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

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RESULTS observations are in excellent agreement with different abundance of FIS and H-NS during the growth cycle and the general repressor role of H-NS [Ball et al., 1992; Dorman, 2004]. 3.1.6 Supercoiling sensitivity of biosynthesis and degradation pathways Interestingly the analysis of the distribution of Hyp and Rel genes among the functional groups involved in essential cellular metabolism demonstrated a substantially higher proportion of Hyp genes in anabolic than in catabolic pathways, which was especially remarkable in wild-type cells (Table 3). It was therefore of interest to investigate some essential metabolic pathways in more detail. Table 3: Supercoiling sensitivity of genes of biosynthesis and degradation pathways. The metabolic pathways comprising 421 genes for biosynthesis and 233 genes from degradation were derived from http://EcoCyc.org. The Hyp to Rel transcript ratios are derived from the data set B for 148, 111 and 134 metabolic genes expressed in the wild-type, fis and hns mutants, respectively. Biosynthesis (Hyp/Rel) Degradation (Hyp/Rel) Wild type 4.29 0.54 fis 2.07 0.87 hns 1.91 1.0 3.1.7 Coordination of metabolic pathways by supercoiling sensitivity Analysis of a pathway of exceptional importance for vitality – the citric acid cycle – demonstrated that the crucial steps producing combustible fuel in the form of reducing equivalents NADH and FADH2, which are required for generation of ATP by oxidative 45
RESULTS phosphorylation, are associated with DNA relaxation. In contrast, the glyoxylate bypass, which is predominantly utilized in aerobically growing cultures where most of the energy is derived by glycolysis is activated by negative superhelicity (Figure 15 A and Table 3). This suggests that high ATP/ADP ratios favouring supercoiling of DNA by gyrase would facilitate glyoxylate bypass and plastic substrate synthesis, whereas DNA relaxation would favour the production of ATP required to maintain gyrase activity. Furthermore we found that the de novo pathway of nucleotide biosynthesis explicitly involves the Hyp genes (Figure 15 B). Purine nucleotides are required during fast growth and the dependence of this pathway on supercoiling levels is in keeping with the prevailing conditions during fast growth. The data presented here thus shows that supercoiling has a role not only in regulation of important individual genes but also in coordinating the activity of metabolic pathways. 46
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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
Page 11 and 12: LIST OF TABLES List of tables Table
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
Page 61: RESULTS transcripts of a growth pha
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 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
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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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