Student project: Enzymatic production and LC-MS/MS analysis of sulfatedoligosaccharides
In the ocean, the carbon cycle is driven by photosynthetic algae, followed by recycling via extensive bacterial degradation of algal biomass. One important constituent of algal biomass are polysaccharides, yet we lack appropriate tools to characterize their structures that are often branched or modified by acetyl or sulfate groups. However, bacteria have evolved enzymes that highly specifically hydrolyze a target polysaccharide. Analogous to restriction enzymes for DNA research, these specific hydrolyses can be used to dissect the structure of polysaccharides.
In this project, we want to characterize novel enzymes and establish them as tools to study environmentally relevant polysaccharides. For example, the polysaccharide fucoidan plays an important role in sequestering carbon in the ocean. Fucoidan is a highly-branched cell wall polysaccharide, but despite its main building block, sulfated L-fucose, we only have very limited structural information and only few available fucoidan-active enzymes. Along known enzymes, we will screen a small library of new enzyme candidates and establish analytical workflows to characterize the structure of released oligosaccharides by LC-MS/MS. You will learn how to work with heterologously expressed enzymes, how to setup new chromatographic methods to separate carbohydrates and analyse complex molecular fragmention patters generates by MS/MS experiments. From this we will not only learn the exact molecular mechanism about how bacteria feed on polysaccharides, but also will be able to identify structures of important biomolecules in the ocean.
The expected duration of this project is 3-6 months. For questions and interest please contact
Suggested reading:
S. Vidal-Melgosa et al., “Diatom fucan polysaccharide precipitates carbon during algal blooms,” Nat. Commun., 2021, doi: 10.1038/s41467-021-21009-6.
A. Sichert et al., “Verrucomicrobia use hundreds of enzymes to digest the algal polysaccharide fucoidan,” Nat. Microbiol., 2020, doi: 10.1038/s41564-020-0720-2.
Ropartz et al., “In-depth structural characterization of oligosaccharides released by GH107 endofucanase MfFcnA reveals enzyme subsite specificity and sulfated fucan substructural features”. Glycobiology, 2022, doi: 10.1093/glycob/cwab125