A dual promoter system regulating λ DNA replication initiation

Nucleic Acids Research

Volumn 42, Issue 7, 2014, Pages 4450-4462

  Olszewski, Paweł ^a   Szambowska, Anna ^a   Barańska, Sylwia ^a   Narajczyk, Magdalena ^a   Wȩgrzyn, Grzegorz ^a   Glinkowska, Monika ^a  

^a UNIVERSITY OF GDA SK   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN LAMBDAO; PROTEIN ORILAMBDA; UNCLASSIFIED DRUG; VIRUS DNA; VIRUS PROTEIN;

ARTICLE; BACTERIOPHAGE; CONTROLLED STUDY; DNA REPLICATION; ESCHERICHIA COLI; GENETIC TRANSCRIPTION; MOLECULAR INTERACTION; MUTATION; NONHUMAN; PLASMID; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN BINDING; VIRUS GENOME;

BACTERIOPHAGE LAMBDA; DNA REPLICATION; DNA, VIRAL; MUTATION; PLASMIDS; PROMOTER REGIONS, GENETIC; REPLICATION ORIGIN; TRANSCRIPTION, GENETIC; VIRAL PROTEINS;

EID: 84898933008     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku103     Document Type: Article

References (70)

1. Wegrzyn, A. and Wegrzyn, G. (2001) Inheritance of the replication complex: a unique or common phenomenon in the control of DNA replication? Arch Microbiol., 175, 86-93. (Pubitemid 32200303)
2. Baranska, S., Glinkowska, M., Herman-Antosiewicz, A., Maciag-Dorszynska, M., Nowicki, D., Szalewska-Palasz, A., Wegrzyn, A. and Wegrzyn, G. (2013) Replicating DNA by cell factories: roles of central carbon metabolism and transcription in the control of DNA replication in microbes, and implications for understanding this process in human cells. Microb. Cell Fact., 12, 55.
3. Jackson, D., Wang, X. and Rudner, D.Z. (2012) Spatio-temporal organization of replication in bacteria and eukaryotes (nucleoids and nuclei). Cold Spring Harb. Perspect. Biol., 4, a010389.
4. Leonard, A.C. and Mechali, M. (2013) DNA Replication Origins. Cold Spring Harb. Perspect. Biol., 5, a010116.
5. Sobetzko, P., Travers, A. and Muskhelishvili, G. (2012) Gene order and chromosome dynamics coordinate spatiotemporal gene expression during the bacterial growth cycle. Proc. Natl Acad. Sci. USA, 109, E42-E50.
6. Sequeira-Mendes, J. and Gomez, M. (2012) On the opportunistic nature of transcription and replication initiation in the metazoan genome. Bioessays, 34, 119-125.
7. Oppenheim, A.B., Kobiler, O., Stavans, J., Court, D.L. and Adhya, S. (2005) Switches in bacteriophage lambda development. Annu. Rev. Genet., 39, 409-429. (Pubitemid 43011121)
8. Wegrzyn, G, Licznerska, K. and Wegrzyn, A. (2012) Phage X-new insights into regulatory circuits. Adv. Virus Res., 82, 155-178.
9. Tsurimoto, T. and Matsubara, K. (1981) Purified bacteriophage lambda O protein binds to four repeating sequences at the lambda replication origin. Nucleic Acids Res., 9, 1789-1799. (Pubitemid 11074428)
10. Dodson, M., Roberts, J., McMacken, R. and Echols, H. (1985) Specialized nucleoprotein structures at the origin of replication of bacteriophage X: complexes with ÀO protein and with ÀO, ÀP, and Escherichia coli DnaB proteins. Proc. Natl Acad. Sci. USA, 82, 4678-4682. (Pubitemid 16239626)
11. Alfano, C. and McMacken, R. (1989) Ordered assembly of nucleoprotein structures at the bacteriophage X replication origin during the initiation of DNA replication. J. Biol. Chem., 264, 10699-10708.
12. Biswas, S.B. and Biswas, E.E. (1987) Regulation of dnaB function in DNA replication in Escherichia coli by dnaC and X P gene products. J. Biol. Chem., 262, 7831-7838.
13. Mallory, J.B., Alfano, C. and McMacken, R. (1990) Host-virus interactions in the initiation of bacteriophage X DNA replication. Recruitment of Escherichia coli DnaB helicase by ÀP replication protein. J. Biol. Chem., 265, 13297-13307.
14. Liberek, K., Georgopoulos, C. and Zylicz, M. (1988) Role of the Escherichia coli DnaK and DnaJ heat shock proteins in the initiation of bacteriophage X DNA replication. Proc. Natl Acad. Sci. USA, 85, 6632-6636.
15. Dodson, M., McMacken, R. and Echols, H. (1989) Specialized nucleoprotein structures at the origin of replication of bacteriophage X. Protein association and disassociation reactions responsible for localized initiation of replication. J. Biol. Chem., 264, 10719-10725.
16. Zylicz, M. (1993) The Escherichia coli chaperones involved in DNA replication. Philos. Trans. R. Soc. Lond. B Biol. Sci., 339, 271-277.
17. Szalewska-Palasz, A., Wegrzyn, A., Herman, A. and Wegrzyn, G. (1994) The mechanism of the stringent control of lambda plasmid DNA replication. EMBO J., 13, 5779-5785. (Pubitemid 24363046)
18. Szalewska-Palasz, A., Wegrzyn, A., Blaszczak, A., Taylor, K. and Wegrzyn, G. (1998a) DnaA-stimulated transcriptional activation of oriÀ: escherichia coli RNA polymerase X subunit as a transcriptional activator contact site. Proc. Natl Acad. Sci. USA, 95, 4241-4246. (Pubitemid 28207896)
19. Dove, W.F., Hargrove, E., Ohashi, M., Haugli, F. and Guha, A. (1969) Replicator activation in lambda. Jpn. J. Genet., 44, 11-22.
20. Nijkamp, H.J.J., Szybalski, W., Ohashi, M. and Dove, W.F. (1971) Gene expression by constitutive mutants of coliphage lambda. Mol. Gen. Genet., 114, 80-88.
21. McMacken, R. (2002) Potent stimulation of transcription-coupled DNA supercoiling by sequence-specific DNA-binding proteins. Proc. Natl Acad. Sci. USA, 99, 9139-9144. (Pubitemid 34764580)
22. Learn, B., Karzai, A.W. and McMacken, R. (1993) Transcription stimulates the establishment of bidirectional X DNA replication in vitro. Cold Spring Harb. Symp. Quant. Biol., 58, 389-402. (Pubitemid 24219501)
23. Baranska, S., Gabig, M., Wegrzyn, A., Konopa, G, Herman-Antosiewicz, A., Hernandez, P., Schvartzman, J.B., Helinski, D.R. and Wegrzyn, G (2001) Regulation of the switch from early to late bacteriophage lambda DNA replication. Microbiology, 147, 535-547. (Pubitemid 32243715)
24. Szambowska, A., Pierechod, M., Wegrzyn, G and Glinkowska, M. (2011) Coupling of transcription and replication machineries in X DNA replication initiation: evidence for direct interaction of Escherichia coli RNA polymerase and the ÀO protein. Nucleic Acids Res., 39, 168-177.
25. Wegrzyn, G and Wegrzyn, A. (2005) Genetic switches during bacteriophage lambda development. Prog. Nucleic Acid Res. Mol. Biol., 79, 1-48. (Pubitemid 43591148)
26. Zylicz, M., Liberek, K., Wawrzynow, A. and Georgopoulos, C. (1998) Formation of the preprimosome protects lambda O from RNA transcription-dependent proteolysis by ClpP/ClpX. Proc. Natl Acad. Sci. USA, 95, 15259-15263. (Pubitemid 29018686)
27. Hayes, S. and Szybalski, W. (1975) Role of oop RNA primer in intitiation of coliphage lambda DNA replication. In: Goulian, M. and Hanawalt, P. (eds), In: DNA Synthesis and its Regulation. Benjamin, Menlo Park, CA, pp. 486-512
28. Wold, M.S., Mallory, J.B., Roberts, J.D., LeBowitz, J.H. and McMacken, R. (1982) Initiation of bacteriophage X DNA replication in vitro with purified X replication proteins. Proc. Natl Acad. Sci. USA, 79, 6176-6180. (Pubitemid 13219828)
29. Mensa-Wilmot, K., Seaby, R., Alfano, C, Wold, M.S., Gomes, B. and McMacken, R. (1989) Reconstitution of a nine-protein system that initiates bacteriophage X DNA replication. J. Biol. Chem., 264, 2853-2861. (Pubitemid 19057780)
30. Krinke, L. and Wulff, D.L. (1987) OOP RNA, produced from multicopy plasmids, inhibits X cII gene expression through an RNase III-dependent mechanism. Genes Dev., 1, 1005-1013.
31. Krinke, L., Mahoney, M. and Wulff, D.L. (1991) The role of the OOP antisense RNA in coliphage X development. Mol. Microbiol., 5, 1265-1272. (Pubitemid 21896152)
32. Potrykus, K., Perzylo, E. and Wegrzyn, G (2002) pO, a promoter for oop RNA synthesis, has a role in replication of plasmids derived from bacteriophage X. Plasmid, 47, 210-215.
33. Szalewska-Palasz, A., Weigel, C, Speck, C, Srutkowska, S., Konopa, G, Lurz, R., Marszalek, J., Taylor, K., Messer, W. and Wegrzyn, G (1998) Interaction of the Escherichia coli DnaA protein with bacteriophage X DNA. Mol. Gen. Genet., 259, 679-688. (Pubitemid 28499413)
34. Flatten, I., Morigen. and Skarstad, K. (2009) DnaA protein interacts with RNA polymerase and partially protects it from the effect of rifampicin. Mol. Microbiol., 71, 1018-1030.
35. Wegrzyn, A., Wegrzyn, G, Herman, A. and Taylor, K. (1996a) Protein inheritance: X plasmid replication perpetuated by the heritable replication complex. Genes Cells, 1, 953-963. (Pubitemid 126670801)
36. Wegrzyn, G, Wegrzyn, A., Pankiewicz, A. and Taylor, K. (1996b) Allele specificity of the Escherichia coli DnaA gene function in the replication of plasmid derived from phage X. Mol. Gen. Genet., 252, 580-586.
37. Miller, J.H. (1972) Experiments in Molecular Genetics. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
38. Zylicz, M., Gorska, I., Taylor, K. and Georgopoulos, C (1984) Bacteriophage lambda replication proteins: formation of a mixed oligomer and binding to the origin of lambda DNA. Mol. Gen. Genet., 196, 401-406. (Pubitemid 14010692)
39. Fuller, R.S., Kaguni, J.M. and Kornberg, A. (1981) Enzmatic replication of the origin of the Escherichia coli chromosome. Proc. Natl Acad. Sci. USA, 78, 7370-7374. (Pubitemid 12186142)
40. Viguera, E., Hernandez, P., Krimer, D.B., Boistov, A.S., Lurz, R., Alonso, J.C. and Schvartzman, J.B. (1996) The ColE1 unidirectional origin acts as a polar replication fork pausing site. J. Biol. Chem., 271, 22414-22421. (Pubitemid 26304675)
41. Srutkowska, S., Caspi, R., Gabig, M. and Wegrzyn, G (1999) Detection of DNA replication intermediates after two-dimensional agarose gel electrophoresis using a fluorescein-labeled probe. Anal. Biochem., 269, 221-222. (Pubitemid 29174292)
42. Viguera, E., Rodriguez, A., Hernandez, P., Krimer, D.B., Trellez, O. and Schvartzman, J.B. (1998) A computer model for the analysis of DNA replication intermediates by two-dimensional (2D) agarose gel electrophoresis. Gene, 217, 41-49. (Pubitemid 28430997)
43. Wegrzyn, G, Szalewska-Palasz, A., Wegrzyn, A., Obuchowski, M. and Taylor, K. (1995) Transcriptional activation of the origin of coliphage lambda DNA replication is regulated by the host DnaA initiator function. Gene, 154, 47-50.
44. Wrobel, B., Herman-Antosiewicz, A., Szalewska-Palasz, A. and Wegrzyn, G (1998) Polyadenylation of oop RNA in the regulation of bacteriophage lambda development. Gene, 212, 57-65. (Pubitemid 28269133)
45. Narajczyk, M., Baranska, S., Szambowska, A., Glinkowska, M., Wegrzyn, A. and Wegrzyn, G (2007a) Modulation of X plasmid and phage DNA replication by Escherichia coli SeqA protein. Microbiology, 153, 1653-1663. (Pubitemid 46780020)
46. Narajczyk, M., Baranska, S., Wegrzyn, A. and Wegrzyn, G (2007b) Switch from y to s replication of bacteriophage X DNA: factors involved in the process and a model for its regulation. Mol. Genet. Genomics, 278, 65-74. (Pubitemid 46911429)
47. Baranska, S., Konopa, G and Wegrzyn, G (2002) Directionality of X plasmid DNA replication carried out by the heritable replication complex. Nucleic Acids Res., 30, 1176-1181. (Pubitemid 34679690)
48. Rothstein, R., Michel, B. and Gangloff, S. (2000) Replication fork pausing and recombination or ''gimme a break''. Genes Dev., 14, 1-10. (Pubitemid 30051572)
49. Lin, Y.L. and Pasero, P. (2012) Interference between DNA replication and transcription as a cause of genomic instability. Curr. Genomics, 13, 65-73.
50. Herman-Antosiewicz, A., Srutkowska, S., Taylor, K. and Wegrzyn, G (1998) Replication and maintenance of X Plasmids devoid of the Cro repressor autoregulatory loop in Escherichia coli. Plasmid, 40, 113-125. (Pubitemid 28409388)
51. Herman-Antosiewicz, A. and Wegrzyn, G (1999) Regulation of copy number and stability of phage X derived pTCÀ 1 plasmid in the light of the dimer/multimer catastrophe hypothesis. FEMS Mirobiol. Lett., 176, 489-493. (Pubitemid 29308977)
52. Summers, D.K., Beton, C.W. and Withers, H.L. (1993) Multicopy plasmid instability: the dimer catastrophe hypothesis. Mol. Microbiol., 8, 1031-1038. (Pubitemid 23187022)
53. Wojtkowiak, D., Georgopoulos, C. and Zylicz, M. (1993) Isolation and characterization of ClpX, a new ATP-dependent specificity component of the Clp protease of Escherichia coli. J. Biol. Chem., 268, 22609-22617. (Pubitemid 23318316)
54. Gottesman, S., Clark, W.P., de Crecy-Lagard, V. and Maurizi, M.R. (1993) ClpX, an alternative subunit for the ATP-dependent Clp protease of Escherichia coli. Sequence and in vivo activities. J. Biol. Chem., 268, 22618-22626. (Pubitemid 23318317)
55. Leng, F., Chen, B. and Dunlap, D.D. (2011) Dividing a supercoiled DNA molecule into two independent topological domains. Proc. Natl Acad. Sci. USA, 108, 19973-19978.
56. Hayes, S. and Szybalski, W. (1973) Control of short leftward transcripts from the immunity and ori regions in induced coliphage lambda. Mol. Gen. Genet., 126, 275-290.
57. Lusky, M. and Hobom, G. (1979) Inceptor and origin of DNA replication in lambdoid coliphages. I the lambda minimal replication system. Gene, 6, 137-172. (Pubitemid 9224822)
58. Potrykus, K., Baranska, S., Wegrzyn, A. and Wegrzyn, G. (2002) Composition of the lambda plasmid heritable replication complex. Biochem. J., 364, 857-862. (Pubitemid 34680863)
59. Shearwin, K.E., Callen, B.P. and Egan, J.B. (2005) Transcriptional interference-a crash course. Trends Genet., 21, 339-345.
60. Simmons, L.A., Breier, A.M., Cozzarelli, N.R. and Kaguni, J.M. (2004) Hyperinitiation of DNA replication in Escherichia coli leads to replication fork collapse and inviability. Mol. Microbiol., 51, 349-358. (Pubitemid 38142125)
61. Su'etsugu, M., Emoto, A., Fujimitsu, K., Keyamura, K. and Katayama, T. (2003) Transcriptional control for initiation of chromosomal replication in Escherichia coli: fluctuation of the level of origin transcription ensures timely initiation. Genes Cells, 8, 731-745. (Pubitemid 37121562)
62. Snyder, M., Sapolsky, R.J. and Davis, R.W. (1988) Transcription interferes with elements important for chromosome maintenance in Saccharomyces cerevisiae. Mol. Cell. Biol., 8, 2184-2194.
63. Greger, I.H., Demarchi, F., Giacca, M. and Proudfoot, N.J. (1998) Transcriptional interference.perturbs the binding of Sp1 to the HIV-1 promoter. Nucleic Acids Res., 26, 1294-1301.
64. Schubert, R.A., Dodd, I.B., Egan, J.B. and Shearwin, K.E. (2007) Cro's role in the CI Cro bistable switch is critical for {lambda}'s transition from lysogeny to lytic development. Genes Dev., 21, 2461-2472. (Pubitemid 47529374)
65. Herman-Antosiewicz, A. and Wegrzyn, G. (1998) Replication of lambda plasmid DNA in the Escherichia coli cell cycle. Biochem. Biophys. Res. Commun., 247, 554-557. (Pubitemid 28418429)
66. Anand, R.P., Lovett, S.T. and Haber, J.E. (2013) Break-induced DNA replication. Cold Spring Harb. Perspect. Biol., 5, a010397.
67. Merrikh, H., Zhang, Y., Grossman, A.D. and Wang, J.D. (2012) Replication-transcription conflicts in bacteria. Nat. Rev. Microbiol., 10, 449-458.
68. Hase, T., Nakai, M. and Masamune, Y. (1989) Transcription of a region downstream from lambda ori is required for replication of plasmids derived from coliphage lambda. Mol. Gen. Genet., 216, 120-125.
69. Hayes, S. (1979) Initiation of coliphage lambda replication, lit, oop RNA synthesis, and effect of gene dosage on transcription from promoters PL, PR, and PR. Virology, 97, 415-438. (Pubitemid 10222413)
70. Hayes, S., Horbay, M.A. and Hayes, C. (2012) A CI-independent form of replicative inhibition: turn off of early replication of bacteriophage lambda. PLoS One, 7, e36498.