Wellcome Senior Research Fellow
Juri Rappsilber is a Wellcome Senior Research Fellow, Professor of Proteomics in the University of Edinburgh and Professor of Bioanalytics in the Technische Universität Berlin. His group develops tools to study the function, location, interactions and structure of proteins in cells. Most of the work involves cross-linking, mass spectrometry, machine learning and software development. Juri Rappsilber took his PhD in Proteomics at the European Molecular Biology Laboratory (EMBL) in Heidelberg and Goethe Universität Frankfurt am Main in the lab of Matthias Mann and followed him as a postdoc to Odense, Denmark. In 2003 he relocated as principle investigator to the FIRC Institute of Molecular Oncology, Milan, which he left in 2006 to move to the University of Edinburgh. He became Wellcome Senior Research Fellow in 2009 and Professor of Proteomics in 2010. He has also held the post of Professor of Bioanalytics in Berlin since 2011.
Genes are not randomly distributed in the genome. In humans, 10% of protein-coding genes are transcribed from bidirectional promoters and many more are organised in larger clusters. Intriguingly, neighbouring genes are frequently coexpressed but rarely functionally related. We could show recently that coexpression of bidirectional gene pairs, and closeby genes in general, is buffered at the protein level (Kustatscher et al., 2017). Taking into account the 3D architecture of the genome, we found that co-regulation of spatially close, functionally unrelated genes is pervasive at the transcriptome level, but does not extend to the proteome. We extended this analysis from human cells to mouse tissues (Grabowski et al., 2018). Chromosomal proximity of genes explains a proportion of this nonfunctional mRNA coexpression also there. However, the main driver of non-functional mRNA coexpression across mouse tissues is epigenetic similarity. Protein-level buffering likely reflects a lack of coordination of post-transcriptional regulation of functionally unrelated genes. The large presence of non-functional coexpression of genes at the transcript but not protein level suggests that proteomics data should surpass transcriptomics data when screening for functional links between genes.
The annotation of protein function is a longstanding challenge of cell biology that suffers from the sheer magnitude of the task. We therefore developed ProteomeHD, which documents the response of 10,323 human proteins to 294 biological perturbations, measured by isotope-labelling mass spectrometry (Kustatscher et al., 2019). Using this data matrix and robust machine learning we create a co-regulation map of the cell that reflects functional associations between human proteins and that outperforms predictions done by STRING based on the NCBI GEO repository currently holding mRNA expression profiling data from more than one million human samples. Our map identifies a functional context for many uncharacterized proteins, including microproteins that are difficult to study with traditional methods. Co-regulation also captures relationships between proteins which do not physically interact or co-localize. For example, co-regulation of the peroxisomal membrane protein PEX11β with mitochondrial respiration factors led us to discover a novel organelle interface between peroxisomes and mitochondria in mammalian cells. The co-regulation map can be explored at www.proteomeHD.net
Our lab is also continuing its development of cross-linking/mass spectrometry as a tool to investigate in cells structures of proteins and their complexes.
Kustatscher, G., Grabowski, P., Schrader, T.A., Passmore, J.B., Schrader, M., and Rappsilber, J. (2019). Co-regulation map of the human proteome enables identification of protein functions. Nat Biotechnol. 37, 1361-1371.
Mendes, M.L., Fischer, L., Chen, Z.A., Barbon, M., O'Reilly, F.J., Giese, S.H., Bohlke-Schneider, M., Belsom, A., Dau, T., Combe, C.W., Graham, M., Eisele, M.R., Baumeister, W., Speck, C., and Rappsilber, J. (2019). An integrated workflow for crosslinking mass spectrometry. Mol Syst Biol. 15, e8994.
Grabowski, P., Hesse, S., Hollizeck, S., Rohlfs, M., Behrends, U., Sherkat, R., Tamary, H., Ünal, E., Somech, R., Patıroğlu, T., Canzar, S., van der Werff Ten Bosch, J., Klein, C., and Rappsilber, J. (2019). Proteome Analysis of Human Neutrophil Granulocytes From Patients With Monogenic Disease Using Data-independent Acquisition. Mol Cell Proteomics. 18, 760-772.
Protein co-regulation predicts functions of unknown proteins. (left) The uncharacterized microprotein TMEM256 has co-regulation partners enriched for the GO term ‘mitochondrial inner membrane’. The uncharacterized HEATR5B protein is positioned next to Vacuolar Protein Sorting factors. (right) For multifunctional proteins, co-regulation can reveal a mix of their functions (DDX3X; n=14 of 81 co-regulated proteins annotated with GO term ‘mRNA splicing’, via spliceosome, n=27 with GO term ‘cytosolic ribosome’), or their main function only (prohibitin, PHB; n=9 of 11 co-regulated proteins annotated as ‘mitochondrial inner membrane’).