The Fis protein has a stimulating role in initiation of replication in Escherichia coli in vivo

PLoS ONE

Volumn 8, Issue 12, 2013, Pages

  Flåtten, Ingvild ^a   Skarstad, Kirsten ^a  

^a OSLO UNIVERSITY HOSPITAL   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

FACTOR FOR INVERSION STIMULATION;

ARTICLE; BACTERIAL CELL; BACTERIAL GROWTH; CELL GROWTH; CELL VOLUME; CONTROLLED STUDY; ESCHERICHIA COLI; FLOW CYTOMETRY; GROWTH RATE; IN VIVO STUDY; NONHUMAN; PROTEIN DETERMINATION; PROTEIN FUNCTION;

CHROMOSOMES, BACTERIAL; DNA REPLICATION; DNA, BACTERIAL; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; FACTOR FOR INVERSION STIMULATION PROTEIN; ORGANISMS, GENETICALLY MODIFIED; PROKARYOTIC INITIATION FACTORS; TRANSCRIPTION INITIATION, GENETIC;

EID: 84892639301     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0083562     Document Type: Article

References (46)

1. Skarstad K, Katayama T (2013) Regulating DNA replication in bacteria.: Cold Spring Harb Perspect Biol. 2013 Apr 1;5(4):a012922. doi: 10.1101/cshperspect.a012922.
2. Fuller RS, Funnell BE, Kornberg A (1984) The DnaA protein complex with the E. coli chromosomal replication origin (oriC) and other DNA sites. Cell 38:889-900.
3. McGarry KC, Ryan VT, Grimwade JE, Leonard AC (2004) Two discriminatory binding sites in the Escherichia coli replication origin are required for DNA strand opening by initiator DnaA-ATP. Proc Natl Acad Sci U S A 101:2811-2816.
4. Ozaki S, Kawakami H, Nakamura K, Fujikawa N, Kagawa W et al.(2008) A Common Mechanism for the ATP-DnaA-dependent Formation of Open Complexes at the Replication Origin. J Biol Chem 283:8351-8362.
5. Speck C, Messer W (2001) Mechanism of origin unwinding: sequential binding of DnaA to double- and single-stranded DNA. EMBO J 20:1469-1476.
6. Ozaki S, Katayama T (2009) DnaA structure, function, and dynamics in the initiation at the chromosomal origin. Plasmid 62:71-82.
7. Finkel SE, Johnson RC (1992) The Fis protein: it's not just for DNA inversion anymore. Mol Microbiol 6:3257-3265.
8. Bradley MD, Beach MB, de Koning AP, Pratt TS, Osuna R (2007) Effects of Fis on Escherichia coli gene expression during different growth stages. Microbiology 153:2922-2940.
9. Browning DF, Grainger DC, Busby SJ (2010) Effects of nucleoid-associated proteins on bacterial chromosome structure and gene expression. Curr Opin Microbiol 13:773-780.
10. Azam TA, Iwata A, Nishimura A, Ueda S, Ishihama A (1999) Growth Phase-Dependent Variation in Protein Composition of the Escherichia coli Nucleoid. J Bacteriol 181:6361-6370.
11. Cassler MR, Grimwade JE, Leonard AC (1995) Cell cycle-specific changes in nucleoprotein complexes at a chromosomal replication origin. EMBO J 14:5833-5841.
12. Filutowicz M, Ross W, Wild J, Gourse RL (1992) Involvement of Fis protein in replication of the Escherichia coli chromosome. J Bacteriol 174:398-407.
13. Gille H, Egan JB, Roth A, Messer W (1991) The FIS protein binds and bends the origin of chromosomal DNA replication, oriC, of Escherichia coli. Nucleic Acids Res 19:4167-4172.
14. Roth A, Urmoneit B, Messer W (1994) Functions of histone-like proteins in the initiation of DNA replication at oriC of Escherichia coli. Biochimie 76:917-923.
15. Ryan VT, Grimwade JE, Camara JE, Crooke E, Leonard AC (2004) Escherichia coli prereplication complex assembly is regulated by dynamic interplay among Fis, IHF and DnaA. Mol Microbiol 51:1347-1359.
16. Hiasa H, Marians KJ (1994) Fis cannot support oriC DNA replication in vitro. J Biol Chem 269:24999-25003.
17. Wold S, Crooke E, Skarstad K (1996) The Escherichia coli Fis protein prevents initiation of DNA replication from oriC in vitro. Nucleic Acids Res 24:3527-3532.
18. Margulies C, Kaguni JM (1998) The FIS protein fails to block the binding of DnaA protein to oriC, the Escherichia coli chromosomal origin. Nucl Acids Res 26:5170-5175.
19. Boye E, Lyngstadaas A, Løbner-Olesen A, Skarstad K, Wold S (1992) Regulation of DNA replication in Escherchia coli. In DNA replication and the Cell Cycle . Fanning E, Knippers R, Winnacker EL., editors Berlin: Mosbacher Kolloquium Springer, 15-26.
20. Cooper S, Helmstetter CE (1968) Chromosome replication and the division cycle of Escherichia coli B/r. J Mol Biol 31:519-540.
21. Skarstad K, Bernander R, Boye E (1995) Analysis of DNA replication in vivo by flow cytometry. Methods Enzymol 262:604-13.
22. Koch C, Vandekerckhove J, Kahmann R (1988) Escherichia coli host factor for site-specific DNA inversion: cloning and characterization of the fis gene. Proc Natl Acad Sci U S A 85:4237-4241.
23. Helmstetter CE (1996) Timing of Synthetic Activities in the Cell Cycle. In Escherichia coli and Salmonella. Cellular and Molecular Biology. 2 edition. Edited by Neidhardt FC et al., editors: ASM Press, 1627-1639.
24. Boye E, Stokke T, Kleckner N, Skarstad K (1996) Coordinating DNA replication initiation with cell growth: differential roles for DnaA and SeqA proteins. Proc Natl Acad Sci U S A 93:12206-12211.
25. Morigen, Løbner-Olesen A, Skarstad K (2003) Titration of the Escherichia coli DnaA protein to excess datA sites causes destabilization of replication forks, delayed replication initiation and delayed cell division. Mol Microbiol 50:349-362.
26. Morigen, Odsbu I, Skarstad K (2009) Growth rate dependent numbers of SeqA structures organize the multiple replication forks in rapidly growing Escherichia coli. Genes Cells 14:643-657.
27. Froelich JM, Phuong TK, Zyskind JW (1996) Fis binding in the dnaA operon promoter region. J Bacteriol 178:6006-6012.
28. Torheim NK, Boye E, Løbner-Olesen A, Stokke T, Skarstad K (2000) The Escherichia coli SeqA protein destabilizes mutant DnaA204 protein. Mol Microbiol 37:629-638.
29. Ball CA, Osuna R, Ferguson KC, Johnson RC (1992) Dramatic changes in Fis levels upon nutrient upshift in Escherichia coli. J Bacteriol 174:8043-8056.
30. Weigel C, Messer W, Preiss S, Welzeck M, Morigen et al. (2001) The sequence requirements for a functional Escherichia coli replication origin are different for the chromosome and a minichromosome. Mol Microbiol 40:498-507.
31. Riber L, Fujimitsu K, Katayama T, Løbner-Olesen A (2009) Loss of Hda activity stimulates replication initiation from I-box, but not R4 mutant origins in Escherichia coli. Mol Microbiol 71:107-122.
32. Leonard AC, Grimwade JE (2005) Building a bacterial orisome: emergence of new regulatory features for replication origin unwinding. Mol Microbiol 55:978-985.
33. Bramhill D, Kornberg A (1988) Duplex opening by DnaA protein at novel sequences in initiation of replication at the origin of the E. coli chromosome. Cell 52:743-755.
34. Bates DB, Asai T, Cao Y, Chambers MW, Cadwell GW et al. (1995) The DnaA box R4 in the minimal oriC is dispensable for initiation of Escherichia coli chromosome replication. Nucleic Acids Res 23:3119-3125.
35. Skarstad K, Baker TA, Kornberg A (1990) Strand separation required for initiation of replication at the chromosomal origin of E.coli is facilitated by a distant RNA-DNA hybrid. EMBO J 9:2341-2348.
36. Asai T, Chen CP, Nagata T, Takanami M, Imai M (1992) Transcription in vivo within the replication origin of the Escherichia coli chromosome: a mechanism for activating initiation of replication. Mol Gen Genet 231:169-178.
37. Leonard AC, Grimwade JE (2010) Regulating DnaA complex assembly: it is time to fill the gaps. Curr Opin Microbiol 13:766-772.
38. Bremer H, Dennis PP (1996) Modulation of Chemical Composition and other Parameters of the Cell by Growth Rate. In Escherichia coli and Salmonella. Cellular and Molecular Biology. 2 edition. Edited by Neidhardt FC et al., editors: ASM Press, 1553-1566.
39. Boye E, Løbner-Olesen A (1991) Bacterial growth control studied by flow cytometry. Res Microbiol 142:131-135.
40. Skarstad K, Boye E, Steen HB (1986) Timing of initiation of chromosome replication in individual Escherichia coli cells. EMBO J 5:1711-1717.
41. Flåtten I, Morigen, Skarstad K (2009) DnaA protein interacts with RNA polymerase and partially protects it from the effect of rifampicin. Mol Microbiol 71:1018-1030.
42. Clark DJ, Maaloe O (1967) DNA replication and the division cycle in Escherichia coli. J Mol Biol 23:99-112.
43. Waldminghaus T, Skarstad K (2010) ChIP on Chip: surprising results are often artifacts. BMC Genomics 11:414.
44. Stokke C, Flåtten I, Skarstad K (2012) An Easy-To-Use Simulation Program Demonstrates Variations in Bacterial Cell Cycle Parameters Depending on Medium and Temperature. PlosONE 7:e30981.
45. Guyer MS, Reed RR, Steitz JA, Low KB (1981) Identification of a sex-factor-affinity site in E. coli as gamma delta. Cold Spring Harb Symp Quant Biol 45:135-140.
46. Jensen KF (1993) The Escherichia coli K-12 "wild types" W3110 and MG1655 have an rph frameshift mutation that leads to pyrimidine starvation due to low pyrE expression levels. J Bacteriol, 175:3401-3407.