Presence of a characteristic D-D-E motif in IS1 transposase

Journal of Bacteriology

Volumn 184, Issue 22, 2002, Pages 6146-6154

  Ohta, Shinya ^a   Tsuchida, Ken ^a   Choi, Sunju ^a   Sekine, Yasuhiko ^a   Shiga, Yasuyuki ^a   Ohtsubo, Eiichi ^a  

^a UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

INTEGRASE; IS1 PROTEIN; POLYPEPTIDE; TRANSPOSASE; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARCHAEBACTERIUM; ARTICLE; ENZYME ACTIVE SITE; GENE INSERTION; PRIORITY JOURNAL; PROTEIN FAMILY; PROTEIN MOTIF; SEQUENCE HOMOLOGY;

ARCHAEA; BACTERIA (MICROORGANISMS); INSERTION SEQUENCES;

EID: 0036843635     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.184.22.6146-6154.2002     Document Type: Article

References (54)

1. Abremski, K. E., and R. H. Hoess. 1992. Evidence for a second conserved arginine residue in the integrase family of recombination protein. Protein Eng. 5:87-91.
2. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
3. Argos, P., A. Landy, K. Abremski, J. B. Egan, E. Haggard-Ljungquist, R. H. Hoess, M. L. Kahn, B. Kariolis, S. V. L. Narayana, L. S. Pierson III, N. Sternberg, and J. M. Leong. 1986. The integrase family of site-specific recombinase: Regional similarities and global diversity. EMBO J. 5:433-440.
4. Baker, T. A., and L. Luo. 1994. Identification of residues in the Mu transposase essential for catalysis. Proc. Natl. Acad. Sci. USA 91:6654-6658.
5. Bolland, S., and N. Kleckner. 1996. The three chemical steps of Tn10/IS10 transposition involve repeated utilization of a single active site. Cell 84:223-233.
6. Davies, D. R., I. Y. Goryshin, W. S. Reznikoff, and I. Rayment. 2000. Three-dimensional Tn5 synaptic complex transposition intermediate. Science 289:77-85.
7. Doak, T. G., F. P. Doerder, C. L. Jahn, and G. Herrick. 1994. A proposed superfamily of transposase genes: Transposon-like elements in ciliated protozoa and a common "D35E" motif. Proc. Natl. Acad. Sci. USA 91:942-946.
8. Dower, W. J., J. M. Miller, and C. W. Ragsdale. 1988. High efficiency transformation of E. coli by high voltage electroporation. Nucleic Acids Res. 16:6127-6145.
9. Dyda, F., A. B. Hickman, T. M. Jenkins, A. Engelman, R. Craigie, and D. R. Davies. 1994. Crystal structure of the catalytic domain of HIV-1 integrase: Similarity to other polynucleotidyl transferases. Science 266:1981-1986.
10. Escoubas, J. M., M. F. Prate, O. Fayet, I. Salvignol, D. Galas, D. Zerbib, and M. Chandler. 1991. Translational control of transposition activity of the bacterial insertion sequence IS1. EMBO J. 10:705-712.
11. Fayet, O., P. Ramond, P. Polard, M. F. Prére, and M. Chandler. 1990. Functional similarities between retroviruses and the IS3 family of bacterial insertion sequences? Mol. Microbiol. 4:1771-1777.
12. Galagan, J. E., C. Nusbaum, A. Roy, M. G. Endrizzi, P. Macdonald, W. FitzHugh, S. Calvo, R. Engels, S. Smirnov, D. Atnoor, A. Brown, N. Allen, J. Naylor, N. Stange-Thomann, K. DeArellano, R. Johnson, L. Linton, P. McEwan, K. McKernan, J. Talamas, A. Tirrell, W. Ye, A. Zimmer, R. D. Barber, I. Cann, D. E. Graham, D. A. Grahame, A. M. Guss, R. Hedderich, C. Ingram-Smith, H. C. Kuettner, J. A. Krzycki, J. A. Leigh, W. Li, J. Liu, B. Mukhopadhyay, J. N. Reeve, K. Smith, T. A. Springer, L. A. Umayam, O. White, R. H. White, E. Conway de Macario, J. G. Ferry, K. F. Jarrell, H. Jing, A. J. Macario, I. Paulsen, M. Pritchett, K. R. Sowers, R. V. Swanson, S. H. Zinder, E. Lander, W. W. Metcalf, and B. Birren. 2002. The genome of M. acetivorans reveals extensive metabolic and physiological diversity. Genome Res. 12:532-542.
13. Galas, D. J., M. P. Calos, and J. H. Miller. 1980. Sequence analysis of Tn9 insertions in the lacZ gene. J. Mol. Biol. 143:19-41.
14. Grindley, N. D. F. 1978. IS1 insertion generates duplication of a nine base pair sequence at its target site. Cell 13:419-426.
15. Guo, M., S. Manulis, H. Mor, and I. Barash. 2002. The presence of diverse IS elements and an avrPphD homologue that acts as a virulence factor on the pathogenicity plasmid of Erwinia herbicola pv. gypsophilae. Mol. Plant-Microbe Interact. 15:709-716.
16. He, M., A. Wilde, and M. A. Kaderbhai. 1990. A simple single-step procedure for small-scale preparation of Escherichia coli plasmid. Nucleic Acids Res. 18:1660.
17. Iida, S., R. Hiestand-Nauer, and W. Arber. 1985. Transposable element IS1 intrinsically generates target duplications of variable length. Proc. Natl. Acad. Sci. USA 82:839-843.
18. Jakowec, M., P. Prentki, M. Chandler, and D. J. Galas. 1988. Mutational analysis of the open reading frames in the transposable element IS1. Genetics 120:47-55.
19. Johnsrud, L. 1979. DNA sequence of the transposable element IS1. Mol. Gen. Genet. 169:213-218.
20. Jones, D. T. 1999. Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292:195-202.
21. Kaneko, T., S. Sato, H. Kotani, A. Tanaka, E. Asamizu, Y. Nakamura, N. Miyajima, M. Hirosawa, M. Sugiura, S. Sasamoto, T. Kimura, T. Hosouchi, A. Matsuno, A. Muraki, N. Nakazaki, K. Naruo, S. Okumura, S. Shimpo, C. Takeuchi, T. Wada, A. Watanabe, M. Yamada, M. Yasuda, and S. Tabata. 1996. Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. DNA Res. 3:109-136.
22. Kawarabayasi, Y., Y. Hino, H. Horikawa, K. Jin-No, M. Takahashi, M. Sekine, S. Baba, A. Ankai, H. Kosugi, A. Hosoyama, S. Fukui, Y. Nagai, K. Nishijima, R. Otsuka, H. Nakazawa, M. Takamiya, Y. Kato, T. Yoshizawa, T. Tanaka, Y. Kudoh, J. Yamazaki, N. Kushida, A. Oguchi, K. Aoki, S. Masuda, M. Yanagi, M. Nishimura, A. Yamagishi, T. Oshima, and H. Kikuchi. 2001. Complete genome sequence of an aerobic thermoacidophilic crenarchaeon, Sulfolobus tokodaii strain 7. DNA Res. 8:123-140.
23. Kulkosky, J., K. S. Jones, R. A. Katz, J. P. G. Mack, and A. M. Skalka. 1992. Residues critical for retroviral integrative recombination in a region that is highly conserved among retroviral/retrotransposon integrases and bacterial insertion sequence transposases. Mol. Cell. Biol. 12:2331-2338.
24. Machida, C., and Y. Machida. 1989. Regulation of IS1 transposition by the insA gene product. J. Mol. Biol. 208:567-574.
25. Machida, Y., C. Machida, and E. Ohtsubo. 1984. Insertion element IS1 encodes two structural genes required for its transposition. J. Mol. Biol. 177:229-245.
26. Machida, Y., C. Machida, H. Ohtsubo, and E. Ohtsubo. 1982. Factors determining frequency of plasmid cointegration mediated by insertion sequence IS1. Proc. Natl. Acad. Sci. USA 79:277-281.
27. McGuffin, L. J., K. Bryson, and D. T. Jones. 2000. The PSIPRED protein structure prediction server. Bioinformatics 16:404-405.
28. Ohtsubo, E., and Y. Sekine. 1996. Bacterial insertion sequences. Curr. Top. Microbiol. Immunol. 204:1-26.
29. Ohtsubo, E., M. Zenilman, and H. Ohtsubo. 1980. Plasmids containing insertion elements are potential transposons. Proc. Natl. Acad. Sci. USA 77:750-754.
30. Ohtsubo, H., and E. Ohtsubo. 1978. Nucleotide sequence of an insertion element, IS1. Proc. Natl. Acad. Sci. USA 75:615-619.
31. Ohtsubo, H., K. Nyman, W. Doroszkiewicz, and E. Ohtsubo. 1981. Multiple copies of iso-insertion sequences of IS1 in Shigella dysenteriae chromosome. Nature 292:640-643.
32. Pearson, W. R., and D. J. Lipman. 1988. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA 85:2444-2448.
33. Raleigh, E. A., N. E. Murray, H. Revel, R. M. Blumenthal, D. Westaway, A. D., P. W. Rigby, J. Elhai, and D. Hanahan. 1988. McrA and McrB restriction phenotypes of some E. coli strains and implications for gene cloning. Nucleic Acids Res. 16:1563-1575.
34. Rezsbhazy, R., B. Hallet, J. Delcour, and J. Mahillon. 1993. The IS4 family of insertion sequences: Evidence for a conserved transposase motif. Mol. Microbiol. 9:1283-1295.
35. Rice, P., and K. Mizuuchi. 1995. Structure of the bacteriophage Mu transposase core: A common structure motif for DNA transposition and retroviral integration. Cell 82:209-220.
36. Sawyer, S. A., D. E. Dykhuizen, R. F. DuBose, L. Green, T. Mutangadura-Mhlanga, D. F. Wolczyk, and D. L. Hartl. 1987. Distribution and abundance of insertion sequences among natural isolates of Escherichia coli. Genetics 115:51-63.
37. Sekine, Y., and E. Ohtsubo. 1989. Frameshifting is required for expression of IS1 transposase. Proc. Natl. Acad. Sci. USA 86:4609-4613.
38. Sekine, Y., and E. Ohtsubo. 1991. Translational frameshifting in IS elements and other genetic systems, p. 243-261. In M. Kimura and N. Takahata (ed.), New Aspects of the Genetics of Molecular Evolution. Japan Science Society Press, Tokyo, Japan.
39. Sekine, Y., H. Nagasawa, and E. Ohtsubo. 1992. Identification of the site of translational frameshifting required for production of the transposase encoded by insertion sequence IS1. Mol. Gen. Genet. 235:317-324.
40. Sekine, Y., K. Izumi, T. Mizuno, and E. Ohtsubo. 1997. Inhibition of transpositional recombination by OrfA and OrfB proteins encoded by insertion sequence IS3. Genes Cells 2:547-557.
41. Sekine, Y., N. Eisaki, and E. Ohtsubo. 1994. Translational control in production of transposase and in transposition of insertion sequence IS3. J. Mol. Biol. 235:1406-1420.
42. Sekine, Y., N. Eisaki, K. Kobayashi, and E. Ohtsubo. 1997. Isolation and characterization of IS1 circles. Gene 191:183-190.
43. Sekino, N., Y. Sekine, and E. Ohtsubo. 1995. IS1-encoded proteins, InsA and the InsA-B′-InsB transframe protein (transposase): Functions deduced from their DNA-binding ability. Adv. Biophys. 31:209-222.
44. Serre, M. C., C. Turlan, M. L. Bortolin, and M. Chandler. 1995. Mutagenesis of the IS1 transposase: Importance of a His-Arg-Tyr triad for activity. J. Bacteriol. 177:5070-5077.
45. She, Q., R. K. Singh, F. Confalonieri, Y. Zivanovic, G. Allard, M. J. Awayez, C. C.-Y. Chan-Weiher, I. G. Clausen, B. A. Curtis, A. de Moors, G. Erauso, C. Fletcher, P. M. K. Gordon, I. H. Jong, A. C. Jeffries, C. J. Kozera, N. Medina, X. Peng, H. P. Thi-Ngoc, P. Redder, M. E. Schenk, C. Theriault, N. Tolstrup, R. L. Charlebois, W. F. Doolittle, M. Duguet, T. Gaasterland, R. A. Garrett, M. A. Ragan, C. W. Sensen, and J. Van der Oost. 2001. The complete genome of the crenarchaeon Sulfolobus solfataricus P2. Proc. Natl. Acad. Sci. USA 98:7835-7840.
46. Shiga, Y., Y. Sekine, Y. Kano, and E. Ohtsubo. 2001. Involvement of H-NS in transpositional recombination mediated by IS1. J. Bacteriol. 183:2476-2484.
47. Shiga, Y., Y. Sekine, and E. Ohtsubo. 1999. Transposition of IS1 circles. Genes Cells 4:551-561.
48. Umeda, M., and E. Ohtsubo. 1991. Four types of IS1 with differences in nucleotide sequence reside in the Escherichia coli K-12 chromosome. Gene 98:1-5.
49. Williams, T. L., E. L. Jackson, A. Carritte, T. A. Baker. 1999. Organization and dynamics of the Mu transpososome: Recombination by communication between two active sites. Genes Dev. 13:2725-2737.
50. Yanisch-Perron, C., J. Vieira, and J. Messing. 1985. Improved M13 phage cloning vectors and host strains: Nucleotide sequences of the M13mp18 and pUC10 vectors. Gene 33:103-109.
51. Yoshioka, Y., H. Ohtsubo, and E. Ohtsubo. 1987. Repressor gene finO in plasmids R100 and F: Constitutive transfer of plasmid F is caused by insertion of IS3 into F finO. J. Bacteriol. 169:619-623.
52. Zerbib, D., M. Jakowec, P. Prentki, D. J. Galas, and M. Chandler. 1987. Expression of proteins essential for IS1 transposition: Specific binding of InsA to the ends of IS1. EMBO J. 6:3163-3169.
53. Zerbib, D., P. Polard, J. M. Escoubas, D. Galas, and M. Chandler. 1990. The regulatory role of the IS1-encoded InsA protein in transposition. Mol. Microbiol. 4:471-477.
54. Zerbib, D., P. Prentki, P. Gamas, E. Freund, D. J. Galas, and M. Chandler. 1990. Functional organization of the ends of IS1: Specific binding site for an IS1-encoded protein. Mol. Microbiol. 4:1477-1486.