Evolution of bHLH transcription factors: Modular evolution by domain shuffling?

Multidomain proteins usually contain several conserved and apparently indep endently evolved domains. As a result, classifications based on only a sing le small domain may obscure the true evolutionary relationships of the prot eins. The current classification of basic helix-loop-helix (bHLH) domain-co ntaining proteins is based on the conserved bHLH domain alone. Herein, we e xplore whether sequence homology and, therefore, evolutionary relationships can be detected among the flanking or non-bHLH components of the amino aci d sequences of 122 bHLH proteins. These 122 proteins were the same proteins previously used to construct the existing classification of the bHLH-domai n-containing proteins. Several possible scenarios are examined in order to explain the observed patterns of sequence divergence, including (1) monophy ly, (2) convergent evolution, (3) addition of functional components to the bHLH domain, and (4) modular evolution with domain shuffling. Drawing on se veral lines of evidence, we suggest that modular evolution by domain shuffl ing may have played an important role in the evolution of this large group of transcriptional regulators.