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

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APPENDIX I gene blattner ratio p-value Function A/B citX b0614 0.4000 0.0370 holo-ACP synthase clpA b0882 0.7887 0.0340 ATP-binding component of serine protease cpsB b2049 0.3934 0.0301 mannose-1-phosphate guanylyltransferase-(GDP) cpxP b3913 2.7585 0.0052 regulator of the Cpx response and possible chaperone involved in resistance to extracytoplasmic stress creA b4397 0.6098 0.0489 hypothetical protein csgA b1042 0.5922 0.0165 curlin, major subunit cydC b0886 0.5727 0.0423 abc-6-cplx dcd b2065 0.5033 0.0057 dCTP deaminase dcp b1538 0.5735 0.0138 dipeptidyl carboxypeptidase II deoB b4383 2.8180 0.0292 phosphopentomutase dgoR b4479 0.3103 0.0080 regulator protein for dgo operon dinB b0231 0.5729 0.0144 DNA polymerase IV (Y-family DNA polymerase; translesion DNA synthesis) dinD b3645 0.5218 0.0499 DNA-damage-inducible protein dld b2133 0.3096 0.0065 D-lactate:Quinone Oxidoreductase dnaG b3066 2.8483 0.0412 DNA biosynthesis; DNA primase dnaQ b0215 0.4868 0.0086 DNA polymerase III, epsilon subunit dppB b3543 0.3745 0.0395 dipeptide ABC transporter elaA b2267 0.3654 0.0026 hypothetical protein elbB b3209 0.7262 0.0373 sigma cross-reacting protein 27A (SCRP-27A) emtA b1193 0.5201 0.0102 murein transglycosylase E entS b0591 5.6019 0.0045 YbdA MFS transporter erfK b1990 0.4581 0.0299 hypothetical protein with similarity to universal stress protein exbB b3006 9.4812 0.0258 ExbB protein; uptake of enterochelin; tonB-dependent uptake of B colicins exbD b3005 4.8930 0.0016 ExbD uptake of enterochelin; tonB-dependent uptake of B colicins fbaB b2097 0.1818 0.0492 fructose bisphosphate aldolase monomer fecA b4291 3.3493 0.0110 outer membrane receptor; citrate-dependent iron transport, outer membrane receptor fecB b4290 8.7354 0.0011 ferric dicitrate uptake system feoA b3408 1.5400 0.0067 ferrous iron transport protein A fepA b0584 3.0382 0.0381 FepA, outer membrane receptor for ferric enterobactin (enterochelin) and colicins B and D fhuF b4367 6.4472 0.0140 acts in reduction of ferrioxamine B iron fimA b4314 0.0474 0.0033 major type 1 subunit fimbrin (pilin) fimI b4315 0.1958 0.0097 fimbrial protein fklB b4207 0.6485 0.0088 FKBP-type 22KD peptidyl-prolyl cis-trans isomerase (a rotamase) fkpA b3347 0.6246 0.0037 peptidyl-prolyl cis-trans isomerase; in protein folding flgJ b1081 2.4784 0.0147 FlgJ flgM b1071 1.3378 0.0033 anti-FliA (anti-sigma) factor; also known as RflB protein flgN b1070 1.6620 0.0138 flagellar biosynthesis protein FlgN flhB b1880 1.7009 0.0337 flagellar biosynthesis protein FlhB fliE b1937 1.4750 0.0088 flagellar basal-body protein FliE fliF b1938 1.6666 0.0306 flagellar M-ring protein FliF; basal-body MS(membrane and supramembrane)- ring and collar protein fliG b1939 2.1045 0.0069 flagellar motor switch protein FliG; component of motor switching and energizing, enabling rotation and determining its direction fliL b1944 2.1945 0.0188 flagellar biosynthesis fliM b1945 2.0791 0.0003 flagellar motor switch protein FliM; component of motor switch and energizing, enabling rotation and determining its direction fliP b1948 1.9491 0.0114 flagellar biosynthesis protein FliP fliQ b1949 3.0936 0.0072 flagellar biosynthesis protein FliQ fliZ b1921 1.4597 0.0276 possible cell-density responsive regulator of sigmaF flxA b1566 1.6260 0.0119 hypothetical protein; gene is regulated by FliA folE b2153 0.6211 0.0207 GTP cyclohydrolase I frmA b0356 1.1962 0.0067 formaldehyde dehydrogenase, glutathione-dependent ftnA b1905 0.4044 0.0002 cytoplasmic ferritin, an iron storage protein) ftsI b0084 2.4213 0.0314 essential cell division protein FtsI; penicillin-binding protein 3 ftsL b0083 1.7997 0.0053 essential cell division protein FtsL 161
APPENDIX I gene blattner ratio p-value Function A/B galR b2837 2.6916 0.0029 GalR-galactose galT b0758 0.6631 0.0384 UDP-glucose-hexose-1-phosphate uridylyltransferase / galactose-1-phosphate uridylyltransferase galU b1236 1.8258 0.0242 UTP-glucose-1-phosphate uridylyltransferase garR b3125 0.6022 0.0007 tartronate semialdehyde reductase gcl b0507 0.3585 0.0257 glyoxylate carboligase ghrA b1033 0.3564 0.0005 glyoxylate reductase glmS b3729 1.0956 0.0218 L-glutamine:D-fructose-6-phosphate aminotransferase gloA b1651 0.8364 0.0384 glyoxalase I gltB b3212 0.5950 0.0474 glutamate synthase (NADPH) large chain precursor gltD b3213 0.5153 0.0061 glutamate synthase (NADPH) small chain glyA b2551 0.5605 0.0266 glycine hydroxymethyltransferase gmhB b0200 0.6287 0.0027 GmhB gpp b3779 2.2141 0.0307 guanosine-5'-triphosphate,3'-diphosphate pyrophosphatase grxB b1064 0.4556 0.0213 oxidized glutaredoxin 2 gst b1635 0.5631 0.0185 glutathione transferase gutQ b2708 0.7061 0.0173 protein with a sugar isomerase domain hdeD b3511 1.5185 0.0068 protein involved in acid resistance hdfR b4480 0.6083 0.0428 transcriptional regulator hemL b0154 0.6270 0.0356 glutamate-1-semialdehyde aminotransferase hepA b0059 0.5258 0.0325 RNA Polymerase (RNAP)-binding ATPase and RNAP recycling factor hflD b1132 0.6486 0.0423 membrane protein in operon with purB hipA b1507 2.1862 0.0158 HipA transcriptional activator hisI b2026 0.7672 0.0436 phosphoribosyl-AMP cyclohydrolase / phosphoribosyl-ATP pyrophosphatase hisJ b2309 0.5028 0.0038 histidine ABC transporter hscA b2526 1.7721 0.0266 chaperone, member of Hsp70 protein family hsdM b4349 0.7275 0.0448 host modification; DNA methylase M hsdS b4348 0.6614 0.0101 specificity determinant for hsdM and hsdR htrA b0161 2.8995 0.0097 DegP hybD b2993 0.4468 0.0191 hydrogenase 2 maturation endopeptidase hydN b2713 1.2745 0.0490 putative electron transport protein HydN ibpA b3687 2.0616 0.0065 small heat shock protein IbpA inaA b2237 1.3823 0.0226 pH-inducible protein involved in stress response infC b1718 1.3280 0.0197 protein chain initiation factor IF-3 iscA b2528 1.4270 0.0242 iron-sulfur cluster assembly protein iscS b2530 1.4016 0.0167 cysteine desulfurase monomer iscU b2529 1.3576 0.0171 scaffold protein involved in iron-sulfur cluster assembly iscX b2524 1.8316 0.0294 protein with possible role in iron-sulfur cluster biogenesis kdgT b3909 2.3520 0.0274 KdgT 2-keto-3-deoxygluconate transporter kduD b2842 0.7186 0.0150 2-deoxy-D-gluconate 3-dehydrogenase kduI b2843 0.7822 0.0384 homolog of pectin degrading enzyme 5-keto 4-deoxyuronate isomerase leuA b0074 2.9952 0.0235 2-isopropylmalate synthase lplA b4386 0.6314 0.0266 lipoyl-protein ligase A lysU b4129 0.3830 0.0029 lysyl-tRNA synthetase (LysRSu), inducible maa b0459 0.6405 0.0004 maltose acetyltransferase malX b1621 0.5038 0.0496 EIIBCMalX malY b1622 0.7775 0.0304 bifunctional: repressor of maltose regulon / cystathionine beta-lyase manA b1613 0.5147 0.0334 mannose-6-phosphate isomerase map b0168 1.5951 0.0157 methionine aminopeptidase marA b1531 5.0995 0.0031 MarA transcriptional activator marR b1530 4.0195 0.0022 MarR-salicylate mbhA b0230 0.4200 0.0113 putative motility protein mdaB b3028 1.9345 0.0233 NADPH quinone reductase mdoD b1424 0.6780 0.0394 glucan biosynthesis protein D mdtH b1065 0.5184 0.0019 YceL MFS transporter menG b3929 0.7805 0.0366 inhibitor of ribonuclease E (RNase E) activity mfd b1114 0.5397 0.0158 transcription-repair coupling factor; mutation frequency decline 162
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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 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 141 and 142: APPENDIX I gene blattner ratio p-va
Page 157 and 158: APPENDIX I gene blattner ratio A/B
Page 177: APPENDIX I gene blattner ratio A/B
Page 205 and 206: Statement of sources Declaration I
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