Extensive regulation compromises the extent to which DNA gyrase controls dna supercoiling and growth rate of Escherichia coli

European Journal of Biochemistry

Volumn 266, Issue 3, 1999, Pages 865-877

  Jensen, Peter Ruhdal ^a   Van Der Weijden, Coen C ^b   Jensen, Lars Bogø ^a   Westerhoff, Hans V ^b   Snoep, Jacky L ^b  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^b VU UNIVERSITY AMSTERDAM   (Netherlands)

Author keywords

galactosidase; Gene expression; Homeostatic control; Lac promoter; Metabolic control analysis; Topoisomerases

Indexed keywords

BETA GALACTOSIDASE; DNA TOPOISOMERASE; DNA TOPOISOMERASE (ATP HYDROLYSING);

ARTICLE; BACTERIAL GROWTH; DNA SUPERCOILING; ENZYME ACTIVITY; ESCHERICHIA COLI; GENE EXPRESSION; METABOLIC REGULATION; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; TRANSCRIPTION REGULATION;

ADENOSINE DIPHOSPHATE; ADENOSINE TRIPHOSPHATE; DNA TOPOISOMERASES, TYPE II; DNA, BACTERIAL; DNA, SUPERHELICAL; ESCHERICHIA COLI; GENE EXPRESSION; GENES, BACTERIAL; ISOPROPYL THIOGALACTOSIDE; MODELS, BIOLOGICAL; PROMOTER REGIONS (GENETICS);

EID: 0033572810     PISSN: 00142956     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1432-1327.1999.00921.x     Document Type: Article

References (55)

1. 1. Drlica, K. (1984) Biology of bacterial deoxyribonucleic acid topoisomerases. Microbiol. Rev. 48, 273-289.
2. 2. Goldstein, E. & Drlica, K. (1984) Regulation of baeterial DNA supercoiling: plasmid linking numbers vary with growth temperature. Proc. Natl Acad. Sci. USA 81, 4046-4050.
3. 3. Mizushima, T., Kataoka, K., Ogata, Y., Inoue, R.I. & Sekimizu, K. (1997) Increase in negative supercoiling of plasmid DNA in Escherichia coli exposed to cold shock. Mol. Microbiol. 23, 381-386.
4. 4. Higgins, C.F., Dorman, C.J., Stirling, D.A., Waddell, L., Booth, I.R., May, G. & Bremer, E. (1988) A physiological role for DNA supercoiling in the osmotic regulation of gene expression in S. typhimurium and E. coli. Cell 52, 569-584.
5. 5. Karem, K. & Foster, J.W. (1993) The influence of DNA topology on the environmental regulation of a pH-regulated locus in Salmonella typhimurium. Mol. Microbiol. 10, 75-86.
6. 6. Balke, V.L. & Gralla, J.D. (1987) Changes in the linking number of supercoiled DNA accompany growth transitions in Escherichia coli. J. Bacteriol. 169, 4499-4506.
7. 7. Jensen, P.R., Loman, L., Petra, B., van der Weijden, C. & Westerhoff, H.V. (1995) Energy buffering of DNA structure fails when Escherichia coli runs out of substrate. J. Bacteriol. 177, 3420-3426.
8. 8. Yamamoto, N. & Droffner, ML. (1985) Mechanisms determining aerobic or anaerobic growth in the facultative anaerobe Salmonella typhimurium. Proc. Natl Acad. Sci. USA 82, 2077-2081.
9. 9. Dorman, C.J., Barr, G.C., Bhriain, N.N. & Higgins, C.F. (1988) DNA supercoiling and the anaerobic and growth phase regulation of tonB gene expression. J. Bacteriol. 170, 2816-2826.
10. 10. Smith, G.R. (1981) DNA supercoiling: another level for regulating gene expression. Cell 24, 599-600.
11. 11. Jovanovich, S.B. & Lebowitz, J. (1987) Estimation of the effect of coumermycin A1 on Salmonella typhimurium promoters by using random operon fusions. J. Bacteriol. 169, 4431-4435.
12. 12. Tan, J., Shu, L. & Wu, H.Y. (1994) Activation of the Leu-500 promoter by adjacent transcription. J. Bacteriol. 176. pp. 1077-1086.
13. 13. Pruss, G.J. & Drlica, K. (1989) DNA supercoiling and prokaryotic transcription. Cell 56, 521-523.
14. 14. Gellert, M. (1981) DNA topoisomerases. Annu. Rev. Biochem. 50, 879-910.
15. 15. Liu, L.F. & Wang, J.C. (1987) Supercoiling of the DNA template during transcription, Proc. Natl Acad. Sci. USA 84, 7024-7027.
16. 16. Westerhoff, H.V., O'Dea, M.H., Maxwell, A. & Gellert, M. (1988) DNA supercoiling by DNA gyrase. A static head analysis. Cell Biophys. 12, 157-181.
17. 17. Pruss, G.J., Manes, S.H. & Drlica, K. (1982) Escherichia coli DNA topoisomerase I mutants: increased supercoiling is corrected by mutations near gyrase genes. Cell 31, 35-42.
18. 18. Hsieh, L.-S., Rouviere-Yaniv, J. & Drlica, K. (1991) Bacterial DNA supercoiling and [ATP]/[ADP] ratio: changes associated with salt shock. J. Bacteriol. 173, 3914-3917.
19. 19. Hsieh, L.S., Burger, R.M. & Drlica, K. (1991) Bacterial DNA supercoiling and (ATP)-(ADP): Changes associated with a transition to anaerobic growth. J. Mol. Biol. 219, 443-450.
20. 20. Van Workum, M., Van Dooren, S., Oldenburg, N., Molenaar, D., Jensen, P., Snoep, J. & Westerhoff, H. (1996) DNA supercoiling depends on the phosphorylation potential in Escherichia coli. Mol. Microbiol. 20, 351-360.
21. 21. Menzel, R. & Gellert, M. (1983) Regulation of the genes for E. coli DNA gyrase: homeostatic control of DNA supercoiling. Cell 34, 105-113.
22. 22. Tse-dinh, Y.C. (1985) Regulation of Escherichia coli DNA topoisomerase I gene by DNA supercoiling. Nucleic Acids Res. 13, 4751-4763.
23. 23. Malik, M., Bensaid, A., Rouviere-Yaniv, J. & Drlica, K. (1996) Histone-like protein HU and bacterial DNA topology: suppression of an HU deficiency by gyrase mutations. J. Mol. Biol. 256, 66-76.
24. 24. Nakanishi, A., Oshida, T., Matsushita, T., Imajoh-Ohmi, S. & Ohnuki, T. (1998) Identification of DNA gyrase inhibitor (GyrI) in Escherichia coli. J. Biol. Chem. 273, 1933-1938.
25. 25. Groen, A.K., Wanders, R.J.A., Westerhoff, H.V., van der Meer, R. & Tager, J.M. (1982) Quantification of the contribution of various steps to the control of mitochondrial respiration. J. Biol. Chem. 257, 2754-2757.
26. 26. Kacser, H. & Burns, J.A. (1973) The control of flux. In Rate Control of Biological Processes (Davies, D.D., ed.), pp. 65-104. Cambridge University Press, London.
27. 27. Heinrich, R. & Rapoport, T.A. (1974) A linear steady-state treatment of enzymatic chains. General properties, control and effector strength. Eur. J. Biochem. 42, 89-95.
28. 28. Drlica, K. & Snyder, M. (1978) Superhelical Escherichia coli DNA: relaxation by coumermycin. J. Mol. Biol. 120, 145-154.
29. 29. Westerhoff, H.V. & Van Workum, M. (1990) Control of DNA structure and gene expression. Biomed. Biochim. Acta 49, 839-853.
30. 30. Wijker, J.E., Jensen, P.R., Snoep. J.L., Vaz Gomez, A., Guiral, M., Jongsma, A.P.M., De Waal, A., Hoving, S., Van Dooren, S., Van der Weijden, C.C., Van Workum, M., Van Heeswijk, W.C., Molenaar, D., Wielinga, P., Richard, P., Diderich, J., Bakker, B.M., Teusink, B., Hemker, M., Rohwer, J.M., Van der Gugten, A.A., Kholodenko, B.N. & Westerhoff, H.V. (1995) Energy, control and DNA structure in the living cell. Biophys. Chem. 55, 153-165.
31. 31. Yanish-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, 103-109.
32. 32. Woodcock, D.M., Crowther, P.J., Doherty, J., Jefferson, S., DeCruz., E., Noyer-Weidner, M., Smith, S.S., Michael, M.Z. & Graham, M.W. (1989) Quantitative evaluation of Escherichia coli host strains for tolerance to cytosine methylation in plasmid and phage recombinants. Nucleic Acids Res. 17, 3469-3478.
33. 33. Casabadan, M.J. & Cohen, S.N. (1980) Analysis of gene control signals by DNA fusion and cloning in Escherichia coli. J. Mol. Biol. 138, 179-207.
34. 34. Neidhardt, F.C., Bloch, P.L. & Smith, D.F. (1974) Culture medium for Enterobacteria. J. Bacteriol. 119, 736-747.
35. +-ATPase. Proc. Natl Acad. Sci. USA 90, 8068-8072.
36. 36. Youngman, P. (1987) Plasmids: a Practical Approach. IRL Press, Oxford.
37. 37. Miller, J.H. (1992) A Short Course in Bacterial Genetics. Cold Spring Harbour Laboratory Press, Cold Spring Harbour, New York.
38. 38. Lutz, R. & Bujard, H. (1997) Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I-1-1-2 regulatory elements. Nucleic Acids Res. 25, 1203-1210.
39. 39. Chang, A.C.Y. & Cohen, S.N. (1978) Construction and characterization of amplifiable multicopy DNA cloning vehicles derived from the P15A cryptic miniplasmid. J. Bacteriol. 134, 1141-1156.
40. 40. Schneider, K. & Beck, C.F. (1986) Promoter-probe vectors for the analysis of divergently arranged promoters. Gene 42, 37-48.
41. 41. Westerhoff, H.V. & Van Dam, K. (1987) Thermodynamics and Control of Biological Free Energy Transduction. Elsevier, Amsterdam.
42. 42. Westerhoff, H.V., Koster, J.G., Van Workum, M. & Rudd, K.E. (1990) On the control of gene expression. In Control of Metabolic Processes (Cornish-Bowden, A., ed.), pp. 399-412. Plenum Press, New York.
43. 43. Westerhoff, H.V, Jensen, PR., Snoep, J.L. & Kholodenko, B.N. (1998) Thermodynamics of complexity - the live cell. Thermochim. Acta 309, 111-120.
44. 44. Menzel, R. & Gellert, M. (1987) Fusions of the Escherichia coli gyrA and gyrB control regions to the galactokinase gene are inducible by coumermycin treatment. J. Bacteriol. 169, 1272-1278.
45. 45. Ruijter, G.J.G., Postma, P.W. & Van Dam, K. (1991) Control of glucose metabolism by enzyme IIGlc of the phosphoenolpyruvate-dependent phosphotranferase system in Escherichia coli. J. Bacteriol. 173, 6184-6191.
46. 46. Van der Vlag, J., Van't Hof, R., Van Dam, K. & Postma, P.W. (1995) Control of glucose metabolism by the enzymes of the glucose transferase system in Salmonella typhimurium. Eur. J. Biochem. 230, 170-182.
47. +-ATPase and inverse respiratory control in Escherichia coli. EMBO J. 12, 1277-1282.
48. 48. Van Heeswijk, W.C., Hoving, S., Molenaar, D., Stegernan, B., Kahn, D. & Westerhoff, H.V. (1996) An alternative P-II protein in the regulation of glutamine synthetase in Escherichia coli. Mol. Microbiol. 21, 133-146.
49. 49. Van Heeswijk, W.C. (1998) The glutamine synthetase adenylylation cascade. PhD thesis, The University of Amsterdam, Amsterdam.
50. 50. Jensen, P.R. & Michelsen, O. (1992) Carbon and energy metabolism of atp mutants of Escherichia coli. J. Bacteriol. 174, 7635-7641.
51. 51. Oliver, S.G. (1996) From DNA sequence to biological function. Nature 379, 597-600.
52. 52. Drlica, K., Pruss, G.J., Manes, S.H. & Chevalier, S.G. (1986) DNA topoisomerase mutations in bacteria. In Bacterial Chromatin (Gualerzi, C.O. & Pon, C.L., eds). pp. 52-63. Springer-Verlag, Heidelberg.
53. 53. Moreno-Sanchez, R. (1985) Contribution of the translocator of adenine nucleotides and the ATP synthase to the control of oxidative phosphorylation and arsenylation in liver mitochondria. J. Biol. Chem. 260, 12554-12560.
54. 54. Fell, D. A. (1992) Metabolic control analysis: a survey of its theoretical and experimental development. Biochem. J. 286, 313-330.
55. 55. Steck, T.R., Franco, R.J., Wang, J.Y. & Drlica, K. (1993) Topoisomerase mutations affect the relative abundance of many Escherichia coli proteins. Mol. Microbiol. 10, 473-481.