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Viral Infection and Propagation in Plant Tissue Culture

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Viral Infection and Propagation in Plant Tissue Culture Viral Infection and Propagation in Plant Tissue Culture by FIONA STELLA SHADWICK Thesis submitted for the degree of Doctor of Philosophy School of Biotechnology and Biomolecular Sciences University of New South Wales January 2007 ACKNOWLEDGEMENTS I wish to thank Professor Pauline Doran for her guidance, encouragement and generous support. I also wish to extend my gratitude to the staff of the school; in particular I would also like to thank Mr. Malcolm Noble, Dr. Russell Cail and Dr. David Chin for their technical advice and assistance. I also wish to thank Caleb Chung from his assistance with HPLC analysis and the assembly and operation of bioreactors. I wish to thank my husband and family for their patience and encouragement. For their companionship and generosity I thank my fellow laboratory members. i TABLE OF CONTENTS page Table of Contents i Abstract xiv CHAPTER 1 – INTRODUCTION 1.1 Foreign Protein Expression in Whole Plants 1 1.1.1 Plants as expression systems 1 1.1.1.1 Expression systems 1 1.1.1.2 Plant-based expression systems 2 1.1.2 Heterologous protein production in whole plants 3 1.1.3 Approaches to increase protein yield 4 1.1.3.1 Promoter sequences 4 1.1.3.2 Protein targeting 6 1.1.3.3 Sequence optimisation 7 1.1.3.4 Alternate host plants 8 1.1.3.5 Plastid expression 8 1.1.3.6 Virus-based expression systems 9 1.2 Plant Tissue Culture 11 1.2.1 Undifferentiated plant tissue culture 11 1.2.2 Differentiated organ culture 12 1.2.2.1 Root cultures 12 Untransformed root cultures 13 Transformed “hairy root” cultures 13 1.2.2.2 Shoot cultures 16 1.3 Plant Tissue Culture as a Production System for Heterologous Proteins 17 1.3.1 Foreign protein production using plant tissue culture 19 1.3.2 Increasing protein expression and recovery 24 1.3.2.1 Increased protein expression 24 Promoter sequences 25 Protein targeting 26 Culture species and type 26 ii Alternate transformation 28 Bioprocess developments 29 1.3.2.2 Increased protein recovery 29 1.4 Plant Viruses as Vectors 32 1.4.1 Plant viruses 32 1.4.2 Plant-virus-based vectors 34 1.4.3 Vector design 36 1.4.4 Approaches for foreign protein expression 38 1.4.4.1 Fusions 38 1.4.4.2 Free proteins 40 Additional open reading frames 41 Expression of foreign proteins as part of the viral polyprotein 41 1.5 Foreign Protein Expression Using Plant Viral Vectors 42 1.5.1 Stability 50 1.5.2 Movement of plant viral vectors 51 1.5.3 Vector and foreign protein accumulation 53 1.5.3.1 Accumulation of viral vectors 54 1.5.3.2 Accumulation of foreign proteins 55 1.5.4 Safety 56 1.6 Tobacco Mosaic Virus 58 1.6.1 Virus structure 58 1.6.2 Genome organization and encoded product function 60 1.6.3 Early events in TMV infection 62 1.6.4 TMV replication and movement 63 1.6.4.1 Virus replication 63 1.6.4.2 Viral movement 64 Cell-to-cell movement 65 Long-distance movement 66 1.7 Tobacco Mosaic Virus as a Vector 67 1.7.1 30B vector 68 1.7.2 30B-GFPC3 70 1.7.3 Movement, host range and stability of 30B and 30B-GFPC3 70 iii 1.7.3.1 Vector stability 71 1.7.3.2 Host range and movement 71 1.8 TMV Infection of Plant Roots 72 1.8.1 TMV accumulation in roots from whole plants 72 1.8.2 TMV accumulation in cultured roots 74 1.9 Virus Infection of Cultured Plant Cells 75 1.9.1 Infection of cultured cells with virus 80 1.9.1.1 Initiation of infection in cultured cells 80 Intentional cell wall injury 80 Natural cell wall breaks 82 1.9.1.2 Culture characteristics 84 1.9.1.3 Culture age 85 1.9.1.4 Viral inoculum 86 1.9.2 Characteristics of viral accumulation in tissue culture 87 1.9.2.1 Kinetics of viral accumulation 87 Viral accumulation in plant cell protoplasts 88 Viral accumulation in plant suspension and callus cultures 89 1.9.2.2 Viral yield 94 1.9.2.3 Effect of viral infection on culture growth 96 1.10 Project Aims 97 CHAPTER 2 – MATERIALS AND METHODS 2.1 Cultures 98 2.1.1 Plant material 98 2.1.2 Viral material 98 2.1.3 Bacterial cultures 98 2.2 Media 99 2.2.1 Plant culture media 99 2.2.2 Bacterial culture media 100 2.3 Initiation and Maintenance of Plant Cultures 101 2.3.1 Surface sterilisation and germination of seeds 101 2.3.2 Maintenance of axenic plantlets 102 iv 2.3.3 Hairy root cultures 102 2.3.3.1 Initiation of Nicotiana benthamiana hairy root cultures 102 2.3.3.2 Maintenance of hairy root cultures 104 2.3.4 Callus and suspension cultures 104 2.3.4.1 N. benthamiana callus and suspension cultures 104 2.3.4.2 N. tabacum callus and suspension cultures 105 2.4 Growth of Plants in Soil 106 2.4.1 N. tabacum plants 106 2.4.2 N. glutinosa plants 106 2.4.3 N. benthamiana plants 107 2.5 Production of TMV 107 2.5.1 Infection of N. tabacum plants with TMV 107 2.5.2 Purification of TMV 108 2.5.3 Concentration and purity of TMV preparations 110 2.6 Production of Transgenic Virus 111 2.6.1 Transformation of E. coli XL1-Blue with plasmid 30B-GFPC3 111 2.6.2 Production of in vitro transcript of 30B-GFPC3 111 2.6.3 Infection of plants with 30B-GFPC3 RNA transcript 112 2.6.4 Purification of TMV-GFPC3 113 2.7 Preliminary Investigations of TMV Accumulation in N. tabacum Suspension and Hairy Root Cultures 114 2.7.1 Growth of N. tabacum suspension and hairy root cultures 114 2.7.1.1 Growth of N. tabacum suspension cultures 114 2.7.1.2 Growth of N. tabacum hairy root cultures 114 2.7.2 Accumulation of TMV in N. tabacum suspension culture 115 2.7.3 Accumulation of TMV in N. tabacum hairy roots 116 2.8 Accumulation of TMV in N. benthamiana Suspension 116 2.9 Accumulation of TMV in N. benthamiana Hairy Roots 118 2.9.1 Selection of N. benthamiana hairy roots with suitable growth and viral accumulation characteristics 119 2.9.2 Time-course of TMV accumulation in N. benthamiana hairy roots 119 v 2.9.3 Effect of hairy root condition at the time of viral inoculation on TMV accumulation 120 2.9.3.1 Effect of root age 120 Variously aged roots in fresh medium 120 Variously aged roots in conditioned media 120 2.9.3.2 Effect of injuring hairy roots prior to viral infection 121 2.9.4 Characteristics of hairy root growth and viral accumulation in N. benthamiana hairy roots over 36 days 122 2.9.5 Effect of medium condition at the time of viral inoculation on TMV accumulation 122 2.9.5.1 Removal of TMV inoculum from cultures after an “inoculation phase” 122 2.9.5.2 Inoculation of hairy roots with virus in phosphate buffer 122 2.9.6 Alteration of viral inoculum concentration 123 2.9.7 Proportional scale-up in shake flasks 123 2.10 Accumulation of TMV in N. benthamiana Hairy Roots with an Established Viral Infection 126 2.10.1 Accumulation of TMV over three generations of culture 126 2.10.2 Effect of increasing the viral inoculum concentration used to initiate a primary viral infection in hairy roots on viral accumulation in a subsequent-generation hairy root culture with an established viral infection 127 2.11 Viral Stability in Medium 128 2.11.1 Viral stability in plant media and phosphate buffer 128 2.11.1.1 Virus stability in fresh media 128 2.11.1.2 Virus infectivity in fresh media 129 2.11.2 Virus characteristics in conditioned media 129 2.11.2.1 Virus stability in conditioned media 130 2.11.2.2 Virus infectivity in conditioned media 130 2.12 Short-Term Virus Association Experiments 131 2.12.1 Concentration of viral inoculum and viral association with hairy roots 131 2.12.2 Viral association with roots during proportional scale-up 131 vi 2.13 Association of Deactivated TMV with Hairy Roots 132 2.13.1 Deactivation of TMV 132 2.13.2 Hairy roots and deactivated virus association 133 2.14 Accumulation of Genetically Modified Virus and GFP in Hairy Roots 134 2.15 Viral Distribution in Hairy Root Clumps in Shake Flasks 134 2.15.1 Distribution of virus in different concentric regions 135 2.15.2 Distribution of virus in radial segments 135 2.16 Accumulation of TMV in N. benthamiana Hairy Roots in a Stirred Bioreactor 136 2.16.1 Bioreactor configuration 136 2.16.2 Bioreactor culture methods 138 2.17 Analytical Procedures 141 2.17.1 Growth 141 2.17.2 Medium characteristics 141 2.17.2.1 Medium pH 141 2.17.2.2 Medium conductivity 142 2.17.2.3 Medium sugar concentration 142 2.17.3 Sample extraction for the analysis of virus, total protein and GFP 143 2.17.3.1 Sample extraction for the detection of virus in plant biomass using ELISA 143 2.17.3.2 Sample extraction for the detection of GFP in plant biomass and for virus detection using Western blot 144 2.17.3.3 Sample extraction for assessment of total soluble protein 145 2.17.4 Quantification and analysis of virus 145 2.17.4.1 Quantification of TMV using ELISA 145 2.17.4.2 Western blot detection of viral coat protein 149 2.17.4.3 Particle size analysis 151 2.17.4.4 Viral infectivity using local lesion assays 152 2.17.5 Detection of GFP 154 2.17.5.1 Detection of GFP using ELISA 154 2.17.5.2 Detection of GFP using Western blotting 156 2.17.5.3 Detection of GFP using fluorescence microscopy 157 vii 2.17.6 Quantification of virus using scanning electron microscopy 158 2.17.7 Total soluble protein 160 2.18 Statistical Analysis 161 CHAPTER 3 – RESULTS 3.1 Tobacco Mosaic Virus Accumulation in N.
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