Genome plasticity in Streptomyces: Identification of 1 Mb TIRs in the S. coelicolor A3(2) chromosome

Molecular Microbiology

Volumn 51, Issue 6, 2004, Pages 1535-1550

  Weaver, David ^a   Karoonuthaisiri, Nitsara ^a   Tsai, Hsiu Hwei ^b   Huang, Chih Hung ^b   Ho, Mai Lan ^a   Gai, Shuning ^a   Patel, Kedar G ^a   Huang, Jianqiang ^c   Cohen, Stanley N ^c   Hopwood, David A ^d   Chen, Carton W ^b   Kao, Camilla M ^a  

^a Stanford University   (United States)

^b NATIONAL YANG MING UNIVERSITY   (Taiwan)

^c STANFORD UNIVERSITY   (United States)

^d JOHN INNES CENTRE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ARTICLE; BACTERIAL CHROMOSOME; BACTERIAL GENOME; BACTERIUM ISOLATE; DNA MICROARRAY; DNA SEQUENCE; GENE EXPRESSION; INVERTED REPEAT; LIQUID CULTURE; LONG TERMINAL REPEAT; MUTAGENESIS; NONHUMAN; POLYACRYLAMIDE GEL ELECTROPHORESIS; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SOIL MICROFLORA; STREPTOMYCES; STREPTOMYCES COELICOLOR; ULTRAVIOLET IRRADIATION; X IRRADIATION;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; CHROMOSOME MAPPING; CHROMOSOMES, BACTERIAL; CLONING, MOLECULAR; DNA, BACTERIAL; ELECTROPHORESIS, GEL, PULSED-FIELD; GENES, BACTERIAL; GENOME, BACTERIAL; HUMANS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID HYBRIDIZATION; RECOMBINATION, GENETIC; RNA, BACTERIAL; SEQUENCE ANALYSIS, DNA; STREPTOMYCES; TERMINAL REPEAT SEQUENCES; TRANSPOSASES;

BACTERIA (MICROORGANISMS); POSIBACTERIA; PROKARYOTA; STREPTOMYCES COELICOLOR; UNCULTURED ACTINOMYCETE;

EID: 12144290764     PISSN: 0950382X     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1365-2958.2003.03920.x     Document Type: Article

References (35)

1. Bao, K., and Cohen, S.N. (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.
2. Bentley, S.D., Chater, K.F., Cerdeno-Tarraga, A.M., Challis, G.L., Thomson, N.R., James, K.D., et al. (2002) Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417: 141-147.
3. Bruton, C.J., and Chater, K.F. (1987) Nucleotide sequence of IS110, an insertion sequence of Streptomyces coelicolor A3(2). Nucleic Acids Res 15: 7053-7065.
4. Bystrykh, L.V., Fernandez-Moreno, M.A., Herrema, J.K., Malpartida, F., Hopwood, D.A., and Dijkhuizen, L. (1996) Production of actinorhodin-related 'blue pigments' by Streptomyces coelicolor A3(2). J Bacteriol 178: 2238-2244.
5. Chater, K.F., Bruton, C.J., Foster, S.G., and Tobek, I. (1985) Physical and genetic analysis of IS110, a transposable element of Streptomyces coelicolor A3(2). Mol Gen Genet 200: 235-239.
6. Chen, C.W., Yu, T.W., Lin, Y.S., Kieser, H.M., and Hopwood, D.A. (1993) The conjugative plasmid SLP2 of Streptomyces lividans is a 50 kb linear molecule. Mol Microbiol 7: 925-932.
7. Chen, C.W., Huang, C.H., Lee, H.H., Tsai, H.H., and Kirby, R. (2002) Once the circle has been broken: dynamics and evolution of Streptomyces chromosomes. Trends Genet 18: 522-529.
8. Dary, A., Martin, P., Wenner, T., Decaris, B., and Leblond, P. (2000) DNA rearrangements at the extremities of the Streptomyces ambofaciens linear chromosome: evidence for developmental control. Biochimie 82: 29-34.
9. Dittrich, W., Betzler, M., and Schrempf, H. (1991) An amplifiable and deletable chloramphenicol-resistance determinant of Streptomyces lividans 1326 encodes a putative transmembrane protein. Mol Microbiol 5: 2789-2797.
10. Eisen, M.B., Spellman, P.T., Brown, P.O., and Botstein, D. (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95: 14863-14868.
11. Erikson, D. (1948) Differentiation of the vegetative and sporogenous phases of the actinomycetes. 3. Variation in the Actinomyces coelicolor species group. J Gen Microbiol 2: 252-259.
12. Fischer, G., Decaris, B., and Leblond, P. (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.
13. Fischer, G., Wenner, T., Decaris, B., and Leblond, P. (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.
14. Flett, F., and Cullum, J. (1987) DNA deletions in spontaneous chloramphenicol-sensitive mutants of Streptomyces coelicolor A3(2) and Streptomyces lividans 66. Mol Gen Genet 207: 499-502.
15. Flett, F., Platt, J., and Cullum, J. (1987) DNA rearrangements associated with instability of an arginine gene in Streptomyces coelicolor A3(2). J Basic Microbiol 27: 3-10.
16. Freeman, R.F., and Hopwood, D.A. (1978) Unstable naturally occurring resistance to antibiotics in Streptomyces. J Gen Microbiol 106: 377-381.
17. Gollub, J., Ball, C.A., Binkley, G., Demeter, J., Finkelstein, D.B., Hebert, J.M., et al. (2003) Microarray Database: data access and quality assessment tools. Nucleic Acids Res 31: 94-96.
18. Henderson, D.J., Brolle, D.F., Kieser, T., Melton, R.E., and Hopwood, D.A. (1990) Transposition of IS117 (the Streptomyces coelicolor A3(2) mini-circle) to and from a cloned target site and into secondary chromosomal sites. Mol Gen Genet 224: 65-71.
19. Hopwood, D.A. (1999) Forty years of genetics with Streptomyces: from in vivo through in vitro to in silico. Microbiology 145: 2183-2202.
20. Huang, C.H., Chen, C.Y., Tsai, H.H., Chen, C., Lin, Y.S., and Chen, C.W. (2003) Linear plasmid SLP2 of Streptomyces lividans is a composite replicon. Mol Microbiol 47: 1563-1576.
21. Huang, J., Lih, C.J., Pan, K.H., and Cohen, S.N. (2001) Global analysis of growth phase responsive gene expression and regulation of antibiotic biosynthetic pathways in Streptomyces coelicolor using DNA microarrays. Genes Dev 15: 3183-3192.
22. Ikeda, H., Ishikawa, J., Hanamoto, A., Shinose, M., Kikuchi, H., Shiba, T., et al. (2003) Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis. Nature Biotechnol 21: 526-531.
23. Kieser, H.M., Kieser, T., and Hopwood, D.A. (1992) A combined genetic and physical map of the Streptomyces coelicolor A3(2) chromosome. J Bacteriol 174: 5496-5507.
24. Kieser, T., Bibb, M.J., Buttner, M.J., Chater, K.F., and Hopwood, D.A. (2000) Practical Streptomyces Genetics. Norwich: John Innes Foundation.
25. Leblond, P., and Decaris, B. (1994) New insights into the genetic instability of streptomyces. FEMS Microbiol Lett 123: 225-232.
26. Leblond, P., Fischer, G., Francou, F., Berger, F., Guerineau, M., and Decaris, B. (1996) 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.
27. Lydiate, D.J., Ikeda, H., and Hopwood, D.A. (1986) A 2.6 kb DNA sequence of Streptomyces coelicolor A3(2) which functions as a transposable element. Mol Gen Genet 203: 79-88.
28. McDaniel, R., Ebert-Khosla, S., Hopwood, D.A., and Khosla, C. (1993) Engineered biosynthesis of novel polyketides. Science 262: 1546-1550.
29. Mahillon, J., and Chandler, M. (1998) Insertion sequences. Microbiol Mol Biol Rev 62: 725-774.
30. Martin, M.C., Schneider, D., Bruton, C.J., Chater, K.F., and Hardisson, C. (1997) A glgC gene essential only for the first of two spatially distinct phases of glycogen synthesis in Streptomyces coelicolor A3(2). J Bacteriol 179: 7784-7789.
31. Pandza, K., Pfalzer, G., Cullum, J., and Hranueli, D. (1997) 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.
32. Pandza, S., Biukovic, G., Paravic, A., Dadbin, A., Cullum, J., and Hranueli, D. (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.
33. Perkins-Balding, D., Duval-Valentin, G., and Glasgow, A.C. (1999) Excision of IS492 requires flanking target sequences and results in circle formation in Pseudoalteromonas atlantica. J Bacteriol 181: 4937-4948.
34. Qin, Z., and Cohen, S.N. (2002) Survival mechanisms for Streptomyces linear replicons after telomere damage. Mol Microbiol 45: 785-794.
35. Redenbach, M., Flett, F., Piendl, W., Glocker, I., Rauland, U., Wafzig, O. et al. (1993) The Streptomyces lividans 66 chromosome contains a 1 MB deletogenic region flanked by two amplifiable regions. Mol Gen Genet 241: 255-262.