Agrobacterium: From Biology to Biotechnology (eBook)

Dr. Tzvi Tzfira is an Assistant Professor in the Department of Molecular, Cellular, and Developmental Biology at the University of Michigan. Dr. Vitaly Citovsky is a Professor in the Department of Biochemistry and Cell Biology at Stony Brook University.

Contributing Authors 6
Table of Contents 11
Preface 27
Color Figures 29
Acknowledgments 30
AGROBACTERIUM: A DISEASE-CAUSING BACTERIUM 31
1 INTRODUCTION 32
2 AGROBACTERIUM HOST RANGE 34
3 DIVERSITY OF NATURAL ISOLATES 35
4 SOURCES OF INFECTION AND CONTROL OF CROWN GALL DISEASE 42
5 ACKNOWLEDGEMENTS 56
6 REFERENCES 56
A BRIEF HISTORY OF RESEARCH ON AGROBACTERIUM TUMEFACIENS: 1900-1980s 77
1 INTRODUCTION 77
2 AGROBACTERIUM— THE PATHOGEN 79
3 A. TUMEFACIENS AS THE VECTOR OF CHOICE FOR PLANT GENETIC ENGINEERING 89
4 CONCLUSIONS 94
5 ACKNOWLEDGEMENTS 94
6 REFERENCES 95
AGROBACTERIUM AND PLANT BIOTECHNOLOGY 103
1 INTRODUCTION 104
2 THE DEVELOPMENT OF AGROBACTERIUM-MEDIATED TRANSFORMATION 105
3 APPLICATIONS OF AGROBACTERIUM-MEDIATED TRANSFORMATION 121
4 GENE FLOW AND MOLECULAR APPROACHES TO TRANSGENE CONTAINMENT/ MONITORING 143
5 GLOBAL STATUS OF AGRICULTURAL BIOTECHNOLOGY AND TECHNOLOGY TRANSFER 146
6 ACKNOWLEDGEMENTS 152
7 REFERENCES 152
THE AGROBACTERIUM TUMEFACIENS C58 GENOME 178
1 INTRODUCTION 179
2 GENERAL FEATURES OF THE GENOME 179
3 THE LINEAR CHROMOSOME 181
4 PHYLOGENY AND WHOLE-GENOME COMPARISON 184
5 DNA REPLICATION AND THE CELL CYCLE 185
6 GENUS-SPECIFIC GENES 186
7 PLANT TRANSFORMATION AND TUMORIGENESIS 187
8 TRANSPORT 188
9 REGULATION 189
10 RESPONSE TO PLANT DEFENSES 191
11 GENERAL METABOLISM 192
12 CONCLUSIONS 195
13 ACKNOWLEDGEMENTS 198
14 REFERENCES 198
AGROBACTERIUM— TAXONOMY OF PLANT- PATHOGENIC RHIZOBIUM SPECIES 211
1 INTRODUCTION 212
2 HISTORICAL PERSPECTIVE— ORIGINS 213
3 AGROBACTERIUM—RHIZOBIUM RELATIONSHIPS 223
4 GENOTYPIC RELATIONSHIPS 224
5 PLASMID TRANSFER AND GENUS RECLASSIFICATION 227
6 DIVERSITY WITHIN RHIZOBIUM 228
7 REVISION OF AGROBACTERIUM NOMENCLATURE 232
8 RELATIONSHIP OF RHIZOBIUM TO OTHER MEMBERS OF THE RHIZOBIACEAE 235
9 OTHER ‘ AGROBACTERIUM’ SPECIES 236
10 SUMMARY 237
11 ACKNOWLEDGEMENTS 237
12 REFERENCES 238
THE INITIAL STEPS IN AGROBACTERIUM TUMEFACIENS PATHOGENESIS: CHEMICAL BIOLOGY OF HOST RECOGNITION 249
1 INTRODUCTION 250
2 SIGNAL DIVERSITY 251
3 SIGNAL RECOGNITION, INTEGRATION AND TRANSMISSION 254
4 SUMMARY 264
5 ACKNOWLEDGEMENTS 264
6 REFERENCES 264
AGROBACTERIUM-HOST ATTACHMENT AND BIOFILM FORMATION 270
1 INTRODUCTION 271
2 PRESUMPTIVE ADHERENCE FACTORS 274
3 PLANT RECEPTORS RECOGNIZED DURING A. TUMEFACIENS INFECTION 285
4 BIOFILM FORMATION BY A. TUMEFACIENS 286
5 A MODEL FOR ADHERENCE AND BIOFILM FORMATION 293
6 A WIDE RANGE OF SURFACE INTERACTIONS 294
7 CONCLUSIONS 295
8 ACKNOWLEDGEMENTS 296
9 REFERENCES 296
PRODUCTION OF A MOBILE T-DNA BY AGROBACTERIUM TUMEFACIENS 305
1 INTRODUCTION 306
2 A. TUMEFACIENS—NATURE’S GENETIC ENGINEER 306
3 INTERKINGDOM GENE TRANSFER 307
4 VirD2 INTERACTS WITH HOST PROTEINS 320
5 T-DNA INTEGRATION 323
6 PLANT GENETIC ENGINEERING 325
7 ACKNOWLEDGEMENTS 327
8 REFERENCES 327
TRANSLOCATION OF ONCOGENIC T-DNA AND EFFECTOR PROTEINS TO PLANT CELLS 340
1 INTRODUCTION 341
2 A HISTORICAL OVERVIEW 341
3 A. TUMEFACIENS VIRB/D4 SECRETION SUBSTRATES 345
4 THE VIRB/D4 MACHINE 351
5 VIRB/D4 MACHINE ASSEMBLY AND SPATIAL POSITIONING 358
6 VIRB/D4 CHANNEL/PILUS ARCHITECTURE 364
7 T-DNA TRANSLOCATION ACROSS THE CELL ENVELOPE 366
8 THE AGROBACTERIUM – PLANT CELL INTERFACE 372
9 SUMMARY AND PERSPECTIVES 375
10 ACKNOWLEDGEMENTS 377
11 REFERENCES 377
INTRACELLULAR TRANSPORT OF AGROBACTERIUM T- DNA 390
1 INTRODUCTION 390
2 STRUCTURE AND FUNCTION OF THE T-COMPLEX 392
3 CYTOPLASMIC TRANSPORT 397
4 NUCLEAR IMPORT 399
5 INTRANUCLEAR MOVEMENT OF THE T-COMPLEX 406
6 FROM THE CYTOPLASM TO THE CHROMATIN: A MODEL FOR T- COMPLEX IMPORT 407
7 FUTURE PROSPECTS 409
8 ACKNOWLEDGEMENTS 409
9 REFERENCES 410
MECHANISMS OF T-DNA INTEGRATION 420
1 INTRODUCTION 421
2 THE T-DNA MOLECULE 422
3 PROTEINS INVOLVED IN T-DNA INTEGRATION 423
4 GENOMIC ASPECTS OF T-DNA INTEGRATION/ TARGET- SITE SELECTION 433
5 MODELS FOR T-DNA INTEGRATION 445
6 FUTURE DIRECTIONS 453
7 ACKNOWLEDGEMENTS 454
8 REFERENCES 454
AGROBACTERIUM TUMEFACIENS-MEDIATED TRANSFORMATION: PATTERNS OF T- DNA INTEGRATION INTO THE HOST GENOME 466
1 INTRODUCTION 467
2 T-DNA INTEGRATION MECHANISM: SUCCESSIVE STEPS LEADING TO STABLE INTEGRATION OF THE T- DNA INTO THE PLANT HOST GENOME 468
3 PATTERNS OF T-DNA INTEGRATION INTO THE HOST GENOME 483
4 ACKNOWLEDGMENTS 494
5 REFERENCES 494
FUNCTION OF HOST PROTEINS IN THE AGROBACTERIUM- MEDIATED PLANT TRANSFORMATION PROCESS 507
1 INTRODUCTION 508
2 A GENETIC BASIS EXISTS FOR HOST SUSCEPTIBILITY TO AGROBACTERIUM-MEDIATED TRANSFORMATION 509
3 THE PLANT RESPONSE TO AGROBACTERIUM: STEPS IN THE TRANSFORMATION PROCESS, AND PLANT GENES/ PROTEINS INVOLVED IN EACH OF THESE STEPS 512
4 CONCLUSIONS 531
5 ACKNOWLEDGMENTS 532
6 REFERENCES 532
THE ONCOGENES OF AGROBACTERIUM TUMEFACIENS AND AGROBACTERIUM RHIZOGENES 547
1 INTRODUCTION 548
2 THE A. TUMEFACIENS ONCOGENES 549
3 THE A. RHIZOGENES ONCOGENES 557
4 CONCLUSIONS 573
5 REFERENCES 574
BIOLOGY OF CROWN GALL TUMORS 588
1 INTRODUCTION 589
2 CROWN GALL VASCULARIZATION 590
3 ONCOGENE-INDUCED PHYTOHORMONE CASCADE 593
4 ENHANCEMENT OF WATER AND SOLUTE TRANSPORT 602
5 KINETICS AND FUNCTION OF THE SUGAR-CLEAVING ENZYMES SUCROSE SYNTHASE, ACID CELL WALL AND VACUOLAR INVERTASE 607
6 CONCLUSIONS 607
7 ACKNOWLEDGEMENTS 608
8 REFERENCES 608
THE CELL-CELL COMMUNICATION SYSTEM OF AGROBACTERIUM TUMEFACIENS 615
1 INTRODUCTION 616
2 A MODEL OF QUORUM SENSING IN A. TUMEFACIENS 617
3 STRUCTURE AND FUNCTION STUDIES OF TRAR 625
4 TRAR IN TRANSCRIPTION ACTIVATION 630
5 QUORUM SENSING IN TUMOURS AND INFECTED PLANTS 635
6 ACKNOWLEGEMENTS 636
7 REFERENCES 637
HORIZONTAL GENE TRANSFER 645
1 INTRODUCTION 646
2 FOOTPRINT OF HORIZONTAL GENE TRANSFER FROM AGROBACTERIUM TO TOBACCO PLANTS 646
3 Other CT-DNAs 656
4 GENETIC TUMORS 657
5 ADVANTAGE OF CT-DNA AND CREATION OF NEW SPECIES 661
6 ACKNOWLEDGEMENTS 664
7 REFERENCES 664
AGROBACTERIUM-MEDIATED TRANSFORMATION OF NON- PLANT ORGANISMS 670
1 INTRODUCTION 671
2 NON-PLANT ORGANISMS TRANSFORMED BY AGROBACTERIUM 673
3 EXPERIMENTAL ASPECTS OF AGROBACTERIUM-MEDIATED TRANSFORMATION OF NON- PLANT ORGANISMS 677
4 ROLE OF VIRULENCE PROTEINS IN THE AGROBACTERIUM- MEDIATED TRANSFORMATION OF NON- PLANT ORGANISMS 679
5 TARGETED INTEGRATION OF T-DNA 680
6 PROTEIN TRANSFER FROM AGROBACTERIUM TO NON- PLANT HOSTS 685
7 PROSPECTS 685
8 ACKNOWLEDGEMENTS 687
9 REFERENCES 687
THE BIOETHICS AND BIOSAFETY OF GENE TRANSFER 697
1 INTRODUCTION 698
2 WHICH RISKS ARE RELEVANT? 705
3 CONCERNS BEYOND RISK ASSESSMENT 709
4 CONCLUSIONS 714
5 ACKNOWLEDGEMENTS 715
6 REFERENCES 715
AGROBACTERIUM-MEDIATED GENE TRANSFER: A LAWYER’S PERSPECTIVE 718
1 INTRODUCTION -WHY SHOULD A SCIENTIST CARE ABOUT A LAWYER’S VIEW OF AGROBACTERIUM? 719
2 SOME BASICS ABOUT PATENTS 728
3 AGROBACTERIUM-MEDIATED TRANSFORMATION AND PATENT LAW 732
4 CONCLUSIONS 751
5 ACKNOWLEDGEMENTS 752
6 REFERENCES 752
Index 755