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

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APPENDIX I gene blattner ratio p-value Function A/B acrE b3265 0.1990 0.0005 transmembrane protein affects septum formation and cell membrane permeability acrF b3266 0.4401 0.0079 AcrEF-TolC Drug Efflux Transport System ade b3665 0.4857 0.0346 cryptic adenine deaminase monomer agaA b3135 1.3368 0.0175 AgaA agp b1002 1.7053 0.0169 3-phytase / glucose-1-phosphatase allD b0517 0.8448 0.0140 ureidoglycolate dehydrogenase alsK b4084 2.0491 0.0034 putative D-allose kinase amn b1982 0.6066 0.0233 AMP nucleosidase ampH b0376 0.6290 0.0473 putative enzyme apt b0469 0.4031 0.0012 adenine phosphoribosyltransferase arcB b3210 1.3746 0.0005 ArcB-Phis292 argE b3957 0.4469 0.0206 acetylornithine deacetylase argP b2916 1.8354 0.0114 ArgP transcriptional activator argR b3237 0.8272 0.0077 ArgR transcriptional dual regulator aroG b0754 0.4066 0.0018 2-dehydro-3-deoxyphosphoheptonate aldolase aroL b0388 0.6991 0.0407 shikimate kinase II aroM b0390 1.2587 0.0066 protein of aro operon, regulated by aroR arsR b3501 2.1332 0.0342 ArsR transcriptional regulator artJ b0860 1.4705 0.0115 arginine ABC transporter ascF b2715 0.6756 0.0021 EIIAsc asd b3433 0.3715 0.0107 aspartate semialdehyde dehydrogenase asr b1597 1.4676 0.0477 acid shock protein atoC b2220 1.4762 0.0173 AtoC-Pasp b0165 b0165 0.5609 0.0062 hypothetical protein b0255 b0255 0.4577 0.0292 hypothetical protein b0501 b0501 1.7323 0.0252 hypothetical protein b0582 b0582 1.6254 0.0305 IS186 protein b0609 b0609 1.7352 0.0238 hypothetical protein b1052 b1052 0.6634 0.0425 hypothetical protein b1144 b1144 2.3356 0.0306 hypothetical protein b1371 b1371 1.3289 0.0228 hypothetical protein b1402 b1402 0.5199 0.0099 IS22 protein b1578 b1578 0.3596 0.0018 hypothetical protein b3004 b3004 1.5667 0.0459 hypothetical protein b3044 b3044 0.4341 0.0020 IS21 protein b3975 b3975 0.6083 0.0012 hypothetical protein bcp b2480 0.4248 0.0031 thiol peroxidase bcsB b3532 1.3097 0.0175 cellulose biosynthesis protein bcsZ b3531 1.5108 0.0233 endo-1,4-D-glucanase bfd b3337 1.5485 0.0247 bacterioferritin-associated ferredoxin bglJ b4366 0.6250 0.0347 BglJ transcriptional regulator bisC b3551 0.7735 0.0310 biotin sulfoxide reductase / methionine-S-sulfoxide reductase bolA b0435 1.2797 0.0184 BolA transcriptional regulator borD b0557 0.3304 0.0257 bacteriophage lambda Bor protein homolog btuB b3966 2.9792 0.0085 outer membrane receptor for transport of vitamin B12, E colicins, and bacteriophage BF23 btuF b0158 1.6355 0.0409 periplasmic vitamin B12 binding protein cadA b4131 1.5715 0.0317 lysine decarboxylase caiD b0036 1.4534 0.0482 crotonobetainyl-CoA hydratase / carnitine racemase carA b0032 0.2101 0.0070 carbamoyl phosphate synthetase ccmA b2201 1.6431 0.0142 CcmABCDEFGH cytochrome c biogenesis system cfa b1661 0.6266 0.0211 cyclopropane fatty acid synthase cheY b1882 1.3741 0.0165 CheY-Pasp citX b0614 1.6215 0.0232 holo-ACP synthase clpA b0882 1.3076 0.0196 ATP-binding component of serine protease clpB b2592 1.7953 0.0255 ClpB chaperone cmr b0842 0.6968 0.0355 MdfA/Cmr MFS multidrug transporter 137
APPENDIX I gene blattner ratio p-value Function A/B cobC b0638 2.3925 0.0065 alpha-ribazole-5'-P phosphatase codA b0337 0.3324 0.0112 cytosine deaminase codB b0336 0.3778 0.0284 CodB cytosine NCS1 transporter corA b3816 0.6187 0.0409 CorA magnesium ion MIT transporter cpdA b3032 0.6411 0.0141 cAMP phosphodiesterase cpsB b2049 4.1414 0.0042 mannose-1-phosphate guanylyltransferase-(GDP) cpsG b2048 3.9546 0.0014 phosphomannomutase cpxP b3913 2.3448 0.0199 regulator of the Cpx response and possible chaperone involved in resistance to extracytoplasmic stress creB b4398 0.3912 0.0063 CreB- Phosphorylated transcriptional regulator crl b0240 0.3398 0.0058 Crl transcriptional regulator csgA b1042 1.1757 0.0491 curlin, major subunit csgD b1040 0.3335 0.0298 CsgD transcriptional activator csgE b1039 0.3294 0.0116 curli production assembly/transport component csgG b1037 0.6373 0.0467 curli production component cspA b3556 0.1595 0.0272 cold shock protein CspA cspB b1557 0.0804 0.0020 cold shock protein CspB cspF b1558 0.1563 0.0010 cold shock protein CspF cspI b1552 0.4222 0.0364 cold shock protein CspI cvpA b2313 0.4563 0.0323 membrane protein required for colicin V production cyaY b3807 0.7207 0.0274 iron-binding frataxin homolog cybB b1418 0.4149 0.0121 cytochrome b561 cybC b4236 0.5877 0.0172 cytochrome b562 (soluble) cynR b0338 1.4730 0.0246 CynR-Cyanate transcriptional activator cyoA b0432 1.6203 0.0356 cytochrome bo terminal oxidase subunit II cyoD b0429 1.2541 0.0388 cytochrome bo terminal oxidase subunit IV cyoE b0428 1.7729 0.0214 heme O synthase cysJ b2764 0.8120 0.0324 sulfite reductase flavoprotein subunit cysM b2421 0.7167 0.0338 O-acetylserine (thiol)-lyase B cytR b3934 0.3074 0.0076 CytR-cytidine dapA b2478 0.5629 0.0328 dihydrodipicolinate synthase dapF b3809 0.5061 0.0428 diaminopimelate epimerase dcm b1961 0.8273 0.0436 DNA cytosine methylase dcrB b3472 2.0849 0.0233 conserved protein involved in bacteriophage adsorption ddpA b1487 1.5696 0.0361 YddS ddpC b1485 2.0675 0.0310 YddQ degS b3235 0.4723 0.0130 inner membrane serine protease required for the extracytoplasmic stress response mediated by sigmaE dfp b3639 0.4912 0.0038 P-pantothenate cysteine ligase / P-pantothenoylcysteine decarboxylase dnaB b4052 0.2288 0.0030 chromosome replication; chain elongation; part of primosome dnaG b3066 2.0680 0.0024 DNA biosynthesis; DNA primase dppC b3542 1.7014 0.0194 dipeptide ABC transporter dppF b3540 1.6050 0.0225 dipeptide ABC transporter dsbB b1185 0.7021 0.0043 dsbB protein dsbC b2893 0.5304 0.0070 DsbCoxidized dtd b3887 0.6855 0.0317 D-Tyr-tRNATyr deacylase dxr b0173 1.5005 0.0195 DXP reductoisomerase eda b1850 1.6768 0.0060 oxaloacetate decarboxylase / 2-keto-3-deoxy-6-phosphogluconate aldolase / 2- keto-4-hydroxyglutarate aldolase elaA b2267 0.7645 0.0471 hypothetical protein elaC b2268 0.6841 0.0220 binuclear zinc phosphodiesterase monomer emrE b0543 1.4396 0.0395 EmrE SMR transporter entD b0583 0.7069 0.0132 phosphopantetheinyl transferase entE b0594 0.5193 0.0155 enterobactin synthase multienzyme complex envR b3264 0.6510 0.0447 EnvR transcriptional regulator epd b2927 0.4460 0.0015 erythrose 4-phosphate dehydrogenase eutN b2456 1.0929 0.0134 putative detox protein, ethanolamine utilization 138
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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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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 153: APPENDIX I gene blattner ratio p-va
Page 157 and 158: APPENDIX I gene blattner ratio A/B
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Statement of sources Declaration I
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