Martin Pabst Group

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 de novo metaproteomics papers in Cell Systems (featured article May) Database-independent de novo metaproteomics of complex microbial communities and on bioRxiv: NovoLign: metaproteomics by sequence alignment

Check out our latest article on complex wastewater microbiomes: The different (omics) views on the complex aerobic granular sludge microbiome

Or take a look at our latest preprint on the metabolic potential of a microorganism that can thrive in nutrient-poor environments: The metabolic potential of Aeromonas to utilise the carbohydrate polymer chitin | 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