Expertise:

Activity-based (meta-)proteomics, click chemistry, LC, MS, biochemical assays, organic synthesis

PhD Project: Activity-based Metaproteomics

Microbiomes are the foundation of planetary health, critically influencing ecosystems, human health as well as biogeochemical cycles. The mammoth task caused by the immense taxonomic complexity of microbiomes is the accurate functional characterization of this plethora of microorganisms. While metagenomics and metatranscriptomics allow insights into the taxonomic composition and functional potential of the analyzed samples, metaproteomics can disclose the functional profile and provide an in-depth view of the interactions between microorganisms and their host or their environment (1). They, however, still fail to distinguish between active and inactive proteins.

To bridge this gap, we will advance activity-based metaproteomics (ABMP, Link to short video about Sarah´s PhD thesis), opens an external URL in a new window — a cutting-edge approach that focuses exclusively on active proteins — in our Cluster of Excellence Microplanet, opens an external URL in a new window. Activity-based proteomic profiling (ABPP) employs small molecule probes that bind covalently to the active site of an enzyme. These probes can label proteins in their native state, by penetrating cells and tissues. Tailoring these probes to specific enzyme groups makes ABPP a versatile protein profiling technique (2). By integrating ABPP with high-resolution MS and using it for metaproteomics, our project aims to enable the selective detection of catalytically active proteins within complex microbiomes, providing a functional perspective on microbial ecosystems and their response to environmental changes.

We will establish a high-throughput workflow and perform activity-based metaproteomic analyses of selected bacterial communities, e.g., in wastewater, for identifying members of different enzyme classes (hydrolases and oxidoreductases). Next to the discovery of unknown microbial enzymes and their activity profiles under different conditions, our workflow will enable us to derive relationships between active enzyme abundance and biotransformation rates to assess substrate specificity, inhibition by drugs and biotransformation products, and the potential for biotechnological optimization for key enzymes. This research aligns with the broader goal of the Cluster of Excellence "Microbiomes drive planetary health" of understanding microbiomes as fundamental drivers of planetary health.

1. Salerno, C. (2024b). Metaproteomics: Methods and Protocols. Methods in molecular biology. Springer Protocols. doi:https://doi.org/10.1007/978-1-0716-3910-8.
2. Cravatt, B.F., Wright, A.T. and Kozarich, J.W. (2008). Activity-Based Protein Profiling: From Enzyme Chemistry to Proteomic Chemistry. Annual Review of Biochemistry, 77(1), pp.383–414. doi:https://doi.org/10.1146/annurev.biochem.75.101304.124125.