Low exchangeability of selenocysteine, the 21st amino acid, in vertebrate proteins

Molecular Biology and Evolution

Volumn 26, Issue 9, 2009, Pages 2031-2040

  Castellano, Sergi ^a   Andrés, Aida M ^a   Bosch, Elena ^b   Bayes, Mònica ^c,d   Guigó, Roderic ^c   Clark, Andrew G ^a  

^a Department of Obstetrics Gynecology   (United States)

^b UNIVERSITAT POMPEU FABRA   (Spain)

^c CENTRE FOR GENOMIC REGULATION CRG   (Spain)

^d Centro Nacional de Genotipado CeGen   (Spain)

Author keywords

Cysteine; Exchangeability; Selenium; Selenocysteine; Selenoproteins; Vertebrates

Indexed keywords

AMINO ACID; CYSTEINE; ENZYME; PROTEIN; PROTEOME; SELENIUM; SELENOCYSTEINE; SELENOPROTEIN; THIOREDOXIN REDUCTASE;

ARTICLE; BIOCHEMISTRY; CODON; EVOLUTION; FAMILY; GENOME; GEOGRAPHIC DISTRIBUTION; HUMAN; MOLECULAR BIOLOGY; MOLECULAR EVOLUTION; NONHUMAN; NUTRITIONAL DEFICIENCY; PROTEIN FUNCTION; UNITED STATES; VERTEBRATE;

ANIMALS; EVOLUTION, MOLECULAR; HUMANS; OXYGEN; PHYLOGENY; PROTEINS; PROTEOME; SELENOCYSTEINE; SELENOPROTEINS; VERTEBRATES;

VERTEBRATA;

EID: 68949206430     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msp109     Document Type: Article

References (64)

1. Akashi H, Gojobori T. 2002. Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis. Proc Natl Acad Sci USA. 99:3695-3700.
2. Bamshad M, Wooding SP. 2003. Signatures of natural selection in the human genome. Nat Rev Genet. 4:99-111.
3. Bargelloni L, Marcato S, Patarnello T. 1998. Antarctic fish hemoglobins: evidence for adaptive evolution at subzero temperature. Proc Natl Acad Sci USA. 95:8670-8675.
4. 2. Geochim Cosmochim Acta. 70:5653.
5. Berner RA, VandenBrooks JM, Ward PD. 2007. Oxygen and evolution. Science. 316:557-558.
6. Berry MJ, Mai AL, Kieffer J, Harney JW, Larsen P. 1992. Substitution of cysteine for selenocysteine in type I iodothyronine deiodinase reduces the catalytic efficiency of the protein but enhances its translation. Endocrinology. 131:1448-1852.
7. Canfield DE, Poulton SW, Narbonne GM. 2007. Late-Neoproterozoic deep-ocean oxygenation and the rise of animal life. Science. 315:92-95.
8. Cann HM, de Toma C, Cazes L, Legrand MF, Morel V, Piouffre L, Bodmer J, Bodmer WF, Bonne-Tamir B, Cambon-Thomsen A. 2002. A human genome diversity cell line panel. Science. 296:261-262.
9. Castellano S. 2009. On the unique function of selenocysteine - insights from the evolution of selenoproteins. Biochim Biophys Acta. Advanced online publication. doi:10.1016/j.bbagen.2009.03.027.
10. Castellano S, Gladyshev VN, Guigó R, Berry MJ. 2008. SelenoDB 1.0: a database of selenoprotein genes, proteins and SECIS elements. Nucl Acids Res. 36:D339-D343.
11. Castellano S, Lobanov AV, Chapple C, et al. (11 co-authors). 2005. Diversity and functional plasticity of eukaryotic selenoproteins: identification and characterization of the SelJ family. Proc Natl Acad Sci USA. 102:16188-16193.
12. Castellano S, Novoselov SV, Kryukov GV, Lescure A, Blanco E, Krol A, Gladyshev VN, Guigó R. 2004. Reconsidering the evolution of eukaryotic selenoproteins: a novel nonmammalian family with scattered phylogenetic distribution. EMBO Rep. 5:71-77.
13. Chamary JV, Guigó R, Parmley JL, Hurst LD. 2006. Hearing silence: non-neutral evolution at synonymous sites in mammals. Nat Rev Genet. 7:98-108.
14. Chapple CE, Guigó R. 2008. Relaxation of selective constraints causes independent selenoprotein extinction in insect genomes. PLoS ONE. 3:e2968.
15. Driscoll DM, Copeland DR. 2003. Mechanism and regulation of selenoprotein synthesis. Annu Rev Nutr. 23:17-40.
16. Drosophila 12 Genomes Consortium. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 450:203-218.
17. Ellegren H, Smith NG, Webster MT. 2003. Mutation rate variation in the mammalian genome. Curr Opin Genet Dev. 13:562-568.
18. Eyre-Walker A, Keightley PD. 2007. The distribution of fitness effects of new mutations. Nat Rev Genet. 8:610-618.
19. Farris JS. 1977. Phylogenetic analysis under Dollo's law. Syst Zool. 26:77-88.
20. Fitch WM. 1971. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool. 20:406-416.
21. Foster CB, Aswath A, Chanock SJ, McKay HF, Peters U. 2006. Polymorphism analysis of six selenoprotein genes: support for a selective sweep at the glutathione peroxidase 1 locus (3p21) in Asian populations. BMC Genet. 7:56.
22. Gish W, States DJ. 1993. Identification of protein coding regions by database similarity search. Nat Genet. 3:266-272.
23. Gould SJ, Lewontin RC. 1979. The spandrels of San Marco and the Panglossian paradigm. Proc R Soc Lond. 205:581-598.
24. Grantham R. 1974. Amino acid difference formula to help explain protein evolution. Science. 185:862-864.
25. Gromer S, Johansson L, Bauer H, Arscott LD, Rauch S, Ballou DP, Williams CH Jr, Schirmer RH, Arnér ES. 2003. Active sites of thioredoxin reductases: why selenoproteins? Proc Natl Acad Sci USA. 100:12618-12623.
26. Hasegawa M, Kishino H, Yano T. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol. 22:160-174.
27. Haygood R, Fedrigo O, Hanson B, Yokoyama KD, Wray GA. 2007. Promoter regions of many neural- and nutrition-related genes have experienced positive selection during human evolution. Nat Genet. 39:1140-1144.
28. Hedges SB. 2002. The origin and evolution of model organisms. Nat Rev Genet. 3:838-849.
29. Hein J, Schierup MH, Wiuf C. 2005. From genealogies to sequences. In: Gene genealogies, variation and evolution. A primer in coalescent theory. Oxford: Oxford University Press. pp 57.
30. Hudson RR. 2002. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics. 18:337-338.
31. Jacob G, Giles GI, Giles NM, Sies NH. 2003. Sulfur and selenium: the role of oxidation state in protein structure and function. Angew Chem Int Ed. 42:4742-4758.
32. Johansson L, Gafvelin G, Arnér ES. 2005. Selenocysteine in proteins - properties and biotechnological use. Biochim Biophys Acta. 1726:1-13.
33. Jukes TH. 1990. Genetic code 1990. Experientia. 46:1149-1157.
34. Kanzok SM, Fechner A, Bauer H, Ulschmid JK, Müller HM, Botella-Muñoz J, Schneuwly S, Schirmer R, Becker K. 2001. Substitution of the thioredoxin system for glutathione reductase in Drosophila melanogaster. Science. 291:643-646.
35. Kawashima S, Pokarowski P, Pokarowska M, Kolinski A, Katayama T, Kanehisa M. 2008. AAindex: amino acid index database, progress report 2008. Nucleic Acids Res. 36:D202-D205.
36. Kim HY, Gladyshev VN. 2005. Different catalytic mechanisms in mammalian selenocysteine- and cysteine-containing methionine-R-sulfoxide reductases. PLoS Biol. 3:e375.
37. Kryukov GV, Castellano S, Novoselov SV, Lobanov AV, Zehtab O, Guigó R, Gladyshev VN. 2003. Characterization of mammalian selenoproteomes. Science. 300:1439-1443.
38. Leinfelder W, Zehelein E, Mandrand-Berthelot M, Böck A. 1988. Gene for a novel tRNA species that accepts L-serine and cotranslationally inserts selenocysteine. Nature. 331:723-725.
39. Levander OA. 1987. A global view of human selenium nutrition. Ann Rev Nutr. 7:227-250.
40. Lobanov AV, Fomenko DE, Zhang Y, Sengupta A, Hatfield DL, Gladyshev VN. 2007. Evolutionary dynamics of eukaryotic selenoproteomes: large selenoproteomes may associate with aquatic life and small with terrestrial life. Genome Biol. 8:R198.
41. Lobanov AV, Hatfield DL, Gladyshev VN. 2008a. Reduced reliance on the trace element selenium during evolution of mammals. Genome Biol. 9:R62.
42. Lobanov AV, Hatfield DL, Gladyshev VN. 2008b. Selenoproteinless animals: selenophosphate synthetase SPS1 functions in a pathway unrelated to selenocysteine biosynthesis. Protein Sci. 17:176-182.
43. Lynch M. 2007. The frailty of adaptive hypotheses for the origins of organismal complexity. Proc Natl Acad Sci USA. 104:8597-8604.
44. Maiorino M, Aumann KD, Brigelius-Flohé R, Doria D, van den Heuvel J, McCarthy J, Roveri A, Ursini F, Flohé L. 1995. Probing the presumed catalytic triad of selenium-containing peroxidases by mutational analysis of phospholipid hydroperoxide glutathione peroxidase (PHGPx). Biol Chem Hoppe Seyler. 376:651-660.
45. Margulies EH, Vinson JP. NISC Comparative Sequencing Program, et al. (11 co-authors). 2005. An initial strategy for the systematic identification of functional elements in the human genome by low-redundancy comparative sequencing. Proc Natl Acad Sci USA. 102:3354-3359.
46. Marth GT, Czabarka E, Murvai J, Sherry ST. 2004. The allele frequency spectrum in genome-wide human variation data reveals signals of differential demographic history in three large world populations. Genetics. 166:351-372.
47. Mehta A, Rebsch CM, Kinzy SA, Fletcher JE, Copeland PR. 2004. Efficiency of mammalian selenocysteine incorporation. J Biol Chem. 279:37852-37859.
48. Mitchell-Olds T, Willis JH, Goldstein DB. 2007. Which evolutionary processes influence natural genetic variation for phenotypic traits? Nat Rev Genet. 8:845-856.
49. Miyata T, Miyazawa S, Yasunaga T. 1979. Two types of amino acid substitutions in protein evolution. J Mol Evol. 12:219-236.
50. Nielsen R, Hellmann I, Hubisz M, Bustamante C, Clark AG. 2007. Recent and ongoing selection in the human genome. Nat Rev Genet. 8:857-868.
51. Nikolaev S, Montoya-Burgos JI, Margulies EH, ISC Comparative Sequencing Program. Rougemont J, Nyffeler B, Antonarakis SE. 2007. Early history of mammals is elucidated with the ENCODE multiple species sequencing data. PLoS Genet. 3:e2.
52. Rambaut A, Grassly NC. 1997. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput Appl Biosci. 13:235-238.
53. Rocher C, Lalanne JL, Chaudière J. 1992. Purification and properties of a recombinant sulfur analog of murine selenium-glutathione peroxidase. Eur J Biochem. 205:955-960.
54. Rosenberg MS, Subramanian S, Kumar S. 2003. Patterns of transitional mutation biases. within and among mammalian genomes. Mol Biol Evol. 20:988-993.
55. Shamberger RJ. 1981. Selenium in the environment. Sci Total Environ. 17:59-74.
56. Shchedrina VA, Novoselov SV, Malinouski MY, Gladyshev VN. 2007. Identification and characterization of a selenoprotein family containing a diselenide bond in a redox motif. Proc Natl Acad Sci USA. 104:13919-13924.
57. Stadtman TC. 1996. Selenocysteine. Ann Rev Biochem. 65:83-100.
58. Valentine JL. 1997. Environmental occurrence of selenium in waters and related health significance. Biomed Environ Sci. 10:292-299.
59. Venter JC, Adams MD, Myers EW, et al. (275 co-authors). 2001. The sequence of the human genome. Science. 291:1304-1351.
60. Williamson SH, Hernandez R, Fledel-Alon A, Zhu L, Nielsen R, Bustamante CD. 2005. Simultaneous inference of selection and population growth from patterns of variation in the human genome. Proc Natl Acad Sci USA. 102:7882-7887.
61. Xu XM, Carlson BA, Mix H, Zhang Y, Saira K, Glass RS, Berry MJ, Gladyshev VN, Hatfield DL. 2007. Biosynthesis of Selenocysteine on Its tRNA in Eukaryotes. PLoS Biol. 5:e4.
62. Yampolsky LY, Stoltzfus A. 2005. The exchangeability of amino acids in proteins. Genetics. 170:1459-1472.
63. Zhong L, Holmgren A. 2000. Essential role of selenium in the catalytic activities of mammalian thioredoxin reductase revealed by characterization of recombinant enzymes with selenocysteine mutations. J Biol Chem. 275:18121-18128.
64. Zmasek CM, Eddy SR. 2001. A simple algorithm to infer gene duplication and speciation events on a gene tree. Bioinformatics. 17:821-828.