Research Group Network Analysis and Modelling
Head: Dr. Andrea Bräutigam
The group focuses on the dissection, modeling, and evolution of complex traits in plants using systems biotechnology, i.e. RNA-seq and genome-seq in conjunction with phenotypic data from metabolomics, phenotyping and physiological analyses.
Figure 1: Conceptual model of the branched C4 cycle with key enzymes and energy consumption annotated.
Plants with the C4 trait are able to supercharge their carbon fixation using a carbon pump. Plants without the trait, also called C3 plants, use only Rubisco to fix CO2. This enzyme is not only a slow enzyme but also not very specific for CO2 and hence inefficient. C4 plants largely resolve problem by concentrating CO2 at the site of Rubisco through a cycle of biochemical reactions which require compartmentation. C4 photosynthesis is a complex trait, the sum of anatomical, regulatory and metabolic subtraits, yet it evolved independently more than 60 times. Using a combination of RNA-seq and model building we dissect the complex trait and its evolution. The complex trait of C4 photosynthesis offers three outstanding advantages: (i) a trait directly related to yield, as many of the very productive crop plants are indeed C4 plants, (ii) a large collection of plants with the trait available for study and corresponding multi-level omics data, and (iii) active efforts to recreate the trait using synthetic biology.
Past projects include the molecular identification of enzymes and transport proteins contributing to the C4 cycle and conceptual models of the cycle for Gynandropsis gynandra, different Flaveria species, Panicum maximum, and Zea mays, model extension to a branched rather than linear cycle, identification of energy requirements depending on decarboxylation enzymes, developmental control of cycle architecture, modeling of limits for cycle architecture, conceptual models about the architectural trait components, the role of photorespiration in the trait, and stoichiometric models to understand evolution.
Current projects include a meta-analysis of ten independent origins of C4 photosynthesis to test model predictions, stoichiometric model development, and regulatory networks underlying the C4 trait.
The methods, concepts, and models developed for the analyses of the complex trait C4 photosynthesis are largely transferable to other complex traits such as yield. Transfer is under development.
RNA-seq to understand complex phenotypes
The transcriptional abundance of all transcripts in a sample reflects the combined output of the transcriptional regulatory networks that result in transcription, transcript stability, and transcript decay. For conditions within the range of the ecological niche of the plant (i.e. conditions which the plants population has encountered in recent evolutionary time), the transcriptional abundance informs about the regulatory network itself and about the output evolved to maximize reproductive success. For conditions outside this range (i.e. mutations, conditions beyond the ecological niche, or combinations thereof), the plant still processes the available information and enacts a response, however, it may not present itself as logical in the sense that it may not maximize reproductive success since it was not shaped by evolution. Both experimental approaches yield insights into the regulatory networks, their inputs and their information processing, and into the outputs which shape the observable phenotypes. Projects related to RNA-seq analyses are frequently carried out with collaborations partners.
Currently ongoing projects include Arabidopsis mutant stress responses, secondary metabolite production in desert plants, iron tolerance in rice, hypoxia memory in tomato, cryopreservation in various species, barley grain development, Azolla filiculoides genome sequencing and N-influenced transcriptome analyses, and RNA-seq based population level analyses of biomass.
Past projects include the SO2 responses of Arabidopsis, prey digestion in the venus flytrap, the pea transcriptome, the Azolla filiculoides transcriptome, nitrogen/phosphor balance in maize, the CAM trait, a mutant involved in salt stress, and the regulatory network underlying systemic acquired resistance.