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

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Gene regulation by RR09 in S. pneumoniae SP0647 PTS system, galactitol-specific IIC component, putative 0.19 1.47E-04 SP0648 beta-galactosidase, bgaA 0.10 2.42E-03 SP0782 hypothetical protein 0.38 5.20E-03 SP0923 Cof family protein 0.49 3.68E-02 SP1190 tagatose 1,6-diphosphate aldolase, lacD 0.15 8.23E-05 SP1191 tagatose-6-phosphate kinase, lacC 0.12 7.43E-06 SP1192 galactose-6-phosphate isomerase, lacB 0.03 1.19E-02 SP1193 galactose-6-phosphate isomerase, lacA 0.14 1.57E-04 SP1197 PTS system, galactitol-specific IIB component, putative 0.16 6.20E-03 SP1804 general stress protein 24, putative 0.48 3.88E-05 SP1845 exodeoxyribonuclease, exoA 0.45 3.91E-02 SP1883 dextran glucosidase dexS, putative 0.34 7.58E-05 SP1884 trehalose PTS system, IIABC components 0.44 7.00E-05 SP2108 maltose/maltodextrin ABC transporter, malX 0.36 6.10E-04 SP2110 maltodextrin ABC transporter, permease protein, malD 0.49 1.46E-02 53 53
Chapter 2 Table S2. Genes up- and downregulated in D39 Δrr09 at an optical density of 0.2 grown in THY-broth. Ratios are given as Δrr09 / wild type. Gene Upregulated Annotation Ratio (fold change) p-value SP0018 competence protein, comW 22.08 3.44E-02 SP0042 competence factor transporting protein comA 6.56 3.19E-03 SP0043 competence factor transport protein comB 6.12 5.65E-04 SP0430 hypothetical protein 2.42 2.56E-02 SP0502 glutamine synthetase, glnA 4.59 2.26E-02 SP0545 immunity protein blpY 3.49 1.05E-03 SP0701 orotidine 5'-phosphate decarboxylase, pyrF 2.73 2.75E-03 SP0702 orotate phosphoribosyltransferase pyrE 2.82 3.19E-04 SP0963 dihydroorotate dehydrogenase pyrDII 3.41 9.85E-04 SP0964 dihydroorotate dehydrogenase B, pyrD 2.56 7.03E-03 SP0965 endo-beta-N-acetylglucosaminidase, lytB 3.11 2.07E-02 SP1110 riboflavin kinase / FMN adenylyltransferase, mreA 6.74 3.87E-05 SP1277 aspartate carbamoyltransferase catalytic chain, pyrB 2.14 2.50E-05 SP1278 pyrimidine operon regulatory protein, pyrR 2.83 1.10E-04 SP1380 putative ABC-2 type transport system permease 2.25 3.22E-02 SP1549 polypeptide deformylase, def 3.08 2.06E-02 SP1716 ABC transporter permease - Na+ export, natB 2.58 5.84E-06 SP1717 ABC transporter permease - Na+ export, natA 2.57 1.14E-04 SP1870 ABC transporter membrane-spanning permease, fatC 3.95 3.19E-02 SP1941 competence/damage-inducible protein, cinA 2.78 2.31E-03 SP2047 hypothetical protein 2.51 3.08E-04 SP2048 competence protein comGF 2.69 7.91E-04 SP2050 competence protein cglD 2.34 3.54E-03 SP2051 competence protein cglC 2.65 2.87E-02 SP2052 competence protein cglB 2.09 5.20E-05 SP2053 competence protein cglA CDP-diacylglycerol-glycerol-3-p 3- 3.75 2.33E-04 SP2222 phosphatidyltransferase, pgsA 2.23 2.24E-02 SP2235 response regulator comE 10.09 3.79E-04 SP2236 sensor histidine kinase comD 22.01 1.49E-05 Downregulated SP0060 beta-galactosidase, bgaA 0.10 5.97E-04 SP0061 PTS system, mannose-specific IIB component, putative 0.27 2.19E-03 SP0062 PTS system, mannose-specific IIC component, putative 0.19 2.86E-03 SP0063 PTS system, mannose-specific IID component, putative 0.18 6.47E-04 SP0064 PTS system, mannose-specific IIA component, putative 0.36 4.66E-04 SP0065 sugar isomerase domain protein, agaS 0.16 8.04E-05 SP0066 aldose 1-epimerase, galM 0.10 2.61E-03 SP0303 6-phospho-beta-glucosidase, bglA 0.03 2.25E-05 SP0306 transcriptional regulator bglG, putative 0.01 2.77E-03 SP0307 PTS system, IIA component 0.01 1.05E-04 SP0308 PTS system, cellobiose-specific IIA component 0.01 3.95E-04 SP0309 hypothetical protein 0.10 1.49E-03 SP0310 PTS system, cellobiose-specific IIC component 0.08 2.01E-04 SP0342 glucan 1,6-alpha-glucosidase, dexB 0.48 4.02E-03 SP0645 PTS system, galactitol-specific IIA component, putative 0.13 5.17E-06 54 54
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 52 and 53: genome sequence of a virulent isola
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
Page 186 and 187:
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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