Endogenous Amdoparvovirus-Related Elements Reveal Insights Into the Biology and Evolution of Vertebrate Parvoviruses Judit J
Total Page：16
File Type：pdf, Size：1020Kb
Virus Evolution, 2018, 4(2): vey026 doi: 10.1093/ve/vey026 Research article Endogenous amdoparvovirus-related elements reveal insights into the biology and evolution of vertebrate parvoviruses Judit J. Pe´nzes1,*, Soledad Marsile-Medun2,3, Mavis Agbandje-McKenna1, and Robert James Gifford3,*,† 1University of Florida McKnight Brain Institute, 1149 Newell Dr, Gainesville, FL 32610, USA, 2Agrocampus Ouest, 65 Rue de Saint-Brieuc, 35000 Rennes, France and 3MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow, UK *Corresponding author: E-mails: judit.penzes@ufl.edu; [email protected] †http://orcid.org/0000-0003-4028-9884 Abstract Amdoparvoviruses (family Parvoviridae: genus Amdoparvovirus) infect carnivores, and are a major cause of morbidity and mor- tality in farmed animals. In this study, we systematically screened animal genomes to identify endogenous parvoviral ele- ments (EPVs) disclosing a high degree of similarity to amdoparvoviruses, and investigated their genomic, phylogenetic and protein structural features. We report the first examples of full-length, amdoparvovirus-derived EPVs in the genome of the Transcaucasian mole vole (Ellobius lutescens). We also identify four EPVs in mammal and reptile genomes that are intermediate between amdoparvoviruses and their sister genus (Protoparvovirus) in terms of their phylogenetic placement and genomic fea- tures. In particular, we identify a genome-length EPV in the genome of a pit viper (Protobothrops mucrosquamatus) that is more similar to a protoparvovirus than an amdoparvovirus in terms of its phylogenetic placement and the structural features of its capsid protein (as revealed by homology modeling), yet exhibits characteristically amdoparvovirus-like genome features in- cluding: (1) a putative middle ORF gene; (2) a capsid gene that lacks a phospholipase A2 domain; (3) a genome structure consis- tent with an amdoparvovirus-like mechanism of capsid gene expression. Our findings indicate that amdoparvovirus host range extends to rodents, and that parvovirus lineages possessing a mixture of proto- and amdoparvovirus-like characteristics have circulated in the past. In addition, we show that EPV sequences in the mole vole and pit viper encode intact, expressible replicase genes that have potentially been co-opted or exapted in these host species. Key words: parvovirus; amdoparvovirus; paleovirology; protoparvovirus; endogenous virus. 1. Introduction exhibiting a low level of sequence similarity, parvovirus genomes Parvoviruses (family Parvoviridae) are small, single-stranded DNA are highly conserved in overall structure, containing two large viruses that infect vertebrate (subfamily Parvovirinae) and inverte- gene cassettes responsible for encoding the nonstructural (NS) brate (subfamily Densovirinae) hosts. The small (4–6 kb) genome is and the structural (VP) proteins. The N-terminal region of the mi- encompassed by characteristic terminal palindromic repeats, nor capsid protein VP1 includes a highly conserved phospholy- which form hairpin-like secondary structures characteristic for pase A2 (PLA2) motif that is required for escape from the each genus (Tijssen et al. 2011; Cotmore et al. 2014). Despite endosomal compartments after entering the host cell (Zadori VC The Author(s) 2018. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. 1 2|Virus Evolution, 2018, Vol. 4, No. 2 et al. 2001). The parvovirus capsid is icosahedral with a T ¼ 1 examining their genomic, phylogenetic and protein structural symmetry, displaying a jelly roll fold of conserved b-sheets linked characteristics. by variable surface loops, designated variable region (VR) I to IX (Chapman and Agbandje-McKenna 2006). Endogenous parvoviral elements (EPVs) are genomic sequen- 2. Methods ces homologous to parvovriuses that are thought to have been 2.1 In silico genome screening generated when parvoviral DNA sequences were incorporated into the germline of the ancestral host species, such that they We used the database-integrated genome screening (DIGS) tool were subsequently inherited as host alleles (Holmes 2011; (Zhu et al. 2018) to screen whole-genome sequence (WGS) as- Feschotte and Gilbert 2012). The identification of orthologous semblies for EPVs. The DIGS tool provides a framework for simi- EPVs in the genomes of distantly related species demonstrates larity-search–based genome screening. It uses the basic local that these sequences were generated millions of years ago alignment search tool (BLAST) program (Altschul et al. 1997)to (Belyi et al. 2010; Kapoor et al. 2010; Katzourakis and Gifford systematically screen WGS files for sequences matching to a 2010; Smith et al. 2016), and they can therefore provide a useful nucleotide or peptide ‘probe’. Sequences that disclose above- source of retrospective information about the longer-term evo- threshold similarity to the probe are extracted and classified, lutionary relationships between parvoviruses and their hosts. with results being captured in an MySQL relational database Amdoparvovirus is a recently defined genus in the family (Axmark and Widenius 2015). To identify EPVs, we used parvo- Parvoviridae (Cotmore et al. 2014). The type species was originally virus peptide sequences to screen all 362 vertebrate genome as- called Aleutian mink disease virus (AMDV)—hence the genus semblies available in the NCBI WGS database as of the 15 name. However, AMDV is now considered to represent a variant December 2017. Sequences that produced statistically signifi- of the renamed species Carnivore amdoparvovirus 1 (Cotmore et al. cant matches to these probes were extracted and classified by 2014). AMDV causes an immune complex-associated progressive BLAST-based comparison to a set of reference peptide sequen- syndrome in American mink (Neovison vison) called Aleutian dis- ces selected to represent the broad range of diversity in subfam- ease or plasmacytosis (Bloom et al. 1994) which is considered to ily Parvovirinae. be one of the most important infectious diseases affecting farm- raised mink (Canuti et al. 2016). AMDV infection is known to be 2.2 Sequence analyses widespread in wild mink as well as in farmed animals (Canuti Characterization and annotation of EPVs was performed using et al. 2015), and related amdoparvoviruses have been identified in the Artemis Genome Browser (Carver et al. 2012). Putative pep- other carnivore species, including raccoon dogs, foxes, skunks, tide sequences encoded by EPVs were inferred and aligned and red pandas (Pennick et al. 2007; Li et al. 2011; Shao et al. 2014; using MUSCLE (Edgar 2004), PAL2NAL (Suyama et al. 2006), and LaDouceur et al. 2015; Alex et al. 2018). Findings from metage- T-coffee Expresso (Armougom et al. 2006). Phylogenies were nomic studies suggest that amdoparvoviruses may infect a reconstructed from aa alignments incorporating structural data broader range of mammalian orders (Lau et al. 2017), but this has (at least one high-resolution structure from all available gen- yet to be fully demonstrated. era), and using maximum likelihood (ML) as implemented in Phylogenetic studies support a common evolutionary origin for PhyML-3.1, with 1000 bootstrap replicates (Guindon et al. 2010). amdoparvoviruses and protoparvoviruses (genus Protoparvovirus) The RtEV (NS) and the LG (VP) protein substitution models—as (Cotmore et al. 2014). Protoparvoviruses infect a wide range of selected using ProTest (Abascal et al. 2005)—were used for mammalian hosts, encompassing several distinct mammalian reconstructing phylogenies. orders (Tijssen et al. 2011; Sasaki et al. 2015). For example, rodent To detect structural homology, we applied the pGenTHREADER protoparvoviruses are known for their oncolytic properties and pDomTHREADER algorithms of the PSIPRED Protein Sequence (Marchini et al. 2015), while carnivore and ungulate protoparvovi- Analysis Workbench (Lobley et al. 2009). The selected PDB struc- ruses are significant pathogens of domestic pets and livestock tures were applied as templates for homology modeling, carried (Hueffer and Parrish 2003; Kailasan et al. 2015; Meszaros et al. out by SWISS-MODEL (Biasini et al. 2014). Polymers of the acquired 2017). capsid monomer models were constructed by the Oligomer Although they are relatively closely related, amdoparvoviruses Generator feature of the Viper web database (http://viperdb. and protoparvoviruses are distinguished by certain features of scripps.edu/) (Carrillo-Tripp et al. 2009). The generated polymers their genomes and replication strategies. In particular, amdopar- were rendered as well as ribbon diagrams compared using PYMOL vovirus mRNAs are transcribed from one single upstream pro- (Schro¨ dinger). moter and are polyadenylated at two distinct polyadenylation signals. To provide the VP1 encoding transcript, an intron is spliced out, leaving a short, three amino acid (aa)–encoding exon 3. Results leader sequence (transcribed from a short, upstream ORF) posi- 3.1 Identification and characterization of EPVs tioned in-frame with the VP ORF (Qiu et al. 2006). In contrast, the NS- and VP-encoding mRNAs of protoparvoviruses are transcribed We screened WGS assemblies of 688 animal species for EPVs dis- from two different promoters, being polyadenylated at a mutual closing a high degree