Journal
NUCLEIC ACIDS RESEARCH
Volume 38, Issue 13, Pages 4231-4245Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkq162
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Funding
- Marie Curie Host Fellowships for the Transfer of Knowledge [MTKD-CT-2004]
- Centre National de la Recherche Scientifique
- Agence Nationale de la Recherche [ANR-08-BLAN-0206-01]
- Agence Nationale de la Recherche (ANR) [ANR-08-BLAN-0206] Funding Source: Agence Nationale de la Recherche (ANR)
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Domains in Arabidopsis proteins NRPE1 and SPT5-like, composed almost exclusively of repeated motifs in which only WG or GW sequences and an overall amino-acid preference are conserved, have been experimentally shown to bind multiple molecules of Argonaute (AGO) protein(s). Domain swapping between the WG/GW domains of NRPE1 and the human protein GW182 showed a conserved function. As classical sequence alignment methods are poorly-adapted to detect such weakly-conserved motifs, we have developed a tool to carry out a systematic analysis to identify genes potentially encoding AGO-binding GW/WG proteins. Here, we describe exhaustive analysis of the Arabidopsis genome for all regions potentially encoding proteins bearing WG/GW motifs and consider the possible role of some of them in AGO-dependent mechanisms. We identified 20 different candidate WG/GW genes, encoding proteins in which the predicted domains range from 92aa to 654aa. These mostly correspond to a limited number of families: RNA-binding proteins, transcription factors, glycine-rich proteins, translation initiation factors and known silencing-associated proteins such as SDE3. Recent studies have argued that the interaction between WG/GW-rich domains and AGO proteins is evolutionarily conserved. Here, we demonstrate by an in silico domain-swapping simulation between plant and mammalian WG/GW proteins that the biased amino-acid composition of the AGO-binding sites is conserved.
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