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PLANT MOLECULAR BIOLOGY MANUAL

PLANT MOLECULAR BIOLOGY MANUAL

Second edition

Edited by

STANTON B. GELVIN

Purdue University, West Lafayette, Indiana, USA

ROBBERT A. SCHILPEROORT

Leiden University, Leiden, the Netherlands

Kluwer Academic Publishers Dordrecht I Boston I London

Supplement 2 ISBN 0--792~205-4

Neither Kluwer Academic Publishers nor any person acting on its behalf is responsible for the use which might be made of the information contained herein.

Published by Kluwer Academic Publishers, P.O. Box 17,3300 AA Dordrecht, The Netherlands.

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All Rights Reserved © 1997 Kluwer Academic Publishers

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Plant Molecular Biology Manual, 2nd Edition Supplement 2, 1997

INSTRUCTIONS FOR SUPPLEMENT 2

Preliminary pages Pages I-XV should be replaced by new pages i-xviii.

Section C Add after Chapter C3:

Chapter C4:

Chapter C5:

Section F Add after Chapter F4:

Chapter F5:

Chapter F6:

Section G Add after Chapter G3:

Index Replace

Chapter G4:

H. Knight, A.J. Trewavas & M.R. KnightlRecombi­nant aequorin methods for measurement of intra­cellular calcium in plants

Jeong Hee Lee & F. SchOfflIGUS activity staining -a powerful tool in plant molecular biology

M.J. LaskowskilRNA differential display

A. Fischer, G. Theissen & H. SaedlerlExpression analysis of mUltigene families by RFLP-coupled domain-directed differential display (RC4D)

Ho-Hyung WoolIn-cell RT-PCR in a single, de­tached plant cell

Contents

SECTION A: IN VITRO METHODS OF GENE TRANSFER TO PLANT CELLS

1. PEG-mediated direct gene transfer and electroporation Roland Bilang, Andreas Kloti, Martin Schrott & logo Potrykus

2. Gene transfer to plants via particle bombardment Paul Christou

SECTION B: AGROBACTERIUM-MEDIATED GENE TRANFER TO PLANT CELLS

1. Agrobacterium-mediated gene transfer to plant cells: Cointegrate and binary vectors Cindy R. Walkerpeach & J. Velten

2. Specialized vectors for gene tagging and expression studies Csaba Koncz, Norbert Martini, Uszl6 Szabados, Milan Hrouda, Andreas Bachmair & Jeff Schell

3. Agrobacterium molecular genetics Paul J.J. Hooykaas

4. Genetic manipulation of Agrobacterium tumefaciens strains to improve transformation of recalcitrant plant species Stanton B. Gelvin & Chang-Nong Liu

5. Transient expression assays using GUS constructs and fluorometric detection for analysis of T-DNA transfer Linda A. Castle & Roy O. Morris

6. Agrobacterium inoculation techniques for plant tissues Nancy L. Mathis & Maud A.W. Hinchee

SECTION C: SELECTABLE AND SCREENABLE MARKERS FOR PLANT TRANSFORMATION

1. Antibiotic-resistance markers for plant tranformation M. van Montagu

2. Reporter genes for plants Luis Herrera-Estrella, Patricia Le6n, Olof Olsson & Teemu H. Teeri

3. Opines as screenable markers for plant transformation Yves Dessaux & Annik Petit

x

**4. Recombinant aequorin methods for measurement of intracellular calcium in plants H. Knight, A.J. Trewavas & M.R. Knight

**5. GUS activity staining - a powerful tool in plant molecular biology Jeong Hee Lee & F. SchOffl

SECTION D: NUCLEIC ACID EXTRACTION FROM PLANT TISSUE

1. Extraction of total cellular DNA from plants, algae and fungi Scott O. Rogers & Arnold J. Bendich

2. Isolation and characterization of nuclear scaffolds Gerald E. Hall, Jr. & Steven Spiker

3. Isolation of plant mitochondria and mitochondrial nucleic acids Sally A. Mackenzie

4. Isolation of chloroplasts and chloroplast DNA C.A. Price, Nourredine Hadjeb, Lee Newman & Ellen M. Raerdon

5. Isolation of total, poly (A) and polysomal RNA from plant tissues Katharina Pawlowski, Reinhard Kunze, Jacco de Vries & Ton Bisseling

SECTION E: TRANSCRIPTION AND TRANSLATION SYSTEMS

1. Assay for gene expression using run-on transcription in isolated nuclei Imre E. Somssich

2. Preparation of an in vitro transcription system of plant origin, with methods and templates for assessing its fidelity Yukki Yamaguchi, Fujio Mukumoto, Hidemasa Imasehi & Ken-Ichi Yamazaki

SECTION F: BLOTTING AND GENE DETECTION SYSTEMS

1. Southern, Northern and Western blot analysis Johan Memelink, Kathleen M.M. Swords, L. Andrew Staehelin & J. Harry C. Hoge

2. Screening of cDNA expression libraries with synthetic oligonucleotides for DNA binding proteins Wolfgang Werr, Barbel Uberlacker & Bethina Klinge

3. Non-radiative nucleic acid detection systems Susan J. Karcher

** Included in Supplement 2.

4. Polymerase chain reaction: gene detection. inverse PCR and genetic engineering Jerry L. Slightom. Roger F. Drong & Paula P. Chee

**5. RNA differential display M.J. Laskowski

**6. Expression analysis of multigene families by RFLP-coupled domain-directed differential display (RC4D) A. Fischer. G. Theissen & H. Saedler

xi

SECTION G: IN SITU HYBRIDIZATION AND IMMUNODETECTION

1. RNA in situ hybridization in plants Nicholas B. Duck

2. In situ hybridization to plant metaphase chromosomes using digoxigenin labeled nucleic acid sequences S. Hinnisdaels. I. Farbos. J. Del-Favero. J. Veuskens. M. Jacobs & A. Mouras

*3. Light microscopic applications of immunocytochemistry K. Vandenbosch. D.J. Sherrier & D.A. Dreyer

**4. In-cell RT-PCR in a single. detached plant cell Ho-Hyung Woo

SECTION B: CLONING AND DETECTION OF DNA SEQUENCES FROM LARGE DNA MOLECULES

1. Methods for generating plant genomic libraries Marjory A. Snaed. Patricia L. Kretz & Jay M. Short

2. Construction of plant yeast artificial chromosome libraries Gregory B. Martin

3. Preparation of heigh molecular weight plant DNA and analysis by pulsed field gel electrophoresis Raymond A.J.J. van Daelen & Pim Zabel

4. Random amplified polymorphic DNA (RAPD) markers Anton Rafalski. Scott Tingey & John G.K. Williams

* Included in Supplement 1. ** Included in Supplement 2.

xii

SECTION I: PROTEIN-NUCLEIC ACID INTERACTION ANALYSES

1. Gel mobility shift assay Koji Mikami, Hisabumi Takase & Masaki Iwabuchi

2. Optimization of DNAse I footprinting experiments Susan J. Martino-Catt & Steve A. Key

3. Analysis of plant chromatin and in vivo protein-DNA interactions Robert J. Ferl & Anna-Lisa Paul

4. Expression and characterization of recombinant plant trans-acting factors Eric Lam & Lee Meisel

SECTION J: SUBCELLULAR TARGETTING OF POTEINS

1. In vitro import of proteins into chloroplasts Barrj D. Bruce, Sharyn Perry, John Froehlich & Kenneth Keegstra

2. In vitro targetting of proteins to mitochondria Marc A. Boutry, Didier Thomas & Fran~ois Chaumont

3. Targetting of proteins to the vacuole James E. Dombrowski, Luis Gomez, Maarten J. Chrispeels & Natasha V. Raikhel

4. Visualizing protein import into the plant cell nucleus Vitaly Citovsky

SECTION K: GENE TAGGING USING TRANSPOSONS

1. Gene tagging by endogenous transposons Wolf-Ekkehard Lonnig & Peter Huijser

2. Heterologous transposon tagging as a tod for the isolation of plant genes Erik A. van der Biezen, Mark J.J. van Haaren, Bert Overduin, H. John J. Nijkamp & Jacques Hille

*3. T-DNA tagging in Arabidopsis thaliana: Cloning by gene disruption B. Schulz, M.J. Bennett, B.P. Dilkes & K.A. Feldman

SECTION L: VIRAL MEDIATED GENE TRANSFER

*1. High level gene expression in plants using RNA viruses as transient expression vectors C.M. Kearney, S.N. Chapman, T.H. Turpen & W.O. Dawson

* Included in Supplement 1.

*2. Caulimovirus mediated gene transfer I. Jupin & B. Gronenbom

*3. Gerninivirus mediated gene transfer D.M. Bisaro & G. Sunter

* Index

* Included in Supplement 1.

xiii

xiv

List of Contributors

Author Chapter Address

Bendich, A.J. Dl Botany Dept. KB-15, University of Washing-ton, Seattle WA 98195, USA

Bennett, M.J. K3 University of Warwick, Dept. of Biological Sciences, Coventry CV4 7AL, Great Britain

Bisaro, D.M. L2 Ohio State University, Biotechnology Center, 1060 Carmack Road, Columbus OH 43210, U.S.A.

Bisseling, T. D5 Dept. of Molecular Biology, Transitarium, Dreyeolaan 3, 6703 HA Wageningen, The Netherlands

Boutry, M.A. J2 Biochemie Physiology, University of Lou-vain, Croix du Sud 2-20, 1348 Louvain-La-Neuve, Belgium

Castle, L.A. B5 Oklahoma State University, Botany LSE 104, Stillwater OK 74078, USA

Chapman, S.N. L1 University of Florida, CREC, Lake Alfred, FL 33850, USA

Chee, P.P. F4 Molecular Biology Unit 7242, The Upjohn Company, Kalamazoo, MI 49007, USA

Christou, P A2 Agracetus, Inc., Research & Development, 8520 University Green, Middleton WI 53562, USA

Citovsky, V. J4 U.C. Berkeley, Plant Biology, Berkeley CA 94720, USA

Dawson, W.O. L1 University of Florida, CREC, Lake Alfred, FL 33850, USA

Dessaux, Y. C3 Institut des Sciences Vegetaies, Biitiment 23 C.N.R.S., Avenue de la Terrasse, 91198 Gif-sur-Yvette Cedex, France

Dilkes, B.P. K3 University of Arizona, Dept. of Plant Sci-ences, Tucson, Arizona 85721, USA

Dreyer, D.A. G3 Texas A & M University, Biology Dept., College Station, TX 77843-3258, USA

Drong, R.E F4 Molecular Biology Unit 7242, The Upjohn Company, Kalamazoo, MI 49007, USA

Duck, N. Gl Monsanto Company, 700 Chesterfield Village Parkway, St. Louis MO 63198, USA

Feldmann, K.A. K3 University of Arizona, Dept. of Plant Sci-ences, Tucson, Arizona 85721, USA

Ferl, R.J. I3 Dept. of Botany, University of FLorida, Gainesville FL 32611, USA

xv

Fischer, A. F6 c/o F. Hoffmann-LaRoche AG, PRPG 66n04, Grenzacherstrasse, CH-4070 Basel, Switzerland

Gelvin, S.B. B4 Dept. of Biological Sciences, Purdue Univer-sity, Lilly Hall of Life Sciences, West Lafay-ette IN 47907, USA

Gronenbom, B. L3 C.N.R.S., Institut des Sciences Vegetales, 91198 Gif-sur -Yvette, France

Hille, J. K2 Genetics, Free University, De Boelelaan 1007, 1001 HV Amsterdam, The Netherlands

Hinchee, M. B6 Monsanto, Plant Protection Improvement, 700 Chesterfield VP, St. Louis MO 63198, USA

Hooykaas, P.J.J. B3 Clusius Laboratory, Wassenaarseweg 64, 2333 AL Leiden, The Netherlands

Huijser, P. K1 MPI fUr Ziichtungsforschung, Carl von Linne Weg 10,5000 KOln 30, Germany

Iwabuchi, M. 11 Kyoto University, Faculty of Science/botany, Ktrashirikawa, Kyoto 606-01, Japan

Jacobs, M. G2 Plantengenetica VUB, University of Brus-sels, Paardenstraat 65, St. Genesius Rode, 1640 Belgium

Jupin, I. L3 Institut des Sciences Vegetales, CNRS, 91198 Gif sur Yvette, Cedex, Fran~e

Karcher, S.J. F3 Dept. of Biological Sciences, Purdue Univer-sity, B-315 Lilly Hall, W. Lafayette IN 47907-13902, USA

Kay, S.A. 12 Dept. of Biology, Gilmer Hall, University of Virginia, Charlottesville WV 22901, USA

Kearney, C.M. L1 University of FLorida, CREC, Lake Alfred FL 33850, USA

Keegstra, K. 11 University of Wisconsin, Dept. of Botany, 430 Lincoln Drive, Madison WI 53706, USA

Knight, H. C4 University of Oxford, Dept. of Plant Sci-ences, Oxford, OXI 3RB, UK

Knight, M.R. C4 University of Oxford, Dept. of Plant Sci-ences, Oxford, OXI 3RB, UK

Koncz, C. B2 Max-Planck Institut fUr Ziichtungsforschung, 5000 KOln 30, Germany

Lam,E. 14 Rutgers University, AgroBiotech Center, Waksman University, Piscataway NJ 08854, USA

Laskowski, M.J. F5 Dept. of Biology, Williams College, William-stown, MA 01267, USA

xvi

Lee, leong Hee C5 Universitat Tiibingen, Lehrstuhl flir Allge-meine Genetik, Auf der Morgenstelle 28, 0-72076 TUbingen, Germany

MacKenzie, S. 03 Dept. of Agronomy, Lilly Hall of Life Sci-ences, Purdue University, Lafayette IN 47907, USA

Martin, G.B. H2 Purdue University, Dept. of Agronomy, 1150 Lilly Hall, West Lafayette IN 47907-1150, USA

Memelink, 1. Fl Clusius Lab.lMolecular Plant Sciences Inst., Leiden University, Wassenaarsewag 64, 2333 AL Leiden, The Netherlands

Potrykus, 1. Al Institute of Plant Sciences, Eth Zentrum LFV-E20, 8092 Ziirich, Switzerland

Price, C.A. D4 Waksman Institute, Rutgers State University, Piscataway Nl 08855-0759, USA

Rafalski, A. H4 DuPont Co. Agricultural Products & Bio-technology, P.O. Box 80402, Wilmington DE 19880-0402, USA

Raikhel, N. 13 Michigan State University, Plant Research Laboratory, East Lansing MI 48824, USA

Saedler, H. F6 Max-Planck-Institut flir Ziichtungsforschung, Carl-von-Linne-Weg 10,0-50829, KOln, Germany

SchOffl, F. C5 Universitat Tiibingen, Lehrstuhl flir Allge-meine Genetik, Auf der Morgenstelle 28, 0-72076 Tiibingen, Germany

Schulz, B. K3 University of Arizona, Dept. of Plant Sci-ences, Tucson, Arizona 85721, USA

Sherrier, 0.1. G3 Texas A & M University, Biology Dept., College Station, TX 77843-3258, USA

Slightom,l.L. F4 Molecular Biology Unit 7242, The Up john Co., Kalamazoo MI 49007-0199, USA

Snaed, M. HI Strategene Cloning Systems, La 10lla CA 92037, USA

Sommsich, I.E. El Max-Planck Institut, Biochemie, Carl von Linne Weg 10, 5000 KOln 30, Germany

Spiker, S. 02 3530 Gardner Hall, North Carolina State University, Raleigh NC 27695, USA

Sunter, G. L2 Ohio State University, Biotechnology Center, 1060 Carmack Road, COlumbus OH 43210, USA

Teeri, T. C2 Dept. of Genetics, University of Helsinki, Arkadiankatu 7, 00100 Helsinki, Finland

Theissen, G.

Trewavas, AJ.

Turpen, T.H.

Vandenbosch, K.

Van Montagu, M.

Velten, J.

Werr, W.

Woo, Ho-Hyung

Yamazaki, K.

Zabel, P.

F6

C4

L1

G3

Cl

Bl

F2

G4

E2

H3

xvii

Max-Planck -Institut fUr Ztichtungsforschung, Carl-von-Linne-Weg 10, D-50829, K61n, Germany University of Edingburgh, Institute of Cell and Molecular Biology, Edinburgh, EH9 3JH, UK Biosource Genetics Corporation, 3333 Vaca Valley Pkwy., Vacaville, CA 957688, USA Texas A & M University, Biology Dept., College Station TX 77843, USA Laboratorium Genetica, University Gent, Ledeganckstraat 35, 9000 Gent, Belgie P.G.E.L., New Mexico State University, Box 3GL, Las Cruces NM 88003, USA Institut flir Genetik, Universitiit zu K61n, Germany University of Zrizona, Dept. of Plant Pathol­ogy and Molecular and Cellular Biology, Tucson, AZ 85721, USA Research Institute for Biochemical Regula­tion, School of Agricultural Sciences, Nagoya University, Nagoya, 46401, Japan Dept. of Molecular Biology, Agriculture Uni­versity, Dreyenlaan 3, 6703 HA Wageningen, The Netherlands