Molecular interactions of plant cell wall polymers

Specialised plant cells produce thickened cell walls, called secondary cell walls comprised of lignocellulose. The main polymers in lignocellulose are cellulose, xylan, galactoglucomannan and lignin. Lignocellulose forms the majority of biomass on the planet and its utilization for construction, energy production, materials and pharmaceuticals may be important for a more sustainable future. For each of these applications, the interactions between the polymers in secondary cell walls are important. Previously, it was proposed that glucuronic acid side chains on xylan form ester bonds with lignin, and that this cross-linking might be important for cell wall properties. These bonds have been hypothesized to form if the glucuronic acid substitutions of xylan participate in lignin polymerization reactions and thereby cross-link xylan and lignin. Supporting this potentially important role in cell wall cross-linking, previous investigations in the model plant Arabidopsis showed that the glucuronic acid branches of xylan are crucial to the recalcitrance of lignocellulose to enzymatic digestion. In this thesis the molecular basis of this change in recalcitrance was investigated. The gux1 gux2 mutant, which lacks glucuronic acid in secondary cell walls, was found to be more accessible to hydrolytic enzymes, likely due to an increase in the porosity of the cell wall. Investigations with solid-state NMR revealed a reduction in the interactions between lignin and xylan in the mutant plants. Specific lignin synthesis mutants, which have altered lignification chemistry preventing the xylan-lignin cross-linking, were shown to share enzyme accessibility and lignin-xylan interaction phenotypes with the gux1 gux2 mutant. The presence of ester bonds between lignin and xylan was investigated and introduction of novel xylan-lignin cross-links was attempted. Solid-state NMR was used to extend our understanding of the interactions between the cell wall polymers, in industrially relevant conifer cell walls, which have a significantly higher content of galactoglucomannan than Arabidopsis. It was found that both xylan and galactoglucomannan bind to the cellulose surface and that these polysaccharides interact with lignin. This work demonstrates that some similarities in interactions between lignin and hemicelluloses occur in Angiosperms and Gymnosperms and that these interactions may play roles in the maintenance of plant material properties, such as the recalcitrance to enzymatic digestion

Combinatorial peptidomics: a generic approach for protein expression profiling

Traditional approaches to protein profiling were built around the concept of investigating one protein at a time and have long since reached their limits of throughput. Here we present a completely new approach for comprehensive compositional analysis of complex protein mixtures, capable of overcoming the deficiencies of current proteomics techniques. The Combinatorial methodology utilises the peptidomics approach, in which protein samples are proteolytically digested using one or a combination of proteases prior to any assay being carried out. The second fundamental principle is the combinatorial depletion of the crude protein digest (i.e. of the peptide pool) by chemical crosslinking through amino acid side chains. Our approach relies on the chemical reactivities of the amino acids and therefore the amino acid content of the peptides (i.e. their information content) rather than their physical properties. Combinatorial peptidomics does not use affinity reagents and relies on neither chromatography nor electrophoretic separation techniques. It is the first generic methodology applicable to protein expression profiling, that is independent of the physical properties of proteins and does not require any prior knowledge of the proteins. Alternatively, a specific combinatorial strategy may be designed to analyse a particular known protein on the basis of that protein sequence alone or, in the absence of reliable protein sequence, even the predicted amino acid translation of an EST sequence. Combinatorial peptidomics is especially suitable for use with high throughput micro- and nano-fluidic platforms capable of running multiple depletion reactions in a single disposable chip