REFERENCES Rochman, M., Aviv, M., Glaser, G., and Muskhelishvili, G. (2002) Promoter protection <strong>by</strong> a transcription factor acting as a local topological homeostat. EMBO Rep 3: 355-360. Ryals, J., Little, R., and Bremer, H. (1982) Control <strong>of</strong> rRNA and tRNA syntheses in Escherichia coli <strong>by</strong> guanosine tetraphosphate. J Bacteriol 151: 1261-1268. Sadler, J.R., and Novick, A. (1965) The Properties <strong>of</strong> Repressor and the Kinetics <strong>of</strong> Its Action. J Mol Biol 12: 305-327. Saeed, A.I., Sharov, V., White, J., Li, J., Liang, W., Bhagabati, N., Braisted, J., Klapa, M., Currier, T., Thiagarajan, M., Sturn, A., Snuffin, M., Rezantsev, A., Popov, D., Ryltsov, A., Kostukovich, E., Borisovsky, I., Liu, Z., Vinsavich, A., Trush, V., and Quackenbush, J. (2003) TM4: a free, open-source system for microarray data management and analysis. Biotechniques 34: 374-378. Sambrook, J. and Russell, D.W. (2001) Molecular cloning : a laboratory manual. Third edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York. Sander, P., Langert, W., and Mueller, K. (1993) Mechanisms <strong>of</strong> upstream activation <strong>of</strong> the rrnD promoter P1 <strong>of</strong> Escherichia coli. J Biol Chem 268: 16907-16916. Schneider, R., Travers, A., and Muskhelishvili, G. (1997) FIS modulates growth phasedependent topological transitions <strong>of</strong> DNA in Escherichia coli. Mol Microbiol 26: 519-530. Schneider, R., Travers, A., Kutateladze, T., and Muskhelishvili, G. (1999) A DNA architectural protein couples cellular physiology and DNA topology in Escherichia coli. Mol Microbiol 34: 953-964. Schneider, R., Travers, A., and Muskhelishvili, G. (2000) The <strong>expression</strong> <strong>of</strong> the Escherichia coli fis <strong>gene</strong> is strongly dependent on the superhelical density <strong>of</strong> DNA. Mol Microbiol 38: 167-175. Schneider, R., Lurz, R., Luder, G., Tolksdorf, C., Travers, A., and Muskhelishvili, G. (2001) An architectural role <strong>of</strong> the Escherichia coli chromatin protein FIS in organising DNA. Nucleic Acids Res 29: 5107-5114. 77
REFERENCES Schroder, O., and Wagner, R. (2000) The bacterial DNA-binding protein H-NS represses ribosomal RNA transcription <strong>by</strong> trapping RNA polymerase in the initiation complex. J Mol Biol 298: 737-748. Sinden, R.R., and Pettijohn, D.E. (1981) Chromosomes in living Escherichia coli cells are segregated into domains <strong>of</strong> supercoiling. Proc Natl Acad Sci U S A 78: 224- 228. Snoep, J.L., van der Weijden, C.C., Andersen, H.W., Westerh<strong>of</strong>f, H.V., and Jensen, P.R. (2002) DNA supercoiling in Escherichia coli is under tight and subtle homeostatic control, involving <strong>gene</strong>-<strong>expression</strong> and metabolic <strong>regulation</strong> <strong>of</strong> both topoisomerase I and DNA gyrase. Eur J Biochem 269: 1662-1669. Staczek, P., and Higgins, N.P. (1998) Gyrase and Topo IV modulate chromosome domain size in vivo. Mol Microbiol 29: 1435-1448. Stein, R.A., Deng, S., and Higgins, N.P. (2005) Measuring chromosome dynamics on different time scales using resolvases with varying half-lives. Mol Microbiol 56: 1049-1061. Tao, H., Bausch, C., Richmond, C., Blattner, F.R., and Conway, T. (1999) Functional genomics: <strong>expression</strong> analysis <strong>of</strong> Escherichia coli growing on minimal and rich media. J Bacteriol 181: 6425-6440. Thanbichler, M., Viollier, P.H., and Shapiro, L. (2005) The structure and function <strong>of</strong> the bacterial chromosome. Curr Opin Genet Dev 15: 153-162. Tippner, D., Afflerbach, H., Bradaczek, C., and Wagner, R. (1994) Evidence for a regulatory function <strong>of</strong> the histone-like Escherichia coli protein H-NS in ribosomal RNA synthesis. Mol Microbiol 11: 589-604. Travers, A.A. (1980) Promoter sequence for stringent control <strong>of</strong> bacterial ribonucleic acid synthesis. J Bacteriol 141: 973-976. Travers, A., and Muskhelishvili, G. (1998) DNA microloops and microdomains: a <strong>gene</strong>ral mechanism for transcription activation <strong>by</strong> torsional transmission. J Mol Biol 279: 1027-1043. 78
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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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- Page 97 and 98: REFERENCES Willenbrock, H., and Uss
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