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

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APPENDIX I gene blattner ratio p-value Function A/B ykgJ b0288 0.5411 0.0198 putative ferredoxin ymgA b1165 1.8693 0.0273 hypothetical protein ymgC b1167 13.1366 0.0366 hypothetical protein ymgD b1171 0.3867 0.0100 hypothetical protein ynaA b1368 0.9570 0.0079 putative alpha helix protein yncA b1448 1.1679 0.0391 putative N-acetyltransferase yneG b1523 1.1135 0.0464 conserved hypothetical protein ynfA b1582 5.9471 0.0110 inner membrane protein yniB b1726 3.4656 0.0443 hypothetical protein yoaG b1796 0.5357 0.0394 hypothetical protein yobB b1843 0.7096 0.0410 conserved hypothetical protein yohC b2135 3.0037 0.0304 putative transport protein yohD b2136 0.6268 0.0385 hypothetical protein yohJ b2141 0.8408 0.0481 putative transmembrane protein yphA b2543 2.8374 0.0476 hypothetical protein yqjE b3099 1.9245 0.0368 conserved protein yraM b3147 0.8763 0.0122 putative glycosylase yrbD b3193 1.2481 0.0359 YrbD yrdA b3279 0.4732 0.0240 putative transferase yrfG b3399 0.5282 0.0267 putative hydrolase with a phophatase-like domain ytfF b4210 0.4613 0.0484 putative transmembrane subunit ytfK b4217 11.1610 0.0296 hypothetical protein ytjB b4387 0.5306 0.0382 membrane protein znuA b1857 0.4613 0.0187 ZnuA/ZnuB/ZnuC ABC transporter zraP b4002 0.2157 0.0093 zinc homeostasis protein b0395 2.2058 0.0439 b0322 1.4431 0.0208 b3948 0.7342 0.0285 Supplementary table - IV: CSH50 wild-type (A) Vs CSH50 hns-205::Tn10 (B), Mid-exponential phase gene blattner ratio p-value Function A/B acrE b3265 0.4232 0.0319 transmembrane protein affects septum formation and cell membrane permeability ade b3665 0.0880 0.0027 cryptic adenine deaminase monomer agaB b3138 0.5821 0.0060 EIIAga agaC b3139 0.5600 0.0258 EIIAga allD b0517 0.3467 0.0295 ureidoglycolate dehydrogenase alsA b4087 1.4648 0.0056 YjcW alsK b4084 1.6686 0.0186 putative D-allose kinase aniC b4115 0.1952 0.0013 AdiC Arginine:Agmatine Antiporter artJ b0860 1.3014 0.0092 arginine ABC transporter asnA b3744 4.5645 0.0110 aspartate-ammonia ligase azoR b1412 1.7670 0.0328 acyl carrier protein phosphodiesterase b0501 b0501 0.3204 0.0148 hypothetical protein b1172 b1172 0.3230 0.0046 conserved hypothetical protein b1364 b1364 1.7953 0.0104 hypothetical protein b1437 b1437 2.0579 0.0149 hypothetical protein b2084 b2084 0.2573 0.0018 hypothetical protein b2680 b2680 0.2973 0.0151 YgaY MFS transporter b4283 b4283 0.7779 0.0431 IS911 protein basR b4113 0.5152 0.0269 BasR-Phosphorylated transcriptional regulator bcsE b3536 0.7416 0.0435 putative protease 97
APPENDIX I gene blattner ratio p-value Function A/B bglG b3723 0.3084 0.0458 BglG monomer bioF b0776 0.5910 0.0182 8-amino-7-oxononanoate synthase cadA b4131 0.4186 0.0251 lysine decarboxylase cfa b1661 1.7766 0.0466 cyclopropane fatty acid synthase chaC b1218 0.6361 0.0124 cation transport regulator chbB b1738 0.7761 0.0260 EIIChb chbR b1735 0.6426 0.0292 ChbR transcriptional regulator citC b0618 0.4542 0.0028 citrate lyase ligase citD b0617 0.4617 0.0403 subunit of acyl carrier protein clpA b0882 2.1712 0.0279 ATP-binding component of serine protease clpB b2592 1.8746 0.0335 ClpB chaperone copA b0484 2.0211 0.0020 YbaR csgA b1042 0.3262 0.0123 curlin, major subunit csgB b1041 0.3223 0.0205 curlin, minor subunit precursor csgD b1040 0.2580 0.0060 CsgD transcriptional activator csgF b1038 0.3660 0.0143 curli assembly component csiE b2535 2.3439 0.0459 hypothetical protein cspC b1823 0.5094 0.0463 cold shock protein CspC cspI b1552 0.1583 0.0104 cold shock protein CspI cutC b1874 0.6803 0.0402 copper homeostasis protein cysH b2762 1.3960 0.0442 3'-phospho-adenylylsulfate reductase cysP b2425 1.7696 0.0110 thiosulfate ABC transporter dcrB b3472 1.7334 0.0438 conserved protein involved in bacteriophage adsorption dctR b3507 0.4226 0.0328 protein involved in metabolism of C4-dicarboxylates dcuS b4125 1.6044 0.0224 DcuS-Phis349 ddpC b1485 1.3826 0.0444 YddQ dgoR b3694 1.6453 0.0106 regulator protein for dgo operon djlC b0649 0.6688 0.0445 Hsc56; a DnaJ-like protein that activates ATPase activity of Hsc62 dmsB b0895 1.5182 0.0340 dimethyl sulfoxide reductase, chain B dmsC b0896 1.4176 0.0279 dimethyl sulfoxide reductase, chain C dmsD b1591 1.3281 0.0123 DMS reductase maturation protein dpiA b0620 0.2993 0.0020 CitB transcriptional regulator dpiB b0619 0.2370 0.0054 DpiB dsbC b2893 0.3743 0.0137 DsbCoxidized elaD b2269 0.7119 0.0344 putative sulfatase / phosphatase entA b0596 1.8924 0.0444 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase exbB b3006 3.9960 0.0236 ExbB protein; uptake of enterochelin; tonB-dependent uptake of B colicins exbD b3005 3.9950 0.0076 ExbD uptake of enterochelin; tonB-dependent uptake of B colicins fdoG b3894 1.9381 0.0090 formate dehydrogenase-O, α subunit fecR b4292 3.3052 0.0019 regulator for fec operon, periplasmic feoB b3409 8.1963 0.0108 FeoB ferrous iron transporter fepC b0588 2.0669 0.0123 Ferric Enterobactin Transport System fhuA b0150 3.0188 0.0173 FhuA outer membrane protein receptor for ferrichrome, colicin M, and phages T1, T5, and phi80 fhuB b0153 1.7527 0.0468 ferrichrome uptake system fhuC b0151 2.1582 0.0127 ferrichrome uptake system fic b3361 1.3570 0.0403 stationary-phase protein with possible role in p-aminobenzoate or folate biosynthesis fimB b4312 0.1579 0.0019 regulator for fimA fimC b4316 0.2925 0.0204 periplasmic chaperone, required for type 1 fimbriae fimD b4317 0.2625 0.0115 outer membrane protein; export and assembly of type 1 fimbriae, interrupted fimE b4313 0.4518 0.0341 regulator for fimA fimF b4318 0.1795 0.0195 fimbrial morphology fimG b4319 0.3289 0.0425 fimbrial morphology fimH b4320 0.3630 0.0420 minor fimbrial subunit, D-mannose specific adhesin fixA b0041 0.2419 0.0368 probable flavoprotein subunit required for anaerobic carnitine metabolism flgA b1072 5.3030 0.0410 flagellar biosynthesis; assembly of basal-body periplasmic P ring flgC b1074 13.7652 0.0406 flagellar basal-body rod protein FlgC 98
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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
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
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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 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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