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

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APPENDIX I gene blattner ratio A/B p-value Function yegD b2069 0.1096 0.0022 actin family protein yegP b2080 0.7106 0.0331 conserved hypothetical protein yegS b2086 0.6537 0.0417 conserved protein yegV b2100 0.6305 0.0488 putative kinase yejK b2186 0.5169 0.0083 nucleoid component yfaE b2236 1.5204 0.0066 conserved hypothetical protein, 2Fe-2S ferredoxin-related yfaY b2249 0.6445 0.0134 putative competence-damage protein yfbB b2263 0.4472 0.0003 putative enzyme yfcZ b2343 0.5741 0.0249 conserved hypothetical protein yfdG b2350 2.8866 0.0223 hypothetical protein yfdH b2351 4.5779 0.0047 putative glycan biosynthesis enzyme yfdZ b2379 0.4718 0.0255 putative aminotransferase yfhA b2554 0.6241 0.0138 putative 2-component transcriptional regulator yfiF b2581 0.3793 0.0154 hypothetical protein yfiH b2593 2.3518 0.0047 conserved hypothetical protein yfiQ b2584 0.6139 0.0054 putative NAD(P)-binding and ATP-binding acyl-CoA synthetase ygaF b2660 0.3095 0.0000 hypothetical protein ygaZ b2682 2.9721 0.0184 hypothetical protein ygcL b2760 0.7291 0.0047 hypothetical protein with possible relationship to novobiocin and deoxycholate resistance ygeA b2840 0.4954 0.0300 putative resistance protein ygeO b2857 1.8523 0.0339 hypothetical protein ygfJ b2877 0.6146 0.0146 conserved protein ygfS b2886 1.7328 0.0364 putative oxidoreductase, Fe-S subunit yggJ b2946 1.6239 0.0074 conserved hypothetical protein yggL b2959 0.6458 0.0023 conserved hypothetical protein yggW b2955 1.3703 0.0151 putative oxidase yghB b3009 0.7895 0.0308 putative integral membrane protein yghU b2989 0.2467 0.0025 glutathione transferase-like protein possibly involved in glutathionylspermidine metabolism ygiA b3036 1.6742 0.0177 hypothetical protein yhaV b3130 0.5692 0.0077 conserved hypothetical protein yhcA b3215 2.1510 0.0365 putative chaperone yhdE b3248 0.4955 0.0496 conserved hypothetical protein yhdH b3253 0.3436 0.0006 putative dehydrogenase yheL b3343 3.0897 0.0190 conserved hypothetical protein yheM b3344 4.4555 0.0202 conserved hypothetical protein yheN b3345 2.6968 0.0330 conserved hypothetical protein yheO b3346 2.2685 0.0223 hypothetical protein yhfA b3356 0.5425 0.0352 conserved hypothetical protein yhhM b3467 0.7356 0.0202 putative receptor yhhT b3474 1.3859 0.0171 hypothetical protein yhiQ b3497 1.6969 0.0181 putative methyltransferase yhjK b3529 1.4678 0.0029 conserved protein yiaT b3584 0.8971 0.0295 putative outer membrane protein yibI b3598 1.5584 0.0342 hypothetical protein yicC b3644 0.6226 0.0107 conserved protein yifN b3777 0.6923 0.0355 conserved hypothetical protein yigZ b3848 2.8187 0.0073 putative elongation factor yiiR b3921 0.6478 0.0117 putative membrane protein yijP b3955 0.4791 0.0024 hypothetical protein; related to invasion protein of pathogenic E. coli yjbQ b4056 0.2981 0.0075 conserved hypothetical protein yjcZ b4110 1.2700 0.0269 hypothetical protein yjdM b4108 0.3921 0.0080 hypothetical protein yjgB b4269 0.6383 0.0112 putative oxidoreductase yjiG b4329 0.6702 0.0021 putative membrane protein yjjA b4360 0.6315 0.0065 putative glycoprotein/receptor yjjQ b4365 1.8874 0.0056 putative regulator ykfG b0247 1.4225 0.0448 putative DNA repair protein 159
APPENDIX I gene blattner ratio A/B p-value Function ykgB b0301 0.2697 0.0126 putative membrane protein ykgI b0303 0.1371 0.0142 hypothetical protein yliD b0832 0.5942 0.0294 YliA/YliB/YliC/YliD ABC transporter ymgA b1165 0.1880 0.0008 hypothetical protein ynaJ b1332 0.6770 0.0219 conserved hypothetical protein ynfD b1586 0.4744 0.0302 conserved hypothetical protein ynjH b1760 0.1079 0.0001 conserved hypothetical protein yoaB b1809 0.4229 0.0064 conserved protein yoaC b1810 0.4432 0.0033 conserved hypothetical protein yphC b2545 0.7253 0.0435 predicted oxidoreductase yqeG b2845 2.3330 0.0145 YqeG STP transporter yqfB b2900 0.5018 0.0235 conserved hypothetical protein yqiA b3031 1.8528 0.0482 putative hydrolase yqiI b3048 1.5915 0.0251 conserved protein yqjD b3098 0.5135 0.0398 conserved hypothetical protein yraM b3147 0.6915 0.0206 putative glycosylase yrbA b3190 1.6358 0.0200 hypothetical protein yrdC b3282 1.9330 0.0102 RNA-binding protein with unique protein fold yrdD b3283 3.2410 0.0102 putative DNA topoisomerase yrfF b3398 3.1897 0.0119 putative dehydrogenase ytfA b4205 0.6230 0.0360 hypothetical protein znuA b1857 3.6361 0.0065 ZnuA/ZnuB/ZnuC ABC transporter znuC b1858 1.3426 0.0008 ZnuA/ZnuB/ZnuC ABC transporter zraR b4004 2.5337 0.0077 ZraR-Phosphorylated transcriptional activator Supplementary table – XI: LZ54 wild-type (A) Vs LZ54 fis::cm (B) gene blattner ratio p-value Function A/B aaeX b3242 0.3200 0.0268 hypothetical protein abgB b1337 0.4513 0.0162 hypothetical protein aceF b0115 1.4049 0.0029 AceF-lipoate acs b4069 0.0998 0.0401 putative hydroxycinnamate-CoA ligase / acetyl-CoA synthetase adk b0474 0.4908 0.0443 adenylate kinase aegA b2468 0.4339 0.0331 putative oxidoreductase, Fe-S subunit ahpC b0605 0.4949 0.0199 AhpC component aldB b3588 0.6066 0.0090 putative aminobutyraldehyde dehydrogenase / aldehyde dehydrogenase B allR b0506 0.3675 0.0004 AllR transcriptional regulator amyA b1927 1.4397 0.0367 alpha-amylase, cytoplasmic aniC b4115 0.9075 0.0200 AdiC Arginine:Agmatine Antiporter argR b3237 0.5889 0.0462 ArgR transcriptional dual regulator aroA b0908 0.7038 0.0037 3-phosphoshikimate-1-carboxyvinyltransferase artQ b0862 1.3759 0.0198 arginine ABC transporter atpG b3733 1.3528 0.0009 ATP synthase, F1 complex, gamma subunit b0309 b0309 0.3686 0.0298 hypothetical protein b0373 b0373 0.5710 0.0097 hypothetical protein b1364 b1364 1.7894 0.0168 hypothetical protein baeS b2078 0.5383 0.0205 BaeS-Phis bglG b3723 1.2005 0.0036 BglG monomer cbl b1987 0.7237 0.0159 Cbl transcriptional activator chbG b1733 2.1422 0.0047 hypothetical protein, encoded by an operon required for growth on N,N'- diacetylchitobiose cheB b1883 2.0876 0.0004 CheB-Pasp / PGluMase / protein-glutamine glutaminase cheZ b1881 1.3201 0.0444 CheZ citE b0616 2.1449 0.0394 subunit of citryl-ACP lyase 160
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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 125 and 126: 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 and 158: APPENDIX I gene blattner ratio A/B
Page 175: APPENDIX I gene blattner ratio A/B
Page 205 and 206: Statement of sources Declaration I
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