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

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genome sequence of a virulent isolate of Streptococcus pneumoniae. Science 293:498- 506. 29. Throup, J. P., K. K. Koretke, A. P. Bryant, K. A. Ingraham, A. F. Chalker, Y. Ge, A. Marra, N. G. Wallis, J. R. Brown, D. J. Holmes, M. Rosenberg, and M. K. Burnham. 2000. A genomic analysis of two-component signal transduction in Streptococcus pneumoniae. Mol. Microbiol. 35:566-576. 30. Titgemeyer, F., and W. Hillen. 2002. Global control of sugar metabolism: a gram- positive solution. Antonie Leeuwenhoek 82:59-71. 31. van Hijum, S. A., A. de Jong, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok, and O. P. Kuipers. 2005. A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC Genomics 6:77. 32. van Hijum, S. A., J. Garcia de la Nava, O. Trelles, J. Kok, and O. P. Kuipers. 2003. MicroPreP: a cDNA microarray data pre-processing framework. Appl. Bioinformatics 2:241-244. Gene regulation by RR09 in S. pneumoniae 51 51
Chapter 2 Supplemental material Table S1. Genes up- and downregulated in D39 Δrr09 at an optical density of 0.1 grown in THY-broth. Ratios are given as Δrr09 / wild type. Gene Upregulated Annotation Ratio (fold change) p-value SP0042 competence factor transporting protein comA 4.88 2.14E-04 SP0043 competence factor transport protein comB 5.00 2.60E-03 SP0430 hypothetical protein 2.50 8.67E-03 SP0545 immunity protein blpY 2.05 1.47E-02 SP0963 dihydroorotate dehydrogenase pyrDII 2.06 1.82E-03 SP1110 riboflavin kinase / FMN adenylyltransferase, mreA 4.01 2.36E-04 SP1266 DNA processing protein dprA, putative 2.16 3.55E-02 SP1277 aspartate carbamoyltransferase catalytic chain, pyrB 4.19 2.49E-02 SP1278 pyrimidine operon regulatory protein, pyrR 2.73 5.75E-04 SP1286 uracil permease, pyrP 2.17 4.28E-02 SP1549 polypeptide deformylase, def 2.66 1.17E-02 SP1716 ABC transporter permease - Na+ export, natB 5.99 1.88E-02 SP1717 ABC transporter permease - Na+ export, natA 2.29 1.53E-06 SP1941 competence/damage-inducible protein, cinA 2.46 1.26E-04 SP2006 transcriptional regulator, comX 10.84 3.74E-02 SP2047 hypothetical protein 2.33 2.82E-02 SP2048 competence protein comGF 3.17 2.20E-03 SP2050 competence protein cglD 2.87 5.36E-03 SP2051 competence protein cglC 4.53 2.20E-02 SP2052 competence protein cglB 3.74 4.07E-04 SP2053 competence protein cglA 8.25 8.94E-04 SP2156 SPFH domain/band 7 family 2.05 9.86E-04 SP2235 response regulator comE 11.29 1.50E-04 SP2236 sensor histidine kinase comD 15.54 2.67E-04 SPXX57 SP1908; single strand binding protein, ssb 2.61 2.68E-03 Downregulated SP0060 beta-galactosidase, bgaA 0.16 1.51E-04 SP0061 PTS system, mannose-specific IIB component, putative 0.33 6.50E-04 SP0062 PTS system, mannose-specific IIC component, putative 0.22 2.19E-03 SP0063 PTS system, mannose-specific IID component, putative 0.16 2.48E-02 SP0064 PTS system, mannose-specific IIA component, putative 0.30 9.47E-04 SP0065 sugar isomerase domain protein, agaS 0.35 2.40E-02 SP0066 aldose 1-epimerase, galM 0.35 5.68E-03 SP0303 6-phospho-beta-glucosidase, bglA 0.08 1.97E-04 SP0306 transcriptional regulator bglG, putative 0.04 1.84E-03 SP0307 PTS system, IIA component 0.09 5.91E-03 SP0308 PTS system, cellobiose-specific IIA component 0.09 1.40E-02 SP0309 hypothetical protein 0.25 7.67E-04 SP0310 PTS system, cellobiose-specific IIC component branched-chain amino acid transport system II carrier 0.14 6.37E-04 SP0626 protein, brnQ 0.34 1.76E-02 SP0645 PTS system, galactitol-specific IIA component, putative 0.29 3.13E-03 SP0646 PTS system, galactitol-specific IIA component, putative 0.29 2.25E-03 52 52
Page 1 and 2: Gene regulation in Streptococcus pn
Page 3 and 4: Cover image by Duve van Boggelen (w
Page 5 and 6: 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 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 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
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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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