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

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APPENDIX I gene blattner ratio p-value Function A/B flgD b1075 11.0115 0.0367 flagellar biosynthesis, initiation of hook assembly flgG b1078 5.4828 0.0333 flagellar basal-body rod protein FlgG flgI b1080 2.4887 0.0470 flagellar P-ring protein FlgI fliE b1937 1.6564 0.0329 flagellar basal-body protein FliE fliH b1940 1.5432 0.0196 flagellar biosynthesis protein FliH fliL b1944 5.3308 0.0268 flagellar biosynthesis fliN b1946 4.7917 0.0295 flagellar motor switch protein FliN; component of motor switch and energizing, enabling rotation and determining its direction fliZ b1921 4.2696 0.0330 possible cell-density responsive regulator of sigmaF folC b2315 0.7311 0.0443 folylpoly-γ-glutamate synthetase / dihydrofolate synthetase fpr b3924 2.5348 0.0149 flavodoxin NADP+ reductase frdD b4151 1.6186 0.0382 fumarate reductase membrane protein frlB b3371 2.2009 0.0184 fructoselysine 6-phosphate deglycase monomer fruB b2169 0.3434 0.0332 EIIFru fruK b2168 0.4896 0.0376 1-phosphofructokinase monomer fsaA b0825 7.7628 0.0036 Fsa ftnA b1905 0.5763 0.0388 cytoplasmic ferritin, an iron storage protein) gadA b3517 0.0773 0.0039 glutamate decarboxylase A subunit gadC b1492 0.1005 0.0061 XasA GABA APC transporter gadE b3512 0.1805 0.0075 GadE transcriptional activator gadW b3515 0.2415 0.0112 GadWtranscriptional repressor gadX b3516 0.2187 0.0018 GadX transcriptional activator gcl b0507 1.3668 0.0281 glyoxylate carboligase glf b2036 0.8672 0.0128 UDP-galactopyranose mutase glk b2388 1.8333 0.0429 glucokinase glnB b2553 1.3692 0.0068 PII-UMP glnQ b0809 1.7145 0.0305 glutamine ABC transporter glpK b3926 1.4158 0.0147 glycerol kinase gltF b3214 0.3892 0.0017 regulator of gltBDF operon, induction of Ntr enzymes gltJ b0654 1.5962 0.0062 glutamate ABC transporter gor b3500 1.5677 0.0412 glutathione reductase (NADPH) groE b4142 1.7003 0.0104 GroES, 10 Kd chaperone binds to Hsp60 in pres. Mg-ATP, suppressing its ATPase activity groL b4143 1.6506 0.0412 GroEL, chaperone Hsp60, peptide-dependent ATPase, heat shock protein grpE b2614 2.1870 0.0236 phage lambda replication; host DNA synthesis; heat shock protein; protein repair hdeD b3511 0.1890 0.0048 protein involved in acid resistance hemA b1210 0.5195 0.0126 glutamyl-tRNA reductase hlyE b1182 0.1049 0.0060 hemolysin E hofB b0107 1.8089 0.0424 protein involved in plasmid replication hsdS b4348 1.3534 0.0115 specificity determinant for hsdM and hsdR htrL b3618 0.3544 0.0428 involved in lipopolysaccharide biosynthesis hycF b2720 1.3712 0.0000 formate hydrogenlyase complex hyfA b2481 1.4088 0.0450 hydrogenase 4, component A hyfI b2489 1.2438 0.0144 hydrogenase 4, small subunit hypB b2727 1.7286 0.0223 guanine-nucleotide binding protein, functions as nickel donor for large subunit of hydrogenase 3 iaaA b0828 1.6736 0.0020 beta cleavage product of IaaA idnD b4267 0.5169 0.0436 L-idonate 5-dehydrogenase idnR b4264 1.1480 0.0279 IdnR-5-ketogluconate ilvC b3774 1.6530 0.0410 acetohydroxy acid isomeroreductase ilvY b3773 1.7029 0.0090 IlvY transcriptional dual regulator infB b3168 0.8211 0.0337 protein chain initiation factor IF-2 intG b1936 0.3431 0.0453 hypothetical protein katG b3942 1.3880 0.0202 hydroperoxidase I kdsB b0918 1.5677 0.0297 3-deoxy-D-manno-octulosonate-cytidylyltransferase ldhA b1380 2.9107 0.0129 D-lactate dehydrogenase lrhA b2289 0.4409 0.0449 LrhA transcriptional repressor 99
APPENDIX I gene blattner ratio p-value Function A/B mak b0394 1.4938 0.0390 manno(fructo)kinase malQ b3416 1.2649 0.0206 maltose degrading enzyme 2 / maltose degrading enzyme / amylomaltase map b0168 2.1116 0.0092 methionine aminopeptidase mcrC b4345 0.7384 0.0462 MrcC subunit of 5-methylcytosine restriction system mdtC b2076 0.7845 0.0383 MdtABC RND-type Drug Exporter mdtF b3514 0.4998 0.0195 YhiV mdtM b4337 0.6514 0.0140 YjiO drug MFS transporter menF b2265 0.6845 0.0468 isochorismate synthase, menaquinone-specific menG b3929 1.4163 0.0172 inhibitor of ribonuclease E (RNase E) activity mfd b1114 1.2470 0.0009 transcription-repair coupling factor; mutation frequency decline mntH b2392 2.1445 0.0446 MntH manganese ion NRAMP transporter mobA b3857 2.0022 0.0164 molybdopterin guanine dinucleotide synthase molR_1 b2115 0.5716 0.0391 molybdate metabolism regulator, interrupted mppA b1329 0.3284 0.0002 periplasmic murein tripeptide binding protein msbA b0914 0.7297 0.0302 ATP-binding transport protein; multicopy suppressor of htrB mtlA b3599 1.2772 0.0244 EIIMtl murA b3189 0.6703 0.0265 UDP-N-acetylglucosamine enolpyruvoyl transferase mutS b2733 0.7424 0.0275 MutHLS complex, methyl-directed mismatch repair nrdH b2673 4.4358 0.0460 glutaredoxin-like protein; hydrogen donor nrdI b2674 2.8928 0.0050 stimulates ribonucleotide reduction nuoB b2287 1.3211 0.0440 NADH dehydrogenase I ompF b0929 2.0493 0.0041 outer membrane porin OmpF ompR b3405 1.5638 0.0031 OmpR transcriptional dual regulator ompW b1256 1.5536 0.0299 OmpW, outer membrane protein osmC b1482 0.3366 0.0477 osmotically inducible peroxidase OsmC paaH b1395 1.6745 0.0471 putative 3-hydroxy-acyl-CoA dehydrogenase of phenylacetate degradation paaI b1396 1.5659 0.0497 hypothetical protein with some similarity to thioesterases pagP b0622 0.2030 0.0037 PagP monomer pfkA b3916 2.4655 0.0114 6-phosphofructokinase-1 monomer / putative NAD+ kinase pflB b0903 2.0318 0.0371 pyruvate formate-lyase (inactive) pflD b3951 1.4252 0.0361 formate acetyltransferase 2 pflE b0824 4.1008 0.0376 putative pyruvate formate-lyase 2 activating enzyme pgaA b1024 1.9171 0.0243 putative outer membrane protein pgaB b1023 0.5469 0.0305 putative membrane protein pgk b2926 1.3537 0.0305 phosphoglycerate kinase pinR b1374 0.2637 0.0145 putative transposon resolvase pmrF b2254 0.3626 0.0319 undecaprenyl phosphate-L-Ara4FN transferase pptA b1461 0.5373 0.0206 probable 4-oxalocrotonate tautomerase (4-OT) monomer prlC b3498 1.6015 0.0034 oligopeptidase A proV b2677 0.1318 0.0010 proline ABC transporter proW b2678 0.1876 0.0048 proline ABC transporter pspF b1303 1.5821 0.0168 PspF transcriptional activator pspG b4050 0.7424 0.0314 phage shock protein PspG pta b2297 1.5264 0.0118 phosphate acetyltransferase pyrB b4245 2.0111 0.0261 aspartate carbamoyltransferase, PyrB subunit rdgC b0393 0.7189 0.0182 nonspecific DNA binding protein; nucleoid component recA b2699 0.7639 0.0133 DNA strand exchange and renaturation, DNA-dependent ATPase, DNA- and ATPdependent coprotease recN b2616 0.2723 0.0087 protein used in recombination and DNA repair recX b2698 0.4849 0.0425 inhibitor of RecA relE b1563 0.7927 0.0031 toxin of the RelE-RelB toxin-antitoxin system; cleaves mRNA in ribosome rfaG b3631 0.6527 0.0257 lipopolysaccharide core biosynthesis; glucosyltransferase I rfaQ b3632 0.5460 0.0077 lipopolysaccharide core biosynthesis rhsA b3593 0.4066 0.0429 RhsA protein in rhs element rhsD b0497 0.1528 0.0099 RhsD protein in rhs element rihB b2162 0.4066 0.0069 ribonuceloside hydrolase 2 (pyrimidine-specific) rihC b0030 2.2156 0.0351 ribonucleoside hydrolase 3 100
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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
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 115: 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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