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

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APPENDIX I gene blattner ratio p-value Function A/B pqqL b1494 2.4892 0.0097 putative zinc peptidase prkB b3355 0.6558 0.0194 probable phosphoribulokinase prmA b3259 1.1549 0.0237 methylation of 50S ribosomal subunit protein L11 proB b0242 0.4436 0.0305 gamma-glutamyl kinase-GP-reductase multienzyme complex proQ b1831 0.4270 0.0085 protein that affects osmoregulation of ProP transporter prpR b0330 1.3979 0.0217 PrpR transcriptional regulator pspE b1308 1.3420 0.0120 thiosulfate sulfurtransferase pssA b2585 0.3090 0.0108 phosphatidylserine synthase ptsA b3947 1.4554 0.0198 PEP-protein phosphotransferase system enzyme I purA b4177 0.5294 0.0086 adenylosuccinate synthase purC b2476 0.1639 0.0003 phosphoribosylaminoimidazole-succinocarboxamide synthase purE b0523 0.2509 0.0013 N5-carboxyaminoimidazole ribonucleotide mutase purF b2312 0.2414 0.0192 amidophosphoribosyl transferase purM b2499 0.1577 0.0004 phosphoribosylformylglycinamide cyclo-ligase purN b2500 0.5155 0.0120 phosphoribosylglycinamide formyltransferase purR b1658 0.3655 0.0001 PurR transcriptional repressor purT b1849 0.6975 0.0250 GAR transformylase 2 purU b1232 0.4724 0.0343 formyltetrahydrofolate deformylase puuC b1300 1.2759 0.0124 aldehyde dehydrogenase pykA b1854 1.2788 0.0072 pyruvate kinase II monomer pykF b1676 0.6019 0.0200 pyruvate kinase I monomer pyrC b1062 0.5738 0.0154 dihydroorotase pyrF b1281 0.3505 0.0074 orotidine-5'-phosphate-decarboxylase qseB b3025 0.5963 0.0366 putative 2-component transcriptional regulator radC b3638 0.7993 0.0107 hypothetical protein rarA b0892 1.3775 0.0153 recombination factor rbsA b3749 1.3686 0.0067 ribose ABC transporter rdoA b3859 0.3650 0.0037 cytoplasmic protein of low abundance recB b2820 1.3049 0.0003 RecB; DNA helicase, ATP-dependent dsDNA/ssDNA exonuclease V subunit, ssDNA endonuclease recF b3700 1.8782 0.0203 ssDNA and dsDNA binding, ATP binding recN b2616 3.2489 0.0013 protein used in recombination and DNA repair rfaJ b3626 2.9390 0.0359 UDP-D-glucose:(galactosyl)lipopolysaccharide glucosyltransferase rfaK b3623 2.5429 0.0162 lipopolysaccharide core biosynthesis; probably hexose transferase rfaS b3629 2.4712 0.0160 lipopolysaccharide core biosynthesis rfaY b3625 2.7443 0.0257 lipopolysaccharide core biosynthesis rfaZ b3624 2.8758 0.0135 protein involved in KdoIII attachment during lipopolysaccharide core biosynthesis rfbX b2037 1.5328 0.0192 RfbX lipopolysaccharide PST transporter rfc b2035 2.1537 0.0085 O-antigen polymerase rfe b3784 0.2504 0.0025 undecaprenyl-phosphate α-N-acetylglucosaminyl transferase rffC b3790 1.8384 0.0174 TDP-fucosamine acetyltransferase rhaR b3906 1.5371 0.0023 RhaR-L-rhamnose transcriptional activator rhlE b0797 0.5998 0.0306 DEAD-box-containing ATP-dependent RNA helicase family member rhsD b0497 0.3038 0.0094 RhsD protein in rhs element ribB b3041 0.4756 0.0036 3,4-dihydroxy-2-butanone 4-phosphate synthase ribC b1662 0.6034 0.0484 riboflavin synthase ribF b0025 0.2311 0.0048 riboflavin kinase / FMN adenylyltransferase rimI b4373 1.2616 0.0232 acetylates N-terminal alanine of 30S ribosomal subunit protein S18 / ribosomalprotein-alanine N-acetyltransferase rimJ b1066 0.3654 0.0033 acetylates N-terminal alanine of 30S ribosomal subunit protein S5 / ribosomalprotein-alanine N-acetyltransferase rluE b1135 1.5925 0.0139 23S rRNA pseudouridine synthase rnc b2567 0.3545 0.0116 RNase III, ds RNA rpmA b3185 1.2009 0.0086 50S ribosomal subunit protein L27 rpmB b3637 0.7069 0.0448 50S ribosomal subunit protein L28 rpmF b1089 1.3157 0.0137 50S ribosomal subunit protein L32 rpoD b3067 2.3387 0.0271 sigma70 factor 143
APPENDIX I gene blattner ratio p-value Function A/B rpoE b2573 0.6299 0.0405 sigmaE rpoH b3461 1.4151 0.0363 sigma32 factor rseA b2572 0.4158 0.0006 anti-sigma factor that inhibits sigmaE rseB b2571 0.5185 0.0085 negative regulator of sigmaE; interacts with RseA and stimulates binding of RseA to sigmaE rssA b1234 0.5582 0.0116 hypothetical protein rssB b1235 0.6895 0.0442 RssB-P rsxA b1627 1.9291 0.0099 integral membrane protein of SoxR-reducing complex rsxB b1628 1.6538 0.0104 member of SoxR-reducing complex rsxC b1629 2.0272 0.0303 member of SoxR-reducing complex rsxD b1630 1.5930 0.0439 integral membrane protein of SoxR-reducing complex rsxE b1632 2.2544 0.0002 integral membrane protein of SoxR-reducing complex rsxG b1631 2.4324 0.0084 member of SoxR-reducing complex rtn b2176 1.1293 0.0298 hypothetical protein sanA b2144 0.4376 0.0187 vancomycin sensitivity sbcD b0398 1.3094 0.0159 ATP-dependent dsDNA exonuclease sdaB b2797 1.2729 0.0279 L-threonine deaminase II / L-serine deaminase 2 sdhA b0723 2.4428 0.0087 succinate dehydrogenase flavoprotein sdhB b0724 1.8201 0.0024 succinate dehydrogenase iron-sulfur protein sdhC b0721 2.3445 0.0253 succinate dehydrogenase membrane protein sdhD b0722 1.9449 0.0060 succinate dehydrogenase membrane protein sdiA b1916 0.5260 0.0202 SdiA transcriptional activator secE b3981 0.2013 0.0210 Sec Protein Secretion Complex secG b3175 0.5355 0.0233 Sec Protein Secretion Complex sfsB b3188 1.4450 0.0295 Nlp transcriptional regulator shiA b1981 0.3314 0.0445 ShiA shikimate MFS transporter skp b0178 1.3482 0.0022 periplasmic chaperone smg b3284 0.4759 0.0018 hypothetical protein smpA b2617 2.0368 0.0327 SmpA small membrane protein A smtA b0921 0.1981 0.0013 S-adenosylmethionine-dependent methyltransferase sodC b1646 0.5884 0.0295 superoxide dismutase precursor (Cu-Zn) speC b2965 1.1224 0.0484 ornithine decarboxylase, biosynthetic speG b1584 0.4098 0.0187 spermidine acetyltransferase spr b2175 0.3174 0.0244 putative lipoprotein spy b1743 1.6823 0.0465 periplasmic protein related to spheroblast formation sra b1480 0.5126 0.0007 30S ribosomal subunit protein S22; sub-stoichiometric stationary phase ribosomal component srlR b2707 0.4372 0.0018 GutR-sorbitol srmB b2576 0.2487 0.0347 SrmB, DEAD-box RNA helicase sscR b2765 0.5881 0.0085 putative 6-pyruvoyl tetrahydrobiopterin synthase sspA b3229 1.4235 0.0255 regulator of transcription; stringent starvation protein A sthA b3962 1.4674 0.0398 soluble pyridine nucleotide transhydrogenase sucA b0726 1.7215 0.0420 subunit of E1(0) component of 2-oxoglutarate dehydrogenase sufS b1680 1.4919 0.0303 L-selenocysteine lyase (and L-cysteine desulfurase) monomer sulA b0958 0.3282 0.0018 suppressor of lon; inhibits cell division and ftsZ ring formation tam b1519 1.3876 0.0359 trans-aconitate methyltransferase tap b1885 2.0690 0.0425 MCP-IV tatB b3838 1.3899 0.0436 TatABCE protein export complex tatC b3839 1.3590 0.0079 TatABCE protein export complex tdcB b3117 1.5829 0.0012 threonine dehydratase (catabolic) tdcC b3116 0.6742 0.0130 TdcC threonine STP transporter tesA b0494 0.4687 0.0017 lysophospholipase L1 / thioesterase I thyA b2827 2.4688 0.0437 thymidylate synthase tktA b2935 0.7435 0.0147 transketolase I tolC b3035 0.6930 0.0345 TolC outer membrane channel torS b0993 0.8969 0.0128 TorS-Phis850 torY b1873 0.3115 0.0139 trimethylamine N-oxide reductase III, c-type cytochrome subunit 144
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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 109 and 110: 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 159: 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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