Evolution and Regulation of Plant Specialized Metabolism
In our group we aim to better understand the evolution of plant specialized metabolic pathways and their regulation from the organismal down to the single-cell level.
Plants produce an enormous diversity of specialized metabolites (natural products). While some of them are unique and only occur in specific lineages, others are conserved and more widespread. Interestingly, in some cases the biosynthesis of even complex natural products was invented more than once in nature. Studying such independently evolved metabolic pathways offers insights into the evolution of pathways and their regulation, and can inform pathway engineering approaches.
As a model pathway system, we currently use ipecac alkaloid biosynthesis, a remarkable example of independently evolved complex natural products. These monoterpenoid-derived tetrahydroisoquinoline alkaloids occur in the Cornales and Gentianales orders, which diverged at least 100 million years ago. Ipecac alkaloid-producing species are traditional medicinal plants and particularly known for their emetic activities. “Ipecac syrup”, an extract prepared from Carapichea ipecacuanha rhizome, was an over-the-counter emetic drug used for many decades.
We have been elucidating ipecac alkaloid biosynthesis in Alangium salviifolium (Cornales), C. ipecacuanha (Gentianales, Rubiaceae, Rubioideae) and Pogonopus speciosus (Gentianales, Rubiaceae, Ixoroideae) using classic pathway discovery methods i.e. generating genomics, transcriptomics and metabolomics data and subsequent pathway reconstitution in Nicotiana benthamiana as well as in vitro enzymatic activity assays using recombinantly produced proteins. In silico approaches such as phylogenetic analyses and protein model comparisons (alphafold) are used to understand evolutionary relationships between the discovered enzymes. We also compare subcellular localization and protein-protein-interactions of pathway enzymes.
Such comparative analyses recently revealed a nearly identical chemical logic of ipecac alkaloid biosynthesis in these species but striking differences in the evolutionary strategies of enzyme recruitment, showcasing how nature uses different ways to reach the same outcome. We are currently unravelling the remaining pathway steps.
Single-cell omics to boost enzyme discovery and to unravel pathway partitioning
Recently, we have been focusing on applying new methods to study pathways and regulation down to the single cell level. In collaboration with other department members (Project Group Natural Product Pathways in Plants and Single Cells) and external collaborators (https://buell-lab.github.io/) we perform single cell metabolomics and single-cell transcriptomics to better understand how specialized metabolic pathways are organized at the cell-type-specific level.
The use of single-cell omics data recently enabled the discovery of the long sought-after missing iridoid cyclase and will accelerate the elucidation of missing ipecac alkaloid biosynthesis steps. Additionally, it will further our understanding about why cell-type-specific pathway partitioning occurs and how plants regulate this.
An independent method development study has focused on analyzing the protein level of regulators of cell type-specific processes. Because detecting lowly abundant regulatory proteins is still a major challenge in single-cell proteomics we use protein proximity labelling to pull down and analyze regulatory nuclear proteins from distinct cell layers. This study has been performed in the model plant Arabidopsis thaliana because it is easily transformable and essential prior knowledge about cell type-specific promoters is available.
Alumni:
Clara Morweiser MSc thesis, MPI fellowship 2024-2025
Ketil Krabbe MSc thesis 2024
Chloée Tymen MSc thesis 2024
Olivia Dittberner, Master internship 2023