Nucleic Acids and Molecular Biology

Transcription

1 Nucleic Acids and Molecular Biology 20 Series Editor H. J. Gross

2 H. Ulrich Göringer (Ed.) RNA Editing

3 Professor Dr. H. Ulrich Göringer Institute of Microbiology and Genetics Technical University Darmstadt Schnittspahnstr Darmstadt Germany ISSN ISBN-13: e-isbn-13: Library of Congress Control Number: This work is subject to copyright. All rights are reserved, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilm or in any other way, and storage in data banks. Duplication of this publication or parts thereof is permitted only under the provisions of the German Copyright Law of September 9, 1965, in its current version, and permission for use must always be obtained from Springer. Violations are liable for prosecution under the German Copyright Law. Springer is a part of Springer Science+Business Media springer.com Springer-Verlag Berlin Heidelberg 2008 The use of registered names, trademarks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. Printed on acid-free paper

4 Preface Editing a book on editing has a certain tongue in cheek connotation to it, and I must admit that I was not aware what the job truly entailed when the project started. However, over the many months that it took to complete the book, it was interesting to realize that indeed printing-type editing and biological editing have many matching characteristics. Therefore, the quote by the well-known film editor Verna Fields ( ), I wish the word editing had never been invented, editing implies correcting, and it s not, can function as a motto for the book: the various biological phenomena that are controlled by the different editing reactions are by far more complex than a simple correction process, and it is astounding how multifaceted the field has become. All chapters of the book focus, as a general editorial subtext, on the correlation between RNA structure and function, and on complexity. This involves different length scales: from complex molecular machineries, to the interplay of complex biochemical pathways, and to evolutionary processes. The chapters are organized in a sequence beginning with a status quo account of RNA editing reactions from the focused perspective of RNA structure. This is followed by a chapter on the structure/function correlation in trna editing, and a chapter on RNA editing by adenosine deaminases that act on RNA (ADARs). A to I editing is perhaps today s best example for the wide spectrum of biological functions that are impacted by RNA editing. Especially the recently discovered interaction of the ADAR editing pathway with the microrna/rnai machinery is an excellent illustration of this. The next chapter summarizes the remarkable progress in the insertion/deletion-type editing reaction in Physarum polycephalum, and the following two chapters are dedicated to editing processes in plant mitochondria and chloroplasts. Three chapters deal with the U insertion/u deletion-type RNA editing reaction in kinetoplastid parasites. This incorporates a description of the molecular editing machinery, a chapter on accessory factors of the reaction pathway, and a detailed discussion of its biological function including the recently discovered alternative editing phenomenon. A final chapter is dedicated to evolutionary aspects of RNA editing. I hope that the book will prove useful not only to those working directly in this domain, but also to advanced students and researchers, including those in sister disciplines, who wish to re-edit their knowledge on RNA editing. v

5 vi Preface Finally, I would like to thank all contributing authors for their work and efforts, and the series editor H.J. Gross for his help and advice. A special thank you goes to Ursula Gramm for her patient and calm editorial work, and to Monique T. Delafontaine for her superb copy-editing: a perfect example of editing as a conditio sine qua non. Darmstadt, June 2007 Uli Göringer

6 Contents Preface... v Contributors... ix Editing Reactions from the Perspective of RNA Structure... 1 Matthias Homann Editing of trna for Structure and Function Juan D. Alfonzo RNA Editing by Adenosine Deaminases that Act on RNA (ADARs) Michael F. Jantsch and Marie Öhman Insertion/Deletion Editing in Physarum polycephalum Jonatha M. Gott and Amy C. Rhee RNA Editing in Plant Mitochondria Mizuki Takenaka, Johannes A. van der Merwe, Daniil Verbitskiy, Julia Neuwirt, Anja Zehrmann, and Axel Brennicke RNA Editing in Chloroplasts Masahiro Sugiura Working Together: the RNA Editing Machinery in Trypanosoma brucei Jason Carnes and Kenneth Stuart RNA Editing Accessory Factors the Example of mhel61p H. Ulrich Göringer, Michael Brecht, Cordula Böhm, and Elisabeth Kruse The Function of RNA Editing in Trypanosomes Torsten Ochsenreiter and Stephen Hajduk vii

7 viii Contents Evolutionary Aspects of RNA Editing Dave Speijer Index

8 Contributors Juan D. Alfonzo Department of Microbiology and The Ohio State Biochemistry Program, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, USA, Cordula Böhm Genetics, Darmstadt University of Technology, Schnittspahnstr. 10, Darmstadt, Germany Michael Brecht Genetics, Darmstadt University of Technology, Schnittspahnstr. 10, Darmstadt, Germany Axel Brennicke Molekulare Botanik, Universität Ulm, Ulm, Germany Jason Carnes Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, USA, and Department of Pathobiology, University of Washington, Seattle, WA 98195, USA H. Ulrich Göringer Genetics, Darmstadt University of Technology, Schnittspahnstr. 10, Darmstadt, Germany, Jonatha M. Gott Center for RNA Molecular Biology, Euclid Avenue, Case Western Reserve University, Cleveland, OH 44106, USA, Stephen Hajduk Department of Biochemistry and Molecular Biology, University of Georgia, 120 Green Street, Athens, GA , USA, ix

9 x Contributors Matthias Homann Genetics, Darmstadt University of Technology, Schnittspahnstr. 10, Darmstadt, Germany, Michael F. Jantsch Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr Gasse 1, 1030 Vienna, Austria, Elisabeth Kruse Genetics, Darmstadt University of Technology, Schnittspahnstr. 10, Darmstadt, Germany Julia Neuwirt Molekulare Botanik, Universität Ulm, Ulm, Germany Torsten Ochsenreiter Department of Biochemistry and Molecular Biology, University of Georgia, 120 Green Street, Athens, GA , USA Marie Öhman Department of Molecular Biology & Functional Genomics, Stockholm University, Stockholm, Sweden Amy C. Rhee Center for RNA Molecular Biology, Euclid Avenue, Case Western Reserve University, Cleveland, OH 44106, USA Dave Speijer Academic Medical Center (AMC), Department of Medical Biochemistry, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands, Kenneth Stuart Seattle Biomedical Research Institute, 307 Westlake Ave N, Suite 500, Seattle, WA 98109, USA, and Department of Pathobiology, University of Washington, Seattle, WA 98195, USA, Masahiro Sugiura Graduate School of Natural Sciences, Nagoya City University, Nagoya , Japan, Mizuki Takenaka Molekulare Botanik, Universität Ulm, Ulm, Germany,

10 Contributors xi Daniil Verbitskiy Molekulare Botanik, Universität Ulm, Ulm, Germany Dré van der Merwe Molekulare Botanik, Universität Ulm, Ulm, Germany Anja Zehrmann Molekulare Botanik, Universität Ulm, Ulm, Germany