Drosophila selenophosphate synthetase 1 regulates vitamin B6 metabolism: Prediction and confirmation

BMC Genomics

Volumn 12, Issue , 2011, Pages

  Lee, Kwang H ^a   Shim, Myoung S ^a   Kim, Jin Y ^a   Jung, Hee K ^a   Lee, Eunji ^a   Carlson, Bradley A ^b   Xu, Xue Ming ^b   Park, Jin M ^c   Hatfield, Dolph L ^b   Park, Taesung ^a   Lee, Byeong J ^a  

^a Seoul National University   (South Korea)

^b NATIONAL CANCER INSTITUTE   (United States)

^c MASSACHUSETTS GENERAL HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED RNA; DROSOPHILA PROTEIN; PYRIDOXAL 5 PHOSPHATE; PYRIDOXINE; SELENOPHOSPHATASE SYNTHETASE 1; TRANSCRIPTOME; UNCLASSIFIED DRUG; PHOSPHOTRANSFERASE; SELD PROTEIN, DROSOPHILA; SMALL INTERFERING RNA;

ANIMAL CELL; ARTICLE; BIOSYNTHESIS; CELL GROWTH; CONTROLLED STUDY; DOWN REGULATION; DROSOPHILA; GENE CLUSTER; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GROWTH INHIBITION; IMMUNE RESPONSE; INNATE IMMUNITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PREDICTION; VITAMIN METABOLISM; ANIMAL; CELL CULTURE; DRUG ANTAGONISM; ENZYMOLOGY; GENETICS; METABOLISM; RNA INTERFERENCE;

EUKARYOTA;

ANIMALS; CELLS, CULTURED; DROSOPHILA; DROSOPHILA PROTEINS; PHOSPHOTRANSFERASES; PYRIDOXAL PHOSPHATE; RNA INTERFERENCE; RNA, SMALL INTERFERING; VITAMIN B 6;

EID: 80052022855     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-426     Document Type: Article

References (45)

1. Boosalis MG. The Role of Selenium in Chronic Disease. Nutr Clin Pract 2008, 23(2):152-160. 10.1177/0884533608314532, 18390782.
2. Flohé L. Selenium in mammalian spermiogenesis. J Biol Chem 2007, 388(10):987-995.
3. Hatfield DL, Berry MJ, Gladyshev VN. Selenium: Its molecular biology and role in human health 2006, New York: Springer-Verlag Inc., 2.
4. Tamura T, Yamamoto S, Takahata M, Sakaguchi H, Tanaka H, Stadtman TC, Inagaki K. Selenophosphate synthetase genes from lung adenocarcinoma cells: Sps1 for recycling L-selenocysteine and Sps2 for selenite assimilation. Proc Natl Acad Sci USA 2004, 101(46):16162-16167. 10.1073/pnas.0406313101, 528966, 15534230.
5. Ehrenreich A, Forchhammer K, Tormay P, Veprek B, Böck A. Selenoprotein synthesis in E. coli. Purification and characterisation of the enzyme catalysing selenium activation. Eur J Biochem 1992, 206(3):767-773. 10.1111/j.1432-1033.1992.tb16983.x, 1606960.
6. Glass RS, Singh WP, Jung W, Veres Z, Scholz TD, Stadtman TC. Monoselenophosphate: synthesis, characterization, and identity with the prokaryotic biological selenium donor, compound SePX. Biochemistry 1993, 32(47):12555-12559. 10.1021/bi00210a001, 8251472.
7. Lu J, Holmgren A. Selenoproteins. J Biol Chem 2009, 284(2):723-727.
8. Leinfelder W, Forchhammer K, Veprek B, Zehelein E, Böck A. In vitro synthesis of selenocysteinyl-tRNAUCA from seryl-tRNAUCA: involvement and characterization of the selD gene product. Proc Natl Acad Sci USA 1990, 87(2):543-547. 10.1073/pnas.87.2.543, 53301, 2405383.
9. Guimaraes MJ, Peterson D, Vicari A, Cock BG, Copeland NG, Gilbert DJ, Jenkins NA, Ferrick DA, Kastelein RA, Bazan JF, Zlotnik A. Identification of a novel selD homolog from eukaryotes, bacteria, and archaea: Is there an autoregulatory mechanism in selenocysteine metabolism?. Proc Natl Acad Sci USA 1996, 93(26):15086-15091. 10.1073/pnas.93.26.15086, 26360, 8986768.
10. Low SC, Harney JW, Berry MJ. Cloning and functional characterization of human selenophosphate synthetase, an essential component of selenoprotein synthesis. J Biol Chem 1995, 270(37):21659-21664. 10.1074/jbc.270.37.21659, 7665581.
11. Xu XM, Carlson BA, Mix H, Zhang Y, Saira K, Glass RS, Berry MJ, Gladyshev VN, Hatfield DL. Biosynthesis of selenocysteine on its tRNA in eukaryotes. PLoS Biol 2007, 5(1):e4. 10.1371/journal.pbio.0050004, 1717018, 17194211.
12. Xu XM, Carlson BA, Irons R, Mix H, Zhong N, Gladyshev VN, Hatfield DL. Selenophosphate synthetase 2 is essential for selenoprotein biosynthesis. Biochem J 2007, 404(1):115-120. 10.1042/BJ20070165, 1868833, 17346238.
13. Lobanov AV, Hatfield DL, Gladyshev VN. Selenoproteinless animals: selenophosphate synthetase SPS1 functions in a pathway unrelated to selenocysteine biosynthesis. Protein Sci 2008, 17(1):176-182. 2144598, 18156471.
14. Alsina B, Serras F, Baguna J, Corominas M. Patufet, the gene encoding the Drosophila melanogaster homologue of selenophosphate synthetase, is involved in imaginal disc morphogenesis. Mol Gen Genet 1998, 257(2):113-123. 10.1007/s004380050630, 9491069.
15. Morey M, Corominas M, Serras F. DIAP1 suppresses ROS-induced apoptosis caused by impairment of the selD/sps1 homolog in Drosophila. J Cell Sci 2003, 116(22):4597-4604. 10.1242/jcs.00783, 14576353.
16. Morey M, Serras F, Baguñà J, Hafen E, Corominas M. Modulation of the Ras/MAPK signalling pathway by the redox function of selenoproteins in Drosophila melanogaster. Dev Biol 2001, 238(1):145-156. 10.1006/dbio.2001.0389, 11784000.
17. Shim MS, Kim JY, Jung HK, Lee KH, Xu XM, Carlson BA, Kim KW, Kim IY, Hatfield DL, Lee BJ. Elevation of glutamine level by selenophosphate synthetase 1 knockdown induces megamitochondrial formation in Drosophila cells. J Biol Chem 2009, 284(47):32881-32894. 10.1074/jbc.M109.026492, 2781704, 19755423.
18. Small-Howard A, Morozova N, Stoytcheva Z, Forry EP, Mansell JB, Harney JW, Carlson BA, Xu XM, Hatfield DL, Berry MJ. Supramolecular complexes mediate selenocysteine incorporation in vivo. Mol Cell Biol 2006, 26(6):2337-2346. 10.1128/MCB.26.6.2337-2346.2006, 1430297, 16508009.
19. Xu XM, Carlson BA, Zhang Y, Mix H, Kryukov GV, Glass RS, Berry MJ, Gladyshev VN, Hatfield DL. New developments in selenium biochemistry: selenocysteine biosynthesis in eukaryotes and archaea. Biol Trace Elem Res 2007, 119(3):234-241. 10.1007/s12011-007-8003-9, 17916946.
20. Forchhammer K, Böck A. Selenocysteine synthase from Escherichia coli. Analysis of the reaction sequence. J Biol Chem 1991, 266(10):6324-6328.
21. Ganichkin OM, Xu XM, Carlson BA, Mix H, Hatfield DL, Gladyshev VN, Wahl MC. Structure and catalytic mechanism of eukaryotic selenocysteine synthase. J Biol Chem 2008, 283(9):5849-5865.
22. Fitzpatrick TB, Amrhein N, Kappes B, Macheroux P, Tews I, Raschle T. Two independent routes of de novo vitamin B6 biosynthesis: not that different after all. Biochem J 2007, 407(1):1-13. 10.1042/BJ20070765, 17822383.
23. Mooney S, Leuendorf JE, Hendrickson C, Hellmann H. Vitamin B6: A long known compound of surprising complexity. Molecules 2009, 14(1):329-351. 10.3390/molecules14010329, 19145213.
24. Gonza'lez E, Danehower D, Daub ME. Vitamer levels, stress response, enzyme activity, and gene regulation of Arabidopsis lines mutant in the pyridoxine/pyridoxamine 5'-phosphate oxidase (PDX3) and the pyridoxal kinase (SOS4) genes involved in the vitamin B6 salvage pathway1[W][OA]. Plant Physiol 2007, 145(3):985-996. 10.1104/pp.107.105189, 2048783, 17873088.
25. Yoshimura T, Goto M. D-amino acids in the brain: structure and function of pyridoxal phosphate-dependent racemases. FEBS J 2008, 275(14):3527-3537. 10.1111/j.1742-4658.2008.06516.x, 18564179.
26. Esaki N, Nakamura T, Tanaka H, Suzuki T, Morino Y, Soda K. Enzymatic synthesis of selenocysteine in rat liver. Biochemistry 1981, 20(15):4492-4496. 10.1021/bi00518a039, 6456763.
27. Meier M, Janosik M, Kery V, Kraus JP, Burkhard P. Structure of human cystathionine β-synthase: a unique pyridoxal 5'-phophate-dependent heme protein. EMBO J 2001, 20(15):3910-3916. 10.1093/emboj/20.15.3910, 149156, 11483494.
28. Aitken SM, Kirsch JF. The enzymology of cystathionine biosynthesis: strategies for the control of substrate and reaction specificity. Arch Biochem Biophys 2005, 433(1):166-175. 10.1016/j.abb.2004.08.024, 15581575.
29. Soda K, Oikawa T, Esaki N. Vitamin B6 enzymes participating in selenium amino acid metabolism. BioFactors 1999, 10(2):257-262. 10.1002/biof.5520100225, 10609891.
30. Tobe R, Mihara H, Kurihara T, Esaki N. Identification of proteins interacting with selenocysteine lyase. Biosci Biotechnol Biochem 2009, 73(5):1230-1232. 10.1271/bbb.90065, 19420685.
31. Tamayo P, Slonim D, Mesirov J, Zhu Q, Kitareewan S, Dmitrovsky E, Lander ES, Golub TR. Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation. Proc Natl Acad Sci USA 1999, 96(6):2907-2912. 10.1073/pnas.96.6.2907, 15868, 10077610.
32. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardsom E, Ringwald M, Rubin GM, Sherlock G. Gene ontology: tool for the unification of biology. Nat Genet 2000, 25(1):25-29. 10.1038/75556, 3037419, 10802651.
33. Maere S, Heymans K, Kuiper M. BiNGO: a cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 2005, 21(16):3448-3449. 10.1093/bioinformatics/bti551, 15972284.
34. Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Roy Stat Soc B 1995, 57:289-300.
35. Musayev FN, Di Salvo ML, Ko TP, Schirch V, Safo MK. Structure and properties of recombinant human pyridoxine 5'-phosphate oxidase. Protein Sci 2003, 12(7):1455-1463. 10.1110/ps.0356203, 2323923, 12824491.
36. Drewke C, Klein M, Clade D, Arenz A, Müller R, Leistner E. 4-O-Phosphoryl-L-threonine, a substrate of the pdxC(serC) gene product involved in vitamin B6 biosynthesis. FEBS Lett 1996, 390(2):179-182. 10.1016/0014-5793(96)00652-7, 8706854.
37. Foley E, O'Farrell PH. Functional dissection of an innate immune response by a genome-wide RNAi screen. PLoS Biol 2004, 2(8):e203. 10.1371/journal.pbio.0020203, 434151, 15221030.
38. Kim JY, Lee KH, Shim MS, Shin H, Xu XM, Carlson BA, Hatfield DL, Lee BJ. Human selenophosphate synthetase 1 has five splice variants with unique interactions, subcellular localizations and expression patterns. Biochem Biophys Res Commun 2010, 397(1):53-58. 10.1016/j.bbrc.2010.05.055, 2924440, 20471958.
39. Bolstad BM, Irizarry RA, Astrand M, Speed TP. A Comparison of normalization methods for high density oligonucleotide array data based on bias and variance. Bioinformatics 2003, 19(2):185-193. 10.1093/bioinformatics/19.2.185, 12538238.
40. Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 2003, 31(4):e15. 10.1093/nar/gng015, 150247, 12582260.
41. Park T, Yi SG, Lee S, Lee S, Yoo DH, Ahn JI, Lee YS. Statistical tests for identifying differentially expressed genes in time course microarray experiments. Bioinformatics 2003, 19(6):694-703. 10.1093/bioinformatics/btg068, 12691981.
42. Westfall PH, Young SS. Resampling-based multiple testing: examples and methods for p-value adjustment 1993, New York, Wiley.
43. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13(11):2498-2504. 10.1101/gr.1239303, 403769, 14597658.
44. Schmittgen TD, Livak KJ. Analyzing real-time PCR data by the comparative CT method. Nat Protoc 2008, 3(6):1101-1108. 10.1038/nprot.2008.73, 18546601.
45. Perry C, Yu S, Chen J, Matharu KS, Stover PJ. Effect of vitamin B6 availability on serine hydroxymethyltransferase in MCF-7 cells. Arch Biochem Biophys 2007, 462(1):21-27. 10.1016/j.abb.2007.04.005, 1976282, 17482557.