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

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Table 2. Differentially expressed genes in D39 ΔglnAP. Gene identifier GlnR-regulon and pneumococcal virulence D39 TIGR4/R6 a Gene name Annotation Ratio b spd0051 sp0044 purC phosphoribosylaminoimidazole-succinocarboxamide synthase 1.1 spd0111 spr0103 argininosuccinate lyase 1.1 spd0142 sp0139 hypothetical protein 1.3 spd0143 spr0139 UDP-glucose 6-dehydrogenase 1.9 spd0144 sp0141 mutR transcriptional regulator 2.0 spd0145 sp0142 hypothetical protein 3.8 spd0146 sp0143 CAAX amino terminal protease family protein 3.9 spd0147 sp0144 CAAX amino terminal protease family protein 4.0 spd0148 sp0145 ABC transporter, substrate-binding protein 3.9 spd0149 sp0146 hypothetical protein 1.7 spd0161 sp0159 hypothetical protein 3.9 spd0283 sp0310 PTS system, IIC component 1.5 spd0300 sp0327 hypothetical protein 1.5 spd0334 sp0366 aliA oligopeptide ABC transporter 2.1 spd0335 sp0368 cell wall surface anchor family protein 1.4 spd0361 sp0395 transcriptional regulator, putative 1.4 spd0364 spr0361 ABC-type polar amino acid transport system 3.5 spd0404 sp0445 ilvB acetolactate synthase large subunit 3.2 spd0405 sp0446 ilvN acetolactate synthase, small subunit 3.4 spd0406 sp0447 ilvC ketol-acid reductoisomerase 3.1 spd0407 sp0448 hypothetical protein 2.5 spd0408 sp0449 hypothetical protein 2.7 spd0409 sp0450 ilvA threonine dehydratase 2.7 spd0424 sp0474 PTS system, cellobiose-specific IIC component 1.1 spd0541 spr0470 blpO bacteriocin 2.4 spd0652 sp0749 livJ branched-chain amino acid ABC transporter 1.0 spd0653 sp0750 livH branched-chain amino acid ABC transporter 1.4 spd0654 sp0751 livM branched-chain amino acid ABC transporter, permease protein 1.7 spd0655 sp0752 livG branched-chain amino acid ABC transporter 1.7 spd0656 sp0753 livF branched-chain amino acid ABC transporter 1.7 spd0749 sp0856 ilvE branched-chain amino acid aminotransferase 1.8 spd0751 sp0858 hypothetical protein 1.8 spd0752 sp0859 hypothetical protein 1.6 spd0753 sp0860 pcp pyrrolidone-carboxylate peptidase 1.7 spd0778 spr0786 hypothetical protein 2.4 spd0778 sp0882 hypothetical protein 2.3 spd0780 sp0884 hypothetical protein 2.0 spd0780 spr0788 hypothetical protein 1.9 spd0781 sp0885 hypothetical protein 2.3 spd0844 sp0955 celB competence protein 1.1 spd0900 sp1013 asd aspartate-semialdehyde dehydrogenase 2.0 spd0901 sp1014 dapA dihydrodipicolinate synthase 2.1 spd1004 sp1119 gapN glyceraldehyde-3-phosphate dehydrogenase, NADP-dependent 2.2 spd1011 sp1126 glxK glycerate kinase 1.1 spd1156 spr1179 putative iron-dependent peroxidase 1.0 spd1158 c sp1306 gdhA NADP-specific glumatate dehydrogenase 2.1 spd1190 sp1356 Atz/Trz family protein 1.1 spd1191 sp1357 ABC transporter, ATP-binding/permease protein 1.1 spd1192 sp1358 ABC transporter, ATP-binding/permease protein 1.3 spd1276 spr1302 hypothetical protein 1.3 spd1464 sp1651 psaD thiol peroxidase 1.3 spd1472 sp1659 ileS isoleucyl-tRNA synthetase 1.1 spd1500 sp1688 ABC transporter, permease protein 1.1 spd1563 spr1598 dicarboxylate/amino acid:cation (Na+ or H+) symporter 1.3 spd1564 sp1754 hypothetical protein 1.1 spd1585 spr1620 ABC transporter, sugar-binding protein 1.7 spd1596 sp1811 trpA tryptophan synthase, alpha subunit 1.1 171 171
Chapter 6 spd1602 sp1817 trpE anthranilate synthase component I 1.1 spd1649 sp1869 fatD iron-compound ABC transporter, permease protein 1.5 spd1650 sp1870 fatC ABC transporter membrane-spanning permease - ferric iron transport 1.5 spd1651 sp1871 fecA ABC transporter ATP-binding protein - ferric iron transport 1.1 spd1652 sp1872 fatB iron-compound ABC transporter, iron-compound-binding protein 1.1 spd1667 sp1887 amiF ABC transporter ATP-binding protein - oligopeptide transport 1.1 spd1668 sp1888 amiE ABC transporter ATP-binding protein - oligopeptide transport 1.3 spd1669 sp1889 amiD ABC transporter membrane-spanning permease - oligopeptide transport 1.2 spd1670 sp1890 amiC ABC transporter membrane-spanning permease - oligopeptide transport 1.1 spd1783 sp1986 hypothetical protein 1.1 spd1840 sp2031 predicted Zn-dependent hydrolases of the beta-lactamase fold 1.3 spd1845 sp2036 PTS system, ascorbate-specific IIA component, PTS-EII 1.3 spd1954 sp2125 hypothetical protein 2.2 spd1981 spr1961 hypothetical protein 1.1 spd1985 sp2157 adh2 alcohol dehydrogenase, iron-containing 1.0 spd1988 sp2160 hypothetical protein 1.1 spd1994 sp2166 fucA L-fuculose-phosphate aldolase 1.2 spd0096 sp0100 transcriptional regulator, PadR family protein -1.0 spd0381 sp0418 acp acyl carrier protein -1.0 spd0448 c sp0502 glnA glnA, glutamine synthetase -6.5 spd0803 sp0910 hypothetical protein -1.1 spd1098 c sp1241 glnP glutamine/glutamate transporter -6.2 spd1099 c sp1242 glnQ glutamine/glutamate transporter -3.2 spd1402 sp1572 dpr starved cells-like peroxide resistance protein -1.1 spd1524 sp1714 transcriptional regulator, GntR family protein -1.3 spd1526 spr1560 hypothetical protein (ABC-2 transporter) -1.1 spd1526 sp1715 hypothetical protein, ABC-2 type transporter -1.2 spd1607 sp1824 ABC transporter, permease protein (Fe(III)) -1.2 spd2068 sp2239 htrA serine protease -1.1 a Gene identifier as deposited in the NCBI Gene Expression Omnibus (GEO) database under GEO Series accession number GSE9850 ( TIGR4, sp; R6, spr). b Microarray ratio is given as log2-transformed expression of ∆glnPA / expression of wild-type. c Genes directly regulated by GlnR are indicated in bold fonts. 172 172
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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
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Introduction Figure 1. Infections c
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Interestingly, autolysis induced by
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histidine kinase is the sensor prot
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metabolism are often required for v
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egulatory systems, aiming to elucid
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11. Cockeran, R., A. J. Theron, H.
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33. Li, S., S. J. Kelly, E. Lamani,
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53. Romero, P., R. Lopez, and E. Ga
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CHAPTER 2 Regulation of gene expres
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Introduction Streptococcus pneumoni
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Materiaals and Meethods Gene regula
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(Invitrogen), 0.2 mM aminoallyl dUT
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Isolation of pneumococcal RNA durin
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Resultss and Discuussion Gene regul
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Table 1. Genes regulated by RR09 in
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phosphofructokinase, and a fructose
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Figure 4. Expression of rlrA and rr
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correlated well with our in vitro m
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Figure 7. Bacterial loads in blood
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Acknowledgments This work was suppo
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10. Ibrahim, Y. M., A. R. Kerr, J.
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genome sequence of a virulent isola
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Gene regulation by RR09 in S. pneum
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Gene regulation by RR09 in S. pneum
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Table S4. Genes up- and downregulat
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Table S6. Genes up- and downregulat
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Chapter 3 Abstract 62 62 Previous s
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Chapter 3 between the wild-type and
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Chapter 3 S. pneumoniae TIGR4 by CS
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Chapter 3 performance liquid chroma
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Chapter 3 Results Transcriptional a
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Chapter 3 Table 3. Differentially e
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Chapter 3 Figure 2. Colonization mo
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Chapter 3 than the D39ΔpsaR-infect
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Chapter 3 effect was more severe fo
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Chapter 3 in TIGR4ΔpsaR. However,
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Chapter 3 References 1. Adrian, P.
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Chapter 3 21. Hemsley, C., E. Joyce
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Chapter 3 40. McCluskey, J., J. Hin
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CHAPTER 4 CodY of Streptococcus pne
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Introduction Bacteria encounter var
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Materials and Methods Bacterial str
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Table 2. Oligonucleotide primers us
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The CodY regulon of S. pneumoniae I
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The CodY regulon of S. pneumoniae w
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Accession numbers The microarray da
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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
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 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
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