Year: 2019
Type: article
Abstract: The molecular and cellular basis of novelty is an active area of research in evolutionary biology. Until very recently, the vast majority of cellular phenomena were so difficult to sample that cross-species studies of biochemistry were rare and comparative analysis at the level of biochemical systems was almost impossible. Recent advances in systems biology are changing what is possible, however, and comparative phylogenetic methods that can handle this new data are wanted. Here, we introduce the term "phylogenetic latent variable models" (PLVMs, pronounced "plums") for a class of models that has recently been used to infer the evolution of cellular states from systems-level molecular data, and develop a new parameterization and fitting strategy that is useful for comparative inference of biochemical networks. We deploy this new framework to infer the ancestral states and evolutionary dynamics of protein-interaction networks by analyzing >16,000 predominantly metazoan co-fractionation and affinity-purification mass spectrometry experiments. Based on these data, we estimate ancestral interactions across unikonts, broadly recovering protein complexes involved in translation, transcription, proteostasis, transport, and membrane trafficking. Using these results, we predict an ancient core of the Commander complex made up of CCDC22, CCDC93, C16orf62, and DSCR3, with more recent additions of COMMD-containing proteins in tetrapods. We also use simulations to develop model fitting strategies and discuss future model developments.
Source: PLoS Computational Biology
Institution: The University of Texas at Austin
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $2,350
Awards: G1346015802, G2366074401, G2850145367, Evolutionary Biophysics of Slo3 Potassium Channels, G3667756519, G3899806454, G4714635365, Network-Guided Predictions and Characterization of Genes Governing Pattern Recognition Receptor-Mediated Immunity in Cereals, G6043510538, Mapping the blood cell protein complexosome, Proteomics and model organism humanization to decode human genetics, Mapping the ciliary interactome, an extensive protein interaction network underlying human ciliopathies
OpenAlex ID: W2981475932