Skip to Main content Skip to Navigation
Journal articles

Genome-wide computational identification of WG/GW Argonaute-binding proteins in Arabidopsis.

Abstract : 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.
Complete list of metadata

https://hal.archives-ouvertes.fr/hal-00788371
Contributor : Elisabeth Goetschy Connect in order to contact the contributor
Submitted on : Thursday, February 14, 2013 - 12:14:23 PM
Last modification on : Wednesday, March 16, 2022 - 4:06:01 PM

Links full text

Identifiers

Collections

Citation

Wojciech M Karlowski, Andrzej Zielezinski, Julie Carrère, Dominique Pontier, Thierry Lagrange, et al.. Genome-wide computational identification of WG/GW Argonaute-binding proteins in Arabidopsis.. Nucleic Acids Research, Oxford University Press, 2010, 38 (13), pp.4231-45. ⟨10.1093/nar/gkq162⟩. ⟨hal-00788371⟩

Share

Metrics

Record views

85