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

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RESULTS Figure 13: Genomic wheels showing spatiotemporal distribution of supercoiling associated transcripts. Rel (red), Hyp (blue), Act (green) and Rep (yellow) transcripts among the growth-phase-dependent genes (grey) in CSH50 wild-type (outer wheels) and fis (A) or hns (B) (inner wheels). ME- mid-exponential phase; TS-transition phase; LS-late stationary phase; Ori-origin of replication; Ter-terminus of replication. 41
RESULTS During the entire growth cycle, 820 genes were found to be regulated by fis and 611 by hns. From the former, 371 genes were activated (up-regulated in the wildtype background) and 475 repressed (up-regulated in the mutant background) by fis. The corresponding numbers for hns are 292 activated and 327 repressed genes. From experiment 1 of set B, 1,596 genes were identified to be associated with supercoiling (either hypernegative or relaxed DNA), exceeding by five times the number identified previously [Peter et al., 2004]. Out of 1,596 Hyp and Rel transcripts identified, only 145 were common to wild-type, fis and hns backgrounds indicating that the supercoiling response depends on genetic context and explaining the expanded repertoire of supercoiling sensitive genes identified. The growth phase dependent genes were then mapped on the supercoiling associated genes (see Figure 11). Among all the growth phase dependent genes, 397 out of 820 (fis experiment) and 329 out of 611 (hns experiment) were found by mapping to be associated with either Rel or Hyp condition. The dependence of supercoiling response on genetic context and high proportion (almost 50%) of supercoiling sensitive genes in each genetic background indicate that regulation involves a cross talk between the chromatin proteins and supercoiling, wherein both change in an interdependent manner. 3.1.5 Variations of supercoiling-associated transcripts The growth phase dependent genes were further analyzed based on their distribution in four classes of supercoiling associated genes. Out of total of 302 unique genes upregulated from all the 3 growth phases in hns mutant, 210 could be mapped as supercoiling associated genes. From the table 2 we can see that, among these 70% (148 genes) were associated with the Rep group, while the corresponding number in fis mutant is 39% only (94 out of total 239 mapped). The wild-type strain compared to fis had similar proportion of Act & Rep genes while the fis mutant from the same experiment had approximately three times more Rep than Act genes. In the hns experiment the distribution of growth phase dependent genes is different compared to 42
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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
Page 7 and 8: ACKNOWLEDGEMENTS first impression o
Page 9 and 10: 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: RESULTS furthermore the colour of t
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 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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