Unexpected complexity of the Reef-Building Coral Acropora millepora transcription factor network

Taewoo Ryu,Charalampos Harris Mavromatis,Till Bayer,Christian R Voolstra,Timothy Ravasi

doi:10.1186/1752-0509-5-58

Taewoo Ryu, Charalampos Harris Mavromatis + Show 3 more

Open Access

https://doi.org/10.1186/1752-0509-5-58

Copy DOI

Abstract

BackgroundCoral reefs are disturbed on a global scale by environmental changes including rising sea surface temperatures and ocean acidification. Little is known about how corals respond or adapt to these environmental changes especially at the molecular level. This is mostly because of the paucity of genome-wide studies on corals and the application of systems approaches that incorporate the latter. Like in any other organism, the response of corals to stress is tightly controlled by the coordinated interplay of many transcription factors.ResultsHere, we develop and apply a new system-wide approach in order to infer combinatorial transcription factor networks of the reef-building coral Acropora millepora. By integrating sequencing-derived transcriptome measurements, a network of physically interacting transcription factors, and phylogenetic network footprinting we were able to infer such a network. Analysis of the network across a phylogenetically broad sample of five species, including human, reveals that despite the apparent simplicity of corals, their transcription factors repertoire and interaction networks seem to be largely conserved. In addition, we were able to identify interactions among transcription factors that appear to be species-specific lending strength to the novel concept of "Taxonomically Restricted Interactions".ConclusionsThis study provides the first look at transcription factor networks in corals. We identified a transcription factor repertoire encoded by the coral genome and found consistencies of the domain architectures of transcription factors and conserved regulatory subnetworks across eumetazoan species, providing insight into how regulatory networks have evolved.

Highlights

Coral reefs are disturbed on a global scale by environmental changes including rising sea surface temperatures and ocean acidification
We developed and applied a systemswide integrative approach to assess the complexity of the Acropora millepora transcription factor (TF) network by reconstructing a transcription factors (TFs) interaction map from known interactions and comparing it to those of four model organisms
To identify coral proteins whose orthologs exist in other species, all coding sequences were queried against NCBI non-redundant database using BLASTp [20], the best-hit sequence for each contig or singleton was chosen

Summary

Introduction

Coral reefs are disturbed on a global scale by environmental changes including rising sea surface temperatures and ocean acidification. Little is known about how corals respond or adapt to these environmental changes especially at the molecular level. This is mostly because of the paucity of genome-wide studies on corals and the application of systems approaches that incorporate the latter. Deciphering and predicting transcriptional regulatory networks is of considerable importance in understanding how organisms function, adapt, and respond to changes in their environment. Little effort has been made so far in understanding the structure, function, and conversation of transcriptional networks in non-model organisms, e.g. corals, despite their ecological importance. The emerging picture from these studies is that corals are complex organisms as revealed by a diverse set of receptors and a comprehensive innate immunity reservoir which are important for responses to the environment [15]

Methods

Results

Conclusion