Toward an elucidation of the process underlying the evolution of gene regulation several billion years ago

Because the DNA of primeval organisms no longer remains, the earliest ages of world history are generally considered off limits to molecular evolutionary analysis.However, a new method can measure evolutionary distances between existing and ancestral organisms by focusing on repeating sequences.This approach utilizes the similarity in intramolecular direct repeats present in the transcription initiation factors TBP and TFIIB as an evolutionary measure revealing the degree of similarity between the genes of present offspring and those of their ancestors.The approach also reveals the properties of the ancestors and the order of emergence of TBP and TFIIB.While both archaeal and eukaryotic transcription initiation systems utilize TBP and TFIIB, eukaryotic systems include larger numbers of initiation factors.It remains uncertain how eukaryotic transcription initiation systems have evolved.Inter-repeat sequence dissimilarity indicates that the asymmetry of two repeats in TBP and TFIIB has gradually increased during evolution.Interspecies sequence diversity indicates that the resultant asymmetric structure, which is related to the ability to interact with multiple factors, diverged in archaeal TBP and archaeal/eukaryotic TFIIB during evolution.This suggests that eukaryotic TBP initially acquired multiple Eukarya-specific interactors through asymmetric evolution of the two repeats.After the asymmetric TBP generated the complexity of the eukaryotic transcription initiation systems, its diversification halted, and its asymmetric structure spread throughout eukaryotic species.This approach provides a new way to discuss mechanistic and system evolution quantitatively.