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

More documents

Recommendations

Info

Gene regulation by RR09 in S. pneumoniae SP0646 PTS system, galactitol-specific IIA component, putative 0.07 1.05E-05 SP0647 PTS system, galactitol-specific IIC component, putative 0.18 2.14E-04 SP0648 beta-galactosidase, bgaA 0.09 5.41E-04 SP0758 PTS system, glucose-specific IIABC components, ptsG 0.30 4.30E-03 SP0782 hypothetical protein 0.38 1.10E-04 SP1182 lactose phosphotransferase system repressor, lacR 0.47 9.21E-04 SP1190 tagatose 1,6-diphosphate aldolase, lacD 0.06 1.01E-03 SP1191 tagatose-6-phosphate kinase, lacC 0.08 3.71E-05 SP1192 galactose-6-phosphate isomerase, lacB 0.05 1.32E-04 SP1193 galactose-6-phosphate isomerase, lacA 0.03 2.26E-03 SP1197 PTS system, galactitol-specific IIB component, putative 0.09 1.70E-04 SP1626 30S ribosomal protein S15, rpsO 0.31 2.58E-02 SP1883 dextran glucosidase dexS, putative 0.18 7.71E-03 SP1884 trehalose PTS system, IIABC components 0.35 3.84E-05 SP2108 maltose/maltodextrin ABC transporter, malX 0.35 5.14E-04 SP2110 maltodextrin ABC transporter, permease protein, malD 0.31 6.30E-03 SPXX36 SP2063; LysM domain protein (spr1875) 0.24 1.39E-02 55 55
Chapter 2 Table S3. Genes up- and downregulated in D39 Δrr09 at an optical density of 0.6 grown in BHI-broth. Ratios are given as Δrr09 / wild type. Gene Upregulated Annotation Ratio (fold change) p-value SP0501 transcriptional regulator, MerR family 2.85 1.08E-02 SP0502 glutamine synthetase, type I 3.02 1.54E-03 SP0875 lactose phosphotransferase system repressor 15.26 2.70E-04 SP0876 1-phosphofructokinase, putative 13.35 2.36E-05 SP0877 PTS system, fructose specific IIABC components 8.35 2.72E-03 SP1922 conserved hypothetical protein 3.42 1.56E-03 SP1923 pneumolysin 4.60 2.41E-03 SP1924 hypothetical protein 2.92 3.00E-03 SP1925 hypothetical protein 3.09 4.14E-03 SP1926 hypothetical protein 2.90 2.32E-04 Downregulated SP0057 beta-N-acetylhexosaminidase 0.17 1.21E-03 SP0060 beta-galactosidase 0.03 7.48E-05 SP0061 PTS system, IIB component 0.07 9.99E-05 SP0062 PTS system, IIC component 0.03 1.03E-04 SP0063 PTS system, IID component 0.03 7.25E-05 SP0064 PTS system, IIA component 0.04 1.14E-04 SP0065 sugar isomerase domain protein AgaS 0.20 2.23E-02 SP0066 aldose 1-epimerase 0.12 2.97E-04 SP0090 ABC transporter, permease protein 0.25 6.19E-03 SP0285 alcohol dehydrogenase, zinc-containing 0.36 2.61E-03 SP0303 6-phospho-beta-glucosidase 0.04 8.93E-05 SP0305 PTS system, IIB component 0.09 7.50E-04 SP0306 transcriptional regulator, putative 0.21 3.50E-03 SP0307 PTS system, IIA component 0.30 2.35E-02 SP0308 PTS system, IIA component 0.25 4.82E-03 SP0310 PTS system, IIC component 0.16 1.62E-04 SP0368 Cell wall surface anchor family protein 0.22 6.38E-04 SP0386 sensor histidine kinase, putative 0.41 1.60E-02 SP0498 endo-beta-N-acetylglucosaminidase, putative 0.19 5.05E-04 SP0577 PTS system, beta-glucosides-specific IIABC 0.27 9.38E-03 SP1027 conserved hypothetical protein 0.25 1.37E-02 SP1471 oxidoreductase, putative 0.33 6.98E-03 SP1695 acetyl xylan esterase, putative 0.23 1.41E-03 SP1802 hypothetical protein 0.19 2.12E-03 SP2026 alcohol dehydrogenase, iron-containing 0.25 2.78E-03 SP2055 alcohol dehydrogenase, zinc-containing 0.35 1.87E-04 SP2056 N-acetylglucosamine-6-phosphate deacetylase 0.34 8.35E-04 SP2107 4-alpha-glucanotransferase 0.27 3.81E-03 SP2141 glycosyl hydrolase-related protein 0.08 7.90E-04 SP2142 ROK family protein 0.08 5.19E-04 SP2143 conserved hypothetical protein 0.16 2.36E-03 SP2144 conserved hypothetical protein 0.09 3.47E-04 SP2146 conserved hypothetical protein 0.20 2.06E-03 SP2239 serine protease 0.18 7.39E-04 SP2240 spspoJ protein 0.21 5.54E-03 56 56
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 54 and 55: 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
Page 106 and 107:
Binding of CodY to target promoters
Page 108 and 109:
The CodY regulon of S. pneumoniae E
Page 110 and 111:
The CodY regulon of S. pneumoniae F
Page 112 and 113:
Discussion CodY has been described
Page 114 and 115:
levels of adherence in D39. Using a
Page 116 and 117:
References The CodY regulon of S. p
Page 118 and 119:
Glass. 2001. Genome of the bacteriu
Page 120 and 121:
40. Shivers, R. P., S. S. Dineen, a
Page 122 and 123:
CHAPTER 5 Regulation of glutamine a
Page 124 and 125:
Introduction Regulation of nitrogen
Page 126 and 127:
Materials and Methods Nitrogen Meta
Page 128 and 129:
TK136 D39 Δcps; Km R capsule-less
Page 130 and 131:
gene from pORI28, was fused to the
Page 132 and 133:
Construction of lacZ fusions Chromo
Page 134 and 135:
Enzyme assays Cell-free extracts, u
Page 136 and 137:
Reverse-transcriptase PCR RNA isola
Page 138 and 139:
Table 3. Summary of transcriptome c
Page 140 and 141:
effect caused by altered intracellu
Page 142 and 143:
examine whether zwf is only transcr
Page 144 and 145:
(http://www.bd.com/ds/technicalCent
Page 146 and 147:
H6-GlnR alone at the concentration
Page 148 and 149:
Discussion In this study, we charac
Page 150 and 151:
Acknowledgements TK, JB and HB are
Page 152 and 153:
11. den Hengst, C. D., S. A. van Hi
Page 154 and 155:
Nitrogen Metabolism in S. pneumonia
Page 156 and 157:
52. Wray, L. V., Jr., J. M. Zalieck
Page 158 and 159:
CHAPTER 6 Site-specific contributio
Page 160 and 161:
Introduction GlnR-regulon and pneum
Page 162 and 163:
Materials and Methods Bacterial str
Page 164 and 165:
eferred to as t=0. Bacteriology res
Page 166 and 167:
Results GlnR-regulon and pneumococc
Page 168 and 169:
Figure 3. Colonization model. Bacte
Page 170 and 171:
GlnR-regulon and pneumococcal virul
Page 172 and 173:
Table 2. Differentially expressed g
Page 174 and 175:
Discussion The ability to adequatel
Page 176 and 177:
The microarray data showed that pre
Page 178 and 179:
Acknowledgments WTH is supported by
Page 180 and 181:
12. Ibrahim, Y. M., A. R. Kerr, J.
Page 182 and 183:
33. Zalieckas, J. M., L. V. Wray, J
Page 184 and 185:
CHAPTER 7 Pneumococcal gene regulat
Page 186 and 187:
Introduction Regulation of gene exp
Page 188 and 189:
Gene regulation and metabolism in S
Page 190 and 191:
makes it possible for the pneumococ
Page 192 and 193:
A CcpA homologue exists in the pneu
Page 194 and 195:
double mutant, suggesting direct re
Page 196 and 197:
References Gene regulation and meta
Page 198 and 199:
23. Kerr, A. R., P. V. Adrian, S. E
Page 200 and 201:
45. Sonenshein, A. L. 2005. CodY, a
Page 202 and 203:
CHAPTER 8 Summarizing discussion 20
Page 204 and 205:
that the observed virulence phenoty
Page 206 and 207:
CodY was found to be required for a
Page 208 and 209:
References Summarizing discussion 1
Page 210 and 211:
Summarizing discussion 21. Orihuela
Page 212 and 213:
Samenvatting en discussie Curriculu
Page 214 and 215:
Samenvatting en discussie kunnen ge
Page 216 and 217:
Bevindingen die dit onderbouwen, we
Page 218 and 219:
Curriculum Vitae Curriculum Vitae W
Page 220 and 221:
Dankwoord Jeetje, dat het dan toch
Page 222:
oekje en ik kijk uit naar de bijbeh
show all

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

Create successful ePaper yourself

Delete template?

Save as template?