Phylogeny, functional annotation, and protein interaction network analyses of the Xenopus tropicalis basic helix-loop-helix transcription factors

Abstract

The previous survey identified 70 basic helix-loop-helix (bHLH) proteins, but it was proved to be incomplete, and the functional information and regulatory networks of frog bHLH transcription factors were not fully known. Therefore, we conducted an updated genome-wide survey in the Xenopus tropicalis genome project databases and identified 105 bHLH sequences. Among the retrieved 105 sequences, phylogenetic analyses revealed that 103 bHLH proteins belonged to 43 families or subfamilies with 46, 26, 11, 3, 15, and 4 members in the corresponding supergroups. Next, gene ontology (GO) enrichment analyses showed 65 significant GO annotations of biological processes and molecular functions and KEGG pathways counted in frequency. To explore the functional pathways, regulatory gene networks, and/or related gene groups coding for Xenopus tropicalis bHLH proteins, the identified bHLH genes were put into the databases KOBAS and STRING to get the signaling information of pathways and protein interaction networks according to available public databases and known protein interactions. From the genome annotation and pathway analysis using KOBAS, we identified 16 pathways in the Xenopus tropicalis genome. From the STRING interaction analysis, 68 hub proteins were identified, and many hub proteins created a tight network or a functional module within the protein families.

Figure 1

Alignment of 105 Xenopus tropicalis bHLH domains. Designation of basic, helix 1, loop, and helix 2 follows Ferre-D'Amare et al. [–43] and bHLH domains were shaded using GeneDoc. Family and bHLH protein names and high-order groups were organized according to Table 1 in the paper of Ledent et al. [4]. Highly conserved sites are shaded in black and indicated with asterisks on the top.

Figure 2

STRING mapping profiles of protein interaction network (PIN) representing bHLH transcription factor protein interactions. Panel (a) showed the main figure of PIN profile and connectivity of hub proteins and the others. The protein interacting gene products are marked in blue and green lines. There are totally 68 hub proteins identified and many hub proteins created a tight network or a functional module within their protein families. Panel (b) magnified the implication of different connective lines with different data sources in the main figure.