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Identification and Characterization of Genes Involved in the Biosynthesis of the Plant Cell Wall Polysaccharide Xyloglucan by Al

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Identification and Characterization of Genes Involved in the Biosynthesis of the Plant Cell Wall Polysaccharide Xyloglucan by Al Identification and characterization of genes involved in the biosynthesis of the plant cell wall polysaccharide xyloglucan By Alexander Christiaan Schultink A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Plant Biology in the Graduate Division of the University of California, Berkeley Committee in charge: Professor Markus Pauly, Chair Professor Chris Somerville Professor Michelle Chang Fall 2013 Abstract Identification and characterization of genes involved in the biosynthesis of the plant cell wall polysaccharide xyloglucan by Alexander Christiaan Schultink Doctor of Philosophy in Plant Biology University of California, Berkeley Professor Markus Pauly, Chair Xyloglucan (XyG) represents the most abundant hemicellulose in the primary cell wall of many dicot and non‐graminaceous monocot plant species. Found throughout the land plant lineage, the structure of this polysaccharide varies by species, tissue, and developmental stage. Some proteins responsible for the biosynthesis and metabolism of XyG have been previously identified but additional genes remain to be uncovered. In the work presented here, several genetic and genomic approaches were used to identify previously unknown genes involved in XyG biosynthesis and metabolism. A forward genetic screen of mutagenized Arabidopsis thaliana resulted in the identification of the Altered Xyloglucan 9 (AXY9) gene, coding for a protein of unknown function, as part of an apparently plant‐specific pathway for the acetylation of polysaccharides. The AXY9 protein may be part of a system for shuttling activated acetyl groups across the Golgi membrane for use by polysaccharide‐specific acetyltransferases. A transcriptional profiling approach used on developing XyG‐rich Tropaeolum majus seeds revealed a galactosyltransferase that acts on XyG, as demonstrated by mutant analysis in A. thaliana. By utilizing comparative genomics, two putative XyG arabinofuranosyltransferase genes were discovered from tomato, which are able to act in vivo to arabinosylate XyG. Expression of these genes rescued mechanical and morphological phenotypes of an A. thaliana mutant deficiency for XyG galactosylation, providing insight into the function of XyG substitution. To provide a testing platform for candidate genes involved in XyG biosynthesis and to investigate the activities of these genes independently from endogenous plant proteins, an attempt was made to reconstruct the XyG biosynthetic pathway in a heterologous host. This effort resulted in the production of a glucan backbone and the UDP‐xylose donor substrate required for the xylosyltransferases, but a XyG polysaccharide was not detected. 1 Table of Contents List of figures ................................................................................................................................... ix List of tables .................................................................................................................................... xi 1 Introduction ............................................................................................................................. 1 1.1 Plant cell wall polysaccharides ......................................................................................... 1 1.1.1 Function .................................................................................................................... 1 1.1.2 Structures .................................................................................................................. 2 1.1.3 Biosynthesis .............................................................................................................. 5 1.2 XyG ................................................................................................................................... 7 1.2.1 Function .................................................................................................................... 7 1.2.2 Structures and diversity ............................................................................................ 8 1.2.3 XyG Biosynthesis ..................................................................................................... 11 1.2.4 XyG Metabolism ...................................................................................................... 13 1.2.5 Applications............................................................................................................. 13 1.3 Thesis objective .............................................................................................................. 14 2 Materials and methods ......................................................................................................... 15 2.1 Media and growth conditions ........................................................................................ 15 2.1.1 Growth media ......................................................................................................... 15 2.1.2 Induction of transgene expression in Pichia pastoris ............................................. 16 2.1.3 Sterilization of A. thaliana seed surface ................................................................. 16 2.1.4 Growth of A. thaliana on plates and soil ................................................................ 16 2.1.5 Growth of N. benthamiana on soil ......................................................................... 16 2.2 Molecular biology ........................................................................................................... 16 2.2.1 Extraction of genomic DNA from plant tissue ........................................................ 16 2.2.2 Genotyping A. thaliana and Pichia pastoris using PCR ........................................... 16 2.2.3 Genetic mapping with SSLP and CAPS markers ...................................................... 17 2.2.4 Amplification of genes for cloning using PCR ......................................................... 17 2.2.5 Cloning methods ..................................................................................................... 17 2.2.6 Restriction digest analysis of plasmids ................................................................... 18 i 2.2.7 DNA sequencing of plasmids and gene fragments ................................................. 18 2.2.8 Transformation of P. pastoris ................................................................................. 18 2.2.9 Excision of selectable marker from genome of P. pastoris .................................... 19 2.2.10 Transformation of A. tumefaciens .......................................................................... 19 2.2.11 Transformation of A. thaliana ................................................................................ 19 2.2.12 Infiltration of N. benthamiana ................................................................................ 19 2.2.13 Transcriptional analysis using qRT‐PCR .................................................................. 20 2.2.14 Transcriptional analysis using RT‐PCR .................................................................... 20 2.2.15 High‐throughput sequencing of A. thaliana ........................................................... 20 2.3 Microscopy ..................................................................................................................... 20 2.3.1 Subcellular localization ........................................................................................... 20 2.3.2 Light microscopy (for stem sections) and staining ................................................. 21 2.4 Bioinformatic methods ................................................................................................... 21 2.4.1 Analysis of high‐throughput sequencing data ........................................................ 21 2.4.2 Phylogenetic tree construction ............................................................................... 21 2.5 Analytical methods ......................................................................................................... 21 2.5.1 Preparation of alcohol insoluble residue (AIR) from plant tissue .......................... 21 2.5.2 Preparation of alcohol insoluble residue (AIR) from P. pastoris ............................ 22 2.5.3 Analysis of XEG‐released oligosaccharides by MALDI‐TOF MS (XyG OLIMP) ......... 22 2.5.4 Analysis of XEG‐released oligosaccharides using HPAEC‐PAD ................................ 22 2.5.5 Desalting / purification of XyG oligosaccharides .................................................... 23 2.5.6 Purification of novel oligosaccharide (XXSG) .......................................................... 23 2.5.7 Glycosidic linkage analysis ...................................................................................... 23 2.5.8 Extraction of XyG from olive fruit ........................................................................... 24 2.5.9 Nucleotide sugar extraction and analysis ............................................................... 24 2.5.10 Measurement of acetic acid content of AIR material ............................................. 25 2.5.11 NMR spectroscopy of the oligosaccharide ............................................................. 25 2.5.12 OREX protein purification and digestion ................................................................ 25 2.5.13 Leaf extensibility ....................................................................................................
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