Coordinated regulation of gene expression by E ... - Jacobs University

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REFERENCES 6 References Ali Azam, T., Iwata, A., Nishimura, A., Ueda, S., and Ishihama, A. (1999) Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid. J Bacteriol 181: 6361-6370. Auner, H., Buckle, M., Deufel, A., Kutateladze, T., Lazarus, L., Mavathur, R., Muskhelishvili, G., Pemberton, I., Schneider, R., and Travers, A. (2003) Mechanism of transcriptional activation by FIS: role of core promoter structure and DNA topology. J Mol Biol 331: 331-344. Azam, T.A., and Ishihama, A. (1999) Twelve species of the nucleoid-associated protein from Escherichia coli. Sequence recognition specificity and DNA binding affinity. J Biol Chem 274: 33105-33113. Balke, V.L., and Gralla, J.D. (1987) Changes in the linking number of supercoiled DNA accompany growth transitions in Escherichia coli. J Bacteriol 169: 4499-4506. Ball, C.A., Osuna, R., Ferguson, K.C., and Johnson, R.C. (1992) Dramatic changes in Fis levels upon nutrient upshift in Escherichia coli. J Bacteriol 174: 8043-8056. Bartlett, M.S., Gaal, T., Ross, W., and Gourse, R.L. (2000) Regulation of rRNA transcription is remarkably robust: FIS compensates for altered nucleoside triphosphate sensing by mutant RNA polymerases at Escherichia coli rrn P1 promoters. J Bacteriol 182: 1969-1977. Blot, N., Mavathur, R., Geertz, M., Travers, A., and Muskhelishvili, G. (2006) Homeostatic regulation of supercoiling sensitivity coordinates transcription of the bacterial genome. EMBO Rep 7: 710-715. Bokal, A.J.t., Ross, W., and Gourse, R.L. (1995) The transcriptional activator protein FIS: DNA interactions and cooperative interactions with RNA polymerase at the Escherichia coli rrnB P1 promoter. J Mol Biol 245: 197-207. 69
REFERENCES Bordes, P., Conter, A., Morales, V., Bouvier, J., Kolb, A., and Gutierrez, C. (2003) DNA supercoiling contributes to disconnect sigmaS accumulation from sigmaSdependent transcription in Escherichia coli. Mol Microbiol 48: 561-571. Bowater, R.P., Chen, D., and Lilley, D.M. (1994) Modulation of tyrT promoter activity by template supercoiling in vivo. Embo J 13: 5647-5655. Browning, D.F., and Busby, S.J. (2004) The regulation of bacterial transcription initiation. Nat Rev Microbiol 2: 57-65. Burgess, R.R. (1969) Separation and characterization of the subunits of ribonucleic acid polymerase. J Biol Chem 244: 6168-6176. Cheung, K.J., Badarinarayana, V., Selinger, D.W., Janse, D., and Church, G.M. (2003) A microarray-based antibiotic screen identifies a regulatory role for supercoiling in the osmotic stress response of Escherichia coli. Genome Res 13: 206-215. Crozat, E., Philippe, N., Lenski, R.E., Geiselmann, J., and Schneider, D. (2005) Longterm experimental evolution in Escherichia coli. XII. DNA topology as a key target of selection. Genetics 169: 523-532. Dame, R.T., Wyman, C., and Goosen, N. (2001) Structural basis for preferential binding of H-NS to curved DNA. Biochimie 83: 231-234. Dame, R.T. (2005) The role of nucleoid-associated proteins in the organization and compaction of bacterial chromatin. Mol Microbiol 56: 858-870. Deng, S., Stein, R.A., and Higgins, N.P. (2005) Organization of supercoil domains and their reorganization by transcription. Mol Microbiol 57: 1511-1521. DiNardo, S., Voelkel, K.A., Sternglanz, R., Reynolds, A.E., and Wright, A. (1982) Escherichia coli DNA topoisomerase I mutants have compensatory mutations in DNA gyrase genes. Cell 31: 43-51. Dorman, C.J. (1996) Flexible response: DNA supercoiling, transcription and bacterial adaptation to environmental stress. Trends Microbiol 4: 214-216. Dorman, C.J., and Deighan, P. (2003) Regulation of gene expression by histone-like proteins in bacteria. Curr Opin Genet Dev 13: 179-184. 70
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Coordinated regulation of gene expr
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Parts of this work has been publish
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ABSTRACT promoter region determines
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ACKNOWLEDGEMENTS first impression o
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TABLE OF CONTENTS 2.2.5 Preparation
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LIST OF TABLES List of tables Table
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LIST OF FIGURES List of Figures Fig
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ABBREVIATIONS Abbreviations ∆61
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ABBREVIATIONS TBE Tris TS tyrT35U t
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INTRODUCTION Salmonella: “In more
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INTRODUCTION Figure 1: Schematic il
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INTRODUCTION UP element -35 -10 Spa
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INTRODUCTION can also influence elo
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INTRODUCTION have more base-pairs t
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INTRODUCTION Figure 6: Graphical re
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INTRODUCTION shown that H-NS reache
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INTRODUCTION formed as a repercussi
Page 35 and 36: MATERIALS AND METHODS 2 Materials a
Page 37 and 38: MATERIALS AND METHODS NaCl 10 gm YT
Page 39 and 40: MATERIALS AND METHODS LZ41 3 pyrF28
Page 41 and 42: MATERIALS AND METHODS 2.2 Methods 2
Page 43 and 44: MATERIALS AND METHODS given using a
Page 45 and 46: MATERIALS AND METHODS phenol: chlor
Page 47 and 48: MATERIALS AND METHODS Filtered (by
Page 49 and 50: MATERIALS AND METHODS free water (A
Page 51 and 52: RESULTS 3 Results Growth phase-depe
Page 53 and 54: RESULTS Neither the fis nor the hns
Page 55 and 56: RESULTS these identified genes (by
Page 57 and 58: RESULTS furthermore the colour of t
Page 59 and 60: RESULTS During the entire growth cy
Page 61 and 62: RESULTS transcripts of a growth pha
Page 63 and 64: RESULTS phosphorylation, are associ
Page 65 and 66: RESULTS Table 4: RT-PCR analysis of
Page 67 and 68: RESULTS Figure 16: Schematic repres
Page 69 and 70: RESULTS parC) which allows the supe
Page 71 and 72: RESULTS Figure 19: In vitro transcr
Page 73 and 74: RESULTS contrast the tyrTD promoter
Page 75 and 76: DISCUSSION 4 Discussion The idea of
Page 77 and 78: DISCUSSION In a study by Balke & Gr
Page 79 and 80: DISCUSSION cells maintain viability
Page 81 and 82: DISCUSSION writhe in the UAS by FIS
Page 83 and 84: DISCUSSION 4.3.2 Mechanism of trans
Page 85: CONCLUSION 5 Conclusion Regulation
Page 89 and 90: REFERENCES Gruber, T.M., and Gross,
Page 91 and 92: REFERENCES molecular basis for sele
Page 93 and 94: REFERENCES Pan, C.Q., Finkel, S.E.,
Page 95 and 96: REFERENCES Schroder, O., and Wagner
Page 97 and 98: REFERENCES Willenbrock, H., and Uss
Page 99 and 100: APPENDIX I gene blattner ratio p-va
Page 127 and 128: APPENDIX I Supplementary table - VI
Page 129 and 130: APPENDIX I fabB b2323 0.6336 0.0043
Page 131 and 132: APPENDIX I ibpA b3687 2.4960 0.0181
Page 133 and 134: APPENDIX I pepP b2908 1.2182 0.0368
Page 135 and 136: APPENDIX I speG b1584 0.4151 0.0001
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APPENDIX I ycjX b1321 4.0841 0.0141
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APPENDIX I yhfY b3382 1.4063 0.0453
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APPENDIX I gene blattner ratio p-va
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APPENDIX I gene blattner ratio A/B
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Statement of sources Declaration I
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