Gene regulation in Streptococcus pneumoniae - RePub - Erasmus ...

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Table S6. Genes up- and downregulated in TIGR4 Δrr09 at an optical density of 0.6 grown in BHI-broth. Ratios are given as Δrr09 / wild type. Gene regulation by RR09 in S. pneumoniae Gene Annotation Ratio (fold change) p-value Upregulated SP0044 phosphoribosylaminoimidazole-succinocarboxamide synthase 5.29 2.30E-04 SP0045 phosphoribosylformylglycinamidine synthase, putative 6.10 1.02E-04 SP0046 amidophosphoribosyltransferase 13.52 1.30E-04 SP0047 phosphoribosylformylglycinamide cyclo-ligase 8.18 2.21E-04 SP0048 phosphoribosylglycinamide formyltransferase 8.07 1.44E-04 SP0050 phosphoribosylaminoimidazolecarboxamide formyltransferase 7.51 5.00E-05 SP0051 phosphoribosylamine--glycine ligase 7.85 1.07E-05 SP0053 phosphoribosylaminoimidazole carboxylase, catalytic subunit 7.60 2.03E-05 SP0054 phosphoribosylaminoimidazole carboxylase, ATPase subunit 11.82 2.81E-05 SP0056 adenylosuccinate lyase 3.10 3.59E-05 SP0287 xanthine/uracil permease family protein 7.66 7.24E-05 SP0288 conserved hypothetical protein 3.21 4.35E-04 SP0289 dihydropteroate synthase 2.19 5.46E-04 SP0462 cell wall surface anchor family protein 5.87 3.16E-04 SP0463 cell wall surface anchor family protein 7.54 2.29E-04 SP0464 cell wall surface anchor family protein 6.67 3.70E-04 SP0466 sortase, putative 2.87 4.60E-04 SP0845 lipoprotein 2.60 1.94E-04 SP0875 lactose phosphotransferase system repressor 2.75 8.13E-05 SP0876 1-phosphofructokinase, putative 2.59 2.61E-04 SP1229 formate--tetrahydrofolate ligase 3.23 6.25E-04 SP1249 conserved hypothetical protein 2.55 5.77E-04 SP1587 oxalate:formate antiporter 6.93 3.33E-05 Downregulated SP0117 pneumococcal surface protein A 0.40 5.25E-04 SP0338 ATP-dependent Clp protease, ATP-binding subunit, putative 0.37 1.31E-02 SP0424 (3R)-hydroxymyristoyl-(acyl-carrier-protein) dehydratase 0.46 1.50E-03 SP0515 heat-inducible transcription repressor HrcA 0.41 4.40E-04 SP0516 heat shock protein GrpE 0.32 8.74E-04 SP0517 dnaK protein 0.40 1.21E-03 SP0519 dnaJ protein 0.49 5.98E-04 SP0647 PTS system, IIC component, putative 0.46 4.36E-03 SP0648 beta-galactosidase 0.29 4.47E-04 SP0724 hydroxyethylthiazole kinase, putative 0.47 1.12E-04 SP1804 general stress protein 24, putative 0.49 1.55E-02 SP1883 dextran glucosidase DexS, putative 0.37 1.46E-02 SP1884 trehalose PTS system, IIABC components 0.27 2.07E-03 SP1895 sugar ABC transporter, permease protein 0.41 2.30E-03 SP1896 sugar ABC transporter, permease protein 0.45 1.48E-03 SP1897 sugar ABC transporter, sugar-binding protein 0.37 1.34E-03 59 59
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Gene regulation in Streptococcus pn
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Cover image by Duve van Boggelen (w
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Promotiecommissie Promotoren: Prof.
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CHAPTER 1 Introduction 7
Page 10 and 11: Introduction Figure 1. Infections c
Page 12 and 13: Interestingly, autolysis induced by
Page 14 and 15: histidine kinase is the sensor prot
Page 16 and 17: metabolism are often required for v
Page 18 and 19: egulatory systems, aiming to elucid
Page 20 and 21: 11. Cockeran, R., A. J. Theron, H.
Page 22 and 23: 33. Li, S., S. J. Kelly, E. Lamani,
Page 24 and 25: 53. Romero, P., R. Lopez, and E. Ga
Page 26 and 27: CHAPTER 2 Regulation of gene expres
Page 28 and 29: Introduction Streptococcus pneumoni
Page 30 and 31: Materiaals and Meethods Gene regula
Page 32 and 33: (Invitrogen), 0.2 mM aminoallyl dUT
Page 34 and 35: Isolation of pneumococcal RNA durin
Page 36 and 37: Resultss and Discuussion Gene regul
Page 38 and 39: Table 1. Genes regulated by RR09 in
Page 40 and 41: phosphofructokinase, and a fructose
Page 42 and 43: Figure 4. Expression of rlrA and rr
Page 44 and 45: correlated well with our in vitro m
Page 46 and 47: Figure 7. Bacterial loads in blood
Page 48 and 49: Acknowledgments This work was suppo
Page 50 and 51: 10. Ibrahim, Y. M., A. R. Kerr, J.
Page 52 and 53: genome sequence of a virulent isola
Page 54 and 55: Gene regulation by RR09 in S. pneum
Page 56 and 57: Gene regulation by RR09 in S. pneum
Page 58 and 59: Table S4. Genes up- and downregulat
Page 62 and 63: CHAPTER 3 Strain-specific impact on
Page 64 and 65: Introduction PsaR and pneumococcal
Page 66 and 67: Materials and Methods Bacterial str
Page 68 and 69: DNA microarray data analysis Dual-c
Page 70 and 71: this small volume, only the nose of
Page 72 and 73: adjacent genes, encoding a MerR fam
Page 74 and 75: PsaR and pneumococcal virulence sp0
Page 76 and 77: 1.5 x 10 5 vs 5.8 x 10 4 CFU/ml at
Page 78 and 79: Discussion PsaR and pneumococcal vi
Page 80 and 81: PsaR and pneumococcal virulence mut
Page 82 and 83: Acknowledgments WTH is supported by
Page 84 and 85: 10. Dawid, S., A. M. Roche, and J.
Page 86 and 87: PsaR and pneumococcal virulence 31.
Page 88: 49. van Hijum, S. A., J. Garcia de
Page 91 and 92: Chapter 4 Abstract 90 90 CodY is a
Page 93 and 94: Chapter 4 is found that is, at leas
Page 95 and 96: Chapter 4 HindIII and PstI to creat
Page 97 and 98: Chapter 4 spr1436 EMSA fw TGCGTAAAC
Page 99 and 100: Chapter 4 codY coding sequence was
Page 101 and 102: Chapter 4 homogenizer (polytron PT
Page 103 and 104: Chapter 4 Results The CodY regulon
Page 105 and 106: Chapter 4 fatD sp1869 spd1649 iron-
Page 107 and 108: Chapter 4 Figure 1. Electrophoretic
Page 109 and 110: Chapter 4 Figure 2. DNase1 Footprin
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Chapter 4 role of CodY in this proc
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Chapter 4 112 112 Using DNAse1 foot
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Chapter 4 Acknowledgements We would
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Chapter 4 10. Claverys, J. P., B. G
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Chapter 4 30. Lanie, J. A., W. L. N
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Chapter 4 49. van Hijum, S. A., J.
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Chapter 5 Abstract 122 122 Several
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Chapter 5 pneumoniae contains a put
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Chapter 5 Table 1. Strains and plas
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Chapter 5 128 128 pTK21 pORI13 Pzwf
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Chapter 5 glnA-his # GGCGGTCTCTCATG
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Chapter 5 Scientific BV) per ml of
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Chapter 5 phenol/chloroform, 500 mg
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Chapter 5 Results Prediction of put
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Chapter 5 glutamine ABC transporter
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Chapter 5 repression of glnA expres
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Chapter 5 Regulation of gdhA by Gln
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Chapter 5 H6-GlnA and H6-GlnR are f
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Chapter 5 Figure 7. Adhesion of S.
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Chapter 5 148 148 Both GlnR and Cod
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Chapter 5 References 1. Almassy, R.
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Chapter 5 21. Kharat, A. S., and A.
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Chapter 5 43. Tamura, G. S., A. Nit
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156
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Chapter 6 Abstract 158 158 The tran
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Chapter 6 homologue is present, ind
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Chapter 6 dilutions were plated on
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Chapter 6 data were processed using
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Chapter 6 attenuated phenotype. Aft
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Chapter 6 Figure 4. Pneumonia model
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Chapter 6 170 170 Twelve genes were
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Chapter 6 spd1602 sp1817 trpE anthr
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Chapter 6 candidate for fibronectin
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Chapter 6 with the supply of nutrie
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Chapter 6 References 1. Beckmann, C
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Chapter 6 180 180 of variance and a
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182
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Chapter 7 Abstract 184 184 Efficien
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Chapter 7 Nitrogen metabolism 186 1
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Chapter 7 Figure 1. Models of trans
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Chapter 7 levels did not change exp
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Chapter 7 severely affected in thei
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Chapter 7 Enterococcus faecalis, Ba
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Chapter 7 11. Dineen, S. S., A. C.
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Chapter 7 33. Ochi, K., J. Kandala,
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200
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Chapter 8 202 202 Being one of the
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Chapter 8 for virulence in a seroty
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Chapter 8 206 206 Another important
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Chapter 8 11. Hava, D. L., and A. C
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Chapter 8 31. Song, X. M., W. Conno
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Samenvatting en discussie 212 212 S
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eguleren namelijk, twee two-compone
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met behulp van muizen. Ook is er na
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List of Publications List of public
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jou en de rest van de Molecular Med
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