Interactions of the Streptomyces lividans initiator protein DnaA with its target

European Journal of Biochemistry

Volumn 260, Issue 2, 1999, Pages 325-335

  Majka, Jerzy ^a,b   Jakimowicz, Dagmara ^a   Messer, Walter ^b   Schrempf, Hildgund ^c   Lisowski, Marek ^c   Zakrzewska Czerwińska, Jolanta ^a  

^a INSTITUTE OF IMMUNOLOGY AND EXPERIMENTAL THERAPY   (Poland)

^b MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

^c NONE

Author keywords

DnaA box; DnaA promoter region; DnaA protein; Streptomyces; Surface plasmon resonance

Indexed keywords

DEOXYRIBONUCLEASE; DEOXYRIBONUCLEOPROTEIN;

AMINO TERMINAL SEQUENCE; ARTICLE; BACILLUS SUBTILIS; DNA FOOTPRINTING; DNA REPLICATION; DNA SEQUENCE; DNA STRUCTURE; ESCHERICHIA COLI; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN ANALYSIS; PROTEIN PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; STREPTOMYCES LIVIDANS; SURFACE PLASMON RESONANCE;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BASE SEQUENCE; BIOSENSING TECHNIQUES; BLOTTING, WESTERN; DNA FOOTPRINTING; DNA, FUNGAL; DNA-BINDING PROTEINS; ELECTROPHORESIS, POLYACRYLAMIDE GEL; MOLECULAR SEQUENCE DATA; MOLECULAR WEIGHT; PROMOTER REGIONS (GENETICS); SEQUENCE ALIGNMENT; STREPTOMYCES;

BACILLUS SUBTILIS; BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; PROKARYOTA; STREPTOMYCES; STREPTOMYCES LIVIDANS;

EID: 0033106405     PISSN: 00142956     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1432-1327.1999.00168.x     Document Type: Article

References (49)

1. Skarstad, K. & Boye, E. (1994) The initiator protein DnaA: evolution. properties and function. Biochim. Biophys. Acta 1217, 111-130.
2. Messer, W. & Weigel, C. (1996) Initiation of chromosome replication. In Escherichia coli and Salmonella. Cellular and Molecular Biology (Neidhardt, F.C., Curtiss, R. III, Ingraham, J., Lin, E.C.C., Low, K.B., Magasanik, B., Reznikoff, W.S., Riley, M., Schaechter, M. & Umbarger, H., eds.) 2nd edn, pp. 1579-1601, American Society for Microbiology, Washington, DC.
3. Kornberg, A. & Baker, T. (1992) DNA Replication, 2nd edn. W. H. Freeman, New York.
4. 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.
5. Ogasawara, N. & Yoshikawa, H. (1992) Genes and their organisation in the replication origin region of the bacterial chromosome. Mol. Microbiol. 6, 629-634.
6. Roth, A. & Messer, W. (1995) The DNA binding domain of the initiator protein DnaA. EMBO J. 14, 2106-2111.
7. Schaper, S. & Messer, W. (1997) Prediction of the structure of the replication inititor protein DnaA. Proteins 28, 1-9.
8. Kützner, H.J. (1981) The family Streptomycetaceae. In The Prokaryotes: a Handbook on Habitats, Isolation and Identification of Bacteria (Stair, M.P., Stolp, H., Truper, H.G., Balows, A. & Schlegel, H., eds.), pp. 2028-2090. Springer-Verlag KG, Berlin.
9. Radenbach, M., Kieser, H.M., Denapaite, D., Eicher, A., Cullumn, J., Kinashi, H. & Hopwood, D.A. (1996) A set of ordered cosmids and detailed genetic and physical map for the 8 Mb Streptomyces coelicolor A3(2) chromosome. Mol. Microbiol. 21, 77-96.
10. Zakrzewska-Czerwińska, J. & Schrempf, H. (1992) Characterization of an autonomously replicating region from the Streptomyces lividans chromosome. J. Bacteriol. 174, 2688-2693.
11. Zakrzewska-Czerwińska, J., Majka, J. & Schrempf, H. (1995) Minimal requirements of the Streptomyces lividans 66 oriC region and its transcriptional and translational activities. J. Bacteriol. 177, 4765-4771.
12. Jakimowicz, D., Majka, J., Messer, W., Speck, Ch., Sanchez, J., Fernandez, M., Cruz Martin, M., Keller, U., Schauwecker, F., Schrempf, H. & Zakrzewska-Czerwińska, J. (1998) Structural elements of the Streptomyces oriC region and their interactions with the DnaA protein. Microbiology 144, 1281-1290.
13. Majka, J., Messer, W., Schrempf, H. & Zakrzewska-Czerwińska, J. (1997) Purification and characterization of the Streptomyces lividans initiator protein DnaA. J. Bacteriol. 179, 2426-2432.
14. Messer, W. & Weigel, Ch. (1997) DnaA initiator - also a transcription factor. Mol. Microbiol. 24, 1-6.
15. Zhou, Z. & Syvanen, M. (1990) Identification and sequence of the drpA gene from Escherichia coli. Mol. Gen. Genet. 172, 281-286.
16. Wang, Q. & Kaguni, J.M. (1989) DnaA protein regulates transcription of the rpoH gene of Escherichia coli. J. Biol. Chem. 264, 7338-7344.
17. van den Berg, E.A., Geerse, R.H., Memelink, J., Bovenberg, R.A.L., Magnée, F.A. & van de Putte, P. (1985) Analysis of regulatory sequences upstream of the E. coli uvrB gene; involvement of the DnaA protein. Nucleic Acids Res. 13, 1829-1840.
18. Mizushima, T., Tomura, A., Shinpuku, T., Miki, T. & Sekimizu, K. (1994) Loss of flagellation in dnaA mutants of Escherichia coli. J. Bacteriol. 176, 5544-5546.
19. Augustin, L.B., Jacobson, B.A. & Fuchs, J.A. (1994) Escherichia coli Fis and DnaA proteins bind specifically to the nrd promoter region and affect expression of an nrd-lac fusion. J. Bacteriol. 176, 378-387.
20. Schaefer, C. & Messer, W. (1989) Directionality of DnaA protein/DNA interaction. Active orientation of the DnaA protein/dnaA box in transcription termination. EMBO J. 8, 1609-1613.
21. Zakrzewska-Czerwińska, J., Nardmann, J. & Schrempf, H. (1994) Inducible transcription of the dnaA gene from Streptomyces lividans 66. Mol. Gen. Genet. 242, 440-447.
22. Sambrook, J., Fritsch, E.F. & Maniatis, T. (1989) Molecular Cloning. A Laboratory Manual, 2nd edn. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
23. 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. USA 85, 4237-4241.
24. Mattern, S. (1992) Regulation of the galactose operon of Streptomyces lividans. PhD Thesis, Universität Osanbrück, Osanbrück, Germany.
25. Pahl, A., Ühlein, M., Bang, H., Schlumbohm, W. & Keller, U. (1992) Streptomycetes possess peptidyl-prolyl cis-trans isomerases that strongly resemble cyclophilins from eukaryotic organisms. Mol. Microbiol. 6, 3551-3558.
26. Hopwood, D.A., Bibb, M.J., Chater, K.F., Kieser, T., Bruton, C.J., Kieser, H.M., Lydiate, D.J., Smith, C.P., Ward, J.M. & Schrempf, H. (1985) Genetic Manipulation of Streptomyces: A Laboratory Manual. The John Innes Foundation, Norwich, UK.
27. Schlochtermeier, A., Walter, S., Schröder, J., Moorman, M. & Schrempf, H. (1992) The gene encoding the cellulase (Avicelase) Cell from Streptomyces reticuli and analysis of protein domains. Mol. Microbiol. 6, 3611-3621.
28. Sanger, F., Nicklen, S. & Coulson, A.R. (1977) DNA sequencing with chain-terminating inhibitors. Proc. Natl Acad. Sci. USA 74, 5463-5467.
29. Majka, J., Jakimowicz, D., Zarko-Postawka, M. & Zakrzewska-Czerwińska, J. (1997) Glutathione S-transferase fusions proteins as an affinity reagent for rapid isolation of specific sequence directly from genomic DNA. Nucleic Acids Res. 25, 2537-2538.
30. Laemmli, U.K. (1970) Cleavage of structural proteins during assembly of the head of the bacteriophage T4. Nature 227, 680-685.
31. Provencher, S.W. & Glöckner, J. (1981) Estimation of globular protein structure from circular dichroism. Biochemistry 20, 33-37.
32. 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.
33. Carey, J. (1991) Gel retardation. Methods Enzymol. 208, 103-117.
34. Malmqvist, M. (1993) Biospecific interaction analysis using biosensor technology. Nature 361, 186-187.
35. Fisher, R.J. & Fivash, M. (1994) Surface plasmon resonance based methods for measuring the kinetics and binding affinities of biomolecular interactions. Curr. Opin. Biotechnol. 5, 389-395.
36. Krause, M. & Messer, W. (1997) Complex at the replication origin of Bacillus subtilis with homologous and heterologous DnaA protein. J. Mol. Biol. 274, 365-380.
37. Svaren, J., Schmitz, J. & Horz, W. (1994) The transactivation domain of Pho4 is required for nucleosome disruption at the PHO5 promoter. EMBO J. 13, 4856-4862.
38. Venter, U., Svaren, J., Schmitz, J., Schmid, A. & Horz, W. (1994) A nucleosome precludes binding of the transcription factor Pho4 in vivo to a critical target site in the PHO5 promoter. EMBO J. 13, 4848-4855.
39. Schaper, S. & Messer, W. (1995) Interaction of the initiator protein DnaA of Escherichia coli with its DNA target. J. Biol. Chem 270, 17622-17626.
40. Bondeson, K., Frostell-Karlsson, A., Fagerstam, L. & Magnusson, G. (1993) Lactose repressor-operator DNA interactions: kinetic analysis by a surface plasmon resonance biosensor. Analyt. Biochem. 214, 245-251.
41. Atlung, T., Clausen, E. & Hansen, F.G. (1985) Autoregulation of the dnaA gene of Escherichia coli. Mol. Gen. Genet. 200, 442-450.
42. Braun, R.E., O'Day, K. & Wright, A. (1985) Autoregulation of the DNA replication gene dnaA in E. coli. Cell 40, 159-169.
43. Kücherer, C., Lother, H., Kölling, R., Schauzu, M.A. & Messer, W. (1986) Regulation of transcription of the chromosomal dnaA gene of Escherichia coli. Mol. Gen. Genet. 205, 115-121.
44. Yoshikawa, H. & Wake, R.G. (1993) Initiation and termination of chromosome replication. In Bacillus subtilis and Other Gram-Positive Bacteria: Biochemistry, Physiology, and Molecular Genetics (Sonenshein, A.L., Hoch. J.A. & Losick, R., eds.), pp. 507-528. American Society for Microbiology, Washington, D.C.
45. Sutton, M.D. & Kaguni, J.M. (1997) The Escherichia coli dnaA Gene: four functional domains. J. Med. Biol. 274, 546-561.
46. Darimont, B. & Sterner, R. (1994) Sequence, assembly and evolution of a primordial ferredoxin from Thermotoga maritima. EMBO J. 13, 1772-1781.
47. Fujita, M.Q., Yoshikawa, H. & Ogasawara, N. (1989) Structure of the DnaA region of Pseudomonas putida: conservation among three bacteria. Bacillus subtilis, Escherichia coli and P. putida. Mol. Gen. Genet. 215, 381-387.
48. Fujita, M.Q., Yoshikawa, H. & Ogasawara, N. (1992) Structure of the dnaA and DnaA-box in the Mycoplasma capricolum chromosome: Conservation and variations in the course of evolution. Gene 110, 17-23.
49. Kimura, M. & Ohta, T. (1974) On some principles governing molecular evolution. Proc. Natl Acad. Sci. USA 71, 2848-2852.