Our research topics

Our research revolves around identification of molecular mechanisms leading to the emergence of complex phenotypes, and providing strategies for crop improvement via directed mutagenesis or precise breeding. The phenotypes of interest include most importantly performance and quality traits of crops. Our methodology builds up on integration of multi-omic data in the context of metabolic and regulatory networks. Current research in the group includes three major directions:

  1. evolution and modelling of C4 photosynthesis,
  2. modelling and engineering of plant lipid metabolism,
  3. molecular principles of metabolic traits emergence.

Additionally, we conduct collaborative projects with other groups of the IPK Gatersleben providing computational expertise, high throughput data analysis and modelling tools

Evolution and modeling of C4 Photosynthesis

Figure 1: (A) Comparison of C3 and C4 plants based on leaf cross section and metabolism. (B) Comparison of C4 cycle modes.

 

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 mostly resolve this problem by concentrating CO2 at the site of Rubisco through a cycle of biochemical reactions which requires compartmentation. C4 photosynthesis is a complex trait, the sum of anatomical, regulatory and metabolic sub-traits is numerous, yet it evolved more than 60 times independently. Using a combination of RNA-seq and model building we dissect the complex trait and its evolution. The complex C4 trait 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 extensive 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.

 

 

 

Modelling and engineering of plant lipid metabolism

Lipid compounds are central determinants of oil crops quality traits, but due to their multiple molecular functions, they also control the overall plant performance. The structural diversity of lipids reflects their wide range of functions. Nowadays, mass-spectrometry-based profiling of plant tissues enables routine identification and quantification of more than 300 lipid compounds, many of which exhibit developmental- and/or stress-specific accumulation. In the same time, the biosynthetic pathways and modes of regulation are known only for a relatively small set of these compounds.

Therefore in this project, we employ metabolomic, chemometric and transcriptomic analysis of tissues and isolated organelles to reconstruct and study plant lipid assembly pathways. Our primary goal is to explain and simulate observed plant lipid diversity and devise strategies for bioengineering and targeted breeding of oil crops.

In parallel, we build and extend metabolic models of plant seed and study the interaction between acyl lipid turnover and primary of the plant cell in different developmental and genetic contexts. The project relies on close collaboration with labs of the Molecular Genetics department. Our external collaboration partners include Max Planck Institute of Molecular Plant Physiology, Germany, Weizmann Institute of Science, Israel, and Argonne National Labs, IL, US.

Molecular origins of complex traits

Many complex phenotypes such as stress resistance, increased nutritional value or alteration of colouration originate from the rearrangement of metabolic fluxes under selective pressure. Metabolic fluxes, however, are system-scale properties controlled by multiple enzymatic and regulatory processes and therefore are controlled by multiple loci.

In this project, we utilise the capacity of IPK phenomic and genomic infrastructure with access to high throughput RNAseq and metabolomic technology to generate and multi-omic QTL data describing the trait emergence on multiple levels of system complexity. We use metabolic modelling and tools of network analysis and inference in combination with QTL and GWAS analysis to study the emergence of complex traits on a system scale and identify biochemical cues required to achieve given phenotype. We are also interested in applying our methodology to devise strategies for precise breeding of new crop cultivars, investigate the transferability of beneficial phenotypic traits between crop cultivars and their wild ancestors, and study metabolic principles of heterosis.


In the frame of this research area, we conduct projects in close collaboration with experimental labs of the Molecular Genetics department. Our external collaborators include Max Planck Institute of Molecular Plant Physiology, Germany, and Weizmann Institute of Sciences, Israel.