Changes in the plant host factors induced upon viral infection of Nicotiana benthamiana with peanut stunt virus (PSV) [strain P] with and without satellite RNA

Peanut stunt virus (PSV) belongs to cucumoviruses which infect many agriculturally important plants. Certain PSV strains contain a small RNA molecule, referred to as satellite RNA (satRNA), which has a propensity to modulate pathogenesis process.Plant viruses with ssRNA genomes are known to replicate in cytoplasm, however, they utilize other cellular structures to their life cycle as well. Among them the role of chloroplast is recently particularly underlined. Here, we tried to indicate the host factors associated with various cellular structures, the levels of which are changed during virus infection. To this end we did transcriptome profiling of N. benthamiana challenged by PSV-P with/ without satRNA using species-specific microarrays. Agilent microarrays in 2x105k format (two microarrays per slide) were used for hybridization of labeled RNA from upper parts of treated N. benthamiana plants (infected PSV-P, PSV-P+satRNA) labeled with Cy5 versus a common reference (ref): pooled RNA extracted from a mix of tissues and treatments, labeled with Cy3. Three biological replicates were used for each treatment.

花生矮化病毒（Peanut stunt virus, PSV）隶属于黄瓜花叶病毒属（cucumoviruses），可侵染多种具有重要农业经济价值的植物。部分PSV毒株携带一类被称为卫星RNA（satellite RNA, satRNA）的小分子RNA，该分子可调控病毒的致病进程。已知基因组为单链RNA（single-stranded RNA, ssRNA）的植物病毒可在细胞质中进行复制，同时也会利用其他细胞结构完成自身生命周期，其中叶绿体在病毒侵染过程中的作用近来受到了特别关注。本研究旨在筛选出与各类细胞结构相关、且在病毒侵染过程中表达水平发生显著变化的宿主因子。为此，本研究采用物种特异性基因芯片（microarrays）技术，对分别接种PSV-P毒株、PSV-P与卫星RNA共接种的本氏烟（Nicotiana benthamiana）进行转录组分析。本研究采用安捷伦（Agilent）2×105k阵列格式基因芯片（每张玻片搭载两张芯片），对以Cy5标记的处理组本氏烟上部组织RNA（分别为接种PSV-P、PSV-P+satRNA的植株）与以Cy3标记的共同参照（common reference, ref）进行杂交；共同参照为混合提取自不同组织与处理组的总RNA。每个处理组均设置三次生物学重复。