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The Role of Glycosyltransferase 61 and BAHD Genes in Determining Ferulate & Para-Coumarate Content of the Cell Walls of the Poaceae

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The Role of Glycosyltransferase 61 and BAHD Genes in Determining Ferulate & Para-Coumarate Content of the Cell Walls of the Poaceae The role of glycosyltransferase 61 and BAHD genes in determining ferulate & para-coumarate content of the cell walls of the Poaceae Lucy Sarah Hyde Doctor of Philosophy University of York Biology September 2016 Abstract Lignocellulosic biomass, composed largely of plant cell walls, of economically important cereal crops is remarkably recalcitrant to digestion, both in second generation biofuel production and ruminant nutrition applications. Ferulic acid (FA) esterified to arabinoxylan (AX) forms oxidatively-linked dimers and oligomers which cross-link polysaccharide chains. FA is also a nucleation site for lignin formation. These cross-links are major inhibitors of enzymatic digestion, and therefore FA is a key target for improving the digestibility of grass cell walls. Also, para-coumaric acid (pCA) esterified to AX may be involved in the polymerisation of lignin. Despite the importance of cell wall-bound hydroxycinnamic acids, many of the genes and enzymes responsible for the esterification of pCA and FA to AX remain to be elucidated. The BAHD and glycosyltransferase (GT)61 gene families have previously been identified as likely to be involved in the process (Mitchell et al., 2007). Here, the role of candidate genes within the BAHD and GT61 families in pCA and FA esterification to AX is investigated in the model organism Brachypodium distachyon (Brachypodium). Jasmonic acid induced large increases in cell wall-esterified pCA, and moderate increases in FA and FA dimer in Brachypodium callus, accompanied by up-regulation of genes within the BAHD and GT61 families. Furthermore, transformation of Brachypodium with RNAi constructs designed to knock-down expression of paralogues BdGT61.9p1 and BdGT61.9p2 resulted in decreased cell wall-esterified FA. Overexpression of BdGT61.9p1 in Brachypodium resulted in a small increase in the 8-8-coupled FA dimer. These findings complemented the existing body of evidence for the involvement of genes within the BAHD and GT61 families in hydroxycinnamic acid esterification to AX. 2 Table of Contents Abstract…………………………………………………………………………………………....2 Table of contents…………………………………………………………………………………3 List of Figures………………………………………………………………………………........8 List of Tables……………………………………………………………………………………12 Acknowledgements………………………………………………………………………….....13 Declaration………………………………………………………………………………………15 General Introduction ..................................................................................17 1.1 The Poaceae and the commelinid monocots ...................................................17 1.2 Second generation liquid biofuels ...................................................................18 1.3 Ruminant nutrition .........................................................................................19 1.4 Cell walls .........................................................................................................19 1.5 Xylan structure ...............................................................................................21 1.6 Cell wall-bound hydroxycinnamic acids (HCAs) ............................................25 1.6.1 Cell wall-bound ferulic acid (FA) .............................................................25 1.6.2 Cell wall-bound ferulic acid (FA) dimers .................................................26 1.6.3 FA cross-link to lignin ..............................................................................29 1.6.4 FA cross-linking in digestibility ...............................................................30 1.6.5 Cell wall-bound para-coumaric acid (pCA) ..............................................30 1.6.6 Cell wall-bound sinapic acid ....................................................................31 1.7 Glucurono- and arabinoxylan synthesis .........................................................32 1.7.1 Discovery of xylan synthesis genes ..........................................................32 1.7.2 Synthesis of the β-(1-4)-xylan backbone ..................................................33 1.7.3 Dicot GX side chain synthesis ..................................................................34 1.7.4 Arabinoxylan (AX) synthesis in the Poaceae ...........................................34 1.7.5 Conservation of IRX genes .......................................................................36 1.7.6 The xylan synthase complex ....................................................................36 3 1.8 FA synthesis genes ..........................................................................................39 1.8.1 BAHD acyl transferases in feruloylation .................................................39 1.8.2 Glycosyltransferase 61 family in feruloylation .......................................42 1.9 Brachypodium .................................................................................................46 1.10 Project aims .....................................................................................................48 General Materials and Methods .................................................................49 2.1 Chemicals and reagents ..................................................................................49 2.2 Plant growth and harvest ...............................................................................49 2.3 Tissue preparation ..........................................................................................49 2.4 Alcohol insoluble residue (AIR) preparation ..................................................49 2.5 Destarching of alcohol insoluble residue ........................................................50 2.6 Matrix polysaccharides extraction and analysis ............................................51 2.7 Crystalline cellulose extraction and analysis .................................................51 2.8 Lignin extraction and analysis .......................................................................52 2.9 Silica analysis ..................................................................................................52 2.10 Saccharification ...............................................................................................53 2.11 Cell wall-bound phenolic acid extraction ........................................................53 2.12 High performance liquid chromatography (HPLC) ........................................54 2.13 Standard cloning procedure ............................................................................55 2.14 Agrobacterium transformation .......................................................................55 2.15 Callus generation ............................................................................................56 2.16 Brachypodium transformation ........................................................................56 2.17 DNA isolation ..................................................................................................57 2.18 Quantitative PCR (qPCR) to determine zygosity ...........................................58 2.19 RNA isolation ..................................................................................................58 2.20 Western blotting ..............................................................................................60 2.21 Microscopy .......................................................................................................61 4 The Effect of Mechanical Stress on Cell Wall Composition in Brachypodium distachyon .............................................................................................62 3.1 Introduction .....................................................................................................62 3.2 Chapter 3 specific methods .............................................................................66 3.2.1 Plant growth .............................................................................................66 3.2.2 Mechanical stress .....................................................................................66 3.2.3 Overview of mechanical stress experiments............................................66 3.2.4 Statistics ...................................................................................................70 3.3 Results .............................................................................................................71 3.3.1 Plant growth .............................................................................................71 3.3.2 Cell wall-bound phenolic acids.................................................................72 3.3.3 Cell wall monosaccharides and lignin .....................................................74 3.3.4 Silica .........................................................................................................74 3.3.5 Digestibility ..............................................................................................77 3.4 Discussion ........................................................................................................79 3.4.1 Stem length ..............................................................................................79 3.4.2 Cell wall-bound FA and FA dimers .........................................................79 3.4.3 Lignin .......................................................................................................81 3.4.4 Cell wall monosaccharides .......................................................................81 3.4.5 Silica .........................................................................................................83
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