A permuted set of a trinucleotide circular code coding the 20 amino acids in variant nuclear codes

Michel, Christian; Pirillo, Giuseppe

doi:10.1016/j.jtbi.2012.11.023

Cited by 15 publications

(6 citation statements)

References 35 publications

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“…No maximal circular code among these 12,964,440 ones codes for 20 or 19 amino acids with SGC. Ten maximal circular codes code for 18 amino acids with SGC (see Michel and Pirillo 2013 , Introduction). Interestingly, we identify 52 maximal 1-circular codes among ones, i.e.…”

Section: Biological Consequencesmentioning

confidence: 99%

The Relation Between k-Circularity and Circularity of Codes

et al. 2020

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A code X is k-circular if any concatenation of at most k words from X , when read on a circle, admits exactly one partition into words from X. It is circular if it is k-circular for every integer k. While it is not a priori clear from the definition, there exists, for every pair (n,), an integer k such that every k-circular-letter code over an alphabet of cardinality n is circular, and we determine the least such integer k for all values of n and. The k-circular codes may represent an important evolutionary step between the circular codes, such as the comma-free codes, and the genetic code.

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Section: Biological Consequencesmentioning

confidence: 99%

The Relation Between k-Circularity and Circularity of Codes

et al. 2020

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“…Indeed, coding sequences include much more information than generally believed, even beyond RNA editing (RDD [91]), systematic transformations during replication [44][45][46] and transcription [39,[47][48][49][50][51], and translation along expanded codons [32][33][34][35][36][37][38][39][40][41][42][43]. Cryptic codes [92,93] such as the well-developed theory of the natural circular code [94][95][96][97][98][99][100][101][102][103][104][105][106][107][108][109][110][111][112] regulate the ribosomal translation frame [113][114][115][116], and protein cotranslational folding …”

Section: Coding Redundancy Between Frames and Tolerating Ribosomal Frmentioning

confidence: 99%

Directed Mutations Recode Mitochondrial Genes: From Regular to Stopless Genetic Codes

Seligmann¹

2018

Mitochondrial DNA - New Insights

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Mitochondrial genetic codes evolve as side effects of stop codon ambiguity: suppressor tRNAs with anticodons translating stops transform genetic codes to stopless genetic codes. This produces peptides from frames other than regular ORFs, potentially increasing protein numbers coded by single sequences. Previous descriptions of marine turtle Olive Ridley mitogenomes imply directed stop-depletion of noncoding +1 gene frames, stop-creation recodes regular ORFs to stopless genetic codes. In this analysis, directed stop codon depletion in usually noncoding gene frames of the spiraling whitefly Aleurodicus dispersusʼ mitogenome produces new ORFs, introduces stops in regular ORFs, and apparently increases coding redundancy between different gene frames. Directed stop codon mutations switch between peptides coded by regular and stopless genetic codes. This process seems opposite to directed stop creation in HIV ORFs within genomes of immunized elite HIV controllers. Unknown DNA replication/edition mechanisms probably direct stop creation/depletion beyond natural selection on stops. Switches between genetic codes regulate translation of different gene frames.

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“…By excluding the homopolymer trinucleotides and dividing the 60 remaining trinucleotides into three disjoint classes, a circular code of trinucleotides has at most 20 trinucleotides (called a maximal circular code). There exist 12,964,440 maximal circular codes, although it has been shown that there is no maximal circular code that can code 20 or 19 amino acids and only 10 can code for 18 amino acids (Michel and Pirillo 2013). Remarkably, one of the maximal circular codes, called the X circular code (Fig.…”

Section: Introductionmentioning

confidence: 99%

Circular code motifs in the ribosome: a missing link in the evolution of translation?

Dila

Ripp

Mayer

et al. 2019

RNA

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The origin of the genetic code remains enigmatic five decades after it was elucidated, although there is growing evidence that the code coevolved progressively with the ribosome. A number of primordial codes were proposed as ancestors of the modern genetic code, including comma-free codes such as the RRY, RNY, or GNC codes (R = G or A, Y = C or T, N = any nucleotide), and the X circular code, an error-correcting code that also allows identification and maintenance of the reading frame. It was demonstrated previously that motifs of the X circular code are significantly enriched in the protein-coding genes of most organisms, from bacteria to eukaryotes. Here, we show that imprints of this code also exist in the ribosomal RNA (rRNA). In a large-scale study involving 133 organisms representative of the three domains of life, we identified 32 universal X motifs that are conserved in the rRNA of >90% of the organisms. Intriguingly, most of the universal X motifs are located in rRNA regions involved in important ribosome functions, notably in the peptidyl transferase center and the decoding center that form the original "proto-ribosome." Building on the existing accretion models for ribosome evolution, we propose that error-correcting circular codes represented an important step in the emergence of the modern genetic code. Thus, circular codes would have allowed the simultaneous coding of amino acids and synchronization of the reading frame in primitive translation systems, prior to the emergence of more sophisticated start codon recognition and translation initiation mechanisms.

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A permuted set of a trinucleotide circular code coding the 20 amino acids in variant nuclear codes

Cited by 15 publications

References 35 publications

The Relation Between k-Circularity and Circularity of Codes

The Relation Between k-Circularity and Circularity of Codes

Directed Mutations Recode Mitochondrial Genes: From Regular to Stopless Genetic Codes

Circular code motifs in the ribosome: a missing link in the evolution of translation?

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