Once the circle has been broken: Dynamics and evolution of Streptomyces chromosomes

Trends in Genetics

Volumn 18, Issue 10, 2002, Pages 522-529

  Chen, Carton W ^a   Huang, Chih Hung ^a   Lee, Hsuan Hsuan ^a   Tsai, Hsiu Hui ^a   Kirby, Ralph ^b  

^a NATIONAL YANG MING UNIVERSITY   (Taiwan)

^b RHODES UNIVERSITY   (South Africa)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL CHROMOSOME; BIOINFORMATICS; CHROMOSOME ANALYSIS; CHROMOSOME STRUCTURE; GENETIC RECOMBINATION; GENETIC STABILITY; GENETIC VARIABILITY; MOLECULAR DYNAMICS; MOLECULAR EVOLUTION; NONHUMAN; PLASMID; PRECURSOR; PRIORITY JOURNAL; REVIEW; STREPTOMYCES; TRANSPOSON;

CHROMOSOMES, BACTERIAL; COMPUTATIONAL BIOLOGY; DNA TRANSPOSABLE ELEMENTS; EVOLUTION; MODELS, GENETIC; PLASMIDS; STREPTOMYCES; TERMINAL REPEAT SEQUENCES;

ACTINOBACTERIA (CLASS); BACTERIA (MICROORGANISMS); INSERTION SEQUENCES; PROKARYOTA; STREPTOMYCES; TRANSPOSONS; UNCULTURED ACTINOMYCETE;

EID: 0036804584     PISSN: 01689525     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0168-9525(02)02752-X     Document Type: Review

References (75)

1. Lin Y-S., et al. The chromosomal DNA of Streptomyces lividans 66 is linear. Mol. Microbiol. 10:1993;923-933.
2. Ferdows M.S., Barbour A.G. Megabase-sized linear DNA in the bacterium Borrelia burgdorferi, the Lyme disease agent. Proc. Natl. Acad. Sci. U. S. A. 86:1989;5969-5973.
3. Casjens S., et al. Linear chromosomes of Lyme disease agent spirochetes: genetic diversity and conservation of gene order. J. Bacteriol. 177:1995;2769-2780.
4. Baril C., et al. Linear chromosome of Borrelia burgdorferi. Res. Microbiol. 140:1989;507-516.
5. Allardet-Servent A., et al. Presence of one linear and one circular chromosome in the Agrobacterium tumefaciens C58 genome. J. Bacteriol. 175:1993;7869-7874.
6. Wang S-J., et al. Streptomyces genomes: circular genetic maps from the linear chromosomes. Microbiology. 145:1999;2209-2220.
7. Stahl F.W. Circular genetic maps. J. Cell. Physiol. 70:1967;1-12.
8. Fraser C.M., et al. Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi. Nature. 390:1997;580-586.
9. Bentley S.D., et al. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature. 417:2002;141-147.
10. Chater K.F. Taking a genetic scalpel to the Streptomyces colony. Microbiology. 144:1998;1465-1478.
11. Chater K.F. Developmental decision during sporulation in the aerial mycelium in Streptomyces. Prokaryotic Development. 2000;33-48 American Society for Microbiology.
12. Miguelez E.M., et al. Streptomycetes: a new model to study cell death. Int. Microbiol. 3:2000;153-158.
13. Yang M.C., Losick R. Cytological evidence for association of the ends of the linear chromosome in Streptomyces coelicolor. J. Bacteriol. 183:2001;5180-5186.
14. Lezhava A., et al. Physical map of the linear chromosome of Streptomyces griseus. J. Bacteriol. 177:1995;6492-6498.
15. Pandza K., et al. Physical mapping shows that the unstable oxytetracycline gene cluster of Streptomyces rimosus lies close to one end of the linear chromosome. Microbiology. 143:1997;1493-1501.
16. Leblond P., et al. The unstable region of Streptomyces ambofaciens includes 210-kb terminal inverted repeats flanking the extremities of the linear chromosomal DNA. Mol. Microbiol. 19:1996;261-271.
17. Omura S., et al. Genome sequence of an industrial microorganism Streptomyces avermitilis: deducing the ability of producing secondary metabolites. Proc. Natl. Acad. Sci. U. S. A. 98:2001;12215-12220.
18. Huang C-H., et al. The telomeres of Streptomyces chromosomes contain conserved palindromic sequences with potential to form complex secondary structures. Mol. Microbiol. 28:1998;905-926.
19. Chang P.C., Cohen S.N. Bidirectional replication from an internal origin in a linear Streptomyces plasmid. Science. 265:1994;952-954.
20. Musialowski M.S., et al. Functional evidence that the principal DNA replication origin of the Streptomyces coelicolor chromosome is close to the dnaA-gyrB region. J. Bacteriol. 176:1994;5123-5125.
21. Chen C.W. Complications and implications of linear bacterial chromosomes. Trends Genet. 12:1996;192-196.
22. Qin Z., Cohen S.N. Replication at the telomeres of the Streptomyces linear plasmid pSLA2. Mol. Microbiol. 28:1998;893-904.
23. Volff J.N., Altenbuchner J. Genetic instability of the Streptomyces chromosome. Mol. Microbiol. 27:1998;239-246.
24. Leblond P., Decaris B. New insights into the genetic instability of Streptomyces. FEMS Microbiol. Lett. 123:1994;225-232.
25. Chen C.W. The unstable ends of the Streptomyces linear chromosomes: a nuisance without cures? Trends Biotechnol. 13:1995;157-160.
26. Redenbach M., et al. The Streptomyces lividans 66 chromosome contains a 1 Mb deletogenic region flanked by two amplifiable regions. Mol. Gen. Genet. 241:1993;255-262.
27. Volff J-N., et al. Artificial circularization of the chromosome with concomitant deletion of its terminal inverted repeats enhances genetic instability and genomic rearrangement in Streptomyces lividans. Mol. Gen. Genet. 253:1997;753-760.
28. Schrempf H. Deletion and amplification of DNA sequences in melanin-negative variants of Streptomyces reticuli. Mol. Gen. Genet. 189:1983;501-505.
29. Altenbuchner J., Cullum J. DNA amplification and an unstable arginine gene in Streptomyces lividans 66. Mol. Gen. Genet. 195:1984;134-138.
30. Hasegawa M., et al. Certain chromosomal regions in Streptomyces glaucescens tend to carry amplifications and deletions. Mol. Gen. Genet. 200:1985;375-384.
31. Kameoka D., et al. Analysis of fusion junctions of circularized chromosomes in Streptomyces griseus. J. Bacteriol. 181:1999;5711-5717.
32. Adams D.E., et al. The role of topoisomerase IV in partitioning bacterial replicons and the structure of catenated intermediates in DNA replication. Cell. 71:1992;277-288.
33. Lin Y-S., Chen C.W. Instability of artificially circularized chromosomes of Streptomyces lividans. Mol. Microbiol. 26:1997;709-719.
34. Fischer G., et al. Occurrence of deletions, associated with genetic instability in Streptomyces ambofaciens, is independent of the linearity of the chromosomal DNA. J. Bacteriol. 179:1997;4553-4558.
35. Volff J.N., Altenbuchner J. High-frequency transposition of IS1373, the insertion sequence delimiting the amplifiable element AUD2 of Streptomyces lividans. J. Bacteriol. 179:1997;5639-5642.
36. Eichenseer C., Altenbuchner J. The very large amplifiable element AUD2 from Streptomyces lividans 66 has insertion sequence-like repeats at its ends. J. Bacteriol. 176:1994;7107-7112.
37. Gunes G., et al. Genetic instability associated with insertion of IS6100 into one end of the Streptomyces lividans chromosome. Microbiology. 145:1999;2203-2208.
38. Bey S.J., et al. The homologous terminal sequence of the Streptomyces lividans chromosome and SLP2 plasmid. Microbiology. 146:2000;911-922.
39. Fischer J., et al. The use of an improved transposon mutagenesis system for DNA sequencing leads to the characterization of a new insertion sequence of Streptomyces lividans 66. Gene. 180:1996;81-89.
40. Gray Y.H.M. It takes two transposons to tango. Transposable-element-mediated chromosomal rearrangements. Trends Genet. 16:2000;461-468.
41. Pandza S., et al. Recombination between the linear plasmid pPZG101 and the linear chromosome of Streptomyces rimosus can lead to exchange of ends. Mol. Microbiol. 28:1998;1165-1176.
42. Birch A., et al. Chromosomal deletion and rearrangement in Streptomyces glaucescens. J. Bacteriol. 173:1991;3531-3538.
43. Birch A., et al. Extremely large chromosomal deletions are intimately involved in genetic instability and genomic rearrangements in Streptomyces glaucescens. Mol. Gen. Genet. 217:1989;447-458.
44. Leskiw B.K., et al. The use of a rare codon specifically during development? Mol. Microbiol. 5:1991;2861-2867.
45. Dary A., et al. DNA rearrangements at the extremities of the Streptomyces ambofaciens linear chromosome: evidence for developmental control. Biochimie. 82:2000;29-34.
46. Dary A., et al. Evolution of the linear chromosomal DNA in Streptomyces: is genomic variability developmentally modulated? Res. Microbiol. 150:1999;439-445.
47. Xiao J. Differentiation genes are involved in homologous recombination in Streptomyces coelicolor. Yi Chuan Xue Bao. 27:2000;1108-1113.
48. Fischer G., et al. 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. U. S. A. 95:1998;14296-14301.
49. Yamasaki, M. and Kinashi, H. (2001) Streptomyces coelicolor 2106 contains two chimeric chromosomes formed by single crossover of SCP1 and the wild-type chromosome. Twelfth International Symposium on the Biology of Actinomycetes, pp. 84
50. Gravius B., et al. The 387 kb linear plasmid pPZG101 of Streptomyces rimosus and its interactions with the chromosome. Microbiology. 140:1994;2271-2277.
51. Chen C.W., et al. The conjugative plasmid SLP2 of Streptomyces lividans is a 50 kb linear molecule. Mol. Microbiol. 7:1993;925-932.
52. Volff J.N., Altenbuchner J. Influence of disruption of the recA gene on genetic instability and genome rearrangement in Streptomyces lividans. J. Bacteriol. 179:1997;2440-2445.
53. Mikoc A., et al. Construction and characterization of a Streptomyces rimosus recA mutant: the RecA-deficient strain remains viable. Mol. Gen. Genet. 264:2000;227-232.
54. Muth G., et al. Mutational analysis of the Streptomyces lividans recA gene suggests that only mutants with residual activity remain viable. Mol. Gen. Genet. 255:1997;420-428.
55. Vierling S., et al. Genetics and Molecular Biology of Industrial Microorganisms. 2000;Society for Industrial Microbiology.
56. Aravind L., Koonin E.V. Prokaryotic homologs of the eukaryotic DNA-end-binding protein Ku, novel domains in the Ku protein and prediction of a prokaryotic double-strand break repair system. Genome Res. 11:2001;1365-1374.
57. Reeves A.R., et al. Physical-genetic map of the erythromycin-producing organism Saccharopolyspora erythraea. Microbiology. 144:1998;2151-2159.
58. Redenbach M., et al. Chromosome topology and genome size of selected actinomycetes species. Antonie Van Leeuwenhoek. 78:2000;227-235.
59. Volff J.N., Altenbuchner J. A new beginning with new ends: linearisation of circular chromosomes during bacterial evolution. FEMS Microbiol. Lett. 186:2000;143-150.
60. Redenbach M., et al. A set of ordered cosmids and a detailed genetic and physical map for the 8 Mb Streptomyces coelicolor A3(2) chromosome. Mol. Microbiol. 21:1996;77-96.
61. Friend E.J., Hopwood D.A. The linkage map of Streptomyces rimosus. J. Gen. Microbiol. 68:1971;187-197.
62. Louarn J., et al. Hyperrecombination in the terminus region of the Escherichia coli chromosome: possible relation to nucleoid organization. J. Bacteriol. 176:1994;7524-7531.
63. Bao K., Cohen S.N. Terminal proteins essential for the replication of linear plasmids and chromosomes in Streptomyces. Genes Dev. 15:2001;1518-1527.
64. Yang C-C., et al. The terminal proteins of linear Streptomyces chromosomes and plasmids: A novel class of replication priming proteins. Mol. Microbiol. 43:2002;297-305.
65. Lin N.T., et al. Plasmids carrying cloned fragments of RF DNA from the filamentous phage φLf can be integrated into the host chromosome via site-specific integration and homologous recombination. Mol. Genet. Genomics. 266:2001;425-435.
66. Clerget M. Site-specific recombination promoted by a short DNA segment of plasmid R1 and by a homologous segment in the terminus region of the Escherichia coli chromosome. New Biol. 3:1991;780-788.
67. Barre F.X., et al. Circles: the replication-recombination-chromosome segregation connection. Proc. Natl. Acad. Sci. U. S. A. 98:2001;8189-8195.
68. Fraser C.M., et al. Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi. Nature. 390:1997;580-586.
69. Picardeau M., et al. Physical mapping of an origin of bidirectional replication at the centre of the Borrelia burgdorferi linear chromosome. Mol. Microbiol. 32:1999;437-445.
70. Goodner B., et al. Genome sequence of the plant pathogen and biotechnology agent Agrobacterium tumefaciens C58. Science. 294:2001;2323-2328.
71. Wood D.W., et al. The genome of the natural genetic engineer Agrobacterium tumefaciens C58. Science. 294:2001;2317-2323.
72. Yamasaki M., et al. A complex insertion sequence cluster at a point of interaction between the linear plasmid SCP1 and the linear chromosome of Streptomyces coelicolor A3(2). J. Bacteriol. 182:2000;3104-3110.
73. Yamasaki M., et al. Integrated structures of the linear plasmid SCP1 in two bidirectional donor strains of Streptomyces coelicolor A3(2). Mol. Gen. Genet. 264:2001;634-642.
74. Casjens S. Evolution of the linear DNA replicons of the Borrelia spirochetes. Curr. Opin. Microbiol. 2:1999;529-534.
75. Schardl C.L., et al. Linearization of maize mitochondrial chromosomes by recombination with linear episomes. Nature. 310:1984;292-296.