Functionality of system components: conservation of protein function in protein feature space

Area of Science:

• Bioinformatics
• Computational Biology
• Evolutionary Biology

Background:

• Protein features like posttranslational modifications, subcellular localization, and physicochemical properties can be predicted from amino acid sequences.
• These sequence-derived features are valuable for predicting protein function.

Purpose of the Study:

• To investigate the conservation patterns of sequence-derived protein features between orthologs and paralogs.
• To evaluate the performance of a protein function prediction method (ProtFun) that relies solely on sequence-derived features.
• To assess the cross-species applicability of such a prediction method.

Main Methods:

• Comparative analysis of protein feature conservation between orthologous and paralogous proteins.
• Evaluation of the ProtFun prediction method using sequence-derived features as input.
• Performance assessment across different taxonomic domains (Eukaryota, Archaea, Bacteria).

Main Results:

• Sequence-derived protein features are significantly more conserved among orthologs than paralogs.
• The ProtFun method demonstrates robust performance across most eukaryotes and performs better than expected in archaea and bacteria.
• Posttranslational modifications, including cellular use and sequence motifs, show conservation within Eukarya.

Conclusions:

• Conservation of sequence-derived features in orthologs indicates their importance for protein function and evolutionary selection.
• Protein function prediction methods based on sequence features are effective and transferable across diverse organisms.
• Sequence motifs and cellular roles of posttranslational modifications are conserved within eukaryotic proteins.