Structural/functional analysis of the human OXR1 protein: identification of exon 8 as the anti-oxidant encoding function

BMC Molecular Biology

Volumn 13, Issue , 2012, Pages

  Murphy, Kenan C ^a   Volkert, Michael R ^a  

^a UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; COMPLEMENTARY DNA; OXR1 PROTEIN; PROTEIN; REACTIVE OXYGEN METABOLITE; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ANTIOXIDANT ACTIVITY; ARTICLE; BACTERIAL STRAIN; BACTERIUM MUTANT; CONTROLLED STUDY; DNA LIBRARY; DNA REPAIR; ESCHERICHIA COLI; EXON; GENE; HUMAN; MUTAGENESIS; NONHUMAN; OXR1 GENE; PLASMID; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN FUNCTION; YEAST;

DNA PRIMERS; ESCHERICHIA COLI; EXONS; GENE EXPRESSION REGULATION; GENE LIBRARY; HUMANS; MITOCHONDRIA; MUTAGENESIS; OXIDATIVE STRESS; PLASMIDS; PROTEINS;

EID: 84864536811     PISSN: None     EISSN: 14712199     Source Type: Journal    
DOI: 10.1186/1471-2199-13-26     Document Type: Article

References (50)

1. Cadet J, Douki T, Ravanat JL. Oxidatively generated base damage to cellular DNA. Free Radic Biol Med 2010, 49(1):9-21. 10.1016/j.freeradbiomed.2010.03.025, 20363317.
2. Negre-Salvayre A, Coatrieux C, Ingueneau C, Salvayre R. Advanced lipid peroxidation end products in oxidative damage to proteins Potential role in diseases and therapeutic prospects for the inhibitors. Br J Pharmacol 2008, 153(1):6-20. 10.1038/sj.bjp.0707395, 2199390, 17643134.
3. Sedelnikova OA, Redon CE, Dickey JS, Nakamura AJ, Georgakilas AG, Bonner WM. Role of oxidatively induced DNA lesions in human pathogenesis. Mutat Res 2010, 704(1-3):152-159. 3074954, 20060490.
4. Liochev SI, Fridovich I. The Haber-Weiss cycle -- 70 years later: an alternative view. Redox Rep 2002, 7(1):55-57. author reply 59-60, 10.1179/135100002125000190, 11981456.
5. Hancock JT, Desikan R, Neill SJ. Role of reactive oxygen species in cell signalling pathways. Biochem Soc Trans 2001, 29(Pt 2):345-350.
6. Klaunig JE, Kamendulis LM. The role of oxidative stress in carcinogenesis. Annu Rev Pharmacol Toxicol 2004, 44:239-267. 10.1146/annurev.pharmtox.44.101802.121851, 14744246.
7. Halliwell B. Oxidative stress and cancer: have we moved forward?. Biochem J 2007, 401(1):1-11.
8. Gilgun-Sherki Y, Melamed E, Offen D. The role of oxidative stress in the pathogenesis of multiple sclerosis: the need for effective antioxidant therapy. J Neurol 2004, 251(3):261-268. 10.1007/s00415-004-0348-9, 15015004.
9. Hitchon CA, El-Gabalawy HS. Oxidation in rheumatoid arthritis. Arthritis Res Ther 2004, 6(6):265-278. 10.1186/ar1447, 1064874, 15535839.
10. Delles C, Miller WH, Dominiczak AF. Targeting reactive oxygen species in hypertension. Antioxid Redox Signal 2008, 10(6):1061-1077. 10.1089/ars.2007.2008, 18321202.
11. Thomas B, Beal MF. Parkinson's disease. Hum Mol Genet 2007, 16(R2):R183-R194. 10.1093/hmg/ddm159, 17911161.
12. Lu T, Finkel T. Free radicals and senescence. Exp Cell Res 2008, 314(9):1918-1922. 10.1016/j.yexcr.2008.01.011, 2486428, 18282568.
13. Perry G, Nunomura A, Cash AD, Taddeo MA, Hirai K, Aliev G, Avila J, Wataya T, Shimohama S, Atwood CS, et al. Reactive oxygen: its sources and significance in Alzheimer disease. J Neural Transm Suppl 2002, 62:69-75.
14. Fridovich I. Superoxide radical and superoxide dismutases. Annu Rev Biochem 1995, 64:97-112. 10.1146/annurev.bi.64.070195.000525, 7574505.
15. Hayes JD, McLellan LI. Glutathione and glutathione-dependent enzymes represent a co-ordinately regulated defence against oxidative stress. Free Radic Res 1999, 31(4):273-300. 10.1080/10715769900300851, 10517533.
16. Horsburgh MJ, Wharton SJ, Karavolos M, Foster SJ. Manganese: elemental defence for a life with oxygen. Trends Microbiol 2002, 10(11):496-501. 10.1016/S0966-842X(02)02462-9, 12419613.
17. Demple B, Harrison L. Repair of oxidative damage to DNA: enzymology and biology. Annu Rev Biochem 1994, 63:915-948. 10.1146/annurev.bi.63.070194.004411, 7979257.
18. Fishel ML, Vasko MR, Kelley MR. DNA repair in neurons: so if they don't divide what's to repair?. Mutat Res 2007, 614(1-2):24-36.
19. Wyrzykowski J, Volkert MR. The Escherichia coli methyl-directed mismatch repair system repairs base pairs containing oxidative lesions. J Bacteriol 2003, 185(5):1701-1704. 10.1128/JB.185.5.1701-1704.2003, 148063, 12591888.
20. Wallace SS. Biological consequences of free radical-damaged DNA bases. Free Radic Biol Med 2002, 33(1):1-14. 10.1016/S0891-5849(02)00827-4, 12086677.
21. Michaels ML, Cruz C, Grollman AP, Miller JH. Evidence that MutY and MutM combine to prevent mutations by an oxidatively damaged form of guanine in DNA. Proc Natl Acad Sci USA 1992, 89(15):7022-7025. 10.1073/pnas.89.15.7022, 49637, 1495996.
22. Jiang D, Hatahet Z, Melamede RJ, Kow YW, Wallace SS. Characterization of Escherichia coli Endonuclease VIII. J Biol Chem 1997, 272(51):32230-32239. 10.1074/jbc.272.51.32230, 9405426.
23. Hegde ML, Hazra TK, Mitra S. Early steps in the DNA base excision/single-strand interruption repair pathway in mammalian cells. Cell Res 2008, 18(1):27-47. 10.1038/cr.2008.8, 2692221, 18166975.
24. Volkert MR, Elliott NA, Housman DE. Functional genomics reveals a family of eukaryotic oxidation protection genes. Proc Natl Acad Sci USA 2000, 97(26):14530-14535. 10.1073/pnas.260495897, 18953, 11114193.
25. Stowers RS, Russell S, Garza D. The 82F late puff contains the L82 gene, an essential member of a novel gene family. Dev Biol 1999, 213(1):116-130. 10.1006/dbio.1999.9358, 10452850.
26. Jaramillo-Gutierrez G, Molina-Cruz A, Kumar S, Barillas-Mury C. The Anopheles gambiae oxidation resistance 1 (OXR1) gene regulates expression of enzymes that detoxify reactive oxygen species. PLoS One 2010, 5(6):e11168. 10.1371/journal.pone.0011168, 2887368, 20567517.
27. Natoli R, Provis J, Valter K, Stone J. Expression and role of the early-response gene Oxr1 in the hyperoxia-challenged mouse retina. Invest Ophthalmol Vis Sci 2008, 49(10):4561-4567. 10.1167/iovs.08-1722, 18539939.
28. Choi J, Forster MJ, McDonald SR, Weintraub ST, Carroll CA, Gracy RW. Proteomic identification of specific oxidized proteins in ApoE-knockout mice: relevance to Alzheimer's disease. Free Radic Biol Med 2004, 36(9):1155-1162. 10.1016/j.freeradbiomed.2004.02.002, 15082069.
29. Shenk JC, Liu J, Fischbach K, Xu K, Puchowicz M, Obrenovich ME, Gasimov E, Alvarez LM, Ames BN, Lamanna JC, et al. The effect of acetyl-L-carnitine and R-alpha-lipoic acid treatment in ApoE4 mouse as a model of human Alzheimer's disease. J Neurol Sci 2009, 283(1-2):199-206. 2713369, 19342064.
30. Strum JC, Shehee R, Virley D, Richardson J, Mattie M, Selley P, Ghosh S, Nock C, Saunders A, Roses A. Rosiglitazone induces mitochondrial biogenesis in mouse brain. J Alzheimers Dis 2007, 11(1):45-51.
31. James R, Searcy JL, Le Bihan T, Martin SF, Gliddon CM, Povey J, Deighton RF, Kerr LE, McCulloch J, Horsburgh K. Proteomic analysis of mitochondria in APOE transgenic mice and in response to an ischemic challenge. J Cereb Blood Flow Metab 2011, 32(1):164-176. 3323298, 21878944.
32. Oliver PL, Finelli MJ, Edwards B, Bitoun E, Butts DL, Becker EB, Cheeseman MT, Davies B, Davies KE. Oxr1 Is Essential for Protection against Oxidative Stress-Induced Neurodegeneration. PLoS Genet 2011, 7(10):e1002338. 10.1371/journal.pgen.1002338, 3197693, 22028674.
33. Elliott NA, Volkert MR. Stress induction and mitochondrial localization of Oxr1 proteins in yeast and humans. Mol Cell Biol 2004, 24(8):3180-3187. 10.1128/MCB.24.8.3180-3187.2004, 381681, 15060142.
34. Durand M, Kolpak A, Farrell T, Elliott NA, Shao W, Brown M, Volkert MR. The OXR domain defines a conserved family of eukaryotic oxidation resistance proteins. BMC Cell Biol 2007, 8:13. 10.1186/1471-2121-8-13, 1847813, 17391516.
35. Volkert MR, Wang JY, Elliott NA. A functional genomics approach to identify and characterize oxidation resistance genes. Methods Mol Biol 2008, 477:331-342. 10.1007/978-1-60327-517-0_25, 19082958.
36. Cupples CG, Miller JH. A set of lacZ mutations in Escherichia coli that allow rapid detection of each of the six base substitutions. Proc Natl Acad Sci U S A 1989, 86(14):5345-5349. 10.1073/pnas.86.14.5345, 297618, 2501784.
37. Doerks T, Copley RR, Schultz J, Ponting CP, Bork P. Systematic identification of novel protein domain families associated with nuclear functions. Genome Res 2002, 12(1):47-56. 10.1101/gr.203201, 155265, 11779830.
38. Garnier J, Osguthorpe DJ, Robson B. Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J Mol Biol 1978, 120(1):97-120. 10.1016/0022-2836(78)90297-8, 642007.
39. Shao W, Halachmi S, Brown M. ERAP140, a conserved tissue-specific nuclear receptor coactivator. Mol Cell Biol 2002, 22(10):3358-3372. 10.1128/MCB.22.10.3358-3372.2002, 133794, 11971969.
40. Chen D, Lucey MJ, Phoenix F, Lopez-Garcia J, Hart SM, Losson R, Buluwela L, Coombes RC, Chambon P, Schar P, et al. T:G mismatch-specific thymine-DNA glycosylase potentiates transcription of estrogen-regulated genes through direct interaction with estrogen receptor alpha. J Biol Chem 2003, 278(40):38586-38592. 10.1074/jbc.M304286200, 12874288.
41. Likhite VS, Cass EI, Anderson SD, Yates JR, Nardulli AM. Interaction of estrogen receptor alpha with 3-methyladenine DNA glycosylase modulates transcription and DNA repair. J Biol Chem 2004, 279(16):16875-16882. 10.1074/jbc.M313155200, 14761960.
42. Teo AK, Oh HK, Ali RB, Li BF. The modified human DNA repair enzyme O(6)-methylguanine-DNA methyltransferase is a negative regulator of estrogen receptor-mediated transcription upon alkylation DNA damage. Mol Cell Biol 2001, 21(20):7105-7114. 10.1128/MCB.21.20.7105-7114.2001, 99886, 11564893.
43. Fischer H, Zhang XU, O'Brien KP, Kylsten P, Engvall E. C7, a novel nucleolar protein, is the mouse homologue of the Drosophila late puff product L82 and an isoform of human OXR1. Biochem Biophys Res Commun 2001, 281(3):795-803. 10.1006/bbrc.2001.4345, 11237729.
44. Poteete AR, Fenton AC, Wang HR. Recombination-promoting activity of the bacteriophage lambda Rap protein in Escherichia coli K-12. J Bacteriol 2002, 184(16):4626-4629. 10.1128/JB.184.16.4626-4629.2002, 135263, 12142434.
45. Thomason LC, Costantino N, Shaw DV, Court DL. Multicopy plasmid modification with phage lambda Red recombineering. Plasmid 2007, 58(2):148-158. 10.1016/j.plasmid.2007.03.001, 2706537, 17434584.
46. Murphy KC. Targeted chromosomal gene knockout using PCR fragments. Methods Mol Biol 2011, 765:27-42. 10.1007/978-1-61779-197-0_2, 21815084.
47. Wang JY, Sarker AH, Cooper PK, Volkert MR. The single-strand DNA binding activity of human PC4 prevents mutagenesis and killing by oxidative DNA damage. Mol Cell Biol 2004, 24(13):6084-6093. 10.1128/MCB.24.13.6084-6093.2004, 480877, 15199162.
48. Poteete AR. Expansion of a chromosomal repeat in Escherichia coli: roles of replication, repair, and recombination functions. BMC Mol Biol 2009, 10:14. 10.1186/1471-2199-10-14, 2656507, 19236706.
49. Schagger H, von Jagow G. Tricine-sodium dodecyl sulfate-polyacrylamide gel electrophoresis for the separation of proteins in the range from 1 to 100 kDa. Anal Biochem 1987, 166(2):368-379. 10.1016/0003-2697(87)90587-2, 2449095.
50. Sambrook J, Frisch EF, Maniatis T. Molecular Cloning, a laboratory manual. Cold Spring Harbor 1989, Cold Spring Harbor Laboratory Press, NY.