Evolution of nonstop, no-go and nonsense-mediated mRNA decay and their termination factor-derived components

Abstract

Background: Members of the eukaryote/archaea specific eRF1 and eRF3 protein families have central roles in translation termination. They are also central to various mRNA surveillance mechanisms, together with the eRF1 paralogue Dom34p and the eRF3 paralogues Hbs1p and Ski7p. We have examined the evolution of eRF1 and eRF3 families using sequence similarity searching, multiple sequence alignment and phylogenetic analysis.

Results: Extensive BLAST searches confirm that Hbs1p and eRF3 are limited to eukaryotes, while Dom34p and eRF1 (a/eRF1) are universal in eukaryotes and archaea. Ski7p appears to be restricted to a subset of Saccharomyces species. Alignments show that Dom34p does not possess the characteristic class-1 RF minidomains GGQ, NIKS and YXCXXXF, in line with recent crystallographic analysis of Dom34p. Phylogenetic trees of the protein families allow us to reconstruct the evolution of mRNA surveillance mechanisms mediated by these proteins in eukaryotes and archaea.

Conclusion: We propose that the last common ancestor of eukaryotes and archaea possessed Dom34p-mediated no-go decay (NGD). This ancestral Dom34p may or may not have required a trGTPase, mostly like a/eEF1A, for its delivery to the ribosome. At an early stage in eukaryotic evolution, eEF1A was duplicated, giving rise to eRF3, which was recruited for translation termination, interacting with eRF1. eRF3 evolved nonsense-mediated decay (NMD) activity either before or after it was again duplicated, giving rise to Hbs1p, which we propose was recruited to assist eDom34p in eukaryotic NGD. Finally, a third duplication within ascomycete yeast gave rise to Ski7p, which may have become specialised for a subset of existing Hbs1p functions in non-stop decay (NSD). We suggest Ski7p-mediated NSD may be a specialised mechanism for counteracting the effects of increased stop codon read-through caused by prion-domain [PSI+] mediated eRF3 precipitation.

Figure 1

Architecture and consensus alignments of the eRF1/Dom34p family. A) A schematic representation of the domain architecture of eRF1 is shown along with B) an alignment of separate consensus sequences for paralogues of eRF1/Dom34p for eukaryotes and archaea. Fifty percent conservation consensus sequences were calculated using the Python program ConsensusFinder (G. Atkinson). Uppercase letters indicate amino acids conserved in > 50% of all examined sequences, and lowercase letters indicate a common amino acid substitution group conserved in > 50% of the sequences. A '.' denotes a position that is universally present but not conserved in sequence, and gaps are denoted by "-". Domains are indicated above the alignment with lines terminating in arrows. Other family-specific symbols are as follows: dashed grey box with filled circles below – location of Dom34p residues implicated in endonuclease activity [32,35], filled grey box – eRF1 structural minidomains, open grey box – human eRF3 binding sites [11], dashed line – RNA binding site [30], "^" characters – putative NLS domain [56], and "~" characters – well conserved patches that fall outside previously reported functional motifs. The a/eRF1-specific insertion at positions 356–393 is shown in detail in additional file 4. Secondary structure is indicated below the alignment for human eRF1 (PDB accession code 1DT9, [91]) and S. cerevisae Dom34p (PDB accession code 2VGM, [32]). Blue arrows show β-sheets and red tubes show α-helices. Pale blocks within structural elements indicate positions in the alignment that are not present in the sequence of the protein from which the structure was determined.

Figure 2

Annotated structure of human eRF1 alone and superimposed with yeast Dom34p structure. Panel A: Human eRF1 (PDB accession code 1DT9) structure is shown indicating the location of functional features and patches of residues that are highly conserved across the eRF1 family. Panel B: Superposition of human eRF1 (green) and S. cerevisae Dom34p (PDB accession code 2VGM, light pink). eRF1-specific functional motifs are marked with the same color coding as in panel A. Color code and residue coordinates (from figure 2B) are as follows: GGQ motif (yellow, 198–200), NIKS (blue, 62–65) and YXCXXF (orange, 138–144) motifs, GILRY motif (red, 441–445), a/eRF1-specific insertion (magenta, 356–393) RNA-binding motif [30] (white, 320–352), E41, E/D44 and D 45 residues in Dom34p (violet) and M stem conserved region (cyan, 239–245).

Figure 3

Phylogeny of the eRF1/Dom34p family. The tree shown was derived by Bayesian inference based on 178 universally aligned positions of eRF1 and Dom34p amino acid sequences from the M and C domains. The analysis was terminated after 5 million generations, at which point the SDSF was 0.0205 and 500,000 generations were discarded as burn-in. Branch lengths are drawn to scale as indicated by the scale bar at lower left. Branch support values from this analysis are indicated in black, with BIPP in square brackets and MLBP without brackets. Only MLBP values greater than 50% and BIPP values great than 0.65 are displayed. Branch thickness is drawn proportional to BIPP values from separate phylogenetic analyses of full length a/eRF1 (349 positions, blue branches) and a/eDom34p (292 positions, purple branches) as indicated by the key to the right of the figure. Numbers in blue and purple italics correspond to MLBP support from the separate a/eRF1 and a/eDom34p phylogenetic analyses respectively. The tree topologies generated from these separate analyses are shown in additional files 3 and 4. Archaeal and eukaryotic taxon names are preceded by major group designations as follows: ME: metazoa; EX: excavata; FU: fungi; AM: amoebozoa; AV: alveolates; PL: archaeplastida ("plants"); NA: Nanoarchaea; EU: euryarchaeota; CR: crenarchaeaota. Names are followed by NCBI GI numbers.

Figure 4

Architecture and consensus alignments of the eRF3/Hbs1p family. A) A schematic representation of the domain architecture of eRF3 is shown along with B) an alignment of separate consensus sequences for paralogues of eRF3/Hbs1p families. Sixty percent conservation consensus sequences were calculated using the Python program ConsensusFinder (G. Atkinson). Uppercase letters indicate amino acids conserved in > 60% of all examined sequences, and lowercase letters indicate a common amino acid substitution group conserved in > 60% of the sequences. A '.' denotes a position that is universally present but not conserved in sequence, and gaps are denoted by "-". Domains are indicated above the alignment with lines terminating in arrows. Other family-specific symbols are as follows. Open grey box: E. octocarinatus eRF1 binding sites [62], filled grey boxes: human eRF1 binding site [11], dashed line: S. pombe eRF1 binding site [61]. Secondary structure is indicated below the alignment for S. pombe eRF3 (PDB accession code 1R5B, [65]) and Sulfolobus solfataricus aEF1A (PDB accession code 1JNY, [92]). Striped blocked are disordered regions with undetermined structure. Other structural designations are as in Figure 1.

Figure 5

Phylogeny of the eRF3/Hbs1p family. The tree shown was derived by Bayesian inference phylogeny based on 395 universally aligned positions of eRF3 and Hbs1p amino acid sequences. The analysis was terminated after 5 million generations, at which point the SDSF was 0.0286, and 500,000 generations were discarded as burn-in. Branch lengths designation, support values and major taxon group designation are as in Figure 4.

Figure 6

Phylogeny of the Hbs1p/Ski7p families. The tree shown was derived by Bayesian inference phylogeny based on 395 universally aligned amino acid positions for Ski7p, Hbs1p, and eRF3 sequences. The tree includes all identified Ski7p sequences. The analysis was terminated after 5 million generations, at which point the SDSF was 0.005, and 500,000 generations were discarded as burn-in. For sequences retrieved as nucleotides and translated into amino acids, the numbers in brackets indicate the start and end coordinates of the genomic DNA that was matched in the TBLASTN search. Branch lengths designation, support values and major taxon group designation are as in Figure 4.

Figure 7

Evolution of mRNA quality control mechanisms. A schematic representation of a proposed scenario for the origin and divergence of components of trGTPase-associated mRNA decay mechanisms in archaea and eukaryotes is shown. Abbreviations indicate decay mechanisms known to function in eukaryotes and potentionally functional in archaea as follows: NSD – nonstop decay, NMD – nonsense-mediated decay, and NGD – no-go decay.