The Metabolomics of Desiccation Tolerance in Xerophyta humilis by Halford Dace Dissertation presented for the degree of Master of Science in the Department of Molecular and Cell Biology University of Cape Town February 2014 Supervisors: Prof. J. M. Farrant Dr M. S. Rafudeen University of Cape Town The copyright of this thesis vests in the author. No quotation from it or information derived from it is to be published without full acknowledgement of the source. The thesis is to be used for private study or non- commercial research purposes only. Published by the University of Cape Town (UCT) in terms of the non-exclusive license granted to UCT by the author. University of Cape Town The Metabolomics of Desiccation Tolerance in Xerophyta humilis / Dace 2 Plagiarism Statement I know the meaning of Plagiarism and declare that all of the work in the document, save for that which is properly acknowledged, is my own. The Metabolomics of Desiccation Tolerance in Xerophyta humilis / Dace 3 Abstract Resurrection plants are unique in the ability to survive near complete water loss in vegetative tissues without loss of viability. In order to do so, they employ multifaceted strategies which include structural adaptations, antioxidant and photoprotective mechanisms, and the accumulation of proteins and metabolites that stabilise macromolecules. A full understanding of the phenomenon of vegetative desiccation tolerance will require a systems view of these adaptations at the levels of the genome, the control of gene expression, and the control of metabolic pathways. This dissertation reports a high-throughput metabolomic analysis of the changes that occur in vegetative tissues of resurrection plant Xerophyta humilis during dehydration. A combination of chromatography, mass spectrometry and nuclear magnetic resonance revealed numerous primary and secondary metabolites in the plant. Multivariate statistics identified a subset of metabolites that were significantly up- or down-regulated in response to water deficit stress. These metabolites both confirmed existing observations about the metabolic response of X. humilis to drying and revealed compounds not previously known to be associated with this response. Desiccation-associated metabolites were mapped onto known biochemical pathways, to generate hypotheses concerning possible regulatory schemes in the stress response, inviting deeper investigation in future. The Metabolomics of Desiccation Tolerance in Xerophyta humilis / Dace 4 Table of Contents Chapter One: Introduction and Background .............................................................................. 9 Introduction ............................................................................................................................ 9 Desiccation Biology ............................................................................................................. 11 Metabolomics ....................................................................................................................... 20 This Study ............................................................................................................................ 46 Chapter Two: Materials and Methods ...................................................................................... 50 Plant Source and Maintenance ............................................................................................. 50 Water Content Determination .............................................................................................. 51 Metabolite Extraction ........................................................................................................... 53 GC-MS Experiments ............................................................................................................ 54 LC-MS Experiments ............................................................................................................ 57 NMR Experiments ............................................................................................................... 58 Chapter Three: Numerical Analysis ......................................................................................... 60 Data Pre-Processing ............................................................................................................. 60 Statistical Treatment ............................................................................................................ 63 Compound Identification ..................................................................................................... 66 Pathway Inference ................................................................................................................ 69 Chapter Four: Results and Discussion ..................................................................................... 70 Drying Kinetics .................................................................................................................... 70 Principal Component Analysis ............................................................................................ 72 Partial Least Squares Discriminant Analysis ....................................................................... 86 Targeted Compounds ........................................................................................................... 94 Untargeted Compounds ....................................................................................................... 98 Compound Pathway Inference ........................................................................................... 102 Metabolite Changes in the Context of Plant Desiccation .................................................. 107 Conclusion and Future Prospects ........................................................................................... 112 Appendices ............................................................................................................................. 116 Appendix A: Selection Among Scaling Algorithms .......................................................... 117 The Metabolomics of Desiccation Tolerance in Xerophyta humilis / Dace 5 Appendix B: Untargeted Peak Lists ................................................................................... 121 Appendix C: GC-MS Chromatograms ............................................................................... 140 Appendix D: LC-MS Chromatograms ............................................................................... 173 Appendix E: NMR Spectra ................................................................................................ 190 Appendix F: Perl Code for Unit Mass Consolidation ........................................................ 194 Appendix G: R Code for PCA ........................................................................................... 195 Appendix H: R Code for PLS-DA ..................................................................................... 197 Appendix I: R Code for Pathway Mapping ....................................................................... 202 Bibliography .......................................................................................................................... 205 The Metabolomics of Desiccation Tolerance in Xerophyta humilis / Dace 6 List of Figures Figure 1. Relative Water Content of X. humilis leaves ............................................................ 70 Figure 2. Variance per Principal Component for GC-MS peaks of X. humilis leaf extract. .... 73 Figure 3: Score and loading plots for GC-MS leaf extract data. ............................................. 74 Figure 4: Variance per Principal Component for GC-MS peaks of X. humilis root extract, .. 76 Figure 5: Score and loading plots for GC-MS root extract data. ............................................. 77 Figure 6: Variance per Principal Component for LC-MS peaks of X. humilis leaf extract ..... 79 Figure 7: Score and loading plots for LC-MS leaf extract data. .............................................. 80 Figure 8: Variance per Principal Component for LC-MS peaks of X. humilis root extract. ... 83 Figure 9: Score and loading plots for LC-MS root extract data. ............................................. 84 Figure 10: PLS regression for GC-MS peaks of X. humilis leaf extracts ................................ 87 Figure 11: PLS regression for GC-MS peaks of X. humilis root extracts ................................ 89 Figure 12: PLS regression for LC-MS peaks of X. humilis leaf extracts ................................. 91 Figure 13: PLS regression for LC-MS peaks of X. humilis root extracts ................................ 93 Figure 14: Untargeted compound peak summary .................................................................... 99 Figure 15: Relative activity scores of inferred pathways ....................................................... 104 Figure 16: PCA with no data scaling ..................................................................................... 118 Figure 17: PCA with autoscaled data ..................................................................................... 119 Figure 18: PCA with Pareto-scaled data ................................................................................ 120 The Metabolomics of Desiccation Tolerance in Xerophyta humilis / Dace 7 List of Tables Table 1: A Selection of metabolite classes, with examples and properties ............................ 27 Table 2: Chromatographic modes and their uses ....................................................................