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

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APPENDIX I gene blattner ratio p-value Function A/B yfbT b2293 1.7768 0.0251 putative phosphatase, contains a phophatase-like domain yfcV b2339 0.2396 0.0363 putative fimbrial-like protein yfcZ b2343 1.9842 0.0309 conserved hypothetical protein yfdY b2377 1.9172 0.0152 hypothetical protein yfeH b2410 2.5659 0.0020 putative cytochrome oxidase yfeO b2389 1.3810 0.0219 hypothetical protein yfgH b2505 0.3998 0.0112 putative outer membrane lipoprotein yfgI b2506 0.3691 0.0138 putative membrane protein yfiC b2575 0.5114 0.0115 putative enzyme yfiR b2603 0.4214 0.0315 conserved protein yfjT b2637 1.2855 0.0166 hypothetical protein ygaD b2700 1.5905 0.0380 conserved protein ygaQ b2654 0.5771 0.0145 hypothetical protein ygcG b2778 0.5541 0.0426 putative membrane protein ygcI b2757 0.2705 0.0485 hypothetical protein ygcK b2759 0.1525 0.0146 hypothetical protein ygeH b2852 1.2703 0.0166 putative invasion protein ygfJ b2877 0.5915 0.0145 conserved protein ygiD b3039 1.7851 0.0438 putative enzyme with dioxygenase domain ygiL b3043 0.1979 0.0050 putative fimbrial-like protein ygiP b3060 0.3869 0.0138 putative transcriptional regulator LYSR-type ygjG b3073 0.7150 0.0032 putrescine:2-oxoglutaric acid aminotransferase ygjR b3087 1.7341 0.0151 putative NAD(P)-binding dehydrogenase yhaC b3121 0.7029 0.0259 conserved protein yhaH b3103 1.4810 0.0409 putative cytochrome yheT b3353 0.9395 0.0476 putative hydrolase with an alpha/beta-hydrolase domain yhgG b3410 8.7789 0.0083 putative transcriptional regulator yhhS b3473 1.9023 0.0214 YhhS MFS transporter yhiM b3491 0.3980 0.0150 conserved inner membrane protein yhiS b3504 0.4148 0.0135 conserved protein yhjB b3520 1.6281 0.0425 putative regulator yhjD b3522 1.3548 0.0218 putative membrane protein yhjH b3525 1.9821 0.0096 protein involved in flagellar function yhjX b3547 2.3356 0.0409 YhjX MFS transporter yiaU b3585 0.4160 0.0154 putative transcriptional regulator LYSR-type yibA b3594 0.2851 0.0477 putative lyase yicO b3664 0.2533 0.0165 putative membrane protein with possible relationship to novobiocin and deoxycholate resistance yieI b3716 1.7977 0.0144 putative membrane protein yigF b3817 0.4178 0.0439 conserved hypothetical protein yigL b3826 1.3312 0.0472 conserved protein with a phosphatase-like domain yigZ b3848 1.4946 0.0135 putative elongation factor yihF b3861 0.6315 0.0205 conserved protein yjaG b3999 1.5544 0.0152 conserved protein yjbB b4020 1.4828 0.0113 putative alpha helix protein yjbM b4048 0.5829 0.0309 conserved hypothetical protein yjcZ b4110 0.6510 0.0102 hypothetical protein yjdA b4109 0.3357 0.0151 hypothetical protein yjdL b4130 0.7255 0.0483 YjdL peptide POT transporter yjeJ b4145 0.5658 0.0365 conserved protein yjeN b4157 0.4976 0.0199 conserved hypothetical protein yjeS b4166 1.9051 0.0114 conserved ferredoxin-like protein yjfM b4185 1.4600 0.0495 conserved hypothetical protein yjgK b4252 1.5575 0.0381 conserved hypothetical protein yjgN b4257 0.6494 0.0031 putative membrane protein possible involved in transport yjhE b4282 0.6011 0.0270 KpLE2 phage-like element yjhH b4298 0.2791 0.0089 putative lyase/synthase 103
APPENDIX I gene blattner ratio p-value Function A/B yjhI b4299 0.3015 0.0021 putative regulator yjiP b4338 0.2074 0.0198 hypothetical protein yjiW b4347 0.3864 0.0124 hypothetical protein yjjI b4380 1.2300 0.0003 conserved hypothetical protein yjjN b4358 0.7146 0.0214 putative oxidoreductase yliH b0836 1.4511 0.0323 putative receptor; induced in stationary phase ymdA b1044 1.3743 0.0405 conserved hypothetical protein ymdE b1028 1.2439 0.0093 putative malonyl-CoA:Acyl carrier protein transacylase ymfM b1148 1.3536 0.0483 hypothetical protein ymgD b1171 0.4644 0.0021 hypothetical protein ynaE b1375 0.2665 0.0186 hypothetical protein ynaI b1330 0.5285 0.0218 YnaI ynbD b1411 1.4997 0.0330 putative enzyme yncC b1450 0.6862 0.0367 hypothetical protein yncD b1451 1.5934 0.0332 Probable TonB-dependent receptor yncI b1458 0.1672 0.0266 conserved protein yneI b1525 3.7228 0.0368 putative aldehyde dehydrogenase yneK b1527 0.9040 0.0285 conserved protein ynfN b1551 0.2403 0.0063 hypothetical protein yohJ b2141 2.9847 0.0353 putative transmembrane protein yohN b2107 0.6686 0.0265 hypothetical protein ypfJ b2475 1.4122 0.0100 conserved protein ypjF b2646 1.6516 0.0435 member of the YeeV, YkfI, YpjF family of toxin proteins yqaC b2657 0.3850 0.0243 putative enzyme yqeC b2876 0.6850 0.0170 conserved protein yqeI b2847 0.3106 0.0215 putative sensory transducer yqeJ b2848 0.3761 0.0379 conserved hypothetical protein yqgA b2966 2.0839 0.0160 putative transport protein yrhA b3443 0.7276 0.0181 conserved hypothetical protein ytfR b4485 1.7393 0.0402 subunit of YtfQ/YtfR/YtfS/YtfT/YjfF ABC transporter ytfT b4230 1.5937 0.0012 YtfQ/YtfR/YtfS/YtfT/YjfF ABC transporter zraS b4003 2.0921 0.0305 ZraS-Phis Supplementary table – V: CSH50 wild-type (A) Vs CSH50 hns-205::Tn10 (B), Transition to stationary phase gene blattner ratio p-value Function A/B aaeB b3240 1.1872 0.0075 hypothetical protein aceE b0114 0.2646 0.0654 subunit of E1p component of pyruvate dehydrogenase complex acrD b2470 1.3042 0.1589 AcrD ade b3665 0.0725 0.0088 cryptic adenine deaminase monomer adiA b4117 0.9019 0.0328 Adi agaB b3138 1.1736 0.1822 EIIAga alsC b4086 1.2567 0.1129 YjcV ansB b2957 0.2992 0.0537 asparaginase II arpB_2 b1721 0.9159 0.1043 hypothetical protein artJ b0860 0.8070 0.0643 arginine ABC transporter b1367 b1367 1.2731 0.0856 hypothetical protein b1567 b1567 0.7688 0.1747 hypothetical protein b3808 b3808 1.2642 0.0697 hypothetical protein b4103 b4103 1.4344 0.0818 putative C terminus of split phnE gene product betA b0311 1.2923 0.0890 choline dehydrogenase 104
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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
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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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
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APPENDIX I gene blattner ratio A/B
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APPENDIX I gene blattner ratio p-va
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Statement of sources Declaration I
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