title: Nucleotide sequence of Zygosaccharomyces bailii virus Z: Evidence for +1 programmed ribosomal frameshifting and for assignment to family Amalgaviridae.
abstract: Zygosaccharomyces bailii virus Z (ZbV-Z) is a monosegmented dsRNA virus that infects the yeast Zygosaccharomyces bailii and remains unclassified to date despite its discovery >20years ago. The previously reported nucleotide sequence of ZbV-Z (GenBank AF224490) encompasses two nonoverlapping long ORFs: upstream ORF1 encoding the putative coat protein and downstream ORF2 encoding the RNA-dependent RNA polymerase (RdRp). The lack of overlap between these ORFs raises the question of how the downstream ORF is translated. After examining the previous sequence of ZbV-Z, we predicted that it contains at least one sequencing error to explain the nonoverlapping ORFs, and hence we redetermined the nucleotide sequence of ZbV-Z, derived from the same isolate of Z. bailii as previously studied, to address this prediction. The key finding from our new sequence, which includes several insertions, deletions, and substitutions relative to the previous one, is that ORF2 in fact overlaps ORF1 in the +1 frame. Moreover, a proposed sequence motif for +1 programmed ribosomal frameshifting, previously noted in influenza A viruses, plant amalgaviruses, and others, is also present in the newly identified ORF1-ORF2 overlap region of ZbV-Z. Phylogenetic analyses provided evidence that ZbV-Z represents a distinct taxon most closely related to plant amalgaviruses (genus Amalgavirus, family Amalgaviridae). We conclude that ZbV-Z is the prototype of a new species, which we propose to assign as type species of a new genus of monosegmented dsRNA mycoviruses in family Amalgaviridae. Comparisons involving other unclassified mycoviruses with RdRps apparently related to those of plant amalgaviruses, and having either mono- or bisegmented dsRNA genomes, are also discussed.
authors.affiliation: Department of Microbiology & Immunobiology, Harvard Medical School, Boston, MA 02115, USA; Department of Biology, Program in Biochemistry and Molecular and Cellular Biology, University of Namur, Namur BE 5000, Belgium.
authors.forename: Delphine
authors.initials: D
authors.lastname: Depierreux
authors.affiliation: Department of Microbiology & Immunobiology, Harvard Medical School, Boston, MA 02115, USA; Program in Molecules, Cells and Organisms, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Minh
authors.initials: M
authors.lastname: Vong
authors.affiliation: Department of Microbiology & Immunobiology, Harvard Medical School, Boston, MA 02115, USA. Electronic address: mnibert@hms.harvard.edu.
authors.forename: Max L
authors.initials: ML
authors.lastname: Nibert
mesh_terms: D018965:Frameshifting, Ribosomal; D000067148:Fungal Viruses / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D058889:Molecular Typing; D016366:Open Reading Frames; D010802:Phylogeny; D012328:RNA Viruses / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D012367:RNA, Viral; D017423:Sequence Analysis, RNA; D020068:Zygosaccharomyces / Q000821:virology*
chemical_list: D012367:RNA, Viral
keywords: Amalgaviridae; Fungal virus; Mycovirus; Ribosomal frameshifting; Totiviridae; dsRNA