Stable deletions arising in the readthrough region of Soil-borne wheat mosaic virus RNA2 define the 5′ limit of the functional promoter for the p19 subgenomic RNA

Abstract

The appearance of de novo deletion mutations in the readthrough (RT) region (nucleotide positions 861-2591) downstream of the capsid protein (CP) gene of a Japanese strain of Soil-borne wheat mosaic virus RNA2 was examined using infectious transcripts. Mutant RNA2s with different deletions predominated in independent serial passage experiments but all best-adapted mutants retained the 3'-terminal portion of the RT gene in frame with the CP gene. The longest best-adapted mutation deleted the 1434 nucleotides between positions 1061 and 2494. When the RT protein was truncated by insertion of a termination codon plus an additional nucleotide to give a +1 frame-shift, after serial passages the progeny viruses regained the ability to express the C-terminal region of RT by an internal deletion. The 5' terminus of the p19 subgenomic RNA was identified at position 2598 and an essential transcription signal for this mRNA mapped between positions 2534 and 2563. A mutant in which this essential promoter element has been deleted cannot transcribe the p19 subgenomic RNA and has lost infectivity in planta. These results indicate that the 3'-terminal region of the RT gene has a major function in cis for expression of p19, which is essential for infecting plants. A reason for retaining the RT C-terminal region in stable deletion mutants is still unknown.

Estimation of the Size of Genetic Bottlenecks in Cell-to-Cell Movement of Soil- Borne Wheat Mosaic Virus and the Possible Role of the Bottlenecks in Speeding Up Selection of Variations in trans -Acting Genes or Elements

“…We assumed a 0 ϭ 0.3 and c ϭ 30; a 0 and c determine the inflection point and inclination of the logistic curve, respectively. We used a 0 ϭ 0.3 because an SBWMV RNA2 mutant with ϳ30% transcription efficiency of p19 subgenomic RNA compared to that of wild-type virus could infect plants but showed irregular formed lesions (34), indicating that the virus can infect some cells but not others. With these parameter values, the succession probability of intracellular probability is very low if the frequency of the adaptive genome is below 0.2, while it is close to 1 if the frequency is over 0.4 (Fig.…”

Chinese Wheat Mosaic Virus-Induced Gene Silencing in Monocots and Dicots at Low Temperature

“…As previous studies on furoviruses have shown the coat protein read through region is prone to spontaneous deletions during prolonged infection or mechanical virus transmission. The virus remains fully infectious as this region is not required for viral encapsidation, replication, and systemic infection ( Yang et al, 2016 ) but probably plays a role in viral transmission through soil-borne zoospores ( Yamamiya et al, 2005 ). This read through region is therefore an obvious choice for sequence insertions.…”

A new furovirus infecting barley in France closely related to the Japanese soil-borne wheat mosaic virus

“…The appearance of spontaneous deletion mutants obtained after manual inoculation has been reported for Japanese and American isolates of SBWMV (Shirako & Ehara, 1986;Tsuchizaki, Hibino, & Saito, 1972). These deletions were found in the CP-RT domain in the case of two isolates from the USA (Chen, MacFarlane, & Wilson, 1994Yamamiya, Miyanishi, & Shirako, 2005). Sequencing of SBWMV-Mar RNA2 indicated that the complete RT protein was conserved although this isolate was maintained by mechanical inoculation to barley plants.…”