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. 2011 Mar 15;1(9):847–858. doi: 10.1007/s13238-010-0100-4

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

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,✉
PMCID: PMC4875223  PMID: 21203927

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.

Electronic Supplementary Material

The online version of this article (doi:10.1007/s13238-010-0100-4 contains supplementary material, which is available to authorized users.

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

Electronic Supplementary Material

Table (PDF 24 KB) (22.1KB, pdf)
Table (PDF 96 KB) (93.8KB, pdf)
Table (PDF 16 KB) (12.1KB, pdf)
Figure (PDF 856 KB) (853.6KB, pdf)

Footnotes

Electronic Supplementary Material

The online version of this article (doi:10.1007/s13238-010-0100-4 contains supplementary material, which is available to authorized users.

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Supplementary Materials

Table (PDF 24 KB) (22.1KB, pdf)
Table (PDF 96 KB) (93.8KB, pdf)
Table (PDF 16 KB) (12.1KB, pdf)
Figure (PDF 856 KB) (853.6KB, pdf)

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