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

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APPENDIX I gene blattner ratio p-value Function A/B torZ b1872 0.7072 0.0237 trimethylamine N-oxide reductase III, TorZ subunit trkH b3849 0.6885 0.0381 TrkH potassium ion Trk Transporter trmH b3651 1.8914 0.0192 tRNA (Gm18) 2'-O-methyltransferase trpE b1264 0.3805 0.0021 anthranilate synthase component I trxB b0888 2.0565 0.0480 thioredoxin reductase monomer tsx b0411 0.2461 0.0277 nucleoside channel; receptor of phage T6 and colicin K ttk b3641 0.6729 0.0216 Ttk transcriptional regulator tufA b3339 0.7291 0.0156 elongation factor Tu tyrR b1323 0.7217 0.0246 TyrR-Phenylalanine transcriptional repressor ubiC b4039 0.2269 0.0075 chorismate pyruvate lyase udk b2066 1.5831 0.0047 uridine kinase / cytidine kinase ugpB b3453 1.9109 0.0225 glycerol-3-P ABC transporter / tranport ulaG b4192 1.5035 0.0480 putative L-ascorbate 6-phosphate lactonase uppS b0174 0.6969 0.0442 subunit of undecaprenyl diphosphate synthase uspF b1376 0.5835 0.0176 nucleotide binding protein uvrB b0779 1.7413 0.0390 DNA repair; excision nuclease subunit B uvrY b1914 0.5143 0.0135 UvrY- Phosphorylated transcriptional regulator vsr b1960 0.6583 0.0004 DNA mismatch endonuclease of the very short patch (VSP) mismatch repair pathway wbbI b2034 1.8917 0.0454 hypothetical protein; not required for colanic acid biosynthesis wcaB b2058 3.4010 0.0356 putative transferase wcaC b2057 3.4672 0.0035 putative glycosyl transferase wcaE b2055 2.1253 0.0353 putative colanic acid biosynthesis glycosyl transferase wcaF b2054 2.3400 0.0172 putative transferase wcaJ b2047 3.5268 0.0124 putative colanic acid biosynthsis UDP-glucose lipid carrier transferase wcaK b2045 3.6607 0.0020 putative galactokinase (EC 2.7.1.6). wcaL b2044 3.4923 0.0027 putative colanic biosynthesis glycosyl transferase wcaM b2043 3.6739 0.0018 hypothetical protein wzc b2060 2.2224 0.0433 tyrosine kinase involved in colanic acid biosynthesis wzxC b2046 3.2937 0.0149 WzxC wzxE b3792 1.7476 0.0290 metabolism; biosynthesis of macromolecules (cellular constituents); enterobacterial common antigen (surface glycolipid) transport wzzE b3785 0.5895 0.0452 putative transport protein xapR b2405 0.3135 0.0382 XapR transcriptional activator xdhB b2867 1.1750 0.0243 putative xanthine dehydrogenase subunit, FAD-binding domain xdhD b2881 1.6833 0.0105 putative oxidoreductase; possible component of selenate reductase with possible role in purine salvage xerD b2894 0.4958 0.0395 site-specific recombinase xseB b0422 0.1694 0.0020 exonuclease VII, small subunit xylA b3565 0.4106 0.0021 xylose isomerase xylG b3567 0.8076 0.0315 xylose ABC transporter xylR b3569 0.5108 0.0188 XylR-Xylose transcriptional activator yabP b0056 0.5438 0.0159 conserved hypothetical protein yadL b0137 0.6723 0.0395 putative adhesin-like protein yaeB b0195 1.4683 0.0342 hypothetical protein yaeF b0193 1.3932 0.0097 putative synthase of the YaeF/YiiX family yaeH b0163 0.7470 0.0373 putative structural protein yafK b0224 0.3497 0.0087 conserved protein; in enteroaggregative E. coli, YafK is required for development of biofilms yagA b0267 1.6510 0.0239 hypothetical protein yagK b0277 1.2809 0.0271 hypothetical protein yagL b0278 2.0628 0.0124 DNA-binding protein yagN b0280 0.4906 0.0152 hypothetical protein yagU b0287 0.5401 0.0210 conserved protein yagZ b0293 1.5683 0.0418 conserved hypothetical protein yahA b0315 0.3553 0.0092 hypothetical protein yahG b0321 1.5771 0.0398 conserved protein yahJ b0324 1.6920 0.0040 putative deaminase 145
APPENDIX I gene blattner ratio p-value Function A/B yaiB b0382 0.2451 0.0009 conserved hypothetical protein yajR b0427 1.2541 0.0397 YajR MFS transporter ybaJ b0461 0.2101 0.0016 conserved hypothetical protein ybaN b0468 0.4651 0.0207 hypothetical protein ybaP b0482 0.4012 0.0131 putative ligase ybbK b0489 1.2971 0.0106 putative protease ybbW b0511 1.7524 0.0306 YbbW NCS1 Transporter ybcK b0544 2.1084 0.0046 hypothetical protein ybdM b0601 1.5187 0.0100 conserved protein ybeD b0631 2.1582 0.0344 conserved hypothetical protein ybeY b0659 2.4213 0.0071 conserved hypothetical protein ybeZ b0660 2.9088 0.0292 putative ATP-binding protein ybfE b0685 1.8437 0.0015 hypothetical protein, transcriptionally regulated by LexA ybgA b0707 1.5859 0.0393 conserved protein ybgD b0719 0.5899 0.0284 putative fimbrial-like protein ybhC b0772 0.4417 0.0083 putative pectinesterase ybiN b0807 0.6910 0.0207 putative methyltransferase ybjC b0850 0.5669 0.0359 conserved hypothetical protein; gene is within soxRS regulon ybjK b0846 1.7319 0.0164 putative DEOR-type transcriptional regulator ybjP b0865 1.4541 0.0338 putative enzyme ycaL b0909 0.4083 0.0132 putative heat shock protein ycbB b0925 0.6763 0.0145 putative amidase ycdO b1018 1.6105 0.0013 conserved hypothetical protein yceJ b1057 1.4910 0.0123 putative cytochrome ycfM b1105 0.5966 0.0118 putative fibronectin-binding protein ycfQ b1111 2.1759 0.0130 hypothetical protein ycgE b1162 0.4795 0.0012 putative transcriptional regulator ycgH_1 b1169 1.8719 0.0154 conserved protein; member of the Autotransporter family ycgJ b1177 0.7096 0.0429 hypothetical protein ycgL b1179 0.3597 0.0007 conserved hypothetical protein ycgN b1181 0.2099 0.0018 conserved hypothetical protein ychF b1203 1.8344 0.0127 putative GTP-binding protein ychJ b1233 0.4063 0.0421 conserved hypothetical protein yciK b1271 0.5205 0.0025 putative oxidoreductase yciO b1267 1.3356 0.0473 conserved protein yciS b1279 0.6049 0.0052 conserved hypothetical protein ycjG b1325 0.4886 0.0004 L-Ala-D/L-Glu epimerase, a muconate lactonizing enzyme ycjZ b1328 0.3753 0.0083 putative transcriptional regulator LYSR-type ydaO b1344 0.4843 0.0448 conserved protein ydaT b1358 1.2401 0.0281 hypothetical protein ydbK b1378 1.3365 0.0031 putative pyruvate synthase ydcD b1457 0.4394 0.0073 hypothetical protein ydcV b1443 1.5826 0.0274 YdcS/YdcT/YdcV/YdcU ABC transporter ydeH b1535 0.6334 0.0003 hypothetical protein ydeI b1536 0.7006 0.0434 conserved hypothetical protein ydeO b1499 1.8404 0.0071 putative ARAC-type regulatory protein ydeP b1501 1.8515 0.0329 acid resistance protein ydeQ b1502 1.5966 0.0329 putative adhesin; similar to FimH protein ydeS b1504 2.0807 0.0078 putative fimbrial-like protein ydfH b1540 0.6051 0.0014 hypothetical protein ydfT b1559 1.2620 0.0433 hypothetical protein YdgE b1599 0.5062 0.0374 YdgE SMR Protein ydgI b1605 1.2957 0.0413 ArcD APC transporter ydgT b1625 0.2841 0.0002 conserved hypothetical protein ydhF b1647 0.5142 0.0040 putative oxidoreductase, NAD(P)-linked ydhH b1640 0.5712 0.0220 conserved hypothetical protein 146
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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 111 and 112: 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 161: APPENDIX I gene blattner ratio p-va
Page 205 and 206: Statement of sources Declaration I
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