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

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APPENDIX I xseB b0422 0.1805 0.0061 exonuclease VII, small subunit xylR b3569 0.5246 0.0295 XylR-Xylose transcriptional activator yabP b0056 0.4221 0.0292 conserved hypothetical protein yafK b0224 0.1376 0.0369 conserved protein; in enteroaggregative E. coli, YafK is required for development of biofilms yagA b0267 1.6600 0.0302 hypothetical protein yagI b0272 0.3762 0.0042 putative regulator yagT b0286 1.5660 0.0376 putative oxidoreductase, Fe-S subunit yagU b0287 1.2317 0.0268 conserved protein ybaJ b0461 0.2544 0.0048 conserved hypothetical protein ybaN b0468 0.3530 0.0019 hypothetical protein ybaO b0447 1.2709 0.0229 putative LRP-like transcriptional regulator ybaV b0442 0.5407 0.0434 conserved hypothetical protein ybbO b0493 0.6285 0.0137 putative oxidoreductase ybcJ b0528 0.5730 0.0490 putative RNA-binding protein ybcK b0544 1.1512 0.0052 hypothetical protein ybeA b0636 0.4138 0.0056 conserved hypothetical protein ybeB b0637 0.4743 0.0070 conserved hypothetical protein ybeD b0631 2.5488 0.0424 conserved hypothetical protein ybeY b0659 3.2204 0.0213 conserved hypothetical protein ybeZ b0660 3.8440 0.0151 putative ATP-binding protein ybfF b0686 0.4315 0.0108 putative enzyme ybhK b0780 0.2522 0.0010 putative structural protein ybhO b0789 1.6209 0.0479 cardiolipin synthase 2 ybiR b0818 0.5665 0.0479 YbiR ybjC b0850 0.5750 0.0491 conserved hypothetical protein; gene is within soxRS regulon ycaL b0909 0.5299 0.0354 putative heat shock protein ycbG b0956 0.5827 0.0116 putative dehydrogenase ycbK b0926 0.4469 0.0152 conserved hypothetical protein ycbQ b0938 1.9263 0.0170 putative fimbrial-like protein ycbR b0939 1.8020 0.0084 putative chaperone yccA b0970 0.4983 0.0427 putative carrier/transport protein; substrate or modulator of FtsH-mediated proteolysis yccF b0961 0.5456 0.0466 conserved hypothetical protein yccJ b1003 1.1693 0.0345 hypothetical protein ycdF b1005 0.5798 0.0023 hypothetical protein ycdZ b1036 0.8246 0.0257 putative transport protein yceB b1063 1.4666 0.0413 conserved hypothetical protein yceG b1097 0.2704 0.0009 putative thymidylate kinase (EC 2.7.4.9) yceH b1067 0.4580 0.0122 conserved hypothetical protein yceO b1058 0.6506 0.0348 hypothetical protein ycfJ b1110 0.4082 0.0338 hypothetical protein ycfP b1108 0.4708 0.0147 putative hydrolase ycfR b1112 0.3787 0.0147 conserved hypothetical protein ycfT b1115 1.5947 0.0302 putative transport protein ycgH_2 b1170 1.9107 0.0317 conserved protein; member of the Autotransporter family ycgL b1179 0.3430 0.0036 conserved hypothetical protein ycgM b1180 0.4324 0.0364 putative isomerase ycgN b1181 0.2587 0.0108 conserved hypothetical protein ycgR b1194 1.3756 0.0420 protein involved in flagellar function ycgZ b1164 0.4255 0.0168 hypothetical protein ychF b1203 1.6270 0.0442 putative GTP-binding protein ychJ b1233 0.3905 0.0170 conserved hypothetical protein ychQ b1213 0.6472 0.0161 hypothetical protein yciS b1279 0.4349 0.0229 conserved hypothetical protein ycjD b1289 1.2011 0.0454 conserved hypothetical protein ycjG b1325 0.4835 0.0125 L-Ala-D/L-Glu epimerase, a muconate lactonizing enzyme ycjR b1314 1.8315 0.0473 putative epimerase/isomerase ycjT b1316 1.1203 0.0476 putative enzyme 119
APPENDIX I ycjX b1321 4.0841 0.0141 putative EC 2.1 enzyme ydaO b1344 0.2434 0.0148 conserved protein ydbA_1 b1401 0.7691 0.0006 hypothetical protein product of fragment 1 of a split CDS ydbA_2 b1405 0.7077 0.0491 hypothetical protein product of fragment 2 of a split CDS ydcT b1441 0.4358 0.0233 YdcS/YdcT/YdcV/YdcU ABC transporter ydcX b1445 2.3184 0.0377 hypothetical protein yddE b1464 0.7336 0.0245 conserved protein ydeA b1528 0.2041 0.0058 YdeA MFS transporter ydeJ b1537 1.4392 0.0057 conserved protein ydeK b1510 0.4875 0.0351 YdeK ydfN b1547 1.3671 0.0077 hypothetical protein ydfT b1559 1.3152 0.0336 hypothetical protein ydfX b1568 1.3846 0.0254 hypothetical protein ydgH b1604 0.4280 0.0237 conserved hypothetical protein ydgT b1625 0.1702 0.0097 conserved hypothetical protein ydhA b1639 0.6550 0.0304 conserved hypothetical protein ydhH b1640 0.4726 0.0304 conserved hypothetical protein ydhI b1643 0.3978 0.0137 hypothetical protein ydiA b1703 0.3178 0.0056 conserved protein ydiO b1695 1.6655 0.0206 putative acyl-CoA dehydrogenase ydiR b1698 1.8979 0.0320 putative subunit of YdiQ-YdiR flavoprotein ydjG b1771 1.3397 0.0169 putative oxidoreductase yeaD b1780 1.7584 0.0268 conserved hypothetical protein yeaE b1781 0.4205 0.0018 putative oxidoreductase, NAD(P)-linked yeaZ b1807 0.4660 0.0019 hypothetical protein yebC b1864 1.6986 0.0245 conserved protein yebF b1847 2.0516 0.0108 conserved hypothetical protein yebG b1848 2.3442 0.0088 hypothetical protein; gene is part of SOS regulon yebK b1853 0.5355 0.0044 hypothetical protein yebN b1821 0.4945 0.0468 putative membrane protein, terpenoid synthase-like yebR b1832 0.2435 0.0027 conserved hypothetical protein yebY b1839 0.4488 0.0070 conserved hypothetical protein yebZ b1840 0.5229 0.0048 putative resistance protein yecD b1867 0.4582 0.0236 putative enzyme yecN b1869 0.1959 0.0051 putative membrane protein yecO b1870 0.2973 0.0060 putative methyltransferase yecP b1871 0.4271 0.0274 putative enzyme yedF b1930 1.6425 0.0395 conserved hypothetical protein; might bind RNA yedI b1958 0.5069 0.0041 hypothetical protein yedK b1931 1.5169 0.0377 conserved hypothetical protein yedR b1963 0.5416 0.0326 hypothetical protein yedS_2 b1965 1.4927 0.0201 putative outer membrane protein yeeE b2013 0.2863 0.0317 putative transport system permease protein yeeN b1983 9.6166 0.0005 conserved protein yeeP b1999 0.6937 0.0431 putative histone yeeT b2003 1.9457 0.0049 hypothetical protein yeeZ b2016 0.8883 0.0272 putative enzyme of sugar metabolism yegD b2069 0.2637 0.0019 actin family protein yegR b2085 1.5686 0.0058 hypothetical protein yegW b2101 0.6534 0.0191 putative transcriptional regulator yegX b2102 0.4954 0.0096 putative hydrolase yegZ b2083 1.3932 0.0173 hypothetical protein yehM b2120 1.2804 0.0220 conserved hypothetical protein yeiG b2154 1.0945 0.0217 putative esterase (EC 3.1.1.-). yeiR b2173 0.5560 0.0087 putative enzyme yeiU b2174 0.2626 0.0007 putative permease yfaD b2244 1.4122 0.0462 hypothetical protein yfaH b2238 1.2445 0.0457 hypothetical protein 120
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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
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 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: APPENDIX I speG b1584 0.4151 0.0001
Page 139 and 140: APPENDIX I yhfY b3382 1.4063 0.0453
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 A/B
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Statement of sources Declaration I
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