Structural analysis of substitution patterns in alleles of human immunoglobulin VH genes

Molecular Immunology

Volumn 42, Issue 9, 2005, Pages 1085-1097

  Romo González, Tania ^a   Vargas Madrazo, Enrique ^a  

^a UNIVERSIDAD VERACRUZANA   (Mexico)

Author keywords

Amino acid substitution pattern; Antibody repertoires; Molecular recognition; R S ratio

Indexed keywords

HUMAN IMMUNOGLOBULIN;

ALLELE; AMINO ACID SUBSTITUTION; ARTICLE; GENE LOCUS; GENETIC ANALYSIS; GENETIC VARIABILITY; HUMAN; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BLOOD LEVEL;

EID: 17044417257     PISSN: 01615890     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molimm.2004.11.004     Document Type: Article

References (105)

1. E.E. Adderson, F.H. Azmi, P.M. Wilson, P.G. Shackelford, and W.L. Carroll The human VH3b gene subfamily is highly polymorphic J. Immunol. 151 2 1993 800 809
2. J.S. Andris, B.R. Brodeur, and J.D. Capra Molecular characterization of human antibodies to bacterial antigens: utilization of the less frequently expressed VH2 and VH6 heavy chain variable region gene families Mol. Immunol. 30 17 1993 1601 1616
3. R. Baer, A. Forster, I. Lavenir, and T.H. Rabbitts Immunoglobulin VH genes are transcribed by T cells in association with a new 5′ exon J. Exp. Med. 167 6 1988 2011 2016
4. R.S. Becker, and K.L. Knight Somatic diversification of immunoglobulin heavy chain VDJ genes: evidence for somatic gene conversion in rabbits Cell 63 5 1990 987 997
5. J.E. Berman, S.J. Mellis, R. Pollock, C.L. Smith, H. Suh, B. Heinke, C. Kowal, U. Surti, L. Chess, C.R. Cantor, and F.W. Alt Content and organization of the human Ig VH locus: definition of three new VH families and linkage to the Ig CH locus EMBO J. 7 3 1988 727 738
6. J.E. Berman, K.G. Nickerson, R.R. Pollock, J.E. Barth, R.K. Schuurman, D.M. Knowles, L. Chess, and F.W. Alt VH gene usage in humans: biased usage of the VH6 gene in immature B lymphoid cells Eur. J. Immunol. 21 5 1991 1311 1314
7. R.V. Blanden, H.S. Rothenfluh, P. Zylstra, G.F. Weiller, and E.J. Steele The signature of somatic hypermutation appears to be written into the germline IgV segment repertoire Immunol. Rev. 162 1998 117 132
8. H.P. Brezinschek, R.I. Brezinschek, and P.E. Lipsky Analysis of the heavy chain repertoire of human peripheral B cells using single-cell polymerase chain reaction J. Immunol. 155 1 1995 190 202
9. M.J. Campbell, A.D. Zelenetz, S. Levy, and R. Levy Use of family specific leader region primers for PCR amplification of the human heavy chain variable region gene repertoire Mol. Immunol. 29 2 1992 193 203
10. P.P. Chen Structural analyses of human developmentally regulated Vh3 genes Scand. J. Immunol. 31 3 1990 257 267
11. P.P. Chen, M.F. Liu, S. Sinha, and D.A. Carson A 16/6 idiotype-positive anti-DNA antibody is encoded by a conserved VH gene with no somatic mutation Arthritis Rheum. 31 11 1988 1429 1431
12. C. Chothia, and A.M. Lesk Canonical structures for the hypervariable regions of immunoglobulins J. Mol. Biol. 196 4 1987 901 917
13. C. Chothia, A.M. Lesk, A. Tramontano, M. Levitt, S.J. Smith-Gill, G. Air, S. Sheriff, E.A. Padlan, D. Davies, W.R. Tulip, P.M. Colman, S. Spinelli, P.M. Alzari, and R.J. Poljak Conformations of immunoglobulin hypervariable regions Nature 342 6252 1989 877 883
14. M. Cohn, and R.E. Langman The immune system: a look from a distance Front Biosci. 1 1996 d318 d323
15. G.P. Cook, and I.M. Tomlinson The human immunoglobulin VH repertoire Immunol. Today 16 5 1995 237 242
16. G.P. Cook, I.M. Tomlinson, G. Walter, H. Riethman, N.P. Carter, L. Buluwela, G. Winter, and T.H. Rabbitts A map of the human immunoglobulin VH locus completed by analysis of the telomeric region of chromosome 14q Nat. Genet. 7 2 1994 162 168
17. G.P. Cook, I.M. Tomlinson, G. Walter, H. Riethman, N.P. Carter, L. Buluwela, G. Winter, and T.H. Rabbitts A map of the human immunoglobulin VH locus completed by analysis of the telomeric region of chromosome 14q Nat. Genet. 7 2 1994 162 168
18. A. Coutinho Germ-line selection ensures embryonic autoreactivity and a positive discrimination of self mediated by supraclonal mechanisms Semin. Immunol. 12 3 2000 205 213 (discussion 257-344)
19. X. Cui, and H. Li Discriminating between allelic and interlocus differences among human immunoglobulin VH4 sequences by analyzing single spermatozoa Hum. Genet. 100 1 1997 96 100
20. X. Cui, and H. Li Determination of gene organization in individual haplotypes by analyzing single DNA fragments from single spermatozoa Proc. Natl. Acad. Sci. U.S.A. 95 18 1998 10791 10796
21. X. Cui, and H. Li Human immunoglobulin VH4 sequences resolved by population-based analysis after enzymatic amplification and denaturing gradient gel electrophoresis Eur. J. Immunogenet. 27 1 2000 37 46
22. K. Decanniere, A. Desmyter, M. Lauwereys, M.A. Ghahroudi, S. Muyldermans, and L. Wyns A single-domain antibody fragment in complex with RNase A: non-canonical loop structures and nanomolar affinity using two CDR loops Struct. Fold Des. 7 4 1999 361 370
23. M. Eigen, B.F. Lindemann, M. Tietze, R. Winkler-Oswatitsch, A. Dress, and A. von Haeseler How old is the genetic code? Statistical geometry of tRNA provides an answer Science 244 4905 1989 673 679
24. J. Foote, and G. Winter Antibody framework residues affecting the conformation of the hypervariable loops J. Mol. Biol. 224 2 1992 487 499
25. M. Go, and S. Miyazawa Relationship between mutability, polarity and exteriority of amino acid residues in protein evolution Int. J. Pept. Protein Res. 15 3 1980 211 224
26. S.D. Gorman, M.R. Clark, E.G. Routledge, S.P. Cobbold, and H. Waldmann Reshaping a therapeutic CD4 antibody Proc. Natl. Acad. Sci. U.S.A. 88 10 1991 4181 4185
27. R. Grantham Amino acid difference formula to help explain protein evolution Science 185 4154 1974 862 864
28. M.K. Halushka, J.B. Fan, K. Bentley, L. Hsie, N. Shen, A. Weder, R. Cooper, R. Lipshutz, and A. Chakravarti Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis Nat. Genet. 22 3 1999 239 247
29. L. Hammarstrom, N. Ghanem, C.I. Smith, G. Lefranc, and M.P. Lefranc RFLP of human immunoglobulin genes Exp. Clin. Immunogenet. 7 1 1990 7 19
30. S. Hande, and T. Manser Single amino acid substitutions in V(H) CDR2 are sufficient to generate or enhance the specificity of two forms of an anti-arsonate antibody variable region for DNA Mol. Immunol. 34 18 1997 1281 1290
31. I.J. Harmer, S. Loizou, K.M. Thompson, A.K. So, M.J. Walport, and C. Mackworth-Young A human monoclonal antiphospholipid antibody that is representative of serum antibodies and is germline encoded Arthritis Rheum. 38 8 1995 1068 1076
32. A. Hemminki, S. Niemi, L. Hautoniemi, H. Soderlund, and K. Takkinen Fine tuning of an anti-testosterone antibody binding site by stepwise optimisation of the CDRs Immunotechnology 4 1 1998 59 69 Jun
33. P.T. Jones, P.H. Dear, J. Foote, M.S. Neuberger, and G. Winter Replacing the complementarity-determining regions in a human antibody with those from a mouse Nature 321 6069 1986 522 525
34. T.H. Jukes, and J.L. King Evolutionary nucleotide replacements in DNA Nature 281 5732 1979 605 606
35. E.A. Kabat The structural basis of antibody complementarity Adv. Protein Chem. 32 1978 1 75
36. P.M. Kirkham, F. Mortari, J.A. Newton, and H.W. Schroeder Jr. Immunoglobulin VH clan and family identity predicts variable domain structure and may influence antigen binding EMBO J. 11 2 1992 603 609
37. P.M. Kirkham, and H.W. Schroeder Jr. Antibody structure and the evolution of immunoglobulin V gene segments Semin. Immunol. 6 6 1994 347 360
38. M. Kodaira, T. Kinashi, I. Umemura, F. Matsuda, T. Noma, Y. Ono, and T. Honjo Organization and evolution of variable region genes of the human immunoglobulin heavy chain J. Mol. Biol. 190 4 1986 529 541
39. L. Kruglyak The use of a genetic map of biallelic markers in linkage studies Nat. Genet. 17 1 1997 21 24
40. R. Kuppers, U. Fischer, K. Rajewsky, and A. Gause Immunoglobulin heavy and light chain gene sequences of a human CD5 positive immunocytoma and sequences of four novel VHIII germline genes Immunol. Lett. 34 1 1992 57 62
41. S. Lacroix-Desmazes, S.V. Kaveri, L. Mouthon, A. Ayouba, E. Malanchere, A. Coutinho, and M.D. Kazatchkine Self-reactive antibodies (natural autoantibodies) in healthy individuals J. Immunol. Methods 216 1-2 1998 117 137
42. F. Lara-Ochoa, E. Vargas-Madrazo, and J.C. Almagro Distributions of the use frequencies of amino acids in the hypervariable regions of immunoglobulins J. Mol. E 41 1 1995 98 103
43. K.H. Lee, F. Matsuda, T. Kinashi, M. Kodaira, and T. Honjo A novel family of variable region genes of the human immunoglobulin heavy chain J. Mol. Biol. 195 4 1987 761 768
44. M.P. Lefranc IMGT, the international ImMunoGeneTics database Nucleic Acids Res. 31 1 2003 307 310
45. M.P. Lefranc IMGT-ONTOLOGY and IMGT databases, tools and Web resources for immunogenetics and immunoinformatics Mol. Immunol. 40 10 2004 647 660
46. M.P. Lefranc, and G. Lefranc The Immunoglobulin FactsBook 2001 Academic Press 458
47. M.P. Lefranc, N. Pallares, and J.P. Frippiat Allelic polymorphisms and RFLP in the human immunoglobulin lambda light chain locus Hum. Genet. 104 5 1999 361 369
48. W.-H. Li Molecular Evolution 1997 Sinauer Associates Inc.
49. H. Li, X. Cui, S. Pramanik, and N.O. Chimge Genetic diversity of the human immunoglobulin heavy chain VH region Immunol. Rev. 190 2002 53 68
50. R.M. MacCallum, A.C. Martin, and J.M. Thornton Antibody-antigen interactions: contact analysis and binding site topography J. Mol. Biol. 262 5 1996 732 745
51. F. Matsuda, K. Ishii, P. Bourvagnet, K. Kuma, H. Hayashida, T. Miyata, and T. Honjo The complete nucleotide sequence of the human immunoglobulin heavy chain variable region locus J. Exp. Med. 188 11 1998 2151 2162
52. F. Matsuda, E.K. Shin, H. Nagaoka, R. Matsumura, M. Haino, Y. Fukita, S. Taka-ishi, T. Imai, J.H. Riley, and R. Anand Structure and physical map of 64 variable segments in the 3′0.8-megabase region of the human immunoglobulin heavy-chain locus Nat. Genet. 3 1 1993 88 94
53. E.E. Max Immunoglobulins: Molecular Genetics W. Paul Fundamental immunology fourth ed. 1998 Lippincott-Raven Philadelphia 111 182
54. P.M.H. Mazumdar Species and Specificity. An Interpretation of History of Immunology 1995 Cambridge University Press pp. 3-382
55. W.T. McCormack, L.W. Tjoelker, and C.B. Thompson Avian B-cell development: generation of an immunoglobulin repertoire by gene conversion Annu. Rev. Immunol. 9 1991 219 241
56. E.C. Milner, W.O. Hufnagle, A.M. Glas, I. Suzuki, and C. Alexander Polymorphism and utilization of human VH genes Ann. N.Y. Acad. Sci. 764 1995 50 61
57. A. Nobrega, A. Grandien, M. Haury, L. Hecker, E. Malanchere, and A. Coutinho Functional diversity and clonal frequencies of reactivity in the available antibody repertoire Eur. J. Immunol. 28 4 1998 1204 1215
58. T. Olee, P.M. Yang, K.A. Siminovitch, N.J. Olsen, J. Hillson, J. Wu, F. Kozin, D.A. Carson, and P.P. Chen Molecular basis of an autoantibody-associated restriction fragment length polymorphism that confers susceptibility to autoimmune diseases J. Clin. Invest. 88 1 1991 193 203
59. T. Ota, T. Sitnikova, and M. Nei Evolution of vertebrate immunoglobulin variable gene segments Curr. Top. Microbiol. Immunol. 248 2000 221 245
60. E.A. Padlan On the nature of antibody combining sites: unusual structural features that may confer on these sites an enhanced capacity for binding ligands Proteins 7 2 1990 112 124
61. E.A. Padlan, C. Abergel, and J.P. Tipper Identification of specificity-determining residues in antibodies FASEB J. 9 1 1995 133 139
62. W. Pargent, K.F. Schable, and H.G. Zachau Polymorphisms and haplotypes in the human immunoglobulin kappa locus Eur. J. Immunol. 21 8 1991 1829 1835
63. V. Pascual, and J.D. Capra Human immunoglobulin heavy-chain variable region genes: organization, polymorphism, and expression Adv. Immunol. 49 1991 1 74
64. V. Pascual, I. Randen, K. Thompson, M. Sioud, O. Forre, J. Natvig, and J.D. Capra The complete nucleotide sequences of the heavy chain variable regions of six monospecific rheumatoid factors derived from Epstein-Barr virus-transformed B cells isolated from the synovial tissue of patients with rheumatoid arthritis. Further evidence that some autoantibodies are unmutated copies of germ line genes J. Clin. Invest. 86 4 1990 1320 1328
65. R.M. Perlmutter, B. Berson, J.A. Griffin, and L Hood Diversity in the germline antibody repertoire. Molecular evolution of the T15 VN gene family J. Exp. Med. 162 6 1985 1998 2016
66. S. Pramanik, and H. Li Direct detection of insertion/deletion polymorphisms in an autosomal region by analyzing high-density markers in individual spermatozoa Am. J. Hum. Genet. 71 6 2002 1342 1352
67. M.C. Ramirez-Benites, and J.C. Almagro Analysis of antibodies of known structure suggests a lack of correspondence between the residues in contact with the antigen and those modified by somatic hypermutation Proteins 45 3 2001 199 206
68. L. Riechmann, J. Foote, and G. Winter Expression of an antibody Fv fragment in myeloma cells J. Mol. Biol. 203 3 1988 825 828
69. M. Roe, I.N. Norderhaug, P. Brandtzaeg, and F.E. Johansen Fine specificity of ligand-binding domain 1 in the polymeric Ig receptor: importance of the CDR2-containing region for IgM interaction J. Immunol. 162 10 1999 6046 6052
70. H.S. Rothenfluh, R.V. Blanden, and E.J. Steele Evolution of V genes: DNA sequence structure of functional germline genes and pseudogenes Immunogenetics 42 3 1995 159 171
71. H.S. Rothenfluh, and E.J. Steele Origin and maintenance of germ-line V genes Immunol. Cell Biol. 71 Pt 3 1993 227 232
72. D.B. Rubinstein, R.S. Schwartz, T. Guillaume, P. Leblanc, and A.K. Stewart Germline complexity, restriction fragment length polymorphism, and coding region sequences of the human VH7 gene family identified with family-specific FR3 segment oligonucleotides Mol. Immunol. 31 10 1994 713 721
73. I. Sanz, H. Dang, M. Takei, N. Talal, and J.D. Capra VH sequence of a human anti-Sm autoantibody. Evidence that autoantibodies can be unmutated copies of germline genes J. Immunol. 142 3 1989 883 887
74. E.H. Sasso, J.H. Buckner, and L.A. Suzuki Ethnic differences of polymorphism of an immunoglobulin VH3 gene J. Clin. Invest. 96 3 1995 1591 1600
75. E.H. Sasso, K.W. van Dijk, and E.C. Milner Prevalence and polymorphism of human VH3 genes J. Immunol. 145 8 1990 2751 2757
76. E.H. Sasso, K. Willems van Dijk, A.P. Bull, and E.C. Milner A fetally expressed immunoglobulin VH1 gene belongs to a complex set of alleles J. Clin. Invest. 91 6 1993 2358 2367
77. E.H. Sasso, K. Willems van Dijk, A. Bull, S.M. van der Maarel, and E.C. Milner VH genes in tandem array comprise a repeated germline motif J. Immunol. 149 4 1992 1230 1236
78. F.A. Saul, and R.J. Poljak Structural patterns at residue positions 9, 18, 67 and 82 in the VH framework regions of human and murine immunoglobulins J. Mol. Biol. 230 1 1993 15 20
79. G. Schaible, G.A. Rappold, W. Pargent, and H.G. Zachau The immunoglobulin kappa locus: polymorphism and haplotypes of Caucasoid and non-Caucasoid individuals Hum. Genet. 91 3 1993 261 267
80. M.J. Shlomchik, A. Marshak-Rothstein, C.B. Wolfowicz, T.L. Rothstein, and M.G. Weigert The role of clonal selection and somatic mutation in autoimmunity Nature 328 6133 1987 805 811
81. T. Tanaka, and M. Nei Positive darwinian selection observed at the variable-region genes of immunoglobulins Mol. Biol. E 6 5 1989 447 459
82. I.M. Tomlinson, G. Walter, P.T. Jones, P.H. Dear, E.L. Sonnhammer, and G. Winter The imprint of somatic hypermutation on the repertoire of human germline V genes J. Mol. Biol. 256 5 1996 813 817
83. I.M. Tomlinson, G. Walter, J.D. Marks, M.B. Llewelyn, and G. Winter The repertoire of human germline VH sequences reveals about fifty groups of VH segments with different hypervariable loops J. Mol. Biol. 227 3 1992 776 798
84. S. Tonegawa Somatic generation of antibody diversity Nature 302 5909 1983 575 581
85. S. van der Maarel, K.W. van Dijk, C.M. Alexander, E.H. Sasso, A. Bull, and E.C. Milner Chromosomal organization of the human VH4 gene family. Location of individual gene segments J. Immunol. 150 7 1993 2858 2868
86. K.W. van Dijk, E.H. Sasso, and E.C. Milner Polymorphism of the human Ig VH4 gene family J. Immunol. 146 10 1991 3646 3651
87. I. Van Dijk-Hard, and I. Lundkvist Long-term kinetics of adult human antibody repertoires Immunology 107 1 2002 136 144
88. J.H. van Es, M. Heutink, H. Aanstoot, and T. Logtenberg Sequence analysis of members of the human Ig VH4 gene family derived from a single VH locus. Identification of novel germ-line members J. Immunol. 149 2 1992 492 497
89. E. Vargas-Madrazo, F. Lara-Ochoa, and J.C. Almagro Canonical structure repertoire of the antigen-binding site of immunoglobulins suggests strong geometrical restrictions associated to the mechanism of immune recognition J. Mol. Biol. 254 3 1995 497 504
90. E. Vargas-Madrazo, F. Lara-Ochoa, and M. Jimenez-Montano A skewed distribution of amino acids at recognition sites of the hypervariable region of immunoglobulins J. Mol. E 38 1 1994 100 104
91. E. Vargas-Madrazo, F. Lara-Ochoa, M.C. Ramirez-Benites, and J.C. Almagro Evolution of the structural repertoire of the human V(H) and Vkappa germline genes Int. Immunol. 9 12 1997 1801 1815
92. E. Vargas-Madrazo, and E. Paz-Garcia An improved model of association for VH-VL immunoglobulin domains: asymmetries between VH and VL in the packing of some interface residues J. Mol. Recognit. 16 3 2003 113 120
93. Vargas-Madrazo, E., Paz-Garcia, E., 2001. Interpreting Gene Usage of immunoglobulins: Structural Classification of the Genes of Immunoglobulins According to Their Recognition Properties. EFIS 2000 International Proceedings Division. pp. 81-90.
94. A.C. Viale, A. Coutinho, and A.A. Freitas Differential expression of VH gene families in peripheral B cell repertoires of newborn or adult immunoglobulin H chain congenic mice J. Exp. Med. 175 6 1992 1449 1456
95. J. Voswinkel, M. Pfreundschuh, and A. Gause Evidence for a selected humoral immune response encoded by VH4 family genes in the synovial membrane of a patient with RA Ann. N.Y. Acad. Sci. 815 1997 312 315
96. X. Wang, and B.D. Stollar Immunoglobulin VH gene expression in human aging Clin. Immunol. 93 2 1999 132 142
97. N.P. Weng, J.G. Snyder, L.Y. Yu-Lee, and D.M. Marcus Polymorphism of human immunoglobulin VH4 germ-line genes Eur. J. Immunol. 22 4 1992 1075 1082
98. K. Willems van Dijk, L.A. Milner, E.H. Sasso, and E.C. Milner Chromosomal organization of the heavy chain variable region gene segments comprising the human fetal antibody repertoire Proc. Natl. Acad. Sci. U.S.A. 89 21 1992 10430 10434
99. T.H. Winkler, H. Fehr, and J.R. Kalden Analysis of immunoglobulin variable region genes from human IgG anti-DNA hybridomas Eur. J. Immunol. 22 7 1992 1719 1728
100. J.L. Xu, and M.M. Davis Diversity in the CDR3 region of V(H) is sufficient for most antibody specificities Immunity 13 1 2000 37 45
101. Z.A. Yazici, M. Behrendt, M. Goodfield, L.J. Partridge, and N.J. Lindsey Does the CDR3 of the heavy chain determine the specificity of autoantibodies in systemic lupus erythematosus? J. Autoimmun. 11 5 1998 477 483
102. R.M. Zinkernagel Uncertainties - discrepancies in immunology Immunol. Rev. 185 2002 103 125
103. R.M. Zinkernagel, and P.C. Doherty The concept that surveillance of self is mediated via the same set of genes that determines recognition of allogenic cells Cold Spring Harb. Symp. Quant. Biol. 41 Pt. 2 1977 505 510
104. R.M. Zinkernagel, and H. Hengartner Regulation of the immune response by antigen Science 293 5528 2001 251 253
105. M. Zouali B-cell superantigens: implications for selection of the human antibody repertoire Immunol. Today 16 8 1995 399 405