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Zinc Hyperaccumulation in Thlaspi Caerulescens, the Model Heavy Metal Accumulator Plant

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Zinc Hyperaccumulation in Thlaspi Caerulescens, the Model Heavy Metal Accumulator Plant Zinc Hyperaccumulation in Thlaspi caerulescens By Victoria Mills BSc University of Birmingham MSc (Distinction) University of Nottingham Thesis submitted to the University of Nottingham for the degree of Doctor of Philosophy December 2009 Acknowledgements First and foremost I would like to thank my Mum, Ann, for supporting me both financially and emotionally throughout this course. She has always believed in me and stood by me in my decisions. Without this support and encouragement I would not have achieved everything that I have. I dedicate this thesis to her. Secondly I am grateful for the continued support and belief in me by my fiancé, Phil. Thank you for making sure I was fed during my writing up and for dealing with my stresses! Thanks to my other family members who have always been supportive of me and believed and encouraged me to keep writing, my Grandma Enid, Aunty Vivienne and Uncle Stephen, James and Richard and to my brother and sister, Edward and Emma. Also to my Dad who encouraged me in ways he will never know!! I would like to give a special thank you to my good friend Danny Rigby, my “knight in shining armour” for his expert computer document recovery skills! Thanks for being there to help me in my crisis!! At Nottingham I would like to thank my supervisors Dr M. Broadley and Dr K. Pyke for giving me the opportunity to do my doctoral research, and I would like to thank them for their supervision and guidance. I would like to thank Dr P. White (SCRI) and to Dr J. Hammond, Dr H. Bowen from Warwick HRI for their technical support with Chapter 3. Thanks to PhD students S. O’Lochlainn, for assistance with growing and screening of plants and for continuing on with the research after I left. My thanks go to Dr Fray’s research group, in particular Dr Z. Lui (2006) for his technical support and contribution to chapter 3. Thanks to MSc student A. Patel (2005-6), who under my co-supervision contributed to chapter 4. I am grateful to BSc students who spent time in the lab under my co-supervision, E. Sealey (2004-5) and C. Eustace (2006-7), and who contributed data for Chapters 2 and 5, respectively. I am also grateful for the help from Dr P. Anthony, Ms R. Beacham, Mr M. Meacham and Ms S. Flint. Finally, but by no means least, a special thanks goes to my friend Sarah Kyle- Ferguson, for bringing a smile to the lab and beyond, may we continue to support each other through our teaching careers both emotionally and professionally. v Table of Contents Table of Contents Abstract .................................................................................................................... vi Abbreviations ......................................................................................................... vii 1.Introduction ........................................................................................................... 1 1.1 Zinc is an essential element for plant growth ....................................................... 2 1.1.1 Zn chemical and biological properties .................................................... 2 1.1.2 Zn deficiency in plants ............................................................................ 4 1.1.3 Zn toxicity ............................................................................................... 9 1.1.4 Zinc tolerance vs zinc hyperaccumulation ............................................ 11 1.1.4.1 Sequestering ions in root vacuoles ......................................... 12 1.1.4.2 Mycorrhizas, rhizosphere bacteria .......................................... 14 1.1.4.3 Chelators ................................................................................ 16 1.1.4.3.1 Phytochelatins ........................................................... 16 1.1.4.3.2 Metallothioneins ........................................................ 17 1.1.3.4.3 Organic acids and amino acids ................................. 18 1.2 Species that hyperaccumulate Zinc .................................................................... 18 1.2.1 Elevated Zn soil concentrations and Zn-tolerant plant species ............. 18 1.2.2 Hyperaccumulating plant species ......................................................... 19 1.2.2.1 Ni Hyperaccumulation ............................................................. 21 1.2.2.2 Cd Hyperaccumulation ............................................................ 23 1.2.2.3 Zn Hyperaccumulation ............................................................ 24 1.2.3 Hyperaccumulators; environmental and sociological impacts ............... 33 1.3 The selective advantages of the hyperaccumulation trait ................................... 35 1.4 Mechanisms of hyperaccumulation .................................................................... 39 i Table of Contents 1.4.1 Zincophilic root foraging ........................................................................ 39 1.4.2 Zn uptake, efflux and translocation ....................................................... 40 1.4.3 Metal detoxification ............................................................................... 45 1.4.4 Zn compartmentalisation ...................................................................... 46 1.5 Strategies to determine the genes involved in hyperaccumulation ..................... 48 1.5.1 Yeast Expression Libraries ................................................................... 48 1.5.2 Mutants ................................................................................................. 49 1.5.3 QTL ...................................................................................................... 50 1.5.4 Transcriptomics .................................................................................... 50 1.5.5 Genetic manipulation approaches ........................................................ 51 1.5.6 Localisation studies .............................................................................. 53 1.6 Aims of this thesis .............................................................................................. 53 2. Comparing the accumulation and tolerance of zinc in T. caerulescens and T. arvense .................................................................................................................... 57 2.1 Introduction ........................................................................................................ 57 2.1.1 Plant Hyperaccumulators ...................................................................... 58 2.2. Materials and methods ...................................................................................... 59 2.2.1 Plant Materials, culture media and culture conditions ........................... 59 2.2.2 Plant harvesting .................................................................................... 62 2.2.3 Determining the concentration of Zn using radiolabeled 65Zn ............... 62 2.2.4 Statistical analysis ................................................................................ 64 2.3 Results ............................................................................................................... 66 2.3.1 Plant growth of Thlaspi caerulescens and Thlaspi arvense .................. 67 2.3.2 Zinc accumulation in Thlaspi caerulescens and Thlaspi arvense ......... 72 2.4 Summary ............................................................................................................ 76 ii Table of Contents 3. Transcriptomic analysis of Thlaspi species .................................................... 79 3.1 Introduction ........................................................................................................ 79 3.2 Materials and methods ....................................................................................... 90 3.2.1 Plant material and growth conditions .................................................... 90 3.2.1.1 For microarray analysis ........................................................... 90 3.2.1.2 For quantitative, real time PCR (qPCR) .................................. 92 3.2.2 RNA extraction and hybridisation ............................................... 93 3.2.3 GeneChip® array manufacture ............................................................. 97 3.2.4 Masking strategies employed to allow microarray experiments in heterologous systems .................................................................................... 98 3.2.5 Interpretation of the Thlaspi transcriptome data ................................. 100 3.2.6 In silico alignment of A. thaliana sequences and PM probes with Thlaspi gene sequences .......................................................................................... 102 3.2.7 Quantitative real-time PCR (qPCR) .................................................... 103 3.2.7.1 qPCR primer design ........................................................................ 103 3.2.7.2 RNA extraction and running the qPCR ............................................ 107 3.3 Results ............................................................................................................. 108 3.3.1 Sequence comparison of A. thaliana and T. caerulescens ................. 109 3.3.2 Masking strategies employed to allow microarray experiments in heterologous systems .................................................................................. 109 3.3.3 Microarray analysis to compare differential gene expression between T. caerulescens and T. arvense......................................................................
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