The Group has both a wet lab as well as theoretical approaches.
The effect of the Carbon Status on minor carbohydrates and the cell wall
As the cell wall represents a major carbon sink it seems likely that its metabolism might be affected by the carbon status. Indeed there are several pieces of omics data that suggest at least a coordination of cell wall synthesis by decreasing amounts of C. As an example, it has been consistently observed that the nucleotide sugar converting enzymes seem to be transcriptionally regulated by changing carbon availability. To pursue this question, we have established an LC-MS/MS based method to measure nucleotide-sugar pools which –as the precursors for cell wall synthesis- represent the link between primary metabolism and cell synthesis.
As several enzymatic reactions in the sugar conversion pathways are currently unknown, we are cloning candidate genes and investigating their role in Arabidopsis profiting from the output of the protein classification and network approaches. Furthermore, we have conducted a forward genetic screen where the seed mucilage was used as a simple system to study cell wall polymer synthesis and are currently studying the obtained candidate lines.
Identifying Cell Wall Biosynthesis genes using a simple model
The plant cell wall is complex consisting of cellulosic fibres embedded into a matrix of pectins and hemicelluloses. Whilst a tremendous amount of data was generated using mutant collections, not all cell wall mutants are viable and not in all cases is it possible to directly determine changes in the cell wall composition without a fractionation of the cell wall.
Interestingly Arabidopsis thaliana seeds extrude a substance called mucilage upon contact with water. As it turns out a major component of the mucilage is rhamnogalacturonan-I which is also one of the major components in cell wall pectin. However, the mucilage is extremely easy to extract and Arabidopsis seeds are perfectly viable with relatively little mucilage or in mutants and/or ecotypes not extruding mucilage.
Identifying beneficial cell wall traits in natural populations
(Co-Pi Markus Günl)
Plant cell walls are a major resource which can be used for biofuels or for a material use. Whilst the last few years have seen major advances in our understanding of how the plant cell walls are constructed and plant cell walls can be decomposed, we are still far away from tailoring plants to our needs. We therefore investigate the cell wall composition of naturally occurring plant species or variants (e.g. wild relatives) to identify potentially beneficial traits that could be introduced into modern breeding varieties.
Specifically we focus on the use of residual material such as plant parts that would end up as straw and thus don’t compete with food or feed usage.
Network reconstruction, network learning and biological pathways
Given the ample amount of “omics” data that is being generated, it becomes more and more important to devise schemes to best profit from the mass of generated data and to extract the most likely biological interpretation. The group is thus aiming to develop methods and tools to abstract, visualize and interpret high throughput data.
These tools are applied to data that is generated in the group to find new candidate genes for cell wall synthesis and the response to carbon limitation. Furthermore these approaches are used to build predictive models.
Using Next Generation Sequencing to answer biological problems
Currently the group is involved in various RNASeq projects (454 & Illumina Solexa), the assembly of a wild tomato species and in using sequencing to pinpoint mutations. Here the group is interested in developing new tools and algorithms that expedite the analysis of data and which help a biologist to find answers to biologically relevant questions. The group thus tries to enable biologists to e.g. find new candidate genes.
A first release tool is Trimmomatic which can be used to quality trim and adapter clip NGS data (Illumina Solexa).Databases, Ontology and Tool Development
The group is involved in develop tools to faster evaluate, interpret and visualize omics data. Major tools the group has developed are MapMan a GUI application to visualize omics data on biological pathways. ROBINa is a graphical frontend to BioConductor/R. It allows you to quality control and visualize microarray and RNASeq data. In addition experimental questions can be formulated by visually drawing experiments and the data is then statistically evaluated using state-of-the-art statistical algorithms developed in R. All these tools are supported by forums.
Within the MapMan tool we have also developed a specific ontology to support the annotation of genes and metabolites for plant omics data. This onotology has been expanded to more than 10 plant species and can be applied to any plant species where transcript data is available based on sequence similarity searches. We thus provide an easy way to learn about plant transcriptome projects.
Also the group hosts the GABI PRIMARY database. A database for primary data generated within the BMBF financed German GABI programs.
Funding has been provided by
- MPG society and Helmholtz association
- BMBF in the GABI-II, GABI-Future, BioEnergy2021, KBBE programs and through the goFORSYS grant
- EU FW7
We are always looking for bright and motivated students.
Thus if you want to pursue a career in
- cell wall research
- high throughput data analysis
- cutting edge next generation sequencing data projects
- development of ontologies
Just contact us.