Bioinformatics and Proteogenomics Group
Agroscope research program on microbial biodiversity
What do we do?
Our research at the Bioinformatics and Proteogenomics Group revolves around the bioinformatic integration and analysis of datasets from state-of-the-art omics technologies, which we obtain through close collaboration with experimental biologists. These datasets include genome sequences, gene and protein expression, as well as metabolomics data. One particular focus is to exploit the unique advantages of proteomics data, including strategies to achieve complete proteome coverage (including the membrane proteome) and to identify all proteins encoded in a genome (proteogenomics).
Recently, we started to study the role of microbiomes – e.g. for plant protection – by applying metagenomics, genomics and transcriptomics approaches.
As part of a research consortium led by Professor J.A. Robinson (Chemistry Dept., UZH) and Professor L. Eberl (Microbiology Dept., UZH), our team provided its proteomics data analysis and integration expertise to help uncover the fact that a new peptidomimetic (a small protein-like chain designed to mimic a peptide) active against Gram-negative pathogens, exhibits a novel mode of action (MoA). In this case, it selectively ruptures the outer membrane of Gram-negative bacteria.
Furthermore, our proteogenomics expertise helped to uncover protein expression evidence for novel, unannotated short coding sequences in the rhizobial model organism Bradyrhizobium japonicum. A current focus of the group is to develop a general approach to identify such missed protein-coding genes in prokaryotes.
Main publications 2016
- Urfer M et al. A peptidomimetic antibiotic targets outer membrane proteins and disrupts selectively the outer membrane in Escherichia coli. J Biol Chem 2016;291(4):1921-32.
- Turnbull L et al. Explosive cell lysis as a mechanism for the biogenesis of bacterial membrane vesicles and biofilms. Nat Commun 2016;7:11220.
- Čuklina J et al. Genome-wide transcription start site mapping of Bradyrhizobium japonicum grown free-living or in symbiosis - a rich resource to identify new transcripts, proteins and to study gene regulation. BMC Genomics 2016;17:302.