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

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APPENDIX I gene blattner ratio p-value Function A/B iscX b2524 1.9429 0.0374 protein with possible role in iron-sulfur cluster biogenesis ispA b0421 0.2156 0.0032 geranyl diphosphate synthase / farnesyl diphosphate synthase ispG b2515 0.4793 0.0372 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase kdpA b0698 1.4635 0.0082 potassium ion P-type ATPase transporter kdtA b3633 0.5128 0.0192 KDO transferase kefC b0047 1.4900 0.0328 KefC potassium CPA2 transporter lctD b3605 1.5950 0.0088 L-Lactate:Quinone Oxidoreductase leuA b0074 0.5604 0.0386 2-isopropylmalate synthase leuO b0076 0.4172 0.0372 LeuO transcriptional activator ligT b0147 0.3631 0.0028 hypothetical protein lipB b0630 1.7073 0.0027 lipoyl-protein ligase lolB b1209 0.5077 0.0232 outer membrane lipoprotein, localization of lipoproteins in the outer membrane lon b0439 1.7720 0.0416 DNA-binding, ATP-dependent protease La lpcA b0222 0.5206 0.0283 lipopolysaccharide core biosynthesis; phosphoheptose isomerase lpxP b2378 1.5961 0.0222 palmitoleoyl acyltransferase maa b0459 0.4667 0.0368 maltose acetyltransferase malP b3417 1.6906 0.0124 maltodextrin phosphorylase monomer malT b3418 0.4985 0.0239 MalT-MalK marA b1531 0.5442 0.0225 MarA transcriptional activator mazE b2783 0.8900 0.0434 antitoxin of the MazEF "addiction module" mcrA b1159 0.4973 0.0172 restriction of DNA at 5-methylcytosine residues mcrB b4346 1.3712 0.0144 MrcB subunit of 5-methylcytosine restriction system mdaB b3028 0.5909 0.0179 NADPH quinone reductase mdoG b1048 1.3670 0.0155 periplasmic glucan (MDO) biosynthesis protein mdtF b3514 2.2727 0.0041 YhiV mdtK b1663 0.4631 0.0216 NorE multidrug efflux MATE transporter mdtN b4082 1.4199 0.0116 putative membrane protein menF b2265 0.3329 0.0082 isochorismate synthase, menaquinone-specific metC b3008 1.3616 0.0383 L-cysteine desulfhydrase / cystathionine-beta-lyase mgrB b1826 0.6490 0.0364 hypothetical protein; product of a gene induced by low magnesium minC b1176 0.1945 0.0010 cell division inhibitor of the MinC-MinD-MinE and DicB-MinC systems that regulate septum placement minD b1175 0.3435 0.0101 membrane ATPase of the MinC-MinD-MinE system that regulates septum placement minE b1174 0.3672 0.0145 cell division topological specificity factor and inhibitory component of the MinC- MinD-MinE system that regulates septum placement mltC b2963 0.5062 0.0384 membrane-bound lytic murein transglycosylase C mnmC b2324 0.5470 0.0326 bifunctional enzyme catalyzing the formation of mnm5s2U in tRNA mobA b3857 0.6706 0.0302 molybdopterin guanine dinucleotide synthase motB b1889 0.7051 0.0060 MotB protein, enables flagellar motor rotation, linking torque machinery to cell wall mreB b3251 0.5301 0.0235 rod shape-determining protein msbB b1855 0.3370 0.0177 myristoyl acyltransferase msrB b1778 1.0943 0.0060 methionine sulfoxide reductase B / protein-methionine-S-oxide reductase / methionine sulfoxide reductase mtlD b3600 0.4275 0.0087 mannitol-1-phosphate 5-dehydrogenase mukE b0923 0.4201 0.0052 protein involved in chromosome partitioning mukF b0922 0.2947 0.0054 Ca2+-binding protein involved in chromosome partitioning murC b0091 1.5288 0.0169 UDP-N-acetylmuramate-alanine ligase murI b3967 2.4431 0.0020 glutamate racemase mutM b3635 1.4678 0.0408 formamidopyrimidine DNA glycosylase mutY b2961 0.3818 0.0326 adenine glycosylase; G.C --> T.A transversions nadD b0639 2.2259 0.0009 nicotinate-mononucleotide adenylyltransferase nadE b1740 0.7970 0.0374 NAD+ synthase, glutamine dependent / NAD+ synthase, NH3-dependent nadK b2615 1.2935 0.0461 NAD kinase monomer nagZ b1107 0.5177 0.0214 β-N-acetylglucosaminidase nanR b3226 0.3753 0.0253 NanR transcriptional regulator napC b2202 1.5349 0.0131 cytochrome c protein 141
APPENDIX I gene blattner ratio p-value Function A/B narI b1227 1.4294 0.0314 nitrate reductase A, γ subunit narP b2193 0.5047 0.0363 NarP-Phosphorylated transcriptional regulator narX b1222 0.7241 0.0227 NarX-Phis ndh b1109 0.3534 0.0481 NADH cupric reductase / NADH dehydrogenase II nfo b2159 0.7313 0.0447 endonuclease IV nhaA b0019 1.6748 0.0323 sodium/proton NhaA transporter nhaB b1186 0.7111 0.0329 NhaB sodium/proton transporter nhaR b0020 1.5626 0.0364 NhaR-Na+ transcriptional activator nirD b3366 1.2931 0.0487 nitrite reductase, small subunit nlpB b2477 0.4282 0.0017 lipoprotein-34 nlpD b2742 0.5889 0.0384 NlpD putative outer membrane lipoprotein nmpC b0553 0.2798 0.0066 outer membrane porin protein; locus of qsr prophage nrdH b2673 1.5595 0.0197 glutaredoxin-like protein; hydrogen donor nrfB b4071 1.4551 0.0140 nitrite reductase complex nrfG b4076 0.7857 0.0445 maturation of formate-dependent nitrite reductase complex nth b1633 2.1800 0.0177 endonuclease III; specific for apurinic and/or apyrimidinic sites nudF b3034 0.5025 0.0228 hypothetical protein nudH b2830 0.4636 0.0223 putative invasion protein nuoA b2288 1.6995 0.0472 NADH dehydrogenase I nuoB b2287 1.5197 0.0379 NADH dehydrogenase I nuoE b2285 1.4198 0.0304 NADH dehydrogenase I nuoF b2284 1.4220 0.0317 NADH dehydrogenase I nusG b3982 0.2852 0.0347 component in transcription antitermination ompX b0814 1.4445 0.0493 outer membrane protein X osmB b1283 3.4496 0.0098 OsmB osmotically inducible lipoprotein pabA b3360 1.6781 0.0002 para-aminobenzoate synthase multi-enzyme complex / para-aminobenzoate synthase pabB b1812 0.5495 0.0354 para-aminobenzoate synthase multi-enzyme complex / para-aminobenzoate synthase pabC b1096 0.3442 0.0019 para-aminobenzoate synthase multi-enzyme complex / para-aminobenzoate synthase panB b0134 0.7353 0.0027 3-methyl-2-oxobutanoate hydroxymethyltransferase monomer panE b0425 0.5460 0.0418 2-dehydropantoate reductase parC b3019 0.4320 0.0075 Topoisomerase IV subunit A pcnB b0143 0.6795 0.0070 poly(A) polymerase I pdxA b0052 1.3711 0.0238 PdxA dehydrogenase/decarboxylase pdxK b2418 1.2254 0.0374 pyridoxamine kinase / hydroxymethylpyrimidine kinase / pyridoxal kinase pepA b4260 0.3097 0.0122 aminopeptidase A/I pepB b2523 2.2644 0.0239 aminopeptidase (AP) pepP b2908 1.3593 0.0065 proline aminopeptidase P II pepT b1127 0.6833 0.0395 peptidase T pgm b0688 1.5303 0.0417 phosphoglucomutase pgpB b1278 0.4697 0.0419 phosphatidylglycerophosphatase B pheA b2599 0.6656 0.0384 chorismate mutase / prephenate dehydratase pheT b1713 0.7457 0.0492 phenylalanyl-tRNA synthetase β-chain phoP b1130 0.6028 0.0020 PhoP-Phosphorylated transcriptional dual regulator pitB b2987 0.4848 0.0403 PitB plsC b3018 0.4674 0.0213 1-acylglycerol-3-phosphate acyltransferase pmbA b4235 0.4596 0.0021 protease involved in Microcin B17 maturation and in sensitivity to the DNA gyrase inhibitor LetD pmrF b2254 0.5087 0.0075 undecaprenyl phosphate-L-Ara4FN transferase pncA b1768 1.5147 0.0154 pyrazinamidase / nicotinamidase polB b0060 3.0331 0.0022 DNA polymerase II poxA b4155 0.4978 0.0301 putative regulator of pyruvate oxidase pphB b2734 1.5408 0.0047 protein phosphatase 2 / protein-tyrosine-phosphatase / phosphoprotein phosphatase ppk b2501 0.3409 0.0076 polyphosphate kinase pppA b2972 0.8174 0.0270 prepilin peptidase 142
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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 107 and 108: 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 157: APPENDIX I gene blattner ratio A/B
Page 169 and 170: APPENDIX I gene blattner ratio A/B
Page 205 and 206: Statement of sources Declaration I
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