Albuminoid genes: Evolving at the interface of dispensability and selection

Genome Biology and Evolution

Volumn 6, Issue 11, 2014, Pages 2983-2997

  Mozzi, Alessandra ^a   Forni, Diego ^a   Cagliani, Rachele ^a   Pozzoli, Uberto ^a   Vertemara, Jacopo ^a   Bresolin, Nereo ^a,b   Sironi, Manuela ^a  

^a SCIENTIFIC INSTITUTE   (Italy)

^b UNIVERSITY OF MILAN   (Italy)

Author keywords

Albumin; Albuminoids; Hibernation; Positive selection; Vitamin D; Vitamin D binding protein

Indexed keywords

AFP PROTEIN, HUMAN; ALB PROTEIN, HUMAN; ALPHA FETOPROTEIN; FATTY ACID; PROSTAGLANDIN; PROTEIN BINDING; SERUM ALBUMIN; THYROXINE; VITAMIN D BINDING PROTEIN;

ADAPTATION; ANIMAL; BINDING SITE; CHEMISTRY; GENE LINKAGE DISEQUILIBRIUM; GENETIC SELECTION; GENETICS; HAPLOTYPE; HIBERNATION; HUMAN; METABOLISM; MOLECULAR EVOLUTION; PAN TROGLODYTES;

ADAPTATION, PHYSIOLOGICAL; ALPHA-FETOPROTEINS; ANIMALS; BINDING SITES; EVOLUTION, MOLECULAR; FATTY ACIDS; HAPLOTYPES; HIBERNATION; HUMANS; LINKAGE DISEQUILIBRIUM; PAN TROGLODYTES; PROSTAGLANDINS; PROTEIN BINDING; SELECTION, GENETIC; SERUM ALBUMIN; THYROXINE; VITAMIN D-BINDING PROTEIN;

EID: 84942354155     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evu235     Document Type: Article

References (85)

1. 1000 Genomes Project Consortium, et al. 2010. A map of human genome variation from population-scale sequencing. Nature 467:1061-1073.
2. Ahn J, et al. 2010. Genome-wide association study of circulating vitamin D levels. Hum Mol Genet. 19:2739-2745.
3. Angelucci S, et al. 2006. Proteome analysis of human follicular fluid. Biochim Biophys Acta. 1764:1775-1785.
4. Anisimova M, Bielawski JP, Yang Z. 2002. Accuracy and power of Bayes prediction of amino acid sites under positive selection. Mol Biol Evol. 19:950-958.
5. Anisimova M, Nielsen R, Yang Z. 2003. Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics 164:1229-1236.
6. Anisimova M, Yang Z. 2007. Multiple hypothesis testing to detect lineages under positive selection that affects only a few sites. Mol Biol Evol. 24: 1219-1228.
7. Ascenzi P, et al. 2013. Molecular phylogenetic analyses of albuminoids reveal the molecular evolution of allosteric properties. IUBMB Life 65: 544-549.
8. Auton A, et al. 2012. A fine-scale chimpanzee genetic map from population sequencing. Science 336:193-198.
9. Barreiro LB, et al. 2009. Evolutionary dynamics of human Toll-like receptors and their different contributions to host defense. PLoS Genet. 5: e1000562.
10. Bhattacharya AA, Grune T, Curry S. 2000. Crystallographic analysis reveals common modes of binding of medium and long-chain fatty acids to human serum albumin. J Mol Biol. 303:721-732.
11. Borel P, Preveraud D, Desmarchelier C. 2013. Bioavailability of vitamin E in humans: an update. Nutr Rev. 71:319-331.
12. Capella-Gutierrez S, Silla-Martinez JM, Gabaldon T. 2009. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25:1972-1973.
13. Cereda M, Sironi M, Cavalleri M, Pozzoli U. 2011. GeCo++: a C++ library for genomic features computation and annotation in the presence of variants. Bioinformatics 27:1313-1315.
14. Chaplin G, Jablonski NG. 2009. Vitamin D and the evolution of human depigmentation. Am J Phys Anthropol. 139:451-461.
15. Curry S. 2009. Lessons from the crystallographic analysis of small molecule binding to human serum albumin. Drug Metab Pharmacokinet. 24: 342-357.
16. De Mees C, Bakker J, Szpirer J, Szpirer C. 2007. Alpha-fetoprotein: from a diagnostic biomarker to a key role in female fertility. Biomark Insights. 1:82-85.
17. Delport W, Poon AF, Frost SD, Kosakovsky Pond SL. 2010. Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology. Bioinformatics 26:2455-2457.
18. Fagny M, et al. 2014. Exploring the occurrence of classic selective sweeps in humans using whole-genome sequencing datasets. Mol Biol Evol. 31:1850-1868.
19. Fasano M, et al. 2005. The extraordinary ligand binding properties of human serum albumin. IUBMB Life 57:787-796.
20. Fay JC, Wu CI. 2000. Hitchhiking under positive Darwinian selection. Genetics 155:1405-1413.
21. Florant GL, Healy JE. 2012. The regulation of food intake in mammalian hibernators: a review. J Comp Physiol B. 182:451-467.
22. Forni D, et al. 2013. A 175 million year history of T cell regulatory molecules reveals widespread selection, with adaptive evolution of disease alleles. Immunity 38:1129-1141.
23. Forni D, et al. 2014. An evolutionary analysis of antigen processing and presentation across different timescales reveals pervasive selection. PLoS Genet. 10:e1004189.
24. Gabant P, et al. 2002. Alpha-fetoprotein, the major fetal serum protein, is not essential for embryonic development but is required for female fertility. Proc Natl Acad Sci U S A. 99:12865-12870.
25. Gibbs PE, Witke WF, Dugaiczyk A. 1998. The molecular clock runs at different rates among closely related members of a gene family. J Mol Evol. 46:552-561.
26. Grossman SR, et al. 2013. Identifying recent adaptations in large-scale genomic data. Cell 152:703-713.
27. Ha CE, Bhagavan NV. 2013. Novel insights into the pleiotropic effects of human serum albumin in health and disease. Biochim Biophys Acta. 1830:5486-5493.
28. Hubalek M, et al. 2014. The vitamin E-binding protein afamin increases in maternal serum during pregnancy. Clin Chim Acta. 434:41-47.
29. Hulbert AJ. 2000. Thyroid hormones and their effects: a new perspective. Biol Rev Camb Philos Soc. 75:519-631.
30. Jerkovic L, et al. 2005. Afamin is a novel human vitamin E-binding glyco-protein characterization and in vitro expression. J Proteome Res. 4: 889-899.
31. Koot BG, Houwen R, Pot DJ, Nauta J. 2004. Congenital analbuminaemia: biochemical and clinical implications. A case report and literature review. Eur J Pediatr. 163:664-670.
32. Kosakovsky Pond SL, et al. 2011. A random effects branch-site model for detecting episodic diversifying selection. Mol Biol Evol. 28:3033-3043.
33. Kosakovsky Pond SL, Frost SD. 2005. Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol Biol Evol. 22:1208-1222.
34. Kosakovsky Pond SL, Posada D, Gravenor MB, Woelk CH, Frost SD. 2006. Automated phylogenetic detection of recombination using a genetic algorithm. Mol Biol Evol. 23:1891-1901.
35. Kosiol C, et al. 2008. Patterns of positive selection in six Mammalian genomes. PLoS Genet. 4:e1000144.
36. Kragh-Hansen U. 2013. Molecular and practical aspects of the enzymatic properties of human serum albumin and of albumin-ligand complexes. Biochim Biophys Acta. 1830:5535-5544.
37. Larkin MA, et al. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23:2947-2948.
38. Lasky-Su J, et al. 2012. Genome-wide association analysis of circulating vitamin D levels in children with asthma. Hum Genet. 131: 1495-1505.
39. Lauridsen AL, et al. 2005. Plasma concentrations of 25-hydroxy-vitamin D and 1,25-dihydroxy-vitamin D are related to the phenotype of Gc (vitamin D-binding protein): a cross-sectional study on 595 early post-menopausal women. Calcif Tissue Int. 77:15-22.
40. Madsen O. 2009. Mammals (Mammalia). In: Hedges SB, Kumar S, editors. The timetree of life. New York: Oxford University Press. p. 459-461.
41. Murrell B, et al. 2012. Detecting individual sites subject to episodic diversifying selection. PLoS Genet. 8:e1002764.
42. Nei M, Li WH. 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci U S A. 76: 5269-5273.
43. Nishio H, Heiskanen M, Palotie A, Belanger L, Dugaiczyk A. 1996. Tandem arrangement of the human serum albumin multigene family in the sub-centromeric region of 4q: evolution and chromosomal direction of transcription. J Mol Biol. 259:113-119.
44. Nykjaer A, et al. 1999. An endocytic pathway essential for renal uptake and activation of the steroid 25-(OH) vitamin D3. Cell 96: 507-515.
45. Ortiz RM, MacKenzie DS, Worthy GA. 2000. Thyroid hormone concentrations in captive and free-ranging West Indian manatees (Trichechus manatus). J Exp Biol. 203:3631-3637.
46. Petersen CE, Ha CE, Curry S, Bhagavan NV. 2002. Probing the structure of the warfarin-binding site on human serum albumin using site-directed mutagenesis. Proteins 47:116-125.
47. Petit FM, et al. 2009. A new mutation in the AFP gene responsible for a total absence of alpha feto-protein on second trimester maternal serum screening for Down syndrome. Eur J Hum Genet. 17: 387-390.
48. Petitpas I, et al. 2003. Structural basis of albumin-thyroxine interactions and familial dysalbuminemic hyperthyroxinemia. Proc Natl Acad Sci U S A. 100:6440-6445.
49. Pickrell JK, et al. 2009. Signals of recent positive selection in a worldwide sample of human populations. Genome Res. 19:826-837.
50. Powe CE, et al. 2013. Vitamin D-binding protein and vitamin D status of black Americans and white Americans. N Engl J Med 369:1991-2000.
51. Quach H, et al. 2013. Different selective pressures shape the evolution of Toll-like receptors in human and African great ape populations. Hum Mol Genet. 22:4829-4840.
52. Ramagopalan SV, et al. 2010. A ChIP-seq defined genome-wide map of vitamin D receptor binding: associations with disease and evolution. Genome Res. 20:1352-1360.
53. Safadi FF, et al. 1999. Osteopathy and resistance to vitamin D toxicity in mice null for vitamin D binding protein. J Clin Invest. 103:239-251.
54. Schmidt MM, et al. 2013. Crystal structure of an HSA/FcRn complex reveals recycling by competitive mimicry of HSA ligands at a pH-dependent hydrophobic interface. Structure 21:1966-1978.
55. Shao C, et al. 2010. Shotgun proteomics analysis of hibernating arctic ground squirrels. Mol Cell Proteomics. 9:313-326.
56. Sharony R, Zadik I, Parvari R. 2004. Congenital deficiency of alpha feto-protein. Eur J Hum Genet. 12:871-874.
57. Speeckaert M, Huang G, Delanghe JR, Taes YE. 2006. Biological and clinical aspects of the vitamin D binding protein (Gc-globulin) and its polymorphism. Clin Chim Acta. 372:33-42.
58. Srere HK, Wang LC, Martin SL. 1992. Central role for differential gene expression in mammalian hibernation. Proc Natl Acad Sci U S A. 89: 7119-7123.
59. Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595.
60. Terentiev AA, Moldogazieva NT. 2013. Alpha-fetoprotein: a renaissance. Tumour Biol. 34:2075-2091.
61. Thornton K. 2003. Libsequence: a C++ class library for evolutionary genetic analysis. Bioinformatics 19:2325-2327.
62. Toye JM, Lemire EG, Baerg KL. 2012. Perinatal and childhood morbidity and mortality in congenital analbuminemia. Paediatr Child Health. 17: e20-3.
63. Urade Y, Hayaishi O. 2011. Prostaglandin D2 and sleep/wake regulation. Sleep Med Rev. 15:411-418.
64. Villanueva-Canas JL, Faherty SL, Yoder AD, Alba MM. 2014. Comparative genomics of mammalian hibernators using gene networks. Integr Comp Biol. 54(3):452-462.
65. Voegele AF, et al. 2002. Characterization of the vitamin E-binding properties of human plasma afamin. Biochemistry 41:14532-14538.
66. Voight BF, Kudaravalli S, Wen X, Pritchard JK. 2006. A map of recent positive selection in the human genome. PLoS Biol. 4:e72.
67. Wacker M, Holick MF. 2013. Sunlight and vitamin D: a global perspective for health. Dermatoendocrinology 5:51-108.
68. Wang TJ, et al. 2010. Common genetic determinants of vitamin D insufficiency: a genome-wide association study. Lancet 376:180-188.
69. Ward LD, Kellis M. 2012. HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants. Nucleic Acids Res. 40:D930-D934.
70. Warren WC, et al. 2008. Genome analysis of the platypus reveals unique signatures of evolution. Nature 453:175-183.
71. Watterson GA. 1975. On the number of segregating sites in genetical models without recombination. Theor Popul Biol. 7:256-276.
72. Wernersson R, Pedersen AG. 2003. RevTrans: multiple alignment of coding DNA from aligned amino acid sequences. Nucleic Acids Res. 31:3537-3539.
73. Wilson DJ, Hernandez RD, Andolfatto P, Przeworski M. 2011. A population genetics-phylogenetics approach to inferring natural selection in coding sequences. PLoS Genet. 7:e1002395.
74. Worobey M. 2001. A novel approach to detecting and measuring recombination: new insights into evolution in viruses, bacteria, and mitochondria. Mol Biol Evol. 18:1425-1434.
75. Wright S. 1950. Genetical structure of populations. Nature 166:247-249.
76. Yamaguchi S, et al. 2010. Delta12-prostaglandin J2 as a product and ligand of human serum albumin: formation of an unusual covalent adduct at His146. J Am Chem Soc. 132:824-832.
77. Yang J, Ha CE, Bhagavan NV. 2005. Site-directed mutagenesis study of the role of histidine residues in the neutral-to-basic transition of human serum albumin. Biochim Biophys Acta. 1724:37-48.
78. Yang Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci. 13:555-556.
79. Yang Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 24:1586-1591.
80. Yang Z, Nielsen R. 1998. Synonymous and nonsynonymous rate variation in nuclear genes of mammals. J Mol Evol. 46:409-418.
81. Yang Z, Wong WS, Nielsen R. 2005. Bayes empirical Bayes inference of amino acid sites under positive selection. Mol Biol Evol. 22: 1107-1118.
82. Zeng K, Fu YX, Shi S, Wu CI. 2006. Statistical tests for detecting positive selection by utilizing high-frequency variants. Genetics 174: 1431-1439.
83. Zhang J, Nielsen R, Yang Z. 2005. Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol Biol Evol. 22:2472-2479.
84. Zunszain PA, Ghuman J, Komatsu T, Tsuchida E, Curry S. 2003. Crystal structural analysis of human serum albumin complexed with hemin and fatty acid. BMC Struct Biol. 3:6.
85. Zunszain PA, Ghuman J, McDonagh AF, Curry S. 2008. Crystallographic analysis of human serum albumin complexed with 4Z,15E-bilirubin-IXalpha. J Mol Biol. 381:394-406.