ABSTRACT
Two previously sequenced tobacco rattle virus (TRV) isolates, Slu24 and Deb57, from Polish potato fields have recombinant RNA2 species. The 3'-proximal region of the Slu24 RNA2 is derived from the 3' terminus of its supporting RNA1, while that of the Deb57 RNA2 is derived from the 3' terminus of the unrelated RNA1 from the isolate SYM or PpK20. Gene structure annotation revealed open reading frames encoding truncated 16-kDa proteins in the recombinant regions of the RNA2 of Deb57 and Slu24. Reading frame shifts, single nucleotide substitutions and deletions occurred during recombination, including shifts from a stop codon or replacements of an internal stop codon. In the recombinant region of the Deb57 RNA2, the first reading frameshift event starts from the AUG start codon of the truncated 16-kDa protein. The second frameshift event, caused by a single nucleotide deletion upstream of the stop codon, leads to the splitting of the stop codon into two amino acid codons and the continuation of translation. In addition, a U-to-A substitution changes a potential internal stop codon UAA, which is caused by recombination-related frame shifts, into the codon AAA, encoding lysine. The replacement of this internal stop codon with an amino acid codon prevented the premature translation termination of the truncated 16-kDa protein. These recombination-related reading frame shifts are the driving force underlying the major differences in the translated amino acids, consequently leading to their translation into distinct polypeptides. Conversely, single nucleotide substitutions in the recombinant regions of the RNA2 of Deb57 or Slu24 resulted in only minor changes in the translated amino acids.
Subject(s)
Frameshift Mutation , Plant Diseases/virology , Polymorphism, Single Nucleotide , RNA Viruses/genetics , RNA, Viral/genetics , Base Sequence , Molecular Sequence Data , Open Reading Frames , RNA Viruses/isolation & purification , Recombination, Genetic , Viral Proteins/geneticsABSTRACT
Four tobacco rattle virus (TRV) isolates were identified from tobacco bait seedlings planted in soil samples from Polish potato fields. Sequence analysis of the genomic RNA1 of the isolates revealed significant similarity to the isolates Ho and AL recently found in Germany. Multiple sequence alignments of the genomic RNA2 indicated that the two isolates from northern Poland (Deb57 and Slu24) are in a cluster with the isolates PSG and PLB found in the Netherlands. The remaining two isolates, from central Poland (11r21 and Mlo7), are in a distinct group with the unique isolate SYM found in England. The RNA2 sequences of the studied isolates range from 1998 nt to 2739 nt in length, and all carry deletions of the 2b and/or 2c genes. The isolate Mlo7 has an atypical RNA2 structure, having its cp gene located in its central region.
Subject(s)
Plant Diseases/virology , Plant Viruses/genetics , RNA, Viral/genetics , Solanum tuberosum/virology , Genome, Viral , Plant Viruses/isolation & purification , PolandABSTRACT
The Ns gene confers resistance of potato to Potato virus S (PVS). Sixteen German and Dutch potato cultivars, all registered in Poland, were found to be susceptible to PVS infection. However, scoring of the cultivars for the presence of the Ns-linked SCAR marker SC811(454) revealed additional amplicons with a similar electrophoretic migration rate as that of SC811(454), which resulted in ambiguous determination of the genotype at the Ns locus. MboI or FokI treatment of the PCR products allowed to detect their Ns-unspecificity in PVS-susceptible potato cultivars.
