Characterization of DNA polymerase β from Danio rerio by overexpression in E. coli using the in vivo/in vitro compatible pIVEX plasmid

Microbial Cell Factories

Volumn 10, Issue , 2011, Pages

  Ishido, Tomomi ^a   Yamazaki, Naoshi ^b   Ishikawa, Mitsuru ^a   Hirano, Ken ^a  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^b UNIVERSITY OF TOKUSHIMA   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; COMPLEMENTARY DNA; DNA DIRECTED DNA POLYMERASE BETA; METAL ION; FISH PROTEIN; HYBRID PROTEIN;

ALKALINITY; AMINO ACID SUBSTITUTION; ARTICLE; BIOCHEMICAL COMPOSITION; CARBOXY TERMINAL SEQUENCE; CATALYSIS; DNA BINDING; ESCHERICHIA COLI; GENE EXPRESSION SYSTEM; GENE OVEREXPRESSION; IN VITRO STUDY; IN VIVO STUDY; LOW TEMPERATURE; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN DEGRADATION; ZEBRA FISH; AMINO ACID SEQUENCE; ANIMAL; CHEMISTRY; ENZYME STABILITY; GENE EXPRESSION; GENETICS; KINETICS; METABOLISM; MOLECULAR GENETICS; PLASMID; PROTEIN TERTIARY STRUCTURE; RAT; SEQUENCE HOMOLOGY;

BACTERIA (MICROORGANISMS); DANIO; DANIO RERIO; EUKARYOTA; MAMMALIA; RATTUS;

AMINO ACID SEQUENCE; ANIMALS; DNA POLYMERASE BETA; ENZYME STABILITY; ESCHERICHIA COLI; FISH PROTEINS; GENE EXPRESSION; KINETICS; MOLECULAR SEQUENCE DATA; PLASMIDS; PROTEIN STRUCTURE, TERTIARY; RATS; RECOMBINANT FUSION PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; ZEBRAFISH;

EID: 80054735869     PISSN: None     EISSN: 14752859     Source Type: Journal    
DOI: 10.1186/1475-2859-10-84     Document Type: Article

References (32)

1. Wang TSF. Eukaryotic DNA polymerases. Annu Rev Biochem 1991, 60:513-552. 10.1146/annurev.bi.60.070191.002501, 1883203.
2. Budd ME, Campbell JL. The roles of the eukaryotic DNA polymerases in DNA repair synthesis. Mutat Res 1997, 384:157-167.
3. Cleaver JE, Karpus K, Kashani-Sabet M, Limoli CL. Nucleotide excision repair 'a legacy of creativity'. Mutat Res 2001, 485:23-26.
4. Hubscher U, Nasheuer HP, Syvaoja JE. Eukaryotic DNA polymerases, a growing family. Trends Biochem Sci 2000, 25:143-147. 10.1016/S0968-0004(99)01523-6, 10694886.
5. Burgers PM, Koonin EV, Bruford E, Blanco L, Burtis LC, Christman MF, Copeland WC, Friedberg EC, Hanaoka F, Hinkle DC, Lawrence CW, Nakanishi M, Ohmori H, Prakash L, Prakash S, Reynaud C-A, Sugino A, Todo T, Wang Z, Weill J-C, Woodgate R. Eukaryotic DNA polymerases: proposal for a revised nomenclature. J Biol Chem 2001, 276:43487-43490. 10.1074/jbc.R100056200, 11579108.
6. Fry M, Loeb LA. Animal Cell DNA Polymerases 1986, Boca Raton, FL: CRC Press.
7. Zollner H. Handbook of enzyme inhibitors, 3 rd rev 1999, Wiley VCH.
8. Kornberg A, Baker TA. DNA replication 1992, Sausalito, CA: University Science Books, 2.
9. Matsumoto Y, Kim K. Excision of deoxyribose phosphate residues by DNA polymerase beta during DNA repair. Science 1995, 269:699-702. 10.1126/science.7624801, 7624801.
10. Sawaya MR, Pelletier H, Kumar A, Wilson SH, Kraut JA. Crystal structure of the rat DNA polymerase beta: evidence a common polymerase mechanism. Science 1994, 264:1930-1935. 10.1126/science.7516581, 7516581.
11. Yamaguchi T, Nishimura S, Takahashi K, Yoshikuni M, Masaki J, Hirai T, Saneyoshi M. DNA polymerase βs from liver and testes of Cherry Salmon, Oncorhynchus masou: Purification and characterization of DNA polymerase βs with acidic isoelectric points. J Biochem 1996, 119:186-192.
12. Oehlers LP, Heater SJ, Rains JD, Wells MC, David WM, Walter RB. Gene structure, purification and characterization of DNA polymerase β from Xiphophorus maculatus. Comp Biochem Phys C 2004, 138:311-324.
13. Fishman MC. Genomics. Zebrafish--the canonical vertebrate. Science 2001, 294:1290-1291. 10.1126/science.1066652, 11701913.
14. Dooley K, Zon LI. Zebrafish: a model system for the study of human disease. Curr Opin Genet Dev 2000, 10:252-256. 10.1016/S0959-437X(00)00074-5, 10826982.
15. Berghmans S, Murphey RD, Wienholds E, Neuberg D, Kutok JL, Fletcher CDM, Morris JP, Liu TX, Schulte-Merker S, Kanki JP, Plasterk R, Zon LI, Look AT. tp53 mutant zebrafish develop malignant peripheral nerve sheath tumors. Proc Natl Acad Sci USA 2005, 102:407-412. 10.1073/pnas.0406252102, 544293, 15630097.
16. Xu X, Zhang L, Weng S, Huang Z, Lu J, Lan D, Zhong X, Yu X, Xu A, He J. A zebrafish (Danio rerio) model of infectious spleen and kidney necrosis virus (ISKNV) infection. Virology 2008, 376:1-12. 10.1016/j.virol.2007.12.026, 18423508.
17. Augustine-Rauch K, Zhang CX, Panzica-Kelly JM. In vitro developmental toxicology assays: a review of the state of the science of rodent and zebrafish whole embryo culture and embryonic stem cell assays. Birth Defects Res C Embryo Today 2010, 90:87-98. 10.1002/bdrc.20175, 20544698.
18. Zon LI, Peterson RT. In vivo drug discovery in the zebrafish. Nat Rev Drug Discov 2005, 4:35-44. 10.1038/nrd1606, 15688071.
19. Roge J, Betton J-M. Use of pIVEX plasmids for protein overproduction in Escherichia coli. Microb Cell Fact 2005, 4:18. 10.1186/1475-2859-4-18, 1180468, 15932643.
20. Ghosh S, Thakur MK. Overproduction of mouse estrogen receptor alpha-ligand binding domain decreases bacterial growth. Mol Biol Rep 2008, 35:589-594. 10.1007/s11033-007-9128-9, 17786586.
21. Arndt JW, Gong W, Zhong X, Showalter AK, Liu J, Dunlap CA, Lin Z, Paxson C, Tsai M-D, Chan MK. Insight into the catalytic Mechanism of DNA polymerase β: Structures of intermediate complexes. Biochemistry 2001, 40:5368-5375. 10.1021/bi002176j, 11330999.
22. Hartnett JH, Gracyalny MSJ, Slater MR. The single step (KRX) competent cells: Efficient cloning and high protein yields. Promega Notes 2006, 94:27-30.
23. Maga G, Shevelev I, Villani G, Spadari S, Hübscher. Human replication protein A can suppress the intrinsic in vitro mutator phenotype of human DNA polymerase λ. Nucleic Acids Res 2006, 34:1405-1415. 10.1093/nar/gkl032, 1390690, 16522650.
24. Eigen M. Fast elementary steps in chemical reaction mechanisms. Pure Appl Chem 1963, 6:97-115.
25. Margerum DW, Cayley GR, Weatherburn DC, Pagenkopf GK. Coordination Chemistry 1978, 1-200. Washington, DC: American Chemical Society, Martell AE, Vol. 2..
26. Hays H, Berdis AJ. Manganese Substantially Alters the Dynamics of Translesion DNA Synthesis. Biochemistry 2002, 41:4771-4778. 10.1021/bi0120648, 11939771.
27. Pelletier H, Sawaya MR. Characterization of the Metal Ion Binding Helix-Hairpin-Helix Motifs in Human DNA Polymerase β by X-ray Structural Analysis. Biochemistry 1996, 35:12778-12787. 10.1021/bi960790i, 8841120.
28. Date T, Yamaguchi M, Hirose F, Nishimoto Y, Tanihara K, Matsukage A. Expression of active rat DNA polymerase β in Escherichia coli. Biochemistry 1988, 27:2983-2990. 10.1021/bi00408a048, 3042024.
29. Hirano K, Ishido T, Ishikawa M. Rapid sequencing gel electrophoresis using glycerol-tolerant sodium taurine medium. Anal Biochem 2009, 390:100-101. 10.1016/j.ab.2009.04.006, 19364487.
30. Hirano K, Yoshida Y, Ishido T, Wada Y, Moriya N, Yamazaki N, Mizushina Y, Baba Y, Ishikawa M. Consecutive incorporation of fluorophore-labeled nucleotides by mammalian DNA polymerase β. Anal Biochem 2010, 405:160-167. 10.1016/j.ab.2010.06.005, 20570644.
31. Boosalis MS, Petruska J, Goodman MF. DNA polymerase insertion fidelity: gel assay for site-specific kinetics. J Biol Chem 1987, 262:14689-14696.
32. Creighton S, Bloom LB, Goodman MF. Gel fidelity assay measuring nucleotide misinsertion, exonucleolytic proofreading, and lesion bypass efficiencies. Methods in Enzymology: DNA replication 1995, 262:232-256. San Diego: Academic Press, Campbell JL.