Comparative Functional Analysis of the Basic Helix-Loop-Helix Proteins in the Clawed Frogs' Genomes With Common Essential Pathways and Enriched Gene Ontology Terms

Abstract

The international Gene Ontology (GO) and pathway databases were used to functionally analyze the clawed frogs' Basic Helix-Loop-Helix (bHLH) transcription factors of Xenopus tropicalis and Xenopus laevis in a updated genome-wide survey. There were 41 GO terms and one pathway significantly enriched for Xenopus tropicalis, whereas there were 45 GO terms and 3 pathways significantly enriched for Xenopus laevis. Among those significantly enriched GO terms, the two clawed frogs share 31 common functional GO annotations of these bHLH genes, including DNA-dependent transcription and (negative) transcription regulation, DNA binding and bHLH binding, transcription factor complex and protein heterodimerization activity, (negative) regulation of RNA metabolic processes, nuclear translocator and repressor, myogenic basic muscle-specific protein, neurogenic differentiation factor and NeuroD. Furthermore, these frogs' bHLH genes were also found to play important roles in the regulation of gene expression in some important developmental or physiological processes, such as (skeletal) muscle cell differentiation, muscle organ development, biological rhythms and rhythmic process, hypoxia (adaption) and hypoxia-inducible factors, neurogenesis, neural tube development and neurogenic differentiation, whereas they were commonly significantly enriched in TGF-beta signaling pathway. These resulted data and information are very important for us to understand the functions, classification and evolution of frog bHLH genes.