Substitution patterns in alleles of immunoglobulin V genes in humans and mice

Molecular Immunology

Volumn 43, Issue 6, 2006, Pages 731-744

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

^a UNIVERSIDAD VERACRUZANA   (Mexico)

Author keywords

Immune recognition; Immunoglobulins; Patterns of nucleotide substitutions; Protein evolution; V genes

Indexed keywords

IMMUNOGLOBULIN;

ALLELE; ARTICLE; CONTROLLED STUDY; GENE LOCUS; GENETIC VARIABILITY; HUMAN; MOUSE; NONHUMAN; PRIORITY JOURNAL; SUBSTITUTION REACTION;

ALLELES; AMINO ACID SUBSTITUTION; ANIMALS; ANTIBODY DIVERSITY; COMPLEMENTARITY DETERMINING REGIONS; EVOLUTION, MOLECULAR; HUMANS; IMMUNOGLOBULIN VARIABLE REGION; MICE; MODELS, IMMUNOLOGICAL; VARIATION (GENETICS);

EID: 28944443985     PISSN: 01615890     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molimm.2005.03.018     Document Type: Article

References (81)

1. J.C. Almagro, I. Hernandez, M.C. Ramirez, and E. Vargas-Madrazo Structural differences between the repertoires of mouse and human germline genes and their evolutionary implications Immunogenetics 47 5 1998 355 363
2. J.C. Almagro, I. Hernandez, M. del Carmen Ramirez, and E. Vargas-Madrazo The differences between the structural repertoires of VH germ-line gene segments of mice and humans: implication for the molecular mechanism of the immune response Mol. Immunol. 34 16-17 1997 1199 1214
3. E. Andersson, and T. Matsunaga Evolution of immunoglobulin heavy chain variable region genes: a VH family can last for 150-200 million years or longer Immunogenetics 41 1 1995 18 28
4. V. Barbie, and M.P. Lefranc The human immunoglobulin kappa variable (IGKV) genes and joining (IGKJ) segments Exp. Clin. Immunogenet. 15 3 1998 171 183
5. 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
6. J.K. Booker, and G. Haughton Mechanisms that limit the diversity of antibodies. II. Evolutionary conservation of Ig variable region genes which encode naturally occurring autoantibodies Int. Immunol. 6 9 1994 1427 1436
7. B. Chang, and P. Casali A sequence analysis of human germline Ig VH and VL genes. The CDR1s of a major proportion of VH, but not VL, genes display a high inherent susceptibility to amino acid replacement Ann. N.Y. Acad. Sci. 764 1995 170 179
8. C. Chothia, and A.M. Lesk Canonical structures for the hypervariable regions of immunoglobulins J. Mol. Biol. 196 4 1987 901 917
9. C. Chothia, A.M. Lesk, E. Gherardi, I.M. Tomlinson, G. Walter, J.D. Marks, M.B. Llewelyn, and G. Winter Structural repertoire of the human VH segments J. Mol. Biol. 227 3 1992 799 817
10. G. Cocho, F. Lara-Ochoa, E. Vargas, M.A. Jiménez-Montaño, and J.L. Rius Structural patterns in macromolecules in thinking about biology W. Stein F.J. Varela Santa Fe Institute Studies in the Sciences of Complexity 1993 Addison-Wesley Pu. Co. Reading, Mass 105 119
11. G.P. Cook, and I.M. Tomlinson The human immunoglobulin VH repertoire Immunol. Today 16 5 1995 237 242
12. Coutinho, A., 2000. Germ-line selection ensures embryonic autoreactivity and a positive discrimination of self mediated by supraclonal mechanisms. Semin. Immunol. 12 (3) 205-13; discussion 257-344.
13. M.O. Dayhoff Atlas of Protein Sequence and Structure 5 1972 Natl. Biomed. Res. Found Washington, DC
14. M. Eigen, R. Winkler-Oswatitsch, and A. Dress Statistical geometry in sequence space: a method of quantitative comparative sequence analysis Proc. Natl. Acad. Sci. U.S.A. 85 16 1988 5913 5917
15. A. Ferguson Biochemia Systematcis and Evolution 1980 Blackie Glasgow
16. 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
17. R. Grantham Amino acid difference formula to help explain protein evolution Science 185 4154 1974 862 864
18. 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
19. P.H. Harvey, E.C. Holmes, and S. Nee Model phylogenies to explain the real world Bioessays 16 10 1994 767 770
20. A.L. Hughes Evidence for abundant slightly deleterious polymorphisms in bacterial populations Genetics 169 2 2004 533 538
21. T.H. Jukes, and J.L. King Evolutionary nucleotide replacements in DNA Nature 281 5732 1979 605 606
22. E.A. Kabat, and T.T. Wu Identical V region amino acid sequences and segments of sequences in antibodies of different specificities. Relative contributions of VH and VL genes, minigenes, and complementarity-determining regions to binding of antibody-combining sites J. Immunol. 147 5 1991 1709 1719
23. T. Kataoka, T. Nikaido, T. Miyata, K. Moriwaki, and T. Honjo The nucleotide sequences of rearranged and germline immunoglobulin VH genes of a mouse myeloma MC101 and evolution of VH genes in mouse J. Biol. Chem. 257 1 1982 277 285
24. J.F. Kearney, M. Vakil, and N. Solvason The role of idiotypic interactions and B-cell subsets in development of the B-cell repertoire. Cold Spring Harb. Symp. Quant. Biol. 54 1 1989 203 207
25. 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
26. J. Klein, Y. Satta, C. O'hUigin, and N. Takahata The molecular descent of the major histocompatibility complex Annu. Rev. Immunol. 11 1993 269 295
27. J. Klein Natural History of the Mayor Histocompatibility Complex 1986 Wiley New York
28. U. Krawinkel, T. Christoph, and T. Blankenstein Organization of the Ig VH locus in mice and humans Immunol. Today 10 10 1989 339 344
29. L. Kruglyak The use of a genetic map of biallelic markers in linkage studies Nat. Genet. 17 1 1997 21 24
30. 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. Meth. 216 1-2 1998 117 137
31. F. Lara-Ochoa, J.C. Almagro, E. Vargas-Madrazo, and M. Conrad Antibody-antigen recognition: a canonical structure paradigm J. Mol. E 43 6 1996 678 684
32. M.P. Lefranc, and G. Lefranc The Immunoglobulin FactsBook 2001 Academic Press p. 458
33. W.-H. Li Unbiased estimation of the rates of synonymous and nonsynonymous substitution J. Mol. E 36 1 1993 96 99
34. W.-H. Li Molecular Evolution 1997 Sinauer Associates Sunderland, MA
35. G.W. Litman, M.K. Anderson, and J.P. Rast Evolution of antigen binding receptors Annu. Rev. Immunol. 17 1999 109 147
36. 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
37. A.C. Martin, J.C. Cheetham, and A.R. Rees Molecular modeling of antibody combining sites Meth. Enzymol. 203 1991 121 153
38. C. Martinez-Jean, G. Folch, and M.P. Lefranc Nomenclature and overview of the mouse (Mus musculus and Mus sp.) immunoglobulin kappa (IGK) genes Exp. Clin. Immunogenet. 18 4 2001 255 279
39. Massingham, T., Goldman, N., 2005. Detecting amino acid sites under positive selection and purifying selection. Genetics, [Epub ahead of print].
40. W.T. McCormack, and C.B. Thompson Somatic diversification of the chicken immunoglobulin light-chain gene Adv. Immunol. 48 1990 41 67
41. 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
42. T. Nagylaki, and T.D. Petes Intrachromosomal gene conversion and the maintenance of sequence homogeneity among repeated genes Genetics 100 2 1982 315 337
43. I. Nasman, and I. Lundkvist Evidence for oligoclonal diversification of the VH6-containing immunoglobulin repertoire during reconstitution after bone marrow transplantation Blood 87 7 1996 2795 2804
44. 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
45. L. Noel, T.L. Moores, E.A. van Der Biezen, M. Parniske, M.J. Daniels, J.E. Parker, and J.D. Jones Pronounced intraspecific haplotype divergence at the RPP5 complex disease resistance locus of Arabidopsis Plant Cell 11 11 1999 2099 2112
46. F. Obata, R. Shiiba, M. Iizuka, N. Kashiwagi, F. Kurosu, N. Shimada, M. Nishijima, and H. Tozawa Human T-cell receptor BV6 gene polymorphism in relation to expression level and CD4/CD8 skewness Scand. J. Immunol. 51 6 2000 543 547
47. T. Ota, T. Sitnikova, and M. Nei Evolution of vertebrate immunoglobulin variable gene segments Curr. Top. Microbiol. Immunol. 248 2000 221 245
48. N. Pallares, J.P. Frippiat, V. Giudicelli, and M.P. Lefranc The human immunoglobulin lambda variable (IGLV) genes and joining (IGLJ) segments Exp. Clin. Immunogenet. 15 1 1998 8 18
49. V. Pascual, and J.D. Capra Human immunoglobulin heavy-chain variable region genes: organization, polymorphism, and expression Adv. Immunol. 49 1991 1 74
50. 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
51. R.J. Poljak, L.M. Amzel, H.P. Avey, B.L. Chen, R.P. Phizackerley, and F. Saul Three-dimensional structure of the Fab' fragment of a human immunoglobulin at 2,8-A resolution Proc. Natl. Acad. Sci. U.S.A. 70 12 1973 3305 3310
52. C.A. Reynaud, A. Dahan, V. Anquez, and J.C. Weill Somatic hyperconversion diversifies the single Vh gene of the chicken with a high incidence in the D region Cell 59 1 1989 171 183
53. T. Romo-González, and E. Vargas-Madrazo Structural analysis of substitution patterns in alleles of human immunoglobulin VH genes Mol. Immunol. 42 9 2005 1085 1097
54. 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
55. 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
56. ® http://imgt.cines.fr (Initiator and coordinator: Marie-Paule Lefranc, Montpellier, France).
57. H.W. Schroeder Jr., F. Mortari, S. Shiokawa, P.M. Kirkham, R.A. Elgavish, and F.E. Bertrand Developmental regulation of the human antibody repertoire. Ann. N.Y. Acad. Sci. 29 764 1995 242 260
58. S. Schurmans, J. Merino, H.Y. Qin, G. Kramar, M. Duchosal, O. Skalli, G. Benzonana, G. Gabbiani, and P.H. Lambert Autoimmune syndrome after neonatal induction of tolerance to alloantigens: analysis of the specificity and of the cellular and genetic origin of autoantibodies Autoimmunity 9 4 1991 283 291
59. 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
60. T. Sitnikova, and C. Su Coevolution of immunoglobulin heavy- and light-chain variable-region gene families Mol. Biol. Evol. 15 6 1998 617 625
61. J. Stewart, and F.J. Varela Exploring the meaning of connectivity in the immune network Immunol. Rev. 110 1989 37 61
62. T.S. Takano Rate variation of DNA sequence evolution in the Drosophila lineages Genetics 149 2 1998 959 970
63. I.M. Tomlinson, J.P. Cox, E. Gherardi, A.M. Lesk, and C. Chothia The structural repertoire of the human V kappa domain EMBO J. 14 18 1995 4628 4638
64. 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
65. 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
66. N.J. Tourasse, and M. Gouy Evolutionary distances between nucleotide sequences based on the distribution of substitution rates among sites as estimated by parsimony Mol. Biol. Evol. 14 3 1997 287 298
67. A. Tutter, P. Brodeur, M. Shlomchik, and R. Riblet Structure, map position, and evolution of two newly diverged mouse Ig VH gene families J. Immunol. 147 9 1991 3215 3223
68. 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
69. 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
70. 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
71. A.C. Viale, J.A. Chies, F. Huetz, E. Malenchere, M. Weksler, A.A. Freitas, and A. Coutinho VH-gene family dominance in ageing mice Scand. J. Immunol. 39 2 1994 184 188
72. 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
73. E.S. Ward, D. Gussow, A.D. Griffiths, P.T. Jones, and G. Winter Binding activities of a repertoire of single immunoglobulin variable domains secreted from Escherichia coli Nature 341 6242 1989 544 546
74. J.C. Weill, and C.A. Reynaud Rearrangement/hypermutation/gene conversion: when, where and why? Immunol. Today 17 2 1996 92 97
75. A.C. Wilson, S.S. Carlson, and T.J. White Biochemical evolution Annu. Rev. Biochem. 46 1977 573 639
76. I.A. Wilson, and R.L. Stanfield Antibody-antigen interactions Curr. Opin. Struct. Biol. 3 1993 113 118
77. T.T. Wu, and E.A. Kabat An analysis of the sequences of the variable regions of Bence Jones proteins and myeloma light chains and their implications for antibody complementarity J. Exp. Med. 132 2 1970 211 250
78. Z. Yang, and R. Nielsen Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models Mol. Biol. Evol. 17 1 2000 32 43
79. 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 2 1977 505 510
80. M. Zouali B-cell superantigens: implications for selection of the human antibody repertoire Immunol. Today 16 8 1995 399 405
81. E. Zuckerkandl Evolutionary processes and evolutionary noise at the molecular level. I. functional density in proteins J. Mol. Evol. 7 3 1976 167 183