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

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APPENDIX I gene blattner ratio p-value Function A/B ydhK b1645 0.7743 0.0177 putative membrane protein ydhR b1667 0.5054 0.0468 conserved hypothetical protein ydiA b1703 0.3698 0.0021 conserved protein ydiO b1695 1.7686 0.0429 putative acyl-CoA dehydrogenase ydjF b1770 0.6322 0.0205 putative DEOR-type transcriptional regulator ydjG b1771 1.1870 0.0339 putative oxidoreductase ydjJ b1774 0.7716 0.0258 putative oxidoreductase ydjO b1730 0.7452 0.0045 putative enzyme yeaK b1787 0.5384 0.0111 conserved hypothetical protein yeaL b1789 0.5540 0.0222 hypothetical protein yeaO b1792 0.7835 0.0264 conserved hypothetical protein yeaS b1798 1.1343 0.0208 hypothetical protein yebC b1864 1.9628 0.0112 conserved protein yebE b1846 1.4183 0.0339 conserved hypothetical protein yebF b1847 1.6011 0.0157 conserved hypothetical protein yebG b1848 2.0455 0.0150 hypothetical protein; gene is part of SOS regulon yebK b1853 0.6198 0.0144 hypothetical protein yebN b1821 0.1208 0.0031 putative membrane protein, terpenoid synthase-like yebQ b1828 1.7129 0.0232 YebQ yebR b1832 0.2946 0.0066 conserved hypothetical protein yebY b1839 0.3459 0.0078 conserved hypothetical protein yebZ b1840 0.5397 0.0052 putative resistance protein yecN b1869 0.4794 0.0004 putative membrane protein yecO b1870 0.6886 0.0159 putative methyltransferase yedI b1958 0.7429 0.0417 hypothetical protein yedL b1932 0.8697 0.0339 putative acyl-CoA N-acyltransferase yedS_1 b1964 0.5165 0.0447 putative outer membrane protein yedS_3 b1966 0.5465 0.0327 putative outer membrane protein yedW b1969 0.2470 0.0035 putative 2-component transcriptional response regulator yeeN b1983 7.1154 0.0127 conserved protein yeeT b2003 1.3786 0.0008 hypothetical protein yeeU b2004 2.0721 0.0304 antitoxin of the YeeV-YeeU toxin-antitoxin pair yefM b2017 1.3962 0.0282 antitoxin of the YoeB-YefM toxin-antitoxin pair yegE b2067 1.7115 0.0038 putative sensor-type protein yegI b2070 0.5358 0.0484 putative chaperonin yegS b2086 3.9159 0.0491 conserved protein yehD b2111 2.1221 0.0057 putative fimbrial-like protein yeiE b2157 0.6563 0.0387 LYSR-type transcriptional regulator yejE b2179 1.5636 0.0046 YejA/YejB/YejE/YejF ABC transporter yejG b2181 1.5816 0.0091 conserved hypothetical protein yfaE b2236 1.4667 0.0481 conserved hypothetical protein, 2Fe-2S ferredoxin-related yfbE b2253 0.3390 0.0015 UDP-L-Ara4O C-4" transaminase yfbN b2273 0.6296 0.0373 conserved hypothetical protein yfcL b2325 1.4297 0.0332 conserved hypothetical protein yfcR b2335 1.6257 0.0449 putative fimbrial protein yfdK b2354 0.8266 0.0174 hypothetical protein yfdO b2358 1.7079 0.0258 hypothetical protein yfdP b2359 1.3431 0.0013 hypothetical protein yfgA b2516 0.3616 0.0096 putative membrane protein yfhG b2555 0.4592 0.0050 conserved protein yfiB b2605 0.6708 0.0141 putative outer membrane protein yfiF b2581 0.4349 0.0213 hypothetical protein yfjD b4461 1.1920 0.0274 putative membrane protein, hemolysin-like yfjG b2619 1.8537 0.0213 toxin of a putative toxin-antitoxin pair yfjJ b2626 1.4374 0.0028 hypothetical protein ygaH b2683 0.3070 0.0005 putative transport protein 147
APPENDIX I gene blattner ratio p-value Function A/B ygaZ b2682 0.2806 0.0339 hypothetical protein ygcH b2756 1.5103 0.0470 hypothetical protein ygcK b2759 0.5237 0.0303 hypothetical protein ygcL b2760 0.4734 0.0068 hypothetical protein with possible relationship to novobiocin and deoxycholate resistance ygcT b2773 1.3680 0.0295 hypothetical protein ygdR b2833 2.0681 0.0458 conserved hypothetical protein ygeO b2857 1.4246 0.0028 hypothetical protein ygfB b2909 0.6455 0.0197 conserved hypothetical protein ygfM b2880 1.8759 0.0385 putative oxidoreductase with a FAD-binding domain; possible component of selenate reductase ygfZ b2898 0.6440 0.0118 conserved protein yggG b2936 1.3788 0.0242 conserved protein yggH b2960 0.3883 0.0278 tRNA (m7G46) methyltransferase yggJ b2946 0.4258 0.0253 conserved hypothetical protein yggL b2959 0.4522 0.0265 conserved hypothetical protein yggN b2958 0.5163 0.0247 conserved hypothetical protein yggX b2962 0.3380 0.0026 conserved hypothetical protein with role in oxidation-resistance of iron-sulfur clusters yghO b2981 1.4352 0.0178 putative acyltransferase ygiA b3036 0.6569 0.0453 hypothetical protein ygiD b3039 1.2199 0.0229 putative enzyme with dioxygenase domain ygiF b3054 0.4578 0.0171 conserved hypothetical protein ygiL b3043 0.4481 0.0024 putative fimbrial-like protein ygiU b3022 0.5823 0.0419 putative cyanide hydratase ygjD b3064 0.5001 0.0291 putative O-sialoglycoprotein endopeptidase yhbY b3180 2.4069 0.0493 possible RNA-binding protein yhcE b3217 1.6908 0.0322 hypothetical protein yhdA b3252 0.4853 0.0034 conserved protein yhdN b3293 2.2147 0.0304 conserved hypothetical protein yheN b3345 0.7236 0.0466 conserved hypothetical protein yheO b3346 0.6587 0.0186 hypothetical protein yhfA b3356 0.4740 0.0196 conserved hypothetical protein yhfG b3362 1.5910 0.0072 conserved hypothetical protein yhfL b3369 0.7399 0.0465 hypothetical protein yhfU b3378 1.5087 0.0383 hypothetical protein yhfX b3381 1.4728 0.0231 conserved protein yhhH b3483 0.7173 0.0406 hypothetical protein yhhJ b3485 1.2472 0.0276 YhiH/YhhJ ABC transporter yhhS b3473 0.5354 0.0441 YhhS MFS transporter yhhZ b3442 1.5149 0.0020 conserved protein yhiS b3504 1.7373 0.0348 conserved protein yhjA b3518 1.6786 0.0050 putative cytochrome C peroxidase (EC 1.11.1) yhjR b3535 0.3739 0.0105 hypothetical protein yhjY b3548 1.6225 0.0111 putative lipase yi5A b3557 0.5204 0.0060 IS5 protein yiaA b3562 0.3268 0.0239 hypothetical protein yiaB b3563 0.2619 0.0011 inner membrane protein yiaN b3578 0.5853 0.0361 YiaMNO Binding Protein-dependent Secondary (TRAP) Transporter yiaW b3587 0.4349 0.0065 hypothetical protein yibD b3615 2.3369 0.0409 putative glycosyltransferase yibJ b3595 1.4681 0.0140 hypothetical protein yicE b3654 0.2155 0.0218 YicE NCS2 tranporter yicL b3660 0.5423 0.0107 inhibitor of heme biosynthesis yicN b3663 0.7539 0.0488 conserved hypothetical protein yidF b3674 1.4127 0.0375 putative transcriptional regulator yidP b3684 1.4297 0.0316 putative transcriptional regulator 148
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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
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APPENDIX I gene blattner ratio p-va
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Page 113 and 114: 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 157 and 158: APPENDIX I gene blattner ratio A/B
Page 163: APPENDIX I gene blattner ratio p-va
Page 205 and 206: Statement of sources Declaration I
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