Evolution of Eukaryotic Translation Elongation and Termination Factors: Variations of Evolutionary Rate and Genetic Code Deviations

Bridging the gap between transcriptome and proteome measurements identifies post-translationally regulated genes

MOTIVATION

Despite much dynamical cellular behaviour being achieved by accurate regulation of protein concentrations, messenger RNA abundances, measured by microarray technology, and more recently by deep sequencing techniques, are widely used as proxies for protein measurements. Although for some species and under some conditions, there is good correlation between transcriptome and proteome level measurements, such correlation is by no means universal due to post-transcriptional and post-translational regulation, both of which are highly prevalent in cells. Here, we seek to develop a data-driven machine learning approach to bridging the gap between these two levels of high-throughput omic measurements on Saccharomyces cerevisiae and deploy the model in a novel way to uncover mRNA-protein pairs that are candidates for post-translational regulation.

RESULTS

The application of feature selection by sparsity inducing regression (l₁ norm regularization) leads to a stable set of features: i.e. mRNA, ribosomal occupancy, ribosome density, tRNA adaptation index and codon bias while achieving a feature reduction from 37 to 5. A linear predictor used with these features is capable of predicting protein concentrations fairly accurately (R² = 0.86). Proteins whose concentration cannot be predicted accurately, taken as outliers with respect to the predictor, are shown to have annotation evidence of post-translational modification, significantly more than random subsets of similar size P < 0.02. In a data mining sense, this work also shows a wider point that outliers with respect to a learning method can carry meaningful information about a problem domain.

Release factor one is nonessential in Escherichia coli

Recoding a stop codon to an amino acid may afford orthogonal genetic systems for biosynthesizing new protein and organism properties. Although reassignment of stop codons has been found in extant organisms, a model organism is lacking to investigate the reassignment process and to direct code evolution. Complete reassignment of a stop codon is precluded by release factors (RFs), which recognize stop codons to terminate translation. Here we discovered that RF1 could be unconditionally knocked out from various Escherichia coli stains, demonstrating that the reportedly essential RF1 is generally dispensable for the E. coli species. The apparent essentiality of RF1 was found to be caused by the inefficiency of a mutant RF2 in terminating all UAA stop codons; a wild type RF2 was sufficient for RF1 knockout. The RF1-knockout strains were autonomous and unambiguously reassigned UAG to encode natural or unnatural amino acids (Uaas) at multiple sites, affording a previously unavailable model for studying code evolution and a unique host for exploiting Uaas to evolve new biological functions.

Evolution and diversification of the organellar release factor family

Translation termination is accomplished by proteins of the Class I release factor family (RF) that recognize stop codons and catalyze the ribosomal release of the newly synthesized peptide. Bacteria have two canonical RFs: RF1 recognizes UAA and UAG, RF2 recognizes UAA and UGA. Despite that these two release factor proteins are sufficient for de facto translation termination, the eukaryotic organellar RF protein family, which has evolved from bacterial release factors, has expanded considerably, comprising multiple subfamilies, most of which have not been functionally characterized or formally classified. Here, we integrate multiple sources of information to analyze the remarkable differentiation of the RF family among organelles. We document the origin, phylogenetic distribution and sequence structure features of the mitochondrial and plastidial release factors: mtRF1a, mtRF1, mtRF2a, mtRF2b, mtRF2c, ICT1, C12orf65, pRF1, and pRF2, and review published relevant experimental data. The canonical release factors (mtRF1a, mtRF2a, pRF1, and pRF2) and ICT1 are derived from bacterial ancestors, whereas the others have resulted from gene duplications of another release factor. These new RF family members have all lost one or more specific motifs relevant for bona fide release factor function but are mostly targeted to the same organelle as their ancestor. We also characterize the subset of canonical release factor proteins that bear nonclassical PxT/SPF tripeptide motifs and provide a molecular-model-based rationale for their retained ability to recognize stop codons. Finally, we analyze the coevolution of canonical RFs with the organellar genetic code. Although the RF presence in an organelle and its stop codon usage tend to coevolve, we find three taxa that encode an RF2 without using UGA stop codons, and one reverse scenario, where mamiellales green algae use UGA stop codons in their mitochondria without having a mitochondrial type RF2. For the latter, we put forward a “stop-codon reinvention” hypothesis that involves the retargeting of the plastid release factor to the mitochondrion.

On the Diversification of the Translation Apparatus across Eukaryotes

Diversity is one of the most remarkable features of living organisms. Current assessments of eukaryote biodiversity reaches 1.5 million species, but the true figure could be several times that number. Diversity is ingrained in all stages and echelons of life, namely, the occupancy of ecological niches, behavioral patterns, body plans and organismal complexity, as well as metabolic needs and genetics. In this review, we will discuss that diversity also exists in a key biochemical process, translation, across eukaryotes. Translation is a fundamental process for all forms of life, and the basic components and mechanisms of translation in eukaryotes have been largely established upon the study of traditional, so-called model organisms. By using modern genome-wide, high-throughput technologies, recent studies of many nonmodel eukaryotes have unveiled a surprising diversity in the configuration of the translation apparatus across eukaryotes, showing that this apparatus is far from being evolutionarily static. For some of the components of this machinery, functional differences between different species have also been found. The recent research reviewed in this article highlights the molecular and functional diversification the translational machinery has undergone during eukaryotic evolution. A better understanding of all aspects of organismal diversity is key to a more profound knowledge of life.

Mitochondrial genome evolution in the social amoebae

Most mitochondria contain a core set of genes required for mitochondrial function, but beyond this base there are variable genomic features. The mitochondrial genome of the model species Dictyostelium discoideum demonstrated that the social amoebae mitochondrial genomes have a size between those of metazoans and plants, but no comparative study of social amoebae mitochondria has been performed. Here, we present a comparative analysis of social amoebae mitochondrial genomes using D. discoideum, Dictyostelium citrinum, Dictyostelium fasciculatum, and Polysphondylium pallidum. The social amoebae mitochondria have similar sizes, AT content, gene content and have a high level of synteny except for one segmental rearrangement and extensive displacement of tRNAs. From the species that contain the rearrangement, it can be concluded that the event occurred late in the evolution of social amoebae. A phylogeny using 36 mitochondrial genes produced a well-supported tree suggesting that the pairs of D. discoideum/D. citrinum and D. fasciculatum/P. pallidum are sister species although the position of the root is not certain. Group I introns and endonucleases are variable in number and location in the social amoebae. Phylogenies of the introns and endonucleases suggest that there have been multiple recent duplications or extinctions and confirm that endonucleases have the ability to insert into new areas. An analysis of dN/dS ratios in mitochondrial genes revealed that among groups of genes, adenosine triphosphate synthase complex genes have the highest ratio, whereas cytochrome oxidase and nicotinamide adenine dinucleotide (NADH) dehydrogenase genes had the lowest ratio. The genetic codes of D. citrinum, P. pallidum, and D. fasciculatum are the universal code although D. fasciculatum does not use the TGA stop codon. In D. fasciculatum, we demonstrate for the first time that a mitochondrial genome without the TGA stop codon still uses the release factor RF2 that recognizes TGA. Theories of how the genetic code can change and why RF2 may be a constraint against switching codes are discussed.

Evaluation of the models handling heterotachy in phylogenetic inference

Background

The evolutionary rate at a given homologous position varies across time. When sufficiently pronounced, this phenomenon – called heterotachy – may produce artefactual phylogenetic reconstructions under the commonly used models of sequence evolution. These observations have motivated the development of models that explicitly recognize heterotachy, with research directions proposed along two main axes: 1) the covarion approach, where sites switch from variable to invariable states; and 2) the mixture of branch lengths (MBL) approach, where alignment patterns are assumed to arise from one of several sets of branch lengths, under a given phylogeny.

Results

Here, we report the first statistical comparisons contrasting the performance of covarion and MBL modeling strategies. Using simulations under heterotachous conditions, we explore the properties of three model comparison methods: the Akaike information criterion, the Bayesian information criterion, and cross validation. Although more time consuming, cross validation appears more reliable than AIC and BIC as it directly measures the predictive power of a model on 'future' data. We also analyze three large datasets (nuclear proteins of animals, mitochondrial proteins of mammals, and plastid proteins of plants), and find the optimal number of components of the MBL model to be two for all datasets, indicating that this model is preferred over the standard homogeneous model. However, the covarion model is always favored over the optimal MBL model.

Conclusion

We demonstrated, using three large datasets, that the covarion model is more efficient at handling heterotachy than the MBL model. This is probably due to the fact that the MBL model requires a serious increase in the number of parameters, as compared to two supplementary parameters of the covarion approach. Further improvements of the both the mixture and the covarion approaches might be obtained by modeling heterogeneous behavior both along time and across sites.

Different modes of stop codon restriction by the Stylonychia and Paramecium eRF1 translation termination factors

In universal-code eukaryotes, a single-translation termination factor, eukaryote class-1 polypeptide release factor (eRF1), decodes the three stop codons: UAA, UAG, and UGA. In some ciliates, like Stylonychia and Paramecium, eRF1s exhibit UGA-only decoding specificity, whereas UAG and UAA are reassigned as sense codons. Because variant-code ciliates may have evolved from universal-code ancestor(s), structural features should exist in ciliate eRF1s that restrict their stop codon recognition. In omnipotent eRF1s, stop codon recognition is associated with the N-terminal domain of the protein. Using both in vitro and in vivo assays, we show here that chimeric molecules composed of the N-terminal domain of Stylonychia eRF1 fused to the core domain (MC domain) of human eRF1 retained specificity toward UGA; this unambiguously associates eRF1 stop codon specificity to the nature of its N-terminal domain. Functional analysis of eRF1 chimeras constructed by swapping ciliate N-terminal domain sequences with the matching ones from the human protein highlighted the crucial role of the tripeptide QFM in restricting Stylonychia eRF1 specificity toward UGA. Using the site-directed mutagenesis, we show that Paramecium eRF1 specificity toward UGA resides within the NIKS (amino acids 61-64) and YxCxxxF (amino acids 124-131) motifs. Thus, we establish that eRF1 from two different ciliates relies on different molecular mechanisms to achieve specificity toward the UGA stop codon. This finding suggests that eRF1 restriction of specificity to only UGA might have been an early event occurring in independent instances in ciliate evolutionary history, possibly facilitating the reassignment of UAG and UAA to sense codons.

A nuclear phylogeny of the Florideophyceae (Rhodophyta) inferred from combined EF2, small subunit and large subunit ribosomal DNA: establishing the new red algal subclass Corallinophycidae

Previous studies have indicated that resolution of supraordinal relationships in the red algal class Florideophyceae will require additional characters, improved taxon sampling and optimized methods of phylogenetic analysis. To this end, we have generated data to introduce a novel nuclear marker to red algal systematics, elongation factor 2, as well as expanded ribosomal DNA alignments (SSU and LSU) to include 62 ingroup and 4 outgroup taxa. Both single gene and combined data sets were considered. Our analyses resulted in better resolution of both deep as well as more recent divergences, with higher support realized at many nodes. Distance, parsimony and bayesian analyses of the single gene and combined data sets indicated that the subclasses Hildenbrandiophycidae, Ahnfeltiophycidae and Rhodymeniophycidae were monophyletic, whereas the Nemaliophycidae was polyphyletic: one lineage containing the Rhodogorgonales and Corallinales (CR complex); and the other containing the Acrochaetiales, Balbianiales, Balliales, Batrachospermales, Colaconematales, Nemaliales, Palmariales, and Thoreales (APB complex). Based on these results a new subclass of the Florideophyceae, the Corallinophycidae subclassis nov., is proposed to accommodate the Corallinales and Rhodogorgonales. In addition to resolving supraordinal relationships, the present analyses resolved some novel ordinal affinities within the Nemaliophycidae and Rhodymeniophycidae, which are discussed here.

EFL GTPase in cryptomonads and the distribution of EFL and EF-1alpha in chromalveolates

EFL (EF-like protein) is a member of the GTPase superfamily that includes several translation factors. Because it has only been found in a few eukaryotic lineages and its presence correlates with the absence of the related core translation factor EF-1alpha, its distribution is hypothesized to be the result of lateral gene transfer and replacement of EF-1alpha. In one supergroup of eukaryotes, the chromalveolates, two major lineages were found to contain EFL (dinoflagellates and haptophytes), while the others encode EF-1alpha (apicomplexans, ciliates, heterokonts and cryptomonads). For each of these groups, this distribution was deduced from whole genome sequence or expressed sequence tag (EST) data from several species, with the exception of cryptomonads from which only a single EF-1alpha PCR product from one species was known. By sequencing ESTs from two cryptomonads, Guillardia theta and Rhodomonas salina, and searching for all GTPase translation factors, we revealed that EFL is present in both species, but, contrary to expectations, we found EF-1alpha in neither. On balance, we suggest the previously reported EF-1alpha from Rhodomonas salina is likely an artefact of contamination. We also identified EFL in EST data from two members of the dinoflagellate lineage, Karlodinium micrum and Oxyrrhis marina, and from an ongoing genomic sequence project from a third, Perkinsus marinus. Karlodinium micrum is a symbiotic pairing of two lineages that would have both had EFL (a dinoflagellate and a haptophyte), but only the dinoflagellate gene remains. Oxyrrhis marina and Perkinsus marinus are early diverging sister-groups to dinoflagellates, and together show that EFL originated early in this lineage. Phylogenetic analysis confirmed that these genes are all EFL homologues, and showed that cryptomonad genes are not detectably related to EFL from other chromalveolates, which collectively form several distinct groups. The known distribution of EFL now includes a third group of chromalveolates, cryptomonads. Of the six major subgroups of chromalveolates, EFL is found in half and EF-1alpha in the other half, and none as yet unambiguously possess both genes. Phylogenetic analysis indicates EFL likely arose early within each subgroup where it is found, but suggests it may have originated multiple times within chromalveolates as a whole.

The largest subunit of RNA polymerase II from the Glaucocystophyta: functional constraint and short-branch exclusion in deep eukaryotic phylogeny

BACKGROUND

Evolutionary analyses of the largest subunit of RNA polymerase II (RPB1) have yielded important and at times provocative results. One particularly troublesome outcome is the consistent inference of independent origins of red algae and green plants, at odds with the more widely accepted view of a monophyletic Plantae comprising all eukaryotes with primary plastids. If the hypothesis of a broader kingdom Plantae is correct, then RPB1 trees likely reflect a persistent phylogenetic artifact. To gain a better understanding of RNAP II evolution, and the presumed artifact relating to green plants and red algae, we isolated and analyzed RPB1 from representatives of Glaucocystophyta, the third eukaryotic group with primary plastids.

RESULTS

Phylogenetic analyses incorporating glaucocystophytes do not recover a monophyletic Plantae; rather they result in additional conflicts with the most widely held views on eukaryotic relationships. In particular, glaucocystophytes are recovered as sister to several amoebozoans with strong support. A detailed investigation shows that this clade can be explained by what we call "short-branch exclusion," a phylogenetic artifact integrally associated with "long-branch attraction." Other systematic discrepancies observed in RPB1 trees can be explained as phylogenetic artifacts; however, these apparent artifacts also appear in regions of the tree that support widely held views of eukaryotic evolution. In fact, most of the RPB1 tree is consistent with artifacts of rate variation among sequences and co-variation due to functional constraints related to C-terminal domain based RNAP II transcription.

CONCLUSION

Our results reveal how subtle and easily overlooked biases can dominate the overall results of molecular phylogenetic analyses of ancient eukaryotic relationships. Sources of potential phylogenetic artifact should be investigated routinely, not just when obvious "long-branch attraction" is encountered.

Newly sequenced eRF1s from ciliates: the diversity of stop codon usage and the molecular surfaces that are important for stop codon interactions

The genetic code of nuclear genes in some ciliates was found to differ from that of other organisms in the assignment of UGA, UAG, and UAA codons, which are normally assigned as stop codons. In some ciliate species, the universal stop codons UAA and UAG instead encode glutamine. In some other ciliates, the universal stop codon UGA appears to be translated as cysteine or tryptophan. Eukaryotic release factor 1 (eRF1) is a key protein in stop codon recognition, thus, the protein is believed to play an important role in the stop codon reassignment in ciliates. We have cloned, sequenced, and analyzed the cDNA of eRF1 from four ciliate species of three different classes: Karyorelictea (Loxodes striatus), Heterotrichea (Blepharisma musculus), and Litostomatea (Didinium nasutum, Dileptus margaritifer). Phylogenetic analysis of these eRF1s supports the hypothesis that the genetic code in ciliates has deviated independently several times from the universal genetic code, and that different ciliate eRF1s may have undergone different processes to change the codon specificity. Using computational methods, we have also suggested areas on the surface of eRF1s that are important for stop codon recognition in ciliate eRF1s.

Highly divergent actins from karyorelictean, heterotrich, and litostome ciliates

We have cloned, sequenced, and characterized cDNA of actins from five ciliate species of three different classes of the phylum Ciliophora: Karyorelictea (Loxodes striatus), Heterotrichea (Blepharisma japonicum, Blepharisma musculus), and Litostomatea (Didinium nasutum, Dileptus margaritifer). Loxodes striatus uses UGA as the stop codon and has numerous in-frame UAA and UAG, which are translated into glutamine. The other four species use UAA as the stop codon and have no in-frame UAG nor UGA. The putative amino acid sequences of the newly determined actin genes were found to be highly divergent as expected from previous findings of other ciliate actins. These sequences were also highly divergent from other ciliate actins, indicating that actin genes are highly diverse even within the phylum Ciliophora. Phylogenetic analysis showed high evolutionary rate of ciliate actins. Our results suggest that the evolutionary rate was accelerated because of the differences in molecular interactions.

Dramatic diversity of ciliate histone H4 genes revealed by comparisons of patterns of substitutions and paralog divergences among eukaryotes

The accumulation of divergent histone H4 amino acid sequences within and between ciliate lineages challenges traditional views of the evolution of this essential eukaryotic protein. We analyzed histone H4 sequences from 13 species of ciliates and compared these data with sequences from well-sampled eukaryotic clades. Ciliate histone H4s differ from one another at as many as 46% of their amino acids, in contrast with the highly conserved character of this protein in most other eukaryotes. Equally striking, we find paralogs of histone H4 within ciliate genomes that differ by up to 25% of their amino acids, whereas paralogs in other eukaryotes share identical or nearly identical amino acid sequences. Moreover, the most divergent H4 proteins within ciliates are found in the lineages with highly processed macronuclear genomes. Our analyses demonstrate that the dual nature of ciliate genomes-the presence of a "germline" micronucleus and a "somatic" macronucleus within each cell-allowed the dramatic variation in ciliate histone genes by altering functional constraints or enabling adaptive evolution of the histone H4 protein, or both.

Characterisation of a non-canonical genetic code in the oxymonad Streblomastix strix

The genetic code is one of the most highly conserved characters in living organisms. Only a small number of genomes have evolved slight variations on the code, and these non-canonical codes are instrumental in understanding the selective pressures maintaining the code. Here, we describe a new case of a non-canonical genetic code from the oxymonad flagellate Streblomastix strix. We have sequenced four protein-coding genes from S.strix and found that the canonical stop codons TAA and TAG encode the amino acid glutamine. These codons are retained in S.strix mRNAs, and the legitimate termination codons of all genes examined were found to be TGA, supporting the prediction that this should be the only true stop codon in this genome. Only four other lineages of eukaryotes are known to have evolved non-canonical nuclear genetic codes, and our phylogenetic analyses of alpha-tubulin, beta-tubulin, elongation factor-1 alpha (EF-1 alpha), heat-shock protein 90 (HSP90), and small subunit rRNA all confirm that the variant code in S.strix evolved independently of any other known variant. The independent origin of each of these codes is particularly interesting because the code found in S.strix, where TAA and TAG encode glutamine, has evolved in three of the four other nuclear lineages with variant codes, but this code has never evolved in a prokaryote or a prokaryote-derived organelle. The distribution of non-canonical codes is probably the result of a combination of differences in translation termination, tRNAs, and tRNA synthetases, such that the eukaryotic machinery preferentially allows changes involving TAA and TAG.

Isolation and expression of two genes encoding eukaryotic release factor 1 from Paramecium tetraurelia

Paramecium tetraurelia, like some other ciliate species, uses an alternative nuclear genetic code where UAA and UAG are translated as glutamine and UGA is the only stop codon. It has been postulated that the use of stop codons as sense codons is dependent on the presence of specific tRNAs and on modification of eukaryotic release factor one (eRF1), a factor involved in stop codon recognition during translation termination. We describe here the isolation and characterisation of two genes, eRF1-a and eRF1 b, coding for eRF1 in P. tetraurelia. The two genes are very similar, both in genomic organization and in sequence, and might result from a recent duplication event. The two coding sequences are 1,314 nucleotides long, and encode two putative proteins of 437 amino acids with 98.5% identity. Interestingly, when compared with the eRF1 sequences either of ciliates having the same variant genetic code, or of other eukaryotes, the eRF1 of P. tetraurelia exhibits significant differences in the N-terminal region, which is thought to interact with stop codons. We discuss here the consequences of these changes in the light of recent models proposed to explain the mechanism of stop codon recognition in eukaryotes. Besides, analysis of the expression of the two genes by Northern blotting and primer extension reveals that these genes exhibit a differential expression during vegetative growth and autogamy.

Ancient phylogenetic relationships

Traditional views on deep evolutionary events have been seriously challenged over the last few years, following the identification of major pitfalls affecting molecular phylogeny reconstruction. Here we describe the principally encountered artifacts, notably long branch attraction, and their causes (i.e., difference in evolutionary rates, mutational saturation, compositional biases). Additional difficulties due to phenomena of biological nature (i.e., lateral gene transfer, recombination, hidden paralogy) are also discussed. Moreover, contrary to common beliefs, we show that the use of rare genomic events can also be misleading and should be treated with the same caution as standard molecular phylogeny. The universal tree of life, as described in most textbooks, is partly affected by tree reconstruction artifacts, e.g. (i) the bacterial rooting of the universal tree of life; (ii) the early emergence of amitochondriate lineages in eukaryotic phylogenies; and (iii) the position of hyperthermophilic taxa in bacterial phylogenies. We present an alternative view of this tree, based on recent evidence obtained from reanalyses of ancient data sets and from novel analyses of large combination of genes.