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

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APPENDIX I gene blattner ratio p-value Function A/B ycgN b1181 0.2615 0.0009 conserved hypothetical protein ycgZ b1164 0.3437 0.0011 hypothetical protein ychH b1205 0.3360 0.0075 conserved hypothetical protein yciI b1251 1.8595 0.0266 conserved hypothetical protein yciQ b1268 2.0023 0.0382 putative membrane protein ycjD b1289 1.8598 0.0220 conserved hypothetical protein ycjF b1322 4.5462 0.0002 putative membrane protein ycjR b1314 2.8426 0.0026 putative epimerase/isomerase ycjX b1321 5.2223 0.0078 putative EC 2.1 enzyme ycjZ b1328 0.3330 0.0288 putative transcriptional regulator LYSR-type ydaC b1347 2.1926 0.0196 hypothetical protein ydaL b1340 0.4087 0.0084 hypothetical protein ydaO b1344 0.3090 0.0329 conserved protein ydbK b1378 1.5381 0.0088 putative pyruvate synthase ydcD b1457 0.2425 0.0233 hypothetical protein ydcF b1414 0.3249 0.0248 conserved hypothetical protein ydcP b1435 0.5182 0.0437 putative collagenase ydcQ b1438 0.6588 0.0380 hypothetical protein ydcV b1443 2.3103 0.0430 YdcS/YdcT/YdcV/YdcU ABC transporter ydcX b1445 1.7926 0.0407 hypothetical protein ydcZ b1447 0.6629 0.0339 putative transport protein ydeI b1536 1.4337 0.0167 conserved hypothetical protein ydeK b1510 0.5430 0.0356 YdeK ydeP b1501 1.2063 0.0190 acid resistance protein ydfH b1540 0.4468 0.0056 hypothetical protein ydfX b1568 1.9527 0.0006 hypothetical protein ydgK b1626 0.2396 0.0104 putative oxidoreductase ydgT b1625 0.1619 0.0070 conserved hypothetical protein ydhA b1639 0.3471 0.0143 conserved hypothetical protein ydhC b1660 0.5332 0.0469 YdhC drug MFS transporter ydhF b1647 0.6866 0.0318 putative oxidoreductase, NAD(P)-linked ydhH b1640 0.5178 0.0331 conserved hypothetical protein ydhI b1643 0.3395 0.0016 hypothetical protein ydhX b1671 1.4069 0.0177 putative oxidoreductase, Fe-S subunit ydiA b1703 0.4230 0.0097 conserved protein ydiF b1694 2.3786 0.0350 putative enzyme / putative acetate CoA-transferase ydiU b1706 0.3937 0.0051 conserved protein ydjA b1765 0.2828 0.0032 conserved protein ydjE b1769 1.5337 0.0078 YdjE MFS transporter ydjG b1771 1.5063 0.0105 putative oxidoreductase ydjI b1773 1.8655 0.0163 putative aldolase yeaB b1813 0.3894 0.0148 conserved hypothetical protein, MutT-like yeaD b1780 1.6695 0.0155 conserved hypothetical protein yeaN b1791 1.5049 0.0207 YeaN yeaQ b1795 2.2111 0.0082 conserved hypothetical protein yebF b1847 1.6698 0.0283 conserved hypothetical protein yebK b1853 0.2495 0.0033 hypothetical protein yebQ b1828 1.8190 0.0400 YebQ yebR b1832 0.3530 0.0270 conserved hypothetical protein yebW b1837 0.4682 0.0099 hypothetical protein yecD b1867 0.2234 0.0222 putative enzyme yecN b1869 0.3102 0.0188 putative membrane protein yecP b1871 0.3399 0.0218 putative enzyme yecT b1877 1.0931 0.0431 hypothetical protein yedA b1959 0.5288 0.0316 putative transmembrane subunit yedR b1963 1.5955 0.0146 hypothetical protein 133
APPENDIX I gene blattner ratio p-value Function A/B yedS_1 b1964 2.2882 0.0042 putative outer membrane protein yedS_2 b1965 1.7587 0.0236 putative outer membrane protein yedV b1968 1.8495 0.0385 putative 2-component sensor protein yeeI b1976 0.0966 0.0010 conserved hypothetical protein yeeN b1983 4.9594 0.0148 conserved protein yeeR b2001 2.6686 0.0487 hypothetical protein yeeT b2003 2.3201 0.0034 hypothetical protein yeeV b2005 1.3165 0.0457 toxin of the YeeV-YeeU toxin-antitoxin pair yegK b2072 1.7271 0.0442 conserved hypothetical protein yegS b2086 2.0901 0.0070 conserved protein yegZ b2083 2.2403 0.0450 hypothetical protein yeiB b2152 0.3697 0.0315 putative flavoprotein yeiE b2157 0.3697 0.0245 LYSR-type transcriptional regulator yeiH b2158 0.4992 0.0227 putative membrane protein yeiS b2145 0.4582 0.0020 hypothetical protein yeiU b2174 0.4647 0.0046 putative permease yejO b2190 0.7784 0.0168 putative outer membrane protein yfbE b2253 2.0569 0.0265 UDP-L-Ara4O C-4" transaminase yfbN b2273 2.3173 0.0063 conserved hypothetical protein yfbP b2275 1.8398 0.0323 hypothetical protein yfbS b2292 1.5779 0.0333 putative transport protein yfdG b2350 0.2271 0.0070 hypothetical protein yfdT b2363 1.6042 0.0163 hypothetical protein yfdY b2377 0.3177 0.0340 hypothetical protein yfdZ b2379 0.4370 0.0356 putative aminotransferase yfeT b2427 0.3878 0.0370 conserved protein yffP b2447 0.5387 0.0462 hypothetical protein yfgA b2516 0.3806 0.0060 putative membrane protein yfgB b2517 0.5726 0.0383 putative pyruvate formate lyase activating enzyme 2 yfgC b2494 0.5296 0.0021 conserved protein yfgJ b2510 2.4079 0.0095 putative cytochrome yfhG b2555 0.2458 0.0032 conserved protein yfhL b2562 0.2615 0.0411 putative ferredoxin yfhR b2534 1.6968 0.0195 putative methylase or hydrolase yfiC b2575 0.1195 0.0045 putative enzyme yfiR b2603 0.4114 0.0278 conserved protein yfjD b4461 1.6322 0.0139 putative membrane protein, hemolysin-like yfjG b2619 1.8502 0.0087 toxin of a putative toxin-antitoxin pair yfjL b2628 0.1625 0.0098 hypothetical protein yfjO b2631 0.5072 0.0379 hypothetical protein yfjS b2636 1.9190 0.0123 inner membrane lipoprotein YfjS yfjU b2638 0.5267 0.0020 hypothetical protein ygaD b2700 0.4320 0.0264 conserved protein ygaH b2683 0.4552 0.0216 putative transport protein ygbE b2749 0.1583 0.0105 putative cytochrome oxidase subunit ygcF b2777 2.5383 0.0021 hypothetical protein ygdI b2809 2.2634 0.0305 hypothetical protein ygdK b2811 0.3282 0.0174 conserved hypothetical protein ygdR b2833 0.4614 0.0075 conserved hypothetical protein ygeG b2851 1.7509 0.0180 conserved hypothetical protein ygeK b2855 2.0910 0.0188 putative 2-component transcriptional regulator ygeW b2870 1.8672 0.0031 putative carbamoyl transferase ygfH b2920 1.5120 0.0087 propionyl-CoA:succinate CoA transferase ygfS b2886 1.9879 0.0229 putative oxidoreductase, Fe-S subunit yggH b2960 0.4393 0.0186 tRNA (m7G46) methyltransferase yggJ b2946 0.5103 0.0052 conserved hypothetical protein 134
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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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MATERIALS AND METHODS given using a
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MATERIALS AND METHODS phenol: chlor
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MATERIALS AND METHODS Filtered (by
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MATERIALS AND METHODS free water (A
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RESULTS 3 Results Growth phase-depe
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RESULTS Neither the fis nor the hns
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RESULTS these identified genes (by
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RESULTS furthermore the colour of t
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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
Page 99 and 100: APPENDIX I gene blattner ratio p-va
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 149: APPENDIX I gene blattner ratio p-va
Page 157 and 158: APPENDIX I gene blattner ratio A/B
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APPENDIX I gene blattner ratio p-va
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APPENDIX I gene blattner ratio p-va
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Statement of sources Declaration I
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