Basic-helix-loop-helix (bHLH) transcription factors (TFs) belong to a family of transcriptional regulators present in three eukaryotic kingdoms. Many different functions have been identified for these proteins in animals, including the control of cell proliferation and development of specific cell lineages, and their mechanism for controlling gene transcription often involves homo- or hetero-dimerization. In plants, little is known about the bHLH family but we have determined there are 133 bHLH genes in Arabidopsis thaliana and have confirmed that of these at least 113 are expressed. The AtbHLH genes constitute one of the largest families of transcription factors in A. thaliana with significantly more members than are found in most animal species and about an equivalent number to those in vertebrates. Comparisons with animal sequences suggest that the majority of plant bHLH genes have evolved from the ancestral group B class of bHLH genes. By studying the AtbHLH genes collectively, twelve sub-families have been identified. Within each of these main groups, there are conserved amino acid sequence motifs outside the DNA binding domain. Potential gene redundancy amongst members of smaller sub-groups has been analysed, and the resulting information is presented to provide a simplified visual interpretation of the gen
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