Functional Equivalence of Distant Orthologs and Paralogs

Many animal toolkit proteins, despite over 1 billion years of independent evolution in different lineages, often exhibit functionally equivalent activities in vivo when substituted for one another. These observations indicate that the biochemical properties of these proteins and their interactions with receptors, cofactors, etc. have diverged little over vast expanses of time.

What makes these results so surprising and notable is that the function of any transcription factor or ligand is dependent upon interaction with other endogenous proteins—transcription factors, coactivators, corepressors, and parts of the transcriptional machinery in the case of transcription factors, cell surface receptors in the case of ligands. One might expect that genetic drift or the coadaptation of proteins within lineages would lead to functional incompatibilities among proteins from different taxa, especially those separated by over 1 billion years of independent evolution. Yet, many proteins are so conserved that they can interact and function together with other proteins from long-diverged taxa. These results have been more the rule than the exception for transcription factors. Numerous studies of eukaryotic transcription demonstrate that the basic transcriptional machinery, many coactivators, corepressors, chromatin-remodeling complexes, and the protein motifs through which transcription factors interact with them, are often very well conserved.

Sean B. Carroll. Cell 134, July 11, 2008.