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

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APPENDIX I gene blattner ratio A/B p-value Function beta-hydroxyacyl-ACP dehydrase / beta-hydroxydecanoyl-ACP dehydrase / trans- 2-decenoyl-ACP isomerase fabA b0954 1.3210 0.0488 fabB b2323 0.5971 0.0302 beta-ketoacyl-ACP synthase I / malonyl-ACP decarboxylase fadE b0221 1.6673 0.0495 acyl-CoA dehydrogenase fdnI b1476 1.9523 0.0061 formate dehydrogenase N, γ subunit involved in protein transport; multicopy suppressor of dominant negative ftsH fdrA b0518 1.2709 0.0284 mutants outer membrane receptor; citrate-dependent iron transport, outer membrane fecA b4291 1.7276 0.0273 receptor fecI b4293 3.0790 0.0101 sigma19 factor fhuC b0151 0.5705 0.0007 ferrichrome uptake system fldA b0684 1.1793 0.0126 oxidized flavodoxin 1 flgJ b1081 1.5509 0.0122 FlgJ flhD b1892 0.3498 0.0204 FlhD transcriptional dual regulator fliK b1943 1.5668 0.0293 flagellar hook-length control protein FliK periplasmic cystine-binding protein; member of extracellular bacterial solutebinding fliY b1920 0.5595 0.0124 protein family III fmt b3288 1.4785 0.0271 10-formyltetrahydrofolate:L-methionyl-tRNA(fMet) N-formyltransferase fnr b1334 2.6607 0.0164 FNR transcriptional dual regulator folB b3058 0.5634 0.0051 dihydroneopterin aldolase methyleneTHF enzyme / methenyltetrahydrofolate cyclohydrolase / folD b0529 0.6659 0.0470 methylenetetrahydrofolate dehydrogenase-(NADP+) fre b3844 1.6805 0.0020 FMN reductase frlR b3375 0.7577 0.0058 putative transcriptional regulator frmA b0356 1.5071 0.0219 formaldehyde dehydrogenase, glutathione-dependent frsA b0239 0.4360 0.0232 fermentation/respiration switch protein fruR b0080 0.6025 0.0156 FruR transcriptional dual regulator frvA b3900 1.5012 0.0441 EIIABCFrv frwB b3950 2.0264 0.0163 EIIBCFrw frwC b3949 1.7660 0.0430 EIIBCFrw ftsB b2748 0.3995 0.0032 essential cell division protein FtsB fumB b4122 1.5288 0.0433 fumarase B monomer fur b0683 1.5727 0.0358 Fur transcriptional dual regulator gadX b3516 0.5996 0.0010 GadX transcriptional activator UDP-glucose-hexose-1-phosphate uridylyltransferase / galactose-1-phosphate galT b0758 1.5496 0.0183 uridylyltransferase galU b1236 1.1283 0.0373 UTP-glucose-1-phosphate uridylyltransferase gapC_1 b1417 0.6328 0.0268 split glyceraldehyde 3-phosphate dehydrogenase C gapC_2 b1416 0.7832 0.0228 glyceraldehyde 3-phosphate dehydrogenase C, interrupted gatC b2092 0.5533 0.0229 EIIGat gatD b2091 0.5303 0.0482 galactitol-1-phosphate dehydrogenase gatY b2096 0.2303 0.0083 tagatose-1,6-bisphosphate aldolase 2 gatZ b2095 0.3772 0.0024 tagatose-1,6-bisphosphate aldolase 2 gcvH b2904 0.1767 0.0186 dihydrolipoyl-GcvH-protein gcvR b2479 0.2386 0.0003 GcvR-gly glcA b2975 1.2470 0.0468 YghK transporter glf b2036 1.4291 0.0266 UDP-galactopyranose mutase N-acetylglucosamine-1-phosphate uridyltransferase / glucosamine-1-phosphate glmU b3730 0.2684 0.0006 acetyltransferase glnD b0167 1.5254 0.0066 uridylyltransferase / uridylyl-removing enzyme glpB b2242 1.6094 0.0343 glycerol-3-phosphate-dehydrogenase, anaerobic glpD b3426 0.6947 0.0391 glycerol 3-phosphate dehydrogenase, aerobic gltI b0655 2.1460 0.0238 putative periplasmic binding transport protein gltJ b0654 1.8439 0.0084 glutamate ABC transporter gltL b0652 2.3251 0.0499 glutamate ABC transporter glyA b2551 0.6522 0.0151 glycine hydroxymethyltransferase glyQ b3560 0.7048 0.0451 glycine-tRNA synthetase, alpha subunit gntU b4476 1.5662 0.0354 GntU gluconate Gnt transporter gntY b3414 2.5638 0.0235 predicted membrane-bound protein that is involved in high-affinity gluconate 139
APPENDIX I gene blattner ratio A/B p-value Function transport gpt b0238 0.6101 0.0011 xanthine phosphoribosyltransferase / guanine phosphoribosyltransferase / hypoxanthine phosphoribosyltransferase greA b3181 2.0067 0.0017 transcription elongation factor; stimulates the mRNA cleavage activity of RNA polymerase grxA b0849 1.5161 0.0008 oxidized glutaredoxin grxB b1064 0.6716 0.0024 oxidized glutaredoxin 2 gspC b3324 0.6446 0.0495 putative protein secretion protein for export gspD b3325 0.6169 0.0078 putative protein secretion protein for export gspG b3328 1.3373 0.0380 putative protein secretion protein for export gspJ b3331 1.5637 0.0307 putative protein secretion protein for export gspM b3334 1.6029 0.0266 putative protein secretion protein gst b1635 0.4622 0.0007 glutathione transferase guaB b2508 0.4105 0.0135 IMP dehydrogenase gudX b2788 2.0225 0.0315 putative glucarate dehydratase gyrB b3699 2.0935 0.0014 DNA gyrase, subunit B hcaC b2540 0.6918 0.0184 ferredoxin, 3-phenylpropionate dioxygenase system hcaT b2536 0.7188 0.0131 HcaT MFS transporter hcr b0872 1.7460 0.0357 NADH oxidoreductase hdeA b3510 0.6336 0.0024 acid-resistance protein, possible chaperone hdfR b4480 0.5965 0.0480 transcriptional regulator hemA b1210 2.4332 0.0162 glutamyl-tRNA reductase hemC b3805 0.3060 0.0013 hydroxymethylbilane synthase hemD b3804 0.4619 0.0020 uroporphyrinogen III synthase hemG b3850 0.6070 0.0126 protoporphyrinogen oxidase hemH b0475 1.6618 0.0431 ferrochelatase hflD b1132 0.5428 0.0224 membrane protein in operon with purB hflX b4173 0.6818 0.0118 putative GTPase; possible regulator of HflKC hfq b4172 0.5741 0.0397 RNA-binding protein that affects many cellular processes; homolog of mammalian Sm/Sm-like proteins hha b0460 0.3066 0.0051 haemolysin expression modulating protein hisC b2021 0.5274 0.0366 histidine-phosphate aminotransferase hisD b2020 0.4683 0.0485 histidinal dehydrogenase / histidinol dehydrogenase hisF b2025 0.8078 0.0189 imidazole glycerol phosphate synthase, HisF subunit hisS b2514 0.6173 0.0477 histidyl-tRNA synthetase hns b1237 0.5055 0.0012 H-NS transcriptional dual regulator hofO b3393 2.0366 0.0008 conserved hypothetical protein holA b0640 1.8168 0.0002 DNA polymerase III, delta subunit holC b4259 0.2779 0.0200 DNA polymerase III, chi subunit holE b1842 0.2376 0.0017 DNA polymerase III, theta subunit hslR b3400 1.6952 0.0251 heat shock protein Hsp15 htrA b0161 1.3676 0.0489 DegP htrL b3618 3.3010 0.0333 involved in lipopolysaccharide biosynthesis hycH b2718 1.3428 0.0378 processing of large subunit (HycE) of hydrogenase 3 (part of the FHL complex) hypF b2712 1.5597 0.0001 hydrogenase maturation protein ibpA b3687 1.9972 0.0407 small heat shock protein IbpA iclR b4018 0.3761 0.0272 IclR-PEP idnD b4267 0.6061 0.0334 L-idonate 5-dehydrogenase idnO b4266 0.6120 0.0319 5-keto-D-gluconate 5-reductase / putative acetoin dehydrogenase ilvG_1 b3767 0.3376 0.0394 IlvG_1 ilvM b3769 0.3697 0.0001 acetohydroxybutanoate synthase II / acetolactate synthase II imp b0054 0.6460 0.0370 organic solvent tolerance infA b0884 1.9363 0.0438 protein chain initiation factor IF-1 intR b1345 0.5249 0.0341 putative transposase intZ b2442 0.7707 0.0220 putative prophage integrase iscR b2531 3.2160 0.0490 IscR transcriptional regulator iscU b2529 2.3333 0.0037 scaffold protein involved in iron-sulfur cluster assembly 140
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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 105 and 106: 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 155: APPENDIX I gene blattner ratio p-va
Page 169 and 170: APPENDIX I gene blattner ratio A/B
Page 205 and 206: Statement of sources Declaration I
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