In silico identification of silkworm selenoproteomes

Chinese Science Bulletin

Volumn 51, Issue 23, 2006, Pages 2860-2867

  Chen, Ping ^a,b,c   Duan, Jun ^a   Jiang, Liang ^b   Liu, Qiong ^b   Zhao, Ping ^a   Xia, Qingyou ^a   Xu, Huibi ^c  

^a SOUTHWEST UNIVERSITY   (China)

^b SHENZHEN UNIVERSITY   (China)

^c HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

Author keywords

Genome; Selenium; Selenocysteine; Selenoprotein; Silkworm

Indexed keywords

BOMBYX MORI;

EID: 33845617523     PISSN: 10016538     EISSN: 18619541     Source Type: Journal    
DOI: 10.1007/s11434-006-2206-x     Document Type: Article

References (46)

1. Hatfield D L. Selenium: Its molecular biology and role in human health. Boston: Kluwer Academic Publishers, 2001. 313-319
2. Kryukov G V, Castellano S, Novoselov S V, et al. Characterization of mammalian Selenoproteomes. Science, 2003, 300(30): 1439-1443
3. Atkins J F, Gesteland R F. The twenty-first amino acid. Nature, 2000, 407(6803): 463-465
4. Bock A. Biosynthesis of selenoproteins: An overview. Biofactors, 2000, 11(1-2): 77-78
5. Hatfield D L, Gladyshev V N. How selenium has altered our understanding of the genetic code. Mol Cell Biol, 2002, 22(11): 3565-3576
6. Driscoll D M, Copeland P R. Mechanism and regulation of seleno-protein synthesis. Annu Rev Nutr, 2003, 23: 17-40
7. Berry M J, Banu L, Chen Y Y, et al. Recognition of UGA as a selenocysteine codon in type I deiodinase requires sequences in the 3′ untranslated region. Nature, 1991, 353(6341): 273-276
8. Walczak R, Westhof E, Carbon P, et al. A novel RNA structural motif in the selenocysteine insertion element of eukaryotic seleno-protein mRNAs. RNA, 1996, 2(4): 367-379
9. Tujebajeva R M, Copeland P R, Xu X M, et al. Decoding apparatus for eukaryotic selenocysteine insertion. EMBO Rep, 2000, 1(2): 158-163
10. Zhang Y, Gladyshev V N, An algorithm for identification of bacterial selenocysteine insertion sequence elements and selenoprotein genes. Bioinformatics, 2005, 21(11): 2580-2589
11. Xu H B, Huang K X, Qu X H. Identification of selenocysteine insertion sequence (SECIS) element in eukaryotic selenoproteins by RNA Draw program. Chin Sci Bull, 2001, 46(14): 1159-1160
12. Castellano S, Morozova N, Morey M, et al. In silico identification of novel selenoproteins in the Drosophila melanogaster genome. EMBO Rep, 2001, 2(8): 697-702
13. Burge C B, Karlin S. Finding the genes in genomic DNA. Curr Opin Struct Biol, 1998, 8(3): 346-353
14. Haussler D. Computational genefinding. Trends Biochem Sci, Supplementary Guide to Bioinformatics, 1998. 12-15
15. Cataldo L, Baig K, Oko R, et al. Developmental expression, intracellular localization, and selenium content of the cysteine-rich protein associated with the mitochondrial capsules of mouse sperm. Mol Reprod Dev, 1996, 45(3):320-331
16. Gladyshev V N, Jeang K T, Stadtman T C. Selenocysteine, identified as the penultimate C-terminal residue in human T-cell thioredoxin reductase, corresponds to TGA in the human placental gene. Proc Natl Acad Sci USA, 1996, 93(12): 6146-6151
17. Guimaraes M J, Peterson D, Vicari A, et al. 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
18. Lander E S, Linton L M, Birren B, et al. Initial sequencing and analysis of the human genome. Nature, 2001, 409(6822): 860-921
19. Venter J C, Adams M D, Myers E W, et al. The sequence of the human genome. Science, 2001, 291(5507): 1304-1351.
20. Taskov K, Chapple C, Kryukov G V, et al. Nematode seleno-proteome: The use of the selenocysteine insertion system to decode one codon in an animal genome? Nucleic Acids Res, 2005, 33(7): 2227-2238
21. Zhang Y, Fomenko D E, Gladyshev V N. The microbial seleno-proteome of the Sargasso Sea. Genome Biol, 2005, 6(4): R37
22. Kryukov G V, Gladyshev V N. The prokaryotic selenoproteome. EMBO rep, 2004, 5(5): 538-543
23. Adams M D, Celniker S E, Holt R A, et al. Finishing a whole-genome shotgun: Release 3 of the Drosophila euchromatic genome sequence. Science, 2000, 287(5461): 2185-2195
24. Xia Q Y, Zhou Z Y, Lu C, et al. A draft sequence for the genome of the domesticated silkworm (Bombyx mori). Science, 2004, 306(10): 1937-1940
25. Wang J, Xia Q Y, He X M, et al. SilkDB: A knowledgebase for silkworm biology and genomics. Nucleic Acids Res, 2005, 33(Database issue): D399-D402
26. Hu D C, Liu Q, Cui H R, et al. Effects of amino acids from selenium-rich silkworm pupas on human hepatoma cells. Life Sci, 2005, 77(17): 2098-2110
27. Zha X F, Xia Q Y, Zhao P, et al. Detection and analysis of alternative splicing in the silkworm by aligning expressed sequence tags with the genomic sequence. Insect Mol Biol, 2005, 14 (2): 113-119
28. Wang Z L, Li J, Xia Q Y, et al. Identification and expression pattern of Bmlark, a homolog of the Drosophila gene lark in Bombyx mori. DNA Seq, 2005, 16(3): 224-229
29. Cheng T C, Xia Q Y, Qian J F, et al. Mining single nucleotide polymorphisms from EST data of silkworm, Bombyx mori, inbred strain Dazao. Insect Biochem Mol Biol, 2004, 34(6): 523-530
30. Kryukov G V, Kryukov V M, Gladyshev V N. New mammalian selenocysteine-containing proteins identified with an algorithm that searches for selenocysteine insertion sequence elements. J Biol Chem, 1999, 274(48): 33888-33897
31. Higgins C F. ABC transporters: From microorganisms to man. Annu Rev Cell Biol, 1992, 8: 67-113
32. Kaminski W E, Orso E, Diederich W, et al. Identification of a novel human sterol-sensitive atp-binding cassette transporter (ABCA7). Biochem Biophys Res Commun, 2000, 273(2): 532-538
33. Langmann T, Klucken J, Reil M, et al. Molecular cloning of the human ATP-binding cassette transporter 1 (hABC1): Evidence for sterol-dependent regulation in macrophages. Biochem Biophys Res Commun, 1999, 257(1): 29-33
34. Klucken J, Buchler C, Orso E, et al. ABCG1 (ABC8), the human homolog of the Drosophila white gene, is a regulator of macrophage cholesterol and phospholipid transport. Proc Natl Acad Sci USA, 2000, 97(2): 817-822
35. Dai R M, Chen E, Longo D L, et al. Involvement of valosin-containing protein, an ATPase co-purified with IkappaBalpha and 26 S proteasome, in ubiquitin-proteasome-mediated degradation of IkappaBalpha. J Biol Chem, 1998, 273(6): 3562-3573
36. Yamamoto S, Tomita Y, Hoshida Y, et al. Expression level of valosin-containing protein (VCP) as a prognostic marker for gingival squamous cell carcinoma. Ann Oncol, 2004, 15(9): 1432-1438
37. Asai T, Tomita Y, Nakatsuka S et al. VCP (p97) regulates NfkappaB signaling pathway, which is important for metastasis of osteosarcoma cell line. Jpn J Cancer Res, 2002, 93(3): 296-304
38. Brooks-Wilson A, Marcil M, Clee S M, et al. Mutations in ABC1 in Tangier disease and familial high-density lipoprotein deficiency. Nat Genet, 1999, 22(4): 336-345
39. Rust S, Rosier M, Funke H, et al. Tangier disease is caused by mutations in the gene encoding ATP-binding cassette transporter 1. Nat Genet, 1999, 22(4): 352-355
40. Orso E, Broccardo C, Kaminski W E, et al. Transport of lipids from Golgi to plasma membrane is defective in Tangier disease patients and Abc1 deficient mice. Nat Genet, 2000, 24(2): 192-196
41. Allikmets R, Singh N, Sun H, et al. A photoreceptor cell-specific ATP-binding transporter gene (ABCR) is mutated in recessive Stargardt macular dystrophy. Nat Genet, 1997, 15(3): 236-246
42. Allikmets R, Shroyer N F, Singh N, et al. Mutation of the Stargardt disease gene (ABCR) in age-related macular degeneration. Science, 1997, 277(5333): 1805-1807
43. Martinez-Mir A, Paloma E, Allikmets R, et al. Retinitis pigmentosa caused by a homozygous mutation in the Stargardt disease gene ABCR. Nat Genet, 1998, 18(1): 11-12
44. Yamamoto S, Tomita Y, Nakamori S et al. Elevated expression of valosin-containing protein (p97) in hepatocellular carcinoma is correlated with increased incidence of tumor recurrence. J Clin Oncol, 2003, 21(3): 447-452
45. Yamamoto S, Tomita Y, Hoshida Y, et al. Expression level of valosin-containing protein is strongly associated with progression and prognosis of gastric carcinoma. J Clin Oncol, 2003, 21(13): 2537-2544
46. Tsujimoto Y, Tomita Y, Hoshida Y et al. Elevated expression of Valosin-containing protein (p97) is associated with poor prognosis of prostate cancer. Clin Cancer Res, 2004, 10(9): 3007-3012