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

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APPENDIX I gene blattner ratio p-value Function A/B ygbT b2755 0.1586 0.0012 conserved hypothetical protein ygcG b2778 0.4150 0.0418 putative membrane protein ygcI b2757 0.0266 0.0000 hypothetical protein ygcJ b2758 0.4687 0.0197 conserved hypothetical protein ygcK b2759 0.0180 0.0001 hypothetical protein ygcL b2760 0.1023 0.0021 hypothetical protein with possible relationship to novobiocin and deoxycholate resistance ygdR b2833 0.4092 0.0084 conserved hypothetical protein ygeQ b2863 0.6468 0.0449 hypothetical protein ygeW b2870 0.5789 0.0021 putative carbamoyl transferase yghJ b2973 0.4626 0.0310 predicted inner membrane lipoprotein yghR b2984 1.2529 0.0320 conserved protein ygiL b3043 0.0354 0.0001 putative fimbrial-like protein ygjD b3064 1.4330 0.0151 putative O-sialoglycoprotein endopeptidase yhaB b3120 0.6588 0.0079 conserved protein yhcH b3221 1.4678 0.0226 conserved hypothetical protein; gene is in sialic acid catabolic operon yhdH b3253 1.5233 0.0446 putative dehydrogenase yhfK b3358 0.7711 0.0070 hypothetical protein yhfL b3369 0.1799 0.0003 hypothetical protein yhhI b3484 0.1140 0.0042 conserved protein similar to H-repeat-associated proteins yhiK b3489 0.5909 0.0164 hypothetical protein yhjB b3520 0.6632 0.0240 putative regulator yhjH b3525 15.5314 0.0446 protein involved in flagellar function yhjR b3535 0.3106 0.0149 hypothetical protein yiaA b3562 0.3589 0.0101 hypothetical protein yiaJ b3574 1.4560 0.0188 YiaJ transcriptional repressor yiaN b3578 0.5883 0.0029 YiaMNO Binding Protein-dependent Secondary (TRAP) Transporter yiaT b3584 0.3441 0.0061 putative outer membrane protein yiaU b3585 0.3785 0.0049 putative transcriptional regulator LYSR-type yiaV b3586 0.5890 0.0043 putative membrane protein yiaW b3587 0.2799 0.0038 hypothetical protein yibA b3594 0.1903 0.0047 putative lyase yibJ b3595 0.2186 0.0238 hypothetical protein yieL b3719 0.5420 0.0231 putative xylanase yigF b3817 0.2284 0.0094 conserved hypothetical protein yigZ b3848 1.3342 0.0497 putative elongation factor yihN b3874 0.4333 0.0156 YihN MFS transporter yihO b3876 0.6279 0.0411 YihO GPH transporter yihQ b3878 0.6251 0.0380 putative glycosidase yiiG b3896 0.2402 0.0073 conserved protein yiiS b3922 0.2364 0.0157 conserved hypothetical protein yiiU b3928 1.3852 0.0299 conserved hypothetical protein yjbE b4026 0.0840 0.0029 conserved hypothetical protein yjbM b4048 0.4310 0.0137 conserved hypothetical protein yjeB b4178 1.6962 0.0415 conserved protein with a Winged helix domain yjeJ b4145 0.3840 0.0307 conserved protein yjeM b4156 0.2229 0.0057 YjeM APC transporter yjeN b4157 0.3408 0.0038 conserved hypothetical protein yjfJ b4182 0.6175 0.0334 conserved protein yjfK b4183 0.4529 0.0043 conserved hypothetical protein yjfL b4184 0.5766 0.0073 hypothetical protein yjfN b4188 1.3712 0.0202 conserved hypothetical protein yjfZ b4204 0.3394 0.0322 hypothetical protein yjgM b4256 0.4628 0.0240 putative acyltransferase yjgN b4257 0.5071 0.0145 putative membrane protein possible involved in transport yjhB b4279 0.3122 0.0246 YjhB MFS transporter yjhC b4280 0.3612 0.0064 KpLE2 phage-like element; putative NAD(P)-binding dehydrogenase 177
APPENDIX I gene blattner ratio p-value Function A/B yjhF b4296 0.1057 0.0123 YjhF Gnt tranporter yjhG b4297 0.3226 0.0116 putative dehydratase yjhH b4298 0.0468 0.0002 putative lyase/synthase yjhI b4299 0.1141 0.0053 putative regulator yjhP b4306 0.5874 0.0178 putative methyltransferase yjiW b4347 0.2530 0.0215 hypothetical protein ykgA b0300 0.5109 0.0205 putative ARAC-type regulatory protein ykgB b0301 0.2477 0.0014 putative membrane protein ykgF b0307 0.2214 0.0430 putative dehydrogenase ykgH b0310 0.3306 0.0076 conserved protein ykgI b0303 0.0848 0.0003 hypothetical protein ykiA b0392 0.3451 0.0025 hypothetical protein ylbA b0515 0.4807 0.0467 conserved hypothetical protein yliF b0834 0.7291 0.0466 conserved protein ymcC b0986 0.5145 0.0239 putative synthetase, lipoprotein, and/or outer membrane porin ymfE b1138 0.1606 0.0015 hypothetical protein ymfK b1145 1.3071 0.0271 putative phage repressor ymgA b1165 0.3510 0.0002 hypothetical protein ymgB b1166 0.2729 0.0002 hypothetical protein ymgD b1171 0.1185 0.0000 hypothetical protein ynaE b1375 0.1056 0.0000 hypothetical protein ynaI b1330 0.5331 0.0212 YnaI ynaK b1365 0.2104 0.0022 hypothetical protein ynbB b1409 9.4657 0.0003 putative phosphatidate cytidiltransferase ynbD b1411 8.0957 0.0101 putative enzyme yncD b1451 7.7140 0.0189 Probable TonB-dependent receptor yncH b1455 0.6158 0.0168 hypothetical protein yncI b1458 0.0504 0.0048 conserved protein yneG b1523 1.4493 0.0097 conserved hypothetical protein yneK b1527 0.7595 0.0440 conserved protein ynfC b1585 0.6339 0.0385 YnfC lipoprotein ynfN b1551 0.1481 0.0169 hypothetical protein ynjI b1762 0.5647 0.0434 conserved protein yoaC b1810 0.5527 0.0163 conserved hypothetical protein yobF b1824 0.2638 0.0011 hypothetical protein yodA b1973 0.4038 0.0074 cadmium-induced metal binding protein yodB b1974 0.6011 0.0076 putative cytochrome ypdE b2384 0.1729 0.0092 putative endoglucanase yphE b2547 0.7172 0.0119 YphD/YphE/YphF ABC transporter yqeA b2874 0.7065 0.0379 putative carbamate kinase yqeI b2847 0.5345 0.0347 putative sensory transducer yqeJ b2848 0.5636 0.0205 conserved hypothetical protein yqgF b2949 2.0009 0.0211 possible Holliday junction resolvase yqiH b3047 0.4868 0.0245 putative membrane protein yqiJ b3050 0.3830 0.0118 putative oxidoreductase yqjK b3100 0.7262 0.0339 conserved hypothetical protein yraH b3142 0.2087 0.0035 putative fimbrial-like protein yraI b3143 0.2992 0.0267 putative chaperone ytfT b4230 1.3375 0.0312 YtfQ/YtfR/YtfS/YtfT/YjfF ABC transporter znuB b1859 0.7309 0.0475 ZnuA/ZnuB/ZnuC ABC transporter b0322 0.7535 0.0039 178
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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 Supplementary table - VI
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APPENDIX I fabB b2323 0.6336 0.0043
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APPENDIX I ibpA b3687 2.4960 0.0181
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APPENDIX I pepP b2908 1.2182 0.0368
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APPENDIX I speG b1584 0.4151 0.0001
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APPENDIX I ycjX b1321 4.0841 0.0141
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APPENDIX I yhfY b3382 1.4063 0.0453
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Page 157 and 158: APPENDIX I gene blattner ratio A/B
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