Pseudomonas (eBook)

PREFACE 6
CONTENTS 8
LIST OF CONTRIBUTORS 10
NEW INSIGHTS ON IRON ACQUISITION MECHANISMS IN PATHOGENIC PSEUDOMONAS 12
1. INTRODUCTION 12
2. IRON UPTAKE VIA SIDEROPHORES 14
3. HEME ACQUISITION 29
4. TRANSPORT ACROSS THE INNER MEMBRANE 30
5. IRON TRANSPORT REGULATION 32
6. CONCLUSIONS 34
ACKNOWLEDGMENTS 35
REFERENCES 36
CLONAL VARIATIONS IN PSEUDOMONAS AERUGINOSA 46
1. INTRODUCTION 46
2. INTRA- AND INTERCLONAL GENOME DIVERSITY 47
3. CLONAL VARIATIONS OF PHENOTYPE 63
4. INTRACLONAL EVOLUTION AND DIVERSITY IN CLINICAL HABITATS 66
REFERENCES 74
PSEUDOMONAS AERUGINOSA PHOSPHOLIPASES AND PHOSPHOLIPIDS 80
1. PHOSPHOLIPASE C 81
2. PHOSPHOLIPASE D 85
3. PHOSPHOLIPASE A 85
4. PLCS OF P. AERUGINOSA 87
5. PLDS OF P. AERUGINOSA 95
6. PLA2 (EXOU) OF P. AERUGINOSA 97
7. PHOSPHOLIPASES: HYDROLASE OR SYNTHASE? 99
ACKNOWLEDGMENTS 103
REFERENCES 103
IN VIVO FUNCTIONAL GENOMICS OF PSEUDOMONAS: PCR- BASED SIGNATURE- TAGGED MUTAGENESIS 109
1. INTRODUCTION 109
2. SIGNATURE-TAGGED MUTAGENESIS 111
3. IN VIVO STM OF P. AERUGINOSA 114
4. STM AND CHIP ANALYSIS 123
5. CONCLUSION 124
ACKNOWLEDGMENTS 125
REFERENCES 125
A GENOME-WIDE MUTANT LIBRARY OF PSEUDOMONAS AERUGINOSA 131
1. INTRODUCTION 131
2. CONSTRUCTION OF THE TRANSPOSON MUTANT COLLECTION 132
3. COMPOSITION OF THE MUTANT COLLECTION 138
4. MUTANT DISTRIBUTION 139
5. CONFIRMATION OF MUTANT IDENTITY 140
6. MUTANTS DISTRIBUTED FROM SEATTLE 143
7. WHOLE LIBRARY PHENOTYPIC SCREENS 145
8. CONCLUSIONS 147
ACKNOWLEDGMENTS 148
REFERENCES 148
BIOGENESIS AND FUNCTION OF TYPE IV PILI IN PSEUDOMONAS SPECIES 149
1. INTRODUCTION 149
2. STRUCTURE AND BIOGENESIS OF TYPE IV PILI 150
3. TYPE IV PILI AND NATURAL TRANSFORMATION IN PSEUDOMONAS SPECIES 171
4. ROLES OF TYPE IV PILI IN COLONIZATION AND INFECTION BY PSEUDOMONAS SPECIES 173
5. TWITCHING MOTILITY 176
6. TFP AND BIOFILM DEVELOPMENT 182
7. FUTURE DIRECTIONS 184
ACKNOWLEDGMENTS 184
REFERENCES 185
EVOLUTION OF CATABOLIC PATHWAYS IN PSEUDOMONAS THROUGH GENE TRANSFER 199
1. INTRODUCTION 199
2. CATABOLIC PATHWAYS 200
3. MICROORGANISMS AND CATABOLIC ADAPTATION 206
4. GENETIC ADAPTATION MECHANISMS 207
5. EXPANSION OF CATABOLIC PATHWAYS BY LATERAL GENE TRANSFER 213
6. TOLUENE DEGRADATION AND THE TOL PLASMIDS 214
7. POLYAROMATIC PATHWAYS 218
8. CATABOLIC EXPANSION BY LATERAL GENE TRANSFER 221
9. HERBICIDE DEGRADATION 221
10. CHLORO- AND NITROAROMATIC DEGRADATION 225
11. THE CLC ELEMENT 228
12. CONCLUDING REMARKS 232
ACKNOWLEDGMENTS 232
REFERENCES 232
CONTROLLING REGIOSPECIFIC OXIDATION OF AROMATICS AND THE DEGRADATION OF CHLORINATED ALIPHATICS VIA ACTIVE SITE ENGINEERING OF TOLUENE MONOOXYGENASES 247
1. SUMMARY 247
2. INTRODUCTION 248
3. SUCCESSIVE HYDROXYLATIONS OF TOLUENE MONOXYGENASES 251
4. PHYSIOLOGICAL RELEVANCE OF SUCCESSIVE HYDROXYLATIONS OF TpMO 254
5. DISCOVERY OF RESIDUES THAT CONTROL CATALYTIC ACTIVITY IN TOLUENE MONOOXYGENASES 257
6. SATURATION MUTAGENESIS 264
7. CONTROL OF THE REGIOSPECIFIC HYDROXYLATION OF TOLUENE 265
8. CONTROL OF THE REGIOSPECIFIC HYDROXYLATION OF INDOLE 269
9. CONTROL OF THE REGIOSPECIFIC HYDROXYLATION OF METHYL AND METHOXY AROMATICS BY T4MO 272
10. CONTROL OF THE REGIOSPECIFIC HYDROXYLATION OF METHYL AROMATICS BY ToMO 274
11. CONTROL OF THE REGIOSPECIFIC HYDROXYLATION OF NITRO AROMATICS 278
12. REGIOSPECIFIC HYDROXYLATION OF NAPHTHALENE AND FLUORENE 280
13. TWO-PHASE REACTORS FOR SYNTHESIZING PHENOL AND 2- NAPHTHOL 283
14. DEGRADATION OF PCE, TCE, AND CHLOROFORM 284
15. METABOLIC ENGINEERING FOR DEGRADING CHLORINATED ETHENES 286
16. ENGINEERING DIOXYGENASES FOR SINGLE HYDROXYLATIONS OF AROMATICS 288
17. CONCLUSIONS AND FUTURE DIRECTIONS 289
ACKNOWLEDGMENTS 289
REFERENCES 290
AROMATIC RING HYDROXYLATING DIOXYGENASES 297
1. INTRODUCTION 297
2. DISTRIBUTION OF RING HYDROXYLATING DIOXYGENASES IN CATABOLIC PATHWAYS 298
3. RING HYDROXYLATING DIOXYGENASE STRUCTURE AND FUNCTION 313
4. BIOTECHNOLOGY APPLICATIONS 327
5. CONCLUSIONS 331
ACKNOWLEDGMENTS 332
REFERENCES 332
THE PSEUDOMONAS GENOME DATABASE 351
1. PREAMBLE – THE PSEUDOMONAS GENOME DATABASE PHILOSOPHY AND SCOPE 351
2. INITIAL DATABASE DEVELOPMENT AND COMMUNITY ANNOTATION APPROACH – THE PSEUDOMONAS COMMUNITY COMES TOGETHER 352
3. PSEUDOCAP TODAY – FACILITATING CONTINUALLY UPDATED ANNOTATION 355
4. DATABASE STRUCTURE OVERVIEW 359
5. COMPARATIVE GENOMICS CAPABILITY 360
6. GBROWSE – A DISTRIBUTED ANNOTATION SYSTEM THAT ALLOWS RESEARCHERS TO VIEW ALTERNATE ANNOTATIONS AND ADDITIONAL ANALYSES 361
7. INTEGRATION WITH OTHER DATA VIEWS, SUCH AS PATHWAY- BASED VISUALIZATIONS 363
8. EXAMPLES OF ANALYSIS TOOLS ASSOCIATED WITH THIS DATABASE: UTILITY FOR RESEARCH AND DRUG/ VACCINE DISCOVERY 363
9. CONCLUSIONS 367
ACKNOWLEDGMENTS 368
REFERENCES 369
INDEX 372