Martin Pabst Group
The Microbial Proteomics Group develops novel mass spectrometric approaches and data processing pipelines to explore the remarkable diversity of microbes and their communities they live in.
Prokaryotes—the unseen majority on our planet—encompass an enormous metabolic and biochemical diversity. However, only a small fraction of this potential has been discovered and explored for their use in biotechnology and industry to date; for example, there is a growing demand for novel enzymes with high process performances to replace traditional chemistry, or to realize new bioactive compounds such as promising antimicrobials.
Our laboratory is equipped with micro- and nano-flow separation systems coupled to state-of-the-art high-resolution mass spectrometers (GC-MS and LC-Orbitrap-MS instruments).
In nature, microbes live in diverse communities that fundamentally impact human health and are responsible for global processes, such as the biogeochemical cycles. However, the majority of microbial diversity remains uncultured and poorly characterized. Therefore, advanced, culture-independent approaches are urgently needed that provide molecular-level insights into these ecosystems.
METAPROTEOMICS—the large-scale identification and quantification of proteins from complete microbial communities—is a powerful technology for measuring the link between protein diversity, expressed metabolic pathways, and ecological functions. We aim to advance metaproteomics approaches and expand this emerging technology into new fields of microbial ecologies.
If you want to find out more, please have a look at our recent Cell Systems paper (featured article May) Database-independent de novo metaproteomics of complex microbial communities
Or check out our latest preprint Comparative metaproteomics demonstrates different views on the complex granular sludge microbiome | bioRxiv
Glycosylation—the covalent attachment of carbohydrate chains to proteins—is one of the most abundant but also most diverse protein post-translational modifications found in nature.
PROTEIN GLYCOSYLATION is fundamental to all domains of life, but the many biological roles protein glycosylation serves in bacteria and archaea have yet to be explored. Furthermore, the vast array of carbohydrate structures produced by prokaryotes provide great opportunities for new applications in biotechnology and the pharmaceutical industry (such as the discovery of potential antimicrobials, or the identification of targets for the development of vaccines). Our focus is on developing new large-scale discovery methods that address the considerable chemical diversity and strain variability expressed in prokaryotes.
Please check our paper in Chemical Science (HOT articles February) about the phylogenetic distribution of remarkable nine-carbon sugars (sialic acids), or our recent ISME paper featuring unique anammox surface layers!
YEAST PROTEOMICS: Saccharomyces cerevisiae is one of the best-studied eukaryotic model cells and increasingly used as a cell factory in industry. We establish and apply new approaches to identify and quantify protein dynamics and covalent protein modifications in yeast. The proteome shows a vastly higher diversity compared to the genome, which is by a significant proportion due to covalent protein modifications (e.g., for fast regulation of intermolecular interactions) or by tuning of enzyme activities. Our yeast proteomics activities are in collaboration with the Daran-Lapujade Lab (yeast synthetic biology).
Please have a look to our recent FEMS yeast research review (articles making impact 2020): Shot-gun proteomics: why thousands of unidentified signals matter or our most recent article in Molecular & Cellular Proteomics about: Proteome dynamics in yeast
HOST CELL PROTEOMICS: We develop our novel mass spec approaches for monitoring host cell protein removal to accelerate downstream process development. This project is being performed in collaboration with the Ottens Lab.
Check our most recent article (in collaboration with GSK): The complete E. coli host cell proteome