Functional classes in the three domains of life

The evolutionary divergence among the three major domains of life can now b e addressed through the first set of complete genomes from representative s pecies. These model species from the three domains of life, Haemophilus inf luenzae for Bacteria, Saccharomyces cerevisiae for Eukarya, and Methanococc us jannaschii for Archaea, provide the basis for a universal functional cla ssification and analysis. We have chosen 13 functional classes and three su perclasses (ENERGY, COMMUNICATION and INFORMATION) as global descriptors of protein function. Compositional comparison of the three complete genomes r eveals that functional classes are ubiquitous yet diverse in the three doma ins of life. Proteins related with ENERGY processes are generally represent ed in all three domains, while those related with COMMUNICATION represent t he most distinctive functional feature of each single domain. Finally, func tions related with INFORMATION processing (translation, transcription, and replication) show a complex behaviour. In Archaea, proteins in this supercl ass are related with proteins in either Eukarya. or Bacteria, as recognized previously. The distribution of functional classes in the three domains ac curately reflects the principal characteristics of cellular life forms.