title: Domain Organization and Evolution of the Highly Divergent 5' Coding Region of Genomes of Arteriviruses, Including the Novel Possum Nidovirus.
abstract: In five experimentally characterized arterivirus species, the 5'-end genome coding region encodes the most divergent nonstructural proteins (nsp's), nsp1 and nsp2, which include papain-like proteases (PLPs) and other poorly characterized domains. These are involved in regulation of transcription, polyprotein processing, and virus-host interaction. Here we present results of a bioinformatics analysis of this region of 14 arterivirus species, including that of the most distantly related virus, wobbly possum disease virus (WPDV), determined by a modified 5' rapid amplification of cDNA ends (RACE) protocol. By combining profile-profile comparisons and phylogeny reconstruction, we identified an association of the four distinct domain layouts of nsp1-nsp2 with major phylogenetic lineages, implicating domain gain, including duplication, and loss in the early nsp1 evolution. Specifically, WPDV encodes highly divergent homologs of PLP1a, PLP1b, PLP1c, and PLP2, with PLP1a lacking the catalytic Cys residue, but does not encode nsp1 Zn finger (ZnF) and "nuclease" domains, which are conserved in other arteriviruses. Unexpectedly, our analysis revealed that the only catalytically active nsp1 PLP of equine arteritis virus (EAV), known as PLP1b, is most similar to PLP1c and thus is likely to be a PLP1b paralog. In all non-WPDV arteriviruses, PLP1b/c and PLP1a show contrasting patterns of conservation, with the N- and C-terminal subdomains, respectively, being enriched with conserved residues, which is indicative of different functional specializations. The least conserved domain of nsp2, the hypervariable region (HVR), has its size varied 5-fold and includes up to four copies of a novel PxPxPR motif that is potentially recognized by SH3 domain-containing proteins. Apparently, only EAV lacks the signal that directs -2 ribosomal frameshifting in the nsp2 coding region.IMPORTANCEArteriviruses comprise a family of mammalian enveloped positive-strand RNA viruses that include some of the most economically important pathogens of swine. Most of our knowledge about this family has been obtained through characterization of viruses from five species:Equine arteritis virus,Simian hemorrhagic fever virus,Lactate dehydrogenase-elevating virus,Porcine respiratory and reproductive syndrome virus 1, andPorcine respiratory and reproductive syndrome virus 2Here we present the results of comparative genomics analyses of viruses from all known 14 arterivirus species, including the most distantly related virus, WPDV, whose genome sequence was completed in this study. Our analysis focused on the multifunctional 5'-end genome coding region that encodes multidomain nonstructural proteins 1 and 2. Using diverse bioinformatics techniques, we identified many patterns of evolutionary conservation that are specific to members of distinct arterivirus species, both characterized and novel, or their groups. They are likely associated with structural and functional determinants important for virus replication and virus-host interaction.
authors.affiliation: Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
authors.forename: Anastasia
authors.initials: A
authors.lastname: Gulyaeva
authors.affiliation: Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand M.Dunowska@massey.ac.nz a.e.gorbalenya@lumc.nl.
authors.forename: Magdalena
authors.initials: M
authors.lastname: Dunowska
authors.affiliation: Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
authors.forename: Erik
authors.initials: E
authors.lastname: Hoogendoorn
authors.affiliation: Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand.
authors.forename: Julia
authors.initials: J
authors.lastname: Giles
authors.affiliation: Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.
authors.forename: Dmitry
authors.initials: D
authors.lastname: Samborskiy
authors.affiliation: Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands M.Dunowska@massey.ac.nz a.e.gorbalenya@lumc.nl.|Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.|Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia.
authors.forename: Alexander E
authors.identifier: http://orcid.org/0000-0002-4967-7341
authors.initials: AE
authors.lastname: Gorbalenya
mesh_terms: D018018:Arterivirus / Q000145:classification* / Q000235:genetics*; D019295:Computational Biology; D019143:Evolution, Molecular; D005814:Genes, Viral; D014644:Genetic Variation; D016679:Genome, Viral; D010802:Phylogeny; D000072417:Protein Domains; D017361:Viral Nonstructural Proteins / Q000235:genetics*
chemical_list: D017361:Viral Nonstructural Proteins
keywords: arterivirus; bioinformatics; comparative genomics; duplication; evolution; nidovirus; papain-like proteases; phylogenetic analysis; ribosome frameshifting; wobbly possum disease