A natural classification of the basic helix-loop-helix class of transcription factors

Abstract

A natural (evolutionary) classification is provided for 242 basic helix-loop-helix (bHLH) motif-containing proteins. Phylogenetic analyses of amino acid sequences describe the patterns of evolutionary change within the motif and delimit evolutionary lineages. These evolutionary lineages represent well known functional groups of proteins and can be further arranged into five groups based on binding to DNA at the hexanucleotide E-box, the amino acid patterns in other components of the motif, and the presence/absence of a leucine zipper. The hypothesized ancestral amino acid sequence for the bHLH transcription factor family is given together with the ancestral sequences of the subgroups. It is suggested that bHLH proteins containing a leucine zipper are not a natural, monophyletic group.

Figure 1

Fig. 1. Aligned bHLH motif for representative sequences for major evolutionary lineages in NJ tree in Fig. 2. Designation of basic (B), helix (H), and loop (L) regions and the numbering sequence for the individual amino acids follows Ferre–D’Amare (6). Ancestor of various groups reflects sequence inferred to be hypothetical ancestral sequence from maximum parsimony analysis. Clades are in order, as in Fig. 2.

Figure 2

An NJ phylogenetic tree of 122 bHLH proteins. To simplify the tree, nodes were collapsed to a single horizontal line when statistical support for a particular node was questionable, i.e., when boot strap support was <35%. Furthermore, the boot strap values havebeen coded. All branches subtending a clade supported by >95% of the 500 trials are shown by thickened branches. Branches with support between 80 and 94% are marked with an open circle (○), and those with support between 65 and 79% are delimited with a + sign. Branches with values <65% are unmarked. Clades reflecting proteins containing an LZ are indicated with “LZ.”

Figure 2

An NJ phylogenetic tree of 122 bHLH proteins. To simplify the tree, nodes were collapsed to a single horizontal line when statistical support for a particular node was questionable, i.e., when boot strap support was <35%. Furthermore, the boot strap values havebeen coded. All branches subtending a clade supported by >95% of the 500 trials are shown by thickened branches. Branches with support between 80 and 94% are marked with an open circle (○), and those with support between 65 and 79% are delimited with a + sign. Branches with values <65% are unmarked. Clades reflecting proteins containing an LZ are indicated with “LZ.”