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

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APPENDIX I gene blattner ratio p-value Function A/B mglC b2148 0.1817 0.0059 galactose ABC transporter moeB b0826 0.3297 0.0018 molybdopterin biosynthesis mog b0009 0.6094 0.0062 required for the efficient incorporation of Mo into molybdoproteins motA b1890 1.4410 0.0182 MotA protein, proton conductor component of motor; no effect on switching mpaA b1326 0.6680 0.0238 murein peptide amidase A mraW b0082 1.6512 0.0423 S-adenosyl-dependent methyltransferase msrA b4219 0.3359 0.0142 methionine sulfoxide reductase A / protein-methionine-S-oxide reductase / methionine sulfoxide reductase mug b3068 0.2422 0.0049 stationary phase mismatch/uracil DNA glycosylase mukE b0923 2.2877 0.0118 protein involved in chromosome partitioning mukF b0922 2.1539 0.0075 Ca2+-binding protein involved in chromosome partitioning murC b0091 1.3976 0.0217 UDP-N-acetylmuramate-alanine ligase murD b0088 1.1421 0.0308 UDP-N-acetylmuramoylalanine-D-glutamate ligase mutH b2831 0.4240 0.0337 MutHLS complex, methyl-directed mismatch repair nadR b4390 0.6257 0.0268 NadR transcriptional repressor / NMN adenylyltransferase nagA b0677 0.5678 0.0282 N-acetylglucosamine-6-phosphate deacetylase nagB b0678 0.4101 0.0011 glucosamine-6-phosphate deaminase narL b1221 0.5206 0.0007 NarL-Phosphorylated transcriptional dual regulator narX b1222 0.4355 0.0202 NarX-Phis nfi b3998 0.6846 0.0473 endonuclease V (deoxyinosine 3'endoduclease) nfnB b0578 0.7962 0.0085 dihydropteridine reductase nfrA b0568 0.3236 0.0069 bacteriophage N4 receptor, outer membrane protein nfsA b0851 1.5581 0.0063 NADPH nitroreductase nlpD b2742 0.6439 0.0366 NlpD putative outer membrane lipoprotein nudH b2830 1.4474 0.0158 putative invasion protein ompA b0957 0.7281 0.0106 outer membrane protein 3a (II*;G;d) ompC b2215 2.0986 0.0040 outer membrane porin OmpC ompX b0814 0.6904 0.0223 outer membrane protein X oxyR b3961 0.6290 0.0201 OxyR transcriptional dual regulator paaB b1389 0.0991 0.0404 putative subunit of phenylacetate-CoA oxygenase paaI b1396 1.8933 0.0289 hypothetical protein with some similarity to thioesterases pal b0741 0.5468 0.0040 Tol-Pal Cell Envelope Complex panF b3258 0.7935 0.0164 PanF sodium/pantothenate SSS transporter pepQ b3847 1.5249 0.0184 proline dipeptidase pfkA b3916 0.5688 0.0041 6-phosphofructokinase-1 monomer / putative NAD+ kinase pfkB b1723 0.4510 0.0068 6-phosphofructokinase-2 monomer pgk b2926 1.3521 0.0229 phosphoglycerate kinase pheS b1714 1.4275 0.0242 phenylalanyl-tRNA synthetase α-chain phnI b4099 2.1789 0.0451 phosphonate metabolism plsX b1090 2.1023 0.0467 glycerolphosphate auxotrophy in plsB background pmbA b4235 0.6317 0.0323 protease involved in Microcin B17 maturation and in sensitivity to the DNA gyrase inhibitor LetD pnuC b0751 1.2218 0.0260 PnuC NMN transporter poxA b4155 0.4524 0.0462 putative regulator of pyruvate oxidase ppiD b0441 0.7431 0.0500 peptidyl-prolyl cis-trans isomerase prfA b1211 2.0627 0.0070 peptide chain release factor RF-1 prfH b0236 0.3770 0.0439 probable peptide chain release factor prlC b3498 0.5779 0.0203 oligopeptidase A prmA b3259 0.6861 0.0196 methylation of 50S ribosomal subunit protein L11 proA b0243 0.8509 0.0152 gamma-glutamyl kinase-GP-reductase multienzyme complex ptrA b2821 0.2672 0.0247 protease III purB b1131 0.7424 0.0127 5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole lyase / adenylosuccinate lyase purD b4005 0.6497 0.0099 phosphoribosylamine-glycine ligase purE b0523 0.5049 0.0089 N5-carboxyaminoimidazole ribonucleotide mutase purR b1658 1.3164 0.0433 PurR transcriptional repressor purT b1849 0.4486 0.0494 GAR transformylase 2 163
APPENDIX I gene blattner ratio p-value Function A/B puuA b1297 0.4444 0.0002 putative glutamine synthetase (EC 6.3.1.2) puuR b1299 2.1380 0.0256 putative oxidoreductase/putative regulator racR b1356 1.7456 0.0218 hypothetical protein rcsF b0196 0.7467 0.0352 RcsF-P recB b2820 0.3206 0.0117 RecB; DNA helicase, ATP-dependent dsDNA/ssDNA exonuclease V subunit, ssDNA endonuclease recC b2822 2.3410 0.0070 DNA helicase, ATP-dependent dsDNA/ssDNA exonuclease V subunit, ssDNA endonuclease rep b3778 0.5395 0.0242 rep helicase, a single-stranded DNA dependent ATPase rffD b3787 1.6810 0.0404 UDP-N-acetyl-D-mannosaminuronic acid dehydrogenase rffG b3788 1.4341 0.0315 dTDP-glucose 4,6-dehydratase 2 rhsC_1 b0700 0.2172 0.0239 RhsC protein in rhs element, interrupted rhtB b3824 0.4705 0.0156 RhtB homoserine Rht Transporter rimJ b1066 0.6184 0.0212 acetylates N-terminal alanine of 30S ribosomal subunit protein S5 / ribosomalprotein-alanine N-acetyltransferase rob b4396 0.6252 0.0498 Rob transcriptional activator rplD b3319 1.8347 0.0070 50S ribosomal subunit protein L4, regulates expression of S10 operon rplP b3313 1.3529 0.0061 50S ribosomal subunit protein L16 rpmG b3636 1.7607 0.0218 50S ribosomal subunit protein L33 rpsI b3230 2.3038 0.0446 30S ribosomal subunit protein S9 ruvA b1861 0.6819 0.0478 branch migration of Holliday structures; repair sanA b2144 3.4542 0.0022 vancomycin sensitivity sapB b1293 1.2822 0.0403 peptide uptake ABC transporter sbcC b0397 0.5204 0.0154 ATP-dependent dsDNA exonuclease sbcD b0398 0.5232 0.0154 ATP-dependent dsDNA exonuclease secG b3175 2.8489 0.0079 Sec Protein Secretion Complex secY b3300 1.6629 0.0061 Sec Protein Secretion Complex setB b2170 0.5873 0.0068 YeiO MFS transporter slt b4392 0.7163 0.0041 soluble lytic murein transglycosylase smtA b0921 2.2662 0.0008 S-adenosylmethionine-dependent methyltransferase sodA b3908 1.6251 0.0428 superoxide dismutase (Mn) sodB b1656 0.6871 0.0357 superoxide dismutase (Fe) sohA b3129 0.3949 0.0001 putative protease, affects protein secretion soxS b4062 0.7246 0.0408 SoxS transcriptional activator speC b2965 0.2278 0.0104 ornithine decarboxylase, biosynthetic speD b0120 0.4229 0.0032 adenosylmethionine decarboxylase, proenzyme speE b0121 0.3868 0.0023 spermidine synthase spoT b3650 2.1390 0.0249 GDP diphosphokinase / guanosine-3',5'-bis(diphosphate) 3'-diphosphatase sspB b3228 1.6238 0.0353 SspB monomer stpA b2669 0.6804 0.0362 DNA-binding protein; H-NS-like protein; chaperone activity; RNA splicing? talA b2464 0.5618 0.0078 transaldolase A tauC b0367 1.2163 0.0350 TauA/TauB/TauC ABC transporter tdcA b3118 0.7075 0.0382 TdcA transcriptional activator tesB b0452 0.5076 0.0130 thioesterase II thrA b0002 1.5206 0.0439 aspartate kinase I / homoserine dehydrogenase I thrS b1719 1.2919 0.0110 threonyl-tRNA synthetase tnaB b3709 0.3751 0.0371 TnaB tryptophan ArAAP transporter tolB b0740 0.6004 0.0079 Tol-Pal Cell Envelope Complex tonB b1252 4.8369 0.0178 TonB protein; energy transducer; uptake of iron, cyanocobalimin; sensitivity to phages, colicins topB b1763 2.2188 0.0171 DNA topoisomerase III tpiA b3919 0.5602 0.0113 triose phosphate isomerase monomer tpx b1324 0.5721 0.0037 thiol peroxidase 2 trkH b3849 1.6425 0.0408 TrkH potassium ion Trk Transporter trpA b1260 0.6895 0.0091 tryptophan synthase, alpha subunit / indoleglycerol phosphate aldolase ubiB b3835 1.8429 0.0208 2-octaprenylphenol hydroxylase ulaG b4192 0.5353 0.0428 putative L-ascorbate 6-phosphate lactonase ves b1742 1.6031 0.0028 cold-induced member of the CspA family 164
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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
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 179: APPENDIX I gene blattner ratio p-va
Page 205 and 206: Statement of sources Declaration I
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Coordinated regulation of gene expression by E ... - Jacobs University

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