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

Hwang, Yeen T., Kalischuk, Melanie L., Fusaro, Adriana F., Waterhouse, Peter M., & Kawchuk, Lawrence M. (2013) Small RNA sequencing of potato leafroll virus-infected plants reveals an additional subgenomic RNA encoding a sequence-specific RNA-binding protein. Virology, 438(2), pp. 61-69.

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Abstract

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. © 2013.

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ID Code: 65910
Item Type: Journal Article
Refereed: Yes
Additional URLs:
Keywords: Luteoviridae, ORF7, PLRV, Polerovirus, RNA-binding protein, SgRNA3, Small RNA, glutathione transferase, RNA binding protein, transfer RNA, article, controlled study, gene mapping, internal ribosome entry site, nonhuman, Northern blotting, open reading frame, plant virus, potato, priority journal, protein expression, protein secondary structure, quantitative analysis, real time polymerase chain reaction, RNA sequence, RNA structure, RNA synthesis, transcription initiation site, virus genome, virus replication, Base Sequence, Genome, Viral, Plant Diseases, RNA, Viral, RNA-Binding Proteins, Sequence Analysis, RNA, Solanum tuberosum, Potato leafroll virus, RNA viruses
DOI: 10.1016/j.virol.2012.12.012
ISSN: 0042-6822
Subjects: Australian and New Zealand Standard Research Classification > BIOLOGICAL SCIENCES (060000) > GENETICS (060400)
Australian and New Zealand Standard Research Classification > BIOLOGICAL SCIENCES (060000) > PLANT BIOLOGY (060700)
Divisions: Current > Schools > School of Earth, Environmental & Biological Sciences
Current > QUT Faculties and Divisions > Science & Engineering Faculty
Copyright Owner: Copyright 2013 Academic Press
Deposited On: 09 Jan 2014 01:54
Last Modified: 13 Jan 2014 02:50

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