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

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Table 3. Differentially expressed genes in D39 ΔcodY. Gene name ID TIGR4 ID D39 Annotation a The CodY regulon of S. pneumoniae MA ratio b 2D ratioc EMSA d CodY Kd (nM e ) CodY (10nM ILV) mutR sp0141 spd0144 positive transcriptional regulator of MutA 2.51 + 1115 439 sp0142 spd0145 hypothetical protein (bacteriocin) 2.24 + > 2000 1938 sp0143 spd0146 hypothetical protein 2.48 sp0144 spd0147 hypothetical protein 2.84 sp0145 spd0148 hypothetical protein 2.43 sp0159 spd0161 hypothetical protein 2.46 + 834 73 cps2K - spd0326 UDPglucose 6-dehydrogenase 1.47 aliA sp0366 spd0334 oligopeptide-binding protein 2.18 2.98 pbpA sp0369 spd0336 penicillin-binding protein 1A -0.09 1.92 ilvB sp0445 spd0404 acetolactate synthase large subunit 3.02 + > 2000 284 ilvN sp0446 spd0405 acetolactate synthase small subunit 3.24 ilvC sp0447 spd0406 ketol-acid reductoisomerase 3.03 2.28 sp0448 spd0407 hypothetical protein 2.98 sp0449 spd0408 hypothetical protein 3.70 ilvA sp0450 spd0409 threonine dehydratase 2.95 1.70 grpE sp0516 spd0459 heat shock protein GrpE 0.22 1.26 livJ sp0749 spd0652 ABC transporter substrate-binding protein - BCAA transport 1.88 + 597 52 livH sp0750 spd0653 ABC transporter membrane-spanning permease - BCAA transport 1.58 livM sp0751 spd0654 ABC transporter membrane-spanning permease - BCAA transport 1.90 livG sp0752 spd0655 ABC transporter ATP-binding protein - BCAA transport 2.25 livF sp0753 spd0656 ABC transporter ATP-binding protein - BCAA transport 2.30 acuB sp0754 spd0657 acetoin utilization protein 1.08 + >2000 773 pnp sp0831 spd0726 purine-nucleoside phosphorylase 0.35 1.44 ilvE sp0856 spd0749 branched-chain amino acid aminotransferase 2.08 f + 482 68 sp0857 spd0750 ABC-SBP-internal deletion, aliB-like (blastN) 2.09 sp0858 spd0751 hypothetical protein 2.15 sp0859 spd0752 membrane protein 2.07 pcp sp0860 spd0753 pyrrolidone-carboxylate peptidase 1.39 1.75 sp0882 spr0778 putative esterase, S. suis (blastN) 1.64 sp0884 spd0780 putative esterase S. suis (blastN) 1.78 - sp0885 spd0781 putative Carbamoylphosphate synthase large subunit (blastN) 1.94 asd sp1013 spd0900 aspartate-semialdehyde dehydrogenase 2.06 1.40 + > 2000 120 dapA sp1014 spd0901 dihydrodipicolinate synthase 1.69 gapN sp1119 spd1004 NADP-dependent glyceraldehyde-3phosphate dehydrogenase 1.05 + 752 211 glxK sp1126 spd1011 glycerate kinase 1.33 gdhA sp1306 spd1158 glutamate dehydrogenase (NADP+) 1.71 2.80 + 726 156 rplL sp1354 spd1187 50S ribosomal protein L7/L12 -0.17 2.20 rplJ sp1355 spd1188 50S ribosomal protein L10 -0.10 1.43 nagB sp1415 spd1246 N-acetylglucosamine-6-phosphate isomerase -0.19 1.37 sp1578 spd1408 methyltransferase, putative 1.16 + >2000 368 dctA sp1753 spd1563 dicarboxylate/amino acid:cation (Na+ or H+) symporter 2.81 sp1754 spd1564 hypothetical protein (integral membrane protein) 2.84 103 103
Chapter 4 fatD sp1869 spd1649 iron-compound ABC transporter, permease protein 2.80 + >2000 >2000 fatC sp1870 spd1650 iron-compound ABC transporter, permease protein 2.44 fecE sp1871 spd1651 iron-compound ABC transporter, ATP-binding protein 1.37 fatB sp1872 spd1652 iron-compound ABC transporter, ironcompound-binding protein 1.07 amiD sp1889 spd1669 oligopeptide ABC transporter, permease protein 1.20 amiC sp1890 spd1670 oligopeptide ABC transporter, permease protein 1.72 amiA sp1891 spd1671 oligopeptide ABC transporter, oligopeptide-binding protein 1.21 1.41 + 677 433 sp2125 spd1954 hypothetical protein 2.18 + 754 630 rpoA sp0236 spd0218 DNA-directed RNA polymerase subunit alpha -0.12 -1.86 ABC-NBD sp0483 spd0434 ABC transporter ATP-binding protein - cobalt transport -0.34 -1.96 fba sp0605 spd0526 fructose-bisphosphate aldolase -0.20 -1.64 pepV sp0623 spd0542 dipeptidase -0.21 -2.42 sp1429 spd1258 putative peptidase, U32 family -1.29 -1.81 pgm sp1498 spd1326 phosphoglucomutase 0.11 -1.57 atpB sp1513 spd1340 proton-translocating ATPase, F0 sector, subunit a -0.15 -1.58 dpr sp1572 spd1402 DNA binding protein starved cells-like peroxide resistance protein -2.69 -1.55 codY sp1584 spd1412 transcriptional pleiotropic repressor CodY -1.68 + > 2000 382 gapA sp2012 spd1823 glyceraldehyde-3-phosphate dehydrogenase -0.20 -1.93 pcpA sp2136 spd1965 choline binding protein PcpA -1.36 + > 2000 903 pgsA sp2222 spd2049 CDP-diacylglycerol--glycerol-3phosphate 3-phosphatidyltransferase 0.14 -1.67 a Annotation is according to the Kyoto Encyclopedia of Genes and Genomes database (www.kegg.com). b Microarray (MA) ratios are given as follows: expression of ΔcodY / expression of wild-type (Log2 transformed) c 2D DIGE (2D) ratios are given as: expression of ΔcodY / expression of wild-type (Log2 transformed) d In the EMSA column, a plus indicates a shift, while a minus indicates no shift. e The Kds of the promoter region (concentration of CodY at which 50% of the probe is shifted) without addition of BCAAs and in the presence 10 mM BCAAs are shown. f Only expressed in the codY-mutant. 104 104 Ten proteins were found to be significantly more abundant in the wild-type than the mutant, two of which identified by transcriptional analysis as well (Table 3). Proteins only detected by 2D-DIGE included fructose biphosphate aldolase (Fba, sp0605), glyceraldehyde- 3-phophate dehydrogenase (GapA, sp2012), F-type H+-transporting ATPase a chain (AtpB, sp1513), and the dipeptidase PepV (sp0623). Interestingly, L. lactis PepV belongs to the proteolytic system regulated by CodY, although direct regulation of pepV by CodY has never been shown (16).
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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
Page 54 and 55: Gene regulation by RR09 in S. pneum
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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 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
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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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