Yeast Complexome – The Complex Portal rising to the challenge

The Complex Portal ( www.ebi.ac.uk/complexportal ) is an encyclopedia of macromolecular complexes from 20 model organisms that is manually curated based on literature evidence. In 2018 we completed the first draft of all Saccharomyces cerevisiae complexes, also known as the ‘yeast complexome’. Throughout the project we worked in close collaboration with SGD and UniProt curators to build a list of all known and predicted complexes in yeast. It contains nearly 600 well defined complexes including super-structures like polymerases and ribosomal processomes where complexes act as participants of larger complexes. In total, approx 30% of the yeast proteome are represented in these stable complexes. Additionally, we have roughly 30 potential complexes on a ‘watch list’ for which we could not find enough evidence for their existence in vivo . During the course of this project,1382 new, manually assigned, Gene Ontology (GO) annotations specific to complexes as entities have been produced. We have performed an initial comparison of the 589 Complex Portal curated complexes (CPX) with the 408 manually curated complexes from the Pu et al. (2009) CYC2008 dataset (CYC), previously considered the biggest reference complexome for yeast. An initial comparison showed that there is a good agreement between the 2 datasets for smaller complexes but that there is growing disparity over the subunit composition of the larger complexes. Overall, 281 complexes are identical in both datasets, and this increases to 500 complexes that share at least 50% of subunits. Further analysis of this dataset is ongoing. Further, the Yeast Complexome is now being used a gold standard to validate complexes predicted by topological analyses of networks derived from large-scale experiments and for GO enrichment analysis of participant proteins and genes. Additional complexomes are in preparation, including human, mouse and C.elegans, with that of Escherichia coli scheduled to be completed in 2019.