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(GSNOR1) Function Leads to an Altered DNA and Histone Methylation Pattern in Arabidopsis Thaliana

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(GSNOR1) Function Leads to an Altered DNA and Histone Methylation Pattern in Arabidopsis Thaliana TECHNISCHE UNIVERSITÄT MÜNCHEN Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt (WZW) Lehrstuhl für Biochemische Pflanzenpathologie Loss of S-NITROSOGLUTATHIONE REDUCTASE 1 (GSNOR1) function leads to an altered DNA and histone methylation pattern in Arabidopsis thaliana Eva Rudolf Vollständiger Abdruck der von der Fakultät Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt der Technischen Universität München zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften genehmigten Dissertation. Vorsitzender: Prof. Dr. Frank Johannes Prüfer der Dissertation: 1. Prof. Dr. Jörg Durner 2. apl. Prof. Dr. Ramon A. Torres Ruiz Die Dissertation wurde am 30.01.2020 bei der Technischen Universität München eingereicht und durch die Fakultät Wissenschaftszentrum Weihenstephan für Ernährung, Landnutzung und Umwelt am 20.04.2020 angenommen. To my family, Florian and Tobias. Publications and conference contributions related to this thesis: Izabella Kovacs, Alexandra Ageeva, Eva König and Christian Lindermayr, 2016. Chapter Two – S-Nitrosylation of Nuclear Proteins: New Pathways in Regulation of Gene Expression. In Advances in Botanical Research edited by David Wendehenne. Nitric Oxide and Signaling in Plants. Academic Press, 77, 15–39. Eva Rudolf, Markus Wirtz, Ignasi Forné and Christian Lindermayr. S-Nitrosothiols as architect of the methylome in Arabidopsis thaliana. EMBO Conference - Chromatin and Epigenetics 2017, Heidelberg, Germany, Poster. Eva Rudolf, Alexandra Ageeva-Kieferle, Alexander Mengel, Ignasi Forné, Rüdiger Hell, Axel Imhof, Markus Wirtz, Jörg Durner and Christian Lindermayr. Post-translational modification of histones: Nitric oxide modulates chromatin structure. Symposium - From Proteome to Phenotype: role of post- translational modifications 2017, Edinburgh, United Kingdom, Oral presentation. Alexandra Ageeva-Kieferle, Eva Rudolf and Christian Lindermayr, 2019. Redox-Dependent Chromatin Remodeling: A New Function of Nitric Oxide as Architect of Chromatin Structure in Plants. Frontiers in Plant Science, 10, 625. Christian Lindermayr, Eva Rudolf, Jörg Durner and Martin Groth, 2020. Interaction between metabolism and chromatin in plant models. Molecular Metabolism, 38, 100951. Eva Rudolf, Patrick Hüther, Ignasi Forné, Elisabeth Georgii, Yongtao Han, Markus Wirtz, Rüdiger Hell, Axel Imhof, Claude Becker, Jörg Durner and Christian Lindermayr. S-Nitrosoglutathione reductase regulates demethylation and expression of transposable elements and stress-responsive genes. In progress. Other publications and conference contributions: Felicitas Groß, Eva König, Jörg Durner and Jeremy Astier. Nitric oxide production in Arabidopsis thaliana. 5th Plant NO Club Meeting 2014, Munich, Germany, Poster. Zsuzsanna Kolbert, Árpád Molnár, Dóra Oláh, Gábor Feigl, Edit Horváth, László Erdei, Attila Ördög, Eva Rudolf, Teresa K. Barth and Christian Lindermayr, 2019. S-Nitrosothiol Signaling Is involved in Regulating Hydrogen Peroxide Metabolism of Zinc-Stressed Arabidopsis. Plant and Cell Physiology. 60, 2449–2463. Table of Contents Table of Contents .......................................................................................................................... I Summary ..................................................................................................................................... V Abbreviations ............................................................................................................................. VII List of Figures and Tables ............................................................................................................. IX 1 Introduction ......................................................................................................................... 1 1.1 Nitric oxide in plants ................................................................................................................ 1 1.2 S-Nitrosoglutathione is an intracellular mobile NO reservoir ................................................. 3 1.3 NO-mediated regulation of gene expression .......................................................................... 5 1.4 Chromatin methylation and metaboloepigenetic ................................................................... 6 1.4.1 Histone lysine methylation and demethylation in Arabidopsis ...................................... 7 1.4.2 DNA methylation and demethylation in Arabidopsis ...................................................... 8 1.4.3 Metabolic regulation of DNA and histone methylation ................................................ 10 1.5 Epigenetic effects of NO on DNA and histone methylation .................................................. 12 1.5.1 NO affects DNA and histone methylation pathways ..................................................... 13 1.5.2 NO affects metaboloepigenetic processes interacting with DNA and histone methylation ................................................................................................................................... 16 2 Aim of the thesis ................................................................................................................. 19 3 Materials and Methods ....................................................................................................... 20 3.1 Plant material and cultivation ............................................................................................... 20 3.2 Molecular biology methods................................................................................................... 21 3.2.1 Genomic DNA isolation using cetyltrimethylammonium bromide ............................... 21 3.2.2 Genomic DNA isolation using the DNeasy® Plant Mini Kit ............................................ 21 3.2.3 RNA extraction and cDNA synthesis .............................................................................. 22 3.3 Generation and characterization of transgenic lines ............................................................ 22 3.3.1 Preparation of competent Agrobacterium tumefaciens ............................................... 22 3.3.2 Transformation of Agrobacterium tumefaciens by electroporation ............................. 22 3.3.3 Transformation of Arabidopsis ...................................................................................... 23 3.3.4 Generation of transgenic 35S::AtSAHH1-tagged plants ................................................ 23 3.3.5 PCR-based genotyping of mutants and transgenic lines ............................................... 24 3.4 Epigenetic analysis and next generation sequencing ............................................................ 25 3.4.1 DNA methylation analysis by chop-PCR ........................................................................ 25 3.4.2 Whole genome bisulfite sequencing and data analysis ................................................ 25 3.4.3 RNA-sequencing ............................................................................................................ 27 I 3.4.4 Acid extraction of histones ............................................................................................ 27 3.4.5 Quantification of histone methylation and acetylation by LC-MS/MS ......................... 27 3.5 Protein analysis ..................................................................................................................... 30 3.5.1 Sodium dodecyl sulfate polyacrylamide gel electrophoresis ........................................ 30 3.5.2 Coomassie® staining of SDS-PAGE gels ......................................................................... 30 3.5.3 Immunoblotting ............................................................................................................. 30 3.5.4 Detection of S-nitrosated proteins ................................................................................ 31 3.6 Heterologous protein production and enzymatic activity assays ......................................... 32 3.6.1 Heterologous production of AtSAHH1 .......................................................................... 32 3.6.2 SAHH activity assay ........................................................................................................ 33 3.6.3 GSNOR activity assay ..................................................................................................... 33 3.6.4 GUS activity staining ...................................................................................................... 33 3.7 Metabolic analysis ................................................................................................................. 34 3.7.1 Quantification of chlorophyll contents ......................................................................... 34 3.7.2 Quantification of S-nitrosothiols ................................................................................... 34 3.7.3 Quantification of polyamines ........................................................................................ 35 3.7.4 Quantifications of thiols ................................................................................................ 35 3.8 Statistical data analysis.......................................................................................................... 35 4 Results ................................................................................................................................ 36 4.1 S-Nitrosation of AtSAHH1 .....................................................................................................
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