Conservation and divergence of bHLH genes in the calcisponge Sycon ciliatum.

Maja Adamska,Sofia A. V. Fortunato,Michel Vervoort,Marcin Adamski

doi:10.1186/s13227-016-0060-8

Abstract

BackgroundBasic Helix-Loop-Helix (bHLH) genes encode a large family of eukaryotic transcription factors, categorized into six high-order groups: pan-eukaryotic group B involved in regulation of cell cycle, metabolism, and development; holozoan-specific groups C and F involved in development and maintenance of homeostasis; and metazoan-specific groups A, D and E including well-studied genes, such as Atonal, Twist and Hairy, with diverse developmental roles including control of morphogenesis and specification of neurons. Current scenarios of bHLH evolution in animals are mainly based on the bHLH gene set found in the genome of demosponge Amphimedon queenslandica. In this species, the majority of the 21 identified bHLH genes belong to group B, and the single group A gene is orthologous to several neurogenic bilaterian subfamilies, including atonal and neurogenin.Results Given recently discovered differences in developmental toolkit components between siliceous and calcareous sponges, we have carried out genome-wide analysis of bHLH genes in Sycon ciliatum, an emerging calcisponge model. We identified 30 bHLH genes in this species, representing 12 individual families, including four group A families not found in Amphimedon, and two larger family groupings. Notably, the families represented in Sycon are only partially overlapping with those represented in Amphimedon. Developmental expression analysis of a subset of the identified genes revealed patterns consistent with deeply conserved roles, such as specification of sensory cells by Atona-related and stem cells by Myc genes.Conclusions Our results demonstrate independent gene loss events in demosponges and calcisponges, implying a complex bHLH toolkit in the last common metazoan ancestor.Electronic supplementary materialThe online version of this article (doi:10.1186/s13227-016-0060-8) contains supplementary material, which is available to authorized users.

Highlights

Basic Helix-Loop-Helix genes encode a large family of eukaryotic transcription factors, categorized into six high-order groups: pan-eukaryotic group B involved in regulation of cell cycle, metabolism, and development; holozoan-specific groups C and F involved in development and maintenance of homeostasis; and metazoanspecific groups A, D and E including well-studied genes, such as Atonal, Twist and Hairy, with diverse developmental roles including control of morphogenesis and specification of neurons
Basic Helix-Loop-Helix genes constitute a large family of transcription factors (TFs) that are widely found in eukaryotes [1–4]
Identification and phylogenetic analysis of the Sycon Basic Helix-Loop-Helix (bHLH) genes We identified 30 bHLH genes in the fully sequenced genome of Sycon ciliatum (Table 1)

Summary

Introduction

Basic Helix-Loop-Helix (bHLH) genes encode a large family of eukaryotic transcription factors, categorized into six high-order groups: pan-eukaryotic group B involved in regulation of cell cycle, metabolism, and development; holozoan-specific groups C and F involved in development and maintenance of homeostasis; and metazoanspecific groups A, D and E including well-studied genes, such as Atonal, Twist and Hairy, with diverse developmental roles including control of morphogenesis and specification of neurons. Proteins of the group E, known as Hairy and Enhancer of split-related proteins, are only found in metazoans and mainly act as developmental regulators [10] Most of these proteins contain an additional domain, named the ‘orange’ domain, as well as a C-terminal WRPW peptide, both involved in protein–protein interactions [10]. Group F corresponds to the COE (Collier/Olf/EBF) proteins that are found in metazoans and in Capsaspora owczarzaki [11] These proteins lack the basic domain and are characterized by the presence of the ‘COE’ domain, involved in both dimerization and DNA binding [12]

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