Cloning full-length cDNA of grapevine chrome mosaic nepovirus

Amplification and cloning of a long RNA virus genome using immunocapture-long RT-PCR

A rapid and easy method was developed in order to amplify long fragments of the genome of potato virus Y (PVY), a virus possessing a 10-kb genomic RNA. The method of immunocapture-RT-PCR was adapted, by using thermostable DNA polymerases with proofreading activity and the proper buffers and cycles, to amplify almost the whole genome of PVY in two fragments (5.6 and 4.3 kb) without purifying virions nor viral RNA. Both fragments were cloned subsequently and their ends sequenced. The method is applicable to the rapid cloning and molecular characterization of the genomes of many other RNA viruses.

Comparison of the complete nucleotide sequences of two isolates of lettuce mosaic virus differing in their biological properties

The complete nucleotide sequences of the genomic RNAs of the 0 and E isolates of lettuce mosaic potyvirus (LMV) have been determined. These two isolates differ by their behavior towards two lettuce resistance genes and by their seed transmission properties. LMV-0 is unable to induce disease in lettuce carrying either one of the mol1 and mol2 recessive resistance genes, whereas LMV-E is able to induce disease in the same plants. The genomes of these two isolates are 10080 nucleotides (nt) in length, excluding the poly(A) tract, and encode polyproteins of 3255 amino acids (aa). The open reading frame is flanked by a 5' non-coding region of 103 nt and a 3' non-coding region of 212 nucleotides. Ten proteins were predicted. The P3 protein, with 377 aa, is the longest potyviral P3 protein characterized to date while the P1 protein, with 437 aa, is among the longest P1 proteins reported. Sequence comparisons between the two isolates demonstrated only limited sequence difference. The overall nucleotide and amino acid sequence identities between LMV-0 and LMV-E are 94 and 97% respectively. The greatest variability occurs in the P1 and in the variable N-terminal region of the coat protein, while the NIa protease domain, the NIb protein, the C-terminus of the helper component protease and the 3' non-coding region are extensively conserved. While this sequence analysis does not allow direct identification of determinants involved in the resistance breaking or in the seed transmissibility properties, these data are a first step towards the characterization of these determinants.

Turnip yellow mosaic virus variants produced from DNA clones encoding their genomes

Full-length dsDNA clones that encode the genomes of two Australian turnip yellow mosaic isolates, TYMV-BL and TYMV-CL have been constructed. These clones were transcribed to give 6.3 kb capped ssRNA which infects Chinese cabbages to give symptoms indistinguishable from those produced by the parental viruses. Extensions of up to 26 nucleotides at the 3' end of the TYMV-BL clone delay infections, but virus particles isolated from these plants 4 weeks after inoculation contain RNA with the original TYMV-BL 3' terminus. A 90 nucleotide-long portion of the virion protein gene of TYMV-BL was replaced by a synthetic 90-mer primer with 16 nucleotide changes to decrease the large cytosine content (34-42%) characteristic of tymovirus genomic RNA. No reversion of any of the mutated nucleotides to cytosine occurred during 7 passages in Chinese cabbage. Hybrids between the TYMV-BL and TYMV-CL clones were also constructed, by exchanging various portions of the genome. However, it was not possible to determine definitively which part of the viral genome is responsible for the more severe symptoms caused by TYMV-BL as the hybrids gave intermediate symptoms.

The use of PCR for cloning of large cDNA fragments of turnip mosaic potyvirus

A method is described whereby turnip mosaic virus RNA (TuMV RNA) was reverse transcribed and the resulting cDNA amplified enzymatically using the Taq DNA polymerase and degenerate oligonucleotide primers. Two degenerate oligonucleotide primers based on regions of homology in the amino acid sequence of the cytoplasmic inclusion protein and the nuclear inclusion b protein from five potyviruses were synthesized. Polymerase chain reactions utilizing these degenerate primers in association with specific primers amplified a 1.2 kb and a 3.3 kb fragment. These amplified fragments were dC-tailed and cloned into pUC9. Their partial sequence, when compared to potyvirus sequences, showed that they were derived from TuMV RNA and approximately 4.4 kb of viral genome was cloned.

Nucleotide sequence and genetic organization of Hungarian grapevine chrome mosaic nepovirus RNA2

The complete nucleotide sequence of hungarian grapevine chrome mosaic nepovirus (GCMV) RNA2 has been determined. The RNA sequence is 4441 nucleotides in length, excluding the poly(A) tail. A polyprotein of 1324 amino acids with a calculated molecular weight of 146 kDa is encoded in a single long open reading frame extending from nucleotides 218 to 4190. This polyprotein is homologous with the protein encoded by the S strain of tomato black ring virus (TBRV) RNA2, the only other nepovirus sequenced so far. Direct sequencing of the viral coat protein and in vitro translation of transcripts derived from cDNA sequences demonstrate that, as for comoviruses, the coat protein is located at the carboxy terminus of the polyprotein. A model for the expression of GCMV RNA2 is presented.

Nucleotide sequence of Hungarian grapevine chrome mosaic nepovirus RNA1

The nucleotide sequence of the RNA1 of hungarian grapevine chrome mosaic virus, a nepovirus very closely related to tomato black ring virus, has been determined from cDNA clones. It is 7212 nucleotides in length excluding the 3' terminal poly(A) tail and contains a large open reading frame extending from nucleotides 216 to 6971. The presumably encoded polyprotein is 2252 amino acids in length with a molecular weight of 250 kDa. The primary structure of the polyprotein was compared with that of other viral polyproteins, revealing the same general genetic organization as that of other picorna-like viruses (comoviruses, potyviruses and picornaviruses), except that an additional protein is suspected to occupy the N-terminus of the polyprotein.