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

More documents

Recommendations

Info

INTRODUCTION binding proteins) DNA supercoils and thus, on the composition of DNA-constraining nucleoid proteins (also termed Nucleoid Associated Proteins, NAPs). This composition substantially changes with the growth phase and affects the availability of gene promoters [Ali Azam et al., and Ishihama et al., 1999; McLeod et al., 2001]. Some of the nucleoid-associated proteins modulate the activities of cellular topoisomerases and can therefore also exert indirect effects on the growth phase-dependent gene transcription [Dorman et al., 2003; Muskhelishvili and Travers, 2003; Browning et al., 2004]. Alterations of global DNA topology are known to strongly affect the transcription initiation [Travers et al., 2001; Hatfield et al., 2002]. Experimentally induced changes of global DNA superhelicity in E.coli revealed that at least 300 genes are explicitly sensitive to these changes [Peter et al., 2004]. The alterations of global DNA superhelicity have been observed both during growth phase transitions and also in response to environmental challenges, thus implicating DNA supercoiling in coordination of gene expression with physiological demands [Balke and Gralla, 1987; Dorman et al., 1996; Tse-Dinh et al., 1997; Cheung et al., 2003; Travers and Muskhelishvili, 2005b]. Another switch of the growth phase-dependent gene expression pattern is accomplished by the growth phase-dependent modulation of RNAP by increased concentration of “stringent factor” ppGpp (guanosine-3',5'- (bis)pyrophosphate) and the competition between initiation sigma (σ) subunits, which confer different promoter specificities on the RNAP holoenzyme [Heinemann et al., 1997; Ishihama, 1999 and 2000]. Recently it was also proposed that the composition of the RNAP core is also subject to growth related changes [Geertz et al., 2007] 1.1.1 Is there a common coordinating mechanism? Almost five decades ago, John von Neumann proposed that the flow of genetic information is coordinated by an alternation between the ‘digital’ (discontinuous) properties of unique genes and ‘analog’ (continuous) properties of the gene products [von Neumann, 1958]. 3
INTRODUCTION Figure 1: Schematic illustration of operation of the genetic system involving an alternation of the digital (discontinuous) and analog (continuous) information. Global transcriptional response, represented as a corsstalk between ‘analog’ and ‘digital’ signals points towards a mechanism in which regulation of the gene expression does not function as an on-off switch but rather is the result of interdependent actions of several partially redundant pathways translating into varying analog output. This mode of transcriptional response is termed ‘Rheostatic control’ [Travers and Muskhelishvili, 2005b]. The inter-conversions between digital and analog properties offer multiple possibilities for cellular response, which can explain the dynamism manifest in the transcriptome of E.coli. Though the interplay of coordinating factors (superhelicity of DNA, NAPs & RNAP composition) has been uncovered for some gene promoters, the mechanistic basis for explaining the spatial and temporal coordination of transcription in the genome still remains elusive. 1.2 Global transcription coordination - current knowledge In this section, the current knowledge of transcriptional regulation is briefly outlined to elucidate mechanisms that form the basis of the hypothesis explaining global coordination of transcription in the genome. Starting from individual gene promoter 4
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 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: INTRODUCTION Salmonella: “In more
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 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
Page 101 and 102:
Page 103 and 104:
Page 105 and 106:
Page 107 and 108:
Page 109 and 110:
Page 111 and 112:
Page 113 and 114:
Page 115 and 116:
Page 117 and 118:
Page 119 and 120:
Page 121 and 122:
Page 123 and 124:
Page 125 and 126:
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
Page 141 and 142:
Page 143 and 144:
Page 145 and 146:
Page 147 and 148:
Page 149 and 150:
Page 151 and 152:
Page 153 and 154:
Page 155 and 156:
Page 157 and 158:
APPENDIX I gene blattner ratio A/B
Page 159 and 160:
Page 161 and 162:
Page 163 and 164:
Page 165 and 166:
Page 167 and 168:
Page 169 and 170:
Page 171 and 172:
Page 173 and 174:
Page 175 and 176:
Page 177 and 178:
Page 179 and 180:
Page 181 and 182:
Page 183 and 184:
Page 185 and 186:
Page 187 and 188:
Page 189 and 190:
Page 191 and 192:
Page 193 and 194:
Page 195 and 196:
Page 197 and 198:
Page 199 and 200:
Page 201 and 202:
Page 203 and 204:
Page 205 and 206:
Statement of sources Declaration I
Page 207:
190
show all

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

You also want an ePaper? Increase the reach of your titles

Delete template?

Save as template?