Structural elements of the Streptomyces oriC region and their interactions with the DnaA protein

Microbiology

Volumn 144, Issue 5, 1998, Pages 1281-1290

  Jakimowicz, Dagmara ^a   Majka, Jerzy ^a,b   Messer, Walter ^b   Speck, Christian ^b   Fernandez, Marisol ^c   Martin, M Cruz ^c   Sanchez, Jesus ^c   Schauwecker, Florian ^d   Keller, Ullrich ^d   Schrempf, Hildgund ^e   Zakrzewska Czerwińska, Jolanta ^a  

^a INSTITUTE OF IMMUNOLOGY AND EXPERIMENTAL THERAPY   (Poland)

^b MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

^c UNIVERSITY OF OVIEDO   (Spain)

^d TECHNISCHE UNIVERSITÄT BERLIN   (Germany)

^e UNIVERSITY OF OSNABRÜCK   (Germany)

Author keywords

AT rich sequence; DnaA box; oriC; Streptomyces

Indexed keywords

DNA A; DNA BINDING PROTEIN;

ARTICLE; CHROMOSOME REPLICATION; CONSENSUS SEQUENCE; DISSOCIATION CONSTANT; DNA DENATURATION; DNA REPLICATION ORIGIN; ESCHERICHIA COLI; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; STREPTOMYCES;

ACTINOBACTERIA (CLASS); ESCHERICHIA COLI; PROKARYOTA; STREPTOMYCES; STREPTOMYCES ANTIBIOTICUS; STREPTOMYCES CHRYSOMALLUS; STREPTOMYCES LIVIDANS; STREPTOMYCINEAE; UNCULTURED ACTINOMYCETE;

EID: 17744407606     PISSN: 13500872     EISSN: None     Source Type: Journal    
DOI: 10.1099/00221287-144-5-1281     Document Type: Article

References (55)

1. Bolivar, F., Rodriguez, R. L., Greene, P. J., Betlach, M. C., Heyneker, H. L., Boyer, H. W., Crosa, J. H. & Falkow, S. (1977). Construction and characterization of new cloning vehicles. II. A multipurpose cloning system. Gene 2, 95-113.
2. Bondeson, K., Frostell-Karlsson, A., Fagerstam, L. & Magnusson, G. (1993). Lactose repressor-operator DNA interactions: kinetic analysis by a surface plasmon resonance biosensor. Anal Biochem 214, 245-251.
3. Bramhill, D. & Kornberg, A. (1988). Duplex opening by DnaA protein of novel sequences in initiation of replication at the origin of the E. coli chromosome. Cell 52, 743-755.
4. Calcutt, M. J. & Schmidt, F. J. (1992). Conserved gene arrangement in the origin region of the Streptomyces coelicolor chromosome. J Bacteriol 174, 3220-3226.
5. Chen, C. W. (1996). Complications and implications of linear bacterial chromosomes. Trends Genet 12, 192-196.
6. Diederich, L., Roth, A. & Messer, W. A versatile plasmid vector system for the expression of genes in Escherichia coli. BioTechniques 16, 916-923.
7. Fujita, M. Q., Yoshikawa, H. & Ogasawara, N. (1990). Structure of the dnaA region of Micrococcus luteus: conservation and variations among eubacteria. Gene 93, 73-78.
8. Fujita, M. Q., Yoshikawa, H. & Ogasawara, N. (1992). Structure of the dnaA and DnaA-box region in the Mycoplasma capricolum chromosome: conservation and variations in the course of evolution. Gene 110, 17-23.
9. Fuller, R. S., Funnell, B. E. & Kornberg, A. (1984). The DnaA protein complex with the E. coli chromosomal origin (oriC) and other sites. Cell 38, 889-900.
10. Gille, H. & Messer, W. (1991). Localized unwinding and structural perturbations in the origin of replication, oriC, of Escherichia coli in vitro and in vivo. EMBO J 10, 1579-1584.
11. 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. Norwich: John Innes Foundation.
12. Hsu, J., Bramhill, D. & Thompson, Ch. M. (1994). Open complex formation by DnaA initiation protein at the Escherichia coli chromosomal origin requires the 13-mers precisely spaced relative to the 9-mers. Mol Microbiol 11, 903-911.
13. Koch, C., Vandekerhove, 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.
14. Kornberg, A. & Baker, T. (1992). DNA Replication, 2nd edn. New York: W. H. Freeman.
15. Krause, M., Rückert, B., Lurz, R. & Messer, W. (1997). Complexes at the replication origin of Bacillus subtilis with homologous and heterologous DnaA protein. J Mol Biol 274, 365-380.
16. Kützner, H. J. (1981). The family Streptomycetaceae. In The Prokaryotes: A Handbook on Habitats, Isolation and Identification of Bacteria, pp. 2028-2090. Edited by M. P. Starr, H. Stolp, H. G. Trüper, A. Balows & H. Schlegel. Berlin: Springer.
17. Langer, U., Richter, S., Roth, A., Weigel, Ch. & Messer, W. (1996). A comprehensive set of DnaA-box mutations in the replication origin, oriC, of Escherichia coli. Mol Microbiol 21, 301-311.
18. Leblond, P., Redenbach, M. & Cullumn, J. (1993). Physical map of the Streptomyces lividans 66 genome and comparison with that of the related strain Streptomyces coelicolor A3(2). J Bacteriol 175, 3422-3429.
19. Lezhava, A., Mizukami, T., Kajitani, T., Kameoka, D., Redenbach, M., Shinkawa, H., Nimi, O. & Kinashi, H. (1995). Physical map of the linear chromosome of Streptomyces griseus. J Bacteriol 177, 6492-6498.
20. Lin, Y.-S., Kieser, H. M., Hopwood, D. A. & Chen, C. W. (1993). The chromosomal DNA of Streptomyces lividans 66 is linear. Mol Microbiol 10, 923-933.
21. Majka, J., Jakimowicz, D., Zarko-Postawka, M. & Zakrzewska-Czerwińska, J. (1997a). Glutathione S-transferase fusion proteins as an affinity reagent for rapid isolation of specific sequence directly from genomic DNA. Nucleic Acids Res 25, 2537-2538.
22. Majka, J., Messer, W., Schrempf, H. & Zakrzewska-Czerwińska, J. (1997b). Purification and characterization of the Streptomyces lividans initiator protein DnaA. J Bacteriol 179, 2426-2432.
23. Malmqvist, M. (1993). Biospecific interaction analysis using biosensor technology. Nature 361, 186-187.
24. Marczyński, G. T. & Shapiro, L. (1992). Cell-cycle control of a cloned chromosomal origin of replication from Caulobacter crescens. J Mol Biol 226, 959-977.
25. Margolin, W., Bramhill, D. & Long, S. R. (1995). The dnaA gene of Rhizobium meliloti lies within unusual gene arrangement. J Bacteriol 177, 2892-2900.
26. Mattern, S. (1992). Regulation of the galactose operon of Streptomyces lividans. PhD Thesis. Universität Osnabrück, Osnabrück, Germany.
27. Messer, W. & Weigel, C. (1996). Initiation of chromosome replication. In Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, pp. 1579-1601. Edited by F. C. Neidhardt, J. L. Ingraham, K. Brooks Low, B. Magasanik, M. Schaechter & H. E. Umbarger. Washington, DC: American Society for Microbiology.
28. von Meyenburg, K. & Hansen, F. G. (1987). Regulation of chromosome replication. In Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, pp. 1555-1577. Edited by F. C. Neidhardt, J. L. Ingraham, K. Brooks Low, B. Magasanik, M. Schaechter & H. E. Umbarger. Washington, DC: American Society for Microbiology.
29. Moriya, S., Firshein, W., Yoshikawa, H. & Ogasawara, N. (1994). Replication of a Bacillus subtilis oriC plasmid in vitro. Mol Microbiol 12, 469-478.
30. Musialowski, M. L., Flett, F., Scott, G. B., Hobbins, G., Smith, C. P. & Oliver, S. G. (1994). Functional evidence that the principal DNA replication origin of the Streptomyces coelicolor chromosome is close to the dnaA-gyrB region. J Bacteriol 176, 5123-5125.
31. Novella, I. S., Barbes, C. & Sanchez, J. (1992). Sporulation of Streptomyces antibioticus ETHZ 7451 in submerged culture. Can J Microbiol 38, 769-773.
32. 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.
33. 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.
34. Richter, S. & Messer, M. (1995). Genetic structure of the dnaA region of the cyanobacterium Synechocystis sp. strain PCC6803. J Bacteriol 177, 4245-4251.
35. Richter, S., Hess, W. R., Krause, M. & Messer, W. (1998). Unique organization of the dnaA region from Prochlorococcus marinus CCMP 1375, a marine cyanobacterium. Mol Gen Genet (in press).
36. Rizzio, M., Shapiro, L. & Gober, J. W. (1993). Asymmetric expression of the DNA gyrase B subunit gene from replication-competent chromosome in the Caulobacter predivisional cell. J Bacteriol 175, 6970-6981.
37. Salazar, L., Fsihi, H., de Rossi, E., Riccardi, G., Rios, C., Cole, S. T. & Takiff, H. E. (1996). Organization of the origins of replication of the chromosomes of Mycobacterium tuberculosis and isolation of a functional origin from M. smegmatis. Mol Microbiol 20, 283-293.
38. Sambrook, J., Fritsch, E. F. & Maniatis, T. (1989). Molecular Cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
39. Sanger, F., Nicklen, S. & Coulson, A. R. (1977). DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74, 5463-5467.
40. Schaefer, C. & Messer, W. (1991). DnaA protein DNA interaction. Modulation of the recognition sequence. Mol Gen Genet 226, 34-40.
41. Schaper, S. & Messer, W. (1995). Interaction of the initiator protein DnaA of Escherichia coli with its DNA target. J Biol Chem 270, 17622-17626.
42. Short, J. M., Fernandez, J. M., Sorge, J. A. & Huse, W. D. (1988). A bacteriophage lambda expression vector with in vivo excision properties. Nucleic Acids Res 16, 7583-7600.
43. Shuan, M., Chen, S.-Y., Thompson, H. A., Hoover, T. A., Hill, A. & Williams, J. C. (1994). Cloning and characterization of an autonomous replication sequence from Coxiella burnetii. J Bacteriol 176, 5233-5243.
44. Skarstad, K. & Boye, E. (1994). The initiator protein DnaA: Evolution, properties and function. Biochim Biophys Acta 1217, 111-130.
45. Smith, D. W., Yee, T. W., Baird, C. & Krishnapillai, V. (1991). Pseudomonad replication origins: a paradigm for bacterial origins? Mol Microbiol 5, 2581-2587.
46. Vieira, J. & Messing, J. (1991). New pUC-derived cloning vectors with different selectable markers and DNA replication origins. Gene 100, 189-194.
47. Woelker, B. & Messer, W. (1993). The structure of the initiation complex at the replication origin, oriC, of Escherichia coli. Nucleic Acids Res 21, 5025-5033.
48. Yanisch-Perron, C., Vieira, J. & Messing, J. (1985). Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene 33, 103-119.
49. Ye, F., Renaudin, J., Bove, J.-M. & Laigret, F. (1994). Cloning and sequencing of the replication origin (oriC) of the Spiroplasma citri chromosome and construction of autonomously replicating artificial plasmids. Curr Microbiol 29, 23-29.
50. Yoshikawa, H. & Ogasawara, N. (1991). Structure and function of DnaA and the DnaA-box in eubacteria: evolutionary relationships of bacterial replication origins. Mol Microbiol 5, 2589-2597.
51. Yoshikawa, H. & Wake, R. G. (1993). Initiation and termination of chromosome replication. In Bacillus subtilis and Gram-Positive Bacteria: Biochemistry, Physiology and Molecular Genetics, pp. 507-528. Edited by A. L. Sonenshein, J. A. Hoch & R. Losick. Washington, DC: American Society for Microbiology.
52. Zakrzewska-Czerwińska, J. & Schrempf, H. (1992). Characterization of an autonomously replicating region from Streptomyces lividans. J Bacteriol 174, 2688-2693.
53. Zakrzewska-Czerwińska, J., Nardmann, J. & Schrempf, H. (1994). Inducible transcription of the dnaA gene from Streptomyces lividans 66. Mol Gen Genet 242, 440-447.
54. 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.
55. Zweiger, G. & Shapiro, L. (1994). Expression of Caulobacter dnaA as a function of the cell cycle. J Bacteriol 176, 401-408.