Nucleotide sequence, genomic organization and synthesis of infectious transcripts from a full-length clone of artichoke mottle crinkle virus

Abstract

The complete nucleotide sequence of the genome of artichoke mottle crinkle Virus (AMCV), a member of the tombusvirus group, has been determined. The genome is 4790 nucleotides (nt) in length. A full-length cDNA of the AMCV genome has been cloned in pUC9 downstream of the T7 RNA polymerase promoter. Transcripts were infective when inoculated onto Nicotiana clevelandii and N. benthamiana plants. The AMCV genome contains five open reading frames (ORFs). The first ORF from the 5' terminus (ORF1) encodes a protein with a predicted Mr of 33K. ORF2 extends through the amber termination codon of ORF1 to yield a polypeptide of predicted M r 92K and which is the putative RNAdependent RNA polymerase. ORF3 codes for the coat protein (41K). Two nested ORFs in different reading frames (ORFs 4 and 5) code for a 22K and a 19K polypeptide respectively. Sequence homologies suggest that the 22K protein could be involved in cell-to-cell movement of virus. ORFs 3, 4 and 5 are translated from two 3' coterminal subgenomic (sg) RNAs, the 5' termini of which have been mapped. The two sg RNAs are 2155 (sgl) and 934 (sg2) nt in length. ORF3 is expressed from sgl RNA whereas ORFs 4 and 5 are potentially expressed from sg2 RNA. Time course experiments with Cynara scolymus protoplasts indicate that during AMCV infection both positive and negative strands of genomic and sg RNAs are produced and that sg2 RNA is produced before and at a higher level than sgl RNA.

An RNA Activator of Subgenomic mRNA1 Transcription in Tomato Bushy Stunt Virus

“…late in the infection when progeny genomes are abundant) could also apply. Consistent with this notion are the observed accumulation profiles of sg mRNA1 and sg mRNA2 for TBSV and other tombusviruses during 24-h protoplast infections (17,24,25). sg mRNA2 is detectable earliest in the infection, however, its accumulation then levels out at intermediate time points.…”

Regulatory Activity of Distal and Core RNA Elements in Tombusvirus Subgenomic mRNA2 Transcription

“…A third mechanism that has been proposed is that of premature termination of (Ϫ)-strand synthesis during the copying of the genome and subsequent use of the 3Ј-truncated product as a template for the transcription of sg mRNAs (8 -10). Although there is no compelling experimental evidence validating this latter model, it is supported indirectly by the observation that (Ϫ)-strand sg mRNAs do accumulate in various (ϩ)-strand RNA viral infections (8,(11)(12)(13). However, the origin and function of these (Ϫ)-strand sg mRNAs remain to be determined.…”

Genome organization and gene expression of saguaro cactus carmovirus.

“…Pair-wise sequence comparisons were subsequently performed by the GAP program using 25 randomizations. The significance of sequence alignments was assessed by calculating adjusted alignment score AS [AS l (S o kS r )\α, where S o is the observed score, S r is the average score of 25 randomizations and α is the standard deviation of S r ] (Koonin, 1991 ;Tavazza et al, 1994).…”

“…Table 1. Percentage nucleotide identity, amino acid identity and similarity (in parentheses) between SCV and related viruses Additional abbreviations and sources for sequences used : AMCV, artichoke mottle crinkle virus (Tavazza et al, 1994) ; BYDV, barley yellow dwarf virus (Miller et al, 1988) ; CNV, cucumber necrosis virus (CNV) (Rochon & Tremaine, 1989) ; CRSV, cymbidium ringspot virus (Dalmay et al, 1993) ; MCMV, maize chlorotic mottle virus (Nutter et al, 1989) ; RCNMV, red clover necrotic mosaic virus (Xiong & Lommel, 1989) ; SBMV, southern bean mosaic virus (Wu et al, 1987) ; TBSV, tomato bushy stunt virus (Hearne et al, 1990) ; TNV-A and -D, tobacco necrosis virus strain A (Meulewaeter et al, 1990) and strain D (Coutts et al, 1991).…”