Computationally predicted gene regulatory networks in molluscan biomineralization identify extracellular matrix production and ion transportation pathways.

Victoria A Sleight,Melody S Clark,Francesco Falciani,Philipp Antczak,Lenore Cowen

doi:10.1093/bioinformatics/btz754

Abstract

MotivationThe molecular processes regulating molluscan shell production remain relatively uncharacterized, despite the clear evolutionary and societal importance of biomineralization.ResultsHere we built the first computationally predicted gene regulatory network (GRN) for molluscan biomineralization using Antarctic clam (Laternula elliptica) mantle gene expression data produced over an age-categorized shell damage-repair time-course. We used previously published in vivo in situ hybridization expression data to ground truth gene interactions predicted by the GRN and show that candidate biomineralization genes from different shell layers, and hence microstructures, were connected in unique modules. We characterized two biomineralization modules of the GRN and hypothesize that one module is responsible for translating the extracellular proteins required for growing, repairing or remodelling the nacreous shell layer, whereas the second module orchestrates the transport of both ions and proteins to the shell secretion site, which are required during normal shell growth, and repair. Our findings demonstrate that unbiased computational methods are particularly valuable for studying fundamental biological processes and gene interactions in non-model species where rich sources of gene expression data exist, but annotation rates are poor and the ability to carry out true functional tests are still lacking.Availability and implementationThe raw RNA-Seq data is freely available for download from NCBI SRA (Accession: PRJNA398984), the assembled and annotated transcriptome can be viewed and downloaded from molluscDB (ensembl.molluscdb.org) and in addition, the assembled transcripts, reconstructed GRN, modules and detailed annotations are all available as Supplementary Files.Supplementary information Supplementary data are available at Bioinformatics online.

Highlights

The evolution of biomineralization in the late Precambrian corresponded with a huge expansion in morphological diversity
We present the first computationally predicted gene regulatory network (GRN) for molluscan biomineralization constructed from age-categorized damage-repair mantle gene expression data (Supplementary File S2, Fig. 2, Supplementary Fig. S1)
Owing to the use of mantle tissue-specific gene expression profiles the GRN is constrained by the biomineralization process

Summary

Introduction

The evolution of biomineralization in the late Precambrian corresponded with a huge expansion in morphological diversity. With over 85 000 extant species, molluscs are the second most speciose animal phyla They are essential components in worldwide ecosystem functioning, an important source of protein for growing human demand and show biomimicry potential for the development of strong, lowenergy, materials from vastly abundant soluble calcium carbonate (Finnemore et al, 2012). Molluscan shells form through a controlled biological process producing a composite biomaterial containing 95–99% calcium carbonate (CaCO3) and 1–5% organic matrix. Much of the molluscan shell molecular tool kit remains poorly described and many of these ‘unknown’ genes will play important roles in the biomineralization process. There are currently no data available on gene regulatory networks (GRN) controlling biomineralization in molluscs and tools are urgently required to extend analyses beyond a small set of candidate genes and proteins.

Experimental design

Data analysis

First computationally predicted mantle-specific GRN resource for molluscs

Co-expressed genes are clustered by SOTA

Hypothesized functional roles of the biomineralization modules