An extended genetic scale of reading frame coding

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.

Single-Frame, Multiple-Frame and Framing Motifs in Genes

We study the distribution of new classes of motifs in genes, a research field that has not been investigated to date. A single-frame motif SF has no trinucleotide in reading frame (frame 0) that occurs in a shifted frame (frame 1 or 2), e.g., the dicodon AAACAA is SF as the trinucleotides AAA and CAA do not occur in a shifted frame. A motif which is not single-frame SF is multiple-frame MF. Several classes of MF motifs are defined and analysed. The distributions of single-frame SF motifs (associated with an unambiguous trinucleotide decoding in the two 5′–3′ and 3′–5′ directions) and 5′ unambiguous motifs 5′U (associated with an unambiguous trinucleotide decoding in the 5′–3′ direction only) are analysed without and with constraints. The constraints studied are: initiation and stop codons, periodic codons {AAA,CCC,GGG,TTT}, antiparallel complementarity and parallel complementarity. Taken together, these results suggest that the complementarity property involved in the antiparallel (DNA double helix, RNA stem) and parallel sequences could also be fundamental for coding genes with an unambiguous trinucleotide decoding in the two 5′–3′ and 3′–5′ directions or the 5′–3′ direction only. Furthermore, the single-frame motifs SF with a property of trinucleotide decoding and the framing motifs F (also called circular code motifs; first introduced by Michel (2012)) with a property of reading frame decoding may have been involved in the early life genes to build the modern genetic code and the extant genes. They could have been involved in the stage without anticodon-amino acid interactions or in the Implicated Site Nucleotides (ISN) of RNA interacting with the amino acids. Finally, the SF and MF dipeptides associated with the SF and MF dicodons, respectively, are studied and their importance for biology and the origin of life discussed.

Bijective codon transformations show genetic code symmetries centered on cytosine's coding properties

Homology of some RNAs with template DNA requires systematic exchanges between nucleotides. Such exchanges produce 'swinger' RNA along 23 bijective transformations (nine symmetric, X ↔ Y; and 14 asymmetric, X → Y → Z → X, for example A ↔ C and A → C → G → A, respectively). Here, analyses compare amino acids coded by swinger-transformed codons to those coded by untransformed codons, defining coding invariance after transformations. Swinger transformations cluster according to coding invariance in four groups characterized by transformations into cytosine (C = C, T → C, A → C, and G → C). C's central mutational coding role shows that swinger transformations constrained genetic code genesis. Coding invariance post-transformations correlate positively/negatively with mitochondrial swinger transcription/lepidosaurian body temperature. Presumably, low/high temperatures stabilize/revert rare swinger polymerization modes, producing long swinger sequences/point mutations, respectively. Coding invariance after swinger transformations might compensate effects of swinger polymerizations in species with low body temperatures. Hypothetically, swinger transcription increased coding potential of RNA self-replicating protolife systems under heating/cooling cycles.

Reviewing evidence for systematic transcriptional deletions, nucleotide exchanges, and expanded codons, and peptide clusters in human mitochondria

Polymerization sometimes transforms sequences by (a) systematic deletions of mono-, dinucleotides after trinucleotides, or (b) 23 systematic nucleotide exchanges (9 symmetric, X<>Y, e.g. G<>T, 14 asymmetric, X > Y > Z > X, e.g. A > G > T > A), producing del- and swinger RNAs. Some peptides correspond to del- and swinger RNA translations, also according to tetracodons, codons expanded by a silent nucleotide. Here new analyzes assume different proteolytic patterns, partially alleviating false negative peptide detection biases, expanding noncanonical mitoproteome profiles. Mito-genomic, -transcriptomic and -proteomic evidence for noncanonical transcriptions and translations are reviewed and clusters of del- and swinger peptides (also along tetracodons) are described. Noncanonical peptide clusters indicate regulated expression of cryptically encoded mitochondrial protein coding genes. These candidate noncanonical proteins don't resemble known proteins.

Chimeric mitochondrial peptides from contiguous regular and swinger RNA

Previous mass spectrometry analyses described human mitochondrial peptides entirely translated from swinger RNAs, RNAs where polymerization systematically exchanged nucleotides. Exchanges follow one among 23 bijective transformation rules, nine symmetric exchanges (X ↔ Y, e.g. A ↔ C) and fourteen asymmetric exchanges (X → Y → Z → X, e.g. A → C → G → A), multiplying by 24 DNA's protein coding potential. Abrupt switches from regular to swinger polymerization produce chimeric RNAs. Here, human mitochondrial proteomic analyses assuming abrupt switches between regular and swinger transcriptions, detect chimeric peptides, encoded by part regular, part swinger RNA. Contiguous regular- and swinger-encoded residues within single peptides are stronger evidence for translation of swinger RNA than previously detected, entirely swinger-encoded peptides: regular parts are positive controls matched with contiguous swinger parts, increasing confidence in results. Chimeric peptides are 200 × rarer than swinger peptides (3/100,000 versus 6/1000). Among 186 peptides with > 8 residues for each regular and swinger parts, regular parts of eleven chimeric peptides correspond to six among the thirteen recognized, mitochondrial protein-coding genes. Chimeric peptides matching partly regular proteins are rarer and less expressed than chimeric peptides matching non-coding sequences, suggesting targeted degradation of misfolded proteins. Present results strengthen hypotheses that the short mitogenome encodes far more proteins than hitherto assumed. Entirely swinger-encoded proteins could exist.

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Chimeric peptides are translated from contiguous regular and swinger RNA

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They are 200x rarer than mitochondrial swinger peptides

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Chimeric peptides integrated in regular mitochondrial proteins are downregulated

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Contiguous regular parts are matched positive controls for swinger parts

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The last point validates results beyond other statistical tests for robustness

Dinucleotide circular codes and bijective transformations

The presence of circular codes in mRNA coding sequences is postulated to be involved in informational mechanisms aimed at detecting and maintaining the normal reading frame during protein synthesis. Most of the recent research is focused on trinucleotide circular codes. However, also dinucleotide circular codes are important since dinucleotides are ubiquitous in genomes and associated to important biological functions. In this work we adopt the group theoretic approach used for trinucleotide codes in Fimmel et al. (2015) to study dinucleotide circular codes and highlight their symmetry properties. Moreover, we characterize such codes in terms of n-circularity and provide a graph representation that allows to visualize them geometrically. The results establish a theoretical framework for the study of the biological implications of dinucleotide circular codes in genomic sequences.

The maximal C(3) self-complementary trinucleotide circular code X in genes of bacteria, eukaryotes, plasmids and viruses

In 1996, a set X of 20 trinucleotides is identified in genes of both prokaryotes and eukaryotes which has in average the highest occurrence in reading frame compared to the two shifted frames (Arquès and Michel, 1996). Furthermore, this set X has an interesting mathematical property as X is a maximal C(3) self-complementary trinucleotide circular code (Arquès and Michel, 1996). In 2014, the number of trinucleotides in prokaryotic genes has been multiplied by a factor of 527. Furthermore, two new gene kingdoms of plasmids and viruses contain enough trinucleotide data to be analysed. The approach used in 1996 for identifying a preferential frame for a trinucleotide is quantified here with a new definition analysing the occurrence probability of a complementary/permutation (CP) trinucleotide set in a gene kingdom. Furthermore, in order to increase the statistical significance of results compared to those of 1996, the circular code X is studied on several gene taxonomic groups in a kingdom. Based on this new statistical approach, the circular code X is strengthened in genes of prokaryotes and eukaryotes, and now also identified in genes of plasmids. A subset of X with 18 or 16 trinucleotides is identified in genes of viruses. Furthermore, a simple probabilistic model based on the independent occurrence of trinucleotides in reading frame of genes explains the circular code frequencies and asymmetries observed in the shifted frames in all studied gene kingdoms. Finally, the developed approach allows to identify variant X codes in genes, i.e. trinucleotide codes which differ from X. In genes of bacteria, eukaryotes and plasmids, 14 among the 47 studied gene taxonomic groups (about 30%) have variant X codes. Seven variant X codes are identified with at least 16 trinucleotides of X. Two variant X codes XA in cyanobacteria and plasmids of cyanobacteria, and XD in birds are self-complementary, without permuted trinucleotides but non-circular. Five variant X codes XB in deinococcus, plasmids of chloroflexi and deinococcus, mammals and kinetoplasts, XC in elusimicrobia and apicomplexans, XE in fishes, XF in insects, and XG in basidiomycetes and plasmids of spirochaetes are C(3) self-complementary circular. In genes of viruses, no variant X code is found.