A computational study of bacterial gene regulation and adaptation ...

More documents

Recommendations

Info

List of FiguresTitlePageSummary figure: Summary of transcription initiation in bacteria 5Figure 1.1: Levels of transcriptional regulation 28Figure 1.2: AT content and transcription initiation in E. coli 32Figure 1.3: AT content upstream of pseudogenes. 34Figure 1.4: Lead genes in E. coli, their expression and global transcriptionfactors.36Figure 1.5: Supercoiling and AT content. 39Figure 1.6: Anti-silencing of H-NS-repressed genes. 41Figure 2.1: Regulatory targets of general and specific TFs. 60Figure 2.2: Numbers of TFs controlling metabolic enzymes. 62Figure 2.3: Configurations for neighbouring enzymatic reactions. 63Figure 2.4: Co-regulation and co-expression of metabolic enzyme pairs. 64Figure 2.5: Co-expression of enzyme pairs at different levels of separation inthe metabolic network.Figure 2.6: Conservation and co-expression of metabolic enzymes across 380bacterial genomes.Figure 3.1: Integrated genome-scale regulatory network for small moleculemetabolism in E. coli.666980Figure 3.2: Direct and indirect regulation of E.coli metabolism. 85Figure 3.3: Multilayered regulation of metabolism. 89Figure 4.1: c-di-GMP turnover 97Figure 4.2: Numbers of c-di-GMP proteins and their relationship with genomesize.102Figure 4.3: Organism types and c-di-GMP protein counts. 104Figure 4.4: Regulation of c-di-GMP proteins 108
TitlePageFigure 4.5: Catalytic and allosteric sites in c-di-GMP proteins 114Figure 5.1: Schematic representation of the three stages of the regulatoryprocess in bacteria.Figure 5.2: Comparison of regulatory protein counts between E. coli and M.xanthus.125129Figure 5.3: Histidine kinases in prokaryotic genomes and metagenomes. 131Figure 5.4: Transcriptional and non-transcriptional outputs of two-componentsystems.135Figure 5.5: Signal sensing in two-component systems. 137Figure 5.6: Genomes coding for an enrichment of SMBD-containing TFs. 139
Page 3 and 4: Statement of lengthThis thesis does
Page 5 and 6: molecules also bind to enzymes dire
Page 7: Table of ContentsTitlePagesIntroduc
Page 11 and 12: IntroductionFunctional and comparat
Page 13 and 14: egulation owing to the large amount
Page 15 and 16: (A) Closed complex formationRNA pol
Page 17 and 18: Intuitively negative supercoiling,
Page 19 and 20: I.3. Transcription factors: domain
Page 21 and 22: I.4. Transcriptional regulatory net
Page 23 and 24: (Balazsi et al. 2005). Gene express
Page 25 and 26: metabolism / carbon nutrition with
Page 27 and 28: I.4.5. Signal sensing in transcript
Page 29 and 30: I.5. Non-transcriptional output: cy
Page 31 and 32: transcriptional initiation by c-di-
Page 33 and 34: phosphatase activity of the kinases
Page 35 and 36: I.7. ConclusionIn this chapter, we
Page 37 and 38: Chapter 1: Global regulators of bac
Page 59 and 60:
Chapter 2: Transcriptional control
Page 61 and 62:
Page 63 and 64:
Page 65 and 66:
Page 67 and 68:
Page 69 and 70:
Page 71 and 72:
Page 73 and 74:
Page 75 and 76:
Page 77 and 78:
Page 79 and 80:
Page 81 and 82:
Page 83 and 84:
Page 85 and 86:
Page 87 and 88:
Chapter 3: Transcriptional and post
Page 89 and 90:
Page 91 and 92:
Page 93 and 94:
Page 95 and 96:
Page 97 and 98:
Page 99 and 100:
Page 101 and 102:
Page 103 and 104:
Page 105 and 106:
Chapter 4: Comparative genomics of
Page 107 and 108:
Page 109 and 110:
Page 111 and 112:
Page 113 and 114:
Page 115 and 116:
Page 117 and 118:
Page 119 and 120:
Page 121 and 122:
Page 123 and 124:
Page 125 and 126:
Page 127 and 128:
Page 129 and 130:
Page 131 and 132:
Page 133 and 134:
Page 135 and 136:
two-domain architectures wherethese
Page 137 and 138:
Page 139 and 140:
Page 141 and 142:
Page 143 and 144:
Page 145 and 146:
Page 147 and 148:
Page 149 and 150:
(A)60% of genomes from class4530150
Page 151 and 152:
Page 153 and 154:
Discussion and conclusionsDiscussio
Page 155 and 156:
Discussion and conclusionsD1.1.3. C
Page 157 and 158:
Discussion and conclusionsD2. Futur
Page 159 and 160:
BibliographyAmikam, D., Steinberger
Page 161 and 162:
BibliographyBlattner, F.R., Plunket
Page 163 and 164:
BibliographyChen, S.L., Hung, C.S.,
Page 165 and 166:
BibliographyEchols, N., Harrison, P
Page 167 and 168:
Bibliographysystem level analysis o
Page 169 and 170:
BibliographyHerring, C.D., Raghunat
Page 171 and 172:
BibliographyJenal, U., and Malone,
Page 173 and 174:
BibliographyKeseler, I.M., Collado-
Page 175 and 176:
BibliographyLee, S.H., Angelichio,
Page 177 and 178:
BibliographyMcClelland, M., Sanders
Page 179 and 180:
BibliographyO Croinin, T., Carroll,
Page 181 and 182:
BibliographyPrice, M.N., Dehal, P.S
Page 183 and 184:
BibliographySatriano, J., and Schlo
Page 185 and 186:
BibliographySteinberger, O., Lapido
Page 187 and 188:
BibliographyUssery, D.W., Wassenaar
Page 189 and 190:
BibliographyYanofsky, C. 1981. Atte
Page 191 and 192:
Appendix 1Appendix 1.1: Differences
Page 193 and 194:
!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!
Page 195 and 196:
Appendix 1Appendix 1.5: Gene expres
Page 197 and 198:
Appendix 2Appendix 2.1: Differences
Page 199 and 200:
Appendix 2Appendix 2.3: Co-regulati
Page 201 and 202:
Appendix 2Appendix 2.5: Flux coupli
Page 203 and 204:
Appendix 2Appendix 2.7: Co-regulati
Page 205 and 206:
Appendix 2Appendix 2.8B: Connectivi
Page 207 and 208:
Appendix 2Appendix 2.10: Correlatio
Page 209 and 210:
Appendix 2Appendix 2.12A: Robustnes
Page 212 and 213:
Appendix 3Appendix 3Supplementary m
Page 214 and 215:
Reaction ID Regulatory metabolite I
Page 216 and 217:
Appendix 3Appendix 3.3B: Direct reg
Page 218 and 219:
Appendix 3Appendix 3.4B: Direct reg
Page 220 and 221:
Appendix 4Appendix 4Supplementary m
Page 222 and 223:
Appendix 4Motile organisms are rich
Page 224:
Appendix 4We can expand the analysi
Page 227 and 228:
Appendix 5Appendix 5.1A: PFAMs for
Page 229 and 230:
Appendix 5Appendix 5.1C: PFAMs for
Page 231 and 232:
Appendix 5Appendix 5.2B: Small-mole
Page 233 and 234:
Appendix 5Appendix 5.3: Organisms s
Page 235 and 236:
Appendix 5Appendix 5.5: Partner dom
Page 237 and 238:
Appendix 5fraction of SDRRs would a
Page 239 and 240:
Appendix 5Appendix 5.6C: Non-hybrid
Page 241 and 242:
Appendix 5Appendix 5.8: List of org
Page 244 and 245:
Appendix 6Appendix 6List of genomes
Page 246 and 247:
Appendix 648. Mycobacterium tubercu
Page 248 and 249:
Appendix 6144. Bacillus cereus ATCC
Page 250 and 251:
Appendix 6240. Nitrobacter winograd
Page 252 and 253:
Appendix 6336. Cytophaga hutchinson
Page 254 and 255:
Appendix 6432. Acinetobacter bauman
Page 256 and 257:
Appendix 6528. Enterobacter sakazak
Page 258 and 259:
Appendix 6624. Polynucleobacter nec
Page 260 and 261:
Appendix 7Appendix 7List of genomes
Page 262 and 263:
Appendix 748. Bordetella parapertus
Page 264 and 265:
Appendix 7144. Haemophilus somnus14
Page 266 and 267:
Appendix 7240. Prochlorococcus mari
Page 268 and 269:
Appendix 7336. Synechococcus sp. CC
Page 270 and 271:
Downloaded from genome.cshlp.org on
Page 272 and 273:
Page 274 and 275:
Page 276 and 277:
Page 278 and 279:
Page 280 and 281:
Page 282 and 283:
Page 284 and 285:
JOURNAL OF BACTERIOLOGY, June 2008,
Page 286 and 287:
VOL. 190, 2008 P. MIRABILIS GENOME
Page 288 and 289:
Page 290 and 291:
Page 292 and 293:
Page 294:
Page 297 and 298:
2 Nucleic Acids Research, 2008PCR a
Page 299 and 300:
4 Nucleic Acids Research, 2008Table
Page 301 and 302:
6 Nucleic Acids Research, 2008Table
Page 303 and 304:
8 Nucleic Acids Research, 2008solve
Page 305 and 306:
524 Mol Genet Genomics (2008) 279:5
Page 307 and 308:
Page 309 and 310:
Page 311 and 312:
Page 313 and 314:
Page 315 and 316:
Page 317 and 318:
4378 J.J. James et al. / FEBS Lette
Page 319 and 320:
Page 321 and 322:
Page 324 and 325:
An Assessment of the Role of DNA Ad
Page 326 and 327:
DAM and Transcriptionpotential of s
show all

A computational study of bacterial gene regulation and adaptation ...

You also want an ePaper? Increase the reach of your titles

Delete template?

Save as template?