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

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APPENDIX I recA b2699 6.1477 0.0006 DNA strand exchange and renaturation, DNA-dependent ATPase, DNA- and ATP-dependent coprotease recF b3700 1.5026 0.0018 ssDNA and dsDNA binding, ATP binding recN b2616 5.2322 0.0003 protein used in recombination and DNA repair recX b2698 3.3785 0.0128 inhibitor of RecA relA b2784 0.6144 0.0009 GDP pyrophosphokinase / GTP pyrophosphokinase rfaE b3052 1.6731 0.0393 putative kinase rfaH b3842 0.6886 0.0257 RfaH transcriptional regulator rfaI b3627 3.7837 0.0015 UDP-D-galactose:(glucosyl)lipopolysaccharide-alpha-1,3-D-galactosyltransferase rfaJ b3626 3.0420 0.0174 UDP-D-glucose:(galactosyl)lipopolysaccharide glucosyltransferase rfaK b3623 3.1584 0.0170 lipopolysaccharide core biosynthesis; probably hexose transferase rfaS b3629 2.8794 0.0068 lipopolysaccharide core biosynthesis rfaZ b3624 3.4532 0.0385 protein involved in KdoIII attachment during lipopolysaccharide core biosynthesis rfbB b2041 0.7441 0.0376 RmlB rhlB b3780 0.5316 0.0049 ATP-dependent RNA helicase of the RNA degradosome rhlE b0797 0.2790 0.0010 DEAD-box-containing ATP-dependent RNA helicase family member rhsD b0497 0.5670 0.0166 RhsD protein in rhs element ribB b3041 0.4644 0.0229 3,4-dihydroxy-2-butanone 4-phosphate synthase ribC b1662 0.6318 0.0401 riboflavin synthase ribF b0025 0.1259 0.0103 riboflavin kinase / FMN adenylyltransferase rihA b0651 1.8484 0.0409 ribonucleoside hydrolase 1 (pyrimidine-specific) rimJ b1066 0.4103 0.0066 acetylates N-terminal alanine of 30S ribosomal subunit protein S5 / ribosomalprotein-alanine N-acetyltransferase rluC b1086 0.3153 0.0041 23S rRNA pseudouridine synthase rluD b2594 0.7043 0.0136 23S rRNA pseudouridine synthase rluE b1135 1.6545 0.0240 23S rRNA pseudouridine synthase rnc b2567 0.2112 0.0002 RNase III, ds RNA rng b3247 0.7647 0.0261 ribonuclease G (RNAse G) monomer rnhA b0214 0.3725 0.0125 RNase HI, degrades RNA of DNA-RNA hybrids, participates in DNA replication rnr b4179 0.5088 0.0147 RNAse R rplY b2185 1.4198 0.0156 50S ribosomal subunit protein L25 rpmE b3936 1.9883 0.0287 50S ribosomal subunit protein L31 rpoA b3295 1.7187 0.0281 RNA polymerase, alpha subunit rpoH b3461 1.5408 0.0047 sigma32 factor rpsJ b3321 1.7179 0.0451 30S ribosomal subunit protein S10 rpsL b3342 1.3159 0.0319 30S ribosomal subunit protein S12 rpsU b3065 2.0799 0.0248 30S ribosomal subunit protein S21 rspA b1581 2.2521 0.0444 starvation sensing protein RspA rspB b1580 1.2583 0.0486 putative dehydrogenase RspB rssA b1234 0.2763 0.0088 hypothetical protein rsuA b2183 0.3324 0.0011 16S rRNA pseudouridine synthase rsxE b1632 1.6861 0.0192 integral membrane protein of SoxR-reducing complex sdaC b2796 0.5269 0.0174 SdaC serine STP transporter sdhA b0723 1.8472 0.0183 succinate dehydrogenase flavoprotein sdhB b0724 2.4021 0.0348 succinate dehydrogenase iron-sulfur protein secE b3981 0.1598 0.0033 Sec Protein Secretion Complex secF b0409 0.8540 0.0394 Sec Protein Secretion Complex secG b3175 0.3039 0.0132 Sec Protein Secretion Complex selA b3591 0.7449 0.0144 selenocysteine synthase monomer sgbH b3581 1.2423 0.0155 3-keto-L-gulonate 6-phosphate decarboxylase sieB b1353 0.8425 0.0185 phage superinfection exclusion protein slt b4392 0.6966 0.0171 soluble lytic murein transglycosylase slyA b1642 0.4284 0.0138 SlyA transcriptional activator slyB b1641 0.4100 0.0358 putative outer membrane protein slyD b3349 1.3580 0.0393 FKBP-type rotamase, peptidyl prolyl cis-trans isomerase smf b4473 0.6389 0.0144 hypothetical protein smg b3284 0.3104 0.0016 hypothetical protein smpA b2617 3.0746 0.0330 SmpA small membrane protein A smtA b0921 0.1732 0.0009 S-adenosylmethionine-dependent methyltransferase 117
APPENDIX I speG b1584 0.4151 0.0001 spermidine acetyltransferase spr b2175 0.1856 0.0008 putative lipoprotein spy b1743 1.8051 0.0064 periplasmic protein related to spheroblast formation srmB b2576 0.1828 0.0018 SrmB, DEAD-box RNA helicase sscR b2765 0.2846 0.0014 putative 6-pyruvoyl tetrahydrobiopterin synthase sspA b3229 1.7853 0.0360 regulator of transcription; stringent starvation protein A sspB b3228 1.6995 0.0121 SspB monomer sthA b3962 1.9483 0.0152 soluble pyridine nucleotide transhydrogenase sucA b0726 1.7723 0.0282 subunit of E1(0) component of 2-oxoglutarate dehydrogenase suhB b2533 0.6030 0.0333 inositol monophosphatase sulA b0958 0.4776 0.0294 suppressor of lon; inhibits cell division and ftsZ ring formation syd b2793 0.7172 0.0401 interacts with secY tdcD b3115 1.3690 0.0028 propionate kinase / acetate kinase C tdcE b3114 1.8820 0.0225 2-ketobutyrate formate-lyase / pyruvate formate-lyase 4 tdh b3616 1.6683 0.0198 threonine dehydrogenase tesA b0494 0.4861 0.0342 lysophospholipase L1 / thioesterase I thiI b0423 0.3635 0.0002 ThiI protein thyA b2827 1.6662 0.0186 thymidylate synthase tpiA b3919 1.1555 0.0049 triose phosphate isomerase monomer tra5-5 b2089 0.5946 0.0481 treB b4240 1.9360 0.0274 EIITre treC b4239 1.8400 0.0022 trehalose-6-phosphate hydrolase trkA b3290 1.6751 0.0358 TrkA trkG b1363 1.7115 0.0118 TrkG potassium ion Trk Transporter trmD b2607 1.4999 0.0322 tRNA (guanine-1-)-methyltransferase trpB b1261 0.8425 0.0438 tryptophan synthase, beta subunit trpD b1263 0.5060 0.0140 anthranilate synthase component II trpE b1264 0.4037 0.0115 anthranilate synthase component I trpL b1265 0.7864 0.0299 trp operon leader peptide trpR b4393 1.7569 0.0049 TrpR transcriptional repressor trpS b3384 2.1106 0.0124 tryptophanyl-tRNA synthetase tsgA b3364 0.6442 0.0017 YhfC MFS transporter tsr b4355 0.6068 0.0399 MCP-I tsx b0411 0.1946 0.0016 nucleoside channel; receptor of phage T6 and colicin K ttk b3641 0.4174 0.0019 Ttk transcriptional regulator ubiC b4039 0.2098 0.0001 chorismate pyruvate lyase ubiF b0662 1.5458 0.0334 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinone hydroxylase ubiG b2232 0.7780 0.0016 3-demethylubiquinone 3-methyltransferase / 2-octaprenyl-6-hydroxyphenol methylase uhpB b3668 0.5983 0.0403 UhpB-Phis uidA b1617 1.2711 0.0362 beta-glucuronidase ulaE b4197 0.7571 0.0368 L-xylulose 5-phosphate 3-epimerase ulaF b4198 0.7998 0.0198 L-ribulose 5-phosphate 4-epimerase ung b2580 0.6029 0.0221 uracil-DNA-glycosylase upp b2498 0.4553 0.0208 uracil phosphoribosyltransferase uvrB b0779 1.9034 0.0153 DNA repair; excision nuclease subunit B vacJ b2346 0.6153 0.0168 putative lipoprotein visC b2906 1.7240 0.0071 hypothetical protein waaP b3630 1.9894 0.0370 lipopolysaccharide core biosynthesis; phosphorylation of core heptose wbbI b2034 1.6114 0.0023 hypothetical protein; not required for colanic acid biosynthesis wbbK b2032 1.3531 0.0045 putative transferase wcaA b2059 1.5321 0.0226 putative regulator wcaB b2058 1.4575 0.0374 putative transferase wcaD b2056 1.6890 0.0022 putative colanic acid polymerase wcaJ b2047 1.6790 0.0013 putative colanic acid biosynthsis UDP-glucose lipid carrier transferase wza b2062 1.3425 0.0424 Wza Outer Membrane Auxiliary (OMA) Protein, putative polysaccharide export protein xapR b2405 0.7902 0.0250 XapR transcriptional activator xerD b2894 0.4150 0.0016 site-specific recombinase 118
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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
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 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: APPENDIX I pepP b2908 1.2182 0.0368
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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