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

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APPENDIX I yqiB b3033 0.4189 0.0462 putative enzyme yqiH b3047 2.4661 0.0276 putative membrane protein yqjC b3097 1.5209 0.0227 conserved protein yqjD b3098 1.5220 0.0102 conserved hypothetical protein yraI b3143 1.3222 0.0262 putative chaperone yraM b3147 0.5303 0.0388 putative glycosylase yrbH b3197 0.5469 0.0155 arabinose 5-phosphate isomerase monomer yrbL b3207 0.2776 0.0169 conserved hypothetical protein; transcription is regulated by Mg2+ yrdD b3283 0.4003 0.0038 putative DNA topoisomerase ytfK b4217 0.6795 0.0081 hypothetical protein zipA b2412 0.3991 0.0357 essential cell division protein ZipA zitB b0752 1.9751 0.0090 ZitB zinc CDF transporter znuA b1857 0.5007 0.0149 ZnuA/ZnuB/ZnuC ABC transporter znuC b1858 1.5621 0.0156 ZnuA/ZnuB/ZnuC ABC transporter Supplementary table – VIII: LZ41 fis::cm (A) Vs LZ54 fis::cm (B) gene blattner ratio p-value Function A/B aaeB b3240 1.2701 0.0129 hypothetical protein adk b0474 0.5852 0.0267 adenylate kinase adrA b0385 1.5751 0.0281 putative membrane protein agaB b3138 1.6067 0.0201 EIIAga agaD b3140 2.4760 0.0490 EIIAga agn43 b2000 1.9466 0.0365 outer membrane fluffing protein, sim. to adhesin allC b0516 2.6899 0.0373 allantoate amidohydrolase alpA b2624 0.5764 0.0288 AlpA transcriptional activator alr b4053 0.2726 0.0082 alanine racemase, minor alsK b4084 1.8614 0.0254 putative D-allose kinase apaH b0049 1.3196 0.0053 diadenosine tetraphosphatase appC b0978 1.8506 0.0232 cytochrome bd-II terminal oxidase subunit I aqpZ b0875 0.4831 0.0077 AqpZ - water MIP channel aroA b0908 0.6666 0.0280 3-phosphoshikimate-1-carboxyvinyltransferase aroB b3389 0.6970 0.0352 3-dehydroquinate synthase arsR b3501 2.0062 0.0043 ArsR transcriptional regulator artI b0863 2.0420 0.0102 arginine ABC transporter artP b0864 1.6630 0.0391 arginine ABC transporter ascB b2716 0.4567 0.0314 6-phospho-beta-glucosidase; cryptic ascF b2715 0.3701 0.0083 EIIAsc ascG b2714 0.2203 0.0292 AscG transcriptional regulator asd b3433 0.3109 0.0249 aspartate semialdehyde dehydrogenase astE b1744 1.9337 0.0209 succinylglutamate desuccinylase atpB b3738 0.5641 0.0218 ATP synthase, F0 complex, a subunit atpC b3731 1.8372 0.0366 ATP synthase, F1 complex, epsilon subunit atpI b3739 0.5233 0.0310 AtpI b0165 b0165 0.4909 0.0269 hypothetical protein b0255 b0255 0.3208 0.0410 hypothetical protein b1172 b1172 2.5087 0.0177 conserved hypothetical protein b1364 b1364 1.8486 0.0389 hypothetical protein b1402 b1402 0.6370 0.0207 IS22 protein b2084 b2084 2.3089 0.0387 hypothetical protein b2680 b2680 0.6069 0.0111 YgaY MFS transporter b3808 b3808 0.4513 0.0034 hypothetical protein b4283 b4283 0.3477 0.0343 IS911 protein b4339 b4339 0.4301 0.0234 hypothetical protein 123
APPENDIX I gene blattner ratio p-value Function A/B bax b3570 0.4668 0.0105 putative ATP-binding protein bcp b2480 0.3972 0.0258 thiol peroxidase bcsG b3538 1.5125 0.0251 putative membrane protein bdm b1481 0.4571 0.0254 hypothetical protein betI b0313 0.4422 0.0145 BetI-choline bglF b3722 2.3222 0.0326 EIIBgl btuD b1709 0.4855 0.0190 vitamin B12 transport system caiC b0037 2.6932 0.0083 carnitine-CoA ligase / crotonobetaine-CoA ligase caiT b0040 1.9407 0.0255 CaiT carnitine BCCT transporter carA b0032 0.1987 0.0003 carbamoyl phosphate synthetase carB b0033 0.5195 0.0297 carbamoyl phosphate synthetase cbpM b0999 0.7011 0.0474 chaperone-modulator protein CbpM cdaR b0162 0.2974 0.0285 SdaR transcriptional regulator chaA b1216 1.8253 0.0435 ChaA calcium CaCA transporter cheW b1887 1.4429 0.0031 MCP-II cheY b1882 1.4736 0.0153 CheY-Pasp citD b0617 2.1690 0.0098 subunit of acyl carrier protein citE b0616 1.3927 0.0367 subunit of citryl-ACP lyase citF b0615 1.5300 0.0418 subunit of citrate-ACP transferase clcA b0155 0.5515 0.0298 EriC chloride ion ClC channel clpB b2592 1.6744 0.0098 ClpB chaperone clpS b0881 0.5757 0.0045 specificity factor for ClpA-ClpP chaperone-protease complex cmr b0842 0.3828 0.0352 MdfA/Cmr MFS multidrug transporter coaA b3974 0.2063 0.0077 pantothenate kinase monomer cobC b0638 2.5183 0.0233 alpha-ribazole-5'-P phosphatase cobT b1991 0.6766 0.0163 dimethylbenzimidazole phosphoribosyltransferase cpsG b2048 1.7548 0.0421 phosphomannomutase cpxR b3912 0.3442 0.0296 CpxR-Phosphorylated transcriptional dual regulator creA b4397 0.2676 0.0054 hypothetical protein creB b4398 0.1607 0.0018 CreB- Phosphorylated transcriptional regulator creC b4399 0.4234 0.0038 CreC-Phis crl b0240 0.2018 0.0046 Crl transcriptional regulator csgA b1042 1.4150 0.0203 curlin, major subunit csgC b1043 0.4527 0.0035 putative curli production protein csgD b1040 0.5255 0.0417 CsgD transcriptional activator csiE b2535 0.1601 0.0201 hypothetical protein cspA b3556 0.1189 0.0043 cold shock protein CspA cspB b1557 0.0902 0.0121 cold shock protein CspB cspF b1558 0.0878 0.0007 cold shock protein CspF cspG b0990 0.1566 0.0211 cold shock protein CspG cusR b0571 0.2240 0.0067 CusR transcriptional activator cusS b0570 0.3579 0.0313 putative 2-component sensor protein cutE b0657 2.6030 0.0037 apolipoprotein N-acyltransferase cvpA b2313 0.1480 0.0030 membrane protein required for colicin V production cyaY b3807 0.6324 0.0031 iron-binding frataxin homolog cysE b3607 0.5219 0.0143 cysteine synthase cysM b2421 0.3365 0.0109 O-acetylserine (thiol)-lyase B cytR b3934 0.2132 0.0070 CytR-cytidine dam b3387 1.5263 0.0296 DNA adenine methylase dapF b3809 0.3456 0.0309 diaminopimelate epimerase dcm b1961 0.3666 0.0421 DNA cytosine methylase dcuS b4125 0.5027 0.0194 DcuS-Phis349 degQ b3234 0.4658 0.0158 serine endoprotease degS b3235 0.3105 0.0028 inner membrane serine protease required for the extracytoplasmic stress response mediated by sigmaE deoR b0840 0.2578 0.0132 DeoR transcriptional repressor dgkA b4042 0.4758 0.0169 diacylglycerol kinase 124
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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.,
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 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: 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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