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

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TABLE OF CONTENTS 3.2.2 In vivo expression of tyrT in CSH50 Wt & fis mutant ………………. 50 3.2.3 Dependence of promoter activity on superhelical density in vivo …… 51 3.2.4 Dependence of promoter activity on superhelical density in vitro …... 53 3.2.5 Effects of promoter mutations on the function ………………………. 54 4 Discussion …………………………………………………………………… 58 4.1 Interdependency of supercoiling and NAPs …………………………. 59 4.2 Supercoiling coordinates metabolic functions ……………………….. 61 4.3 Activity of tyrT promoter - Interaction of supercoiling and FIS at the promoter level …………………………………………………………. 63 4.3.1 Promoter structure and function ……………………………………… 64 4.3.2 Mechanism of transcriptional activation of the tyrT promoter ………. 66 5 Conclusion …………………………………………………………………… 68 6 References ……………………………………………………………………. 69 7 Appendix I - Supplementary data: Gene lists from microarray experiments. .. 81 III
LIST OF TABLES List of tables Table 1 Bacterial strains used …………………………………………. 21 Table 2 Table 3 Table 4 Number of single and double-coded transcripts in fis and hns transcript profiles ……………………………………………… 43 Supercoiling sensitivity of genes of biosynthesis and degradation pathways ..………………………………………………………. 45 RT-PCR analysis of some of the genes from TCA cycle and purine biosynthesis ..……………………………………………………. 48 Supplementary table I Supplementary table II Supplementary table III Supplementary table IV Supplementary table V Supplementary table VI CSH50 wild-type Vs CSH50 ∆fis, Midexponential phase ….……………………….. 81 CSH50 wild-type Vs CSH50 ∆fis, Transition to stationary phase ...……………………….. 89 CSH50 wild-type Vs CSH50 ∆fis, Late stationary phase ………………………………………. 92 CSH50 wild-type Vs CSH50 ∆hns, Midexponential phase …………………….. 97 CSH50 wild-type Vs CSH50 ∆hns, Transition to stationary phase ………………....………….. 104 CSH50 wild-type Vs CSH50 ∆hns, Late stationary phase …………………………….. 107 Supplementary table VII : LZ41 wild-type Vs LZ54 wild-type .……….. 110 Supplementary table VIII LZ41 ∆fis Vs LZ54 ∆fis ……...…………….. 123 Supplementary table IX LZ41 ∆hns Vs LZ54 ∆hns ..…………............ 136 Supplementary table X LZ41 wild-type Vs LZ41 ∆fis …..…………. 150 IV
Page 1 and 2: Coordinated regulation of gene expr
Page 3 and 4: Parts of this work has been publish
Page 5 and 6: ABSTRACT promoter region determines
Page 7 and 8: ACKNOWLEDGEMENTS first impression o
Page 9: TABLE OF CONTENTS 2.2.5 Preparation
Page 13 and 14: LIST OF FIGURES List of Figures Fig
Page 15 and 16: ABBREVIATIONS Abbreviations ∆61
Page 17 and 18: ABBREVIATIONS TBE Tris TS tyrT35U t
Page 19 and 20: INTRODUCTION Salmonella: “In more
Page 21 and 22: INTRODUCTION Figure 1: Schematic il
Page 23 and 24: INTRODUCTION UP element -35 -10 Spa
Page 25 and 26: INTRODUCTION can also influence elo
Page 27 and 28: INTRODUCTION have more base-pairs t
Page 29 and 30: INTRODUCTION Figure 6: Graphical re
Page 31 and 32: INTRODUCTION shown that H-NS reache
Page 33 and 34: 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
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RESULTS transcripts of a growth pha
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RESULTS phosphorylation, are associ
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RESULTS Table 4: RT-PCR analysis of
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RESULTS Figure 16: Schematic repres
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RESULTS parC) which allows the supe
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RESULTS Figure 19: In vitro transcr
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RESULTS contrast the tyrTD promoter
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DISCUSSION 4 Discussion The idea of
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DISCUSSION In a study by Balke & Gr
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DISCUSSION cells maintain viability
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DISCUSSION writhe in the UAS by FIS
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DISCUSSION 4.3.2 Mechanism of trans
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CONCLUSION 5 Conclusion Regulation
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REFERENCES Bordes, P., Conter, A.,
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REFERENCES Gruber, T.M., and Gross,
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REFERENCES molecular basis for sele
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REFERENCES Pan, C.Q., Finkel, S.E.,
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REFERENCES Schroder, O., and Wagner
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REFERENCES Willenbrock, H., and Uss
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APPENDIX I gene blattner ratio p-va
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APPENDIX I Supplementary table - VI
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APPENDIX I fabB b2323 0.6336 0.0043
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APPENDIX I ibpA b3687 2.4960 0.0181
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APPENDIX I pepP b2908 1.2182 0.0368
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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 A/B
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Statement of sources Declaration I
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