Evolution of coordinated mutagenesis and somatic hypermutation in VH5

Molecular Immunology

Volumn 49, Issue 3, 2011, Pages 537-548

  Wright, Barbara E ^a   Schmidt, Karen H ^a   Hunt, Aaron T ^a   Reschke, Dennis K ^a   Minnick, Michael F ^a  

^a UNIVERSITY OF MONTANA   (United States)

Author keywords

DNA secondary structures; Evolution of SHM; Model of SHM; Transcription driven mutagenesis

Indexed keywords

ARTICLE; COMPUTER PROGRAM; GENE; GENE MUTATION; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; IN VITRO STUDY; MUTAGENESIS; PRIORITY JOURNAL; SOMATIC HYPERMUTATION; VH5 ANTIBODY GENE;

AUTOANTIGENS; BASE SEQUENCE; HUMANS; IMMUNOGLOBULIN HEAVY CHAINS; MOLECULAR SEQUENCE DATA; MUTAGENESIS; NERVE TISSUE PROTEINS; NUCLEIC ACID CONFORMATION; SOMATIC HYPERMUTATION, IMMUNOGLOBULIN; TRANSCRIPTION, GENETIC;

EID: 81955161847     PISSN: 01615890     EISSN: 18729142     Source Type: Journal    
DOI: 10.1016/j.molimm.2011.10.001     Document Type: Article

References (49)

1. Amosova O., Coulter R., Fresco J.R. Self-catalyzed site-specific depurination of guanine residues within gene sequences. Proc. Natl. Acad. Sci. U.S.A. 2006, 103:4392-4397.
2. Bachl J., Carlson C., Gray-Schopfer V., Dessing M., Olsson C. Increased transcription levels induce higher mutation rates in a hypermutating cell line. J. Immunol. 2001, 166:5051-5057.
3. Bagga R., Ramesh N., Brahmachari S.K. Supercoil-induced unusual DNA structures as transcriptional block. Nucleic Acids Res. 1990, 18:3363-3369.
4. Burkala E., Reimers J.M., Schmidt K.H., Davis N., Wei P., Wright B.E. Secondary structures as predictors of mutation potential in the lacZ gene of Escherichia coli. Microbiology 2007, 153:2180-2189.
5. Chua K.F., Alt F.W., Manis J.P. The function of AID in somatic mutation and class switch recombination: upstream or downstream of DNA breaks. J. Exp. Med. 2002, 195:F37-F41.
6. Cooper D.N., Krawczak M. The mutational spectrum of single base-pair substitutions causing human genetic disease: patterns and predictions. Hum. Genet. 1990, 85:55-74.
7. Dayn A., Malkhosyan S., Mirkin S.M. Transcriptionally driven cruciform formation in vivo. Nucleic Acids Res. 1992, 20:5991-5997.
8. Delker R., Fuggmann S.D., Papavasiliou N. A coming-of-age story: activation-induced cytidine deaminase turns 10. Nat. Immunol. 2009, 10:1147-1153.
9. Di Noia J.M., Neuberger M.S. Molecular mechanisms of antibody somatic hypermutation. Annu. Rev. Biochem. 2007, 76:1-22.
10. Franklin A., Blanden R.V. A/T-targeted somatic hypermutation: critique of the mainstream model. Trends Biochem. Sci. 2006, 31:252-258.
11. Frederico L., Kunkel T.A., Shaw B.R. A sensitive genetic assay for the detection of cytosine deamination: determination of rate constants and the activation energy. Biochemistry 1990, 29:2532-2537.
12. Fukita Y., Jacobs H., Rajewsky K. Somatic hypermutation in the heavy chain locus correlates with transcription. Immunity 1998, 9:105-114.
13. Kim H., Lee B.S., Tomita M., Kanai A. Transcription-associated mutagenesis increases protein sequence diversity more effectively than does random mutagenesis in Escherichia coli. PLoS One 2010, 5:e10567.
14. Kluyver A.J. Die einheit in der biochemie in der biochie. Chem. D. Zelle u Gew. 1926, 13:134-190.
15. Krasilnikov A.S., Podtelezhnikov A., Vologodskii A., Mirkin S.M. Large-scale effects of transcriptional DNA supercoiling in vivo. J. Mol. Biol. 1999, 292:1149-1160.
16. Krohn M., Pardon B., Wagner R. Effects of template topology on RNA polymerase pausing during in vitro transcription of the Escherichia coli rrnB leader region. Mol. Microbiol. 1992, 6:581-589.
17. Li Z., Peled J.U., Zhao C., Svetlanov A., Ronai D., Cohen P.E., Scharff M.D. A role for Mlh3 in somatic hypermutation. DNA Repair (Amst.) 2006, 5:675-682.
18. Lindahl T. Instability and decay of the primary structure of DNA. Nature 1993, 362:709-715.
19. Lindahl T., Nyberg B. Heat-induced deamination of cytosine residues in deoxyribonucleic acid. Biochemistry 1974, 13:3405-3410.
20. Markham N.R., Zuker M. DINAMelt web server for nucleic acid melting prediction. Nucleic Acids Res. 2005, 33:W577-W581.
21. Maxam A.M., Gilbert W. Methods in enzymology. Nucleic Acids Part I 1980, vol. 65:499-560. Academic Press, New York.
22. Mirkin E.V., Mirkin S.M. Replication fork stalling at natural impediments. Microbiol. Mol. Biol. Rev. 2007, 71:13-35.
23. Peck L.J., Wang J.C. Transcriptional block caused by a negative supercoiling induced structural change in an alternating CG sequence. Cell 1985, 4:129-137.
24. Pereira F., Soares P., Carneiro J., Pereira L., Richards M.B., Samuels D.C., Amorim A. Evidence for variable selective pressures at a large secondary structure of the human mitochondrial DNA control region. Mol. Biol. Evol. 2008, 25:2759-2770.
25. Phung Q.H., Winter D.B., Cranston A., Tarone R.E., Bohr V.A., Fishel R., Gearhart P.J. Increased hypermutation at G and C nucleotides in immunoglobulin variable genes from mice deficient in the MSH2 mismatch repair protein. J. Exp. Med. 1998, 187:1745-1751.
26. Rajewsky K. Clonal selection and learning in the antibody system. Nature 1996, 381:751-758.
27. Reimers J.M., Schmidt K.H., Longacre A., Reschke D.K., Wright B.E. Increased transcription rates correlate with increased reversion rates in leuB and argH Escherichia coli auxotrophs. Microbiology 2004, 150:1457-1466.
28. Ripley L.S., Glickman B.W. Unique self-complementarity of palindromic sequences provides DNA structural intermediates for mutation. Cold Spring Harb. Symp. Quant. Biol. 1983, 47(Pt 2):851-861.
29. Rogozin I.B., Diaz M. 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, 172:3382-3384.
30. Ronai D., Iglesias-Ussel M.D., Fan M., Li Z., Martin A., Scharff M.D. Detection of chromatin-associated single-stranded DNA in regions targeted for somatic hypermutation. J. Exp. Med. 2007, 204:181-190.
31. Schmidt K.H., Reimers J.M., Wright B.E. The effect of promoter strength, supercoiling and secondary structure on mutation rates in Escherichia coli. Mol. Microbiol. 2006, 60:1251-1261.
32. Shen H.M., Poirier M.G., Allen M.J., North J., Lal R., Widom J., Storb U. The activation-induced cytidine deaminase (AID) efficiently targets DNA in nucleosomes but only during transcription. J. Exp. Med. 2009, 206:1057-1071.
33. Shen H.M., Tanaka A., Bozek G., Nicolae D., Storb U. Somatic hypermutation and class switch recombination in Msh6(-/-)Ung(-/-) double-knockout mice. J. Immunol. 2006, 177:5386-5392.
34. Shen J.C., Rideout W.M., Jones P.A. The rate of hydrolytic deamination of 5-methylcytosine in double-stranded DNA. Nucleic Acids Res. 1994, 22:972-976.
35. Singer B., Kusmierek J.T. Chemical mutagenesis. Annu. Rev. Biochem. 1982, 51:655-693.
36. Skandalis A., Ford B.N., Glickman B.W. Strand bias in mutation involving 5-methylcytosine deamination in the human hprt gene. Mutat. Res. 1994, 314:21-26.
37. Smith K.C. Spontaneous mutagenesis: experimental, genetic and other factors. Mutat. Res. 1992, 277:139-162.
38. Suo Z., Johnson K.A. DNA secondary structure effects on DNA synthesis catalyzed by HIV-1 reverse transcriptase. J. Biol. Chem. 1998, 273:27259-27267.
39. Todd P.A., Glickman B.W. Mutational specificity of UV light in Escherichia coli: indications for a role of DNA secondary structure. Proc. Natl. Acad. Sci. U.S.A. 1982, 79:4123-4127.
40. Weaver D.T., DePamphilis M.L. The role of palindromic and non-palindromic sequences in arresting DNA synthesis in vitro and in vivo. J. Mol. Biol. 1984, 180:961-986.
41. Wright B.E. Mini review, a biochemical mechanism for nonrandom mutations and evolution. J. Bacteriol. 2000, 182:2993-3001.
42. Wright B.E. Micro review, stress-directed adaptive mutations and evolution. Mol. Microbiol. 2004, 52:643-650.
43. Wright B.E., Reimers J.M., Schmidt K.H., Reschke D.K. Hypermutable bases in the p53 cancer gene are at vulnerable positions in DNA secondary structures. Cancer Res. 2002, 62:5641-5644.
44. Wright B.E., Reschke D.K., Schmidt K.H., Reimers J.M., Knight W. Predicting mutation frequencies in stem-loop structures of derepressed genes: implications for evolution. Mol. Microbiol. 2003, 48:429-441.
45. Wright B.E., Schmidt K.H., Minnick M.F., Davis N. I. VH gene transcription creates stabilized secondary structures for coordinated mutagenesis during somatic hypermutation. Mol. Immunol. 2008, 45:3589-3599.
46. Wright B.E., Schmidt K.H., Davis N., Hunt A.T., Minnick M.F. II. Correlations between secondary structure stability and mutation frequency during somatic hypermutation. Mol. Immunol. 2008, 45:3600-3608.
47. Wright B.E., Schmidt K.H., Hunt A.T., Lodmell J.S., Minnick M.F., Reschke D. The roles of transcription and genotoxins underlying p53 mutagenesis in vivo. Carcinogenesis 2011, 10.1093/carcin/bgr177.
48. Wyatt J.R., Puglist J.D., Tinoco I. RNA pseudoknots: stability and loop size requirements. J. Mol. Biol. 1990, 214:455-470.
49. Zheng N.Y., Wilson K., Jared M., Wilson P.C. Intricate targeting of immunoglobulin somatic hypermutation maximizes the efficiency of affinity maturation. J. Exp. Med. 2005, 201:1467-1478.