PI: Gunnar Wingsle

Staff: Robert Nilsson, PhD student

Background

In the "omics" era proteomic analysis has become one of the basic technologies to obtain essential information of the biological system. In the concept of wood formation there is a huge lack of information on the proteomic stage from the wood developing zone. This kind of information has on the contrary developed to a more mature state when analyzed on a transcriptomic level. The proteome are several levels more complicated to analyze than the transcriptome and techniques are still under strong development. The use of masspectrometry in combination with different fractionation techniques has become central tools to gain information with high resolution and in depth analysis in complex protein mixtures. Such analysis has not only the possibility to identify the proteins but also give quantitative and protein functional information. Particularly post translational modifications (PTMs) as phosphorylation and glycosylation has a central role in many regulatory events in cell biology.

Aims

In FuncFiber we will complement the wood transcriptome with the corresponding proteome to aid in our understanding of the wood forming process. A proteome database will be built by identifying proteins from different developmental stages and subproteomes including samples from different compartments as nucleus, plasmalemma and cell walls. The samples will be pre-fractionated into water soluble and membrane and cell wall extracts. These pre-fractionated samples will then be further fractionated e.g. by SDS-PAGE and/or capillary electrophoreses. The fractions will be analysed by ultra performance LC electro-spray mass spectrometry (ESI-QTOFMS), for protein identification. In depth analysis of PTMs as phosphorylation and glycosylation will also be of central importance for some of the isolated proteomes within the project. To couple changes in gene transcription to changes in protein profiles and their final fiber characteristics the recently developed MS-based method for quantitative differential profiling of peptides will be used. With the outlined techniques it will not only be possible to identify thousands of proteins in specific parts in the wood forming zone but also to identify the proteins that differ in trees with different wood properties. The outlined strategy will also include development of methods and analysis of transgenic plants altered in lignin biosynthesis using superoxide dismutase and MYB transcription factors as target proteins.