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PMID: 15949042 Published · epublish English Journal Article Research Support, Non-U.S. Gov't

Expression of human AID in yeast induces mutations in context similar to the context of somatic hypermutation at G-C pairs in immunoglobulin genes.

BMC immunology ·Vol. 6 ·2005-06-10 ·Pages 10

Mayorov VI, Rogozin IB, Adkison LR, Frahm C, Kunkel TA, Pavlov YI

Abstract

Antibody genes are diversified by somatic hypermutation (SHM), gene conversion and class-switch recombination. All three processes are initiated by the activation-induced deaminase (AID). According to a DNA deamination model of SHM, AID converts cytosine to uracil in DNA sequences. The initial deamination of cytosine leads to mutation and recombination in pathways involving replication, DNA mismatch repair and possibly base excision repair. The DNA sequence context of mutation hotspots at G-C pairs during SHM is DGYW/WRCH (G-C is a hotspot position, R = A/G, Y = T/C, W = A/T, D = A/G/T). To investigate the mechanisms of AID-induced mutagenesis in a model system, we studied the genetic consequences of AID expression in yeast. We constructed a yeast vector with an artificially synthesized human AID gene insert using codons common to highly expressed yeast genes. We found that expression of the artificial hAIDSc gene was moderately mutagenic in a wild-type strain and highly mutagenic in an ung1 uracil-DNA glycosylase-deficient strain. A majority of mutations were at G-C pairs. In the ung1 strain, C-G to T-A transitions were found almost exclusively, while a mixture of transitions with 12% transversions was characteristic in the wild-type strain. In the ung1 strain mutations that could have originated from deamination of the transcribed stand were found more frequently. In the wild-type strain, the strand bias was reversed. DGYW/WRCH motifs were preferential sites of mutations. The results are consistent with the hypothesis that AID-mediated deamination of DNA is a major cause of mutations at G-C base pairs in immunoglobulin genes during SHM. The sequence contexts of mutations in yeast induced by AID and those of somatic mutations at G-C pairs in immunoglobulin genes are significantly similar. This indicates that the intrinsic substrate specificity of AID itself is a primary determinant of mutational hotspots at G-C base pairs during SHM.

MeSH Terms
Amino Acid Transport Systems, Basic/genetics Base Pairing Codon/genetics Cytidine Deaminase Cytosine Deaminase/genetics,physiology Genes, Immunoglobulin Genes, Suppressor Humans Mutagenesis Saccharomyces cerevisiae/genetics Saccharomyces cerevisiae Proteins/genetics Somatic Hypermutation, Immunoglobulin/genetics,physiology Substrate Specificity
Chemicals
Amino Acid Transport Systems, Basic CAN1 protein, S cerevisiae Codon Saccharomyces cerevisiae Proteins AICDA (activation-induced cytidine deaminase) Cytosine Deaminase Cytidine Deaminase
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
Mayorov Vladimir I
Mercer University School of Medicine, Macon, GA 31207, USA. mayorov_vi@mercer.edu
Rogozin Igor B
Adkison Linda R
Frahm Christin
Kunkel Thomas A
Pavlov Youri I
References (97)
97 references, click to expand
  1. Altering the pathway of immunoglobulin hypermutation by inhibiting uracil-DNA glycosylase.
    Nature. 2002 Sep 5;419(6902):43-8 PMID: 12214226
  2. Immunoglobulin isotype switching is inhibited and somatic hypermutation perturbed in UNG-deficient mice.
    Curr Biol. 2002 Oct 15;12(20):1748-55 PMID: 12401169
  3. Induction of somatic hypermutation in immunoglobulin genes is dependent on DNA polymerase iota.
    Nature. 2002 Oct 31;419(6910):944-7 PMID: 12410315
  4. Immunoglobulin genes: generating diversity with AID and UNG.
    Curr Biol. 2002 Oct 29;12(21):R725-7 PMID: 12419200
  5. The roles of REV3 and RAD57 in double-strand-break-repair-induced mutagenesis of Saccharomyces cerevisiae.
    Genetics. 2002 Nov;162(3):1063-77 PMID: 12454056
  6. RNA editing enzyme APOBEC1 and some of its homologs can act as DNA mutators.
    Mol Cell. 2002 Nov;10(5):1247-53 PMID: 12453430
  7. Subpathways of nucleotide excision repair and their regulation.
    Oncogene. 2002 Dec 16;21(58):8949-56 PMID: 12483511
  8. Functions of human DNA polymerases eta, kappa and iota suggested by their properties, including fidelity with undamaged DNA templates.
    DNA Repair (Amst). 2003 Feb 3;2(2):135-49 PMID: 12531385
  9. De novo protein synthesis is required for the activation-induced cytidine deaminase function in class-switch recombination.
    Proc Natl Acad Sci U S A. 2003 Mar 4;100(5):2634-8 PMID: 12591955
  10. Activation-induced cytidine deaminase deaminates deoxycytidine on single-stranded DNA but requires the action of RNase.
    Proc Natl Acad Sci U S A. 2003 Apr 1;100(7):4102-7 PMID: 12651944
  11. Revisiting the codon adaptation index from a whole-genome perspective: analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models.
    Nucleic Acids Res. 2003 Apr 15;31(8):2242-51 PMID: 12682375
  12. Transcription-targeted DNA deamination by the AID antibody diversification enzyme.
    Nature. 2003 Apr 17;422(6933):726-30 PMID: 12692563
  13. A novel cytidine deaminase AIDs in the delivery of error-prone polymerases to immunoglobulin genes.
    DNA Repair (Amst). 2003 May 13;2(5):623-7 PMID: 12713818
  14. Transcription enhances AID-mediated cytidine deamination by exposing single-stranded DNA on the nontemplate strand.
    Nat Immunol. 2003 May;4(5):452-6 PMID: 12692548
  15. Analysis of somatic hypermutation in mouse Peyer's patches using immunoglobulin kappa light-chain transgenes.
    Proc Natl Acad Sci U S A. 1993 Nov 1;90(21):9862-6 PMID: 8234326
  16. Genetic evidence for Gln3p-independent, nitrogen catabolite repression-sensitive gene expression in Saccharomyces cerevisiae.
    J Bacteriol. 1995 Dec;177(23):6910-8 PMID: 7592485
  17. Base analog 6-N-hydroxylaminopurine mutagenesis in the yeast Saccharomyces cerevisiae is controlled by replicative DNA polymerases.
    Mutat Res. 1996 Jul 10;369(1-2):33-44 PMID: 8700180
  18. 3'-->5' exonucleases of DNA polymerases epsilon and delta correct base analog induced DNA replication errors on opposite DNA strands in Saccharomyces cerevisiae.
    Genetics. 1996 Mar;142(3):717-26 PMID: 8849882
  19. Influences of histone stoichiometry on the target site preference of retrotransposons Ty1 and Ty2 in Saccharomyces cerevisiae.
    Genetics. 1996 Mar;142(3):761-76 PMID: 8849886
  20. A novel mutation avoidance mechanism dependent on S. cerevisiae RAD27 is distinct from DNA mismatch repair.
    Cell. 1997 Jan 24;88(2):253-63 PMID: 9008166
  21. Abnormal CD40-mediated activation pathway in B lymphocytes from patients with hyper-IgM syndrome and normal CD40 ligand expression.
    J Immunol. 1997 Mar 15;158(6):2576-84 PMID: 9058789
  22. DNA sequence analysis of spontaneous mutagenesis in Saccharomyces cerevisiae.
    Genetics. 1998 Apr;148(4):1491-505 PMID: 9560369
  23. Both DNA strands of antibody genes are hypermutation targets.
    Proc Natl Acad Sci U S A. 1998 Jul 21;95(15):8791-4 PMID: 9671757
  24. The subclass approach for mutational spectrum analysis: application of the SEM algorithm.
    J Theor Biol. 1998 Jun 21;192(4):475-87 PMID: 9680721
  25. Mutator phenotypes conferred by MLH1 overexpression and by heterozygosity for mlh1 mutations.
    Mol Cell Biol. 1999 Apr;19(4):3177-83 PMID: 10082584
  26. Characteristics of sequences around individual nucleotide substitutions in IgVH genes suggest different GC and AT mutators.
    J Immunol. 1999 Jun 1;162(11):6596-601 PMID: 10352276
  27. Biochemical analysis of hypermutational targeting by wild type and mutant activation-induced cytidine deaminase.
    J Biol Chem. 2004 Dec 3;279(49):51612-21 PMID: 15371439
  28. Repair and genetic consequences of endogenous DNA base damage in mammalian cells.
    Annu Rev Genet. 2004;38:445-76 PMID: 15568983
  29. The exceptionally high rate of spontaneous mutations in the polymerase delta proofreading exonuclease-deficient Saccharomyces cerevisiae strain starved for adenine.
    BMC Genet. 2004;5:34 PMID: 15617571
  30. Activation-induced deaminase: controversies and open questions.
    Trends Immunol. 2005 Feb;26(2):90-6 PMID: 15668124
  31. Somatic hypermutation at A.T pairs: polymerase error versus dUTP incorporation.
    Nat Rev Immunol. 2005 Feb;5(2):171-8 PMID: 15688043
  32. Reward versus risk: DNA cytidine deaminases triggering immunity and disease.
    Biochemistry. 2005 Mar 1;44(8):2703-15 PMID: 15723516
  33. MSH2-MSH6 stimulates DNA polymerase eta, suggesting a role for A:T mutations in antibody genes.
    J Exp Med. 2005 Feb 21;201(4):637-45 PMID: 15710654
  34. Somatic hypermutation of VkappaJkappa rearrangements: targeting of RGYW motifs on both DNA strands and preferential selection of mutated codons within RGYW motifs.
    Eur J Immunol. 1999 Dec;29(12):4011-21 PMID: 10602011
  35. Similarity pattern analysis in mutational distributions.
    Mutat Res. 1999 Nov 29;430(1):55-74 PMID: 10592318
  36. Uracil-DNA glycosylase (UNG)-deficient mice reveal a primary role of the enzyme during DNA replication.
    Mol Cell. 2000 Jun;5(6):1059-65 PMID: 10912000
  37. Class switch recombination and hypermutation require activation-induced cytidine deaminase (AID), a potential RNA editing enzyme.
    Cell. 2000 Sep 1;102(5):553-63 PMID: 11007474
  38. Activation-induced cytidine deaminase (AID) deficiency causes the autosomal recessive form of the Hyper-IgM syndrome (HIGM2).
    Cell. 2000 Sep 1;102(5):565-75 PMID: 11007475
  39. Error-prone candidates vie for somatic mutation.
    J Exp Med. 2000 Nov 20;192(10):F27-30 PMID: 11085756
  40. Use of mutation spectra analysis software.
    Hum Mutat. 2001 Feb;17(2):83-102 PMID: 11180592
  41. Biochemical characterization of human DNA polymerase iota provides clues to its biological function.
    Biochem Soc Trans. 2001 May;29(Pt 2):183-7 PMID: 11356150
  42. The translesion DNA polymerase zeta plays a major role in Ig and bcl-6 somatic hypermutation.
    Immunity. 2001 May;14(5):643-53 PMID: 11371365
  43. Somatic mutation hotspots correlate with DNA polymerase eta error spectrum.
    Nat Immunol. 2001 Jun;2(6):530-6 PMID: 11376340
  44. Induction of somatic hypermutation is associated with modifications in immunoglobulin variable region chromatin.
    Immunity. 2003 Oct;19(4):479-89 PMID: 14563313
  45. DNA-cytosine deaminases: from antibody maturation to antiviral defense.
    DNA Repair (Amst). 2004 Jan 5;3(1):85-9 PMID: 14697763
  46. The generation of antibody diversity through somatic hypermutation and class switch recombination.
    Genes Dev. 2004 Jan 1;18(1):1-11 PMID: 14724175
  47. Immunoglobulin gene conversion in chicken DT40 cells largely proceeds through an abasic site intermediate generated by excision of the uracil produced by AID-mediated deoxycytidine deamination.
    Eur J Immunol. 2004 Feb;34(2):504-8 PMID: 14768055
  48. Somatic hypermutation and B cell receptor selection in normal and transformed human B cells.
    Ann N Y Acad Sci. 2003 Apr;987:173-9 PMID: 12727637
  49. Constitutive expression of AID leads to tumorigenesis.
    J Exp Med. 2003 May 5;197(9):1173-81 PMID: 12732658
  50. AID mediates hypermutation by deaminating single stranded DNA.
    J Exp Med. 2003 May 19;197(10):1291-6 PMID: 12756266
  51. Human activation-induced cytidine deaminase causes transcription-dependent, strand-biased C to U deaminations.
    Nucleic Acids Res. 2003 Jun 15;31(12):2990-4 PMID: 12799424
  52. SIFT: Predicting amino acid changes that affect protein function.
    Nucleic Acids Res. 2003 Jul 1;31(13):3812-4 PMID: 12824425
  53. Immunity through DNA deamination.
    Trends Biochem Sci. 2003 Jun;28(6):305-12 PMID: 12826402
  54. Processive AID-catalysed cytosine deamination on single-stranded DNA simulates somatic hypermutation.
    Nature. 2003 Jul 3;424(6944):103-7 PMID: 12819663
  55. Theoretical analysis of mutation hotspots and their DNA sequence context specificity.
    Mutat Res. 2003 Sep;544(1):65-85 PMID: 12888108
  56. Roles of Saccharomyces cerevisiae DNA polymerases Poleta and Polzeta in response to irradiation by simulated sunlight.
    Nucleic Acids Res. 2003 Aug 1;31(15):4541-52 PMID: 12888515
  57. 129-derived strains of mice are deficient in DNA polymerase iota and have normal immunoglobulin hypermutation.
    J Exp Med. 2003 Aug 18;198(4):635-43 PMID: 12925679
  58. The spectrum of spontaneous mutations in a Saccharomyces cerevisiae uracil-DNA-glycosylase mutant limits the function of this enzyme to cytosine deamination repair.
    J Bacteriol. 1991 Nov;173(21):6807-10 PMID: 1938887
  59. Elimination of the yeast RAD6 ubiquitin conjugase enhances base-pair transitions and G.C----T.A transversions as well as transposition of the Ty element: implications for the control of spontaneous mutation.
    Genetics. 1992 Feb;130(2):285-94 PMID: 1311695
  60. Somatic hypermutagenesis in immunoglobulin genes. II. Influence of neighbouring base sequences on mutagenesis.
    Biochim Biophys Acta. 1992 Nov 15;1171(1):11-8 PMID: 1420357
  61. Passenger transgenes reveal intrinsic specificity of the antibody hypermutation mechanism: clustering, polarity, and specific hot spots.
    Proc Natl Acad Sci U S A. 1993 Mar 15;90(6):2385-8 PMID: 8460148
  62. DNA substrate length and surrounding sequence affect the activation-induced deaminase activity at cytidine.
    J Biol Chem. 2004 Feb 20;279(8):6496-500 PMID: 14645244
  63. 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 Feb 17;101(7):1975-80 PMID: 14769937
  64. Cutting edge: DGYW/WRCH is a better predictor of mutability at G:C bases in Ig hypermutation than the widely accepted RGYW/WRCY motif and probably reflects a two-step activation-induced cytidine deaminase-triggered process.
    J Immunol. 2004 Mar 15;172(6):3382-4 PMID: 15004135
  65. Comparison of the differential context-dependence of DNA deamination by APOBEC enzymes: correlation with mutation spectra in vivo.
    J Mol Biol. 2004 Mar 26;337(3):585-96 PMID: 15019779
  66. Palm mutants in DNA polymerases alpha and eta alter DNA replication fidelity and translesion activity.
    Mol Cell Biol. 2004 Apr;24(7):2734-46 PMID: 15024063
  67. Recombinogenic phenotype of human activation-induced cytosine deaminase.
    J Immunol. 2004 Apr 1;172(7):4308-13 PMID: 15034045
  68. Analysis of strand biased 'G'.C hypermutation in human immunoglobulin V(lambda) gene segments suggests that both DNA strands are targets for deamination by activation-induced cytidine deaminase.
    Mol Immunol. 2004 Mar;40(17):1273-8 PMID: 15128044
  69. AID: how does it aid antibody diversity?
    Immunity. 2004 Jun;20(6):659-68 PMID: 15189732
  70. Replication protein A interacts with AID to promote deamination of somatic hypermutation targets.
    Nature. 2004 Aug 26;430(7003):992-8 PMID: 15273694
  71. Activation-induced cytidine deaminase (AID) can target both DNA strands when the DNA is supercoiled.
    Proc Natl Acad Sci U S A. 2004 Aug 31;101(35):12997-3002 PMID: 15328407
  72. The role of activation-induced cytidine deaminase in antibody diversification, immunodeficiency, and B-cell malignancies.
    J Allergy Clin Immunol. 2004 Oct;114(4):726-35; quiz 736 PMID: 15480307
  73. Mismatch recognition and uracil excision provide complementary paths to both Ig switching and the A/T-focused phase of somatic mutation.
    Mol Cell. 2004 Oct 22;16(2):163-71 PMID: 15494304
  74. DNA glycosylases, endonucleases for apurinic/apyrimidinic sites, and base excision-repair.
    Prog Nucleic Acid Res Mol Biol. 1979;22:135-92 PMID: 392601
  75. Rearrangements of immunoglobulin genes during differentiation and evolution.
    Immunol Rev. 1981;59:33-67 PMID: 6796498
  76. Codon selection in yeast.
    J Biol Chem. 1982 Mar 25;257(6):3026-31 PMID: 7037777
  77. Somatic generation of antibody diversity.
    Nature. 1983 Apr 14;302(5909):575-81 PMID: 6300689
  78. Isolation of a DNA fragment that is expressed as an amber suppressor when present in high copy number in yeast.
    Gene. 1984 Jul-Aug;29(1-2):69-76 PMID: 6092233
  79. Statistical test for the comparison of samples from mutational spectra.
    J Mol Biol. 1987 Apr 5;194(3):391-6 PMID: 3305960
  80. Development of the primary antibody repertoire.
    Science. 1987 Nov 20;238(4830):1079-87 PMID: 3317825
  81. DNA polymerase eta is an A-T mutator in somatic hypermutation of immunoglobulin variable genes.
    Nat Immunol. 2001 Jun;2(6):537-41 PMID: 11376341
  82. Mutator effects of overproducing DNA polymerase eta (Rad30) and its catalytically inactive variant in yeast.
    Mutat Res. 2001 Jul 1;478(1-2):129-39 PMID: 11406177
  83. Linking class-switch recombination with somatic hypermutation.
    Nat Rev Mol Cell Biol. 2001 Jul;2(7):493-503 PMID: 11433363
  84. Expression of error-prone polymerases in BL2 cells activated for Ig somatic hypermutation.
    Proc Natl Acad Sci U S A. 2001 Jul 3;98(14):7976-81 PMID: 11427727
  85. Ammonia regulates VID30 expression and Vid30p function shifts nitrogen metabolism toward glutamate formation especially when Saccharomyces cerevisiae is grown in low concentrations of ammonia.
    J Biol Chem. 2001 Aug 3;276(31):28659-66 PMID: 11356843
  86. Human genetic defects in class-switch recombination (hyper-IgM syndromes).
    Curr Opin Immunol. 2001 Oct;13(5):543-8 PMID: 11544001
  87. Error rate and specificity of human and murine DNA polymerase eta.
    J Mol Biol. 2001 Sep 14;312(2):335-46 PMID: 11554790
  88. In vivo consequences of putative active site mutations in yeast DNA polymerases alpha, epsilon, delta, and zeta.
    Genetics. 2001 Sep;159(1):47-64 PMID: 11560886
  89. Activation-induced cytidine deaminase turns on somatic hypermutation in hybridomas.
    Nature. 2002 Feb 14;415(6873):802-6 PMID: 11823785
  90. Requirement of the activation-induced deaminase (AID) gene for immunoglobulin gene conversion.
    Science. 2002 Feb 15;295(5558):1301-6 PMID: 11847344
  91. Molecular mechanism of class switch recombination: linkage with somatic hypermutation.
    Annu Rev Immunol. 2002;20:165-96 PMID: 11861601
  92. The AID enzyme induces class switch recombination in fibroblasts.
    Nature. 2002 Mar 21;416(6878):340-5 PMID: 11875397
  93. Error-prone repair DNA polymerases in prokaryotes and eukaryotes.
    Annu Rev Biochem. 2002;71:17-50 PMID: 12045089
  94. AID enzyme-induced hypermutation in an actively transcribed gene in fibroblasts.
    Science. 2002 Jun 14;296(5575):2033-6 PMID: 12065838
  95. AID mutates E. coli suggesting a DNA deamination mechanism for antibody diversification.
    Nature. 2002 Jul 4;418(6893):99-103 PMID: 12097915
  96. Correlation of somatic hypermutation specificity and A-T base pair substitution errors by DNA polymerase eta during copying of a mouse immunoglobulin kappa light chain transgene.
    Proc Natl Acad Sci U S A. 2002 Jul 23;99(15):9954-9 PMID: 12119399
  97. Yeast origins establish a strand bias for replicational mutagenesis.
    Mol Cell. 2002 Jul;10(1):207-13 PMID: 12150920
Article Info
Journal
BMC immunology
Abbr.
BMC Immunol
ISSN
1471-2172
DOI
10.1186/1471-2172-6-10
Email
mayorov_vi@mercer.edu
Published
2005-06-10
Epub
2005-00-10
Pages
10
Language
English
Region
England
NLM ID
100966980
PMCID
PMC1180437
Subset
IM
External Links
PubMed source DOI: 10.1186/1471-2172-6-10 PMC Full Text View journal details
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