Henri Grosjean
CNRS, University of Paris

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About this Book

This volume is a timely and comprehensive description of the many facets of DNA and RNA modification-editing processes and to some extent repair mechanisms. Each chapter offers fundamental principles as well as up to date information on recent advances in the field (up to end 2008). They ended by a short ‘conclusion and future prospect’ section and an exhaustive list of 35 to up to 257 references (in average 87). Contributors are geneticists, structural enzymologists and molecular biologists working at the forefront of this exciting, fast-moving and diverse field of researches. This book will be a major interest to PhD students and University teachers alike. It will also serve as an invaluable reference tool for new researchers in the field, as well as for specialists of RNA modification enzymes generally not well informed about what is going on in similar processes acting on DNA and vice-versa for specialists of the DNA modification-editing and repair processes usually not much acquainted with what is going on in the RNA maturation field. The book is subdivided into 41 chapters (740 pages). The common links between them are mainly the enzymatic aspects of the different modification-editing and repair machineries: structural, mechanistic, functional and evolutionary aspects. It starts with two general and historical overview of the discovery of modified nucleosides in DNA and RNA and corresponding modification-editing enzymes. Then follows eleven chapters on DNA modification and editing (mechanistic and functional aspects). Two additional chapters cover problems related to DNA/RNA repair and base editing by C-to-U deaminases, followed by three chapters on RNA editing by C-to-U and A-to-I type of deamination. Discussions about interplay between DNA and RNA modifications and the emergence of DNA are covered in two independent chapters, followed by twenty chapters on different but complementary aspects of RNA modification enzymes and their cellular implications. The last chapter concerns the description of the present state-of-the art for incorporating modified nucleosides by in vitro chemical synthesis. At the end of the book, six appendicies give useful details on modified nucleosides, modification-editing enzymes and nucleosides analogs. This information is usually difficult to obtain from current scientific literature.

Table of Contents

Preface

1. Nucleic Acids Are Not Boring Long Polymers of Only Four Types of Nucleotides: A Guided Tour
Henri Grosjean

2. DNA Methylation: From Bug to Beast
Stephanie R. Coffin, Benjamin A. Youngblood and Norbert O. Reich

3. DNA Restriction‑Modification Systems in Prokaryotes
John H. White, Gareth A. Roberts and David T.F. Dryden

4. Experimental Approaches to Study DNA Base Flipping
Saulius Klimašauskas and Zita Liutkevičiūtė

5. Molecular Modeling of Base Flipping in DNA
U. Deva Priyakumar and Alexander D. MacKerell Jr

6. M⋅HhaI and M⋅EcoRI: Paradigms for Understanding the Conformational Mechanisms of DNA Methyltransferases
Norbert O. Reich and Stephanie R. Coffin

7. Mechanism and Evolution of DNA Recognition by DNA‑(adenine N6)‑Methyltransferases from the EcoDam Family
Albert Jeltsch and Tomasz P. Jurkowski

8. Structures and Activities of Mammalian DNA Methyltransferases
Xiaodong Cheng and Robert M. Blumenthal

9. DNA Methylation and Human Diseases: An Overview
Wolfgang A. Schulz and Olusola Y. Dokun

10. Expanding the Chemical Repertoire of DNA Methyltransferases by Cofactor Engineering
Basar Gider and Elmar Weinhold

11. Studying Antibody MaturationUsing Techniques for Detecting Uracils in DNA
Rachel Parisien and Ashok S. Bhagwat

12. Enzymatic Formation of the Hypermodified DNA Base J (β‑D‑Glucopyranosyloxymethyluracil)
Robert Sabatini, Laura Cliffe, Saara Vainio and Piet Borst

13. DNA Demethylation
Teresa Roldán‑Arjona and Rafael R. Ariza

14. Demethylation of DNA and RNA by AlkB Proteins
Pål Ø. Falnes, Erwin van den Born and Trine J. Meza

15. The APOBEC1 Paradigm for Mammalian Cytidine Deaminases That Edit DNA and RNA
Harold C. Smith

16. Mechanism of Action and Structural Aspects of ADARS (A‑to‑I) and APOBEC‑Related (C‑to‑U) Deaminases
Joseph E. Wedekind and Peter A. Beal

17. Structure of RNA Editing Substrates and Their Recognition by RNA Base Deaminase
Christophe Maris and Frédéric H.‑T. Allain

18. Biological Roles of ADARs
Bret S.E. Heale and Mary A. O’Connell

19. The Interplay between RNA and DNA Modifications: Back to the RNA World
Patrick Forterre and Henri Grosjean

20. Folate‑Dependent Thymidylate‑Forming Enzymes:Parallels between DNA and RNA Metabolic Enzymes and Evolutionary Implications
Hannu Myllykallio, Stephane Skouloubris, Henri Grosjean and Ursula Liebl

21. Folds and Functions of Domains in RNA Modification Enzymes
Anna Czerwoniec, Joanna M. Kasprzak, Katarzyna H. Kaminska, Kristian Rother, Elzbieta Purta and Janusz M. Bujnicki

22. Enzyme‑RNA Substrate Recognition in RNA‑Modifying Enzymes
Robert T. Byrne, David G. Waterman and Alfred A. Antson

23. Molecular Basis of tRNA Processing Reactions
Michelle Mitchell and Hong Li

24. RNA‑Modifying Metalloenzymes
Mohamed Atta, Marc Fontecave and Etienne Mulliez

25. Pseudouridine Formation, the Most Common Transglycosylation in RNA
Eugene G. Mueller and Adrian R. Ferré‑D’Amare

26. Enzymatic Formation of the 7‑Deazaguanosine Hypermodified Nucleosides of tRNA
Dirk Iwata‑Reuyl and Valérie de Crécy‑Lagard

27. Biogenesis and Functions of Thio‑Compounds in Transfer RNA: Comparison of Bacterial and Eukaryotic Thiolation Machineries
Akiko Noma, Naoki Shigi and Tsutomu Suzuki

28. Enzymatic Formation of 5‑Aminomethyl‑Uridine Derivatives in tRNA: Functional and Evolutionary Implications
Yoshitaka Bessho and Shigeyuki Yokoyama

29. Deciphering the Complex Enzymatic Pathway for Biosynthesis of Wyosine Derivatives in Anticodon of tRNA^Phe
Jaunius Urbonavičius, Louis Droogmans, Jean Armengaud and Henri Grosjean

30. Multicomponent 2′‑O‑Ribose Methylation Machines: Evolving Box C/D RNP Structure and Function
Keith T. Gagnon, Guosheng Qu and E. Stuart Maxwell

31. Multicomponent Machines in RNA Modification: H/ACA Ribonucleoproteins
Petar Grozdanov and U. Thomas Meier

32. Spliceosomal snRNA Pseudouridylation
John Karijolich, Chao Huang and Yi‑Tao Yu

33. Transfer RNA Aminoacylation and Modified Nucleosides
Richard Giegé and Jacques Lapointe

34. Crystallographic Studies of Decoding by Modified Bases: Correlation of Structure and Function
Albert Weixlbaumer and Frank V. Murphy IV

35. Roles of the Ultra‑Conserved Ribosomal RNA Methyltransferase KsgA in Ribosome Biogenesis
Jason P. Rife

36. Antibiotic Resistance in Bacteria through Modification of Nucleosides in 16S Ribosomal RNA
Graeme L. Conn, Miloje Savic and Rachel Macmaster

37. Antibiotic Resistance in Bacteria Caused by Modified Nucleosides in 23S Ribosomal RNA
Birte Vester and Katherine S. Long

38. Function of Modified Nucleosides in RNA Stabilization
Armine Hayrapetyan, Salifu Seidu‑Larry and Mark Helm

39. Roles of tRNA Modifications in tRNA Turnover
Eric M. Phizicky, Elizabeth J. Grayhack, Irina Chernyakov and Joseph M. Whipple

40. The “PACE” Concept Pointed at New Key Proteins Involved in RNA Metabolism
Jean Armengaud

41. Chemical Synthesis of DNA and RNA Containing Modified Nucleotides
Sébastien Porcher and Mark Helm

Appendix 1: Chemical Structures, Classification of Modified Nucleosides in RNA and the MODOMICS Database Concerning the Corresponding RNA Modification Enzymes
Kristian Rother, Anna Czerwoniec, Janusz M. Bujnicki and Henri Grosjean

Appendix 2: Databases of DNA Modifications
Kristian Rother, Grzegorz Papaj and Janusz M. Bujnicki

Appendix 3: RNA Modification Subsystems in the SEED Database
Valérie de Crécy‑Lagard and Gary Olsen

Appendix 4: List of Available Phosphoramidites of Modified Nucleotides for Chemical DNA/RNA Synthesis
Salifu Seidu‑Larry, Sebastien Porcher, Ronald Micura and Mark Helm

Appendix 5: S‑Adenosyl‑L‑Methionine and Analogs
Elmar Weinhold and Saulius Klimašauskas

Appendix 6: Web Links to Databases about RNA and DNA Modifications and Related Topics
Henri Grosjean and Kristian Rother