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

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REFERENCES Murray, K.D., and Bremer, H. (1996) Control of spoT-dependent ppGpp synthesis and degradation in Escherichia coli. J Mol Biol 259: 41-57. Muskhelishvili, G., Travers, A.A., Heumann, H., and Kahmann, R. (1995) FIS and RNA polymerase holoenzyme form a specific nucleoprotein complex at a stable RNA promoter. Embo J 14: 1446-1452. Muskhelishvili, G., Buckle, M., Heumann, H., Kahmann, R., and Travers, A.A. (1997) FIS activates sequential steps during transcription initiation at a stable RNA promoter. Embo J 16: 3655-3665. Muskhelishvili, G., and Travers, A. (2003) Transcription factor as a topological homeostat. Front Biosci 8: d279-285. Nachaliel, N., Melnick, J., Gafny, R. and Glaser, G. (1989) Ribosome associated protein(s) specifically bind(s) to the upstream activator sequence of the E. coli rrnA P1 promoter. Nucl. Acids Res., 17, 9811-9822. Nasser, W., Schneider, R., Travers, A., and Muskhelishvili, G. (2001) CRP modulates fis transcription by alternate formation of activating and repressing nucleoprotein complexes. J Biol Chem 276: 17878-17886. Neidhardt, F.C. et al. (1987) Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology Vol. 2. American Society for Microbiology. Nygaard, P., Duckert, P., and Saxild, H.H. (1996) Role of adenine deaminase in purine salvage and nitrogen metabolism and characterization of the ade gene in Bacillus subtilis. J Bacteriol 178: 846-853. Nystrom, T. (2004) Stationary-phase physiology. Annu Rev Microbiol 58: 161-181. Ohlsen, K.L., and Gralla, J.D. (1992) DNA melting within stable closed complexes at the Escherichia coli rrnB P1 promoter. J Biol Chem 267: 19813-19818. Ozoline, O.N., Deev, A.A., and Trifonov, E.N. (1999) DNA bendability--a novel feature in E. coli promoter recognition. J Biomol Struct Dyn 16: 825-831. 75
REFERENCES Pan, C.Q., Finkel, S.E., Cramton, S.E., Feng, J.A., Sigman, D.S., and Johnson, R.C. (1996) Variable structures of Fis-DNA complexes determined by flanking DNAprotein contacts. J Mol Biol 264: 675-695. Pan, W. (2002) A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments. Bioinformatics 18: 546-554. Pedersen, A.G., Jensen, L.J., Brunak, S., Staerfeldt, H.H., and Ussery, D.W. (2000) A DNA structural atlas for Escherichia coli. J Mol Biol 299: 907-930. Pemberton, I.K., Muskhelishvili, G., Travers, A.A., and Buckle, M. (2000) The G+Crich discriminator region of the tyrT promoter antagonises the formation of stable preinitiation complexes. J Mol Biol 299: 859-864. Pemberton, I.K., Muskhelishvili, G., Travers, A.A., and Buckle, M. (2002) FIS modulates the kinetics of successive interactions of RNA polymerase with the core and upstream regions of the tyrT promoter. J Mol Biol 318: 651-663. Perez-Martin, J., and de Lorenzo, V. (1997) Clues and consequences of DNA bending in transcription. Annu Rev Microbiol 51: 593-628. Peter, B.J., Arsuaga, J., Breier, A.M., Khodursky, A.B., Brown, P.O., and Cozzarelli, N.R. (2004) Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli. Genome Biol 5: R87. Pontiggia, A., Negri, A., Beltrame, M., and Bianchi, M.E. (1993) Protein HU binds specifically to kinked DNA. Mol Microbiol 7: 343-350. Postow, L., Hardy, C.D., Arsuaga, J., and Cozzarelli, N.R. (2004) Topological domain structure of the Escherichia coli chromosome. Genes Dev 18: 1766-1779. Pruss, G.J., Manes, S.H., and Drlica, K. (1982) Escherichia coli DNA topoisomerase I mutants: increased supercoiling is corrected by mutations near gyrase genes. Cell 31: 35-42. Rimsky, S., Zuber, F., Buckle, M., and Buc, H. (2001) A molecular mechanism for the repression of transcription by the H-NS protein. Mol Microbiol 42: 1311-1323. 76
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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
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 and 88: REFERENCES Bordes, P., Conter, A.,
Page 89 and 90: REFERENCES Gruber, T.M., and Gross,
Page 91: REFERENCES molecular basis for sele
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
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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