Phylogenetic insight into ABCE gene subfamily in plants.

ATP-BINDING CASSETTE SUBFAMILY E MEMBER (ABCE) proteins are one of the most conserved proteins across eukaryotes and archaea. Yeast and most animals possess a single ABCE gene encoding the critical translational factor ABCE1. In several plant species, including Arabidopsis thaliana and Oryza sativa, two or more ABCE gene copies have been identified, however information related to plant ABCE gene family is still missing. In this study we retrieved ABCE gene sequences of 76 plant species from public genome databases and comprehensively analyzed them with the reference to A. thaliana ABCE2 gene (AtABCE2). Using bioinformatic approach we assessed the conservation and phylogeny of plant ABCEs. In addition, we performed haplotype analysis of AtABCE2 and its paralogue AtABCE1 using genomic sequences of 1,135 A. thaliana ecotypes. Plant ABCE proteins showed overall high sequence conservation, sharing at least 78% of amino acid sequence identity with AtABCE2. We found that over half of the selected species have two to eight ABCE genes, suggesting that in plants ABCE genes can be classified as a low-copy gene family, rather than a single-copy gene family. The phylogenetic trees of ABCE protein sequences and the corresponding coding sequences demonstrated that Brassicaceae and Poaceae families have independently undergone lineage-specific split of the ancestral ABCE gene. Other plant species have gained ABCE gene copies through more recent duplication events. We also noticed that ploidy level but not ancient whole genome duplications experienced by a species impacts ABCE gene family size. Deeper analysis of AtABCE2 and AtABCE1 from 1,135 A. thaliana ecotypes revealed four and 35 non-synonymous SNPs, respectively. The lower natural variation in AtABCE2 compared to AtABCE1 is in consistence with its crucial role for plant viability. Overall, while the sequence of the ABCE protein family is highly conserved in the plant kingdom, many plants have evolved to have more than one copy of this essential translational factor.

ABCE1 is a highly conserved RNA silencing suppressor.

ATP-binding cassette sub-family E member 1 (ABCE1) is a highly conserved protein among eukaryotes and archaea. Recent studies have identified ABCE1 as a ribosome-recycling factor important for translation termination in mammalian cells, yeast and also archaea. Here we report another conserved function of ABCE1. We have previously described AtRLI2, the homolog of ABCE1 in the plant Arabidopsis thaliana, as an endogenous suppressor of RNA silencing. In this study we show that this function is conserved: human ABCE1 is able to suppress RNA silencing in Nicotiana benthamiana plants, in mammalian HEK293 cells and in the worm Caenorhabditis elegans. Using co-immunoprecipitation and mass spectrometry, we found a number of potential ABCE1-interacting proteins that might support its function as an endogenous suppressor of RNA interference. The interactor candidates are associated with epigenetic regulation, transcription, RNA processing and mRNA surveillance. In addition, one of the identified proteins is translin, which together with its binding partner TRAX supports RNA interference.

AtRLI2 is an endogenous suppressor of RNA silencing.

RNA silencing is a mechanism involved in gene regulation during development and anti-viral defense in plants and animals. Although many viral suppressors of this mechanism have been described up to now, this is not the case for endogenous suppressors. We have identified a novel endogenous suppressor in plants: RNase L inhibitor (RLI) of Arabidopsis thaliana. RLI is a very conserved protein among eukaryotes and archaea. It was first known as component of the interferon-induced mammalian 2'-5' oligoadenylate (2-5A) anti-viral pathway. This protein is in several organisms responsible for essential functions, which are not related to the 2-5A pathway, like ribosome biogenesis and translation initiation. Arabidopsis has two RLI paralogs. We have described in detail the expression pattern of one of these paralogs (AtRLI2), which is ubiquitously expressed in all plant organs during different developmental stages. Infiltrating Nicotiana benthamiana green fluorescent protein (GFP)-transgenic line with Agrobacterium strains harboring GFP and AtRLI2, we proved that AtRLI2 suppresses silencing at the local and at the systemic level, reducing drastically the amount of GFP small interfering RNAs.