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

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REFERENCES Travers, A., Schneider, R., and Muskhelishvili, G. (2001) DNA supercoiling and transcription in Escherichia coli: The FIS connection. Biochimie 83: 213-217. Travers, A., and Muskhelishvili, G. (2005) Bacterial chromatin. Curr Opin Genet Dev 15: 507-514. Travers, A., and Muskhelishvili, G. (2005) DNA supercoiling - a global transcriptional regulator for enterobacterial growth? Nat Rev Microbiol 3: 157-169. Travers, A., and Muskhelishvili, G. (2007) A common topology for bacterial and eukaryotic transcription initiation? EMBO Rep 8: 147-151. Tse-Dinh, Y.C. (1985) Regulation of the Escherichia coli DNA topoisomerase I gene by DNA supercoiling. Nucleic Acids Res 13: 4751-4763. Tse-Dinh, Y.C., Qi, H., and Menzel, R. (1997) DNA supercoiling and bacterial adaptation: thermotolerance and thermoresistance. Trends Microbiol 5: 323-326. Ueguchi, C., and Mizuno, T. (1993) The Escherichia coli nucleoid protein H-NS functions directly as a transcriptional repressor. Embo J 12: 1039-1046. Valens, M., Penaud, S., Rossignol, M., Cornet, F., and Boccard, F. (2004) Macrodomain organization of the Escherichia coli chromosome. Embo J 23: 4330- 4341. von Neumann, J., (1958) The Computer and the Brain. New Haven, CT, USA: Yale University Press Weber, H., Polen, T., Heuveling, J., Wendisch, V.F., and Hengge, R. (2005) Genomewide analysis of the general stress response network in Escherichia coli: sigmaSdependent genes, promoters, and sigma factor selectivity. J Bacteriol 187: 1591- 1603. Wei, Y., Lee, J.M., Richmond, C., Blattner, F.R., Rafalski, J.A., and LaRossa, R.A. (2001) High-density microarray-mediated gene expression profiling of Escherichia coli. J Bacteriol 183: 545-556. Weinstein-Fischer, D., and Altuvia, S. (2007) Differential regulation of Escherichia coli topoisomerase I by Fis. Mol Microbiol 63: 1131-1144. 79
REFERENCES Willenbrock, H., and Ussery, D.W. (2004) Chromatin architecture and gene expression in Escherichia coli. Genome Biol 5: 252. Wu, H.Y., Shyy, S.H., Wang, J.C., and Liu, L.F. (1988) Transcription generates positively and negatively supercoiled domains in the template. Cell 53: 433-440. Yanisch-Perron, C., Vieira, J., and Messing, J. (1985) Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene 33: 103-119. Zechiedrich, E.L., Khodursky, A.B., and Cozzarelli, N.R. (1997) Topoisomerase IV, not gyrase, decatenates products of site-specific recombination in Escherichia coli. Genes Dev 11: 2580-2592. Zechiedrich, E.L., Khodursky, A.B., Bachellier, S., Schneider, R., Chen, D., Lilley, D.M., and Cozzarelli, N.R. (2000) Roles of topoisomerases in maintaining steadystate DNA supercoiling in Escherichia coli. J Biol Chem 275: 8103-8113. 80
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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
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MATERIALS AND METHODS 2 Materials a
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MATERIALS AND METHODS NaCl 10 gm YT
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MATERIALS AND METHODS LZ41 3 pyrF28
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MATERIALS AND METHODS 2.2 Methods 2
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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 and 86: CONCLUSION 5 Conclusion Regulation
Page 87 and 88: REFERENCES Bordes, P., Conter, A.,
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: REFERENCES Schroder, O., and Wagner
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
Page 137 and 138: APPENDIX I ycjX b1321 4.0841 0.0141
Page 139 and 140: 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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