Abstract
BackgroundMolecular and genetic analyses conducted in model organisms such as Drosophila and vertebrates, have provided a wealth of information about how networks of transcription factors control the proper development of these species. Much less is known, however, about the evolutionary origin of these elaborated networks and their large-scale evolution. Here we report the first evolutionary analysis of a whole superfamily of transcription factors, the basic helix-loop-helix (bHLH) proteins, at the scale of the whole metazoan kingdom.ResultsWe identified in silico the putative full complement of bHLH genes in the sequenced genomes of 12 different species representative of the main metazoan lineages, including three non-bilaterian metazoans, the cnidarians Nematostella vectensis and Hydra magnipapillata and the demosponge Amphimedon queenslandica. We have performed extensive phylogenetic analyses of the 695 identified bHLHs, which has allowed us to allocate most of these bHLHs to defined evolutionary conserved groups of orthology.ConclusionThree main features in the history of the bHLH gene superfamily can be inferred from these analyses: (i) an initial diversification of the bHLHs has occurred in the pre-Cambrian, prior to metazoan cladogenesis; (ii) a second expansion of the bHLH superfamily occurred early in metazoan evolution before bilaterians and cnidarians diverged; and (iii) the bHLH complement during the evolution of the bilaterians has been remarkably stable. We suggest that these features may be extended to other developmental gene families and reflect a general trend in the evolution of the developmental gene repertoires of metazoans.
Highlights
Molecular and genetic analyses conducted in model organisms such as Drosophila and vertebrates, have provided a wealth of information about how networks of transcription factors control the proper development of these species
We propose an evolutionary scenario in which the diversity of metazoan basic helix-loophelix (bHLH) has been established in two main steps, one during the early evolution of metazoans, before the divergence of demosponges from other metazoans, and the second, later, after this split but before the divergence of cnidarians and bilaterians
We have identified 4 bHLH genes in these expressed sequence tags (ESTs), with two corresponding to the Myc and Hey families found in Amphimedon queenslandica and two to the Mad and Emc families for which no member can be found in Amphimedon queenslandica
Summary
Molecular and genetic analyses conducted in model organisms such as Drosophila and vertebrates, have provided a wealth of information about how networks of transcription factors control the proper development of these species. We report the first evolutionary analysis of a whole superfamily of transcription factors, the basic helix-loophelix (bHLH) proteins, at the scale of the whole metazoan kingdom. Many bHLH proteins include additional domains that are important for their activity as transcriptional regulators, such as 'leucine zipper', 'PAS' or 'orange' domains, which are mainly involved in proteinprotein interactions [3,4,5]. In unicellular eukaryotes, such as Saccharomyces cerevisiae, bHLH proteins mainly regulate metabolic pathways [1,6]. In metazoans and plants, the bHLH proteins are mainly involved in controlling developmental processes, in regulating the cell cycle, and in sensing environmental signals [1,2,7,8]
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