Post-Transcriptional Control of Gene Expression in Plants

418 Pages·1996·14.139 MB·English

by  G. G. Simpson, W. Filipowicz (auth.), Witold Filipowicz, Thomas Hohn (eds.)

POST-TRANSCRIPTIONAL CONTROL OF GENE EXPRESSION IN PLANTS
Post-Transcriptional Control of Gene
Expression in Plants
Edited by
Witold Filipowicz and Thomas Hahn
Reprinted from Plant Molecular Biology, Vol. 32(1, 2), 1996
KLUWER ACADEMIC PUBLISHERS
DORDRECHT/BOSTON/LONDON
Library of Congress Cataloging-in-Publication Data
ISBN-13: 978-94-01 0-6644-0 e-ISBN-13: 978-94-009-0353-1
DOl: 10.1007/978-94-009-0353-1
Published by Kluwer Academic Publishers,
P.O. Box 17,3300 AH Dordrecht, The Netherlands
Kluwer Academic Publishers incorporates
the publishing programmes of
D. Reidel, Martinus Nijhoff, Dr. W. Junk and MTP Press.
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Printed on acid-free paper
All Rights Reserved
© 1996 Kluwer Academic Publishers
Softcover reprint of the hardcover 1s t edition 1996
No part of the material protected by this copyright notice may be reproduced
or utilized in any form or by any means, electronic or mechanical,
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CONTENTS
Preface i-ii
Dedication iii
List of Contributors iv-viii
RNA processing and stability
Splicing of precursors to messenger RNA in higher plants: mechanism, regulation and
sub-nuclear organisation of the spliceosomal machinery
G.G. Simpson, W. Filipowicz 1-41
Plant mRNA 3/-end formation
H.M. Rothnie 43-61
Control of mRNA stability In higher plants
M.L. Abler, P.J. Green 63-78
RNA as a target and an initiator of post-transcriptional gene silencing in transgenic
plants
D.C. Baulcombe 79-88
RNA structure and regulation of gene expression
P. Klatt, D. Riesner, G. Steger 89-106
Trans/ation
The plant translational apparatus
K.S. Browning 107-144
Translational control of cellular and viral mRNAs
D.R Gallie 145-158
Translation in plant: rules and exceptions
J. Futterer, T. Hohn 159-189
Fate of translation products
Molecular chaperones and protein folding in plants
RS. Boston, P. Viitanen, E. Vierling 191-222
Transport of proteins in eukaryotic cells: more questions ahead
M. Bar-Peled, D.C. Bassham, N.V. Raikhel 223-249
Plasmodesma I cell-to-cell transport of proteins and nucleic acids
L.A. Mezitt, w.J. Lucas 251-273
Proteolysis in plants: mechanisms and functions
RD. Vierstra 275-302
Organelles
Regulation of gene expression in plant mitochondria
S. Binder, A. Marchfelder, A. Brennicke 303-314
Regulation of gene expression in chloroplasts of higher plants
M. Sugita, M. Sugiura 315-326
Post-transcriptional regulation of chloroplast gene expression in Chlamydomonas
reinhardtii
J.-D. Rochaix 327-341
RNA editing in plant mitochondria and chloroplasts
A.M. Maier, P. Zeitz, H. Kossel, G. Bannard, J.M. Gualberto, J.M. Grienenberger 343-365
Special topicS
Gene expression from viral RNA genomes
I.G. Maia, K. Seran, A.-L. Haenni, F. Bernardi 367-391
Optimizing expression of transgenes with an emphasis on post-transcriptional events
M.G. Koziel, N.B. Carazzi, N. Desai 393-405
Subject index 407-414
Plasma
Cells in I/ membrane"I ~cells.in
~
3t~ ~ ~'
DomalO-2
2222222 ........
-----. :....
~
Cell Wall
For details see Mezitt and Lucas, pp. 251-273
Plant Molecular Biology 32: i-ii, 1996.
Preface
A recent volume in this series (Signals and Signal Transduction Pathways in Plants (K. Palme, ed.) Plant Mol.
BioI. 26, 2137-1679) described the relay races by which signals are transported in plants from the sites of stimuli
to the gene expression machinery of the cell. Part of this machinery, the transcription apparatus, has been well
studied in the last two decades, and many important mechanisms controlling gene expression at the transcriptional
level have been elucidated. However, control of gene expression is by no means complete, once the RNA has been
produced. Important regulatory devices determine the maturation and usage of mRNA and the fate of its translation
product. Posttranscriptional regulation is especially important for generating a fast response to environmental and
intracellular signals.
This book opens with chapters describing the processing of mRNAs, i.e. splicing (Simpson and Filipowicz) and
polyadenylation (Rothnie). Usually, neither the splicing nor the polyadenylation signals of animals and fungi are
recognized efficiently and correctly in plants, indicating that they are not strictly conserved among the eukaryotic
kingdoms. In contrast to animal introns, the processing of plant introns depends on the presence of AU- and U-rich
clusters. The known plant polyadenylation sites do not include a defined element downstream of the AATAAA
motif as found in animals, the AAUAAA motif is not strictly conserved, and upstream elements are important.
More and more examples of alternative mRNA splicing and polyadenylation sites are being identified in plants.
Degradation of RNA might be as important as RNA production for the well-being of cells. Some mRNAs
encoding regulatory proteins must have a high turnover to avoid undesirable overproduction. Short-lived mRNAs
have been found to contain cis elements that label the RNA for degradation (Abler and Green). An especially
interesting mechanism of mRNA disposal occurs during posttranscriptional silencing (Baulcombe). In this case,
RNA that had apparently been produced originally at high excess is degraded specifically. The mechanism of
posttranscriptional silencing is basically unknown, difficult to explain in mechanistic terms and might involve
events described by chaos theory.
Protein synthesis in eukaryotic cells is much more complex than originally thought. More and more factors
governing pretranslational processes (initiation complex formation and scanning), the initiation itself, and elongation
are becoming known (Browning). Sequences both on the leader and the trailer of mRNAs play important roles in the
efficiency and regulation of translation (Gallie). Furthermore, not all eukaryotic mRNAs are strictly monocistronic.
Plant viral RNAs, in particular, are frequently provided with complex leaders containing short open reading frames
which control translation, and viral RNAs are often polycistronic (Fiitterer and Hohn). In general, strategies of gene
expression from viral genomes are unique and frequently also very complex (Maia et al.). For all the properties and
functions of viral and cellular mRNAs, their secondary and tertiary structure is very important (Klaff et al.). An
increasing number of RNA-binding proteins which specifically recognize different structural elements in RNA are
being characterized.
The correct folding of many proteins has been found to depend on the action of chaperonins (Boston et al.). While
some proteins remain in the cytoplams, others are transported to various subcellular localizations or are secreted
(Bar-Peled et al.). A unique property of plant cells is that some proteins, and also nucleic acids, can be actively
transported between cells using gates in the cell wall, the plasmodesmata. This novel macromolecular trafficking
pathway may playa role in the programming of plant development (Mezitt and Lucas). Like mRNA, turnover,
that of proteins is also regulated. Protein degradation in plants involves many proteolytic pathways operating in
different cellular compartments (Vierstra).
11
Due to their probably origin from prokaryotes, plant organelle gene expression uses mechanisms more related to
those of prokaryotes than those used by the cell for nuclear encoded genes. Regulation of organelle gene expression
occurs mainly at the posttranscriptionallevel, i.e. RNA cis and trans splicing, processing ofpolycistronic transcripts
(Rochaix; Sugita and Sugiura; Binder et al.) and finally, RNA editing (Maier et al.). The latter process occurs both
in mitochondria and chloroplasts but its biochemistry remains largely unknown.
From the many examples of posttranscriptional regulation described in this book it is obvious that optimizing
gene expression in transgenic plants cannot stop with the design of optimal promoters but must also consider
the stability and translatability of the transcripts as well as certain structural properties of the protein products
themselves (Koziel et al.).
We would like to dedicate this volume to the memory of Hans Kossel, our colleague and friend, and also
coauthor of one of the chapters (Meier et al.) of this book, who passed away suddenly in December 1995. For
many years Hans Kossel was a Professor of Molecular Biology and Genetics at the University of Freiburg, Ger
many. His research focused on various aspects of the chemistry and biology of nucleic acids. His more recent work
on the structure and function of chloroplastgenomes culminated in the discovery of RNA editing in these organelles.
Witold Filipowicz and
Thomas Hohn
Guest Editors
iii
Hans Kossel (1934-1995)
Plant Molecular Biology 32: iv-viii, 1996. iv
List of Contributors
RNA processing and stability
Splicing of precursors to messenger RNA in higher
plants: mechanism, regulation and sub-nuclear organ PJ. Green
isation of the spliceosomal machinery Plant Research Laboratory
Michigan State University
G.G. Simpson East Lansing, MI 48824-1312
Friedrich Miescher Institute USA
P.O. Box 2543 Phone: [phone]
CH-4002 Basel Fax: [phone]
Switzerland E-mail: [email protected]
Phone: [phone]
Fax: [phone] RNA as a target and an initiator of post-transcriptional
E-mail: [email protected] gene silencing in transgenic plants
W. Filipowicz D.C. Baulcombe
Friedrich Miescher Institute The Sainsbury Laboratory
P.O. Box 2543 Norwich Research Park
CH-4002 Basel Colney
Switzerland Norwich NR4 7UH
Phone: [phone] UK
Fax: [phone] Phone: [phone]
E-mail: filipowi@fmLch Fax: [phone]
E-mail: [email protected]
Plant mRNA 3' -end formation
RNA structure and regulation of gene expression
H.M. Rothnie
Friedrich Miescher Institute P. Klaff
P.O. Box 2543 Heinrich-Heine-Universitat Dusseldorf
CH-4002 Basel Institut fUr Physikalische Biologie
Switzerland Universitatsstrasse 1
Phone: [phone] D-40225 Dusseldorf 1
Fax: [phone] Germany
E-mail: [email protected] Phone: [phone]
Fax: [phone]
Control of mRNA stability in higher plants
D. Riesner
M.L. Abler Heinrich-Heine-Universitat Dusseldorf
Plant Research Laboratory Institut fur Physikalische Biologie
Michigan State University Universitatsstrasse 1
East Lansing, MI 48824-1312 D-40225 Dusseldorf 1
USA Germany
Phone: [phone] Phone: [phone]
Fax: [phone] Fax: [phone]
v
G. Steger Fate of translation products
Heinrich -Heine-U niversitat Dusseldorf
Institut fUr Physikalische Biologie Molecular chaperones and protein folding in plants
Universitatsstrasse 1
D-40225 Dusseldorf 1 R.S. Boston
Germany Department of Botany
Phone: [phone] North Carolina State University
Fax: [phone] Raleigh, NC 27695
USA
Translation
P. Viitanen
The plant translational apparatus Dupond de Nemours Co.
Central Research and Development
K.S. Browning Bldg,402
Department of Chemistry Wilmington, DE 19880-0402
University of Texas USA
Austin, TX 78712-1096 Phone: [phone]
USA Fax: [phone]
Phone: [phone] or 4562
Fax: [phone] E. Vierling
E-mail: [email protected] Department of Biochemistry
University of Arizona
Translation control of cellular and viral mRNAs Tucson, AZ 85721
USA
D.R. Gallie Phone: [phone] or 3977
Department of Biochemistry Fax: [phone]
University of California E-mail: [email protected]
Riverside, CA 92521
USA Transport of proteins in eukaryotic cells: more
Phone: [phone] questions ahead
Fax: [phone]
M. Bar-Peled
Translation in plant-rules and exceptions Plant Research Laboratory
Michigan State University
J. Futterer East Lansing, MI 48824-1312
Institute of Plant Sciences USA
ETZ Phone: [phone]
Universitatsstrasse 2 Fax: [phone]
CH-8092 Zurich
Switzerland D.C. Bassham
Fax: [phone] Plant Research Laboratory
Michigan State University
T. Hohn East Lansing, MI 48824-1312
Friedrich Miescher Institute USA
P.O. Box 2543 Phone: [phone]
CH-4002 Basel Fax: [phone]
Switzerland
Phone: [phone]
Fax: [phone]
E-mail: [email protected]