A-to-I editing of Malacoherpesviridae RNAs supports the antiviral role of ADAR1 in mollusks

Umberto Rosani,Laura Cendron,Maxwell Shapiro,Thomas Maccarthy,Lorenzo Maso,Chang-Ming Bai,Miriam Abbadi,Paola Venier,Chong-Ming Wang,Stefania Domeneghetti

doi:10.1186/s12862-019-1472-6

Abstract

BackgroundAdenosine deaminase enzymes of the ADAR family are conserved in metazoans. They convert adenine into inosine in dsRNAs and thus alter both structural properties and the coding potential of their substrates. Acting on exogenous dsRNAs, ADAR1 exerts a pro- or anti-viral role in vertebrates and Drosophila.ResultsWe traced 4 ADAR homologs in 14 lophotrochozoan genomes and we classified them into ADAD, ADAR1 or ADAR2, based on phylogenetic and structural analyses of the enzymatic domain. Using RNA-seq and quantitative real time PCR we demonstrated the upregulation of one ADAR1 homolog in the bivalve Crassostrea gigas and in the gastropod Haliotis diversicolor supertexta during Ostreid herpesvirus-1 or Haliotid herpesvirus-1 infection. Accordingly, we demonstrated an extensive ADAR-mediated editing of viral RNAs. Single nucleotide variation (SNV) profiles obtained by pairing RNA- and DNA-seq data from the viral infected individuals resulted to be mostly compatible with ADAR-mediated A-to-I editing (up to 97%). SNVs occurred at low frequency in genomic hotspots, denoted by the overlapping of viral genes encoded on opposite DNA strands. The SNV sites and their upstream neighbor nucleotide indicated the targeting of selected adenosines. The analysis of viral sequences suggested that, under the pressure of the ADAR editing, the two Malacoherpesviridae genomes have evolved to reduce the number of deamination targets.ConclusionsWe report, for the first time, evidence of an extensive editing of Malacoherpesviridae RNAs attributable to host ADAR1 enzymes. The analysis of base neighbor preferences, structural features and expression profiles of molluscan ADAR1 supports the conservation of the enzyme function among metazoans and further suggested that ADAR1 exerts an antiviral role in mollusks.

Highlights

Adenosine deaminase enzymes of the ADAR family are conserved in metazoans
Bayesian phylogenesis performed on the enzymatic domain of lophotrochozoan and Homo sapiens ADAR proteins resulted in three main clades reflecting the ADAR2, ADAR1 and ADAD gene classification (Fig. 1)
Exceptions were represented by the C. virginica genome which encodes one ADAR1 gene only and by the gastropods Lottia gigantea and H. diversicolor supertexta whose two ADAR sequences clustered into the ADAR2 clade

Summary

Introduction

Adenosine deaminase enzymes of the ADAR family are conserved in metazoans. They convert adenine into inosine in dsRNAs and alter both structural properties and the coding potential of their substrates. All cellular organisms have developed antiviral defense mechanisms [2] and the arms race between viruses and their hosts has contributed to shape both their genomes over millions of years [3]. (HTS) supports the investigation of both transcriptional and genomic landscapes, successfully disclosing such features in non-model organisms during in-vivo infections and providing an unprecedented resolution of molecular host-pathogen interactions [18]. Hemocytes have been recently used as an in-vitro model for studying Malacoherpesviridae infections [25, 26], the propagation of these viruses is still relying almost exclusively on in-vivo experiments

Objectives

Methods

Results

Discussion

Conclusion