Location of Repository

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

By Thien Ho, Liang Wang, Linfeng Huang, Zhigang Li, Denise W. Pallett, Tamas Dalmay, Kazusato Ohshima, John A. Walsh and Hui Wang

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

Topics: QK
Publisher: Springer
Year: 2010
OAI identifier: oai:wrap.warwick.ac.uk:3988

Suggested articles

Preview

Citations

  1. (2008). 24 Specificity of ARGONAUTE7-miR390 interaction and dual functionality in TAS3 trans-acting siRNA formation. doi
  2. (2006). A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. doi
  3. (2009). A three-dimensional view of the molecular machinery of RNA interference. doi
  4. (2008). An endogenous small interfering RNA pathway in Drosophila. doi
  5. (2006). Analyses on mutation patterns, detection of population bottlenecks, and suggestion of deleterious-compensatory evolution among members of the genus Potyvirus. doi
  6. (2007). Antiviral immunity directed by small RNAs. doi
  7. (2008). Argonaute proteins: key players in RNA silencing. doi
  8. (2009). Characterization and comparative profiling of the small RNA transcriptomes in two phases of locust. doi
  9. (2008). Characterization of hypovirus-derived small RNAs generated in the chestnut blight fungus by an inducible DCL-2-dependent pathway. doi
  10. (2007). Combinatorial RNAi: a winning strategy for the race against evolving targets? doi
  11. (2007). DCL4 targets Cucumber mosaic virus satellite RNA at novel secondary structures. doi
  12. (2009). Deep sequencing of viroid-derived small RNAs from grapevine provides new insights on the role of RNA silencing in plant-viroid interaction. doi
  13. (2009). Deep-sequencing of plant viral small RNAs reveals effective and widespread targeting of viral genomes. doi
  14. (2008). Evidence for GC preference by monocot Dicer-like proteins. doi
  15. (2007). Evidence for targeting common siRNA hotspots and GC preference by plant Dicer-like proteins. doi
  16. (2010). Evolutionary trajectory of turnip mosaic virus populations adapting to a new host. doi
  17. (2008). Experimental evolution of plant RNA viruses. doi
  18. (2005). Gardening the genome: DNA methylation in Arabidopsis thaliana. doi
  19. (2009). Genome rhetoric and the emergence of compositional bias. doi
  20. (2007). Genome-wide profiling and analysis of Arabidopsis siRNAs. doi
  21. (2005). Heterogeneity in codon usages of sobemovirus genes. doi
  22. (2006). Hierarchical action and inhibition of plant Dicer-like proteins in antiviral defense. doi
  23. (2009). Limitations and possibilities of small RNA digital gene expression profiling. doi
  24. (2005). Mutations in Turnip mosaic virus genomes that have adapted to Raphanus sativus. doi
  25. (2006). On the art of identifying effective and specific siRNAs. doi
  26. (2007). Oryza sativa dicer-like4 reveals a key role for small interfering RNA silencing in plant development. doi
  27. (2005). Passengerstrand cleavage facilitates assembly of siRNA into Ago2-containing RNAi enzyme complexes. doi
  28. (2008). Plant ARGONAUTES. doi
  29. (2005). Plant virus-derived small interfering RNAs originate predominantly from highly structured single-stranded viral RNAs. doi
  30. (2008). Prospects for the therapeutic application of lentivirus-based gene therapy to HIV-1 infection. doi
  31. (2004). RISC Assembly Defects in the Drosophila RNAi Mutant armitage. doi
  32. (2009). RNA-based viral immunity initiated by the Dicer family of host immune receptors. doi
  33. (2009). RNAi targeting of West Nile virus in mosquito midguts promotes virus diversification. PLoS pathogens 5, doi
  34. (2008). Role of silencing suppressor proteins. doi
  35. (2009). Roles of plant small RNAs in biotic stress responses. Annual review of plant biology doi
  36. (2008). Selection on codon bias. doi
  37. (2009). Small RNA deep sequencing reveals role for Arabidopsis thaliana RNA-dependent RNA polymerases in viral siRNA biogenesis. doi
  38. (2008). Small RNA-directed epigenetic natural variation in Arabidopsis thaliana. doi
  39. (2008). Small RNAs in viral infection and host defense. doi
  40. (2008). Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5' terminal nucleotide. doi
  41. (2005). Structural basis for 5'-end-specific recognition of guide RNA by the A. fulgidus Piwi protein. doi
  42. (2005). Structural insights into mRNA recognition from a PIWI domain-siRNA guide complex. doi
  43. (2007). Structure of Aquifex aeolicus argonaute highlights conformational flexibility of the PAZ domain as a potential regulator of RNA-induced silencing complex function. doi
  44. (2007). Targets of RNA-directed DNA methylation. doi
  45. (2010). The Arabidopsis RNA-directed DNA methylation argonautes functionally diverge based on their expression and interaction with target loci. doi
  46. (2008). The Argonaute protein family. doi
  47. (2007). Therapeutic application of RNA interference for hepatitis C virus. doi
  48. (2004). WebLogo: a sequence logo generator. doi
  49. (2008). Widespread translational inhibition by plant miRNAs and siRNAs. doi

To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.