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

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APPENDIX I gene blattner ratio A/B p-value yggX b2962 0.2130 0.0026 Function conserved hypothetical protein with role in oxidation-resistance of iron-sulfur clusters yghQ b2983 1.5927 0.0325 putative serine protease yghS b2985 2.5090 0.0044 conserved protein ygiA b3036 0.4378 0.0239 hypothetical protein ygiF b3054 0.4550 0.0096 conserved hypothetical protein ygiH b3059 0.3702 0.0081 putative membrane protein ygiU b3022 0.2603 0.0069 putative cyanide hydratase ygjG b3073 1.9440 0.0152 putrescine:2-oxoglutaric acid aminotransferase ygjN b3083 0.4759 0.0137 conserved hypothetical protein ygjR b3087 0.4817 0.0398 putative NAD(P)-binding dehydrogenase yhaK b3106 0.6327 0.0013 conserved hypothetical protein yhbP b3154 0.2861 0.0046 conserved protein yhcA b3215 1.7828 0.0096 putative chaperone yhcB b3233 0.4240 0.0252 conserved hypothetical protein yhcD b3216 2.5320 0.0410 putative outer membrane protein yhcM b3232 0.2725 0.0003 hypothetical protein yhdA b3252 0.1678 0.0074 conserved protein yhdJ b3262 1.4106 0.0325 cell cycle-regulated methyltransferase yheN b3345 0.6302 0.0272 conserved hypothetical protein yheO b3346 0.5020 0.0092 hypothetical protein yhfG b3362 1.9518 0.0284 conserved hypothetical protein yhfX b3381 1.9848 0.0205 conserved protein yhhK b3459 0.4123 0.0018 putative acyltransferase yhhM b3467 0.3265 0.0159 putative receptor yhhN b3468 0.4588 0.0073 putative enzyme yhhS b3473 0.3667 0.0188 YhhS MFS transporter yhhT b3474 0.5527 0.0461 hypothetical protein yhiL b3490 2.2476 0.0051 hypothetical protein yhiP b3496 1.3365 0.0190 YhiP peptide POT transporter yhiS b3504 1.6910 0.0222 conserved protein yhjA b3518 2.6298 0.0076 putative cytochrome C peroxidase (EC 1.11.1) yhjC b3521 0.2139 0.0092 putative transcriptional regulator LYSR-type yhjR b3535 0.2767 0.0243 hypothetical protein yiaJ b3574 0.3464 0.0228 YiaJ transcriptional repressor yiaV b3586 2.4422 0.0226 putative membrane protein yibA b3594 2.4261 0.0343 putative lyase yicE b3654 0.0934 0.0007 YicE NCS2 tranporter yidI b3677 0.5721 0.0151 hypothetical protein yieO b3754 0.5670 0.0417 YieO drug MFS transporter yifE b3764 1.7605 0.0381 hypothetical protein yigA b3810 0.4061 0.0291 conserved hypothetical protein yigL b3826 1.9789 0.0325 conserved protein with a phosphatase-like domain yihI b3866 0.3969 0.0382 conserved protein yihN b3874 1.3163 0.0362 YihN MFS transporter yihW b3884 0.5544 0.0009 putative DEOR-type transcriptional regulator yihX b3885 0.1479 0.0070 putative phosphatase yjbE b4026 2.1742 0.0103 conserved hypothetical protein yjbJ b4045 0.8546 0.0153 highly abundant nonessential protein yjbQ b4056 0.3680 0.0272 conserved hypothetical protein yjdA b4109 0.1308 0.0055 hypothetical protein yjeB b4178 0.1691 0.0045 conserved protein with a Winged helix domain yjeK b4146 0.2195 0.0017 hypothetical protein yjeS b4166 5.5584 0.0055 conserved ferredoxin-like protein yjfY b4199 2.3690 0.0232 conserved hypothetical protein yjfZ b4204 1.7639 0.0428 hypothetical protein yjgK b4252 0.7295 0.0143 conserved hypothetical protein 135
APPENDIX I gene blattner ratio p-value Function A/B yjhQ b4307 1.4246 0.0099 hypothetical protein yjiP b4338 2.4980 0.0122 hypothetical protein yjjK b4391 1.7150 0.0293 YjjK yjjV b4378 0.5588 0.0453 putative hydrolase ykfA b0253 0.6499 0.0241 putative GTP-binding protein ykfI b0245 1.4478 0.0135 toxin of the YkfI-YafW toxin-antitoxin pair ymdB b1045 0.3716 0.0228 conserved protein ymfE b1138 0.3125 0.0102 hypothetical protein ymfL b1147 2.2281 0.0426 hypothetical protein ymjA b1295 0.2117 0.0004 hypothetical protein ynaE b1375 0.3494 0.0151 hypothetical protein ynaI b1330 2.3789 0.0357 YnaI yncA b1448 0.2369 0.0176 putative N-acetyltransferase yncI b1458 0.3663 0.0269 conserved protein yneE b1520 0.3459 0.0204 conserved hypothetical protein yneH b1524 0.2425 0.0072 putative glutaminase yoaB b1809 0.7879 0.0038 conserved protein yoaG b1796 1.8050 0.0152 hypothetical protein yoaH b1811 0.4847 0.0212 conserved hypothetical protein yobA b1841 0.4374 0.0151 hypothetical protein yodA b1973 1.4017 0.0256 cadmium-induced metal binding protein ypdA b2380 0.4128 0.0202 putative sensor protein yphA b2543 0.5045 0.0317 hypothetical protein ypjA b2647 1.4597 0.0449 putative outer membrane protein ypjF b2646 2.1806 0.0102 member of the YeeV, YkfI, YpjF family of toxin proteins yqaA b2689 0.3480 0.0062 putative integral membrane protein yqeI b2847 0.2786 0.0052 putative sensory transducer yqgE b2948 0.4450 0.0370 conserved protein yqgF b2949 0.3997 0.0078 possible Holliday junction resolvase yqiA b3031 0.4262 0.0079 putative hydrolase yqiB b3033 0.3117 0.0078 putative enzyme yqiJ b3050 1.4637 0.0242 putative oxidoreductase yqjC b3097 1.4751 0.0229 conserved protein yqjK b3100 1.6055 0.0133 conserved hypothetical protein yraM b3147 0.3549 0.0084 putative glycosylase yraN b3148 0.3605 0.0169 conserved hypothetical protein yrbL b3207 0.3337 0.0259 conserved hypothetical protein; transcription is regulated by Mg2+ yrdD b3283 0.1449 0.0047 putative DNA topoisomerase ytfA b4205 0.8018 0.0308 hypothetical protein ytfG b4211 1.9267 0.0219 putative oxidoreductase ytfN b4221 0.6361 0.0427 conserved protein ytfP b4222 0.5980 0.0212 conserved hypothetical protein ytjB b4387 0.5868 0.0341 membrane protein zapA b2910 0.1619 0.0022 ZapA protein, localizes to the cytokinetic ring zipA b2412 0.2297 0.0272 essential cell division protein ZipA zitB b0752 2.0419 0.0407 ZitB zinc CDF transporter znuA b1857 0.4717 0.0485 ZnuA/ZnuB/ZnuC ABC transporter zur b4046 0.3387 0.0049 Zur transcriptional regulator Supplementary table – IX: LZ41 hns-205::Tn10 (A) Vs LZ54 hns-205::Tn10 (B) gene blattner ratio p-value Function A/B acpS b2563 1.5407 0.0218 holo-[acyl-carrier-protein] synthase 136
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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 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 151: 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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Statement of sources Declaration I
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