Skip to main content
Log in

An Overview of Cytidine Deaminases

  • Progress in Hematology
  • Published:
International Journal of Hematology Aims and scope Submit manuscript

Abstract

Enzymes that deaminate cytidine to uridine play an important role in a variety of pathways from bacteria to man.Ancestral members of this family were able to deaminate cytidine only in a mononucleotide or nucleoside context. Recently, a family of enzymes has been discovered with the ability to deaminate cytidines on RNA or DNA. The first member of this new family is APOBEC1, which deaminates apolipoprotein B messenger RNA to generate a premature stop codon. APOBEC1 has the conserved active site motif found in Escherichia coli cytidine deaminase. In addition, APOBEC1 has a unique motif containing 2 phenylalanine residues and an insert of 4 amino acid residues across the active site motif. This motif is present in APOBEC family members including activation-induced cytidine deaminase (AID), APOBEC2, and APOBEC3A through APOBEC3G. AID is essential for initiating class-switch recombination, somatic hypermutation, and gene conversion. The APOBEC3 family is unique to primates. APOBEC3G is able to protect cells from human immunodeficiency virus and other viral infections.This function is not unique to APOBEC3G; other APOBEC3 family members also have this ability. Overexpression of enzymes in this family can cause cancer, suggesting that the genes for the APOBEC family of proteins are proto-oncogenes. Recent advances in the understanding of the mechanism of action of this family are summarized in this review.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

References

  1. Carter CW Jr. The nucleoside deaminases for cytidine and adenosine: structure, transition state stabilization, mechanism, and evolution. Biochimie. 1995;77:92–98.

    Article  PubMed  CAS  Google Scholar 

  2. Betts L, Xiang S, Short SA, Wolfenden R, Carter CW Jr. Cytidine deaminase: the 2.3 Å crystal structure of an enzyme: transition-state analog complex. J Mol Biol. 1994;235:635–656.

    Article  PubMed  CAS  Google Scholar 

  3. Wilson DK, Rudolph FB, Quiocho FA. Atomic structure of adenosine deaminase complexed with a transition-state analog: understanding catalysis and immunodeficiency mutations. Science. 1991;252:1278–1284.

    Article  PubMed  CAS  Google Scholar 

  4. Teng B, Burant CF, Davidson NO. Molecular cloning of an apolipoprotein B messenger RNA editing protein. Science. 1993;260:1816–1819.

    Article  PubMed  CAS  Google Scholar 

  5. Scott J, Navaratnam N, Bhattacharya S, Morrison JR. The apolipoprotein B messenger RNA editing enzyme. Curr Opin Lipidol. 1994;5:87–93.

    Article  PubMed  CAS  Google Scholar 

  6. Navaratnam N, Morrison JR, Bhattacharya S, et al. The p27 catalytic subunit of the apolipoprotein B mRNA editing enzyme is a cytidine deaminase. J Biol Chem. 1993;268:20709–20712.

    PubMed  CAS  Google Scholar 

  7. Jarmuz A, Chester A, Bayliss J, et al. An anthropoid-specific locus of orphan C to U RNA-editing enzymes on chromosome 22. Genomics. 2002;79:285–296.

    Article  PubMed  CAS  Google Scholar 

  8. Muramatsu M, Sankaranand VS, Anant S, et al. Specific expression of activation-induced cytidine deaminase (AID), a novel member of the RNA-editing deaminase family in germinal center B cells. J Biol Chem. 1999;274:18470–18476.

    Article  PubMed  CAS  Google Scholar 

  9. Rogozin IB, Basu MK, Jordan IK, Pavlov YI, Koonin EV. APOBEC4, a new member of the AID/APOBEC family of polynucleotide (deoxy)cytidine deaminases predicted by computational analysis. Cell Cycle. 2005;4:1281–1285.

    Article  PubMed  CAS  Google Scholar 

  10. Conticello SG, Thomas CJ, Petersen-Mahrt SK, Neuberger MS. Evolution of the AID/APOBEC family of polynucleotide (deoxy)cytidine deaminases. Mol Biol Evol. 2005;22:367–377.

    Article  PubMed  CAS  Google Scholar 

  11. Saunders HL, Magor BG. Cloning and expression of the AID gene in the channel catfish. Dev Comp Immunol. 2004;28:657–663.

    Article  PubMed  CAS  Google Scholar 

  12. Zhao Y, Pan-Hammarstrom Q, Zhao Z, Hammarstrom L. Identification of the activation-induced cytidine deaminase gene from zebrafish: an evolutionary analysis. Dev Comp Immunol. 2005;29:61–71.

    Article  PubMed  CAS  Google Scholar 

  13. Hentze MW, Kulozik AE. A perfect message: RNA surveillance and nonsense-mediated decay. Cell. 1999;96:307–310.

    Article  PubMed  CAS  Google Scholar 

  14. Powell LM, Wallis SC, Pease RJ, Edwards YH, Knott TJ, Scott J. A novel form of tissue-specific RNA processing produces apolipoprotein-B48 in intestine. Cell. 1987;50:831–840.

    Article  PubMed  CAS  Google Scholar 

  15. Chang CN, Doong SL, Zhou JH, et al. Deoxycytidine deaminase-resistant stereoisomer is the active form of (+/-)-2′,3′-dideoxy-3′- thiacytidine in the inhibition of hepatitis B virus replication. J Biol Chem. 1992;267:13938–13942.

    PubMed  CAS  Google Scholar 

  16. Mehta A, Kinter MT, Sherman NE, Driscoll DM. Molecular cloning of apobec-1 complementation factor, a novel RNA-binding protein involved in the editing of apolipoprotein B mRNA. Mol Cell Biol. 2000;20:1846–1854.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  17. Chester A, Scott J, Anant S, Navaratnam N. RNA editing: cytidine to uridine conversion in apolipoprotein B mRNA. Biochim Biophys Acta. 2000;1494:1–13.

    Article  PubMed  CAS  Google Scholar 

  18. Maris C, Masse J, Chester A, Navaratnam N, Allain FH. NMR structure of the apoB mRNA stem-loop and its interaction with the C to U editing APOBEC1 complementary factor. RNA. 2005;11:173–186.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  19. Chester A, Somasekaram A, Tzimina M, et al. The apolipoprotein B mRNA editing complex performs a multifunctional cycle and suppresses nonsense-mediated decay. EMBO J. 2003;22:3971–3982.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  20. Morrison JR, Paszty C, Stevens ME, et al. Apolipoprotein B RNA editing enzyme-deficient mice are viable despite alterations in lipoprotein metabolism. Proc Natl Acad Sci U S A. 1996;93:7154–7159.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  21. Teng B, Blumenthal S, Forte T, et al. Adenovirus-mediated gene transfer of rat apolipoprotein B mRNA-editing protein in mice virtually eliminates apolipoprotein B-100 and normal low density lipoprotein production. J Biol Chem. 1994;269:29395–29404.

    PubMed  CAS  Google Scholar 

  22. Hughes SD, Rouy D, Navaratnam N, Scott J, Rubin EM. Gene transfer of cytidine deaminase apoBEC-1 lowers lipoprotein(a) in transgenic mice and induces apolipoprotein B editing in rabbits. Hum Gene Ther. 1996;7:39–49.

    Article  PubMed  CAS  Google Scholar 

  23. Yamanaka S, Poksay KS, Driscoll DM, Innerarity TL. Hyperediting of multiple cytidines of apolipoprotein B mRNA by APOBEC-1 requires auxiliary protein(s) but not a mooring sequence motif. J Biol Chem. 1996;271:11506–11510.

    Article  PubMed  CAS  Google Scholar 

  24. Anant S, Davidson NO. An AU-rich sequence element (UUUN[A/U]U) downstream of the edited C in apolipoprotein B mRNA is a high-affinity binding site for Apobec-1: binding of Apobec-1 to this motif in the 3′ untranslated region of c-myc increases mRNA stability. Mol Cell Biol. 2000;20:1982–1992.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  25. Muramatsu M, Kinoshita K, Fagarasan S, Yamada S, Shinkai Y, Honjo T. Class switch recombination and hypermutation require activation-induced cytidine deaminase (AID), a potential RNA editing enzyme. Cell. 2000;102:553–563.

    Article  PubMed  CAS  Google Scholar 

  26. Revy P, Muto T, Levy Y, et al. Activation-induced cytidine deaminase (AID) deficiency causes the autosomal recessive form of the hyper-IgM syndrome (HIGM2). Cell. 2000;102:565–575.

    Article  PubMed  CAS  Google Scholar 

  27. Arakawa H, Hauschild J, Buerstedde JM. Requirement of the activation-induced deaminase (AID) gene for immunoglobulin gene conversion. Science. 2002;295:1301–1306.

    Article  PubMed  CAS  Google Scholar 

  28. Petersen-Mahrt SK, Harris RS, Neuberger MS. AID mutates E. coli suggesting a DNA deamination mechanism for antibody diversification. Nature. 2002;418:99–103.

    Article  PubMed  CAS  Google Scholar 

  29. Neuberger MS, Harris RS, Di Noia J, Petersen-Mahrt SK. Immunity through DNA deamination. Trends Biochem Sci. 2003;28:305–312.

    Article  PubMed  CAS  Google Scholar 

  30. Honjo T, Muramatsu M, Fagarasan S. AID: how does it aid antibody diversity? Immunity. 2004;20:659–668.

    Article  PubMed  CAS  Google Scholar 

  31. Stavnezer J, Schrader CE. Mismatch repair converts AID-instigated nicks to double-strand breaks for antibody class-switch recombination. Trends Genet. 2006;22:23–28.

    Article  PubMed  CAS  Google Scholar 

  32. Chaudhuri J, Khuong C, Alt FW. Replication protein A interacts with AID to promote deamination of somatic hypermutation targets. Nature. 2004;430:992–998.

    Article  PubMed  CAS  Google Scholar 

  33. Pham P, Bransteitter R, Petruska J, Goodman MF. Processive AID-catalysed cytosine deamination on single-stranded DNA simulates somatic hypermutation. Nature. 2003;424:103–107.

    Article  PubMed  CAS  Google Scholar 

  34. Reynaud CA, Aoufouchi S, Faili A, Weill JC. What role for AID: mutator, or assembler of the immunoglobulin mutasome? Nat Immunol. 2003;4:631–638.

    Article  PubMed  CAS  Google Scholar 

  35. Rada C, Jarvis JM, Milstein C. AID-GFP chimeric protein increases hypermutation of Ig genes with no evidence of nuclear localization. Proc Natl Acad Sci U S A. 2002;99:7003–7008.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  36. Ito S, Nagaoka H, Shinkura R, et al. Activation-induced cytidine deaminase shuttles between nucleus and cytoplasm like apolipoprotein B mRNA editing catalytic polypeptide 1. Proc Natl Acad Sci U S A. 2004;101:1975–1980.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  37. Barreto V, Reina-San-Martin B, Ramiro AR, McBride KM, Nussenzweig MC. C-terminal deletion of AID uncouples class switch recombination from somatic hypermutation and gene conversion. Mol Cell. 2003;12:501–508.

    Article  PubMed  CAS  Google Scholar 

  38. Ta VT, Nagaoka H, Catalan N, et al. AID mutant analyses indicate requirement for class-switch-specific cofactors. Nat Immunol. 2003;4:843–848.

    Article  PubMed  CAS  Google Scholar 

  39. Basu U, Chaudhuri J, Alpert C, et al. The AID antibody diversification enzyme is regulated by protein kinase A phosphorylation. Nature. 2005;438:508–511.

    Article  PubMed  CAS  Google Scholar 

  40. Pasqualucci L, Kitaura Y, Gu H, Dalla-Favera R. PKA-mediated phosphorylation regulates the function of activation-induced deaminase (AID) in B cells. Proc Natl Acad Sci U S A. 2006;103:395–400.

    Article  PubMed  CAS  Google Scholar 

  41. Okazaki IM, Hiai H, Kakazu N, et al. Constitutive expression of AID leads to tumorigenesis. J Exp Med. 2003;197:1173–1181.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  42. Mikl MC, Watt IN, Lu M, et al. Mice deficient in APOBEC2 and APOBEC3. Mol Cell Biol. 2005;25:7270–7277.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  43. Wedekind JE, Dance GS, Sowden MP, Smith HC. Messenger RNA editing in mammals: new members of the APOBEC family seeking roles in the family business. Trends Genet. 2003;19:207–216.

    Article  PubMed  CAS  Google Scholar 

  44. Bishop KN, Holmes RK, Sheehy AM, Davidson NO, Cho SJ, Malim MH. Cytidine deamination of retroviral DNA by diverse APOBEC proteins. Curr Biol. 2004;14:1392–1396.

    Article  PubMed  CAS  Google Scholar 

  45. Liddament MT, Brown WL, Schumacher AJ, Harris RS. APOBEC3F properties and hypermutation preferences indicate activity against HIV-1 in vivo. Curr Biol. 2004;14:1385–1391.

    Article  PubMed  CAS  Google Scholar 

  46. Yu Q, Chen D, Konig R, Mariani R, Unutmaz D, Landau NR. APOBEC3B and APOBEC3C are potent inhibitors of simian immunodeficiency virus replication. J Biol Chem. 2004;279:53379–53386.

    Article  PubMed  CAS  Google Scholar 

  47. Mangeat B, Turelli P, Caron G, Friedli M, Perrin L, Trono D. Broad antiretroviral defence by human APOBEC3G through lethal editing of nascent reverse transcripts. Nature. 2003;424:99–103.

    Article  PubMed  CAS  Google Scholar 

  48. Sheehy AM, Gaddis NC, Choi JD, Malim MH. Isolation of a human gene that inhibits HIV-1 infection and is suppressed by the viral Vif protein. Nature. 2002;418:646–650.

    Article  PubMed  CAS  Google Scholar 

  49. Harris RS, Liddament MT. Retroviral restriction by APOBEC proteins. Nat Rev Immunol. 2004;4:868–877.

    Article  PubMed  CAS  Google Scholar 

  50. Petersen-Mahrt SK, Neuberger MS. In vitro deamination of cytosine to uracil in single-stranded DNA by apolipoprotein B editing complex catalytic subunit 1 (APOBEC1). J Biol Chem. 2003;278:19583–19586.

    Article  PubMed  CAS  Google Scholar 

  51. Schrofelbauer B, Chen D, Landau NR. A single amino acid of APOBEC3G controls its species-specific interaction with virion infectivity factor (Vif). Proc Natl Acad Sci U S A. 2004;101:3927–3932.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  52. Bishop KN, Holmes RK, Sheehy AM, Malim MH. APOBEC-mediated editing of viral RNA. Science. 2004;305:645.

    Article  PubMed  CAS  Google Scholar 

  53. Wiegand HL, Doehle BP, Bogerd HP, Cullen BR. A second human antiretroviral factor, APOBEC3F, is suppressed by the HIV-1 and HIV-2 Vif proteins. EMBO J. 2004;23:2451–2458.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  54. Zheng YH, Irwin D, Kurosu T, Tokunaga K, Sata T, Peterlin BM. Human APOBEC3F is another host factor that blocks human immunodeficiency virus type 1 replication. J Virol. 2004;78:6073–6076.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  55. Turelli P, Mangeat B, Jost S, Vianin S, Trono D. Inhibition of hepatitis B virus replication by APOBEC3G. Science. 2004;303:1829.

    Article  PubMed  Google Scholar 

  56. Yu Q, Konig R, Pillai S, et al. Single-strand specificity of APOBEC3G accounts for minus-strand deamination of the HIV genome. Nat Struct Mol Biol. 2004;11:435–442.

    Article  PubMed  CAS  Google Scholar 

  57. Gunther S, Sommer G, Plikat U, et al. Naturally occurring hepatitis B virus genomes bearing the hallmarks of retroviral G→A hypermutation. Virology. 1997;235:104–108.

    Article  PubMed  CAS  Google Scholar 

  58. Rosler C, Kock J, Kann M, et al. APOBEC-mediated interference with hepadnavirus production. Hepatology. 2005;42:301–309.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Naveenan Navaratnam.

About this article

Cite this article

Navaratnam, N., Sarwar, R. An Overview of Cytidine Deaminases. Int J Hematol 83, 195–200 (2006). https://doi.org/10.1532/IJH97.06032

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1532/IJH97.06032

Key words

Navigation