Systems Biology Group
Background
Traditional approaches for understanding complex biological systems have employed reductionist methods that have focused on individual components to comprehend the complexity observed. A systems biology approach assumes that every component can influence a system and thus attempts to integrate information from a multitude of experiments from a diverse range of conditions to understand complex biological systems. The large number of experiments required to satisfy this approach have become possible in recent years with the advanced development of microarrays, sequencers and mass spectrometers. The Systems Biology Group within the Feedstocks Division at The Joint BioEnergy Institute is employing integrative strategies to further our fundamental understanding of the plant cell wall.
1. Plant Golgi Proteomics
The plant cell wall is comprised of a variety of complex sugar polymers including cellulose, hemicellulose and pectin. The details of precisely how this complex sugar matrix is constructed are currently poorly understood. The Golgi apparatus is an organelle within the plant cell that produces a large proportion of these matrix polysaccharides (namely the hemicelluloses and pectins) and secretes them to the cell wall for incorporation.
Figure 1. Cartoon outlining the Golgi apparatus and its relationship to the plant cell wall.
In order to better understand the role of this organelle in cell wall biosynthesis we are attempting to characterize this organelle using proteomics. Our current knowledge of the protein constituent that comprise the plant Golgi is relatively poor when compared to other subcellular components within the cell. While several factors have contributed to this shortfall, the major problem has been problems associated with its isolation. We are using an orthogonal approach which employs traditional density centrifugation followed by charge based separation of the organelle on a Free Flow Electrophoresis system.
Figure 2. Strategy for isolation of plant Golgi using density centrifugation and the FFE
The rationale for characterizing the plant Golgi proteome and developing a reproducible isolation procedure is to define currently and better understand known biochemical processes (e.g. glycosyl transferases), identify novel pathways and interactions (e.g. lignin transport) and to enable comparative proteomics of this organelle (e.g. compare the Golgi proteome of a cell wall mutant to wild-type). Such approaches will provide powerful tools and resources to assist our understanding plant cell wall biosynthesis.
2. Plant Cell Wall Structure and Composition
A significant impediment to the identification of novel genes involved in plant cell wall biosynthesis using reveres genetics has been the redundancy of gene families within the genome. Consequently we have been using the advanced imaging and spectroscopic resources of the Lawrence Berkeley National Laboratory to identify new methods of visualizing plant cell walls.
Figure 3. Fluorescence Lifetime Imaging Microscopy (FLIM) of plant vascular tissue
Techniques for contrasting plant cell walls that are developed within the group are being used to analyze a series of geographically distinct Arabidopsis populations. These populations or accessions show a wide variety of phenotypic differences and are likely to have subtle changes within their cell walls. The genes responsible for these differences or QTLs (quantitative trait loci) can be readily mapped and identified through the analysis of recombinant inbred populations (RILs).
Figure 4. A collection of Arabidopsis accessions with obvious phenotypic differences.
Since the differences do not represent massive changes to the genetic background that are observed with reveres genetic procedures, the analysis of accessions for cell wall differences can provide a more subtle understanding of the nuances of cell wall biosynthesis.
Useful Links
SUBA Database (http://suba.plantenergy.uwa.edu.au/): Subcellular proteomics and FP information
PhosPhAt Database (http://phosphat.mpimp-golm.mpg.de/): Phosphoproteomic data for the model plant Arabidopsis
1001 genome project (http://www.1001genomes.org/): Program to sequence 1001 Arabidopsis accessions for resource to allow genome-wide association (GWA) mapping
Arabidopsis SNPs on AnnoJ (http://jbei-exwebapp.lbl.gov/annoj): SNPs from sequenced accessions of Arabidopsis arrayed using the AnnoJ genome browser
Multinational Arabidopsis Steering Committee, Proteomics Subcommittee (http://www.masc-proteomics.org/): Arabidopsis proteomics subcommittee
