DNA knotting caused by head-on collision of transcription and replication

Journal of Molecular Biology

Volumn 322, Issue 1, 2002, Pages 1-6

  Olavarrieta, L ^a   Hernandez P ^a   Krimer, D B ^a   Schvartzman, J B ^a  

^a CENTRO DE INVESTIGACIONES BIOLÓGICAS   (Spain)

Author keywords

DNA replication; Knotting; Supercoiling; Transcription

Indexed keywords

DNA; DOUBLE STRANDED DNA; TETRACYCLINE DERIVATIVE;

ANTIBIOTIC RESISTANCE; ARTICLE; CONTROLLED STUDY; DNA REPLICATION; DNA TRANSCRIPTION; GENE FUNCTION; GENE LOCATION; GENE REPLICATION; GENETIC STABILITY; GENETIC TRANSCRIPTION; NONHUMAN; PLASMID; PRIORITY JOURNAL;

ESCHERICHIA COLI;

EID: 0036965964     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(02)00740-4     Document Type: Article

References (40)

1. Brewer, B. J. (1988). When polymerases collide: replication and the transcriptional organization of the E. coli chromosome. Cell, 53, 679-686.
2. Deshpande, A. M. & Newlon, C. S. (1996). DNA replication fork pause sites dependent on transcription. Science, 272, 1030-1033.
3. Linskens, M. H. K. & Huberman, J. A. (1988). Organization of replication of ribosomal DNA in Saccharomyces cerevisiae. Mol. Cell Biol. 8, 4927-4935.
4. Brewer, B. J. & Fangman, W. L. (1988). A replication fork barrier at the 3‴ end of yeast ribosomal RNA genes. Cell, 55, 637-643.
5. French, S. (1992). Consequences of replication fork movement through transcription units in vivo. Science, 258, 1362-1365.
6. Hernández, P., Martín-Parras, L., Martínez-Robles, M. L. & Schvartzman, J. B. (1993). Conserved features in the mode of replication of eukaryotic ribosomal RNA genes. EMBO J. 12, 1475-1485.
7. López-Estraño, C., Schvartzman, J. B., Krimer, D. B. & Hernández, P. (1998). Co-localization of polar replication fork barriers and rRNA transcription terminators in mouse rDNA. J. Mol. Biol. 277, 249-256.
8. Liu, B., Wong, M. L., Tinker, R. L., Geiduschek, E. P. & Alberts, B. M. (1993). The DNA replication fork can pass RNA polymerase without displacing the nascent transcript. Nature, 366, 33-39.
9. Liu, B. & Alberts, B. M. (1995). Head-on collision between a DNA replication apparatus and RNA polymerase transcription complex. Science, 267, 1131-1137.
10. Elias-Arnanz, M. & Salas, M. (1997). Bacteriophage phi 29 DNA replication arrest caused by codirectional collisions with the transcription machinery. EMBO J. 16, 5775-5783.
11. Elias-Arnanz, M. & Salas, M. (1999). Resolution of head-on collisions between the transcription machinery and bacteriophage Phi 29 DNA polymerase is dependent on RNA polymerase translocation. EMBO J. 18, 5675-5682.
12. Liu, L. F. & Wang, J. C. (1987). Supercoiling of the DNA template during transcription. Proc. Natl Acad. Sci. USA, 84, 7024-7027.
13. Alexandrov, A. I., Cozzarelli, N. R., Holmes, V. F., Khodursky, A. B., Peter, B. J., Postow, L. et al. (1999). Mechanisms of separation of the complementary strands of DNA during replication. Genetica, 106, 131-140.
14. Peter, B. J., Ullsperger, C., Hiasa, H., Marians, K. J. & Cozzarelli, N. R. (1998). The structure of supercoiled intermediates in DNA replication. Cell, 94, 819-827.
15. Ullsperger, C., Vologodskii, A. A. & Cozzarelli, N. R. (1995). Unlinking of DNA by topoisomerases during DNA replication. In Nucleic Acids and Molecular Biology (Lilley, D. M. J. & Eckstein, F., eds), pp. 115-142, Springer, Berlin.
16. Champoux, J. J. & Been, M. D. (1980). Topoisomerases and the swivel problem. In Mechanistic Studies of DNA Replication and Genetic Recombination (Alberts, B., ed.), pp. 809-815, Academic Press, New York.
17. Zechiedrich, E. L. & Cozzarelli, N. R. (1995). Roles of topoisomerase IV and DNA gyrase in DNA unlinking during replication in Escherichia coli. Genes Dev. 9, 2859-2869.
18. Bolívar, F., Rodríguez, R. L., Greene, P. J., Betlach, M. C., Heyneker, H. L., Boyer, H. W. et al. (1977). Construction and characterization of new cloning vehicles, II. A multipurpose cloning system. Gene, 2, 95-113.
19. Wu, H. Y., Shyy, S., Wang, J. C. & Liu, L. F. (1988). Transcription generates positively and negatively supercoiled domains in the template. Cell, 53, 433-440.
20. Shishido, K., Komiyama, M. & Ikawa, S. (1987). Increased production of a knotted form of plasmid pBR322 DNA in Escherichia coli DNA topoisomerase mutants. J. Mol. Biol. 195, 215-218.
21. Shishido, K., Ishii, S. & Komiyaba, N. (1989). The presence of the region on pBR322 that encodes resistance to tetracycline is responsible for high levels of plasmid DNA knotting in Escherichia coli DNA topo-isomerase I deletion mutant. Nucl. Acids Res. 17, 9749-9759.
22. Martín-Parras, L., Lucas, I., Martínez-Robles, M. L., Hernández, P., Krimer, D. B., Hyrien, O. & Schvartzman, J. B. (1998). Topological complexity of different populations of pBR322 as visualized by two-dimensional agarose gel electrophoresis. Nucl. Acids Res. 26, 3424-3432.
23. Chiang, C. S. & Bremer, H. (1988). Stability of pBR322-derived plasmids. Plasmid, 20, 207-220.
24. Viguera, E., Hernández, P., Krimer, D. B., Boistov, A. S., Lurz, R., Alonso, J. C. & Schvartzman, J. B. (1996). The ColE1 unidirectional origin acts as a polar replication fork pausing site. J. Biol. Chem. 271, 22414-22421.
25. Sogo, J. M., Stasiak, A., Martínez-Robles, M. L., Krimer, D. B., Hernández, P. & Schvartzman, J. B. (1999). Formation of knots in partially replicated DNA molecules. J. Mol. Biol. 286, 637-643.
26. Postow, L., Peter, B. J. & Cozzarelli, N. B. (1999). Knot what we thought before: the twisted story of replication. Bioessays, 21, 805-808.
27. Bell, L. & Byers, B. (1983). Separation of branched from linear DNA by two-dimensional gel electrophoresis. Anal. Biochem. 130, 527-535.
28. Brewer, B. J., Sena, E. P. & Fangman, W. L. (1988). Analysis of replication intermediates by two-dimensional agarose gel electrophoresis. Cancer Cells, 6, 229-234.
29. Lucas, I., Germe, T., Chevrier-Miller, M. & Hyrien, O. (2001). Topoisomerase II can unlink replicating DNA by precatenane removal. EMBO J. 20, 6509-6519.
30. Hanai, R. & Roca, J. (1999). Two-dimensional agarose-gel electrophoresis of DNA topoisomers. In DNA Topoisomerase Protocols (Bjornsti, M. A. & Osheroff, N., eds), vol. 94, pp. 19-27, Humana Press, Totowa, NJ.
31. Hill, T. M., Pelletier, A. J., Tecklenburg, M. L. & Kuempel, P. L. (1988). Identification of the DNA sequence from E. coli terminus region that halts replication forks. Cell, 55, 459-466.
32. Bastia, D. & Mohanty, B. K. (1996). Mechanisms for completing DNA replication. In DNA Replication in Eukaryotic Cells (DePamphilis, M. L., ed.), pp. 177-215, Cold Spring Harbor Laboratory Press, New York.
33. Santamaría, D., Hernández, P., Martínez-Robles, M. L., Krimer, D. B. & Schvartzman, J. B. (2000). Premature termination of DNA replication in plasmids carrying two inversely oriented ColE1 origins. J. Mol. Biol. 300, 75-82.
34. Olavarrieta, L., Martínez-Robles, M. L., Sogo, J. M., Stasiak, A., Hernández, P., Krimer, D. B. & Schvartzman, J. B. (2002). Supercoiling, knotting and replication fork reversal in partially replicated plasmids. Nucl. Acids Res. 30, 656-666.
35. Brewer, B. J. & Fangman, W. L. (1987). The localization of replication origins on ARS plasmids in S. cerevisiae. Cell, 51, 463-471.
36. Santamaría, D., delaCueva, G., Martínez-Robles, M. L., Krimer, D. B., Hernández, P. & Schvartzman, J. B. (1998). DnaB helicase is unable to dissociate RNA-DNA hybrids - its implication in the polar pausing of replication forks at ColE1 origins. J. Biol. Chem. 273, 33386-33396.
37. Wasserman, S. A. & Cozzarelli, N. R. (1991). Super-coiled DNA-directed knotting by T4 topoisomerase. J. Biol. Chem. 266, 20567-20573.
38. Krasnow, M. A., Stasiak, A., Spengler, S. J., Dean, F., Koller, T. & Cozzarelli, N. R. (1983). Determination of the absolute handedness of knots and catenanes of DNA. Nature, 304, 559-560.
39. Pieranski, P., Kasas, S., Dietler, G., Dubochet, J. & Stasiak, A. (2001). Localization of breakage points in knotted strings. New J. Phys. 3, 101-1013.
40. Deibler, R. W., Rahmati, S. & Zechiedrich, E. L. (2001). Topoisomerase IV alone, unknots DNA in E. coli. Genes Dev. 15, 748-761.