title: Nucleotide bias of DCL and AGO in plant anti-virus gene silencing.
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.
authors.affiliation: NERC/Centre for Ecology and Hydrology (CEH) Wallingford, Maclean Building, Benson Lane, Wallingford, Oxfordshire, OX10 8BB, UK.
authors.forename: Thien
authors.initials: T
authors.lastname: Ho
authors.forename: Liang
authors.initials: L
authors.lastname: Wang
authors.forename: Linfeng
authors.initials: L
authors.lastname: Huang
authors.forename: Zhigang
authors.initials: Z
authors.lastname: Li
authors.forename: Denise W
authors.initials: DW
authors.lastname: Pallett
authors.forename: Tamas
authors.initials: T
authors.lastname: Dalmay
authors.forename: Kazusato
authors.initials: K
authors.lastname: Ohshima
authors.forename: John A
authors.initials: JA
authors.lastname: Walsh
authors.forename: Hui
authors.initials: H
authors.lastname: Wang
mesh_terms: D017360:Arabidopsis / Q000201:enzymology / Q000235:genetics / Q000821:virology; D001482:Base Composition; D031745:Dactylis / Q000201:enzymology / Q000235:genetics / Q000821:virology; D017343:Genes, Plant; D005814:Genes, Viral; D008957:Models, Genetic; D009149:Mustard Plant / Q000201:enzymology / Q000235:genetics / Q000821:virology; D010935:Plant Diseases / Q000235:genetics / Q000821:virology; D010940:Plant Proteins / Q000378:metabolism; D010942:Plant Viruses / Q000235:genetics* / Q000472:pathogenicity*; D010944:Plants / Q000201:enzymology* / Q000235:genetics / Q000821:virology*; D017800:Potyvirus / Q000235:genetics / Q000472:pathogenicity; D034622:RNA Interference; D018749:RNA, Plant / Q000235:genetics; D034741:RNA, Small Interfering / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D034743:RNA-Induced Silencing Complex / Q000378:metabolism*; D043244:Ribonuclease III / Q000378:metabolism*; D012641:Selection, Genetic; D013379:Substrate Specificity
chemical_list: D010940:Plant Proteins; D018749:RNA, Plant; D034741:RNA, Small Interfering; D012367:RNA, Viral; D034743:RNA-Induced Silencing Complex; D043244:Ribonuclease III