Eukaryotic RNases and their Partners in RNA Degradation and Biogenesis

Preface

Chapter One. Biochemistry and Function of RNA Exosomes

1. Introduction

2. Cellular Functions of the Exosome

3. Composition of Exosomes and Their Related Complexes

4. Exosome Cofactors

5. Concluding Remarks

References

Chapter Two. Plant Exosomes and Cofactors

1. Introduction

2. Composition of the Plant Exosome Core Complex

3. Exosome-Related Activities and Cofactors in Plants

4. Impact of Exosome-Mediated Degradation in Plants

5. Final Remarks

References

Chapter Three. Structure and Activities of the Eukaryotic RNA Exosome

1. Introduction

2. Global Architecture of the Eukaryotic Exosome Core

3. RNase PH-Like Domains Comprise a PH-Like Ring in Eukaryotic Exosomes

4. S1 and KH Domains Cap the PH-Like Ring

5. RRP44, a Hydrolytic Endoribonuclease and Processive Exoribonuclease

6. RRP44 and the 10-Component Exosome

7. RRP6, a Eukaryotic Exosome Subunit with Distributive Hydrolytic Activities

8. RRP44, RRP6, and the 11-Component Nuclear Exosome

9. Conclusions

References

Chapter Four. TRAMP Stimulation of Exosome

1. TRAMP Is a Cofactor of Nuclear Exosome

2. RNA Substrate Repertoire of TRAMP

3. TRAMP Biochemistry and Structure

4. TRAMP Complex in Activation of the Exosome

5. TRAMP Complexes in Different Organisms

References

Chapter Five. XRN1: A Major 5′ to 3′ Exoribonuclease in Eukaryotic Cells

1. Introduction

2. XRN1 in mRNA Decay

3. XRN1 in mRNA Quality Control

4. XRN1 in miRNA-Mediated Decay

5. XRN1 in siRNA-Mediated Decay

6. Localization of XRN1 in Cells

7. XRN1 in lncRNA Decay

8. XRN1 in tRNA Quality Control

9. XRN1 in rRNA and snoRNA Processing

10. Regulation of XRN1 Activity

11. Summary

References

Chapter Six. Structures of 5′–3′ Exoribonucleases

1. Introduction

2. Crystal Structure of RAT1/XRN2

3. Crystal Structures of XRN1

4. Structural Homologs of XRNs

5. Active Site of XRNs

6. Structure of the RAT1–RAI1 Complex

7. Structure of RAI1/DOM3Z

8. Perspectives

References

Chapter Seven. Rat1 and Xrn2: The Diverse Functions of the Nuclear Rat1/Xrn2 Exonuclease

1. Introduction

2. The Life Story of RAT1/XRN2

3. Sequence and Structural Data

4. One Protein, Many Functions

5. Overlapping Functions of RAT1 and XRN1

6. XRN2 as a Silencing Suppressor

7. Perspectives

References

Chapter Eight. Normal and Aberrantly Capped mRNA Decapping

1. Introduction

2. mRNA-Decapping Proteins in the Exonucleolytic Pathway of mRNA Decay

3. Presence of an Aberrant Cap-Decapping Protein in S. cerevisiae

4. Additional Potential Functions of RAI1

5. Future Directions

References

Chapter Nine. Activity and Function of Deadenylases

1. Introduction

2. The Poly(A) Nuclease (PAN)

3. The Poly(A)-Specific Ribonuclease

4. The CCR4–NOT Complex

References

Chapter Ten. The Diverse Functions of Fungal RNase III Enzymes in RNA Metabolism

1. Introduction

2. Phylogenetic Distribution and Conservation of RNase III Enzymes in Fungi

3. Ribosomal RNA Processing and RNA Polymerase I Transcriptional Termination

4. Small Nuclear RNAs Processing

5. Functions in Small Nucleolar RNAs Processing

6. (Pre)-mRNA Surveillance, Degradation, and Regulation

7. RNA Polymerase II Termination

8. Conclusions and Perspectives

References

Author Index

Subject Index