Table Of ContentMOLECULAR BIOLOGY AND BIOTECHNOLOGY OF PLANT ORGANELLES
Molecular Biology and
Biotechnology of
Plant Organelles
Chloroplasts and Mitochondria
Edited by
Henry Daniell
Department of Microbiology and Molecular Biology,
University of Central Florida, Orlando, Florida, U.S.A.
and
Christine Chase
Horticultural Sciences Department, University of Florida,
Gainesville, Florida, U.S..A.
A C.I.P. Catalogue record for this book is available from the Library of Congress.
ISBN 1-4020-2713-3 (HB)
ISBN 1-4020-3166-1 (e-book)
Published by Springer,
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©2004 Springer
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CONTENTS
Preface vii
About the Editors viii
Contributors ix
Color Plates xi
1. Introduction to the Molecular Biology and Biotechnology of Plant 1
Organelles
Henry Daniell and Christine D. Chase
SECTION 1: ORGANELLE GENOMES AND PROTEOMICS
2. The Evolutionary Origins of Plant Organelles 15
Michael W. Gray
3. The Somatic Inheritance of Plant Organelles 37
S. Heinhorst, C. L. Chi-Ham, S. W. Adamson and G. C. Cannon
4. The Sexual Inheritance of Plant Organelles 93
Rudolph Hagemann
5. Plastid Genomes 115
R. M. Maier and C. Schmitz-Linneweber
6. Plant Mitochondrial Genomes 151
C. Fauron, J. Allen, S. Clifton and K. Newton
7. Proteomics, Bioinformatics and Genomics Applied to Plant Organelles 179
C. Colas des Francs-Small, B. Szurek and I. Small
SECTION 2: ORGANELLE GENE EXPRESSION AND SIGNALING
8. The Transcription of Plant Organelle Genomes 213
Andreas Weihe
9. RNA Editing in Plant Organelles 239
R. Michael Mulligan
10. Plastid and Plant Mitochondrial RNA Processing and RNA Stability 261
A. Marchfelder and S. Binder
v
11. Intron Splicing in Plant Organelles 295
Alice Barkan
12. Translational Machinery in Plant Organelles 323
Linda Bonen
13. Regulation of Translation in Chloroplasts 347
William Zerges
14. Targeting Signals and Import Machinery of Plastids and Plant 385
Mitochondria
Elzbieta Glaser and Jürgen Soll
15. Proteolysis in Plant Organelles 419
Zach Adam
SECTION 3: ORGANELLE BIOTECHNOLOGY
16. Chloroplast Genetic Engineering 443
Henry Daniell, Paul R. Cohill, Shashi Kumar, and Nathalie Dufourmantel
17. Engineering Herbicide Resistance Pathways in Plastids 491
Amit Dhingra and Henry Daniell
18. Metabolic Engineering of Chloroplasts for Abiotic Stress Tolerance 513
Joe H. Cherry and Brent L. Nielsen
19. Metabolic Pathway Engineering For Nutrition Enrichment 527
Niranjan Baisakh and Swapan Datta
20. Plastid Metabolic Pathways for Fatty Acid Metabolism 543
Ikuo Nishida
21. Metabolic Engineering: Plastids as Bioreactors 565
Karen Bohmert, Oliver P. Peoples and Kristi D. Snell
22. Cytoplasmic Male Sterility and Fertility Restoration by Nuclear Genes 593
Christine D. Chase and S. Gabay-Laughnan
23. The Use of Cytoplasmic Male Sterility for Hybrid Seed Production 623
Michael J. Havey
24. Somatic Cell Cybrids and Hybrids in Plant Improvement 635
W. W. Guo, X. D. Cai and J. W. Grosser
v i
Preface
We have taught plant molecular biology and biotechnology at the undergraduate and
graduate level for over 20 years. In the past few decades, the field of plant organelle
molecular biology and biotechnology has made immense strides. From the green revolution
to golden rice, plant organelles have revolutionized agriculture. Given the exponential
growth in research, the problem of finding appropriate textbooks for courses in plant
biotechnology and molecular biology has become a major challenge. After years of
handing out photocopies of various journal articles and reviews scattered through out the
print and electronic media, a serendipitous meeting occurred at the 2002 IATPC World
Congress held in Orlando, Florida.
After my talk and evaluating several posters presented by investigators from my
laboratory, Dr. Jacco Flipsen, Publishing Manager of Kluwer Publishers asked me whether
I would consider editing a book on Plant Organelles. I accepted this challenge, after
months of deliberations, primarily because I was unsuccessful in finding a text book in this
area for many years. I signed the contract with Kluwer in March 2003 with a promise to
deliver a camera-ready textbook on July 1, 2004. Given the short deadline and the
complexity of the task, I quickly realized this task would need a co-editor. Dr. Christine
Chase was the first scientist who came to my mind because of her expertise in plant
mitochondria, and she readily agreed to work with me on this book. Both of us made a list
of the topics and the eminent researchers in chloroplasts and mitochondria.
Fortunately almost all invited scientists agreed to contribute a chapter on their
topic of expertise. We are extremely thankful to the authors who contributed their
knowledge to this book, and their commitment to educate students of future generations.
Through meticulous work they ensured that the topics were thoroughly researched, up to
date and well presented. We are thankful that they took time from their very busy schedules
and submitted chapters in a timely manner. Unfortunately, we lost two of our valued
colleagues during the preparation of this book. Professor Rainer Maier died in April 2004
after completing Chapter 5. Professor Lawrence Bogorad died in December 2003 before he
could write an overview of this field. He has been Henry Daniell’s mentor and friend for
two decades, and will be missed very much.
The transformation of the manuscript into a book, in a camera-ready format,
involved a myriad of tasks that required the help of many. Jacco Flipsen and Noeline
Gibson of Springer Press were patient with our questions regarding style, graphics, and
format. Henry Daniell would like to acknowledge the assistance of his lab colleagues Amit
Dhingra, Paul Cohill, and Shashi Kumar; Vijay Pattisapu and Suneel Modani were
unstinting in their efforts. He is deeply indebted to his wife Shobana for help in editing this
book and constant support. Christine Chase would like to thank her first mentor in science,
Dr. Rolf Benzinger, for introducing her to the field of genetic transformation. She also
thanks her colleagues Drs. Daryl Pring, Susan Gabay-Laughnan, and Ken Cline for
countless discussions of organelle biology and genetics over the years and for their
insights regarding the content of this volume.
We dedicate this book to the memory of Professors Lawrence Bogorad and Rainer
Maier. Both of them made major contributions and continue to inspire many scientists to
conduct research in chloroplast molecular biology.
Henry Daniell
Christine Chase
vi i
About the Editors
Henry Daniell was born and educated in India. He moved to the
United States as a post-doctoral fellow at the University of Illinois,
Urbana-Champaign in 1980. Since then he has served on the
faculty of Washington State University, University of Idaho
Auburn University and University of Central Florida (as Pegasus
Professor & Trustee Chair). He has published over 100 research
articles on several areas, including DNA replication in chloroplast
and mitochondria, identification of new genes in the mitochondrial genome, promiscuous
DNA and their evolutionary significance, maternal inheritance, transgene containment,
photosynthesis (Rubisco, electron transport), chlorophyll biosynthesis, chloroplast
development, in organello protein synthesis, transcription, RNA processing, RNA stability,
translation, protein import, proteolysis and regulation of these processes. He pioneered the
chloroplast genetic engineering approach in the 1980s and advanced this concept to confer
useful agronomic traits (for biotic & abiotic stress, photoremediation, cytoplasmic male
sterility, etc.) and to express vaccine antigens, biopharmaceuticals and biomaterials in
transgenic plants. He has extended this technology to major crops, including cotton.
Numerous undergraduates, graduates and post-doctoral fellows were trained to use this
experimental system. Based on his oldest patents in this field, he is the technical founder
of Chlorogen Inc., which is now evaluating chloroplast transgenic crops in the field. He is
an editor of the Plant Biotechnology Journal and has received several Distinguished
Researcher and Teaching Excellence Awards. Dr. Daniell has served as a consultant to the
United Nations in biotechnology and was elected to the National Academy of Sciences,
Italy in 2004, a rare honor bestowed on 14 Americans in the past 222 years.
Christine Chase was born and raised in rural, upstate New York. She
earned a B.S. degree in Science Education from Cornell University in
1973 and a Ph.D. in Biology from the University of Virginia in 1981.
During her graduate studies, she was supported by a NIH Traineeship
in Genetics awarded through the Biology Department. Her introduction
to organelle research began with her postdoctoral training (1981-1984)
in the laboratory of Daryl Pring, USDA-ARS, at the University of
Florida. She joined the faculty of the University of Florida Institute of Food and
Agricultural Sciences in 1985, and she currently holds the rank of Professor in the
Horticultural Sciences Department. She was a founding member of the University of
Florida Interdepartmental Graduate Program in Plant Molecular and Cellular Biology, and
she served as Co-Director (1993-1995) and Director (1995-1997) of that program. Dr.
Chase teaches in graduate-level Advanced Genetics and Plant Molecular Biology courses.
Her research exploits the unique biology and genetics of S cytoplasmic male sterility in
maize to study plant mitochondrial biogenesis and function. This research platform
presents an array of interesting biological questions that can be addressed through a variety
of experimental approaches, and numerous undergraduate and graduate students have been
introduced to research via this experimental system.
vi ii
CONTRIBUTORS
ADAM, Z. - Institute of Plant Sciences, The Hebrew University of Jerusalem, Israel
ADAMSON, S. W. - Department of Chemistry and Biochemistry, University of Southern
Mississippi, Mississippi, Hattiesburg, USA
ALLEN, J. - Biological Sciences, University of Missouri, Columbia, Missouri, USA
BAISAKH, N. - Plant Breeding, Genetics, and Biochemistry Division, International Rice
Research Institute, Manila, Philippines
BARKAN, A. - Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
BINDER, S. - Allgemeine Botanik, Universitäät Ulm, Germany
BOHMERT, K. - Metabolix, Inc., Cambridge, Massachusetts, USA
BONEN, L. - Biology Department, University of Ottawa, Canada
CAI, X. D. - National Key Laboratory of Crop Genetic Improvement, Huazhong
Agricultural University, Wuhan, China
CANNON, G. C. - Department of Chemistry and Biochemistry, University of Southern
Mississippi, Hattiesburg, Mississippi, USA
CHASE, C. - Horticultural Sciences Department, University of Florida, Gainesville, Florida,
USA
CHERRY, J. H. - Auburn University, Auburn, Alabama, USA
CHI-HAM, C. L. - Department of Chemistry and Biochemistry, University of Southern
Mississippi, Hattiesburg, USA
CLIFTON, S. - Genome Sequencing Center, Washington University, St. Louis, Missouri,
USA
COHILL, P. R. - Department of Microbiology and Molecular Biology, University of
Central Florida, Orlando, Florida, USA
COLAS DES FRANCS-SMALL, C. - Institut de Biotechnologie des Plants, Université Paris-
Sud, Orsay, France
DANIELL, H. - Department of Microbiology and Molecular Biology, University of Central
Florida, Orlando, Florida, USA
DATTA, S. - Plant Breeding, Genetics, and Biochemistry Division, International Rice
Research Institute, Manila, Philippines
DHINGRA, A. - Department of Microbiology and Molecular Biology, University of Central
Florida, Orlando, Florida, USA
DUFOURMANTEL, N. - CEA Cadarache, DSV, DEVM, CNRS-CEA, Aix-Marseille II,
Saint-Paul-lez-Durance, France
ix
FAURON, C. - Eccles Institute of Genetics, University of Utah, Salt Lake City, Utah, USA
GABAY-LAUGHNAN, S. - Department of Plant Biology, University of Illinois, Urbana-
Champaign, Illinois, USA
GLASER, E. - Department of Biochemistry and Biophysics, Stockholm University, Sweden
GRAY, M. W. - Department of Biochemistry and Molecular Biology, Dalhousie
University, Halifax, Canada
GROSSER, J. W. - Citrus Research and Education Center, University of Florida, Lake
Alfred, Florida, USA
GUO, W. W. - National Key Laboratory of Crop Genetic Improvement, Huazhong
Agricultural University, Wuhan, China
HAGEMANN, R. - Institut für Genetik, Martin-Luther-Universität, Halle/S, Germany
HAVEY, M. J. - USDA, ARS Vegetable Crops Unit, Department of Horticulture,
University of Wisconsin, Madison, Wisconsin, USA
HEINHORST, S. - Department of Chemistry and Biochemistry, University of Southern
Mississippi, Hattiesburg, Mississippi, USA
KUMAR, S. - Department of Microbiology and Molecular Biology, University of Central
Florida, Orlando, Florida, USA
MAIER, R. M. - Cell Biology, Philipps University, Marburg, Germany
MARCHFELDER, A. - Molekulare Botanik, Universitat Ulm, Germany
MULLIGAN, R. M. - Department of Developmental and Cell Biology, University of
California, Irvine, California, USA
NEWTON, K. - Biological Sciences, University of Missouri, Columbia, Missouri, USA
NIELSEN, B. L. - Department of Microbiology and Molecular Biology, Brigham Young
University, Provo, Utah, USA
NISHIDA, I. - Graduate School of Sciences, University of Tokyo, Japan
PEOPLES, O. P. - Metabolix, Inc., Cambridge, Massachusetts, USA
SCHMITZ-LINNEWEBER, C. - Institute of Molecular Biology, University of Oregon,
Eugene, Oregon, USA
SOLL, J. - Department für Biologie I, Botanik, Ludwig-Maximilians-Universität, München,
Germany
SMALL, I. - Unite de Recherche en Genomique Vegetale, Cremieux, France
SNELL, K. D. - Metabolix, Inc., Cambridge, Massachusetts, USA
SZUREK, B. - Unité de Recherche en Génomique Végétale, Cremieux, France
WEIHE, A. - Institut füür Biologie, Humboldt-Universitäät, Berlin, Germany
ZERGES, W. - Biology Department, Concordia University, Montreal, Canada
x
Plate 1: Comparison of various plant mitochondrial genomes.
See Chapter 6, Figure 3.
xi
