Molecular Genetics of Recombination

by Aguilera, Andres; Rothstein, Rodney

• ISBN13: 9783540710202
• ISBN10: 3540710205
• Edition: 1st
• Format: Hardcover
• Copyright: 2007-06-03
• Publisher: Springer Verlag

Summary

Genetic recombination is an important process involved in shaping the genetic make up of progeny. Increasingly, it has become evident that recombination is a DNA repair pathway crucial during DNA replication in vegetatively growing cells. It plays a critical role in preserving the integrity of the genome by mediating the repair of DNA damage, which can occur during normal cellular metabolism as a result of oxidative stress, transcription, replication fork stalling or breakdown, or after the exposure to DNA damaging agents. Until recently, much of our knowledge on the mechanisms of genetic recombination has come from studies of prokaryotic and simple eukaryotic fungal systems. However, these studies have now been significantly extended to mammals, such that a comparative picture of the general factors and mechanisms of genetic recombination is beginning to emerge. Detailed genetic and biochemical studies have led to the isolation and characterization of many of the recombination-repair proteins in E. coli and S. cerevisiae, which in turn has led to the identification of homologues in human cells. The link between recombination defects and recombination proteins in a number of tumors as well as in human hereditary syndromes makes genetic recombination a cellular process of key importance not only in basic biology but also in biomedical studies.

Table of Contents

Genetics of recombination in the model bacterium Escherichia coli	p. 1
Abstract	p. 1
Introduction	p. 1
Genes and pathways	p. 2
The key steps of the homologous recombination reaction	p. 2
Alternative pathways of DSB repair	p. 6
Homologous recombination in plasmids	p. 7
Ligase and polymerase 1	p. 8
Proteins that antagonize homologous recombination	p. 8
The repair of DNA lesions	p. 8
RecFOR- dependent DNA repair	p. 9
RecBC-dependent recombinational repair	p. 10
Recombination and replication	p. 11
Replication inactivation induces RecA-independent recombination	p. 11
Recombination proteins participate in the resetting of replication forks	p. 13
Acknowledgments	p. 18
References	p. 18
Homologous recombination in low dC + dG Gram-positive bacteria	p. 27
Abstract	p. 27
Proteins required for recombinational repair	p. 27
Recombination avenues	p. 34
DNA damage recognition	p. 35
DNA end-processing	p. 36
DSB coordination	p. 37
RecA loading, homologous pairing and strand exchange	p. 37
Branch migration and resolution	p. 38
Horizontal gene transfer	p. 39
Transport and uptake of dsDNA or ssDNA	p. 39
Fate of the incoming DNA	p. 40
Barriers for HGT	p. 46
Acknowledgements	p. 46
References	p. 46
The bacterial RecA protein: structure, function, and regulation	p. 53
Abstract	p. 53
The role of recombination in DNA metabolism	p. 53
The RecA protein of Escherichia coli	p. 54
Overview	p. 54
Structure	p. 55
Binding to DNA	p. 58
ATP hydrolysis and RecA filament states	p. 59
DNA strand exchange is a multi-step process	p. 61
The role of ATP hydrolysis in DNA strand exchange	p. 63
Regulation of RecA function	p. 65
Autoregulation by the RecA C-terminus	p. 65
Proteins that modulate RecA function	p. 67
The single-strand DNA binding protein (SSB)	p. 67
The RecFOR proteins	p. 67
The DinI and RecX proteins	p. 71
The PsiB and RdgC proteins	p. 73
The UvrD helicase	p. 75
Regulation summary	p. 76
References	p. 77
Biochemistry of eukaryotic homologous recombination	p. 95
Abstract	p. 95
Introduction	p. 95
Homologous recombination in different contexts	p. 97
Biochemistry of recombination proteins	p. 98
Structure of the presynaptic Rad51 filament	p. 99
Presynapsis: different pathways leading to Rad51 filament formation and the function of distinct mediator proteins	p. 103
Synapsis: homology search and DNA strand invasion	p. 113
Postsynapsis: many subpathways call for context-specific factors	p. 114
Regulation of recombination	p. 119
Negative regulation of HR and the roles of the Srs2 DNA helicase and MMR	p. 119
Post-translational modification of HR proteins	p. 120
Conclusion	p. 122
Acknowledgements	p. 123
References	p. 123
DNA helicases in recombination	p. 135
Abstract	p. 135
Recombination pathways and models	p. 135
DNA helicases in mitotic recombination	p. 140
Srs2	p. 141
Fbh1	p. 145
Sgs1	p. 145
WRN	p. 147
BLM	p. 147
Rad3/Rem1	p. 148
Rrm3 and Pif1	p. 149
DNA helicases in meiotic recombination	p. 149
Mer3	p. 150
Srs2	p. 150
Sgs1	p. 151
BLM	p. 151
Replication and repair helicases	p. 152
Mph1	p. 152
HEF/FANCM	p. 152
BRIP1/BACH1/FANCJ	p. 153
HEL308/MUS308	p. 153
RecQ5ß	p. 154
RecQL1	p. 154
Hmi1	p. 154
Conclusions	p. 155
Acknowledgements	p. 156
References	p. 156
Holliday junction resolution	p. 169
Abstract	p. 169
A brief overview of HJ formation and processing	p. 169
The HJ resolvases	p. 172
Structural relationships	p. 172
Junction recognition and distortion	p. 174
Sequence-specific cleavage and the need for branch migration	p. 176
The catalysis of cleavage	p. 177
Coordination of cleavage events	p. 178
Directing the orientation of junction cleavage	p. 179
Searching for the elusive nuclear HJ resolvase	p. 180
Mus81	p. 182
Mus81 is related to the XPF family of endonucleases	p. 182
The substrate specificity of Mus81*	p. 183
The role of Mus81* in meiosis	p. 185
Mus81 and links to cancer	p. 186
Mus81 and DSB repair in vegetative cells	p. 187
Mus81 and stalled replication forks	p. 188
Mus81 and inter-strand cross-link repair	p. 189
Future perspectives	p. 190
Acknowledgements	p. 191
References	p. 191
Replication forks and replication checkpoints in repair	p. 201
Abstract	p. 201
DNA replication, checkpoint proteins, and chromosome integrity	p. 201
Stalled versus collapsed replication forks and fork stabilization versus fork restart	p. 202
Sensing stalled forks and checkpoint mediated stabilization of stalled forks	p. 203
Replication fork restart and repair mechanisms	p. 205
Recombination-mediated fork restart and repair	p. 207
Checkpoint-mediated regulation of recombination	p. 207
Other fork restart mechanisms: damage tolerance or postreplication repair pathways	p. 208
Damage bypass at the fork versus postreplication repair	p. 210
Coordination between DNA replication, topology, and chromatin structure	p. 211
Acknowledgements	p. 213
References	p. 213
Sister chromatid recombination	p. 221
Abstract	p. 221
Introduction	p. 221
Homologous recombination: a mechanism with major activity during replication	p. 222
What makes a replication fork stall or collapse?	p. 222
The role of recombination during DNA replication	p. 224
Methods for the measurement of sister-chromatid recombination	p. 226
5-Bromodeoxyuridine labelling	p. 227
Detection of SCE in circular molecules	p. 227
Genetic assays based on direct repeats	p. 228
Molecular analysis of SCR	p. 229
DNA repair genes required for SCR	p. 230
Specific functions required for SCR	p. 235
Cohesins	p. 235
Other SMC complexes	p. 238
The MRX(N) complex	p. 239
Concluding remarks	p. 240
Acknowledgements	p. 241
References	p. 241
Mating-type switching in S. pombe	p. 251
Abstract	p. 251
Fission yeast life cycle	p. 251
The pattern of switching	p. 252
The mating-type region	p. 253
A site- and strand-specific imprint at matl	p. 254
Cis-acting elements controlling the imprint	p. 257
Trans-acting swi (switch) genes	p. 257
Class Ia	p. 258
Class lb	p. 260
Class II	p. 261
The direction of replication model	p. 263
Imprinting formation is coupled to DNA replication	p. 264
Imprinting protection	p. 267
Mating-type switching	p. 267
Initiation	p. 268
Choice of the donor	p. 269
Gene conversion and its resolution	p. 270
Mus81 is the essential nuclease resolving sister chromatid recombination	p. 272
Outlook and future directions	p. 273
Acknowledgements	p. 275
References	p. 275
Multiple mechanisms of repairing meganuclease-induced double-strand DNAbreaks in budding yeast	p. 285
Abstract	p. 285
Introduction	p. 285
MAT switching in Saccharomyces, a paradigm for DSB repair	p. 286
Physical monitoring of MAT switching	p. 287
Monitoring of recombination protein binding to the DSB	p. 288
Primer extension	p. 289
HO and I-SceI-induced ectopic gene conversions and the control ofreciprocal crossing-over	p. 291
Most ectopic recombination occurs by SDSA	p. 292
Control of crossing-over associated with gene conversion	p. 295
Single-strand annealing (SSA)	p. 297
Break-induced replication (BIR)	p. 299
At least two pathways of BIR can be shown for non-telomere sequences in S. cerevisiae	p. 301
RAD51-dependent BIR	p. 302
Analysis of BIR using plasmids and transformation assays	p. 303
Nonhomologous end-joining (NHEJ)	p. 305
Future prospects	p. 308
Acknowledgements	p. 308
References	p. 308
The cell biology of mitotic recombination in Saccharomyces cerevisiae	p. 317
Abstract	p. 317
Choreography of DNA double-strand break repair	p. 317
Cell cycle regulation of recombination foci	p. 321
The cellular response to stalled and collapsed DNA replication forks	p. 322
Spontaneous foci	p. 324
Dynamics of proteins in foci	p. 324
Centers of recombinational DNA repair	p. 325
Nucleolar exclusion of homologous recombination	p. 326
Cohesins	p. 326
Molecular switches	p. 326
Future perspectives	p. 327
References	p. 328
The cell biology of homologous recombination	p. 335
Abstract	p. 335
Introduction	p. 335
Cell biological analyses of homologous recombination proteins	p. 336
Controlled induction of DNA damage	p. 337
Homologous recombination pathways	p. 340
Detection and processing of DSBs	p. 340
Nucleoprotein filament formation	p. 343
Resolution	p. 347
Recombination and replication	p. 348
The function of DNA damage induced foci	p. 349
References	p. 351
BRCA2: safeguarding the genome through homologous recombination	p. 363
Abstract	p. 363
Introduction	p. 363
BRCA2: a tumor suppressor with diverse domain structures in different organisms	p. 364
BRCA2 in vertebrates	p. 364
BRCA2 in non-vertebrate species	p. 365
Binding Partners of BRCA2	p. 366
Rad51: the BRC repeats	p. 366
Rad51: exon 27-encoded sequences	p. 366
DNA	p. 367
DSS1	p. 367
PALB2 and other proteins	p. 368
BRCA2 and homologous recombination	p. 368
Studies in vitro	p. 368
Studies in vivo	p. 369
BRCA2 is essential for development but dispensable for the survival of cancer cells	p. 370
BRCA2 and cancer predisposition in humans	p. 370
BRCA2 is essential during embryogenesis	p. 371
Tumorigenesis in conditional Brca2 mutants	p. 372
How do BRCA2-deficient cells escape genome surveillance checkpoints?	p. 372
Conclusions	p. 373
Acknowledgments	p. 373
References	p. 374
Meiotic recombination	p. 381
Abstract	p. 381
Overview	p. 381
Meiosis	p. 381
Meiotic chromosome structure and the synaptonemal complex	p. 382
Stages of meiotic prophase 1	p. 384
Recombination nodules	p. 384
Overview of meiotic recombination	p. 385
The pathway of meiotic recombination	p. 385
Monitoring meiotic recombination intermediates	p. 385
Initiation of meiotic recombination	p. 387
The Spo11 complex	p. 387
Other factors that Influence DSB formation	p. 394
Resection of DSB-ends	p. 398
Assembly of the Spo11 complex and triggering of Spo11 cleavage	p. 399
Homolog pairing and formation of joint molecules	p. 400
Dmc1	p. 401
Assembly of the strand-exchange complex	p. 401
The Hop2-Mnd1 complex	p. 403
How do strand-exchange proteins promote homolog pairing?	p. 405
Strand-exchange and joint molecule formation	p. 406
Interhomolog bias	p. 408
Suppression of intersister recombination	p. 408
Interhomolog only functions	p. 412
Crossover control	p. 412
Crossover assurance	p. 412
Crossover interference	p. 413
Crossover and noncrossover pathways	p. 414
Pro-crossover factors	p. 414
A molecular model of crossover and noncrossover pathways	p. 419
Closing remarks	p. 421
Acknowledgements	p. 422
References	p. 422
Site-specific recombination	p. 443
Abstract	p. 443
Introduction	p. 443
The two families of recombinases: tyrosine and serine	p. 445
The tyrosine recombinase family	p. 446
Topoisomerases and tyrosine recombinase active sites	p. 446
Control of the recombination reaction	p. 448
Serine family recombinases	p. 451
Domain organisation and active site of serine family recombinases	p. 451
Mechanism of recombination by serine family recombinases	p. 452
Directing recombination outcome	p. 453
Accessory proteins, sequences, and topological selectivity	p. 453
Recombination between asymmetric accessory sites can give reaction directionality	p. 454
Applications of site-specific recombination	p. 456
Related proteins	p. 457
Large serine recombinases	p. 457
Integrons	p. 457
Conjugative transposons	p. 459
telomeres of linear prokaryotic chromosomes	p. 460
Xer recombination: a multifunctional recombination system	p. 461
Concluding remarks	p. 462
References	p. 463
V(D)J recombination: mechanism and consequences	p. 469
Abstract	p. 469
Introduction	p. 469
General properties of V(D)J recombination	p. 470
Recombination sites	p. 470
The RAG genes and proteins	p. 472
DNA cleavage by the RAG proteins	p. 472
Coupled cleavage	p. 473
RSS recognition	p. 474
RAG protein binding to DNA	p. 475
DNA transposition by RAG1/2	p. 476
implications of RAG1/2 transposition for the evolution of the immune system and for chromosomal translocations	p. 477
Sequence motifs and mutational studies of the RAG proteins	p. 478
Other functions of the RAG proteins	p. 479
End processing and joining in V(D)J recombination	p. 480
References	p. 482
Nonhomologous end-joining: mechanisms, conservation and relationship to illegitimate recombination	p. 487
Abstract	p. 487
Introduction	p. 487
DNA mechanisms of nonhomologous end-joining	p. 488
Double strand breaks	p. 488
Overhang-to-overhang joining	p. 488
Blunt end joining and polymerization across the break	p. 490
Use of internal microhomologies	p. 490
The balance between joining modes	p. 490
Protein pathways for nonhomologous end-joining	p. 491
Ku- and Lig4-dependent NHEJ	p. 491
MMEJ	p. 493
SSA and related mechanisms	p. 494
SSBR applied to DSBs	p. 495
Species conservation of Ku-dependent NHEJ	p. 497
Vertebrates and related	p. 497
Insects and worms	p. 497
S. cerevisiae	p. 498
Other fungi	p. 499
Protozoa	p. 500
Plants	p. 500
Bacteria	p. 500
Viruses	p. 501
NHEJ interplay with host cell processes	p. 502
Chromatin	p. 502
Checkpoints	p. 503
Cell cycle	p. 503
Outcomes of NHEJ and its deficiency	p. 504
Accurate repair and maintenance of genome integrity	p. 504
Adaptive and targeted mutagenesis	p. 504
Concluding remarks	p. 505
References	p. 505
Abbreviations	p. 512
Index	p. 515
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