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

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REFERENCES Dorman, C.J. (2004) H-NS: a universal regulator for a dynamic genome. Nat Rev Microbiol 2: 391-400. Drew, H.R., Weeks, J.R., and Travers, A.A. (1985) Negative supercoiling induces spontaneous unwinding of a bacterial promoter. Embo J 4: 1025-1032. Drlica, K. (1992) Control of bacterial DNA supercoiling. Mol Microbiol 6: 425-433. Dunaway, M., and Ostrander, E.A. (1993) Local domains of supercoiling activate a eukaryotic promoter in vivo. Nature 361: 746-748. Figueroa-Bossi, N., Guerin, M., Rahmouni, R., Leng, M., and Bossi, L. (1998) The supercoiling sensitivity of a bacterial tRNA promoter parallels its responsiveness to stringent control. Embo J 17: 2359-2367. Free, A., and Dorman, C.J. (1994) Escherichia coli tyrT gene transcription is sensitive to DNA supercoiling in its native chromosomal context: effect of DNA topoisomerase IV overexpression on tyrT promoter function. Mol Microbiol 14: 151-161. Gamper, H.B., and Hearst, J.E. (1982) A topological model for transcription based on unwinding angle analysis of E. coli RNA polymerase binary, initiation and ternary complexes. Cell 29: 81-90. Geertz, M., Mavathur, R., Travers, A., Muskhelishvili, G. (2007) RNA polymerase composition is homeostatically coupled with DNA topology in E. coli. Submitted to EMBO reports. Gille, H., Egan, J.B., Roth, A. and Messer, W. (1991) The FIS protein binds and bends the origin of chromosomal DNA replication, oriC, of Escherichia coli. Nucleic Acids Res, 19, 4167-4172. Gomez-Eichelmann, M.C., and Camacho-Carranza, R. (1995) [DNA supercoiling and topoisomerases in Escherichia coli]. Rev Latinoam Microbiol 37: 291-304. Gralla, J.D., Hsieh, M. & Wong, C. (1993) Permanganate probing. In Footprinting Techniques for Studying Nucleic Acid-Protein complexes (Revzin, A., ed.) pp.107-128, Academic Press, Orlando, FL. 71
REFERENCES Gruber, T.M., and Gross, C.A. (2003) Multiple sigma subunits and the partitioning of bacterial transcription space. Annu Rev Microbiol 57: 441-466. Guest, J.R., and Russell, G.C. (1992) Complexes and complexities of the citric acid cycle in Escherichia coli. Curr Top Cell Regul 33: 231-247. Hardy, C.D., and Cozzarelli, N.R. (2005) A genetic selection for supercoiling mutants of Escherichia coli reveals proteins implicated in chromosome structure. Mol Microbiol 57: 1636-1652. Hatfield, G.W., and Benham, C.J. (2002) DNA topology-mediated control of global gene expression in Escherichia coli. Annu Rev Genet 36: 175-203. Heinemann, M., and Wagner, R. (1997) Guanosine 3',5'-bis(diphosphate) (ppGpp)- dependent inhibition of transcription from stringently controlled Escherichia coli promoters can be explained by an altered initiation pathway that traps RNA polymerase. Eur J Biochem 247: 990-999. Helling, R.B., and Kukora, J.S. (1971) Nalidixic Acid-Resistant Mutants of Escherichia coli Deficient in Isocitrate Dehydrogenase. J. Bacteriol. 105: 1224-1226. Hengge-Aronis, R. (2002) Recent insights into the general stress response regulatory network in Escherichia coli. J Mol Microbiol Biotechnol 4: 341-346. Hiasa, H., and Marians, K.J. (1994) Topoisomerase III, but not topoisomerase I, can support nascent chain elongation during theta-type DNA replication. J Biol Chem 269: 32655-32659. Ishihama, A. (1999) Modulation of the nucleoid, the transcription apparatus, and the translation machinery in bacteria for stationary phase survival. Genes Cells 4: 135-143. Ishihama, A. (2000) Functional modulation of Escherichia coli RNA polymerase. Annu Rev Microbiol 54: 499-518. Iuchi, S., and Lin, E.C. (1988) arcA (dye), a global regulatory gene in Escherichia coli mediating repression of enzymes in aerobic pathways. Proc Natl Acad Sci U S A 85: 1888-1892. 72
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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
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 and 86: CONCLUSION 5 Conclusion Regulation
Page 87: REFERENCES Bordes, P., Conter, A.,
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
Page 137 and 138: 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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