The LAB FAX series Series Editors: B.D. HAMES Department of Biochemistry and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK D. RICKWOOD Department of Biology, University of Essex, Wivenhoe Park, Colchester C04 3SQ, UK MOLECULAR BIOLOGY LABFAX CELL BIOLOGY LABFAX CELL CULTURE LABFAX BIOCHEMISTRY LABFAX VIROLOGY LABFAX PLANT MOLECULAR BIOLOGY LABFAX Forthcoming titles IMMUNOCHEMISTRY LABFAX BACTERIOLOGY LABFAX EIMZYMOLOGY LABFAX CELLULAR IMMUNOLOGY LABFAX PLANT MOLECULAR iD(ô)[L©il LABRAX EDITED BY R.R.D. CROY Department of Biological Sciences, University of Durham, Science Laboratories, South Road, Durham, DH1 3LE, UK BIOS SCIENTIFIC PUBLISHERS ACADEMIC PRESS BIOS Scientific Publishers Limited, St Thomas House, Becket Street, Oxford OX 1 1SJ ©BIOS Scientific Publishers Limited, 1993 All rights reserved by the publisher. No part of this book may be reproduced or transmitted, in any form or by any means, without permission in writing from the publisher. ISBN 0 12 198370 6 A CIP catalogue entry for this book is available from the British Library. This Edition published jointly in the United States of America by Academic Press, Inc. and BIOS Scientific Publishers Limited. Distributed in the United States, its territories and dependencies, and Canada exclusively by Academic Press, Inc., 1250 Sixth Avenue, San Diego, California 92101 pursuant to agreement with BIOS Scientific Publishers Limited, St Thomas House, Becket Street, Oxford OX1 1 SJ, UK. The cover illustration is based on an original design by Marianne K. Croy Typeset by Unicus Graphics Ltd, Horsham, UK. Printed by Information Press Ltd, Oxford, UK. The information contained within this book was obtained by BIOS Scientific Publishers Limited from sources believed to be reliable. However, while every effort has been made to ensure its accuracy, no responsibility for loss or injury occasioned to any person acting or refraining from action as a result of the information contained herein can be accepted by the publishers, authors or editors. PREFACE Plant Molecular Biology Labfax is a companion text to its successful forerunner Molecular Biology Labfax, edited by Terry Brown from UMIST, and published 2 years ago. Plant molecular biology has undergone a spectacular expansion over the last 5 years both as an applied science and as an intellectually testing discipline in its own right. The recent appearance of several new journals specializing in the molecular aspects of plant biology and the widespread acceptance of plant molecular biology papers in the established plant journals, are testimony to this development. It is therefore timely for such a laboratory databook as Plant Molecular Biology Labfax to be produced in support of this technology. Plant molecular biology has evolved into a multi-disciplinary science utilizing a great many technologies and I hope that this is reflected in the specialized subject areas covered by the different chapters in Plant Molecular Biology Labfax. These range from simple, though essential, aspects of plant anatomy and classification, to practical details of plant transforma- tion and data on plant nucleic acids and genes, through to highly specialized topics of study such as chloroplast molecular biology, plant gene introns and transposable elements. Although plants have a number of unique biological features amongst living organisms, the manipulation of plant nucleic acids is not a special technology — DNA has more or less the same chemistry irrespective of its source; it can be manipulated using the same enzymes and cloned using the same vectors. Several sections in Plant Molecular Biology Labfax contain information and data of general utility to molecular biologists, for example, Chapter 2 contains details of genomic DNA and RNA isolation techniques, and Chapter 10 deals with PCR technology and gene expression. In this respect I hope that the scientific community will regard Plant Molecular Biology Labfax as a companion text which complements Molecular Biology Labfax and reserve a place for it on the laboratory bench. Wherever practicable the accuracy of the data presented in this book has been checked and most of the information was up-to-date at the time of publication. Inevitably in such a large collection of data and information, mistakes can occur and data rapidly becomes out of date and so I would be grateful to readers for any corrections, additions and constructive comments which might be incorporated into future editions. In editing and writing Plant Molecular Biology Labfax, I concur with Terry Brown on his point about needing to be slightly unbalanced to compile such a databook — I too found that the compilation and presentation of data was almost addictive — many of the one page entries and graphs took several days to arrange and present in a form which was deemed easier to use or clearer for the user to understand. All scientists should experience the challenge of collecting and compiling large amounts of data, if only to appreciate the substantial effort and stamina that is required for the production of such texts, which around the lab are very much taken for granted. The production of this book would not have been possible without the suggestions and contributions from my fellow molecular biologists and also the stimulation and interest in PREFACE ν plant molecular sciences imparted by my past supervisors, for which I am deeply indebted. My particular thanks go to my expert co-contributors listed in the following pages. On a sad note, the final stages of production of this book were marred by the untimely death of one of the contributors, Ray Ellis, who fell foul of the changeable weather conditions in the Cairngorm mountains — an area which he loved and visited often. Ray will be sadly missed by his many friends and colleagues and plant science will be all the poorer for this loss. Finally, special thanks are due to my wife, Liz, for her constant encouragement and support during the lengthy preparation of this book, and who even resorted to writing several of the specialized contributions in order to speed up the submission of the final manuscript. R.R.D. Croy vi PLANT MOLECULAR BIOLOGY LABFAX CONTRBIUTORS J. BROWN Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK E.J. CROY Department of Biological Sciences, University of Durham, South Road, Durham DH1 3LE, UK R.R.D. CROY Department of Biological Sciences, University of Durham, South Road, Durham DH1 3LE, UK T. DYER Cambridge Laboratory, AFRC Institute of Plant Sciences Research, John Innes Centre, Colney, Norwich NR4 7UJ, UK fJ.R. ELLIS ICI Seeds, Jealotts Hill Research Station, Bracknell RG12 6EY, UK I.M. EVANS Department of Biological Sciences, University of Durham, South Road, Durham DH1 3LE, UK A. FORDHAM-SKELTON Department of Biology, Colorado State University, Fort Collins, CO 80523, USA T. FRANKLIN Hybaid, 111-113 Waldegrave Road, Teddington TW11 8LL, UK P. GATES Department of Biological Sciences, University of Durham, South Road, Durham DH1 3LE, UK t Deceased, 1993. CONTRIBUTORS xiii F. GUERINEAU Department of Botany, University of Leicester, University Road, Leicester LEI 7RH, UK D.L HERRIN Department of Botany, University of Texas at Austin, Austin, TX 8713, USA C.J. HOWE Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK T. IKEMURA National Institute of Genetics, Mishima, Shizuoka-ken 411, Japan M. LATTERICH Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA D.J. LEADER Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK P. MULLINEAUX Department of Applied Genetics, John Innes Institute, Colney Lane, Norwich NR4 7UJ, UK A. SHIRSAT School of Biological Sciences, University of Wales at Bangor, Bangor, Gwynned LL57 2UW, UK CG. SIMPSON Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK A. THOMPSON Department of Molecular Biology, Horticultural Research International, Littlehampton, Sussex, UK IP. WALLACE Scotgen Ltd, Aberdeen, UK xiv PLANT MOLECULAR BIOLOGY LABFAX ABBREVAITOINS aa amino acid AFLPs amplification-fragment-length-polymorphisms ALA ό-aminolevulinic acid ALS acetolactate synthase ANS 8-anilino-l-naphthalene sulfonic acid APCR anchored PCR ATA aurintricarboxylic acid ATPase adenosine triphosphatase CaMV cauliflower mosaic virus CAT chloramphenicol acetyltransferase cDNA complementary DNA cpDNA chloroplast DNA DAPI diamidino phenolindole dc7GTP 7-deaza-2'deoxyguanosine DCMU 3-(3,4-dichlorophenyl)-1,1-dimethylurea DEPC diethylpyrocarbonate DHFR dihydrofolate reductase dicot dicotyledonous (plant) DMSO dimethylsulfoxide DNA deoxyribonucleic acid DTPA diethylenetriaminepentaacetic acid EDTA ethylenediaminetetraacetic acid ELISA enzyme-linked immunosorbent assay EPSPS 5-enolpyruvylshikimate-3-phosphate synthase ER endoplasmic reticulum EtBr ethidium bromide GUS ^-glucuronidase IPCR inverse PCR LHC light-harvesting complex LM-PCR ligation-mediated PCR Luc luciferase (firefly gene) LUX luciferase (bacterial gene) MES 2-morpholinoethanesulfonic acid MOPAC mixed oligonucleotide primer amplification mRNA messenger RNA monocot monocotyledonous (plant) MUG 4-methylumbelliferyl glucuronide NPT neomycin phosphotransferase ORF open reading frame PAGE Polyacrylamide gel electrophoresis PCR polymerase chain reaction ABBREVIATIONS xiii PEG polyethylene glycol pre-mRNA precursor mRNA PSI photosystem I PSII photosystem II RACE rapid amplification of cDNA ends RAPD randomly amplified polymorphic DNA rDNA ribosomal RNA genes RFLP restriction fragment length polymorphism RH Β right-hand border RT-PCR reverse transcription-PCR Rubisco ribulose bisphosphate carboxylase/oxygenase SDDTC disodium diethyldithiocarbamate SDS sodium dodecyl sulfate snRNAs small nuclear RNAs snRNPs small nuclear ribonucleoprotein particles T-DNA transfer DNA TINS tri-isopropylnaphthalene 1,5 disulfonate TLC thin-layer chromatography TMAC tetramethylammonium chloride UsnRNAs uracil-rich small nuclear RNAs uv ultraviolet VRCs vanadyl ribonucleoside complex w/v weight/volume X-Gal 5-bromo-4-chloro-3-indolyl-ß-D-galactoside X-Gluc 5-bromo-4-chloro-3-indolyl ß-D-glucuronide YAC yeast artificial chromosome xvi PLANT MOLECULAR BIOLOGY LABFAX CHAPTER 1 PLANT A N A T O M Y, HISTOLOGY A ND T A X O N O MY FOR MOLECULAR BIOLOGISTS P. Gates This brief guide provides an introduction to some basic elements of plant anatomy and histology, and information on simple methods for the examination of plant tissues. Users should be aware that the anatomical information is of a very generalized nature and that many variations are likely to be encountered on the basic ground plans of tissue anatomy described here. Detailed references to the tissue structure o fvarious economic plants can be found in the references (1,2). 1. HISTOLOGY: PLANT CELL TYPES 1.1. Parenchyma Living cells (Figure 1). Usually isodiametric (c. 25-50 μτη). Form the bulk of plant packing tissue. MetabolicaUy active with large intercellular space sand thin walls. Often modified for storage of lipids, proteins and starch. 1.2. Epidermis Living, flattened and elongated cells (Figure 2). Cover the surface of the plant. Protective (often covered with cutin) and sometimes secretory. Epidermal cells are often modified into protective or secretory hairs (trichomes). 1.3. Mesophyll Living cells, primarily active in leaf photosynthesis. Divided into a pallisade layer of columnar cells under the leaf adaxial surface (facing the stem) and the more irregular, roughly iso- diametric spongy mesophyll cells above the leaf abaxial surface. The spongy mesophyll is loosely packed, with large intercellular air spaces (see Figure 10). Figure 1. Parenchyma cells. Cell wall -Nucleus Peripheral cytoplasm Vacuole Intercellular space 25 μιη ANATOMY, HISTOLOGY, TAXONOMY 1