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Exploring the Role of Root Barriers in the Metal Hyperaccumulator Noccaea Caerulescens

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Exploring the Role of Root Barriers in the Metal Hyperaccumulator Noccaea Caerulescens Exploring the role of root barriers in the metal hyperaccumulator Noccaea caerulescens M.Sc. Thesis Dario Galanti September 2016 Exploring the role of root barriers in the metal hyperaccumulator Noccaea caerulescens Dario Galanti 920605249070 September 2016 M.Sc. Thesis Laboratory of Genetics GEN-80436 Supervisors: Tânia Serra and Mark Aarts WAGENINGEN UNIVERSITY i ii Table of contents Abstract ................................................................................................................. iv 1 Introduction ..................................................................................................... 1 1.1 Noccaea caerulescens, a Zn/Cd/Ni hyperaccumulator ___________________________ 1 1.2 Hyperaccumulation in N. caerulescens ________________________________________ 2 1.3 Copper homeostasis and transport in plants ___________________________________ 3 1.4 Root Barriers: a N. caerulescens special feature ________________________________ 8 2 Aims .............................................................................................................. 10 3 Materials and methods .................................................................................. 11 3.1 Mutants pre-selection ____________________________________________________ 11 3.2 Optical microscopy ______________________________________________________ 12 3.2.1 Root clearing and lignin autofluorescence of entire roots ............................................................ 12 3.2.2 Autofluorescence of cross sections ............................................................................................... 12 3.3 Hydroponics ____________________________________________________________ 13 3.4 Ionomics ______________________________________________________________ 13 3.5 Gene expression analysis _________________________________________________ 13 3.5.1 RNA extraction and quality control ............................................................................................... 14 3.5.2 cDNA synthesis .............................................................................................................................. 15 3.5.3 Gene identification and primer design .......................................................................................... 15 3.5.4 Primer testing ................................................................................................................................ 16 3.5.5 qPCR analysis ................................................................................................................................. 18 4 Results ........................................................................................................... 19 4.1 Pre-selected mutants ____________________________________________________ 19 4.2 Optical screening of RB mutants ___________________________________________ 22 4.2.1 Lignin autofluorescence of entire roots ........................................................................................ 22 4.2.2 Autofluorescence of cross sections ............................................................................................... 23 4.3 Ionomics ______________________________________________________________ 25 4.4 Gene expression analysis _________________________________________________ 28 4.4.1 COPT family in N. caerulescens ..................................................................................................... 28 4.4.2 Primer efficiency ........................................................................................................................... 29 4.4.3 Gene expression ............................................................................................................................ 30 5 Discussion ...................................................................................................... 31 5.1 Root barriers and hyperaccumulation _______________________________________ 31 5.2 Copper homeostasis in Noccaea caerulescens _________________________________ 32 6 Conclusions .................................................................................................... 34 7 References ..................................................................................................... 36 Appendix A – Ionomics analysis ............................................................................ 40 Part 1 – Control treatment _______________________________________________________ 40 Part 2 – Cu stress treatment _____________________________________________________ 42 Appendix B – Gene expression analysis ................................................................. 43 Appendix C – Mutant seed availability .................................................................. 44 Acknowledgments ................................................................................................ 45 iii Abstract Noccaea caerulescens is an emergent model species for the study of metal hyperaccumulation, reported to accumulate very high levels of nickel (Ni), zinc (Zn) and cadmium (Cd) in leaves. Several studies partially unravelled the mechanisms underlying metal homeostasis and transport in this plant but many pieces are still to be placed in order to compose the entire puzzle. For this purpose, the first aim of this study was to enlighten the role that specific structures called lignin thickenings (LT), present in N. caerulescens roots, may play in the hyperaccumulation mechanism of this plant. By several selection steps, I was able to select three N. caerulescens mutants probably defective in the production of LT. From preliminary data, these mutants seem to have a lower metal accumulation than the wild- type, suggesting an active role of LT in the accumulation mechanism. Nevertheless a more detailed phenotyping and ionomics characterization of the mutants is needed to confirm this hypothesis. The second approach followed to shed light on N. caerulescens metal homeostasis was to carry out a preliminary study about copper (Cu) homeostasis and transport in this plant. Cu availability can influence homeostasis of other metals in several ways like competing with divalent cations as Zn and Cd for transport and tuning of the amounts and kind of superoxide dismutases (Fe-SOD against Cu/Zn-SOD). Aligning A. thaliana members of the COPT gene family of Cu transporters to the N. caerulescens genome, I was able to identify five orthologs. The ortholog of AtCOPT6 was not found. Ionomics and gene expression analysis performed in N. caerulescens, showed differences in Cu homeostasis between this species and A. thaliana. NcCOPT2 expression between roots and shoots is different compared to A. thaliana, suggesting that this gene could recover some of the functions of the absent copy COPT6. Furthermore NcCOPT5, which in A. thaliana is responsible for Cu mobilization from mesophyll vacuoles, seems to be Cu-responsive. This observation, together with the higher Cu translocation observed under Cu-excess conditions, suggests that N. caerulescens could be special also in the administration of this metal. Regarding interactions with other metals I show here that, under Cu-excess conditions, N. caerulescens seems to be able to distinguish between Cd and Zn xylem loading, to exclusively transport Zn. How this distinction works is still unknown, since Zn and Cd xylem loading is thought to be driven by the same pomp HMA4. With this last observation, I want to highlight how the study of Cu response in N. caerulescens can be useful also to understand mechanisms underlying the transport and homeostasis of other metals. iv v 1 Introduction 1.1 Noccaea caerulescens, a Zn/Cd/Ni hyperaccumulator Soil and water pollution on earth is becoming more and more a threat for environmental and health reasons. Therefore interest in studying heavy metal hyperaccumulation in plants has grown and is growing, aiming to provide alternative solutions to conventional methods for soil cleaning. These methods have indeed the drawback to be expensive and sometimes very invasive for the soil. The phytoremediation approach offers an economic, easy and non invasive solution. Furthermore it is particularly indicated for heavy metal contamination, since these elements cannot be degraded using microorganisms as for organic pollutants (Sas-Nowosielska et al. 2008). In this case the most effective approach is phytoextraction, which is based on the ability of some so called, hyperaccumulator plants, to uptake from the soil high levels of metals and translocate them to the shoots (Reeves 1992). These plants usually stock the metals in vacuoles of mesophyll cells to levels that would be toxic for most of other plants. The first step in the development of plants that can be used for phytoremediation is the comprehension of the mechanisms of hyperaccumulation and tolerance, which is different depending on the metal involved. A first distinction must be done between plant micronutrients, which are toxic at high concentrations but necessary at low concentrations (Zn, Fe, Ni, Mo, Mn and Cu) and elements that are not necessary for plant growth (As, Cd, Pb and Hg). The first ones enter the plant through specific transporters, while the second ones usually enter through transporters of chemically similar elements or by simple diffusion (Epstein and Bloom, 2005). Noccaea caerulescens (Thlaspi caerulescens until few years ago, Al-Shehbaz 2014), from the Brassicaceae family, is an emergent model species to study the hyperaccumulation trait. This plant is able to accumulate
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