Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid

Journal of Bacteriology

Volumn 181, Issue 20, 1999, Pages 6361-6370

  Azam, Talukder Ali ^a,b   Iwata, Akira ^c   Nishimura, Akiko ^a   Ueda, Susumu ^c   Ishihama, Akira ^a  

^a NATIONAL INSTITUTE OF GENETICS   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^c NIPPON INSTITUTE FOR BIOLOGICAL SCIENCE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; BACTERIAL PROTEIN; CELL PROTEIN; DNA BINDING PROTEIN; NUCLEOPROTEIN; STRUCTURAL PROTEIN;

ARTICLE; BACTERIAL GROWTH; CELL LYSATE; CONTROLLED STUDY; ESCHERICHIA COLI; GROWTH CURVE; IMMUNOBLOTTING; NONHUMAN; PHASE CONTRAST MICROSCOPY; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PROTEIN ANALYSIS;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; NEGIBACTERIA; PROKARYOTA;

EID: 0032716841     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/jb.181.20.6361-6370.1999     Document Type: Article

References (63)

1. Almirón, M., A. J. Link, D. Furlong, and R. Kolter. 1992. A novel DNA hinding protein with regulatory and protective roles in starved Escherichia coli. Genes Dev. 6:2646-2654.
2. Atlung, T., and H. Ingmer. 1997. H-NS: a modulator of environmentally regulated gene expression. Mol. Microbiol. 24:7-17.
3. Ball, C. A., R. Osuna, K. C. Ferguson, and R. C. Johnson. 1992. Dramatic changes in Fis levels upon nutrient upshift in Escherichia coli. J. Bacteriol. 174:8043-8056.
4. Calvo, J. M., and R. G. Matthews. 1994. Leucine-responsive regulatory protein: a global regulator of metabolism in Escherichia coli. Microbiol. Rev. 58:466-498.
5. Craig, N. L., and S. E. Nash. 1984. E. coli integration host factor binds to specific sites in DNA. Cell 39:707-716.
6. Ditto, M. D., D. Roberts, and R. A. Weisberg. 1994. Growth phase variation of integration host factor level in Escherichia coli. J. Bacteriol. 176:3738-3748.
7. Dixon, N. E., and A. Kornberg. 1984. Protein HU in the enzymatic replication of the chromosomal origin of Escherichia coli. Proc. Natl. Acad. Sci. USA 81:424-428.
8. Drlica, K., and J. Rouviere-Yaniv. 1987. Histone-like proteins of bacteria. Microbiol. Rev. 51:301-319.
9. Finkel, S. E., and R. C. Johnson. 1992. The Fis protein: it's not just for DNA inversion anymore. Mol. Microbiol. 6:3257-3265.
10. Free, A., and C. J. Dorman. 1995. Coupling of Escherichia coli hns mRNA levels to DNA synthesis by autoregulation: implications for growth phase control. Mol. Microbiol. 18:101-113.
11. Fuller, R. S., B. E. Funnell, and A. Kornberg. 1984. The dnaA protein complex with the E. coli chromosome replication origin (oriC) and other DNA sites. Cell 38:889-900.
12. Galke, V. A., V. L. Balke, and J. D. Gralla. 1987. Changes in the linking number of supercoiled DNA accompany growth transitions in Escherichia coli. J. Bacteriol. 169:4499-4506.
13. Geider, K., and H. Hoffmann-Berling. 1981. Proteins controlling the helical structure of DNA. Annu. Rev. Biochem. 50:233-260.
14. Grant, R. A., D. J. Filman, S. E. Finkel, R. Kolter, and J. M. Hogle. 1998. The crystal structure of Dps, a ferritin homolog that binds and protects DNA. Nat. Struct. Biol. 5:294-303.
15. Hengge-Aronis, R. 1999. Interplay of global regulators and cell physiology in the general stress response of Escherichia coli. Curr. Opin. Microbiol. 2: 148-152.
16. Hiraga, S., H. Niki, T. Ogura, C. Ichinose, H. Mori, B. Ezaki, and A. Jaffe. 1989. Chromosomal partitioning in Escherichia coli: novel mutants producing anucleate cells. J. Bacteriol. 171:1496-1505.
17. Hwang, D. S., B. Thony, and A. Kornberg. 1992. IciA protein, a specific inhibitor of initiation of Escherichia coli chromosomal replication. J. Biol. Chem. 267:2209-2213.
18. Hwang, D. S., and A. Kornberg. 1990. A novel protein binds a key origin sequence to block replication of an E. coli minichromosome. Cell 63:325-331.
19. Ishihama, A. 1997. Promoter selectivity control of Escherichia coli RNA polymerase, p. 53-70. In F. Eckstein and D. Lilley (ed.), Nucleic acids and molecular biology, vol. 11. Mechanism of transcription. Springer-Verlag, Heidelberg, Germany.
20. Ishihama, A. 1997. Adaptation of gene expression in stationary phase bacteria. Curr. Opin. Genet. Dev. 7:582-588.
21. Ishihama, A. 1999. Modulation of the nucleoid, the transcription apparatus, and the translation machinery in bacteria for stationary phase survival. Genes Cells 3:135-143.
22. Jair, K.-W., X. Yu, K. Skarstad, B. Thony, N. Fujita, A. Ishihama, and R. E. Wolf, Jr. 1996. Transcription activation of promoters of the superoxide and multiple antibiotic resistance regulation by Rob, a binding protein of the Escherichia coli origin of chromosomal replication. J. Bacteriol. 178:2507-2513.
23. 38. J. Bacteriol. 177:6832-6835.
24. Jishage, M., and A. Ishihama. 1997. Variation in RNA polymerase sigma subunit composition within different stocks of Escherichia coli W3110. J. Bacteriol. 179:959-963.
25. Jishage, M., A. Iwata, S. Ueda, and A. Ishihama. 1996. Regulation of RNA polymerase sigma subunit synthesis in Escherichia coli: intracellular levels of four species of sigma subunit under various growth conditions. J. Bacteriol. 178:5447-5451.
26. Johnson, R. C., M. F. Bruist, and M. I. Simon. 1986. Host protein requirement for in vitro site-specific DNA inversion. Cell 46:531-539.
27. β. Nucleic Acids Res. 19: 1063-1066.
28. β. J. Bacteriol. 176:531-534.
29. S. Mol. Gen. Genet. 248:629-634.
30. Koch, C., and R. Kahmann. 1986. Purification and properties of the Escherichia coli host factor required for inversion of the G segment in bacteriophage Mu. J. Biol. Chem. 261:15673-15678.
31. 38 holoenzymes: effect of DNA supercoiling. J. Biol. Chem. 271:1998-2004.
32. Landgraf, J. R., J. Wu, and J. M. Calvo. 1996. Effects of nutrition and growth rate on Lrp levels in Escherichia coli. J. Bacteriol. 178:6930-6936.
33. Martinez, A., and R. Kolter. 1997. Protection of DNA during oxidative stress by the nonspecific DNA-binding protein Dps. J. Bacteriol. 179:5188-5194.
34. Messer, W., and C. Weigel. 1997. DnaA initiator - also a transcription factor. Mol. Microbiol. 24:1-6.
35. β RNA replication, is essential for rpoS translation in Escherichia coli. Genes Dev. 10:1143-1151.
36. Nash, H. A., and C. A. Robertson. 1981. Purification and properties of the Escherichia coli protein factor required for lambda integration recombination. J. Biol. Chem. 256:9246-9253.
37. Newman, E. B., R. D'Ari, and R. T. Lin. 1992. The leucine-Lrp regulon in E. coli: a global response in search of a raison d'etre. Cell 68:617-619.
38. Newman, E. B., and R. T. Lin. 1995. Leucine-responsive regulatory protein, a global regulator of gene expression in E. coli. Annu. Rev. Microbiol. 49: 747-775.
39. Oberto, J., K. Drlica, and J. Rouviere-Yaniv. 1994. Histones, HMG, HU, IHF: meme combat. Biochimie 76:901-908.
40. Osuna, R., D. Lienau, K. T. Hughes, and R. C. Johnson. 1995. Sequence, regulation, and functions of fis in Salmonella typhimurium. J. Bacteriol. 177: 2021-2032.
41. Paul, T. T., M. J. Haykinson, and R. C. Johnson. 1993. The nonspecific DNA-binding and -bending proteins HMG1 and HMG2 promote the assembly of complex nucleoprotein structures. Genes Dev. 7:1521-1534.
42. Pettijohn, D. E. 1996. The nucleoid, p. 158-166. In F. C. Neidhardt, R. Curtis III, J. L. Ingraham, E. C. C. Lin, K. B. Low, B. Magasanik, W. S. Reznikoff, M. Riley, M. Schaechter, and H. E. Umbarger (ed.), Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 1. American Society for Microbiology, Washington, D.C.
43. Pontiggia, A., A. Negri, M. Beltrame, and M. E. Bianchi. 1993. Protein HU binds specifically to kinked DNA. Mol. Microbiol. 7:343-350.
44. Rouviere-Yaniv, J., M. Yaniv, and J. E. Germond. 1979. Escherichia coli DNA-binding protein HU forms nucleosome-like structure with circular double-stranded DNA. Cell 17:265-274.
45. Sakakibara, Y., and S. Yuasa. 1982. Continuous synthesis of the dnaA gene product of Escherichia coli in the cell cycle. Mol. Gen. Genet. 186:87-94.
46. Schmid, M. B. 1990. More than just 'histone-like' proteins. Cell 63:451-453.
47. Schneider, R., A. Travers, and G. Muskhelishvili. 1997. FIS modulates growth phase-dependent topological transitions of DNA in Escherichia coli. Mol. Microbiol. 26:519-530.
48. β adapted to host factor-less Escherichia coli. Proc. Natl. Acad. Sci. USA 94:10239-10242.
49. Sekimizu, K., B. Yat-ming Yung, and A. Kornberg. 1988. The DnaA protein of Escherichia coli: abundance, improved purification, and membrane binding. J. Biol. Chem. 263:7136-7140.
50. Shi, X., and G. N. Bennett. 1994. Plasmids bearing hfq and the hns-like gene stpA complement hns mutants in modulating arginine decarboxylase gene expression in Escherichia coli. J. Bacteriol. 176:6769-6775.
51. Skarstad, K., B. Thony, D. S. Hwang, and A. Kornberg. 1993. A novel binding protein of the origin of the Escherichia coli chromosome. J. Biol. Chem. 268:5365-5370.
52. Spassky, A., S. Rimsky, H. Garreau, and H. Buc. 1984. H1a, an E. coli DNA-binding protein which accumulates in stationary phase, strongly compacts DNA in vitro. Nucleic Acids Res. 12:5321-5340.
53. Suryanarayana, T., and A.-R. Subramanian. 1978. Specific association of two homologous DNA-binding proteins to the native 30S ribosomal subunits of Escherichia coli. Biochim. Biophys. Acta 520:342-357.
54. Talukder, A. A., and A. Ishihama. Twelve species of nucleoid-associated protein from Escherichia coli: sequence recognition specificity and DNA binding affinity. J. Biol. Chem., in press.
55. Tanaka, H., N. Goshima, K. Khono, Y. Kano, and F. Imamoto. 1993. Properties of DNA-binding of HU heterotypic and homotypic dimers from Escherichia coli. J. Biochem. 113:568-572.
56. Thompson, J. F., L. Moitoso de Vargas, C. Koch, R. Kahmann, and A. Landy. 1987. Cellular factors couple recombination with growth phase: characterization of a new component in the lambda site-specific recombination pathways. Cell 50:901-908.
57. Ueguchi, C., M. Kakeda, H. Yamada, and T. Mizuno. 1994 An analogue of the DnaJ molecular chaperon in Escherichia coli. Proc. Natl. Acad. Sci. USA 91:1054-1058.
58. Wada, A. 1998. Growth phase coupled modulation of Escherichia coli ribosomes. Genes Cells 3:203-208.
59. Williams, R. M., and S. Rimsky. 1987. Molecular aspects of the E. coli nucleoid protein, H-NS: a central controller of gene regulatory networks. FEMS Microbiol. Lett. 156:175-185.
60. Willins, D. A., C. W. Ryan, J. V. Platko, and J. M. Calvo. 1991. Characterization of Lrp, an Escherichia coli regulatory protein that mediates a global response to leucine. J. Biol. Chem. 266:10768-10774.
61. Yamashino, T., M. Kakeda, C. Ueguchi, and T. Mizuno. 1994. An analogue of the DnaJ molecular chaperone whose expression is controlled by sigma S during the stationary phase and phosphate starvation in Escherichia coli. Mol. Microbiol. 13:475-483.
62. Yasuzawa, K., N. Hayashi, N. Goshima, K. Kohno, F. Imamoto, and Y. Kano. 1992. Histone-like proteins are required for cell growth and restraint of supercoils in DNA. Gene 122:9-14.
63. Zhang, Z., and M. Belfort. 1992. Nucleotide sequence of a newly identified Escherichia coli gene, stpA, encoding an H-NS-like protein. Nucleic Acids Res. 20:6734.