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

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Table S4. Genes up- and downregulated in TIGR4 Δrr09 at an optical density of 0.1 grown in THY-broth. Ratios are given as Δrr09 / wild type. Gene regulation by RR09 in S. pneumoniae Gene Upregulated Annotation Ratio (fold change) p-value SP0089 hypothetical protein 2.42 3.90E-02 SP0090 ABC transporter, permease protein 5.20 4.37E-02 SP0394 PTS system, mannitol-specific IIBC components, mtlA 5.48 2.84E-02 SP0397 mannitol-1-phosphate 5-dehydrogenase 79.70 4.93E-03 SP0504 hypothetical protein 2.40 1.37E-02 SP0784 glutathione reductase, gor 2.04 2.03E-02 SP0978 competence protein coiA 41.15 5.63E-03 SP1058 hypothetical protein 4.05 1.72E-02 SP1059 hypothetical protein 2.20 1.06E-03 SP1774 transcriptional regulator, putative 2.14 4.45E-02 SP1828 UDP-glucose 4-epimerase, galE 2.79 4.92E-02 SP1832 hypothetical protein iron-compound ABC transporter, ATP-binding 2.07 3.32E-02 SP1871 protein, piuD 2.72 2.00E-02 SP1969 type II DNA modification methyltransferase, putative 2.37 1.24E-02 SP2141 glycosyl hydrolase-related protein SP0368; cell wall surface anchor family protein 3.89 2.58E-02 SPXX18 (spr0328) 4.66 8.91E-03 Downregulated SP0156 response regulator 07 0.02 4.40E-02 SP0216 50S ribosomal protein L16, rplP 0.30 3.78E-02 SP0261 undecaprenyl diphosphate synthase, uppS glucosamine--fructose-6-phosphate aminotransferase, 0.30 4.74E-02 SP0266 glmS 0.08 9.26E-03 SP0294 50S ribosomal protein L13, rplM 0.16 4.26E-02 SP0461 transcriptional regulator, rlrA 0.03 1.54E-03 SP0462 cell wall surface anchor family protein, rrgA 0.13 2.50E-03 SP0463 cell wall surface anchor family protein, rrgB 0.13 5.22E-03 SP0464 cell wall surface anchor family protein, rrgC 0.06 2.54E-03 SP0467 sortase srtC, putative 0.20 6.92E-04 SP0468 sortase srtD, putative 0.11 1.74E-02 SP0623 dipeptidase, pepV 0.31 4.95E-02 SP0751 branched-chain amino acid ABC transporter, livM 0.05 2.45E-02 SPXX56 SP0857; ABC transporter, aliA-like 0.33 4.60E-02 SP0858 hypothetical protein 0.28 3.27E-02 SP1023 acetyltransferase, GNAT family 0.46 2.18E-03 SP1278 pyrimidine operon regulatory protein, pyrR 0.13 9.37E-03 SP1805 hypothetical protein 0.48 1.14E-02 SP2005 hypothetical protein 0.47 9.31E-03 SP2094 hypothetical protein 0.39 3.25E-02 SP2202 hypothetical protein 0.01 1.32E-02 57 57
Chapter 2 Table S5. Genes up- and downregulated in TIGR4 Δrr09 at an optical density of 0.2 grown in THY-broth. Ratios are given as Δrr09 / wild type. Gene Annotation Upregulated none 58 58 Ratio (fold change) p-value Downregulated SP0117 pneumococcal surface protein A, pspA 0.47 4.37E-06 SP0266 glucosamine--fructose-6-phosphate aminotransferase, glmS 0.37 4.35E-02 SP0461 transcriptional regulator, rlrA 0.20 3.80E-03 SP0462 cell wall surface anchor family protein, rrgA 0.10 6.33E-03 SP0463 cell wall surface anchor family protein, rrgB 0.23 1.77E-03 SP0464 cell wall surface anchor family protein, rrgC 0.19 8.29E-03 SP0467 sortase srtC, putative 0.18 2.58E-02 SP0468 sortase srtD, putative 0.44 3.00E-03 SP0501 transcriptional regulator, glnR 0.48 7.29E-06 SP0661 response regulator 09 0.49 5.61E-03 SP0964 dihydroorotate dehydrogenase B, pyrD 0.48 3.22E-02 SP1278 pyrimidine operon regulatory protein, pyrR 0.43 2.46E-03 SP1965 hypothetical protein 0.43 2.56E-02
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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.
Page 8 and 9: 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 60: Table S6. Genes up- and downregulat
Page 63 and 64: Chapter 3 Abstract 62 62 Previous s
Page 65 and 66: Chapter 3 between the wild-type and
Page 67 and 68: Chapter 3 S. pneumoniae TIGR4 by CS
Page 69 and 70: Chapter 3 performance liquid chroma
Page 71 and 72: Chapter 3 Results Transcriptional a
Page 73 and 74: Chapter 3 Table 3. Differentially e
Page 75 and 76: Chapter 3 Figure 2. Colonization mo
Page 77 and 78: Chapter 3 than the D39ΔpsaR-infect
Page 79 and 80: Chapter 3 effect was more severe fo
Page 81 and 82: Chapter 3 in TIGR4ΔpsaR. However,
Page 83 and 84: Chapter 3 References 1. Adrian, P.
Page 85 and 86: Chapter 3 21. Hemsley, C., E. Joyce
Page 87 and 88: Chapter 3 40. McCluskey, J., J. Hin
Page 90 and 91: CHAPTER 4 CodY of Streptococcus pne
Page 92 and 93: Introduction Bacteria encounter var
Page 94 and 95: Materials and Methods Bacterial str
Page 96 and 97: Table 2. Oligonucleotide primers us
Page 98 and 99: The CodY regulon of S. pneumoniae I
Page 100 and 101: The CodY regulon of S. pneumoniae w
Page 102 and 103: Accession numbers The microarray da
Page 104 and 105: Table 3. Differentially expressed g
Page 106 and 107: Binding of CodY to target promoters
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The CodY regulon of S. pneumoniae E
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The CodY regulon of S. pneumoniae F
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Discussion CodY has been described
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levels of adherence in D39. Using a
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References The CodY regulon of S. p
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Glass. 2001. Genome of the bacteriu
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40. Shivers, R. P., S. S. Dineen, a
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CHAPTER 5 Regulation of glutamine a
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Introduction Regulation of nitrogen
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Materials and Methods Nitrogen Meta
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TK136 D39 Δcps; Km R capsule-less
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gene from pORI28, was fused to the
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Construction of lacZ fusions Chromo
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Enzyme assays Cell-free extracts, u
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Reverse-transcriptase PCR RNA isola
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Table 3. Summary of transcriptome c
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effect caused by altered intracellu
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examine whether zwf is only transcr
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(http://www.bd.com/ds/technicalCent
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H6-GlnR alone at the concentration
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Discussion In this study, we charac
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Acknowledgements TK, JB and HB are
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11. den Hengst, C. D., S. A. van Hi
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Nitrogen Metabolism in S. pneumonia
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52. Wray, L. V., Jr., J. M. Zalieck
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CHAPTER 6 Site-specific contributio
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Introduction GlnR-regulon and pneum
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Materials and Methods Bacterial str
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eferred to as t=0. Bacteriology res
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Results GlnR-regulon and pneumococc
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Figure 3. Colonization model. Bacte
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GlnR-regulon and pneumococcal virul
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Table 2. Differentially expressed g
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Discussion The ability to adequatel
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The microarray data showed that pre
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Acknowledgments WTH is supported by
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12. Ibrahim, Y. M., A. R. Kerr, J.
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33. Zalieckas, J. M., L. V. Wray, J
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CHAPTER 7 Pneumococcal gene regulat
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Introduction Regulation of gene exp
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Gene regulation and metabolism in S
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makes it possible for the pneumococ
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A CcpA homologue exists in the pneu
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double mutant, suggesting direct re
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References Gene regulation and meta
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23. Kerr, A. R., P. V. Adrian, S. E
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45. Sonenshein, A. L. 2005. CodY, a
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CHAPTER 8 Summarizing discussion 20
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that the observed virulence phenoty
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CodY was found to be required for a
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References Summarizing discussion 1
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Summarizing discussion 21. Orihuela
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Samenvatting en discussie Curriculu
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Samenvatting en discussie kunnen ge
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Bevindingen die dit onderbouwen, we
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Curriculum Vitae Curriculum Vitae W
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Dankwoord Jeetje, dat het dan toch
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oekje en ik kijk uit naar de bijbeh
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