The N-terminal region is important for the nuclease activity and thermostability of the flap endonuclease-1 from Sulfolobus tokodaii

Bioscience, Biotechnology and Biochemistry

Volumn 71, Issue 4, 2007, Pages 855-865

  Horie, Masanori ^a,d   Fukui, Kôichi ^a   Xie, Minjue ^a   Kageyama, Yoshitaka ^a   Hamada, Kazuo ^a   Sakihama, Yuri ^a   Sugimori, Kenji ^b   Matsumoto, Kazuko ^a,c  

^a JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^b TOHO UNIVERSITY SCHOOL OF MEDICINE   (Japan)

^c WASEDA UNIVERSITY   (Japan)

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

Author keywords

Flap endonuclease; Sulfolobus tokodaii; Thermoplasma acidophilum

Indexed keywords

BACTERIA; DATABASE SYSTEMS; GENES; NUCLEOTIDES; THERMODYNAMIC STABILITY;

FLAP ENDONUCLEASE; N-TERMINAL REGIONS; SULFOLOBUS TOKODAII; THERMOPLASMA ACIDOPHILUM;

ENZYME ACTIVITY;

BACTERIAL DNA; FLAP ENDONUCLEASE; MAGNESIUM CHLORIDE; PRIMER DNA; RECOMBINANT PROTEIN;

ARTICLE; BACTERIAL GENE; CHEMISTRY; CODON; ENZYMOLOGY; ESCHERICHIA COLI; GENETIC DATABASE; GENETICS; HEAT; METABOLISM; MOLECULAR CLONING; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PH; POLYACRYLAMIDE GEL ELECTROPHORESIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SULFOLOBUS; THERMOPLASMA; WESTERN BLOTTING;

BASE SEQUENCE; BLOTTING, WESTERN; CLONING, MOLECULAR; CODON; DATABASES, GENETIC; DNA PRIMERS; DNA, BACTERIAL; ELECTROPHORESIS, POLYACRYLAMIDE GEL; ESCHERICHIA COLI; FLAP ENDONUCLEASES; GENES, BACTERIAL; HEAT; HYDROGEN-ION CONCENTRATION; MAGNESIUM CHLORIDE; MOLECULAR SEQUENCE DATA; RECOMBINANT PROTEINS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SULFOLOBUS; THERMOPLASMA;

CRENARCHAEOTA; SULFOLOBUS; SULFOLOBUS TOKODAII; SULFOLOBUS TOKODAII STR. 7; THERMOPLASMA ACIDOPHILUM;

EID: 34247484991     PISSN: 09168451     EISSN: 13476947     Source Type: Journal    
DOI: 10.1271/bbb.60326     Document Type: Article

References (29)

1. Liu, Y., Kao, H. I., and Bambara, R. A., Flap endonuclease 1: a central component of DNA metabolism. Annu. Rev. Biochem., 73, 589-615 (2004).
2. Yoon, J. H., Swiderski, P. M., Kaplan, B. E., Takao, M., Yasui, A., Shen, B., and Pfeifer, G. P., Processing of UV damage in vitro by FEN-1 proteins as part of an alternative DNA excision repair pathway. Biochemistry, 38, 4809-4817 (1999).
3. Dionne, I., Robinson, N. P., McGeoch, A. T., Marsh, V. L., Reddish, A., and Bell, S. D., DNA replication in the hyperthermophilic archaeon Sulfolobus solfataricus. Biochem. Soc. Trans., 31, 674-676 (2003).
4. Cann, I. K., and Ishino, Y., Archaeal DNA replication: identifying the pieces to solve a puzzle. Genetics, 152, 1249-1267 (1999).
5. Lyamichev, V., Brow, M. A., and Dahlberg, J. E., Structure-specific endonucleolytic cleavage of nucleic acids by eubacterial DNA polymerases. Science, 260, 778-783 (1993).
6. Shen, B., Qiu, J., Hosfield, D., and Tainer, J. A., Flap endonuclease homologs in archaebacteria exist as independent proteins. Trends Biochem. Sci., 23, 171-173 (1998).
7. Matsui, E., Kawasaki, S., Ishida, H., Ishikawa, K., Kosugi, Y., Kikuchi, H., Kawarabayashi, Y., and Matsui, I., Thermostable flap endonuclease from the archaeon, Pyrococcus horikoshii, cleaves the replication fork-like structure endo/exonucleolytically. J. Biol. Chem., 274, 18297-18309 (1999).
8. Hosfield, D. J., Frank, G., Weng, Y., Tainer, J. A., and Shen, B., Newly discovered archaebacterial flap endonucleases show a structure-specific mechanism for DNA substrate binding and catalysis resembling human flap endonuclease-1. J. Biol. Chem., 273, 27154-27161 (1998).
9. Olivier, M., The Invader assay for SNP genotyping. Mutat. Res., 573, 103-110 (2005).
10. Lyamichev, V., Mast, A. L., Hall, J. G., Prudent, J. R., Kaiser, M. W., Takova, T., Kwiatkowski, R. W., Sander, T. J., de Arruda, M., Arco, D. A., Neri, B. P., and Brow, M. A., Polymorphism identification and quantitative detection of genomic DNA by invasive cleavage of oligonucleotide probes. Nat. Biotechnol., 17, 292-296 (1999).
11. Dionne, I., Nookala, R. K., Jackson, S. P., Doherty, A. J., and Bell, S. D., A heterotrimeric PCNA in the hyperthermophilic archaeon Sulfolobus solfataricus. Mol. Cell, 11, 275-282 (2003b).
12. Collins, B. K., Tomanicek, S. J., Lyamicheva, N., Kaiser, M. W., and Mueser, T. C., A preliminary solubility screen used to improve crystallization trials: crystallization and preliminary X-ray structure determination of Aeropyrum pernix flap endonuclease-1. Acta Crystallogr. D Biol. Crystallogr., 60, 1674-1678 (2004).
13. Wakagi, T., and Oshima, T., Membrane-bound ATPase of a thermoacidophilic archaebacterium, Sulfolobus acidocaldarius. Biochim. Biophys. Acta, 817, 33-41 (1985).
14. Kawarabayasi, Y., Hino, Y., Horikawa, H., Jin-no, K., Takahashi, M., Sekine, M., Baba, S., Ankai, A., Kosugi, H., Hosoyama, A., Fukui, S., Nagai, Y., Nishijima, K., Otsuka, R., Nakazawa, H., Takamiya, M., Kato, Y., Yoshizawa, T., Tanaka, T., Kudoh, Y., Yamazaki, J., Kushida, N., Oguchi, A., Aoki, K., Masuda, S., Yanagii, M., Nishimura, M., Yamagishi, A., Oshima, T., and Kikuchi, H., Complete genome sequence of an aerobic thermoacidophilic crenarchaeon, Sulfolobus tokodaii strain 7. DNA Res., 8, 123-140 (2001).
15. DiRuggiero, J., Brown, J. R., Bogert, A. P., and Robb, F. T., DNA repair systems in archaea: mementos from the last universal common ancestor? J. Mol. Evol., 49, 474-484 (1999).
16. Klenk, H. P., Clayton, R. A., Tomb, J. F., White, O., Nelson, K. E., Ketchum, K. A., Dodson, R. J., Gwinn, M., Hickey, E. K., Peterson, J. D., Richardson, D. L., Kerlavage, A. R., Graham, D. E., Kyrpides, N. C., Fleischmann, R. D., Quackenbush, J., Lee, N. H., Sutton, G. G., Gill, S., Kirkness, E. F., Dougherty, B. A., McKenney, K., Adams, M. D., Loftus, B., Peterson, S., Reich, C. I., McNeil, L. K., Badger, J. H., Glodek, A., Zhou, L., Overbeek, R., Gocayne, J. D., Weidman, J. F., McDonald, L., Utterback, T., Cotton, M. D., Spriggs, T., Artiach, P., Kaine, B. P., Sykes, S. M., Sadow, P. W., D'Andrea, K. P., Bowman, C., Fujii, C., Garland, S. A., Mason, T. M., Olsen, G. J., Fraser, C. M., Smith, H. O., Woese, C. R., and Venter, J. C., The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature, 390, 364-370 (1997).
17. Kaiser, M. W., Lyamicheva, N., Ma, W., Miller, C., Neri, B., Fors, L., and Lyamichev, V., A comparison of eubacterial and archaeal structure-specific 5′-exonucleases. J. Biol. Chem., 274, 21387-21394 (1999).
18. Ruepp, A., Graml, W., Santos-Martinez, M. L., Koretke, K. K., Volker, C., Mewes, H. W., Frishman, D., Stocker, S., Lupas, A. N., and Baumeister, W., The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum. Nature, 407, 508-513 (2000).
19. Laemmli, U. K., Cleavage of structual proteins during the assembly of the the head of bacteriophage T4. Nature, 227, 680-685 (1970).
20. Patnaik, M., Dlott, J. S., Fontaine, R. N., Subbiah, M. T., Hessner, M. J., Joyner, K. A., Ledford, M. R., Lau, E. C., Moehlenkamp, C., Amos, J., Zhang, B., and Williams, T. M., Detection of genomic polymorphisms associated with venous thrombosis using the invader biplex assay. J. Mol. Diagn., 6, 137-144 (2004).
21. Zhu, H., Qu, F., and Zhu, L. H., Isolation of genomic DNAs from plants, fungi and bacteria using benzyl chloride. Nucleic Acids Res., 21, 5279-5280 (1993).
22. Feng, M., Patel, D., Dervan, J. J., Ceska, T., Suck, D., Haq, I., and Sayers, J. R., Roles of divalent metal ions in flap endonuclease-substrate interactions. Nat. Struct. Mol. Biol., 11, 450-456 (2004).
23. Harrington, J. J., and Lieber, M. R., The characterization of a mammalian DNA structure-specific endonuclease. EMBO J., 13, 1235-1246 (1994).
24. Torarinsson, E., Klenk, H. P., and Garrett, R. A., Divergent transcriptional and translational signals in Archaea. Environ. Microbiol., 7, 47-54 (2005).
25. Peabody, D. S., Translation initiation at non-AUG triplets in mammalian cells. J. Biol. Chem., 264, 5031-5035 (1989).
26. Kopke, A. K., and Leggatt, P. A., Initiation of translation at an AUA codon for an archaebacterial protein gene expressed in E. coli. Nucleic Acids Res., 19, 5169-5172 (1991).
27. Hannenhalli, S. S., Hayes, W. S., Hatzigeorgiou, A. G., and Fickett, J. W., Bacterial start site prediction. Nucleic Acids Res., 27, 3577-3582 (1999).
28. MacNeill, S. A., DNA replication: partners in the Okazaki two-step. Curr. Biol., 11, R842-844 (2001).
29. Roberts, J. A., Bell, S. D., and White, M. F., An archaeal XPF repair endonuclease dependent on a heterotrimeric PCNA. Mol. Microbiol., 48, 361-371 (2003).