Circularized chromosome with a large palindromic structure in Streptomyces griseus mutants

Journal of Bacteriology

Volumn 186, Issue 11, 2004, Pages 3313-3320

  Uchida, Tetsuya ^a   Ishihara, Naoto ^a   Zenitani, Hiroyuki ^a   Hiratsu, Keiichiro ^a   Kinashi, Haruyasu ^a  

^a HIROSHIMA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

DNA FRAGMENT; PALINDROMIC DNA;

AMINO ACID SEQUENCE; ARTICLE; CHROMOSOME; CHROMOSOME DELETION; CHROMOSOME STRUCTURE; DELETION MUTANT; DNA SEQUENCE; NONHUMAN; OPEN READING FRAME; PRIORITY JOURNAL; SOUTHERN BLOTTING; STREPTOMYCES; STREPTOMYCES GRISEUS;

AMINO ACID SEQUENCE; BASE SEQUENCE; CHROMOSOME DELETION; CHROMOSOMES, BACTERIAL; GENE AMPLIFICATION; MOLECULAR SEQUENCE DATA; MUTATION; STREPTOMYCES GRISEUS; TERMINAL REPEAT SEQUENCES;

NEGIBACTERIA; STREPTOMYCES; STREPTOMYCES GRISEUS;

EID: 2442690441     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.186.11.3313-3320.2004     Document Type: Article

References (40)

1. Bao, K., and S. N. Cohen. 2001. Terminal proteins essential for the replication of linear plasmids and chromosomes in Streptomyces. Genes Dev. 15:1518-1527.
2. Bao, K., and S. N. Cohen. 2003. Recruitment of terminal protein to the ends of Streptomyces linear plasmids and chromosomes by a novel telomere-binding protein essential for linear DNA replication. Genes Dev. 17:774-785.
3. Bentley, S. D., K. F. Chater, A. M. Cerdeno-Tarraga, G. L. Challis, N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C. H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M. A. Ralandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill, and D. A. Hopwood. 2002. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417:141-147.
4. Birch, A., A. Hausler, C. Rottener, and R. Hutter. 1991. Chromosomal deletion and rearrangement in Streptomyces glaucescens. J. Bacteriol. 173:3531-3538.
5. Chen, C. W., C. H. Huang, H. H. Lee, H. H. Tsai, and R. Kirby. 2002. Once the circle has been broken: dynamics and evolution of Streptomyces chromosomes. Trends Genet. 18:522-529.
6. Cox, M. M. 2001. Recombinational DNA repair of damaged replication forks in Escherichia coli: questions. Annu. Rev. Genet. 35:53-82.
7. Fischer, G., B. Decaris, and P. Leblond. 1997. Occurrence of deletions, associated with genetic instability in Streptomyces ambofaciens, is independent of the linearity of the chromosomal DNA. J. Bacteriol. 179:4553-4558.
8. Fischer, G., T. Wenner, B. Decaris, and P. Leblond. 1998. Chromosomal arm replacement generates a high level of intraspecific polymorphism in the terminal inverted repeats of the linear chromosomal DNA of Streptomyces ambofaciens. Proc. Natl. Acad. Sci. USA 95:14296-14301.
9. Goshi. K., T. Uchida, A. Lezhava, M. Yamasaki, K. Hiratsu, H. Shinkawa, and H. Kinashi. 2002. Cloning and analysis of the telomere and terminal inverted repeat of the linear chromosome of Streptomyces griseus. J. Bacteriol. 184:3411-3415.
10. Hayakawa, T., T. Tanaka, K. Sakaguchi, N. Otake, and H. Yonehara. 1979. A linear plasmid-like DNA in Streptomyces sp. producing lankacidin group antibiotics. J. Gen. Appl. Microbiol. 25:255-260.
11. Hirochika, H., K. Nakamura, and K. Sakaguchi. 1984. A linear DNA plasmid from Streptomyces rochei with an inverted terminal repetition of 614 base pairs. EMBO J. 3:761-766.
12. Huang, C. H., Y. S. Lin, Y. L. Yang, S. W. Huang, and C. W. Chen. 1998. The telomeres of Streptomyces chromosomes contain conserved palindromic sequences with potential to form complex secondary structures. Mol. Microbiol. 28:905-916.
13. Huang, C. H., C. Y. Chen, H. H. Tsai, C. Chen, Y. S. Lin, and C. W. Chen. 2003. Linear plasmid SLP2 of Streptomyces lividans is a composite replicon. Mol. Microbiol. 47:1563-1576.
14. Ikeda, H., J. Ishikawa, A. Hanamoto, M. Shinose, H. Kikuchi, T. Shiba, Y. Sakaki, M. Hattori, and S. Omura. 2003. Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis. Nat. Biotechnol. 21:526-531.
15. Inoue, S., K. Higashiyama, T. Uchida, K. Hiratsu, and H. Kinashi. 2003. Chromosomal circularization in Streptomyces griseus by nonhomologous recombination of deletion ends. Biosci. Biotechnol. Biochem. 67:1101-1108.
16. Ishikawa, J., and K. Hotta. 1999. FramePlot: a new implementation of the frame analysis for predicting protein-coding regions in bacterial DNA with a high G+C content. FEMS Microbiol. Lett. 174:251-253.
17. Kameoka, D., A. Lezhava, H. Zenitani, K. Hiratsu, M. Kawamoto, K. Goshi, K. Inada, H. Shinkawa, and H. Kinashi. 1999. Analysis of fusion junctions of circularized chromosomes in Streptomyces griseus. J. Bacteriol. 181:5711-5717.
18. Kieser, T., and R. E. Melton. 1988. Plasmid pIJ699, a multi-copy positive-selection vector for Streptomyces. Gene 65:83-91.
19. Kinashi, H. 1994. Linear plasmids from actinomycetes. Actinomycetologica 8:87-96.
20. Kinashi, H. 1994. Pulsed field gel electrophoresis: isolation and analysis of large linear plasmids, p. 227-240. In J. W. Dale and P. G. Sanders (ed.), Methods in gene technology, vol. 2. JAJ Press, London, United Kingdom.
21. Kinashi, H., M. Shimaji, and A. Sakai. 1987. Giant linear plasmids in Streptomyces which code for antibiotic biosynthesis genes. Nature 328:454-456.
22. Kinashi, H., E. Mori, A. Hatani, and O. Nimi. 1994. Isolation and characterization of large linear plasmids from lankacidin-producing Streptomyces species. J. Antibiot. 47:1447-1455.
23. Leblond, P., and B. Decaris. 1994. New insights into the genetic instability of Streptomyces. FEMS Microbiol. Lett. 123:225-232.
24. Lezhava, A., T. Mizukami, T. Kajitani, D. Kameoka, M. Redenbach, H. Shinkawa, O. Nimi, and H. Kinashi. 1995. Physical map of the linear chromosome of Streptomyces griseus. J. Bacteriol. 177:6492-6498.
25. Lezhava, A., D. Kameoka, H. Sugino, K. Goshi, H. Shinkawa, O. Nimi, S. Horinouchi, T. Beppu, and H. Kinashi. 1997. Chromosomal deletions in Streptomyces griseus that remove the afsA locus. Mol. Gen. Genet. 253:478-483.
26. Lin, Y. S., H. M. Kieser, D. A. Hopwood, and C. W. Chen. 1993. The chromosomal DNA of Streptomyces lividans 66 is linear. Mol. Microbiol. 10:923-933.
27. Pandza, S., G. Biukovic, A. Paravic, A. J. Dadbin, J. Cullum, and D. Hranueli. 1998. Recombination between the linear plasmid pPZG101 and the linear chromosome of Streptomyces rimosus can lead to exchange of ends. Mol. Microbiol. 28:1165-1176.
28. Pang, X., X. Zhou, Y. Sun, and Z. Deng. 2002. Physical map of the linear chromosome of Streptomyces hygroscopicus 10-22 deduced by analysis of overlapping large chromosomal deletions. J. Bacteriol. 184:1958-1965.
29. Qin, Z., and S. N. Cohen. 1998. Replication at the telomeres of the Streptomyces linear plasmid pSLA2. Mol. Microbiol. 28:893-903.
30. Qin, Z., and S. N. Cohen. 2000. Long palindromes formed in Streptomyces by nonhomologous intra-strand annealing. Genes Dev. 14:1789-1796.
31. Qin, Z., and S. N. Cohen. 2002. Survival mechanism for Streptomyces linear replicons after telomere damage. Mol. Microbiol. 45:785-794.
32. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
33. Smith, G. R. 2001. Homologous recombination near and far from DNA breaks: alternative roles and contrasting views. Annu. Rev. Genet. 35:243-274.
34. Suwa, M., H. Sugino, A. Sasaoka, E. Mori, S. Fujii, H. Shinkawa, O. Nimi, and H. Kinashi. 2000. Identification of two polyketide synthase gene clusters on the linear plasmid pSLA2-L in Streptomyces rochei. Gene 246:123-131.
35. Uchida, T., M. Miyawaki, and H. Kinashi. 2003. Chromosomal arm replacement in Streptomyces griseus. J. Bacteriol. 185:1120-1124.
36. Volff, J. N., and J. Altenbuchner. 1998. Genetic instability of the Streptomyces chromosome. Mol. Microbiol. 27:239-246.
37. Volff, J. N., and J. Altenbuchner. 2000. A new beginning with new ends: linearisation of circular chromosomes during bacterial evolution. FEMS Microbiol. Lett. 186:143-150.
38. Wenner, T., V. Roth, G. Fischer, C. Fourrier, B. Aigle, B. Decaris, and P. Leblond. 2003. End-to-end fusion of linear deleted chromosomes initiates a cycle of genome instability in Streptomyces ambofaciens. Mol. Microbiol. 50:411-425.
39. Yang, C. C., C. H. Huang, C. Y. Li, Y. G. Tsay, S. C. Lee, and C. W. Chen. 2002. The terminal proteins of linear Streptomyces chromosomes and plasmids: a novel class of replication priming proteins. Mol. Microbiol. 43:297-305.
40. Yang, M. C., and R. Losick. 2001. Cytological evidence for association of the ends of the linear chromosome in Streptomyces coelicolor. J. Bacteriol. 183:5180-5186.