Chromosomal circularization in streptomyces griseus by nonhomologous recombination of deletion ends

Bioscience, Biotechnology and Biochemistry

Volumn 67, Issue 5, 2003, Pages 1101-1108

  Inoue, Shoichi ^a   Higashiyama, Koji ^a   Uchida, Tetsuya ^a   Hiratsu, Keiichiro ^a   Kinashi, Haruyasu ^a  

^a HIROSHIMA UNIVERSITY   (Japan)

Author keywords

Chromosomal circularization; Chromosomal deletion; Genome fluidity; Nonhomologous recombination; Streptomyces

Indexed keywords

FUNGAL DNA;

AMINO ACID SEQUENCE; ARTICLE; BIOSYNTHESIS; CHROMOSOME; CHROMOSOME DELETION; CULTURE MEDIUM; GENETIC RECOMBINATION; GENETICS; HYBRIDIZATION; MOLECULAR GENETICS; MUTATION; NUCLEOTIDE SEQUENCE; PLASMID; PULSED FIELD GEL ELECTROPHORESIS; SOUTHERN BLOTTING; STREPTOMYCES GRISEUS; ULTRAVIOLET SPECTROPHOTOMETRY;

AMINO ACID SEQUENCE; BASE SEQUENCE; BLOTTING, SOUTHERN; CHROMOSOME DELETION; CHROMOSOMES, FUNGAL; CULTURE MEDIA; DNA, FUNGAL; ELECTROPHORESIS, GEL, PULSED-FIELD; HYBRIDIZATION, GENETIC; MOLECULAR SEQUENCE DATA; MUTATION; PLASMIDS; RECOMBINATION, GENETIC; SPECTROPHOTOMETRY, ULTRAVIOLET; STREPTOMYCES GRISEUS;

STREPTOMYCES; STREPTOMYCES GRISEUS;

EID: 1542649868     PISSN: 09168451     EISSN: 13476947     Source Type: Journal    
DOI: 10.1271/bbb.67.1101     Document Type: Article

References (30)

1. Lin, Y.-S., Kieser, H. M., Hopwood, D. A., and Chen, C. W., The chromosomal DNA of Strep-tomyces lividans 66 is linear. Mol. Microbiol., 10, 923-933 (1993).
2. Lezhava, A., Mizukami, T., Kajitani, T., Kameoka, D., Redenbach, M., Shinkawa, H., Nimi, O., and Kinashi, H., Physical map of the linear chromosome of Streptomyces griseus. J. Bacteriol., 177, 6492-6498 (1995).
3. Redenbach, M., Kieser, H. M., Denapaite, D., Eichner, A., Cullum, J., Kinashi, H., and Hopwood, D. A., A set of ordered cosmids and a detailed genetic and physical map for the 8 Mb Streptomyces coe-licolor A3(2) chromosome. Mol. Microbiol., 21, 77-96 (1996).
4. Leblond, P., Fischer, G., Francou, F.-X., Berger, F., Guerineau, M., and Decaris, B., The unstable region of Streptomyces ambofaciens includes 210-kb terminal inverted repeats flanking the extremities of the linear chromosomal DNA. Mol. Microbiol., 19, 261-271 (1996).
5. Pandza, K., Pfalzer, G., Cullum, J., and Hranueli, D., Physical mapping shows that the unstable oxytetracycline gene cluster of Streptomyces rimosus lies close to one end of the linear chromosome. Microbiology, 143, 1493-1501 (1997).
6. Omura, S., Ikeda, H., Ishikawa, J., Hanamoto, A., Takahashi, C., Shinose, M., Takahashi, Y., Horikawa, H., Nakazawa, H., Osonoe, T., Kikuchi, H., Shiba, T., Sakaki, Y., and Hattori, M., Genome sequence of an industrial microorganism Streptomyces avermitilis: Deducing the ability of producing secondary metabolites. Proc. Natl. Acad. Sci. USA, 98, 12215-12220 (2001).
7. Pang, X., Zhou, X., Sun, Y., and Deng, Z., Physical map of the linear chromosome of Streptomyces hygroscopicus 10-22 deduced by analysis of overlapping large chromosomal deletions. J. Bacteriol., 184, 1958-1965 (2002).
8. Bentley, S. D., Chater, K. F., Cerdeno-Tarraga, A. M., Challis, G. L., Thomson, N. R., James, K. D., Harris, D. E., Quail, M. A., Kieser, H., Harper, D., Bateman, A., Brown, S., Chandra, G., Chen, C. W., Collins, M., Cronin, A., Fraser, A., Goble, A., Hidalgo, J., Hornsby, T., Howarth, S., Huang, C. H., Kieser, T., Larke, L., Murphy, L., Oliver, K., O’Neil, S., Rabbinowitsch, E., Rajandream, M. A., Rutherford, K., Rutter, S., Seeger, K., Saunders, D., Sharp, S., Squares, R., Squares, S., Taylor, K., Warren, T., Wietzorrek, A., Woodward, J., Barrell, B. G., Parkhill, J., and Hopwood, D. A., Complete genome sequence of the model actinomycete Strep-tomyces coelicolor A3(2). Nature, 417, 141-147 (2002).
9. Kinashi, H., Linear plasmids from actinomycetes. Actinomycetologica, 8, 87-96 (1994).
10. Leblond, P., and Decaris, B., New insight into the genetic instability of Streptomyces. FEMS Microbiol. Lett., 123, 225-232 (1994).
11. Volff, J.-N., and Altenbuchner, J., Genetic instability of the Streptomyces chromosome. Mol. Microbiol., 27, 239-246 (1998).
12. Fischer, G., Decaris, B., and Leblond, P., Occurrence of deletions, associated with genetic instability in Streptomyces ambofaciens, is independent of the linearity of the chromosomal DNA. J. Bacteriol., 179, 4553-4558 (1997).
13. Redenbach, M., Flett, F., Piendl, W., Glocker, I., Rauland, U., Wafzig, O., Kliem, R., Leblond, P., and Cullum, J., The Streptomyces lividans 66 chromosome contains a 1 MB deletogenic region flanked by two amplifiable regions. Mol. Gen. Genet., 241, 255-262 (1993).
14. Kameoka, D., Lezhava, A., Zenitani, H., Hiratsu, K., Kawamoto, M., Goshi, K., Inada, K., Shinkawa, H., and Kinashi, H., Analysis of fusion junctions of circularized chromosomes in Streptomyces griseus. J. Bacteriol., 181, 5711-5717 (1999).
15. Qin, Z., and Cohen, S. N., Survival mechanism for Streptomyces linear replicons after telomere damage. Mol. Microbiol., 45, 785-794 (2002).
16. Lezhava, A., Kameoka, D., Sugino, H., Goshi, K., Shinkawa, H., Nimi, O., Horinouchi, S., Beppu, T., and Kinashi, H., Chromosomal deletions in Strep-tomyces griseus that remove the afsA locus. Mol. Gen. Genet., 253, 478-483 (1997).
17. Suwa, M., Sugino, H., Sasaoka, A., Mori, E., Fujii, S., Shinkawa, H., Nimi, O., and Kinashi, H., Identification of two polyketide synthase gene clusters on the linear plasmid pSLA2-L in Streptomyces rochei. Gene, 246, 123-131 (2000).
18. Kinashi, H., Pulsed field gel electrophoresis: Isolation and analysis of large linear plasmids. In “Methods in Gene Technology” vol. 2, eds. Dale, J. W., and Sanders, P. G., JAI Press, London, pp. 227-240 (1994).
19. Chu, G., Vollrath, D., and Davis, R. W., Separation of large DNA molecules by contour-clamped homogeneous electric fields. Science, 234, 1582-1585 (1986).
20. Sambrook, J., Fritsch, E. F., and Maniatis, T., Molecular cloning, a laboratory manual, second ed., Cold Spring Harbor Laboratory Press (1989).
21. Ishikawa, J., and Hotta, K., 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 (1999).
22. Goshi, K., Uchida, T., Lezhava, A., Yamasaki, M., Hiratsu, K., Shinkawa, H., and Kinashi, H., Cloning and analysis of the telomere and terminal inverted repeat of the linear chromosome of Streptomyces griseus. J. Bacteriol., 184, 3411-3415 (2002).
23. Bibb, M. J., Findlay, P. R., and Johnson, M. W., The relationship between base composition and codon usage in bacterial genes and its use for the simple and reliable identification of protein-coding sequences. Gene, 30, 157-166 (1984).
24. Qin, Z., and Cohen, S. N., Replication at the telomeres of the Streptomyces linear plasmid pSLA2. Mol. Microbiol., 28, 893-903 (1998).
25. Huang, C.-H., Lin, Y.-S., Yang, Y.-L., Huang, S.-W., and Chen, C. W., The telomeres of Streptomyces chromosomes contain conserved palindromic sequences with potential to form complex secondary structures. Mol. Microbiol., 28, 905-916 (1998).
26. Fischer, G., Wenner, T., Decaris, B., and Leblond, P., 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 (1998).
27. Uchida, T., Miyawaki, M., and Kinashi, H., Chromosomal arm replacement in Streptomyces griseus. J. Bacteriol., 185, 1120-1124 (2003).
28. Pandza, S., Biukovic, G., Paravic, A., Dadbin, A., Cullum, J., and Hranueli, D., Recombination between the linear plasmid pPZG101 and the linear chromosome of Streptomyces rimosus can lead to exchange of ends. Mol. Microbiol., 28, 1165-1176 (1998).
29. Qin, Z., and Cohen, S. N., Long palindromes formed in Streptomyces by nonhomologous intra-strand annealing. Genes Dev., 14, 1789-1796 (2000).
30. Kinashi, H., Mori, E., Hatani, A., and Nimi, O., Isolation and characterization of large linear plasmids from lankacidin-producing Streptomyces species. J. Antibiot., 47, 1447-1455 (1994)