Biologically active transcripts of a large satellite RNA from arabis mosaic nepovirus and the importance of 5' end sequences for its replication

Genetic variability, evolution, and biological effects of Grapevine fanleaf virus satellite RNAs

Large satellite RNAs (type B satRNAs) of Grapevine fanleaf virus (GFLV) from the genus Nepovirus, family Secoviridae were identified in a naturally infected vineyard and a grapevine germplasm collection. These GFLV satRNA variants had a higher nucleotide sequence identity with satRNAs of Arabis mosaic virus (ArMV) strains NW and J86 (93.8 to 94.6%) than with the satRNA of GFLV strain F13 and those of other ArMV strains (68.3 to 75.0%). Phylogenetic analyses showed no distinction of GFLV and ArMV satRNAs with respect to the identity of the helper virus. Seven stretches of 8 to 15 conserved nucleotides (I-VII) were identified in the 5' region of subgroup A nepovirus genomic RNAs GFLV, ArMV, and Grapevine deformation virus) and nepovirus type B satRNAs, including previously reported motif I, suggesting that large satRNAs might have originated from recombination between an ancestral subgroup A nepovirus RNA and an unknown RNA sequence with the 5' region acting as a putative cis-replication element. A comparative analysis of two GFLV strains carrying or absent of satRNAs showed no discernable effect on virus accumulation and symptom expression in Chenopodium quinoa, a systemic herbaceous host. This work sheds light on the origin and biological effects of large satRNAs associated with subgroup A nepoviruses.

A RT/PCR-partial restriction enzymatic mapping (PREM) method for the molecular characterisation of the large satellite RNAs of Arabis mosaic virus isolates

The satellite RNA of the grapevine isolate NW of Arabis mosaic virus (ArMV) was cloned and sequenced, and showed 75% identity at the nucleotide level to the satellite RNA of the lilac isolate of ArMV. In order to survey ArMV isolates from various geographical origins and natural hosts for the presence of large satellite RNAs and analyse their degree of variability, a RT/PCR-partial restriction enzymatic mapping (PREM) method was developed. The method is based on the incorporation of 5-methyl-dCTP in the RT/PCR reaction, and the subsequent digestion of the RT/PCR products by methyl-sensitive restriction enzymes. Satellites RNAs were detected by RT/PCR in eight isolates out of 47, six of them originating from grapevine, one from hop and one from lilac. The partial restriction digestion patterns allowed to distinguish six different types of satellites. Cloning and sequencing of the different satellites confirmed these results, the PREM proving able to discriminate sequences with 96% identity. The sizes of the different satellites varied between 1092 and 1139 nucleotides, their encoded proteins between 338 and 360 amino acids. Conserved domains were found in the amino and carboxy-termini between the sequences of the proteins encoded by the satellites of the different isolates of ArMV.

Structural and mutational analyses of cis-acting sequences in the 5'-untranslated region of satellite RNA of bamboo mosaic potexvirus

The satellite RNA of Bamboo mosaic virus (satBaMV) contains on open reading frame for a 20-kDa protein that is flanked by a 5'-untranslated region (UTR) of 159 nucleotides (nt) and a 3'-UTR of 129 nt. A secondary structure was predicted for the 5'-UTR of satBaMV RNA, which folds into a large stem-loop (LSL) and a small stem-loop. Enzymatic probing confirmed the existence of LSL (nt 8-138) in the 5'-UTR. The essential cis-acting sequences in the 5'-UTR required for satBaMV RNA replication were determined by deletion and substitution mutagenesis. Their replication efficiencies were analyzed in Nicotiana benthamiana protoplasts and Chenopodium quinoa plants coinoculated with helper BaMV RNA. All deletion mutants abolished the replication of satBaMV RNA, whereas mutations introduced in most of the loop regions and stems showed either no replication or a decreased replication efficiency. Mutations that affected the positive-strand satBaMV RNA accumulation also affected the accumulation of negative-strand RNA; however, the accumulation of genomic and subgenomic RNAs of BaMV were not affected. Moreover, covariation analyses of natural satBaMV variants provide substantial evidence that the secondary structure in the 5'-UTR of satBaMV is necessary for efficient replication.

Properties of the satellite RNA of nepoviruses

Satellite RNA depend for their multiplication on the co-infection of a host cell by a helper virus which can itself multiply independently of the satellite. Four types of satellite RNA have been distinguished on the basis of the size of the RNA and what sort, if any, of protein they encode. One of them, the B-type, comprises relatively large RNA which are messenger RNA for non-structural proteins. Many of these satellites are typified by having nepoviruses as helper viruses. In general, the presence of nepovirus mRNA satellites in a virus culture causes little or no modification to the symptoms of infection by the helper virus and has little effect on its yield. Some satellites appear to be highly specific to a strain of helper virus but others can be helped by heterologous viruses. The proteins encoded by nepovirus mRNA satellites have a M(r) of 38,000 to 48,000 and are relatively basic, in particular in the N-terminal and C-terminal parts of the molecules. However, there is little similarity in amino acid sequence between proteins encoded by different satellites and no peptide motif could be found in all satellite proteins. The results of reverse genetics experiments with satellites suggest that the satellite-encoded protein is essential for the multiplication of the satellite RNA. This system has considerable potential for the study of the mechanisms of replication both of satellite and helper virus RNA.