The Mechanisms of Codon Reassignments in Mitochondrial Genetic Codes

Many cases of non-standard genetic codes are known in mitochondrial genomes. We carry out analysis of phylogeny and codon usage of organisms for which the complete mitochondrial genome is available, and we determine the most likely mechanism for codon reassignment in each case. Reassignment events can be classified according to the gain-loss framework. The gain represents the appearance of a new tRNA for the reassigned codon or the change of an existing tRNA such that it gains the ability to pair with the codon. The loss represents the deletion of a tRNA or the change in a tRNA so that it no longer translates the codon. One possible mechanism is Codon Disappearance, where the codon disappears from the genome prior to the gain and loss events. In the alternative mechanisms the codon does not disappear. In the Unassigned Codon mechanism, the loss occurs first, whereas in the Ambiguous Intermediate mechanism, the gain occurs first. Codon usage analysis gives clear evidence of cases where the codon disappeared at the point of the reassignment and also cases where it did not disappear. Codon disappearance is the probable explanation for stop to sense reassignments and a small number of reassignments of sense codons. However, the majority of sense to sense reassignments cannot be explained by codon disappearance. In the latter cases, by analysis of the presence or absence of tRNAs in the genome and of the changes in tRNA sequences, it is sometimes possible to distinguish between the Unassigned Codon and Ambiguous Intermediate mechanisms. We emphasize that not all reassignments follow the same scenario and that it is necessary to consider the details of each case carefully.Comment: 53 pages (45 pages, including 4 figures + 8 pages of supplementary information). To appear in J.Mol.Evo

The RNA polymerase III-dependent family of genes in hemiascomycetes: comparative RNomics, decoding strategies, transcription and evolutionary implications

We present the first comprehensive analysis of RNA polymerase III (Pol III) transcribed genes in ten yeast genomes. This set includes all tRNA genes (tDNA) and genes coding for SNR6 (U6), SNR52, SCR1 and RPR1 RNA in the nine hemiascomycetes Saccharomyces cerevisiae, Saccharomyces castellii, Candida glabrata, Kluyveromyces waltii, Kluyveromyces lactis, Eremothecium gossypii, Debaryomyces hansenii, Candida albicans, Yarrowia lipolytica and the archiascomycete Schizosaccharomyces pombe. We systematically analysed sequence specificities of tRNA genes, polymorphism, variability of introns, gene redundancy and gene clustering. Analysis of decoding strategies showed that yeasts close to S.cerevisiae use bacterial decoding rules to read the Leu CUN and Arg CGN codons, in contrast to all other known Eukaryotes. In D.hansenii and C.albicans, we identified a novel tDNA-Leu (AAG), reading the Leu CUU/CUC/CUA codons with an unusual G at position 32. A systematic ‘p-distance tree’ using the 60 variable positions of the tRNA molecule revealed that most tDNAs cluster into amino acid-specific sub-trees, suggesting that, within hemiascomycetes, orthologous tDNAs are more closely related than paralogs. We finally determined the bipartite A- and B-box sequences recognized by TFIIIC. These minimal sequences are nearly conserved throughout hemiascomycetes and were satisfactorily retrieved at appropriate locations in other Pol III genes

Genes adopt non-optimal codon usage to generate cell cycle-dependent oscillations in protein levels

Most cell cycle-regulated genes adopt non-optimal codon usage, namely, their translation involves wobbly matching codons. Here, the authors show that tRNA expression is cyclic and that codon usage, therefore, can give rise to cell-cycle regulation of proteins

Systems biology of energetic and atomic costs in the yeast transcriptome, proteome, and metabolome

Proteins vary in their cost to the cell and natural selection may favour the use of proteins that are cheaper to produce. We develop a novel approach to estimate the amino acid biosynthetic cost based on genome-scale metabolic models, and directly investigate the effects of biosynthetic cost on transcriptomic, proteomic and metabolomic data in _Saccharomyces cerevisiae_. We find that our systems approach to formulating biosynthetic cost produces a novel measure that explains similar levels of variation in gene expression compared with previously reported cost measures. Regardless of the measure used, the cost of amino acid synthesis is weakly associated with transcript and protein levels, independent of codon usage bias. In contrast, energetic costs explain a large proportion of variation in levels of free amino acids. In the economy of the yeast cell, there appears to be no single currency to compute the cost of amino acid synthesis, and thus a systems approach is necessary to uncover the full effects of amino acid biosynthetic cost in complex biological systems that vary with cellular and environmental conditions

Gene organization and sequence analyses of transfer RNA genes in Trypanosomatid parasites

<p>Abstract</p> <p>Background</p> <p>The protozoan pathogens <it>Leishmania major</it>, <it>Trypanosoma brucei </it>and <it>Trypanosoma cruzi </it>(the Tritryps) are parasites that produce devastating human diseases. These organisms show very unusual mechanisms of gene expression, such as polycistronic transcription. We are interested in the study of tRNA genes, which are transcribed by RNA polymerase III (Pol III). To analyze the sequences and genomic organization of tRNA genes and other Pol III-transcribed genes, we have performed an <it>in silico </it>analysis of the Tritryps genome sequences.</p> <p>Results</p> <p>Our analysis indicated the presence of 83, 66 and 120 genes in <it>L. major, T. brucei </it>and <it>T. cruzi</it>, respectively. These numbers include several previously unannotated selenocysteine (Sec) tRNA genes. Most tRNA genes are organized into clusters of 2 to 10 genes that may contain other Pol III-transcribed genes. The distribution of genes in the <it>L. major </it>genome does not seem to be totally random, like in most organisms. While the majority of the tRNA clusters do not show synteny (conservation of gene order) between the Tritryps, a cluster of 13 Pol III genes that is highly syntenic was identified. We have determined consensus sequences for the putative promoter regions (Boxes A and B) of the Tritryps tRNA genes, and specific changes were found in tRNA-Sec genes. Analysis of transcription termination signals of the tRNAs (clusters of Ts) showed differences between <it>T. cruzi </it>and the other two species. We have also identified several tRNA isodecoder genes (having the same anticodon, but different sequences elsewhere in the tRNA body) in the Tritryps.</p> <p>Conclusion</p> <p>A low number of tRNA genes is present in Tritryps. The overall weak synteny that they show indicates a reduced importance of genome location of Pol III genes compared to protein-coding genes. The fact that some of the differences between isodecoder genes occur in the internal promoter elements suggests that differential control of the expression of some isoacceptor tRNA genes in Tritryps is possible. The special characteristics found in Boxes A and B from tRNA-Sec genes from Tritryps indicate that the mechanisms that regulate their transcription might be different from those of other tRNA genes.</p

The universal YrdC/Sua5 family is required for the formation of threonylcarbamoyladenosine in tRNA

Threonylcarbamoyladenosine (t6A) is a universal modification found at position 37 of ANN decoding tRNAs, which imparts a unique structure to the anticodon loop enhancing its binding to ribosomes in vitro. Using a combination of bioinformatic, genetic, structural and biochemical approaches, the universal protein family YrdC/Sua5 (COG0009) was shown to be involved in the biosynthesis of this hypermodified base. Contradictory reports on the essentiality of both the yrdC wild-type gene of Escherichia coli and the SUA5 wild-type gene of Saccharomyces cerevisiae led us to reconstruct null alleles for both genes and prove that yrdC is essential in E. coli, whereas SUA5 is dispensable in yeast but results in severe growth phenotypes. Structural and biochemical analyses revealed that the E. coli YrdC protein binds ATP and preferentially binds RNAThr lacking only the t6A modification. This work lays the foundation for elucidating the function of a protein family found in every sequenced genome to date and understanding the role of t6A in vivo

Codon-triplet context unveils unique features of the Candida albicans protein coding genome

<p>Abstract</p> <p>Background</p> <p>The evolutionary forces that determine the arrangement of synonymous codons within open reading frames and fine tune mRNA translation efficiency are not yet understood. In order to tackle this question we have carried out a large scale study of codon-triplet contexts in 11 fungal species to unravel associations or relationships between codons present at the ribosome A-, P- and E-sites during each decoding cycle.</p> <p>Results</p> <p>Our analysis unveiled high bias within the context of codon-triplets, in particular strong preference for triplets of identical codons. We have also identified a surprisingly large number of codon-triplet combinations that vanished from fungal ORFeomes. <it>Candida albicans </it>exacerbated these features, showed an unbalanced tRNA population for decoding its pool of codons and used near-cognate decoding for a large set of codons, suggesting that unique evolutionary forces shaped the evolution of its ORFeome.</p> <p>Conclusion</p> <p>We have developed bioinformatics tools for large-scale analysis of codon-triplet contexts. These algorithms identified codon-triplets context biases, allowed for large scale comparative codon-triplet analysis, and identified rules governing codon-triplet context. They could also detect alterations to the standard genetic code.</p

Curation and analysis of tRNA and aminoacyl-tRNA synthetase genes in the nuclear genome of Myceliophthora thermophila

Transfer ribonucleic acids (tRNAs) and aminoacyl-tRNA synthetases (AARSs) have long been known for their indispensable roles in the translational process to synthesize proteins in living cells. Therefore, detecting and analyzing the comprehensive sets of tRNA and AARS genes would enhance understanding of the translation system and the results could potentially be used to optimize the translation efficiency for the protein production in the organisms of interest. This research aims to detect the complete sets of cytoplasmic tRNA genes and AARS genes from the nuclear genome of Myceliophthora thermophila, a filamentous fungus used in the enzyme production industry and the first thermophilic eukaryote with a finished genome sequence. In this study, 194 cytoplasmic tRNA genes and 35 aminoacyl-tRNA synthetase genes in M. thermophila were determined by comparing the gene models predicted from the genome with the sequenced RNAs and the experimentally characterized tRNA and AARS genes. The experimentally verified tRNA genes in M. thermophila can encode all of the 20 universal amino acids. The 35 AARS genes code for cytoplasmic and mitochondrial AARS enzymes of all of the 20 amino acid specificities except for the mitochondrial glutaminyl-tRNA synthetase. Four commonly used tools – tRNAscan-SE, SPLITSX, ARAGORN and tRNAfinder – were deployed for the tRNA gene prediction, and we showed that tRNAscan-SE and SPLITSX give more accurate results than ARAGORN and tRNAfinder. Analysis of the tRNA genes showed that there are significant correlations between tRNA gene number in the genome and tRNA abundance in the cell, as well as between tRNA gene number and codon usage bias of protein-encoding genes in M. thermophila. Based on the complete tRNA gene set and the codon frequencies in the protein-encoding gene set, a set of preferred codons in M. thermophila was determined. The manually curated tRNA and AARS genes of M. thermophila, as well as the experimentally characterized ones collected from tRNA and protein databases along with the supporting literature provided in this study, can be used as reliable datasets for tRNA and AARS gene annotation processes

Comparative Genomics and the Evolution of Transposable Elements in Unicellular Eukaryotes

Background Transposable elements are mobile DNA sequences, which are ubiquitous in the majority of eukaryotic genomes. Unicellular eukaryotes have limited research on transposable elements and therefore the picture of evolution is far from conclusive. Similarly, codon usage bias, the frequency of synonymous codons present in a host species coding DNA, has been focused on multicellular organisms, with no clear explanation of the evolutionary pressures that drive bias in unicellular eukaryotic species. Methods Eight Kazachstania budding yeast species, and choanoflagellate species, Salpingoeca rosetta, were screened for the presence of mobile elements, with use of homology based methods. Protein and nucleotide phylogenies were constructed to review ancestral patterns and similarity across superfamilies. Codon usage statistics were employed to review patterns of bias in the host genes and mobile elements of the Kazachstania species, and S.rosetta, as well as two additional holozoan species, Monosiga brevicollis and Capsaspora owczarzaki. Results A diverse repetoire of transposable element families were uncovered in the species reviewed. A complete absence of DNA transposons was found in the Kazachstania species, however both classes of elements were uncovered in S. rosetta. Element phylogenies indicated vertical transfer for the majority of families, with the exception of one family in S. rosetta, which suggested acquisition by horizontal transfer. Patterns of codon usage were revealed in the genus Kazachstania and conservation was seen in the three holozoan species, with similar trends observed in the majority of host species mobile elements. Conclusions The known diversity of TE families for the yeast superfamily, and Choanoflagellatea has increased as a result of the study presented here. Codon usage bias for host genes and mobile elements provided evidence of selection, as well as mutational bias, suggesting that models of evolutionary pressures are more complex in unicellular eukaryotes