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

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APPENDIX I gene blattner ratio p-value Function A/B rplX b3309 3.5468 0.0478 50S ribosomal subunit protein L24 rpmA b3185 0.4113 0.0210 50S ribosomal subunit protein L27 rpmI b1717 6.8633 0.0383 50S ribosomal subunit protein A rpoA b3295 2.8507 0.0294 RNA polymerase, alpha subunit rpsD b3296 5.2826 0.0441 30S ribosomal subunit protein S4 rpsE b3303 12.4222 0.0115 30S ribosomal subunit protein S5 rpsH b3306 4.2597 0.0254 30S ribosomal subunit protein S8, and regulator rpsN b3307 6.6163 0.0259 30S ribosomal subunit protein S14 rpsR b4202 1.8126 0.0017 30S ribosomal subunit protein S18 rsd b3995 0.6020 0.0268 regulator of sigma D rseB b2571 0.2066 0.0278 negative regulator of sigmaE; interacts with RseA and stimulates binding of RseA to sigmaE rusA b0550 0.6409 0.0385 endodeoxyribonuclease RUS (Holliday junction resolvase) sdhB b0724 1.7743 0.0237 succinate dehydrogenase iron-sulfur protein sfsA b0146 3.3885 0.0017 SfsA sgrR b0069 0.5711 0.0195 SgrR transcriptional regulator slp b3506 1.8331 0.0144 outer membrane protein induced after carbon starvation slyA b1642 4.5810 0.0274 SlyA transcriptional activator smf b4473 1.0372 0.0064 hypothetical protein sohB b1272 0.5393 0.0272 putative protease somA b0877 0.7299 0.0121 putative enzyme speD b0120 0.5703 0.0350 adenosylmethionine decarboxylase, proenzyme speE b0121 1.3579 0.0421 spermidine synthase speG b1584 0.4922 0.0388 spermidine acetyltransferase spoT b3650 0.4810 0.0407 GDP diphosphokinase / guanosine-3',5'-bis(diphosphate) 3'-diphosphatase sucA b0726 8.0970 0.0066 subunit of E1(0) component of 2-oxoglutarate dehydrogenase surE b2744 1.5675 0.0023 phosphatase with broad substrate specificity / 3'-nucleotidase / 5'-nucleotidase talA b2464 7.9764 0.0051 transaldolase A tauA b0365 1.1408 0.0442 TauA/TauB/TauC ABC transporter tfaQ b1546 4.3804 0.0443 hypothetical protein trkA b3290 0.8203 0.0039 TrkA trmD b2607 8.9475 0.0351 tRNA (guanine-1-)-methyltransferase trmU b1133 0.5271 0.0381 catalyzes 2-thiouridine modification of tRNA ttk b3641 3.3439 0.0494 Ttk transcriptional regulator ubiE b3833 0.8435 0.0494 S-adenosylmethionine:2-DMK methyltransferase / 2-octaprenyl-6-methoxy-1,4- benzoquinone methylase upp b2498 0.5649 0.0007 uracil phosphoribosyltransferase uspG b0607 2.9614 0.0340 universal stress protein of the UspA family uxuA b4322 0.8406 0.0459 mannonate dehydratase uxuR b4324 0.7367 0.0352 UxuR transcriptional regulator wrbA b1004 4.9428 0.0377 WrbA xapA b2407 0.7936 0.0468 xanthosine phosphorylase xylA b3565 2.0099 0.0081 xylose isomerase xylB b3564 0.5746 0.0049 xylulokinase xylF b3566 0.7195 0.0419 xylose ABC transporter yaaH b0010 0.6869 0.0271 putative transport protein yabI b0065 1.8964 0.0149 putative integral membrane protein yadH b0128 3.3596 0.0418 YadG/YadH ABC transporter yadR b0156 2.8838 0.0285 conserved hypothetical protein yafS b0213 0.6999 0.0147 putative methyltransferase yahC b0317 0.8078 0.0212 putative membrane protein yahK b0325 1.3928 0.0045 putative oxidoreductase ybbP b0496 0.7792 0.0036 YbbA/YbbP ABC transporter ybcO b0549 0.6231 0.0253 hypothetical protein ybdL b0600 0.4618 0.0229 methionine aminotransferase ybeB b0637 1.7480 0.0389 conserved hypothetical protein ybeR b0645 0.5813 0.0326 conserved hypothetical protein 95
APPENDIX I gene blattner ratio p-value Function A/B ybhA b0766 0.7300 0.0055 putative phosphatase ybhL b0786 2.1462 0.0351 putative transport protein ybhN b0788 0.7033 0.0260 hypothetical protein ycbU b0942 0.7402 0.0421 putative fimbrial-like protein yccJ b1003 5.6972 0.0370 hypothetical protein ycdF b1005 3.8775 0.0307 hypothetical protein ycdJ b1009 2.2829 0.0227 putative acetyltransferase ycdN b1016 1.7264 0.0325 hypothetical protein of the OFeT transport family yceK b1050 0.9386 0.0468 hypothetical protein ycjF b1322 2.8255 0.0176 putative membrane protein ycjO b1311 0.5416 0.0001 YcjN/YcjO/YcjP ABC transporter yddL b1472 0.6258 0.0181 putative outer membrane porin protein ydeI b1536 3.2270 0.0014 conserved hypothetical protein ydfJ b1543 0.2900 0.0231 YdfJ yeaK b1787 1.5080 0.0319 conserved hypothetical protein yebQ b1828 0.8734 0.0441 YebQ yebS b1833 0.8160 0.0391 putative membrane protein yecC b1917 0.7788 0.0141 putative ATP-binding component of a transport system yeeA b2008 0.6257 0.0087 putative membrane protein, transport yeeL_2 b1979 0.6176 0.0176 putative transport protein yeeO b1985 0.5128 0.0485 YeeO MATE Transporter yeeT b2003 0.5966 0.0348 hypothetical protein yejB b2178 1.2896 0.0364 YejA/YejB/YejE/YejF ABC transporter yfbE b2253 0.5801 0.0012 UDP-L-Ara4O C-4" transaminase yfeC b2398 0.3352 0.0137 hypothetical protein yfeK b2419 0.6148 0.0371 conserved protein yfgM b2513 0.4685 0.0406 conserved protein yfhG b2555 0.9007 0.0264 conserved protein yfhR b2534 0.8297 0.0101 putative methylase or hydrolase yfiP b2583 1.7964 0.0494 conserved hypothetical protein yfjX b2643 0.7308 0.0082 hypothetical protein ygdQ b2832 0.6379 0.0085 putative transport protein ygeF b2850 0.8063 0.0120 conserved hypothetical protein yggC b2928 6.2501 0.0187 putative kinase yggN b2958 0.7475 0.0321 conserved hypothetical protein yghJ b2974 1.1108 0.0216 predicted inner membrane lipoprotein yghU b2989 1.1448 0.0338 glutathione transferase-like protein possibly involved in glutathionylspermidine metabolism ygiH b3059 0.6438 0.0454 putative membrane protein ygiU b3022 3.8905 0.0267 putative cyanide hydratase ygjJ b3079 0.9097 0.0041 hypothetical protein yhaK b3106 2.4963 0.0437 conserved hypothetical protein yhbN b3200 0.6192 0.0050 YhbG/YhbN ABC transporter yhfX b3381 1.2679 0.0037 conserved protein yhhX b3440 0.7634 0.0300 putative galactose 1-dehydrogenase yhjD b3522 2.7084 0.0452 putative membrane protein yiaD b3552 2.3769 0.0160 putative outer membrane protein yiaV b3586 0.5516 0.0468 putative membrane protein yicH b3655 1.5065 0.0436 conserved protein yifN b3777 0.5132 0.0378 conserved hypothetical protein yigF b3817 0.4341 0.0171 conserved hypothetical protein yiiX b3937 0.6653 0.0054 conserved hypothetical protein of the NlpC/P60 peptidase superfamily yjdK b4128 0.6048 0.0143 hypothetical protein yjeQ b4161 0.9234 0.0275 GTPase and putative translation factor / GTPase yjgR b4263 0.7614 0.0369 putative enzyme with P-loop containing nucleotide triphosphate hydrolase domain yjhB b4279 4.7570 0.0247 YjhB MFS transporter yjhT b4310 0.8659 0.0460 putative enzyme contains galactose oxidase-like domain 96
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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
Page 61 and 62: RESULTS transcripts of a growth pha
Page 63 and 64: RESULTS phosphorylation, are associ
Page 65 and 66: RESULTS Table 4: RT-PCR analysis of
Page 67 and 68: RESULTS Figure 16: Schematic repres
Page 69 and 70: RESULTS parC) which allows the supe
Page 71 and 72: RESULTS Figure 19: In vitro transcr
Page 73 and 74: RESULTS contrast the tyrTD promoter
Page 75 and 76: DISCUSSION 4 Discussion The idea of
Page 77 and 78: DISCUSSION In a study by Balke & Gr
Page 79 and 80: DISCUSSION cells maintain viability
Page 81 and 82: DISCUSSION writhe in the UAS by FIS
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 111: 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
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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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