Sequence-based coevolutionary prediction of species-specific interactomes

Evolutionarily conserved protein-protein interactions (PPIs) reveal fundamental biological processes. However, predicting protein function solely from these interactions provides an incomplete picture of biological systems. Computational methods for predicting PPIs often struggle due to limited functional annotations in databases, making it difficult to fully understand unique biological systems. This study introduces ContextMirror2.0 (CM2.0), a coevolution-based method designed to address these limitations. Coevolutionary approaches, unlike supervised machine learning methods, do not rely on labelled datasets, proving valuable in addressing the scarcity of data for species-specific PPIs. Around 40% of CM2.0's top-1000 predicted PPIs for E. coli, S. enterica, and S. aureus are supported by experimental PPI databases. However, comparative analysis of the resulting functional communities further revealed both highly conserved interaction patterns and species-specific interactions. CM2.0 leverages coevolutionary information at the phylogenetic level to explore protein interaction dynamics and understand the functional consequences of species-specific variations. This information can inform further studies on the emergence of novel functions, adaptation to specific environments, and the development of targeted therapies.