV-1 Replication. J Virol. 2016;90:4681-4695 pubmed publisher
    ..JRCSF and JRCSFvifH42/43D, but not JRCSFvifW79S or JRCSFvifH42/43DW79S, degraded APOBEC3D. With one exception, JRCSFs expressing mutant Vifs that replicated acquired enforced vif mutations...
  20. Berriri S, Gangappa S, Kumar S. SWR1 Chromatin-Remodeling Complex Subunits and H2A.Z Have Non-overlapping Functions in Immunity and Gene Regulation in Arabidopsis. Mol Plant. 2016;9:1051-65 pubmed publisher
    ..analyzed the roles of the SWR1c subunits, PHOTOPERIOD-INDEPENDENT EARLY FLOWERING1 (PIE1), ACTIN-RELATED PROTEIN6 (ARP6), and SWR1 COMPLEX 6 (SWC6), as well as H2A.Z, in defense and gene regulation...
  21. Luo Y, Chen Z, Zhu D, Tu H, Pan S. Yeast Actin-Related Protein ARP6 Negatively Regulates Agrobacterium-Mediated Transformation of Yeast Cell. Biomed Res Int. 2015;2015:275092 pubmed publisher
    ..Here our genetic screening of yeast knockout mutants identified a yeast actin-related protein ARP6 as a negative regulator of AMT...
  22. Zhu M, Wang Y, Wang C, Shen W, Liu J, Geng L, et al. The eQTL-missense polymorphisms of APOBEC3H are associated with lung cancer risk in a Han Chinese population. Sci Rep. 2015;5:14969 pubmed publisher
    ..polymorphisms in the exon regions of 10 APOBEC core genes (APOBEC1, APOBEC2, APOBEC3A, APOBEC3B, APOBEC3C, APOBEC3D, APOBEC3F, APOBEC3G, APOBEC3H, and APOBEC4) and evaluated them with a case-control study including 1200 cases and ..
  23. Suen D, Tsai Y, Cheng Y, Radjacommare R, Ahirwar R, Fu H, et al. The Deubiquitinase OTU5 Regulates Root Responses to Phosphate Starvation. Plant Physiol. 2018;176:2441-2455 pubmed publisher
    ..The root hair phenotype of otu5 was synergistic to that of actin-related protein6 (arp6), harboring a mutation in the SWR1 chromatin-remodeling complex...
  24. Kitamura H, Matsumori H, Kalendová A, Hozak P, Goldberg I, Nakao M, et al. The actin family protein ARP6 contributes to the structure and the function of the nucleolus. Biochem Biophys Res Commun. 2015;464:554-60 pubmed publisher
    ..b>ARP6, one of the nuclear ARPs, is part of the Snf-2-related CREB-binding protein activator protein (SRCAP) chromatin ..
  25. Choi K, Kim J, Müller S, Oh M, Underwood C, Henderson I, et al. Regulation of MicroRNA-Mediated Developmental Changes by the SWR1 Chromatin Remodeling Complex. Plant Physiol. 2016;171:1128-43 pubmed publisher
    ..Z deposition mutants (which are embryonically lethal), Arabidopsis SWR1-C component mutants, including arp6, survive and display a pleiotropic developmental phenotype...
  26. Land A, Wang J, Law E, Aberle R, Kirmaier A, Krupp A, et al. Degradation of the cancer genomic DNA deaminase APOBEC3B by SIV Vif. Oncotarget. 2015;6:39969-79 pubmed publisher
    ..Several APOBEC3 family members function to restrict virus replication. For instance, APOBEC3D, APOBEC3F, APOBEC3G, and APOBEC3H combine to restrict HIV-1 in human lymphocytes...
  27. Siriwardena S, Chen K, Bhagwat A. Functions and Malfunctions of Mammalian DNA-Cytosine Deaminases. Chem Rev. 2016;116:12688-12710 pubmed publisher
    ..Members of the APOBEC3 subfamily in humans (APOBEC3A, APOBEC3B, APOBEC3C, APOBEC3D, APOBEC3F, APOBEC3G, and APOBEC3H) inhibit infections of viruses such as HIV-1, HBV, and HCV, and ..
  28. Leonard B, Starrett G, Maurer M, Oberg A, Van Bockstal M, Van Dorpe J, et al. APOBEC3G Expression Correlates with T-Cell Infiltration and Improved Clinical Outcomes in High-grade Serous Ovarian Carcinoma. Clin Cancer Res. 2016;22:4746-55 pubmed publisher
    ..TCGA data analyses revealed that expression of APOBEC3D and APOBEC3H also correlates with CD3D across multiple cancer types...
  29. Aydin H, Taylor M, Lee J. Structure-guided analysis of the human APOBEC3-HIV restrictome. Structure. 2014;22:668-84 pubmed publisher
    ..Here, we summarize data from recent A3 structural and functional studies to provide perspectives into the interactions between cellular A3 proteins and HIV-1 macromolecules throughout the viral replication cycle. ..
  30. Duggal N, Fu W, Akey J, Emerman M. Identification and antiviral activity of common polymorphisms in the APOBEC3 locus in human populations. Virology. 2013;443:329-37 pubmed publisher
    ..However, we found that two common novel polymorphisms in APOBEC3D decrease antiviral activity against HIV-1, and one polymorphism decreases activity against Alu retrotransposons...
  31. Haché G, Harris R. CEM-T4 cells do not lack an APOBEC3G cofactor. PLoS Pathog. 2009;5:e1000528 pubmed publisher
  32. Arias J, Koyama T, Kinomoto M, Tokunaga K. Retroelements versus APOBEC3 family members: No great escape from the magnificent seven. Front Microbiol. 2012;3:275 pubmed publisher
    ..This review summarizes the recent advances in our understanding of the interplay between the retroelements currently active in the human genome and the anti-retroelement A3 proteins...
  33. Hultquist J, Binka M, LaRue R, Simon V, Harris R. Vif proteins of human and simian immunodeficiency viruses require cellular CBF? to degrade APOBEC3 restriction factors. J Virol. 2012;86:2874-7 pubmed publisher
  34. Zhou T, Han Y, Dang Y, Wang X, Zheng Y. A novel HIV-1 restriction factor that is biologically distinct from APOBEC3 cytidine deaminases in a human T cell line CEM.NKR. Retrovirology. 2009;6:31 pubmed publisher
    ..When the levels of APOBEC3 expression were determined, all these clones retained similar low levels of APOBEC3DE, APOBEC3F, APOBEC3G and APOBEC3H expression, and no APOBEC3B expression was detected...
  35. Olson M, Harris R, Harki D. APOBEC Enzymes as Targets for Virus and Cancer Therapy. Cell Chem Biol. 2018;25:36-49 pubmed publisher
    Human DNA cytosine-to-uracil deaminases catalyze mutations in both pathogen and cellular genomes. APOBEC3D, APOBEC3F, APOBEC3G, and APOBEC3H restrict human immunodeficiency virus 1 (HIV-1) infection in cells deficient in the viral ..
  36. Desimmie B, Delviks Frankenberrry K, Burdick R, Qi D, Izumi T, Pathak V. Multiple APOBEC3 restriction factors for HIV-1 and one Vif to rule them all. J Mol Biol. 2014;426:1220-45 pubmed publisher
    ..Specifically, APOBEC3DE, APOBEC3F, APOBEC3G, and APOBEC3H haplotypes II, V, and VII provide protection against HIV-1Δvif through ..
  37. Feng Y, Baig T, Love R, Chelico L. Suppression of APOBEC3-mediated restriction of HIV-1 by Vif. Front Microbiol. 2014;5:450 pubmed publisher
  38. Niewiadomska A, Yu X. Host restriction of HIV-1 by APOBEC3 and viral evasion through Vif. Curr Top Microbiol Immunol. 2009;339:1-25 pubmed publisher
    ..Here we review the research that led up to the identification of A3G, the mechanisms by which APOBEC3 proteins can inhibit retroelements, and the counter-mechanisms that HIV-1 Vif has developed to evade its antiviral activities. ..
  39. Moris A, Murray S, Cardinaud S. AID and APOBECs span the gap between innate and adaptive immunity. Front Microbiol. 2014;5:534 pubmed publisher
    ..Herein this review we discuss AID and APOBEC cytodine deaminases as a link between innate and adaptive immunity uncovered by recent studies. ..
  40. Liang W, Xu J, Yuan W, Song X, Zhang J, Wei W, et al. APOBEC3DE Inhibits LINE-1 Retrotransposition by Interacting with ORF1p and Influencing LINE Reverse Transcriptase Activity. PLoS ONE. 2016;11:e0157220 pubmed publisher
    ..This study demonstrates that different A3 proteins have been evolved to inhibit LINE-1 activity through distinct mechanisms. ..
  41. Wang Z, Wakae K, Kitamura K, Aoyama S, Liu G, Koura M, et al. APOBEC3 deaminases induce hypermutation in human papillomavirus 16 DNA upon beta interferon stimulation. J Virol. 2014;88:1308-17 pubmed publisher
    ..This study demonstrates that endogenous A3s upregulated by IFN-? induce E2 hypermutation of HPV16 in cervical keratinocytes, and a pathogenic consequence of E2 hypermutation is discussed. ..
  42. Harris R, Hultquist J, Evans D. The restriction factors of human immunodeficiency virus. J Biol Chem. 2012;287:40875-83 pubmed publisher
    ..These HIV restriction and counter-restriction mechanisms suggest strategies for new therapeutic interventions...
  43. Shandilya S, Bohn M, Schiffer C. A computational analysis of the structural determinants of APOBEC3's catalytic activity and vulnerability to HIV-1 Vif. Virology. 2014;471-473:105-16 pubmed publisher
  44. Kitamura S, Ode H, Nakashima M, Imahashi M, Naganawa Y, Kurosawa T, et al. The APOBEC3C crystal structure and the interface for HIV-1 Vif binding. Nat Struct Mol Biol. 2012;19:1005-10 pubmed publisher
    ..These findings provide insight into Vif-A3 interactions and could lead to the development of new pharmacologic anti-HIV-1 compounds...
  45. Phalora P, Sherer N, Wolinsky S, Swanson C, Malim M. HIV-1 replication and APOBEC3 antiviral activity are not regulated by P bodies. J Virol. 2012;86:11712-24 pubmed publisher
    ..Localization to P bodies may therefore provide a means of sequestering APOBEC3 enzymatic activity away from cellular DNA or may be linked to as yet unidentified cellular functions. ..
  46. Desimmie B, Burdick R, Izumi T, Doi H, Shao W, Alvord W, et al. APOBEC3 proteins can copackage and comutate HIV-1 genomes. Nucleic Acids Res. 2016;44:7848-65 pubmed publisher
    Although APOBEC3 cytidine deaminases A3G, A3F, A3D and A3H are packaged into virions and inhibit viral replication by inducing G-to-A hypermutation, it is not known whether they are copackaged and whether they can act additively or ..
  47. Sura W, Kabza M, Karlowski W, Bieluszewski T, Kus Slowinska M, Pawełoszek Ł, et al. Dual Role of the Histone Variant H2A.Z in Transcriptional Regulation of Stress-Response Genes. Plant Cell. 2017;29:791-807 pubmed publisher
    ..the impact of this histone variant on gene expression in Arabidopsis thaliana We demonstrate that the arp6 mutant exhibits anomalies in response to osmotic stress...
  48. Kitamura S, Ode H, Iwatani Y. Structural Features of Antiviral APOBEC3 Proteins are Linked to Their Functional Activities. Front Microbiol. 2011;2:258 pubmed publisher
    ..Here, we review the biological functions of A3 family members with special focus on A3G and base our analysis on the available structural information. ..
  49. Sheehy A, Erthal J. APOBEC3 versus Retroviruses, Immunity versus Invasion: Clash of the Titans. Mol Biol Int. 2012;2012:974924 pubmed publisher
    ..The emerging story implicates the A3 family as not only defense proteins, but also as participants in the broader innate immune response. ..
  50. Hultquist J, Harris R. Leveraging APOBEC3 proteins to alter the HIV mutation rate and combat AIDS. Future Virol. 2009;4:605 pubmed
    ..The current state of mechanistic information is reviewed and the possible risks and benefits of increasing (via hypermutation) or decreasing (via hypomutation) the HIV-1 mutation rate through APOBEC3 proteins are discussed. ..
  51. Bouzidi M, Caval V, Suspène R, Hallez C, Pineau P, Wain Hobson S, et al. APOBEC3DE Antagonizes Hepatitis B Virus Restriction Factors APOBEC3F and APOBEC3G. J Mol Biol. 2016;428:3514-28 pubmed publisher
    ..b>APOBEC3DE (A3DE) stands out in that it is catalytically inactive due to a fixed Tyr320Cys substitution in the C-terminal ..
  52. Kim D. The assembly of Vif ubiquitin E3 ligase for APOBEC3 degradation. Arch Pharm Res. 2015;38:435-45 pubmed publisher
  53. Sato K, Takeuchi J, Misawa N, Izumi T, Kobayashi T, Kimura Y, et al. APOBEC3D and APOBEC3F potently promote HIV-1 diversification and evolution in humanized mouse model. PLoS Pathog. 2014;10:e1004453 pubmed publisher
    Several APOBEC3 proteins, particularly APOBEC3D, APOBEC3F, and APOBEC3G, induce G-to-A hypermutations in HIV-1 genome, and abrogate viral replication in experimental systems, but their relative contributions to controlling viral ..
  54. Samuel C. Introduction to thematic minireview series: Understanding human immunodeficiency virus-host interactions at the biochemical level. J Biol Chem. 2012;287:40838-40 pubmed publisher
  55. Chiu Y, Greene W. APOBEC3G: an intracellular centurion. Philos Trans R Soc Lond B Biol Sci. 2009;364:689-703 pubmed publisher
    ..LMM A3G opposes the external threat posed by exogenous retroviruses, while HMM A3G complexes oppose the internal threat posed by the retrotransposition of select types of retroelements. ..