Béatrice Clouet-d’Orval is Research Director at the CNRS and works at the Center for Integrative Biology, Toulouse, France. Her main research areas focus on the post-transcriptional regulation of gene expression.Bruno Franzetti is Research Director at the CNRS, France, where he specializes in the structural biology of archaea. His research areas include biophysical and cellular mechanisms that maintain proteome integrity under extreme conditions.Philippe Oger is Research Director at the CNRS, France. His research areas include understanding the adaptations of prokaryotes in response to extreme conditions, using a multidisciplinary approach combining the methods derived from atomic physics and cutting-edge molecular biology and modeling.

• Preface xiBéatrice CLOUET-D'ORVAL, Bruno FRANZETTI and Philippe OGERChapter 1. Replication of Archaeal Chromosomes 1Ghislaine HENNEKE, Roxane LESTINI, Marc NADAL and Didier FLAMENT1.1. Replication initiation 21.2. The elongation phase of replication 81.3. Okazaki fragment maturation 101.4. Restarting replication forks 151.5. Replication termination 181.6. Chromosome segregation and decatenation 181.7. References 19Chapter 2. Archaeal DNA Repair 25Caroline L'HERMITTE-STEAD, Anaïs BAYARD, Alexey ALEKSANDROV, Roxane LESTINI and Hannu MYLLYKALLIO2.1. General introduction 252.2. Several different types of DNA damages occur in archaea 282.3. Different archaeal DNA repair pathways 312.4. Coordination of the different pathways by the replication clamp 402.5. Summary and conclusion 422.6. References 43Chapter 3. Transcription in Archaea 45Thomas FOUQUEAU, Duy KHANH PHUNG and Ludovic SAUGUET3.1. RNA polymerase 473.2. The three stages of transcription 513.3. Transcription regulation 643.4. References 66Chapter 4. RNA Classes and Their Maturation and Degradation Enzymes 77Manon BATISTA, Béatrice CLOUET-D'ORVAL and Marie BOUVIER4.1. Introduction 774.2. RNA classes in archaea 794.3. Ribonuclease families in archaea 844.4. Ubiquitous RNA-binding proteins in archaea 954.5. Conclusion 1004.6. References 100Chapter 5. Ribosome and Transfer RNA Biogenesis 115Tamara BASTA and Sébastien FERREIRA-CERCA5.1. Ribosome biogenesis 1165.2. Synthesis and maturation of tRNAs 1335.3. Methodical toolboxes 1565.4. References 158Chapter 6. The Diversity and Function of Noncoding RNAs in Archaea 167Hubert F. BECKER and Christine GASPIN6.1. Introduction 1676.2. Noncoding RNA diversity 1686.3. ncRNA identification 1786.4. Circularization of noncoding RNAs 1826.5. Conclusion 1856.6. References 186Chapter 7. Translation in Archaea 193Emmanuelle SCHMITT and Yves MECHULAM7.1. Initiating the translation 1957.2. Elongation peptide synthesis 2067.3. Translation termination and ribosome recycling 2147.4. Conclusion 2197.5. References 220List of Authors 233Index 237

Béatrice Clouet-d’Orval is Research Director at the CNRS and works at the Center for Integrative Biology, Toulouse, France. Her main research areas focus on the post-transcriptional regulation of gene expression.Bruno Franzetti is Research Director at the CNRS, France, where he specializes in the structural biology of archaea. His research areas include biophysical and cellular mechanisms that maintain proteome integrity under extreme conditions.Philippe Oger is Research Director at the CNRS, France. His research areas include understanding the adaptations of prokaryotes in response to extreme conditions, using a multidisciplinary approach combining the methods derived from atomic physics and cutting-edge molecular biology and modeling.

• Preface xiBéatrice CLOUET-D'ORVAL, Bruno FRANZETTI and Philippe OGERChapter 1. Replication of Archaeal Chromosomes 1Ghislaine HENNEKE, Roxane LESTINI, Marc NADAL and Didier FLAMENT1.1. Replication initiation 21.2. The elongation phase of replication 81.3. Okazaki fragment maturation 101.4. Restarting replication forks 151.5. Replication termination 181.6. Chromosome segregation and decatenation 181.7. References 19Chapter 2. Archaeal DNA Repair 25Caroline L'HERMITTE-STEAD, Anaïs BAYARD, Alexey ALEKSANDROV, Roxane LESTINI and Hannu MYLLYKALLIO2.1. General introduction 252.2. Several different types of DNA damages occur in archaea 282.3. Different archaeal DNA repair pathways 312.4. Coordination of the different pathways by the replication clamp 402.5. Summary and conclusion 422.6. References 43Chapter 3. Transcription in Archaea 45Thomas FOUQUEAU, Duy KHANH PHUNG and Ludovic SAUGUET3.1. RNA polymerase 473.2. The three stages of transcription 513.3. Transcription regulation 643.4. References 66Chapter 4. RNA Classes and Their Maturation and Degradation Enzymes 77Manon BATISTA, Béatrice CLOUET-D'ORVAL and Marie BOUVIER4.1. Introduction 774.2. RNA classes in archaea 794.3. Ribonuclease families in archaea 844.4. Ubiquitous RNA-binding proteins in archaea 954.5. Conclusion 1004.6. References 100Chapter 5. Ribosome and Transfer RNA Biogenesis 115Tamara BASTA and Sébastien FERREIRA-CERCA5.1. Ribosome biogenesis 1165.2. Synthesis and maturation of tRNAs 1335.3. Methodical toolboxes 1565.4. References 158Chapter 6. The Diversity and Function of Noncoding RNAs in Archaea 167Hubert F. BECKER and Christine GASPIN6.1. Introduction 1676.2. Noncoding RNA diversity 1686.3. ncRNA identification 1786.4. Circularization of noncoding RNAs 1826.5. Conclusion 1856.6. References 186Chapter 7. Translation in Archaea 193Emmanuelle SCHMITT and Yves MECHULAM7.1. Initiating the translation 1957.2. Elongation peptide synthesis 2067.3. Translation termination and ribosome recycling 2147.4. Conclusion 2197.5. References 220List of Authors 233Index 237

Béatrice Clouet-d’Orval is Research Director at the CNRS and works at the Center for Integrative Biology, Toulouse, France. Her main research areas focus on the post-transcriptional regulation of gene expression.Bruno Franzetti is Research Director at the CNRS, France, where he specializes in the structural biology of archaea. His research areas include biophysical and cellular mechanisms that maintain proteome integrity under extreme conditions.Philippe Oger is Research Director at the CNRS, France. His research areas include understanding the adaptations of prokaryotes in response to extreme conditions, using a multidisciplinary approach combining the methods derived from atomic physics and cutting-edge molecular biology and modeling.

• Preface xiBéatrice CLOUET-D'ORVAL, Bruno FRANZETTI and Philippe OGERChapter 1. Replication of Archaeal Chromosomes 1Ghislaine HENNEKE, Roxane LESTINI, Marc NADAL and Didier FLAMENT1.1. Replication initiation 21.2. The elongation phase of replication 81.3. Okazaki fragment maturation 101.4. Restarting replication forks 151.5. Replication termination 181.6. Chromosome segregation and decatenation 181.7. References 19Chapter 2. Archaeal DNA Repair 25Caroline L'HERMITTE-STEAD, Anaïs BAYARD, Alexey ALEKSANDROV, Roxane LESTINI and Hannu MYLLYKALLIO2.1. General introduction 252.2. Several different types of DNA damages occur in archaea 282.3. Different archaeal DNA repair pathways 312.4. Coordination of the different pathways by the replication clamp 402.5. Summary and conclusion 422.6. References 43Chapter 3. Transcription in Archaea 45Thomas FOUQUEAU, Duy KHANH PHUNG and Ludovic SAUGUET3.1. RNA polymerase 473.2. The three stages of transcription 513.3. Transcription regulation 643.4. References 66Chapter 4. RNA Classes and Their Maturation and Degradation Enzymes 77Manon BATISTA, Béatrice CLOUET-D'ORVAL and Marie BOUVIER4.1. Introduction 774.2. RNA classes in archaea 794.3. Ribonuclease families in archaea 844.4. Ubiquitous RNA-binding proteins in archaea 954.5. Conclusion 1004.6. References 100Chapter 5. Ribosome and Transfer RNA Biogenesis 115Tamara BASTA and Sébastien FERREIRA-CERCA5.1. Ribosome biogenesis 1165.2. Synthesis and maturation of tRNAs 1335.3. Methodical toolboxes 1565.4. References 158Chapter 6. The Diversity and Function of Noncoding RNAs in Archaea 167Hubert F. BECKER and Christine GASPIN6.1. Introduction 1676.2. Noncoding RNA diversity 1686.3. ncRNA identification 1786.4. Circularization of noncoding RNAs 1826.5. Conclusion 1856.6. References 186Chapter 7. Translation in Archaea 193Emmanuelle SCHMITT and Yves MECHULAM7.1. Initiating the translation 1957.2. Elongation peptide synthesis 2067.3. Translation termination and ribosome recycling 2147.4. Conclusion 2197.5. References 220List of Authors 233Index 237