Chain termination codons and polymerase-induced frameshift mutations

Localized Context-Dependent Effects of the "Ambush" Hypothesis: More Off-Frame Stop Codons Downstream of Shifty Codons

The ambush hypothesis speculates that off-frame stop codons increase translational efficiency after ribosomal frameshifts by stopping early frameshifted translation. Some evidences fit this hypothesis: (1) synonymous codon usages increase with their potential contribution to off-frame stops; (2) the genetic code assigns frequent amino acids to codon families contributing to off-frame stops; (3) positive biases for off-frame stops (AT rich) occur despite adverse nucleotide (GC) biases; and (4) mitochondrial off-frame stop codon densities increase with ribosomal structural instability, potential proxy of frameshift frequencies. In this study, analyses of vertebrate mitogenes and tRNA synthetase genes from all superkingdoms and viruses test a new prediction of the ambush hypothesis: sequences immediately downstream of frameshift-inducing homopolymer codons (AAA, CCC, GGG, and TTT) are off-frame stop rich. Codons immediately downstream of homopolymer codons form more than average off-frame stops, biases are stronger than for corresponding upstream distances and for any other group of synonymous codons. Sequences downstream of that high-density region are off-frame stop depleted. This decrease suggests that off-frame stops, combined with suppressor tRNAs regulate translation of overlapping coding sequences. Results show the predictive power of the ambush hypothesis, from macroevolutionary (genetic code structure) to detailed gene sequence anatomy.

Transcripts with systematic nucleotide deletion of 1-12 nucleotide in human mitochondrion suggest potential non-canonical transcription

Raw transcriptomic data contain numerous RNA reads whose homology with template DNA doesn't match canonical transcription. Transcriptome analyses usually ignore such noncanonical RNA reads. Here, analyses search for noncanonical mitochondrial RNAs systematically deleting 1 to 12 nucleotides after each transcribed nucleotide triplet, producing deletion-RNAs (delRNAs). We detected delRNAs in the human whole cell and purified mitochondrial transcriptomes, and in Genbank's human EST database corresponding to systematic deletions of 1 to 12 nucleotides after each transcribed trinucleotide. DelRNAs detected in both transcriptomes mapped along with 55.63% of the EST delRNAs. A bias exists for delRNAs covering identical mitogenomic regions in both transcriptomic and EST datasets. Among 227 delRNAs detected in these 3 datasets, 81.1% and 8.4% of delRNAs were mapped on mitochondrial coding and hypervariable region 2 of dloop. Del-transcription analyses of GenBank's EST database confirm observations from whole cell and purified mitochondrial transcriptomes, eliminating the possibility that detected delRNAs are false positives matches, cytosolic DNA/RNA nuclear contamination or sequencing artefacts. These detected delRNAs are enriched in frameshift-inducing homopolymers and are poor in frameshift-preventing circular code codons (a set of 20 codons which regulate reading frame detection, over- and underrepresented in coding and other frames of genes, respectively) suggesting a motif-based regulation of non-canonical transcription. These findings show that rare non-canonical transcripts exist. Such non canonical del-transcription does increases mitochondrial coding potential and non-coding regulation of intracellular mechanisms, and could explain the dark DNA conundrum.

Evolution of Nucleotide Punctuation Marks: From Structural to Linear Signals

We present an evolutionary hypothesis assuming that signals marking nucleotide synthesis (DNA replication and RNA transcription) evolved from multi- to unidimensional structures, and were carried over from transcription to translation. This evolutionary scenario presumes that signals combining secondary and primary nucleotide structures are evolutionary transitions. Mitochondrial replication initiation fits this scenario. Some observations reported in the literature corroborate that several signals for nucleotide synthesis function in translation, and vice versa. (a) Polymerase-induced frameshift mutations occur preferentially at translational termination signals (nucleotide deletion is interpreted as termination of nucleotide polymerization, paralleling the role of stop codons in translation). (b) Stem-loop hairpin presence/absence modulates codon-amino acid assignments, showing that translational signals sometimes combine primary and secondary nucleotide structures (here codon and stem-loop). (c) Homopolymer nucleotide triplets (AAA, CCC, GGG, TTT) cause transcriptional and ribosomal frameshifts. Here we find in recently described human mitochondrial RNAs that systematically lack mono-, dinucleotides after each trinucleotide (delRNAs) that delRNA triplets include 2x more homopolymers than mitogenome regions not covered by delRNA. Further analyses of delRNAs show that the natural circular code X (a little-known group of 20 translational signals enabling ribosomal frame retrieval consisting of 20 codons {AAC, AAT, ACC, ATC, ATT, CAG, CTC, CTG, GAA, GAC, GAG, GAT, GCC, GGC, GGT, GTA, GTC, GTT, TAC, TTC} universally overrepresented in coding versus other frames of gene sequences), regulates frameshift in transcription and translation. This dual transcription and translation role confirms for X the hypothesis that translational signals were carried over from transcriptional signals.

Crystalizing the genetic code

New developments are presented in the framework of the model introduced bythe authors in References [1, 2] and in which nucleotides as well ascodons are classified in crystal bases of the quantum group U(q)(sl(2) ⊕ sl (2)) in the limit q → 0. An operator whichgives the correspondence between the amino-acids and the codons isobtained for any known genetic code. The free energy released by basepairing of dinucleotides as well as the relative hydrophilicity andhydrophobicity of the dinucleosides are also computed. For the vertebrateseries, a universal behaviour in the ratios of codon usage frequencies isput in evidence and is shown to fit nicely in our model. Then a firstattempt to represent the mutations relative to the deletion of apyrimidine by action of a suitable crystal spinor operator is proposed.Finally recent theoretial descriptions are reviewed and compared with ourmodel.PACS number: 87.10.+e, 02.10.-v.

Optimization models and the structure of the genetic code

The codon assignment of the quasi-universal genetic code can be assumed to have resulted from the evolutionary pressures that prevailed when the code was still evolving. Here, we review studies of the structure of the genetic code based on optimization models. We also review studies that, from the structure of the code, attempt to derive aspects of the primordial circumstances in which the genetic code froze. Different rationales are summarized, compared with experimental data, discussed in the context of the transition from a RNA world to a DNA-protein world, and linked to the emergence of the last universal common ancestor.

Error-reducing structure of the genetic code indicates code origin in non-thermophile organisms

During the RNA World, organisms experienced high rates of genetic errors, which implies that there was strong evolutionary pressure to reduce the errors' phenotypical impact by suitably structuring the still-evolving genetic code. Therefore, the relative rates of the various types of genetic errors should have left characteristic imprints in the structure of the genetic code. Here, we show that, therefore, it is possible to some extent to reconstruct those error rates, as well as the nucleotide frequencies, for the time when the code was fixed. We find evidence indicating that the frequencies of G and C in the genome were not elevated. Since, for thermodynamic reasons, RNA in thermophiles tends to possess elevated G+C content, this result indicates that the fixation of the genetic code occurred in organisms which were either not thermophiles or that the code's fixation occurred after the rise of DNA.

Cost minimization of ribosomal frameshifts

Properties of mRNA leading regions that modulate protein synthesis are little known (besides effects of their secondary structure). Here I explore how coding properties of leading regions may account for their disparate efficiencies. Trinucleotides that form off frame stop codons decrease costs of ribosomal slippages during protein synthesis: protein activity (as a proxy of gene expression, and as measured in experiments using artificial variants of 5' leading sequences of beta galactosidase in Escherichia coli) increases proportionally to the number of stop motifs in any frame in the 5' leading region. This suggests that stop codons in the 5' leading region, upstream of the recognized coding sequence, terminate eventual translations that sometimes start before ribosomes reach the mRNA's recognized start codon, increasing efficiency. This hypothesis is confirmed by further analyses: mRNAs with 5' leading regions containing in the same frame a start preceding a stop codon (in any frame) produce less enzymatic activity than those with the stop preceding the start. Hence coding properties, in addition to other properties, such as the secondary structure of the 5' leading region, regulate translation. This experimentally (a) confirms that within coding regions, off frame stops increase protein synthesis efficiency by early stopping frameshifted translation; (b) suggests that this occurs for all frames also in 5' leading regions and that (c) several alternative start codons that function at different probabilities should routinely be considered for all genes in the region of the recognized initiation codon. An unknown number of short peptides might be translated from coding and non-coding regions of RNAs.

Degeneracy in the genetic code and its symmetries by base substitutions

Degeneracy in the genetic code is known to minimise the deleterious effects of the most frequent base substitutions: transitions at the third base of codons are generally synonymous substitutions. Transversions that alter degeneracy were reported by Rumer. Here the other transversions are shown to leave invariant degeneracy when applied to the first base of codons. As a summary, degeneracy is considered with respect to all three types of base substitutions, the transitions and the two types of transversions. The symmetries of degeneracy by base substitutions are independent of the representation of the genetic code and discussed with respect to the quasi-universality of the genetic code.

Directed enzyme evolution and selections for catalysis based on product formation

Enzyme engineering by molecular modelling and site-directed mutagenesis can be remarkably efficient. Directed enzyme evolution appears as a more general strategy for the isolation of catalysts as it can be applied to most chemical reactions in aqueous solutions. Selections, as opposed to screening, allow the simultaneous analysis of protein properties for sets of up to about 10(14) different proteins. These approaches for the parallel processing of molecular information 'Is the protein a catalyst?' are reviewed here in the case of selections based on the formation of a specific reaction product. Several questions are addressed about in vivo and in vitro selections for catalysis reported in the literature. Can the selection system be extended to other types of enzymes? Does the selection control regio- and stereo-selectivity? Does the selection allow the isolation of enzymes with an efficient turnover? How should substrates be substituted or mimicked for the design of efficient selections while minimising the number of chemical synthesis steps? Engineering sections provide also some clues to design selections or to circumvent selection biases. A special emphasis is put on the comparison of in vivo and in vitro selections for catalysis.

A mathematical model accounting for the organization in multiplets of the genetic code

A model using suitable mathematical operators in the crystal basis model of the genetic code is presented. This model retains a requirement for stability of the genetic code against misreading or translation errors. The main features (including number of encoded amino-acids, nucleotide content, and synonymous codons multiplet dimension) are described for mitochondrial and eukaryotic genetic codes.

Construction of genetic code from evolutionary stability

The construction of the genetic code is investigated based on a stability principle. The concept and formulation of mutational deterioration (MD) of the genetic code is proposed. It is proved that the degeneracies of codon multiplets obey the rule to best resist MD. The MD for each ideal multiplet of codons is expressed by four parameters and it takes on a minimum value for real distributions of codons in the multiplet. Then the global mutational deterioration (GMD) of code table is calculated and the minimal code is deduced. The domain-like distribution of hydrophobic and hydrophilic amino acids on the genetic code is explained from the minimization of GMD. It is demonstrated that the standard code is approximately GMD-minimal. By introducing some constraints that are related to the initial condition of the system, we have deduced the standard genetic code from the minimization of GMD. The minimization shows the general trend of evolutionary process to some stable state while the constraints reflect a 'frozen accident.' Many deviant codon assignments are also explained through MD minimization assuming the changeable degrees of degeneracies for some multiplets. So, a possible answer to the question of "Why are synonymous codons and amino acids distributed in the code table just as they are?" is given.