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

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APPENDIX I gene blattner ratio p-value Function A/B hcaD b2542 1.6383 0.0207 ferredoxin NAD+ reductase hcaE b2538 0.5174 0.0278 3-phenylpropionate dioxygenase, alpha subunit hcr b0872 2.8116 0.0329 NADH oxidoreductase hdeD b3511 2.0630 0.0226 protein involved in acid resistance hdfR b4480 0.3225 0.0184 transcriptional regulator hemC b3805 0.4388 0.0311 hydroxymethylbilane synthase hemG b3850 0.4767 0.0075 protoporphyrinogen oxidase hemH b0475 1.6086 0.0151 ferrochelatase hemN b3867 0.4698 0.0211 coproporphyrinogen III oxidase, anaerobic hflD b1132 0.4773 0.0130 membrane protein in operon with purB hha b0460 0.3786 0.0126 haemolysin expression modulating protein hipB b1508 0.0870 0.0061 HipB transcriptional activator hmp b2552 1.8564 0.0046 nitric oxide dioxygenase / dihydropteridine reductase 2 hofN b3394 0.3123 0.0307 conserved protein holA b0640 2.0348 0.0021 DNA polymerase III, delta subunit holB b1099 1.5205 0.0029 DNA polymerase III, delta prime subunit holC b4259 0.5840 0.0321 DNA polymerase III, chi subunit holE b1842 0.2431 0.0003 DNA polymerase III, theta subunit hscC b0650 1.6203 0.0217 Hsc62; an Hsp70-family ATPase that negatively regulates sigma70 / nonchaperonin molecular chaperone ATPase hslU b3931 4.1300 0.0123 ATPase component of the HslVU protease htpG b0473 1.8306 0.0130 HtpG monomer htrL b3618 6.9782 0.0063 involved in lipopolysaccharide biosynthesis hyaA b0972 2.2684 0.0027 hydrogenase I, HyaA subunit hybF b2991 1.6921 0.0285 protein involved with the maturation of hydrogenases 1 and 2 hycE b2721 2.0488 0.0454 formate hydrogenlyase complex iaaA b0828 0.1133 0.0019 beta cleavage product of IaaA ibpA b3687 4.2244 0.0016 small heat shock protein IbpA ibpB b3686 7.6875 0.0014 small heat shock protein IbpB icdA b1136 0.3462 0.0100 Icd iclR b4018 0.2325 0.0125 IclR-PEP idnR b4264 0.2909 0.0338 IdnR-5-ketogluconate idnT b4265 0.3169 0.0249 IdnT idonate Gnt tranporter ihfB b0912 1.9863 0.0061 IHF transcriptional dual regulator ilvA b3772 0.4362 0.0424 threonine dehydratase (biosynthetic) inaA b2237 0.2907 0.0071 pH-inducible protein involved in stress response insA_5 b1894 0.3935 0.0446 insA_5 1977239-1976964 : IS1 protein InsA / insA_1 20508-20233 : IS1 protein InsA / insA_6 3581506-3581781 : IS1 protein InsA intR b1345 0.2551 0.0239 putative transposase intS b2349 1.9457 0.0169 putative prophage Sf6-like integrase iscU b2529 1.8083 0.0053 scaffold protein involved in iron-sulfur cluster assembly ispA b0421 0.1813 0.0151 geranyl diphosphate synthase / farnesyl diphosphate synthase ispD b2747 0.4908 0.0411 4-diphosphocytidyl-2C-methyl-D-erythritol synthetase monomer katE b1732 1.7021 0.0305 hydroperoxidase II kdtA b3633 0.3601 0.0028 KDO transferase kduD b2842 1.5255 0.0331 2-deoxy-D-gluconate 3-dehydrogenase kefG b3351 1.3584 0.0057 KefG ldcA b1192 1.7002 0.0372 L,D-carboxypeptidase A leuB b0073 1.7972 0.0055 3-isopropylmalate dehydrogenase leuC b0072 1.6773 0.0000 isopropylmalate isomerase leuD b0071 2.0207 0.0112 isopropylmalate isomerase ligT b0147 0.1852 0.0026 hypothetical protein lipB b0630 2.1877 0.0000 lipoyl-protein ligase livH b3457 1.9033 0.0131 leucine ABC transporter livM b3456 1.6094 0.0498 leucine ABC transporter lolA b0891 0.7885 0.0361 periplasmic chaperone, effects translocation of lipoproteins from inner membrane to outer 127
APPENDIX I gene blattner ratio p-value Function A/B lolB b1209 0.4806 0.0227 outer membrane lipoprotein, localization of lipoproteins in the outer membrane lolE b1118 0.4575 0.0420 LolCDE ABC lipoprotein transporter lon b0439 2.6981 0.0091 DNA-binding, ATP-dependent protease La lpcA b0222 0.2400 0.0125 lipopolysaccharide core biosynthesis; phosphoheptose isomerase lrp b0889 0.4179 0.0402 Lrp-Leucine transcriptional activator lsrG b1518 1.4543 0.0022 conserved hypothetical protein lysA b2838 1.7920 0.0487 diaminopimelate decarboxylase macB b0879 2.0724 0.0127 MacAB macrolide efflux transporter complex malT b3418 0.1905 0.0107 MalT-MalK malY b1622 0.4203 0.0185 bifunctional: repressor of maltose regulon / cystathionine beta-lyase mdl b0449 2.7100 0.0423 MdlB mdoC b1047 0.1432 0.0145 protein required for succinyl modification of osmoregulated periplasmic glucans mdoH b1049 1.6043 0.0230 membrane glycosyltransferase; synthesis of membrane-derived oligosaccharide (MDO) mdtF b3514 1.8716 0.0244 YhiV mdtN b4082 2.2488 0.0020 putative membrane protein mdtO b4081 1.5951 0.0435 YjcQ menD b2264 0.3726 0.0138 putative 2-hydroxyglutarate synthase / SHCHC synthase / 2-oxoglutarate decarboxylase menF b2265 0.3477 0.0276 isochorismate synthase, menaquinone-specific mfd b1114 0.5650 0.0126 transcription-repair coupling factor; mutation frequency decline mhpF b0351 1.8446 0.0238 acetaldehyde dehydrogenase 2 minC b1176 0.2414 0.0115 cell division inhibitor of the MinC-MinD-MinE and DicB-MinC systems that regulate septum placement minD b1175 0.4152 0.0065 membrane ATPase of the MinC-MinD-MinE system that regulates septum placement minE b1174 0.3703 0.0160 cell division topological specificity factor and inhibitory component of the MinC- MinD-MinE system that regulates septum placement mioC b3742 1.6938 0.0341 flavoprotein involved in biotin synthesis mltC b2963 0.4421 0.0091 membrane-bound lytic murein transglycosylase C mmuP b0260 0.3741 0.0038 MmuP APC transporter mnmC b2324 0.5136 0.0357 bifunctional enzyme catalyzing the formation of mnm5s2U in tRNA mntH b2392 0.3161 0.0066 MntH manganese ion NRAMP transporter moaA b0781 0.2797 0.0039 molybdopterin biosynthesis, protein A mobA b3857 0.2268 0.0063 molybdopterin guanine dinucleotide synthase mobB b3856 0.7633 0.0125 molybdopterin-guanine dinucleotide biosynthesis protein B modE b0761 0.3788 0.0052 Molybdate-responsive transcription factor monomer moeB b0826 2.0014 0.0025 molybdopterin biosynthesis mpaA b1326 0.4207 0.0207 murein peptide amidase A mrr b4351 0.4108 0.0084 restriction of methylated adenine msbB b1855 0.2154 0.0023 myristoyl acyltransferase mtlD b3600 0.3066 0.0272 mannitol-1-phosphate 5-dehydrogenase mukE b0923 0.3600 0.0166 protein involved in chromosome partitioning mukF b0922 0.2126 0.0048 Ca2+-binding protein involved in chromosome partitioning murI b3967 2.6898 0.0094 glutamate racemase murP b2429 0.3862 0.0083 MurP mutY b2961 0.3526 0.0252 adenine glycosylase; G.C --> T.A transversions mviM b1068 0.7293 0.0284 putative virulence factor nadD b0639 2.8386 0.0006 nicotinate-mononucleotide adenylyltransferase nadR b4390 0.5652 0.0094 NadR transcriptional repressor / NMN adenylyltransferase nanR b3226 0.2529 0.0184 NanR transcriptional regulator narQ b2469 1.8665 0.0482 NarQ-Phis narV b1465 1.9002 0.0087 nitrate reductase Z, γ subunit nfnB b0578 0.7030 0.0451 dihydropteridine reductase nfrB b0569 0.4153 0.0012 bacteriophage N4 receptor, outer membrane protein nhaA b0019 1.9281 0.0447 sodium/proton NhaA transporter nhaR b0020 2.4259 0.0270 NhaR-Na+ transcriptional activator nikA b3476 2.3805 0.0063 nickel ABC transporter 128
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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
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 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 143: 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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APPENDIX I gene blattner ratio A/B
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Statement of sources Declaration I
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