Small RNA sequencing of Potato leafroll virus-infected plants reveals an additional subgenomic RNA encoding a sequence-specific RNA-binding protein

Potato leafroll virus (PLRV) is a positive-strand RNA virus that generates subgenomic RNAs (sgRNA) for expression of 3′ proximal genes. Small RNA (sRNA) sequencing and mapping of the PLRV-derived sRNAs revealed coverage of the entire viral genome with the exception of four distinctive gaps. Remarkably, these gaps mapped to areas of PLRV genome with extensive secondary structures, such as the internal ribosome entry site and 5′ transcriptional start site of sgRNA1 and sgRNA2. The last gap mapped to ∼500 nt from the 3′ terminus of PLRV genome and suggested the possible presence of an additional sgRNA for PLRV. Quantitative real-time PCR and northern blot analysis confirmed the expression of sgRNA3 and subsequent analyses placed its 5′ transcriptional start site at position 5347 of PLRV genome. A regulatory role is proposed for the PLRV sgRNA3 as it encodes for an RNA-binding protein with specificity to the 5′ of PLRV genomic RNA.

► Small RNA mapping of PLRV-derived sRNAs revealed an additional subgenomic RNA.
► Quantitative PCR and northern blot analysis confirmed the expression of sgRNA3.
► 5′ initiation site of PLRV sgRNA3 mapped to position 5347 of the PLRV genome.
► A regulatory role is proposed for the PLRV sgRNA3 sequence specific RNA-binding protein.