Program in Evolutionary Biology, Canadian Institute for Advanced Research, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
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Abstract |
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Introduction |
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Translation terminationrecognition of stop codons UAA, UAG, and UGA in the A site of ribosomes and hydrolysis of peptidyl-tRNAis the least understood of these processes, from either mechanistic or evolutionary perspectives. Because this process is essential, we might expect the proteins (release factors) responsible to be ancient and highly conserved. However, neither of the two principal bacterial release factors, bacterial release factor 1 (RF1) (which recognizes stop codons UAA and UAG) or RF2 (which recognizes UAA and UGA), shows obvious similarity to the single principal release factor in eukaryotes, eukaryotic release factor 1 (eRF1) (which recognizes all three stop codons). Furthermore, although both bacteria and eukaryotes employ additional GTPase factors (RF3 and eRF3, respectively) that stimulate termination, the genes encoding these factors are not orthologous (Sogin 1997
). It is remarkable that this essential system is so differently constituted in bacteria and eukaryotes.
All six completed archaeal genomes contain an archaeal RF (archael release factor 1; aRF1) clearly related to the principal eukaryotic release factor, eRF1 (Bult et al. 1996
; Klenk et al. 1997
; Smith et al. 1997
; Kawarabayashi et al. 1998, 1999
). Although there have been no biochemical studies on translation termination in archaea, aRF1 is presumed to bind all three stop codons, based on the sequence similarity to the eukaryotic factor (Dennis 1997). However, no eRF3 or RF3 homolog has been identified so far in any archaeon (Bult et al. 1996
; Klenk et al. 1997
; Smith et al. 1997
; Kawarabayashi et al. 1998, 1999
).
At the biochemical and genetic levels, the eukaryotic translation termination system has been studied most extensively in Saccharomyces cerevisiae. The eRF1 gene was first described as an omnipotent nonsense suppressor gene, sup45 (Breining and Piepersberg 1986
). In 1994, the product of this gene (eRF1) was shown to recognize all three stop codons on ribosomes and catalyze peptidyl-tRNA hydrolysis (Frolova et al. 1994
). Subsequently, the product of another nonsense suppressor gene, sup35, was found to assist eRF1. The Sup35 protein, termed eRF3, binds tightly to eRF1 and stimulates its translation termination activity in a GTP-dependent manner (Stansfield et al. 1995
; Zhouravleva et al. 1995
). Comparisons between eRF3 homologs from animals, fungi, and one plant revealed that this protein has an N-terminal domain of varying length and amino acid (aa) sequence and a C-terminal domain that is highly conserved, with strong similarity to elongation factor 1
(EF-1
). In yeast, the EF-1
-like C-terminal domain is necessary and sufficient for maintenance of translation fidelity and cell viability, but the N-terminal domain can be deleted (Ter-Avanesyan et al. 1993
).
Interestingly, the N-terminal domain of yeast eRF3 is responsible for the propagation of a prion-like [+] phenotype, which is inherited in a non-Mendelian manner (Kochneva-Pervukhova et al. 1998
). Overexpression of this domain or mutations affecting it trigger protein aggregation both in vitro and in vivo, as do mutations in mammalian PrPSc (Kochneva-Pervukhova et al. 1998
). The [
+] phenotype appears advantageous to yeast under stress conditions (Eaglestone, Cox, and Tuite 1999
). However, no [
+]-like protein aggregation is known for other eRF3 proteins, and the primary and conserved function of the N-terminal domain of eRF3 remains unclear.
Humans, mice, Caenorhabditis elegans, and yeast contain another open reading frame (ORF), called HBS1 (or eRFS), showing strong sequence similarity to EF-1 and eRF3 (Garcia-Cantalejo et al. 1994
; Wallrapp et al. 1998
). Like eRF3, HBS1 proteins have an additional sequence at the N-terminus of the highly conserved domain corresponding to EF-1
. Although the two molecules share unique structural features, mammalian HBS1 cannot complement a temperature-sensitive (ts) mutation in yeast eRF3 and does not interact with eRF1 (Wallrapp et al. 1998
). In yeast, the HBS1 gene is not essential for cell viability, but an increased copy number of this gene can suppress the growth defect of double mutation in the SSB1 and SSB2 genes (Nelson et al. 1992
). SSB1 and SSB2, which are molecular chaperones of the HSP70 family, are believed to interact directly with nascent polypeptides on ribosomes and support their transport through the ribosome channel into the cytosol. Therefore, yeast HBS1 may escort aminoacyl-tRNA to the ribosome more efficiently than normal EF-1
and relieve "protein sticking" in the channel (Nelson et al. 1992
).
We sought to retrace the evolution of the translation termination system, focusing here on the origins of eRF1 and eRF3. Considering eukaryotes other than animals, plants, and fungi, the GenBank database contains no eRF3 sequences and only two eRF1 sequences (Plasmodium falciparum, AE001492; Tetrahymena thermophila, AB026195). In this study, we amplified, cloned, and sequenced eRF3 genes from two ciliates, Euplotes aediculatus and Oxytricha trifallax, and two amitochondriate protists, Trichomonas vaginalis (Parabasalia) and Giardia lamblia (Diplomonada), as well as the G. lamblia eRF1 gene. In the public databases, we found previously unidentified HBS1 genes for Drosophila melanogaster, Schizosaccharomyces pombe, and Candida albicans. Phylogenetic analyses of these sequences allowed us to trace some of the early stages in the evolution of the eukaryotic version of the translation termination system and provided evidence for G. lamblia as one of the first-diverging lineages among eukaryotes.
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Materials and Methods |
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Exact-match primers based on these partial G. lamblia sequences were used for Uneven PCR (Chen and Wu 1997
). The basic strategy of this method is to amplify unknown N- and C-terminal regions with an exact-match primer and a short primer with an arbitrary sequence (arbitrary primer) that can hybridize to many sites on a template DNA. For each amplified fragment, multiple clones were completely sequenced to avoid PCR artifacts. The sequenced regions for the G. lamblia eRF1 and eRF3 genes were 2.7 and 2.0 kb, respectively. The detailed conditions of Uneven PCR were as described in the original paper (Chen and Wu 1997
). Arbitrary primers used in this study were provided by J. M. Logsdon (Dalhousie University, Halifax, Nova Scotia, Canada).
The EF-1-like domains of the O. trifallax and E. aediculatus eRF3 genes were partially amplified with degenerate primers 35F2A and 35R2A. In the macronuclei of hypotrich ciliates (such as O. trifallax and E. aediculatus), each single gene is known to be composed of a chromosome with telomere ends (Prescott 1994
). Therefore, using PCR with exact-match primers for ciliate eRF3 genes and a primer designed to bind the telomere sequence, 5'-(CCCCAAAA)n-3', we succeeded in amplifying the entire macronuclear chromosomes for the two ciliate eRF3 genes. These amplifications were carried out as follows: denaturation at 94°C for 1 min, annealing at 57°C for 30 s, and extension at 72°C for 30 s for 35 cycles. DNA sequences of these amplified fragments were confirmed by multiple clones. The macronuclear chromosomes containing the O. trifallax and E. aediculatus eRF3 genes were 3.3 and 2.6 kb, respectively. Primers for telomeric repeats were provided by D. M. Prescott (University of Colorado, Boulder).
The 0.4-kb region of the T. vaginalis eRF3 gene was obtained by PCR with primers 35F1A (GTCTTTATCGGCCAYGTNGAYGCNGG) and 35R2A. With this PCR product as a probe, a T. vaginalis genomic DNA library (provided by J. M. Logsdon and N. M. Fast, Dalhousie University) was screened, and one clone containing the entire eRF3 gene (1,764 bp) was isolated. Both DNA strands of this gene were completely sequenced by primer walking. All sequences determined in this study were deposited in GenBank under accession numbers AF198107AF198111.
Identifying HBS1 Genes in Databases
Homologs of the yeast HBS1 gene, which have an EF-1-like domain at their C-terminus, have been described only for C. elegans and two mammals (Nelson et al. 1992;
Wallrapp et al. 1998
). We found two previously unidentified HBS1 genes from D. melanogaster and S. pombe in the GenBank nonredundant (nr) database using TBLASTN (Altschul et al. 1997
). The D. melanogaster homolog was found in the region 62A1062B5 on chromosome 3L (positions 9973009 in AC005557). We also identified several partial cDNA sequences for this gene (e.g., AA952043, AI388068, and AI455532). In S. pombe chromosome II cosmid c2G5 (AL033385), the HBS1 homolog was identified (positions 1857520447). Searching the database for C. albicans at the Stanford DNA Sequence and Technology Center, the ORF found in the contig 33135 (positions 11629) appeared to encode an HBS1 homolog. Although the N-terminus of this ORF is truncated, the entire EF-1
-like domain of HBS1 is covered by this contig. Sequence data for C. albicans were obtained from the Stanford DNA Sequencing and Technology Center website at http://www-sequence.stanford.edu/group/candida.
Phylogenetic Analyses
Eleven eRF1 and six aRF1 sequences ({eRF1 + aRF1}) were aligned by CLUSTAL W (Higgins and Sharp 1988
) and subsequently edited by eye. An unambiguous alignment (358 positions) was used for reconstruction of the eRF1 phylogeny. The best protein maximum-likelihood (ML) tree was chosen among 1,000 trees constructed by quick-add-OTU (heuristic) search using the JTT-F substitution model, implemented in PROTML, version 2.2 (Adachi and Hasegawa 1996
). For further tests of the eRF1 phylogeny, we performed bootstrap analyses using PROTML. One hundred data sets were generated from the original alignment using SEQBOOT (Felsenstein 1993
). For each data set, we searched for the best ML tree among 100 trees constructed by heuristic search with JTT-F. The bootstrap scores were generated from a consensus of the best ML trees obtained from the 100 resampling data sets using CONSENSE (Felsenstein 1993
).
The EF-1-like domains of eRF3 and HBS1 were manually added to an EF-1
alignment provided by S. L. Baldauf (University of York, U.K.) and edited by eye. The resultant unambiguous alignment (372 positions) includes 16 eRF3, 7 HBS1, 16 eukaryotic EF-1
(eEF-1
), and 9 archaeal EF-1
(aEF-1
) sequences. The best ML tree and resampling estimated log likelihood (RELL) values were obtained from 1,000 trees constructed by heuristic search with JTT-F inferred from this master alignment.
It is well documented that the choice of sequences used for an outgroup can significantly affect phylogenetic inferences (e.g., Roger et al. 1999
). For the eRF3 phylogeny, eEF-1
, HBS1, and aEF-1
are available as potential outgroups. From the master alignment including 48 sequences, we generated data sets including 16 eRF3 sequences and 3 sequences for the outgroup, such as human (P04720), Porphyra purpurea (U08844), and G. lamblia (D14342) eEF-1
({eRF3 + eEF-1
}); human (U87791), C. elegans (Z81098), and yeast (Z28309) HBS1 ({eRF3 + HBS1}); or Methanococcus jannaschii, (U67486), Archaeoglobus fulgidus (AE001039), and Desulfurococcus mobilis (X73582) aEF-1
({eRF3 + aEF-1
}). For each of three data sets, the best ML tree was selected from a heuristic search, and bootstrap analyses were performed using resampling data sets.
In PROTML (Adachi and Hasegawa 1996
), all sites are treated as freely changeable with the same evolutionary rate, although in reality such sites evolve at various rates. Therefore, some portion of constant sites in our data sets might be invariable and potentially violate phylogenetic assumptions made by PROTML. In fact, a previous study found that constant (or invariable) site removal from several data sets significantly reduced statistical support for early divergence of G. lamblia and T. vaginalis (Hirt et al. 1999
). To examine the effect of constant-site removal on our analyses, we removed these sites from our data sets, {eRF3 + eEF-1
}, {eRF3 + HBS1}, and {eRF1 + aRF1}, and performed bootstrap analyses again.
For the calibration of site-by-site evolutionary rates in eRF1 and eRF3, we calculated a discrete distribution (one invariable and eight rate categories) over the neighbor-joining (NJ) tree with the JTT using PUZZLE, version 4.0 (Strimmer and von Haeseler 1996
), for each of the former data sets. Based on the ML distance matrices that were calibrated by
distributions, the NJ trees were constructed by NEIGHBOR (Felsenstein 1993
). For bootstrap analyses, 500 resampling data sets were generated by SEQBOOT (Felsenstein 1993
), and these ML distance matrices were subsequently calculated by PUZZLE (Strimmer and von Haeseler 1996
) and PUZZLEBOOT, version 1.02 (A. J. Roger and M. E. Holder, http://members.tripod.de/korbi/puzzle/), using the portion of invariable sites and the shape parameter obtained from an original data set. Using these matrices, bootstrap scores were obtained by NEIGHBOR and CONSENSE (Felsenstein 1993
).
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Results |
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The genes for O. trifallax, E. aediculatus, and T. vaginalis eRF3 should encode 937-, 806-, and 588-aa proteins, respectively. No evidence for introns was found in these genes. The top BLASTX matches of the O. trifallax, E. aediculatus, and T. vaginalis sequences were to the N. tabacum eRF3 (L38828), with e-values of 10-120, 10-115, and 10-101, respectively. Like all eRF3 genes except that of G. lamblia, the O. trifallax, E. aediculatus, and T. vaginalis genes appeared to encode 412, 302, and 155 aa of N-terminal domains that are not found in EF-1 (fig. 1B
). While the N-terminal domains of the two ciliate eRF3 have no apparently repetitive sequence, we found 13 "PEPK" repeats in the T. vaginalis protein (data not shown). Compared with the yeast eRF3, unique C-terminal extensions of 87 and 67 aa were found in the O. trifallax and E. aediculatus proteins (data not shown).
We identified the D. melanogaster and S. pombe homologs of yeast HBS1 in the GenBank databases. The top BLASTX matches of the D. melanogaster and S. pombe sequences were human HBS1 (AAD00645), with e-values of 10-175 and 10-90, respectively. The D. melanogaster HBS1 (671 aa) has an N-terminal domain of 240 aa, as well as the EF-1-like domain (fig. 1B
). The D. melanogaster gene seems to contain no introns. The S. pombe gene should encode a 592-aa protein, with an N-terminal domain of 170 aa. Comparison with the 5' end sequence of its cDNA (AU013219) reveals that there are two short introns (54 and 43 bp) in this gene (data not shown).
A partial gene sequence for HBS1 was also found in the C. albicans sequence database at the Stanford DNA Sequence and Technology Center. The top BLASTX match of the C. albicans sequence is the S. cerevisiae HBS1 (P32769), with an e-value of 3 x 10-81. Although the 5' end of this gene is truncated, the partial gene encodes 105 aa of an N-terminal domain and the entire EF-1-like domain (422 aa) (fig. 1B
).
Phylogenetic Analyses
Bootstrap analysis for the {eRF1 + aRF1} data set statistically supported the initial divergence of G. lamblia and defined clades for A. thaliana and animal sequences (bootstrap scores 88, 99, and 76) in the inferred best ML tree (lnL = -6,900.46) (fig. 2A
). The removal of 37 constant sites did not significantly affect the support for the three branches mentioned above (fig. 2A
). We noticed that the number of invariable sites estimated by PUZZLE (Strimmer and von Haeseler 1996
) was only 10, which is significantly different from the number of constant sites. Nevertheless, the bootstrap scores in the absence of 10 invariable sites did not drastically change (fig. 2A
). In the NJ tree based on the ML distance matrix, G. lamblia was inferred as the basal eukaryote (data not shown), although the bootstrap score for this node was only 30 (fig. 2A
). Support for the animal clade also dropped (bootstrap score 43), and the only node supported by a bootstrap score over 50 was for the A. thaliana clade (bootstrap score 88) (fig. 2A
).
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The best ML tree based on the {eRF3 + aEF-1} data set (lnL = -9,125.38) had a different topology than the two trees mentioned above (data not shown); the first eRF3 branch was T. vaginalis, with G. lamblia being connected to ciliates. However, the bootstrap analysis for this data set poorly supported the basal separation of T. vaginalis (bootstrap score 45) and the node for the G. lambliaciliates clade (bootstrap score 35). We did not perform bootstrap analysis in the absence of constant sites or with calibration of rate heterogeneity across sites for this data set.
Regardless of the outgroup or method used for the reconstruction of eRF3 phylogeny, the clades for animals, fungi, and ciliates were highly supported (partially listed in fig. 2B
), but the phylogenetic positions for ciliates and T. vaginalis were unresolved. Interestingly, N. tabacum was most closely related to the animals-fungi clade in the ML distance trees using the {eRF3 + eEF-1} and {eRF3 +HBS1} data sets (bootstrap scores 60 and 52).
The best ML tree (lnL = -20,460.3) inferred from the data set including 48 sequences confirmed monophyly of eRF3, HBS1, eEF-1, and aEF-1
sequences with RELL values at or near 100 (fig. 3
). The three HBS1 sequences (newly identified in this study) formed a robust clade with the previously reported HBS1 orthologs. Consistent with the previous report (Wallrapp et al. 1998
), the eRF3 and HBS1 clades form a robust sister relationship (RELL value 100).
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Discussion |
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Nevertheless, it seems reasonable to suppose that some eukaryotic lineages diverge before the crown radiation. One might hope to identify them by their possession of "more primitive," or at least differently composed, versions of molecular machinery than are known to be conserved among crown eukaryotes. For instance, early-diverging eukaryotic lineages might have only one or two tubulins (an outgroup to , ß, and/or
) or exhibit a translation termination system more like that of archaea, with no eRF3 and eRF1 lacking a C-terminal tail for eRF3 binding (fig. 1A
and below). Our analyses show that the EF-1
gene duplication which gave rise to eRF3 is found in those protist lineages generally thought the deepest, such as G. lamblia and T. vaginalis. Unless some as-yet-uncharacterized protist group claims that honor, we must conclude that this gene duplication occurred at the "base of the eukaryotes."
However, we provide two lines of evidence for G. lamblia being the most basal branch examined so far. First, there is reasonable bootstrap support for its branching earlier than T. vaginalis in eRF3 trees rooted by eEF-1 and HBS1 (fig. 2B
). The support for this node is not drastically reduced by removal of constant sites (fig. 2B
). Our results are in contrast to the recent report that the support for G. lamblia and T. vaginalis as branching prior to the crown radiation in the trees of the largest subunit of RNA polymerase II or EF-2 greatly depends on constant (or invariable) sites in the data set that potentially disturb phylogenetic inferences using PROTML (Hirt et al. 1999
). In our case, even if the rate heterogeneity across sites in these data sets was fully compensated (using a discrete
distribution), the basal position of G. lamblia was statistically supported (fig. 2B
). We have no evidence that the position of G. lamblia deduced from the eRF3 phylogenies is artifactual, resulting from long-branch attraction.
The bootstrap scores obtained from the eRF1 phylogeny inferred from ML distance analysis (the NJ method considering a distribution) supported only the A. thaliana clade, while, in contrast, the earliest branching of G. lamblia and the animal clade were robust in the ML analyses (fig. 2A
). The eRF3 phylogeny rooted with aEF-1
suggested no strongly supported basal taxon (see Results). Therefore, these trees did not provide further support for or against the G. lamblia position that was inferred from the former analyses.
Second, our data from the structure of the G. lamblia eRF3 gene, which differs from all other eRF3 genes in lacking an N-terminal domain (fig. 1B ), are most consistent with the basal divergence of this protist. If this is a primitive feature (i.e., the ancestral eRF3 lacked the N-terminal domain), then parsimony would dictate that G. lamblia is deeper than T. vaginalis (or any other eukaryote which has this additional domain). Further exploration of informative molecular characters (e.g., indels, presence/absence of molecular machineries) is essential to determine the relative branching points of G. lamblia and T. vaginalis among eukaryotes.
At this point, we cannot, unfortunately, be certain of the ancestral structure of eRF3. The available HBS1 genes all show an N-terminal domain not found for EF-1, and our phylogenetic analysis indicates a close relationship between the two gene families (fig. 3
). If HBS1 and eRF3 are products of a gene duplication occurring after the acquisition of this domain, the parsimony argument does not hold. However, there is no obvious sequence similarity between the N-terminal (nonEF-1
) portions of HBS1 and eRF3. The branches for eRF3 and HBS1 are extremely long (fig. 3 ), and thus the sister relationship of HBS1 and eRF3 may be a long-branch attraction artifact. More HBS1 data (particularly from protists) are very much needed to examine this possibility.
Evolution of the Translation Termination System
The ribosome and associated proteins arguably comprise the cell's most complex (and possibly oldest) macromolecular machine. Several of the constituent molecules responsible for its conserved and essential functions are, not surprisingly, conserved among bacteria, archaea, and eukaryotes. There are, however, substantial differences in function and molecular composition within and between domains, and homology of components has not always been easy to demonstrate (Kyrpides and Woese 1998a, 1998b
).
Translation termination is the probably the least well understood facet of the translation process in either functional or evolutionary terms. Figure 4
presents a summary of the possible relationships between release factors based on our results and those of others (Keeling and Doolittle 1995
; Ito et al. 1996
). The principal release factors (bacterial RF1/RF2, archaeal/eukaryotic RF1) are probably all homologous to each other. Although we failed to detect any similarity between RF1/RF2 and eRF1 with sensitive local alignment programs such as TBLASTN and PSI-BLAST (Altschul et al. 1997
), Ito et al. (1996)
have presented convincing alignments of the bacterial and eukaryotic sequences and suggested further that both are homologous to EF-G. Similarity between aRF1 and eRF1 is much more apparent (fig. 2A
). Archaeal translation termination, like most archaeal replication, transcription, and translation functions, is probably most like the corresponding process in eukaryotes. It also seems simplest to imagine that bacterial RF1 and RF2 are products of a bacterial domainspecific duplication (fig. 4
, numeral 3). However, it is formally possible that the use of a single factor to recognize all three stop codons is a derived condition for eukaryotes (and archaea).
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Our results most directly address the evolution of the translation termination system in eukaryotes after their divergence from prokaryotes. All examined eukaryotes, including T. vaginalis and G. lamblia, have eRF3. All described eRF1 proteins, including that of G. lamblia, have the C-terminal tail necessary for interaction with eRF3. Until eukaryotes branching before the divergence of G. lamblia are identified and shown to lack these features, it seems reasonable to suppose that the duplication of eEF-1 which produced eRF3 and the addition of the eRF3-binding domain to eRF1 occurred at the base of the eukaryotes (fig. 4
, numerals 5 and 5'). It is possible, although not proven here, that G. lamblia diverged prior to the acquisition by eRF3 of its N-terminal ("prion") domain (fig. 4
, numeral 6 and asterisk).
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Acknowledgements |
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Footnotes |
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1 Abbreviations: aRF1, archaeal release factor 1; eEF-1, eukaryotic EF-1
; aEF-1
, archaeal EF-1
; eRF1, eukaryotic release factor 1; eRF3, eukaryotic release factor 3; ML, maximum likelihood; PCR, polymerase chain reaction; RF1, bacterial release factor 1; RF2, bacterial release factor 2; RF3, bacterial release factor 3; ts, temperature-sensitive.
2 Keywords: translation termination
eukaryotic release factor
EF-1
HBS1
gene duplication
Giardia.
3 Address for correspondence and reprints: Yuji Inagaki, Program in Evolutionary Biology, Canadian Institute for Advanced Research, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4H7. E-mail: yinagai{at}is.dal.ca
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