Unequal access of chromosomal regions to each other in Salmonella: Probing chromosome structure with phage λ integrase-mediated long-range rearrangements

Molecular Microbiology

Volumn 52, Issue 2, 2004, Pages 329-344

  Garcia Russell, Nathalie ^a   Harmon, Timothy G ^a   Le, Tien Q ^a   Amaladas, Nelusha H ^a   Mathewson, Richard D ^a   Segall, Anca M ^a  

^a SAN DIEGO STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

INTEGRASE;

ARTICLE; BACTERIOPHAGE LAMBDA; CHROMOSOME; CHROMOSOME STRUCTURE; CONTROLLED STUDY; NONHUMAN; PLASMID; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; SALMONELLA;

ATTACHMENT SITES, MICROBIOLOGICAL; BACTERIAL PROTEINS; BACTERIOPHAGE LAMBDA; BACTERIOPHAGES; CHROMOSOMES, BACTERIAL; DNA TRANSPOSABLE ELEMENTS; DNA, BACTERIAL; DNA, VIRAL; INTEGRASES; PLASMIDS; RECOMBINATION, GENETIC; SALMONELLA TYPHIMURIUM;

BACTERIOPHAGE LAMBDA; NEGIBACTERIA; PROKARYOTA; SALMONELLA;

EID: 1942436944     PISSN: 0950382X     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1365-2958.2004.03976.x     Document Type: Article

References (49)

1. Azam, T.A., Hiraga, S., and Ishihama, A. (2000) Two types of localization of the DNA-binding proteins within the Escherichia coli nucleoid. Genes Cells 5: 613-626.
2. Bankhead, T.M., Etzel, B.J., Wolven, F., Bordenave, S., Boldt, J.L., Larsen, T.A., and Segall, A.M. (2003) Mutations at residues 282, 286, and 293 of phage lambda integrase exert pathway-specific effects on synapsis and catalysis in recombination. J Bacteriol 185: 2653-2666.
3. Bendich, A.J. (2001) The form of chromosomal DNA molecules in bacterial cells. Biochimie 83: 177-186.
4. Benjamin, K.R., Abola, A.P., Kanaar, R., and Cozzarelli, N.R. (1996) Contributions of supercoiling to Tn3 resolvase and phage Mu Gin site-specific recombination. J Mol Biol 256: 50-65.
5. Christ, N., and Droge, P. (1999) Alterations in the directionality of lambda site-specific recombination catalyzed by mutant integrases in vivo. J Mol Biol 288: 825-836.
6. Datsenko, K.A., and Wanner, B.L. (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci USA 97: 6640-6645.
7. DeBoy, R.T., and Craig, N.L. (1996) Tn7 transposition as a probe of cis interactions between widely separated (190 kilobases apart) DNA sites in the Escherichia coli chromosome. J Bacteriol 178: 6184-6191.
8. Gordon, G.S., and Wright, A. (2000) DNA segregation in bacteria. Annu Rev Microbiol 54: 681-708.
9. Han, Y.W., Gumport, R.I., and Gardner, J.F. (1994) Mapping the functional domains of bacteriophage lambda integrase protein. J Mol Biol 235: 908-925.
10. Heiner, C.R., Hunkapiller, K.L., Chen, S.M., Glass, J.I., and Chen, E.Y. (1998) Sequencing multimegabase-template DNA with BigDye terminator chemistry. Genome Res 8: 557-561.
11. Higgins, N.P., Yang, X., Fu, Q., and Roth, J.R. (1996) Surveying a supercoil domain by using the gamma delta resolution system in Salmonella typhimurium. J Bacteriol 178: 2825-2835.
12. Hiraga, S. (2000) Dynamic localization of bacterial and plasmid chromosomes. Annu Rev Genet 34: 21-59.
13. Kavenoff, R., and Bowen, B.C. (1976) Electron microscopy of membrane-free folded chromosomes from Escherichia coli. Chromosoma 59: 89-101.
14. Keener, J., and Nomura, M. (1996) Regulation of ribosome synthesis. In Escherichia coli and Salmonella typhimurium. Neidhardt, F.C. (ed.). Washington, DC: American Society for Microbiology Press, pp. 1417-1431.
15. Kleckner, N., Bender, J., and Gottesman, S. (1991) Uses of transposons with emphasis on Tn10. Methods Enzymol 204: 139-180.
16. Krause, M., Ruckert, B., Lurz, R., and Messer, W. (1997) Complexes at the replication origin of Bacillus subtilis with homologous and heterologous DnaA protein. J Mol Biol 274: 365-380.
17. Krug, P.J., Gileski, A.Z., Code, R.J., Torjussen, A., and Schmid, M.B. (1994) Endpoint bias in large Tn10-catalyzed inversions in Salmonella typhimurium. Genetics 136: 747-756.
18. Lanzer, M., and Bujard, H. (1988) Promoters largely determine the efficiency of repressor action. Proc Natl Acad Sci USA 85: 8973-8977.
19. Leibowitz, P.J., and Schaechter, M. (1975) The attachment of the bacterial chromosome to the cell membrane. Int Rev Cytol 41: 1-28.
20. Liu, L.F., and Wang, J.C. (1987) Supercoiling of the DNA template during transcription. Proc Natl Acad Sci USA 84: 7024-7027.
21. Lu, M., Campbell, J.L., Boye, E., and Kleckner, N. (1994) SeqA: a negative modulator of replication initiation in E. coli. Cell 77: 413-426.
22. Manna, D., and Higgins, N.P. (1999) Phage Mu transposition immunity reflects supercoil domain structure of the chromosome. Mol Microbiol 32: 595-606.
23. Miesel, L., Segall, A., and Roth, J.R. (1994) Construction of chromosomal rearrangements in Salmonella by transduction: inversions of non-permissive segments are not lethal. Genetics 137: 919-932.
24. Murphy, K.C., Campellone, K.G., and Poteete, A.R. (2000) PCR-mediated gene replacement in Escherichia coli. Gene 246: 321-330.
25. Nash, H.A., and Pollock, T.J. (1983) Site-specific recombination of bacteriophage lambda. The change in topological linking number associated with exchange of DNA strands. J Mol Biol 170: 19-38.
26. Nash, H.A., and Robertson, C.A. (1989) Heteroduplex substrates for bacteriophage lambda site-specific recombination: cleavage and strand transfer products. EMBO J 8: 3523-3533.
27. Niki, H., and Hiraga, S. (1998) Polar localization of the replication origin and terminus in Escherichia coli nucleoids during chromosome partitioning. Genes Dev 12: 1036-1045.
28. Niki, H., Yamaichi, Y., and Hiraga, S. (2000) Dynamic organization of chromosomal DNA in Escherichia coli. Genes Dev 14: 212-223.
29. Ohsumi, K., Yamazoe, M., and Hiraga, S. (2001) Different localization of SeqA-bound nascent DNA clusters and MukF-MukE-MukB complex in Escherichia coli cells. Mol Microbiol 40: 835-845.
30. Pettijohn, D.E. (1996) The nucleoid. In Escherichia coli and Salmonella typhimurium. Neidhardt, F.C. (ed.). Washington, DC: American Society for Microbiology Press, pp. 158-166.
31. Pogliano, J. (2002) Dynamic cellular location of bacterial plasmids. Curr Opin Microbiol 5: 586-590.
32. Pogliano, J., Ho, T.Q., Zhong, Z., and Helinski, D.R. (2001) Multicopy plasmids are clustered and localized in Escherichia coli. Proc Natl Acad Sci USA 98: 4486-4491.
33. Pollock, T.J., and Nash, H.A. (1983) Knotting of DNA caused by a genetic rearrangement. Evidence for a nucleosome-like structure in site-specific recombination of bacteriophage lambda. J Mol Biol 170: 1-18.
34. Poteete, A.R., and Fenton, A.C. (2000) Genetic requirements of phage lambda red-mediated gene replacement in Escherichia coli K-12. J Bacteriol 182: 2336-2340.
35. Rebollo, J.E., Francois, V., and Louarn, J.M. (1988) Detection and possible role of two large nondivisible zones on the Escherichia coli chromosome. Proc Natl Acad Sci USA 85: 9391-9395.
36. Roberts, R.C., Burioni, R., and Helinski, D.R. (1990) Genetic characterization of the stabilizing functions of a region of broad-host-range plasmid RK2. J Bacteriol 172: 6204-6216.
37. Schagger, H., and von Jagow, G. (1987) Tricine-sodium dodecyl sulfate-polyacrylamide gel electrophoresis for the separation of proteins in the range from 1 to 100 kDa. Anal Biochem 166: 368-379.
38. Schmid, M.B. (1988) Structure and function of the bacterial chromosome. Trends Biochem Sci 13: 131-135.
39. Schmid, M.B., and Roth, J.R. (1987) Gene location affects expression level in Salmonella typhimurium. J Bacteriol 169: 2872-2875.
40. Segall, A.M. (1998) Analysis of higher order intermediates and synapsis in the bent-L pathway of bacteriophage lambda site-specific recombination. J Biol Chem 273: 24258-24265.
41. Segall, A.M., and Roth, J.R. (1989) Recombination between homologies in direct and inverse orientation in the chromosome of Salmonella: intervals which are nonpermissive for inversion formation. Genetics 122: 737-747.
42. Segall, A.M., and Roth, J.R. (1994) Approaches to half-tetrad analysis in bacteria: recombination between repeated, inverse-order chromosomal sequences. Genetics 136: 27-39.
43. Segall, A., Mahan, M.J., and Roth, J.R. (1988) Rearrangement of the bacterial chromosome: forbidden inversions. Science 241: 1314-1318.
44. Segall, A.M., Goodman, S.D., and Nash, H.A. (1994) Architectural elements in nucleoprotein complexes: interchangeability of specific and non-specific DNA binding proteins. EMBO J 13: 4536-4548.
45. Sinden, R.R., and Pettijohn, D.E. (1981) Chromosomes in living Escherichia coli cells are segregated into domains of supercoiling. Proc Natl Acad Sci USA 78: 224-228.
46. Skarstad, K., Boye, E., and Steen, H.B. (1986) Timing of initiation of chromosome replication in individual Escherichia coli cells. EMBO J 5: 1711-1717.
47. Thomas, C.M. (1981) Molecular genetics of broad host range plasmid RK2. Plasmid 5: 10-19.
48. Ussery, D., Larsen, T.S., Wilkes, K.T., Friis, C., Worning, P., Krogh, A., and Brunak, S. (2001) Genome organization and chromatin structure in Escherichia coli. Biochimie 83: 201-212.
49. Watson, M.A., Boocock, M.R., and Stark, W.M. (1996) Rate and selectivity of synapsis of res recombination sites by Tn3 resolvase. J Mol Biol 257: 317-329.