Trends in selenium utilization in marine microbial world revealed through the analysis of the global ocean sampling (GOS) project

PLoS Genetics

Volumn 4, Issue 6, 2008, Pages

  Zhang, Yan ^a   Gladyshev, Vadim N ^a  

^a UNIVERSITY OF NEBRASKA LINCOLN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE DEHYDROGENASE; SELENIUM; SELENOPROTEIN; SERINE PROTEINASE; THIOREDOXIN; BACTERIAL PROTEIN; SEA WATER;

ARTICLE; CONTROLLED STUDY; GENE SEQUENCE; MARINE ENVIRONMENT; MICROORGANISM; NONHUMAN; PROTEIN ANALYSIS; PROTEIN LOCALIZATION; WATER SAMPLING; AMINO ACID SEQUENCE; ANIMAL; ATLANTIC OCEAN; BACTERIUM; CHEMISTRY; CLASSIFICATION; CONFORMATION; DNA SEQUENCE; EUKARYOTIC CELL; GENETICS; METABOLISM; MICROBIOLOGY; MOLECULAR GENETICS; MULTIGENE FAMILY; NUCLEOTIDE SEQUENCE; PACIFIC OCEAN; PHYLOGENY; PHYSIOLOGY; PROTEIN TERTIARY STRUCTURE; PROTEOMICS; SEQUENCE HOMOLOGY;

EUKARYOTA;

AMINO ACID SEQUENCE; ANIMALS; ATLANTIC OCEAN; BACTERIA; BACTERIAL PROTEINS; BASE SEQUENCE; EUKARYOTIC CELLS; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; NUCLEIC ACID CONFORMATION; PACIFIC OCEAN; PHYLOGENY; PROTEIN STRUCTURE, TERTIARY; PROTEOMICS; SEAWATER; SELENIUM; SELENOPROTEINS; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 46249109847     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1000095     Document Type: Article

References (64)

1. Hatfield DL, Berry MJ, Gladyshev VN (2006) Selenium: a historical perspective. In: Hatfield DL, Berry MJ, Gladyshev VN, eds. Selenium: Its molecular biology and role in human health, 2nd edition. New York: Springer. pp 1-6.
2. Thomson CD (2004) Assessment of requirements for selenium and adequacy of selenium status: a review. Eur J Clin Nutr 58: 391-402.
3. Dodig S, Cepelak I (2004) The facts and controversies about selenium. Acta Pharm 54: 261-276.
4. Stadtman TC (1996) Selenocysteine. Annu Rev Biochem 65: 83-100.
5. Driscoll DM, Copeland PR (2003) Mechanism and regulation of selenoprotein synthesis. Annu Rev Nutr 23: 17-40.
6. Papp LV, Lu J, Holmgren A, Khanna KK (2007) From selenium to selenoproteins: synthesis, identity, and their role in human health. Antioxid Redox Signal 9: 775-806.
7. Low S, Berry MJ (1996) Knowing when not to stop: selenocysteine incorporation in eukaryotes. Trends Biochem Sci 21: 203-208.
8. Böck A (2000) Biosynthesis of selenoproteins-an overview. Biofactors 11: 77-78.
9. st amino acid. Mol Microbiol 5: 515-520.
10. Rother M, Resch A, Wilting R, Böck A (2001) Selenoprotein synthesis in archaea. Biofactors 14: 75-83.
11. Yuan J, Palioura S, Salazar JC, Su D, O'Donoghue P, et al. (2006) RNA-dependent conversion of phosphoserine forms selenocysteine in eukaryotes and archaea. Proc Natl Acad Sci U S A 103: 18923-18927.
12. Xu XM, Carlson BA, Mix H, Zhang Y, Saira K, et al. (2007) Biosynthesis of selenocysteine on its tRNA in eukaryotes. PloS Biol 5: e4.
13. Böck A, Forchhammer K, Heider J, Baron C (1991) Selenoprotein synthesis: an expansion of the genetic code. Trends Biochem Sci 16: 463-467.
14. Berry MJ, Banu L, Harney JW, Larsen PR (1993) Functional characterization of the eukaryotic SECIS elements which direct selenocysteine insertion at UGA codons. EMBO J 12: 3315-3322.
15. Thanbichler M, Böck A (2002) The function of SECIS RNA in translational control of gene expression in Escherichia coli. EMBO J 21: 6925-6934.
16. Liu Z, Reches M, Groisman I, Engelberg-Kulka H (1998) The nature of the minimal 'selenocysteine insertion sequence' (SECIS) in Escherichia coli. Nucleic Acids Res 26: 896-902.
17. Hatfield DL, Gladyshev VN (2002) How selenium has altered our understanding of the genetic code. Mol Cell Biol 22: 3565-3576.
18. Kryukov GV, Kryukov VM, Gladyshev VN (1999) New mammalian selenocysteine-containing proteins identified with an algorithm that searches for selenocysteine insertion sequence elements. J Biol Chem 274: 33888-33897.
19. Lescure A, Gautheret D, Carbon P, Krol A (1999) Novel selenoproteins identified in silico and in vivo by using a conserved RNA structural motif. J Biol Chem 274: 38147-38154.
20. Castellano S, Morozova N, Morey M, Berry MJ, Serras F, et al. (2001) In silico identification of novel selenoproteins in the Drosophila melanogaster genome. EMBO Rep 2: 697-702.
21. Zhang Y, Gladyshev VN (2005) An algorithm for identification of bacterial selenocysteine insertion sequence elements and selenoprotein genes. Bioinformatics 21: 2580-2589.
22. Kryukov GV, Castellano S, Novoselov SV, Lobanov AV, Zehtab O, et al. (2003) Characterization of mammalian selenoproteomes. Science 300: 1439-1443.
23. Castellano S, Novoselov SV, Kryukov GV, Lescure A, Blanco E, et al. (2004) Reconsidering the evolution of eukaryotic selenoproteins: a novel nonmammalian family with scattered phylogenetic distribution. EMBO Rep 5: 71-77.
24. Kryukov GV, Gladyshev VN (2004) The prokaryotic selenoproteome. EMBO Rep 5: 538-543.
25. Zhang Y, Fomenko DE, Gladyshev VN (2005) The microbial selenoproteome of the Sargasso Sea. Genome Biol 6: R37.
26. nd amino acids, selenocysteine and pyrrolysine, in a symbiotic deltaproteobacterium of gutless worm Olavius algarvensis. Nucleic Acids Res 35: 4952-4963.
27. Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, et al. (2007) The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PloS Biol 5: e16.
28. Kannan N, Taylor SS, Zhai Y, Venter JC, Manning G (2007) Structural and functional diversity of the microbial kinome. PloS Biol 5: e17.
29. Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, et al. (2007) The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PloS Biol 5: e77.
30. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, et al. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66-74.
31. Fomenko DE, Xing W, Adair BM, Thomas DJ, Gladyshev VN (2007) High-throughput identification of catalytic redox-active cysteine residues. Science 315: 387-389.
32. Zhang Y, Romero H, Salinas G, Gladyshev VN (2006) Dynamic evolution of selenocysteine utilization in bacteria: a balance between selenoprotein loss and evolution of selenocysteine from redox active cysteine residues. Genome Biol 7: R94.
33. Yutin N, Suzuki MT, Teeling H, Weber M, Venter JC, et al. (2007) Assessing diversity and biogeography of aerobic anoxygenic phototrophic bacteria in surface waters of the Atlantic and Pacific Oceans using the Global Ocean Sampling expedition metagenomes. Environ Microbiol 9: 1464-1475.
34. Schürmann P (2003) Redox signaling in the chloroplast: the ferredoxin/ thioredoxin system. Antioxid Redox Signal 5: 69-78.
35. Droux M, Jacquot JP, Miginac-Maslow M, Gadal P, Huet JC, et al. (1987) Ferredoxin-thioredoxin reductase, an iron-sulfur enzyme linking light to enzyme regulation in oxygenic photosynthesis: purification and properties of the enzyme from C3, C4, and cyanobacterial species. Arch Biochem Biophys 252: 426-439.
36. Buchanan BB (1984) The ferredoxin/thioredoxin system: a key element in the regulatory function of light in photosynthesis. Bioscience 34: 378-383.
37. Dai S, Friemann R, Glauser DA, Bourquin F, Manieri W, et al. (2007) Structural snapshots along the reaction pathway of ferredoxin-thioredoxin reductase. Nature 448: 92-96.
38. Kim HY, Fomenko DE, Yoon YE, Gladyshev VN (2006) Catalytic advantages provided by selenocysteine in methionine-S-sulfoxide reductases. Biochemistry 45: 13697-13704.
39. Lobanov AV, Fomenko DE, Zhang Y, Sengupta A, Hatfield DL, et al. (2007) Evolutionary dynamics of eukaryotic selenoproteomes: large selenoproteomes may associate with aquatic life and small with terrestrial life. Genome Biol 8: R198.
40. 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 U S A 104: 13919-13924.
41. Arunachalam B, Phan UT, Geuze HJ, Cresswell P (2000) Enzymatic reduction of disulfide bonds in lysosomes: characterization of a gamma-interferon- inducible lysosomal thiol reductase (GILT). Proc Natl Acad Sci U S A 97: 745-750.
42. Phan UT, Arunachalam B, Cresswell P (2000) Gamma-interferon-inducible lysosomal thiol reductase (GILT). Maturation, activity, and mechanism of action. J Biol Chem 275: 25907-25914.
43. Pané-Farré J, Lewis RJ, Stülke J (2005) The RsbRST stress module in bacteria: a signaling system that may interact with different output modules. J Mol Microbiol Biotechnol 9: 65-76.
44. Delumeau O, Dutta S, Brigulla M, Kuhnke G, Hardwick SW, et al. (2004) Functional and structural characterization of RsbU, a stress signaling protein phosphatase 2C. J Biol Chem 279: 40927-40937.
45. Obuchowski M, Madec E, Delattre D, Boël G, Iwanicki A, et al. (2000) Characterization of PrpC from Bacillus subtilis, a member of the PPM phosphatase family. J Bacteriol 182: 5634-5638.
46. Duncan L, Alper S, Arigoni F, Losick R, Stragier P (1995) Activation of cell-specific transcription by a serine phosphatase at the site of asymmetric division. Science 270: 641-644.
47. Vijay K, Brody MS, Fredlund E, Price CW (2000) A PP2C phosphatase containing a PAS domain is required to convey signals of energy stress to the sigmaB transcription factor of Bacillus subtilis. Mol Microbiol 35: 180-188.
48. Yang X, Kang CM, Brody MS, Price CW (1996) Opposing pairs of serine protein kinases and phosphatases transmit signals of environmental stress to activate a bacterial transcription factor. Genes Dev 10: 2265-2275.
49. Carniol K, Ben-Yehuda S, King N, Losick R (2005) Genetic dissection of the sporulation protein SpoIIE and its role in asymmetric division in Bacillus subtilis. J Bacteriol 187: 3511-3520.
50. Ching WM, Alzner-DeWeerd B, Stadtman TC (1985) A selenium-containing nucleoside at the first position of the anticodon in seleno-tRNAGlu from Clostridium sticklandii. Proc Natl Acad Sci U S A 82: 347-350.
51. Wittwer AJ, Ching WM (1989) Selenium-containing tRNA(Glu) and tRNA(Lys) from Escherichia coli: purification, codon specificity and translational activity. Biofactors 2: 27-34.
52. Romero H, Zhang Y, Gladyshev VN, Salinas G (2005) Evolution of selenium utilization traits. Genome Biol 6: R66.
53. Kramer GF, Ames BN (1988) Isolation and characterization of a selenium metabolism mutant of Salmonella typhimurium. J Bacteriol 170: 736-743.
54. Wolfe MD, Ahmed F, Lacourciere GM, Lauhon CT, Stadtman TC, et al. (2004) Functional diversity of the rhodanese homology domain: the Escherichia coli ybbB gene encodes a selenophosphate-dependent tRNA 2-selenouridine synthase. J Biol Chem 279: 1801-1809.
55. Hallam SJ, Putnam N, Preston CM, Detter JC, Rokhsar D, et al. (2004) Reverse methanogenesis: testing the hypothesis with environmental genomics. Science 305: 1457-1462.
56. Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, et al. (2005) Comparative metagenomics of microbial communities. Science 308: 554-557.
57. Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, et al. (2006) Metagenomic analysis of the human distal gut microbiome. Science 312: 1355-1359.
58. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
59. Thain D, Tannenbaum T, Livny M (2003) Condor and the Grid. In: Berman F, Hey AJG, Fox G, eds. Grid Computing: Making The Global Infrastructure a Reality. New York: John Wiley & Sons. pp 299-332.
60. Frey J, Tannenbaum T, Foster I, Livny M, Tuecke S (2001) Condor-G: A Computation Management Agent for Multi-Institutional Grids. In Proceedings of the Tenth IEEE Symposium on High Performance Distributed Computing (HPDC10): 7-9 August, 2001; San Francisco, CA.
61. Higgins D, Thompson J, Gibson T, Thompson JD, Higgins DG, et al. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680.
62. Felsenstein J (1989) PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166.
63. Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696-704.
64. Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.