Richard Ed Engel

Recombination and Meiosis: Models, Means, and Evolution - Genome Dynamics and Stability Richard Ed Engel 2008 edition

Marc Notes: Includes bibliographical references and index. Jacket Description/Back: Once per life cycle, mitotic nuclear divisions are replaced by meiosis I and II reducing chromosome number from the diploid level to a haploid genome and recombining chromosome arms by crossing-over. In animals, all this happens during formation of eggs and sperm in yeasts before spore formation. The mechanisms of reciprocal exchange at crossover/chiasma sites are central to mainstream meiosis. To initiate the meiotic exchange of DNA, surgical cuts are made as a form of calculated damage that subsequently is repaired by homologous recombination. These key events are accompanied by ancillary provisions at the level of chromatin organization, sister chromatid cohesion and differential centromere connectivity. Great progress has been made in recent years in our understanding of these mechanisms. Questions still open primarily concern the placement of and mutual coordination between neighboring crossover events. Of overlapping significance, this book features two comprehensive treatises of enzymes involved in meiotic recombination, as well as the historical conceptualization of meiotic phenomena from genetical experiments. More specifically, these mechanisms are addressed in yeasts as unicellular model eukaryotes. Furthermore, evolutionary subjects related to meiosis are treated."Table of Contents: Evolution of Models of Homologous Recombination / James E. Haber -- 1. Introduction -- 1.1. Prelude -- 1.2. The First Molecular Models of Recombination -- 2. Robin Holliday's Remarkable Model -- 2.1. Strand Exchange by Single-Strand Annealing -- 2.2. Evidence Favoring Holliday's Model: Hotspots and Gradients of Gene Conversion -- 2.3. Challenges to the Holliday Model -- 2.4. The 5:3 Paradox -- 2.5. An Absence of Double-Crossovers -- 2.6. Alleles that Show a High PMS Fail to Show a High Proportion of Aberrant 4:4 Asci -- 3. Molecular Models Based on a Single Initiating DNA Lesion -- 4. The Meselson-Radding Model (1975) -- 4.1. A Transition from 5:3 to Ab4:4 Tetrads: Branch Migration of a Holliday Junction can Produce Symmetric Heteroduplex -- 4.2. Evidence Supporting the Meselson-Radding Model: One or Two Heteroduplex Regions Within a Gene -- 4.3. More Evidence: a Large Heterology Apparently Blocks Branch Migration -- 5. Problems with the Meselson-Radding Model -- 5.1. Where are the Crossovers? -- 5.2. Hotspots Appear to be Eliminated by Gene Converted -- 6. Alternative Ways to Initiate Recombination -- 6.1. Several Provocative Suggestions -- 6.2. The First Recombination Model Based on Double-Strand Breaks -- 6.3. A Key Experimental Transition: Studying Recombination in Mitotic Rather than Meiotic Cells -- 7. The Double Holliday DSB Repair Model of Szostak, Orr-Weaver, Rothstein and Stahl -- 7.1. Processing of Double-Strand Break Ends -- 7.2. The Double Holliday Junction -- 8. Identification of DNA Intermediates of Recombination -- 8.1. Physical Monitoring of Meiotic and Mitotic Recombination -- 8.2. Evidence of 5' to 3' Resection -- 8.3. Strand Invasion and 3' End Primer Extension -- 8.4. Physical Analysis of Double Holliday Junctions -- 8.5. Control of Crossing-Over in Meiosis by Stabilizing dHJs -- 8.6. Identification of a HJ Resolvase -- 9. Multiple Pathways Meiotic Recombination -- 9.1. Meiotic Recombination in Many Organisms Depends on a Second Strand Exchange Protein -- 10. Single-Strand Annealing Causes Primarily Intrachromosomal Deletions -- 11. Synthesis-Dependent Strand Annealing Accounts for Most Mitotic Recombination and Noncrossovers in Meiosis -- 12. Evolution of Gene Conversion Models in the Present -- 13. Another Major Source of Creative Thinking: Nonreciprocal Recombination in Phage [lambda] -- 14. Re-Emergence of Old Ideas in New Guises: Break-Induced Replication -- References -- Searching for Homology by Filaments of RecA-Like Proteins / Chantal Prevost -- 1. RecA-Like Proteins and Homologous Recombination -- 1.1. The Universal Function of Homologous Recombination -- 1.2. Nucleoprotein Filaments, the Active Form of Recombinases -- 1.3. Protein/DNA Interactions Inside the Filament -- 1.4. Characteristics of Sequence Recognition in Homologous Recombination -- 2. Sequence Effects in Homologous Recombination -- 2.1. A Non-specific Reaction? -- 2.2. Sequence Effects in Recombinase-DNA Association -- 2.3. Tolerance for Heterology in RecA-Catalyzed DNA Recognition and Strand Exchange -- 3. Homology Search in the Cell -- 4. Models of Homology Search at the Molecular Level -- 4.1. Dynamic Monte Carlo Approach: A Numerical Model of Recognition at the Molecular Level -- 4.2. Role of ATP Hydrolysis in Recognition and Strand Exchange -- 4.3. The Kinetics of Homology Search -- 5. Homology Recognition at the Atomic Level -- 5.1. Hypothesis -- 5.2. Looking for Reaction Intermediates -- 6. Conclusion -- References -- Biochemistry of Meiotic Recombination: Formation, Processing, and Resolution of Recombination Intermediates / Kirk T. Ehmsen, Wolf-Dietrich Heyer -- 1. Introduction -- 2. Biochemistry of Meiotic Recombination -- 2.1. DSB Formation: Spo11 and its Control -- 2.2. Resection -- 2.3. Rad51/Dmc1 Filament Formation -- 2.4. Formation of Heteroduplex DNA by Rad51 and Dmc1: Cofilaments or Asymmetry -- 2.5. Roles of the Rad54 and Rdh54-Tid1 Motor Proteins in Presynapsis, Synapsis and Postsynapsis -- 2.6. DNA Synthesis: Involvement of the PCNA/RFC-Dependent Pol[delta] and Possibly Pol[lambda] -- 2.7. D-Loop Dissolution and Strand Annealing in SDSA -- 2.8. Second End Capture in DSBR -- 2.9. Branch Migration in D-Loops and Double Holliday Junctions -- 2.10. Meiotic MMR -- 2.11. Double Holliday Junction Processing: Roads to Crossover and Non-Crossover -- 2.12. Other Junctions and Alternative Mechanisms for Crossover Formation: Possible Roles of Mus81-Mms4 and XPF -- 3. Conclusions and Outlook -- References -- Meiotic Chromatin: The Substrate for Recombination Initiation / Michael Lichten -- 1. Introduction -- 2. Double-Strand Breaks and Chromatin Structure in Saccharomyces cerevisiae -- 2.1. DSBs Form in Open Chromatin -- 2.2. Chromatin Structure and Postinitiation Events -- 2.3. A Meiotic Chromatin Transition at Active DSB Sites -- 2.4. Other Factors that Influence DSB Patterns -- 2.5. Areas for Future Study -- 3. Recombination Hotspots and Chromatin Structure in Schizosaccharomyces pombe -- 3.1. M26, a Transcription Factor-Associated Recombination Hotspot -- 3.2. Other Recombination/DSB Hotspots -- 3.3. Recombination Repression by Heterochromatin -- 3.4. Areas for Future Study -- 4. Hints from Multicellular Organisms -- 4.1. Recombination Deserts -- 4.2. Recombination Suppression by DNA Methylation in Filamentous Fungi -- 4.3. Recombination Hotspots -- 4.4. Areas for Future Research -- References -- Meiotic Recombination in Schizosaccharomyces pombe: A Paradigm for Genetic and Molecular Analysis / Gareth Cromie, Gerald R. Smith -- 1. S. pombe: An Excellent Model Organism for Studying Meiotic Recombination -- 2. Overview: A Pathway for S. pombe Meiotic Recombination -- 3. Nuclear Movement Promotes Chromosome Alignment: Bouquet and Horsetail Formation -- 4. Meiosis-specific Sister Chromatid Cohesins: Behavior Change -- 5. DSB Formation by Rec12: Preparation and Partnership -- 5.1. S. pombe: A Second Eukaryote with Directly Observed Meiotic DSBs -- 5.2. Modification of Sister Chromatid Cohesion: A Foundation for Meiosis-specific DSB Formation -- 5.3. Formation of Linear Elements: Structures Reminiscent of the Synaptonemal Complex -- 5.4. Rec12: The Active Site Protein for DSB Formation -- 5.5. Other Proteins Essential for DSB Formation: Potential Rec12 Partners and Regulators -- 6. DSB Hotspots and Coldspots: Regulating Where Recombination Occurs -- 6.1. M26: A Eukaryotic Sequence-specific Hotspot -- 6.2. Hotspots in Large Intergenic Regions: Another Role for Junk DNA? -- 6.3. Region-specific Activation by Cohesins: Megabase-scale Control of DSB Formation -- 6.4. Recombination in DSB-poor Intervals: Action at a Distance or Novel Lesions? -- 6.5. Coldspots: Forbidden Regions for Recombination -- 7. Processing of Rec12-generated DSBs: Converting a Lesion into a Recombinogenic DNA-Protein Complex -- 7.1. The MRN Complex Is Needed for Removing Rec12 from DSBs But Not for DSB Formation -- 7.2. Loading Strand-Exchange Proteins: Many Actors with Overlapping Roles -- 8. Strand Invasion and Partner Choice -- 8.1. The Dmc1 and Rad51 Strand Exchange Proteins: Finding a Homologous Partner for Recombination -- 8.2. The Rhp54 and Rdh54 Proteins: Enabling Strand Exchange in a Chromatin Context? -- 8.3. Intersister vs. Interhomolog Recombination: Any Partner Will Do? -- 9. Joint Molecule Resolution -- 9.1. Single Holliday Junctions: An Unexpected Recombination Intermediate -- 9.2. Mus81-Eme1: The Meiotic Holliday Junction Resolvase of S. pombe -- 10. Mismatch Correction -- 11. Relation of Gene Conversion and Crossing-over -- 12. Species-specific Strategies for Ensuring, With or Without Interference, the Crossovers Required for Chromosome Segregation -- 13. Differences Between S. pombe and S. cerevisiae Meiotic Recombination: A Reprise -- References -- Nuclear Movement Enforcing Chromosome Alignment in Fission Yeast-Meiosis Without Homology Synapsis / Da-Qiao Ding, Yasushi Hiraoka -- 1. Introduction -- 2. Alignment of Homologous Chromosomes -- 2.1. Meiosis in S.pombe -- 2.2. Contribution of Telomere Clustering and Nuclear Movement to Homologous Chromosome Alignment -- 2.3. Chromosome Architecture in the Alignment of Homologous Chromosomes -- 3. Regulation of Telomere Clustering -- 3.1. Mating Pheromone, MAP Kinase and Mei2 -- 3.2. Integrity of the Telomere -- 3.3. Integrity of the SPB -- 3.4. Dragging Telomeres to the SPB -- 4. Regulation of Nuclear Movement -- 4.1. Dynein and Dynactin -- 4.2. Concentrating the Microtubule Bundles at the SPB -- 5. Conclusion and Outlook -- References -- On the Origin of Meiosis in Eukaryotic Evolution: Coevolution of Meiosis and Mitosis from Feeble Beginnings / Richard Egel, David Penny -- 1. Introduction -- 2. A Conserved Core of Meiotic Proteins -- 3. The Complex Eukaryotic Signature -- 4. The Universal Trifurcation -- 5. The RNA World Scenario -- 6. Dynamic Implications of Eigen's Quasi-Species Concept -- 7. Woese's Phase Shift at Decreasing Evolutionary Temperature -- 8. Early Traits with Preadaptive Value for Meiosis -- 9. Meiosis vs. Mitosis - Alternative Programs Responding to Different Selective Needs -- 10. Coevolution of Meiosis and Mitosis -- 11. Variations on the Meiotic System in the World of Protists -- 11.1. Fission Yeast as a Haploid Model Organism: Zygotic Meiosis Before Sporulation -- 11.2. Amoebic Slime Molds: Formation of Cannibalistic Zygotes -- 12. Concluding Remarks References -- The Legacy of the Germ Line - Maintaining Sex and Life in Metazoans: Cognitive Roots of the Concept of Hierarchical Selection / Dirk-Henner Lankenau -- 1. Introduction -- 2. The Legacy of the Germ Line -- 2.1. Germ Line: Definitions -- 2.2. The Continuity of Weismann's Germ Plasm and the Theory of Inheritance -- 2.3. The Emergence of Multicellular Organisms During Evolution and the Germ Line -- 2.4. Amphimixis and Meiosis -- 2.5. On the Value of the Volvocinae as a Line of Evolution Towards Multicellularity -- 2.6. Chromatin Diminution: The First Hints in History Towards Germ-Line/Soma Segregation -- 2.7. Biodiversity, Germ-Line Versus Soma Segregation and Preformation Versus Epigenesis -- 2.8. Linking Weismann's to Current Views on the Germ Plasm -- 3. The Allmacht of Selection -- 3.1. Different Levels of Selection-Kin Selection -- 3.2. Hamilton's Rule and the Evolutionary Criterion of Altruistic Behavior -- 4. Maintaining Sex in Metazoans -- 4.1. Introduction -- 4.2. Emergence of Diploidy -- 4.3. Recombination as a Means to Fix Beneficial Mutations -- 4.4. Recombination: Quantum Dimension Versus Ecological Dimension -- 4.5. Recombination as a Means to Eliminate Detrimental Mutations -- 5. Finale -- References -- Lessons to Learn from Ancient Asexuals / Isa Schon, Dunja K. Lamatsch, Koen Martens -- 1. The Paradox of Sex -- 2. What is an Ancient Asexual? -- 2.1. Classical Non-genetic Methods -- 2.2. Classical Genetic Techniques -- 3. Novel Genetic Tests - Meiosis Proteins -- 4. Conclusions -- References -- Subject Index. Publisher Marketing: Once per life cycle, mitotic nuclear divisions are replaced by meiosis I and II reducing chromosome number from the diploid level to a haploid genome and recombining chromosome arms by crossing-over. In animals, all this happens during formation of eggs and sperm in yeasts before spore formation. The mechanisms of reciprocal exchange at crossover/chiasma sites are central to mainstream meiosis. To initiate the meiotic exchange of DNA, surgical cuts are made as a form of calculated damage that subsequently is repaired by homologous recombination. These key events are accompanied by ancillary provisions at the level of chromatin organization, sister chromatid cohesion and differential centromere connectivity. Great progress has been made in recent years in our understanding of these mechanisms. Questions still open primarily concern the placement of and mutual coordination between neighboring crossover events. Of overlapping significance, this book features two comprehensive treatises of enzymes involved in meiotic recombination, as well as the historical conceptualization of meiotic phenomena from genetical experiments. More specifically, these mechanisms are addressed in yeasts as unicellular model eukaryotes. Furthermore, evolutionary subjects related to meiosis are treated."