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

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APPENDIX I gene blattner ratio p-value Function A/B creB b4398 0.4846 0.0434 CreB- Phosphorylated transcriptional regulator creC b4399 0.3937 0.0326 CreC-Phis csdA b2810 0.5874 0.0365 cysteine sulfinate desulfinase csgC b1043 1.2044 0.0112 putative curli production protein cspD b0880 16.0799 0.0280 DNA replication inhibitor cspE b0623 8.6680 0.0365 CspE transcriptional repressor cspG b0990 0.6140 0.0016 cold shock protein CspG csrA b2696 3.9886 0.0476 carbon storage regulator; controls glycogen synthesis, gluconeogenesis, cell size and surface properties cusF b0573 0.7829 0.0248 periplasmic copper-binding protein cynS b0340 0.3529 0.0120 cyanase monomer cysW b2423 0.6881 0.0280 sulfate ABC transporter cysZ b2413 0.4629 0.0035 required for sulfate transport ddpX b1488 0.5345 0.0362 D-Ala-D-Ala dipeptidase deoC b4381 9.0692 0.0321 deoxyribose-phosphate aldolase dhaR b1201 0.6436 0.0124 putative 2-component regulator dksA b0145 1.6863 0.0313 DksA dnaE b0184 0.5435 0.0106 DNA polymerase III, alpha subunit dnaG b3066 0.4222 0.0495 DNA biosynthesis; DNA primase dppA b3544 1.7303 0.0446 dipeptide ABC transporter dsbA b3860 1.1918 0.0084 disulfide oxidoreductase ecpD b0140 0.4814 0.0137 probable pilin chaperone similar to PapD elbB b3209 1.9231 0.0350 sigma cross-reacting protein 27A (SCRP-27A) eutL b2439 0.6724 0.0490 hypothetical protein exuR b3094 0.8492 0.0144 ExuR transcriptional repressor fabF b1095 0.6295 0.0460 beta-ketoacyl-ACP synthase II fdrA b0518 0.5497 0.0092 involved in protein transport; multicopy suppressor of dominant negative ftsH mutants fecA b4291 0.8222 0.0069 outer membrane receptor; citrate-dependent iron transport, outer membrane receptor fimC b4316 0.4900 0.0315 periplasmic chaperone, required for type 1 fimbriae flgB b1073 0.5473 0.0051 flagellar basal-body rod protein FlgB fliD b1924 0.5664 0.0104 flagellar cap protein FliD; filament capping protein; enables filament assembly fliK b1943 2.0042 0.0318 flagellar hook-length control protein FliK fliY b1920 4.1059 0.0296 periplasmic cystine-binding protein; member of extracellular bacterial solute-binding protein family III frlC b3372 1.1884 0.0410 fructoselysine and psicoselysine degradation fruA b2167 1.6009 0.0416 EIIFru frvX b3898 0.6284 0.0373 frv operon protein fsaB b3946 0.5115 0.0025 fructose 6-phosphate aldolase 2 ftsW b0089 1.6371 0.0330 essential cell division protein FtsW fumB b4122 1.4742 0.0092 fumarase B monomer fumC b1611 4.5730 0.0410 fumarase C monomer fusA b3340 7.4644 0.0072 elongation factor G g30K b1088 4.4609 0.0486 hypothetical protein gatY b2096 7.4188 0.0456 tagatose-1,6-bisphosphate aldolase 2 glgS b3049 12.4340 0.0183 glycogen biosynthesis, rpoS dependent glk b2388 2.4011 0.0080 glucokinase glnA b3870 0.6508 0.0408 adenylyl-[glutamine synthetase] gloB b0212 0.7455 0.0328 glyoxalase II glpA b2241 1.8004 0.0339 glycerol-3-phosphate-dehydrogenase, anaerobic gntU b4476 0.6904 0.0450 GntU gluconate Gnt transporter greA b3181 0.5847 0.0466 transcription elongation factor; stimulates the mRNA cleavage activity of RNA polymerase groL b4143 0.1600 0.0302 GroEL, chaperone Hsp60, peptide-dependent ATPase, heat shock protein grxB b1064 3.0152 0.0423 oxidized glutaredoxin 2 gyrA b2231 1.2523 0.0381 DNA gyrase, subunit A hemC b3805 0.7502 0.0425 hydroxymethylbilane synthase hemH b0475 1.2367 0.0211 ferrochelatase 93
APPENDIX I gene blattner ratio p-value Function A/B hflX b4173 1.1608 0.0414 putative GTPase; possible regulator of HflKC htrA b0161 0.3477 0.0251 DegP htrL b3618 0.4161 0.0089 involved in lipopolysaccharide biosynthesis hyfI b2489 0.6981 0.0143 hydrogenase 4, small subunit ibpB b3686 0.1277 0.0168 small heat shock protein IbpB iscU b2529 4.5133 0.0350 scaffold protein involved in iron-sulfur cluster assembly kch b1250 0.6951 0.0255 potassium VIC channel kgtP b2587 2.2993 0.0011 KgtP α-ketoglutarate MFS transporter lpxC b0096 2.7942 0.0029 UDP-3-O-acyl-N-acetylglucosamine deacetylase lrhA b2289 0.3796 0.0348 LrhA transcriptional repressor lsrB b1516 0.7399 0.0208 YneA lysC b4024 0.8123 0.0155 aspartate kinase III lyxK b3580 0.6681 0.0402 L-xylulose kinase macB b0879 0.1409 0.0120 MacAB macrolide efflux transporter complex manZ b1819 2.2877 0.0294 EIIMan mdtA b2074 1.2909 0.0336 MdtABC RND-type Drug Exporter metI b0198 0.8178 0.0151 L- and D-methionine uptake ABC permease modF b0760 0.8025 0.0038 ModF mqo b2210 0.6329 0.0302 malate dehydrogenase mutT b0099 0.7175 0.0241 dGTP pyrophosphohydrolase mviM b1068 2.0452 0.0053 putative virulence factor napG b2205 1.8609 0.0363 ferredoxin-type protein narG b1224 2.2871 0.0317 nitrate reductase A, α subunit narJ b1226 0.6000 0.0278 NarJ, private chaperone for NarG nitrate reductase subunit nlpA b3661 0.6811 0.0025 lipoprotein-28 nlpD b2742 4.4441 0.0000 NlpD putative outer membrane lipoprotein nrdI b2674 0.5413 0.0160 stimulates ribonucleotide reduction nuoE b2285 0.9495 0.0379 NADH dehydrogenase I nuoM b2277 1.8342 0.0080 NADH dehydrogenase I ompA b0957 10.3993 0.0496 outer membrane protein 3a (II*;G;d) osmY b4376 4.2860 0.0255 hyperosmotically inducible periplasmic protein pbpC b2519 5.9984 0.0419 putative peptidoglycan enzyme pckA b3403 2.7797 0.0438 phosphoenolpyruvate carboxykinase (ATP) pepD b0237 0.5596 0.0476 peptidase D pgaB b1023 0.3651 0.0064 putative membrane protein pgpA b0418 0.3457 0.0195 phosphatidylglycerophosphatase A pheT b1713 16.3765 0.0495 phenylalanyl-tRNA synthetase β-chain phnP b4092 0.7634 0.0242 phosphonate metabolism polB b0060 0.6608 0.0120 DNA polymerase II ppa b4226 2.0727 0.0063 inorganic pyrophosphatase proY b0402 0.6754 0.0227 ProY cryptic proline APC transporter pspA b1304 0.3241 0.0349 negative transcriptional regulator of the psp operon pstB b3725 0.9267 0.0131 phosphate ABC transporter ptsI b2416 5.6371 0.0485 PTS enzyme I pykA b1854 0.8489 0.0169 pyruvate kinase II monomer rfaI b3627 0.4462 0.0388 UDP-D-galactose:(glucosyl)lipopolysaccharide-alpha-1,3-D-galactosyltransferase rhsD b0497 1.6558 0.0321 RhsD protein in rhs element rhsE b1456 1.1728 0.0329 RhsE protein in rhs element ribD b0414 0.6515 0.0084 pyrimidine reductase / pyrimidine deaminase rimJ b1066 1.7516 0.0255 acetylates N-terminal alanine of 30S ribosomal subunit protein S5 / ribosomalprotein-alanine N-acetyltransferase rimM b2608 3.7205 0.0153 protein required for wild-type 16S rRNA processing rluA b0058 0.4039 0.0494 23S rRNA and tRNA pseudouridine synthase rnhB b0183 0.4660 0.0478 RNAse HII, degrades RNA of DNA-RNA hybrids rplE b3308 5.5781 0.0305 50S ribosomal subunit protein L5 rplI b4203 2.4184 0.0300 50S ribosomal subunit protein L9 rplR b3304 7.8773 0.0179 50S ribosomal subunit protein L18 94
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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
Page 59 and 60: RESULTS During the entire growth cy
Page 61 and 62: RESULTS transcripts of a growth pha
Page 63 and 64: 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
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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 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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