Abstract
The yeast protein Dom34 has been described to play a critical role in a newly identified mRNA decay pathway called No-Go decay. This pathway clears cells from mRNAs inducing translational stalls through endonucleolytic cleavage. Dom34 is related to the translation termination factor eRF1 and physically interacts with Hbs1, which is itself related to eRF3. We have solved the 2.5-A resolution crystal structure of Saccharomyces cerevisiae Dom34. This protein is organized in three domains with the central and C-terminal domains structurally homologous to those from eRF1. The N-terminal domain of Dom34 is different from eRF1. It adopts a Sm-fold that is often involved in the recognition of mRNA stem loops or in the recruitment of mRNA degradation machinery. The comparison of eRF1 and Dom34 domains proposed to interact directly with eRF3 and Hbs1, respectively, highlights striking structural similarities with eRF1 motifs identified to be crucial for the binding to eRF3. In addition, as observed for eRF1 that enhances eRF3 binding to GTP, the interaction of Dom34 with Hbs1 results in an increase in the affinity constant of Hbs1 for GTP but not GDP. Taken together, these results emphasize that eukaryotic cells have evolved two structurally related complexes able to interact with ribosomes either paused at a stop codon or stalled in translation by the presence of a stable stem loop and to trigger ribosome release by catalyzing chemical bond hydrolysis.
Highlights
In living cells, elaborate quality control mechanisms are essential for ensuring the highest fidelity in the transfer and decoding of the genetic information, i.e. during DNA replication, transcription and translation of mRNAs into proteins
The translation elongation factor eEF-1A that delivers aminoacyl-tRNAs to the ribosomal A-site [37] is the representative of this protein family that further includes eRF3 [38, 39] and Ski7, which is involved in exosome-mediated mRNA degradation and in the non-stop decay (NSD) pathway [19, 21]
The Hbs1-Dom34 complex from S. cerevisiae has been implicated in a newly described mRNA decay pathway called No-Go decay. This pathway releases ribosomes stalled in translation due to the presence of a stable stem loop within the mRNA and this complex triggers direct endonucleolytic cleavage of aberrant mRNA
Summary
Elaborate quality control mechanisms are essential for ensuring the highest fidelity in the transfer and decoding of the genetic information, i.e. during DNA replication, transcription and translation of mRNAs into proteins (for reviews, see Refs. 1–5). The translation elongation factor eEF-1A that delivers aminoacyl-tRNAs to the ribosomal A-site [37] is the representative of this protein family that further includes eRF3 [38, 39] and Ski, which is involved in exosome-mediated mRNA degradation and in the NSD pathway [19, 21]. Overexpression of Hbs suppresses this phenotype in yeast ssb1/ssb mutant strains Based on these observations, Inagaki and co-workers [35] have suggested that during translation elongation, Hbs may help in stop codon-independent peptide release from ribosomes stalled by the absence of Hsp70-mediated nascent polypeptide channeling. Inagaki and co-workers [35] have suggested that during translation elongation, Hbs may help in stop codon-independent peptide release from ribosomes stalled by the absence of Hsp70-mediated nascent polypeptide channeling This is further supported by the involvement of Hbs and Dom in the NGD pathway [26]. Lee and colleagues [41] showed in vitro that the N-terminal domains from both T. acidophilum and Saccharomyces cerevisiae Dom34/Pelota display endonuclease activity against mRNAs that contain a stem loop, supporting the hypothesis that Dom is the endonuclease involved in the NGD pathway
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