植物类病毒是如何影响寄主体内转录组变化？JV，2017

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Comprehensive transcriptome analyses reveal that potato spindle tuber viroid triggers genome-wide changes in alternative splicing, inducible trans-acting activity of phasiRNAs and immune responses

• Yi Zhenga,
• Ying Wangb,c#,
• Biao Dingb and
• Zhangjun Feia,d#
  

-Author Affiliations

• Boyce Thompson Institute, Cornell University, Ithaca, NY, USAa
• Department of Molecular Genetics, The Ohio State University, Columbus, OH, USAb
• Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USAc
• USDA Robert W. Holley Center for Agriculture and Health, Ithaca, NY, USAd
  

Many pathogens express non-coding RNAs (ncRNAs) during infection processes. In the most extreme case, pathogenic ncRNAs alone (such as viroids) can infect eukaryotic organisms leading to diseases. While a few of pathogenic ncRNAs have been implicated in regulating gene expression, functions of most pathogenic ncRNAs in host-pathogen interactions remain unclear. Here we employ potato spindle tuber viroid (PSTVd)-infecting tomato as a system to dissect host interactions with pathogenic ncRNAs, using comprehensive transcriptome analyses. We uncover various new activities in regulating gene expression during PSTVd infection, such as genome-wide alteration in alternative splicing of host protein-coding genes, enhanced guided-cleavage activities of a host microRNA and the induction of trans-acting function of phased secondary short interfering RNAs. Furthermore, we reveal that PSTVd infection massively activates genes involved in plant immune responses, mainly those in the calcium-dependent protein kinase and mitogen-activated protein kinase cascades as well as prominent genes involved in hypersensitive responses, cell wall fortification and various hormone signaling. Intriguingly, our data supports a notion that plant immune systems can respond to pathogenic ncRNAs, which has broad implications in providing new opportunities to understand the complex of immune systems in differentiating “self” and “non-self” as well as lays the foundation to resolve the long-standing question regarding the pathogenesis mechanisms of viroids and perhaps other infectious RNAs.

IMPORTANCE Numerous pathogens, including viruses, express pathogenic non-coding transcripts during infection. In the most extreme case, pathogenic non-coding RNAs alone (i.e. viroids) can cause disease in plants. While some work has demonstrated that pathogenic non-coding RNAs interact with host factors for function, it remains largely unclear regarding the biological significance of pathogenic non-coding RNAs in host-pathogen interactions. Here we apply comprehensive genome-wide analyses on plant-viroid interactions and discover several novel molecular activities underlying nuclear-replicating viroid infection processes in plants, including effects on the expression and function of host non-coding transcripts as well as the alternative splicing of host protein-coding genes. Importantly, we show that plant immunity is activated upon the infection of a neclear-replicating viroid, which is a new concept that helps to understand viroid-based pathogenesis. Our finding has broad implications for understanding the complexity of host immune system and the diverse functions of non-coding RNAs.