Protein & Cell

, Volume 1, Issue 9, pp 847–858 | Cite as

Nucleotide bias of DCL and AGO in plant anti-virus gene silencing

  • Thien Ho
  • Liang Wang
  • Linfeng Huang
  • Zhigang Li
  • Denise W. Pallett
  • Tamas Dalmay
  • Kazusato Ohshima
  • John A. Walsh
  • Hui Wang
Research Article

Abstract

Plant Dicer-like (DCL) and Argonaute (AGO) are the key enzymes involved in anti-virus post-transcriptional gene silencing (AV-PTGS). Here we show that AV-PTGS exhibited nucleotide preference by calculating a relative AV-PTGS efficiency on processing viral RNA substrates. In comparison with genome sequences of dicot-infecting Turnip mosaic virus (TuMV) and monocot-infecting Cocksfoot streak virus (CSV), viral-derived small interfering RNAs (vsiRNAs) displayed positive correlations between AV-PTGS efficiency and G+C content (GC%). Further investigations on nucleotide contents revealed that the vsiRNA populations had G-biases. This finding was further supported by our analyses of previously reported vsiRNA populations in diverse plant-virus associations, and AGO associated Arabidopsis endogenous siRNA populations, indicating that plant AGOs operated with G-preference. We further propose a hypothesis that AV-PTGS imposes selection pressure(s) on the evolution of plant viruses. This hypothesis was supported when potyvirus genomes were analysed for evidence of GC elimination, suggesting that plant virus evolution to have low GC% genomes would have a unique function, which is to reduce the host AV-PTGS attack during infections.

Keywords

anti-virus post-transcriptional gene silencing siRNA nucleotide bias Dicer-like Argonaute plant virus evolution 

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Copyright information

© Higher Education Press and Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • Thien Ho
    • 1
    • 2
  • Liang Wang
    • 3
  • Linfeng Huang
    • 1
  • Zhigang Li
    • 1
  • Denise W. Pallett
    • 1
  • Tamas Dalmay
    • 4
  • Kazusato Ohshima
    • 5
  • John A. Walsh
    • 6
  • Hui Wang
    • 1
  1. 1.NERC/Centre for Ecology and Hydrology (CEH) WallingfordWallingfordUK
  2. 2.Department of BiochemistryUniversity of OxfordOxfordUK
  3. 3.Beijing Institute of GenomicsChinese Academy of SciencesBeijingChina
  4. 4.School of Biological SciencesUniversity of East AngliaNorwichUK
  5. 5.Laboratory of Plant Virology, Faculty of AgricultureSaga UniversitySagaJapan
  6. 6.Plant-Virus Interactions Group, Warwick HRIWarwick UniversityWellesbourneUK
  7. 7.AF BuildingUniversity of Dundee at SCRIInvergowrieUK
  8. 8.Immune Disease InstituteBostonUSA

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