Molecular Genetics of Recombination

Molecular Genetics of Recombination
 
Author:
Andrés Aguilera & Rodney Rothstein
Release at: 2007
Pages: 536
Edition:
First Edition
File Size: 19 MB
File Type: pdf
Language: English


Content of Molecular Genetics of Recombination



Genetics of recombination in the model bacterium Escherichia coli................1 Bénédicte Michel, Zeynep Baharoglu, and Roxane Lestini...............................1 Abstract.........................................................................................................1 1 Introduction................................................................................................1 2 Genes and pathways...................................................................................2 2.1 The key steps of the homologous recombination reaction..................2 2.2 Alternative pathways of DSB repair...................................................6 2.3 Homologous recombination in plasmids.............................................7 2.4 Ligase and polymerase I.....................................................................8 2.5 Proteins that antagonize homologous recombination..........................8 3 The repair of DNA lesions.........................................................................8 3.1 RecFOR- dependent DNA repair........................................................9 3.2 RecBC-dependent recombinational repair........................................10 4 Recombination and replication.................................................................11 4.1 Replication inactivation induces RecA-independent  recombination.........................................................................................11 4.2 Recombination proteins participate in the resetting of replication forks........................................................................................................13 Acknowledgments.......................................................................................18 References...................................................................................................18 Homologous recombination in low dC + dG Gram-positive bacteria.............27 Humberto Sanchez, Begoña Carrasco, Silvia Ayora, and Juan C. Alonso......27 Abstract.......................................................................................................27 1 Proteins required for recombinational repair............................................27 2 Recombination avenues............................................................................34 2.1 DNA damage recognition.................................................................35 2.2 DNA end-processing.........................................................................36 2.3 DSB coordination.............................................................................37 2.4 RecA loading, homologous pairing and strand exchange.................37 2.5 Branch migration and resolution.......................................................38 3 Horizontal gene transfer...........................................................................39 3.1 Transport and uptake of dsDNA or ssDNA......................................39 4 Fate of the incoming DNA.......................................................................40 5 Barriers for HGT......................................................................................46 Acknowledgements.....................................................................................46 References...................................................................................................46 The bacterial RecA protein: structure, function, and regulation....................53 Michael M. Cox...............................................................................................53 Abstract.......................................................................................................53 
1 The role of recombination in DNA metabolism.......................................53 2 The RecA protein of Escherichia coli......................................................54 2.1 Overview..........................................................................................54 2.2 Structure............................................................................................55 2.3 Binding to DNA................................................................................58 2.4 ATP hydrolysis and RecA filament states........................................59 2.5 DNA strand exchange is a multi-step process..................................61 2.6 The role of ATP hydrolysis in DNA strand exchange......................63 3 Regulation of RecA function....................................................................65 3.1 Autoregulation by the RecA C-terminus..........................................65 3.2 Proteins that modulate RecA function..............................................67 3.3 The single-strand DNA binding protein (SSB).................................67 3.4 The RecFOR proteins.......................................................................67 3.5 The DinI and RecX proteins.............................................................71 3.6 The PsiB and RdgC proteins.............................................................73 3.7 The UvrD helicase............................................................................75 4 Regulation summary................................................................................76 References...................................................................................................77 Biochemistry of eukaryotic homologous recombination..................................95 Wolf-Dietrich Heyer........................................................................................95 Abstract.......................................................................................................95 1 Introduction..............................................................................................95 2 Homologous recombination in different contexts....................................97 3 Biochemistry of recombination proteins..................................................98 3.1 Structure of the presynaptic Rad51 filament.....................................99 3.2 Presynapsis: different pathways leading to Rad51 filament  formation and the function of distinct mediator proteins......................103 3.3 Synapsis: homology search and DNA strand invasion...................113 3.4 Postsynapsis: many subpathways call for context-specific factors.114 4 Regulation of recombination..................................................................119 4.1 Negative regulation of HR and the roles of the Srs2 DNA  helicase and MMR................................................................................119 4.2 Post-translational modification of HR proteins..............................120 5 Conclusion.............................................................................................122 Acknowledgements...................................................................................123 References.................................................................................................123 DNA helicases in recombination......................................................................135 Hannah L. Klein............................................................................................135 Abstract.....................................................................................................135 1 Recombination pathways and models....................................................135 2 DNA helicases in mitotic recombination...............................................140 2.1 Srs2.................................................................................................141 2.2 Fbh1................................................................................................145 2.3 Sgs1................................................................................................145 
2.4 WRN...............................................................................................147 2.5 BLM................................................................................................147 2.6 Rad3/Rem1.....................................................................................148 2.7 Rrm3 and Pif1.................................................................................149 3 DNA helicases in meiotic recombination...............................................149 3.1 Mer3................................................................................................150 3.2 Srs2.................................................................................................150 3.3 Sgs1................................................................................................151 3.4 BLM................................................................................................151 4 Replication and repair helicases.............................................................152 4.1 Mph1...............................................................................................152 4.2 HEF/FANCM..................................................................................152 4.3 BRIP1/BACH1/FANCJ..................................................................153 4.4 HEL308/MUS308...........................................................................153 4.5 RecQ5β...........................................................................................154 4.6 RecQL1...........................................................................................154 4.7 Hmi1...............................................................................................154 5 Conclusions............................................................................................155 Acknowledgements...................................................................................156 References.................................................................................................156 Holliday junction resolution.............................................................................169 Matthew C. Whitby.......................................................................................169 Abstract.....................................................................................................169 1 A brief overview of HJ formation and processing..................................169 2. The HJ resolvases..................................................................................172 2.1 Structural relationships...................................................................172 2.2 Junction recognition and distortion.................................................174 2.3 Sequence-specific cleavage and the need for branch migration......176 2.4 The catalysis of cleavage................................................................177 2.5 Coordination of cleavage events.....................................................178 2.6 Directing the orientation of junction cleavage................................179 2.7 Searching for the elusive nuclear HJ resolvase...............................180 3 Mus81.....................................................................................................182 3.1 Mus81 is related to the XPF family of endonucleases....................182 3.2 The substrate specificity of Mus81*...............................................183 3.3 The role of Mus81* in meiosis.......................................................185 3.4 Mus81 and links to cancer..............................................................186 3.5 Mus81 and DSB repair in vegetative cells......................................187 3.6 Mus81 and stalled replication forks................................................188 3.7 Mus81 and inter-strand cross-link repair........................................189 4 Future perspectives.................................................................................190 Acknowledgements...................................................................................191 References.................................................................................................191 
Replication forks and replication checkpoints in repair................................201 Dana Branzei and Marco Foiani....................................................................201 Abstract.....................................................................................................201 1 DNA replication, checkpoint proteins, and chromosome integrity........201 2 Stalled versus collapsed replication forks and fork stabilization  versus fork restart......................................................................................202 3 Sensing stalled forks and checkpoint mediated stabilization of stalled forks..........................................................................................................203 4 Replication fork restart and repair mechanisms.....................................205 4.1 Recombination-mediated fork restart and repair............................207 4.2 Checkpoint-mediated regulation of recombination.........................207 4.3 Other fork restart mechanisms: damage tolerance or  postreplication repair pathways............................................................208 4.4 Damage bypass at the fork versus postreplication repair................210 5 Coordination between DNA replication, topology, and chromatin  structure.....................................................................................................211 Acknowledgements...................................................................................213 References.................................................................................................213 Sister chromatid recombination.......................................................................221 Felipe Cortés-Ledesma, Félix Prado and Andrés Aguilera............................221 Abstract.....................................................................................................221 1 Introduction............................................................................................221 2 Homologous recombination: a mechanism with major activity  during replication......................................................................................222 2.1 What makes a replication fork stall or collapse?............................222 2.2 The role of recombination during DNA replication........................224 3 Methods for the measurement of sister-chromatid recombination.........226 3.1 5-Bromodeoxyuridine labelling......................................................227 3.2 Detection of SCE in circular molecules..........................................227 3.3 Genetic assays based on direct repeats...........................................228 3.4 Molecular analysis of SCR.............................................................229 4 DNA repair genes required for SCR......................................................230 5 Specific functions required for SCR......................................................235 5.1 Cohesins..........................................................................................235 5.2 Other SMC complexes....................................................................238 5.3 The MRX(N) complex....................................................................239 6 Concluding remarks...............................................................................240 Acknowledgements...................................................................................241 References.................................................................................................241 Mating-type switching in S. pombe..................................................................251 Benoit Arcangioli, Laura Roseaulin, and Allyson Holmes............................251 Abstract.....................................................................................................251 1 Fission yeast life cycle...........................................................................251
2 The pattern of switching.........................................................................252 3 The mating-type region..........................................................................253 4 A site- and strand-specific imprint at mat1............................................254 5 Cis-acting elements controlling the imprint...........................................257 6 Trans-acting swi (switch) genes.............................................................257 6.1 Class Ia............................................................................................258 6.2 Class Ib...........................................................................................260 6.3 Class II............................................................................................261 7 The direction of replication model.........................................................263 8 Imprinting formation is coupled to DNA replication.............................264 9 Imprinting protection..............................................................................267 10 Mating-type switching..........................................................................267 10.1 Initiation........................................................................................268 10.2 Choice of the donor.......................................................................269 10.3 Gene conversion and its resolution...............................................270 11 Mus81 is the essential nuclease resolving sister chromatid  recombination............................................................................................272 12 Outlook and future directions...............................................................273 Acknowledgements...................................................................................275 References.................................................................................................275 Multiple mechanisms of repairing meganuclease-induced double-strand DNA breaks in budding yeast....................................................................................285 James E. Haber..............................................................................................285 Abstract.....................................................................................................285 1 Introduction............................................................................................285 2 MAT switching in Saccharomyces, a paradigm for DSB repair.............286 2.1 Physical monitoring of MAT switching..........................................287 2.2 Monitoring of recombination protein binding to the DSB..............288 2.3 Primer extension.............................................................................289 3 HO and I-SceI-induced ectopic gene conversions and the control of reciprocal crossing-over............................................................................291 3.1 Most ectopic recombination occurs by SDSA................................292 3.2 Control of crossing-over associated with gene conversion.............295 4 Single-strand annealing (SSA)...............................................................297 5 Break-induced replication (BIR)............................................................299 5.1 At least two pathways of BIR can be shown for non-telomere sequences in S. cerevisiae.....................................................................301 5.2 RAD51-dependent BIR...................................................................302 5.3 Analysis of BIR using plasmids and transformation assays............303 6 Nonhomologous end-joining (NHEJ).....................................................305 7 Future prospects.....................................................................................308 Acknowledgements...................................................................................308 References.................................................................................................308
The cell biology of mitotic recombination in Saccharomyces cerevisiae.......317 Michael Lisby and Rodney Rothstein............................................................317 Abstract.....................................................................................................317 1 Choreography of DNA double-strand break repair................................317 2 Cell cycle regulation of recombination foci...........................................321 3 The cellular response to stalled and collapsed DNA replication forks...322 4 Spontaneous foci....................................................................................324 5 Dynamics of proteins in foci..................................................................324 6 Centers of recombinational DNA repair.................................................325 7 Nucleolar exclusion of homologous recombination...............................326 8 Cohesins.................................................................................................326 9 Molecular switches.................................................................................326 10 Future perspectives...............................................................................327 References.................................................................................................328 The cell biology of homologous recombination...............................................335 Sheba Agarwal, Roland Kanaar, and Jeroen Essers.......................................335 Abstract.....................................................................................................335 1 Introduction............................................................................................335 2 Cell biological analyses of homologous recombination proteins...........336 3 Controlled induction of DNA damage...................................................337 4 Homologous recombination pathways...................................................340 4.1 Detection and processing of DSBs.................................................340 4.2 Nucleoprotein filament formation...................................................343 4.3 Resolution.......................................................................................347 5 Recombination and replication...............................................................348 6 The function of DNA damage induced foci...........................................349 References.................................................................................................351 BRCA2: safeguarding the genome through homologous recombination.....363 Nicole Christ, Mary Ellen Moynahan, Maria Jasin.......................................363 Abstract.....................................................................................................363 1 Introduction............................................................................................363 2 BRCA2: a tumor suppressor with diverse domain structures in  different organisms....................................................................................364 2.1 BRCA2 in vertebrates.....................................................................364 2.2 BRCA2 in non-vertebrate species...................................................365 3 Binding Partners of BRCA2...................................................................366 3.1 Rad51: the BRC repeats..................................................................366 3.2 Rad51: exon 27-encoded sequences...............................................366 3.3 DNA...............................................................................................367 3.4 DSS1...............................................................................................367 3.5 PALB2 and other proteins..............................................................368 4 BRCA2 and homologous recombination................................................368 4.1 Studies in vitro................................................................................368 
4.2 Studies in vivo.................................................................................369 5 BRCA2 is essential for development but dispensable for the  survival of cancer cells..............................................................................370 5.1 BRCA2 and cancer predisposition in humans.................................370 5.2 BRCA2 is essential during embryogenesis.....................................371 5.3 Tumorigenesis in conditional Brca2 mutants.................................372 5.4 How do BRCA2-deficient cells escape genome surveillance checkpoints?.........................................................................................372 6 Conclusions............................................................................................373 Acknowledgments.....................................................................................373 References.................................................................................................374 Meiotic recombination......................................................................................381 Neil Hunter....................................................................................................381 Abstract.....................................................................................................381 1 Overview................................................................................................381 2 Meiosis...................................................................................................381 2.1 Meiotic chromosome structure and the synaptonemal complex.....382 2.2 Stages of meiotic prophase I...........................................................384 2.3 Recombination nodules...................................................................384 3 Overview of meiotic recombination.......................................................385 3.1 The pathway of meiotic recombination..........................................385 3.2 Monitoring meiotic recombination intermediates...........................385 4 Initiation of meiotic recombination........................................................387 4.1 The Spo11 complex........................................................................387 4.2 Other factors that Influence DSB formation...................................394 4.3 Resection of DSB-ends...................................................................398 4.4 Assembly of the Spo11 complex and triggering of  Spo11 cleavage.....................................................................................399 5 Homolog pairing and formation of joint molecules...............................400 5.1 Dmc1...............................................................................................401 5.2 Assembly of the strand-exchange complex.....................................401 5.3 The Hop2–Mnd1 complex..............................................................403 5.4 How do strand-exchange proteins promote homolog pairing?.......405 5.5 Strand-exchange and joint molecule formation..............................406 6 Interhomolog bias...................................................................................408 6.1 Suppression of intersister recombination........................................408 6.2 Interhomolog only functions...........................................................412 7 Crossover control...................................................................................412 7.1 Crossover assurance........................................................................412 7.2 Crossover interference....................................................................413 7.3 Crossover and noncrossover pathways...........................................414 7.4 Pro-crossover factors......................................................................414 7.5 A molecular model of crossover and noncrossover pathways........419 8 Closing remarks......................................................................................421 Acknowledgements...................................................................................422 
References.................................................................................................422 Site-specific recombination...............................................................................443 Ian Grainge and David J. Sherratt..................................................................443 Abstract.....................................................................................................443 1 Introduction............................................................................................443 2 The two families of recombinases: tyrosine and serine..........................445 3 The tyrosine recombinase family...........................................................446 3.1 Topoisomerases and tyrosine recombinase active sites..................446 3.2 Control of the recombination reaction............................................448 4 Serine family recombinases...................................................................451 4.1 Domain organisation and active site of serine family  recombinases........................................................................................451 4.2 Mechanism of recombination by serine family recombinases........452 5 Directing recombination outcome..........................................................453 5.1 Accessory proteins, sequences, and topological selectivity............453 5.2 Recombination between asymmetric accessory sites can  give reaction directionality...................................................................454 6 Applications of site-specific recombination...........................................456 7 Related proteins......................................................................................457 7.1 Large serine recombinases..............................................................457 7.2 Integrons.........................................................................................457 7.3 Conjugative transposons.................................................................459 7.4 telomeres of linear prokaryotic chromosomes................................460 7.5 Xer recombination: a multifunctional recombination system.........461 8 Concluding remarks...............................................................................462 References.................................................................................................463 V(D)J recombination: mechanism and consequences....................................469 Martin Gellert................................................................................................469 Abstract.....................................................................................................469 1 Introduction............................................................................................469 2 General properties of V(D)J recombination...........................................470 2.1 Recombination sites........................................................................470 3 The RAG genes and proteins.................................................................472 3.1 DNA cleavage by the RAG proteins...............................................472 3.2 Coupled cleavage............................................................................473 3.3 RSS recognition..............................................................................474 3.4 RAG protein binding to DNA.........................................................475 3.5 DNA transposition by RAG1/2.......................................................476 3.6 implications of RAG1/2 transposition for the evolution of the immune system and for chromosomal translocations...........................477 3.7 Sequence motifs and mutational studies of the RAG proteins........478 3.8 Other functions of the RAG proteins..............................................479 4 End processing and joining in V(D)J recombination.............................480 References.................................................................................................482 
Nonhomologous end-joining: mechanisms, conservation and  relationship to illegitimate recombination.......................................................487 Thomas E. Wilson.........................................................................................487 Abstract.....................................................................................................487 1 Introduction............................................................................................487 2 DNA mechanisms of nonhomologous end-joining................................488 2.1 Double strand breaks......................................................................488 2.2 Overhang-to-overhang joining........................................................488 2.3 Blunt end joining and polymerization across the break..................490 2.4 Use of internal microhomologies....................................................490 2.5 The balance between joining modes...............................................490 3 Protein pathways for nonhomologous end-joining.................................491 3.1 Ku- and Lig4-dependent NHEJ.......................................................491 3.2 MMEJ.............................................................................................493 3.3 SSA and related mechanisms..........................................................494 3.4 SSBR applied to DSBs...................................................................495 4 Species conservation of Ku-dependent NHEJ........................................497 4.1 Vertebrates and related...................................................................497 4.2 Insects and worms...........................................................................497 4.3 S. cerevisiae....................................................................................498 4.4 Other fungi......................................................................................499 4.5 Protozoa..........................................................................................500 4.6 Plants...............................................................................................500 4.7 Bacteria...........................................................................................500 4.8 Viruses............................................................................................501 5 NHEJ interplay with host cell processes................................................502 5.1 Chromatin.......................................................................................502 5.2 Checkpoints....................................................................................503 5.3 Cell cycle........................................................................................503 6 Outcomes of NHEJ and its deficiency....................................................504 6.1 Accurate repair and maintenance of genome integrity....................504 6.2 Adaptive and targeted mutagenesis.................................................504 7 Concluding remarks...............................................................................505 References.................................................................................................505 Abbreviations............................................................................................512 Index...................................................................................................................515 

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