RNA sequence of astrovirus: distinctive genomic organization and a putative retrovirus-like ribosomal frameshifting signal that directs the viral replicase synthesis.

Abstract

The genomic RNA of human astrovirus was sequenced and found to contain 6797 nt organized into three open reading frames (la, lb, and 2). A potential ribosomal frameshift site identified in the overlap region of open reading frames la and lb consists of a "shifty" heptanucleotide and an RNA stem-loop structure that closely resemble those at the gag-pro junction of some retroviruses. This translation frameshift may result in the suppression of in-frame amber termination at the end of open reading frame la and the synthesis of a nonstructural, fusion polyprotein that contains the putative protease and RNA-dependent RNA polymerase. Comparative sequence analysis indicated that the protease and polymerase of astrovirus are only distantly related to the respective enzymes of other positive-strand RNA viruses. The astrovirus polyprotein lacks the RNA helicase domain typical of other positivestrand RNA viruses of similar genome size. The genomic organization and expression strategy of astrovirus, with the protease and the polymerase brought together by predicted frameshift, most dosely resembled those of plant luteoviruses.

The complete sequence of a human astrovirus

“…There is a presumptive 85 nt non-translated region (NTR) at the 5' terminus preceding the first AUG, which is in a good environment for translational initiation (AXXAUGG: Kozak, 1989). These features are very similar to those reported for a serotype 2 virus (accession number L13745; Jiang et al, 1993). The 5' NTR is well conserved (73 %), the exact 5' terminus and first 40 nt of the virus RNA are identical between the two serotypes ( Fig.…”

Molecular characterization of a novel astrovirus associated with disease in mink

“…It was, therefore, of great help that we initially obtained two sequences located about 2 kb apart, facilitating the rapid amplification and sequence determination of the 39 two-thirds of the genome. The presence of poly(A) tails in all 39 most sequence parts indicated that the genome is polyadenylated, as is the case for all other astroviruses for which full-length sequences have been determined to date (Imada et al, 2000;Jiang et al, 1993;Koci et al, 2000;Lewis et al, 1994;Mendez-Toss et al, 2000;Oh & Schreier, 2001;Willcocks et al, 1994). The 59 most extreme sequence proved to be more difficult to obtain.…”

Ribosomal Frameshift Signals in Viral Genomes

“…The genome has three ORFs, with the first two overlapping. A frameshift signal that separates the protease and the RdRP was identified in the Human astrovirus and subsequently shown to be functional (Jiang et al, 1993;Marczinke et al, 1994). More recently frameshift signals have been identified in the Chicken, Mink, Ovine and Turkey astroviruses (Bekaert & Rousset, 2005;Bekaert et al, 2010).…”