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

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APPENDIX I minE b1174 0.3218 0.0180 cell division topological specificity factor and inhibitory component of the MinC- MinD-MinE system that regulates septum placement mioC b3742 2.8032 0.0061 flavoprotein involved in biotin synthesis mltC b2963 0.3174 0.0208 membrane-bound lytic murein transglycosylase C mngB b0732 1.4808 0.0136 alpha-mannosidase moaA b0781 0.3113 0.0250 molybdopterin biosynthesis, protein A modE b0761 0.5883 0.0400 Molybdate-responsive transcription factor monomer mokC b0018 1.6023 0.0201 regulatory peptide whose translation enables hokC (gef) expression mraW b0082 0.6100 0.0309 S-adenosyl-dependent methyltransferase mrdB b0634 0.6931 0.0113 rod shape-determining membrane protein; sensitivity to radiation and drugs mreB b3251 0.4151 0.0130 rod shape-determining protein mreC b3250 0.5547 0.0187 rod shape-determining protein mreD b3249 0.4030 0.0041 rod shape-determining protein msbB b1855 0.2631 0.0138 myristoyl acyltransferase mukE b0923 0.2778 0.0005 protein involved in chromosome partitioning mukF b0922 0.2472 0.0062 Ca2+-binding protein involved in chromosome partitioning mutY b2961 0.2826 0.0046 adenine glycosylase; G.C --> T.A transversions nadA b0750 1.2867 0.0026 quinolinate synthetase A nagZ b1107 0.3709 0.0144 β-N-acetylglucosaminidase nanR b3226 0.6046 0.0191 NanR transcriptional regulator narG b1224 1.4419 0.0422 nitrate reductase A, α subunit narP b2193 0.4244 0.0046 NarP-Phosphorylated transcriptional regulator ndh b1109 0.2794 0.0021 NADH cupric reductase / NADH dehydrogenase II ndk b2518 0.5490 0.0297 nucleoside diphosphate kinase / UDP kinase / CDP kinase / dUDP kinase / dCDP kinase / dTDP kinase / dADP kinase / dGDP kinase / GDP kinase nhaA b0019 2.7531 0.0189 sodium/proton NhaA transporter nhaR b0020 1.8006 0.0051 NhaR-Na+ transcriptional activator nirD b3366 1.2750 0.0385 nitrite reductase, small subunit nlpB b2477 0.3204 0.0188 lipoprotein-34 nlpC b1708 0.8276 0.0132 NlpC-putative lipoprotein hydrolase nlpD b2742 0.4725 0.0091 NlpD putative outer membrane lipoprotein npr b3206 1.1115 0.0239 phosphocarrier protein HPr-like NPr, nitrogen related, exchanges phosphate with Enzyme I, Hpr nth b1633 2.1070 0.0198 endonuclease III; specific for apurinic and/or apyrimidinic sites nudF b3034 0.4112 0.0010 hypothetical protein nudG b1759 0.6794 0.0394 CTP pyrophosphohydrolase nudH b2830 0.4781 0.0025 putative invasion protein nuoA b2288 1.6603 0.0436 NADH dehydrogenase I nuoB b2287 2.1552 0.0017 NADH dehydrogenase I nuoC b2286 1.5429 0.0056 NADH dehydrogenase I nuoE b2285 1.4073 0.0195 NADH dehydrogenase I nuoF b2284 1.6783 0.0075 NADH dehydrogenase I nusB b0416 0.5649 0.0227 transcription termination; L factor nusG b3982 0.1716 0.0023 component in transcription antitermination ogrK b2082 1.8738 0.0121 OgrK transcriptional regulator ompX b0814 1.3900 0.0297 outer membrane protein X osmB b1283 1.9992 0.0416 OsmB osmotically inducible lipoprotein oxyR b3961 3.1506 0.0058 OxyR transcriptional dual regulator paaJ b1397 1.4298 0.0499 putative beta-keto-thiolase of phenylacetate degradation pabA b3360 1.4655 0.0359 para-aminobenzoate synthase multi-enzyme complex / para-aminobenzoate synthase pabC b1096 0.3015 0.0413 para-aminobenzoate synthase multi-enzyme complex / para-aminobenzoate synthase pagP b0622 2.7254 0.0221 PagP monomer panB b0134 0.5034 0.0001 3-methyl-2-oxobutanoate hydroxymethyltransferase monomer panF b3258 0.6070 0.0178 PanF sodium/pantothenate SSS transporter parC b3019 0.3991 0.0037 Topoisomerase IV subunit A pcnB b0143 0.5626 0.0040 poly(A) polymerase I pdxH b1638 0.5820 0.0297 pyridoxine 5'-phosphate oxidase / pyridoxamine 5'-phosphate oxidase pepB b2523 1.8383 0.0128 aminopeptidase (AP) 115
APPENDIX I pepP b2908 1.2182 0.0368 proline aminopeptidase P II pepQ b3847 2.4602 0.0335 proline dipeptidase pfkB b1723 1.4328 0.0085 6-phosphofructokinase-2 monomer pflA b0902 2.1225 0.0090 pyruvate formate-lyase activating enzyme pgaC b1022 1.4003 0.0250 predicted N-glycosyltransferase pgi b4025 0.7116 0.0462 phosphoglucose isomerase pgpA b0418 0.5727 0.0094 phosphatidylglycerophosphatase A pheP b0576 0.4252 0.0250 PheP phenylalanine APC transporter phoE b0241 1.3013 0.0094 PhoE phoH b1020 1.4888 0.0191 PhoB-dependent, ATP-binding pho regulon component; may be helicase; induced by P starvation phoP b1130 0.4417 0.0115 PhoP-Phosphorylated transcriptional dual regulator phoQ b1129 0.6685 0.0013 PhoQ-Phis pitB b2987 1.3798 0.0445 PitB plsC b3018 0.3763 0.0024 1-acylglycerol-3-phosphate acyltransferase pmbA b4235 0.5564 0.0213 protease involved in Microcin B17 maturation and in sensitivity to the DNA gyrase inhibitor LetD pmrD b2259 0.4652 0.0050 polymyxin resistance protein pncB b0931 0.2923 0.0110 nicotinate phosphoribosyltransferase pnp b3164 0.2968 0.0110 polynucleotide phosphorylase polB b0060 4.3621 0.0499 DNA polymerase II potB b1125 0.5130 0.0375 putrescine/spermidine ABC transporter potC b1124 0.5813 0.0046 putrescine/spermidine ABC transporter poxA b4155 0.5427 0.0338 putative regulator of pyruvate oxidase ppiD b0441 0.6513 0.0198 peptidyl-prolyl cis-trans isomerase ppk b2501 0.3301 0.0114 polyphosphate kinase ppsA b1702 0.7593 0.0328 phosphoenolpyruvate synthase priC b0467 0.5875 0.0232 primosomal replication protein N'' prmC b1212 0.7663 0.0275 protein-(glutamine-N5) methyltransferase proP b4111 0.4204 0.0214 ProP proline/betaine MFS transporter proQ b1831 0.5181 0.0394 protein that affects osmoregulation of ProP transporter proV b2677 0.3005 0.0108 proline ABC transporter proW b2678 0.3934 0.0291 proline ABC transporter psd b4160 0.5710 0.0213 phosphatidylserine decarboxylase, proenzyme pspB b1305 1.6459 0.0420 stimulates PspC-mediated transcriptional activation of the psp operon; antitoxin of a PspC-PspB toxin-antitoxin pair pssA b2585 0.1873 0.0040 phosphatidylserine synthase purA b4177 0.5024 0.0178 adenylosuccinate synthase purB b1131 0.6679 0.0119 5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole lyase / adenylosuccinate lyase purC b2476 0.1510 0.0007 phosphoribosylaminoimidazole-succinocarboxamide synthase purE b0523 0.3132 0.0136 N5-carboxyaminoimidazole ribonucleotide mutase purF b2312 0.2208 0.0011 amidophosphoribosyl transferase purK b0522 0.2617 0.0039 N5-carboxyaminoimidazole ribonucleotide synthase monomer purM b2499 0.0976 0.0007 phosphoribosylformylglycinamide cyclo-ligase purN b2500 0.3565 0.0063 phosphoribosylglycinamide formyltransferase purR b1658 0.1999 0.0032 PurR transcriptional repressor purT b1849 0.5923 0.0436 GAR transformylase 2 purU b1232 0.4050 0.0031 formyltetrahydrofolate deformylase puuD b1298 0.6547 0.0166 probable amidotransferase subunit pyrB b4245 0.4134 0.0108 aspartate carbamoyltransferase, PyrB subunit pyrC b1062 0.6009 0.0278 dihydroorotase pyrD b0945 0.3694 0.0012 dihydroorotate oxidase radA b4389 0.5088 0.0089 DNA recombination protein rbfA b3167 0.7704 0.0239 ribosome-binding factor A rbsB b3751 2.1321 0.0323 ribose ABC transporter rcsB b2217 0.5589 0.0202 RcsB transcriptional activator rcsC b2218 0.6588 0.0017 RcsC-Phis rdgC b0393 0.4658 0.0035 nonspecific DNA binding protein; nucleoid component 116
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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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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
Page 127 and 128: APPENDIX I Supplementary table - VI
Page 129 and 130: APPENDIX I fabB b2323 0.6336 0.0043
Page 131: APPENDIX I ibpA b3687 2.4960 0.0181
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 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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