A +1 ribosomal frameshifting motif prevalent among plant amalgaviruses.
Sequence accessions attributable to novel plant amalgaviruses have been found in the Transcriptome Shotgun Assembly database. Sixteen accessions, derived from 12 different plant species, appear to encompass the complete protein-coding regions of the proposed amalgaviruses, which would substantially expand the size of genus Amalgavirus from 4 current species. Other findings include evidence for UUU_CGN as a +1 ribosomal frameshifting motif prevalent among plant amalgaviruses; for a variant version of this motif found thus far in only two amalgaviruses from solanaceous plants; for a region of α-helical coiled coil propensity conserved in a central region of the ORF1 translation product of plant amalgaviruses; and for conserved sequences in a C-terminal region of the ORF2 translation product (RNA-dependent RNA polymerase) of plant amalgaviruses, seemingly beyond the region of conserved polymerase motifs. These results additionally illustrate the value of mining the TSA database and others for novel viral sequences for comparative analyses.
Department of Microbiology & Immunobiology, Harvard Medical School, Boston, MA 02115, USA; Harvard Ph.D. Program in Virology, Division of Medical Sciences, Harvard University, Boston, MA 02115, USA. Electronic address: mnibert@hms.harvard.edu.
Max L
ML
Nibert
Harvard Ph.D. Program in Virology, Division of Medical Sciences, Harvard University, Boston, MA 02115, USA. Electronic address: jessepyle@g.harvard.edu.
Jesse D
JD
Pyle
Division of Virology, Department of Pathology, Addenbrooke's Hospital, University of Cambridge, Cambridge CB2 0QQ, UK. Electronic address: aef24@cam.ac.uk.
Andrew E
AE
Firth
D001483:Base Sequence; D016000:Cluster Analysis; D003062:Codon; D017124:Conserved Sequence; D018965:Frameshifting, Ribosomal; D016679:Genome, Viral; D059372:Nucleotide Motifs; D016366:Open Reading Frames; D010802:Phylogeny; D010942:Plant Viruses / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D012333:RNA, Messenger / Q000737:chemistry* / Q000235:genetics*; D012367:RNA, Viral
D003062:Codon; D012333:RNA, Messenger; D012367:RNA, Viral
Amalgaviridae; Coiled coil; Database mining; Fungal virus; Plant virus; Ribosomal frameshifting; dsRNA virus