Essential molecular functions associated with the circular code evolution

Ahmed, Ahmed; Frey, Gabriel; Michel, Christian

doi:10.1016/j.jtbi.2010.02.006

Cited by 40 publications

(23 citation statements)

References 30 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Obtaining this empirical result within natural gene sequences, considering all possible combinations of 20 codons, has P = 6.2 × 10 -8 . These codons code for their assigned amino acid, and also constitute the natural circular code ‘X’, which enables to retrieve the ribosomal translational frame (Arquès and Michel, 1996; Ahmed et al, 2007, 2010; Michel, 2012; El Soufi and Michel, 2014, 2015). …”

Section: Introductionmentioning

confidence: 99%

Evolution of Nucleotide Punctuation Marks: From Structural to Linear Signals

Houmami

Seligmann

2017

Front. Genet.

View full text Add to dashboard Cite

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.

show abstract

Section: Introductionmentioning

confidence: 99%

Evolution of Nucleotide Punctuation Marks: From Structural to Linear Signals

Houmami

Seligmann

2017

Front. Genet.

View full text Add to dashboard Cite

show abstract

“…If x and y belong to the class C, then the distance δ x,y between them is defined as δ x,y = 20 − card{x ∩ y} (see also Ahmed et al, 2010). The result is reported in Fig.…”

Section: Discussionmentioning

confidence: 99%

“…Moreover, recent works Michel, 2003, 2006) reveal the presence of many other circular codes in different organisms; also, the existence of evolutionary mechanisms responsible of codon variations from the archetypical common X0 circular code are hypothesized (Arquès et al, 1999;Ahmed et al, 2010). Moreover, Michel et al (2008) identify a relation between the comma-free codes and the circular codes by constructing a hierarchy of these two classes of codes.…”

Section: Circular Codesmentioning

confidence: 98%

Circular codes revisited: A statistical approach

González¹,

Giannerini²,

Rosa³

2011

Journal of Theoretical Biology

View full text Add to dashboard Cite

In 1996 Arquès & Michel [(1996) J. Theor. Biol. 182, [45][46][47][48][49][50][51][52][53][54][55][56][57][58] discovered the existence of a common circular code in eukaryote and prokaryote genomes.Since then, circular code theory has provoked great interest and underwent a rapid development. In this paper we discuss some theoretical issues related to the synchronization properties of coding sequences and circular codes with particular emphasis on the problem of retrieval and maintenance of the reading frame. Motivated by the theoretical discussion, we adopt a rigorous statistical approach in order to try to answer to different questions. First, we investigate the covering capability of the whole class of 216 self-complementary, coding sequences are tailored as to maximize or minimize the coverage of circular codes on specific reading frames. Such optimization clearly relates the function of circular codes with reading frame synchronization.

show abstract

“…This role seems fulfilled by the natural circular code X, a set of 20 regular codons overrepresented in the coding frame of genes versus other frames. X possesses peculiar mathematical properties that enable retrieval of translational frame [3], [4], [5], [6], [7], [8], [9], [10]. This punctuation code can also be considered as cryptic superimposed information.…”

Section: Introductionmentioning

confidence: 99%

“…The reading frame retrieval capacity (RFR) of circular codes can be quantified [5]. The RFRs of these transformations of X correlate with properties of corresponding detected swinger RNAs [34].…”

Section: Introductionmentioning

confidence: 99%

Unbiased Mitoproteome Analyses Confirm Non-canonical RNA, Expanded Codon Translations

Seligmann

2016

Computational and Structural Biotechnology Journal

View full text Add to dashboard Cite

Proteomic MS/MS mass spectrometry detections are usually biased towards peptides cleaved by experimentally added digestion enzyme(s). Hence peptides resulting from spontaneous degradation and natural proteolysis usually remain undetected. Previous analyses of tryptic human proteome data (cleavage after K, R) detected non-canonical tryptic peptides translated according to tetra- and pentacodons (codons expanded by silent mono- and dinucleotides), and from transcripts systematically (a) deleting mono-, dinucleotides after trinucleotides (delRNAs), (b) exchanging nucleotides according to 23 bijective transformations. Nine symmetric and fourteen asymmetric nucleotide exchanges (X ↔ Y, e.g. A ↔ C; and X → Y → Z → X, e.g. A → C → G → A) produce swinger RNAs. Here unbiased reanalyses of these proteomic data detect preferentially non-canonical tryptic peptides despite assuming random cleavage. Unbiased analyses couldn't reconstruct experimental tryptic digestion if most detected non-canonical peptides were false positives. Detected non-tryptic non-canonical peptides map preferentially on corresponding, previously described non-canonical transcripts, as for tryptic non-canonical peptides. Hence unbiased analyses independently confirm previous trypsin-biased analyses that showed translations of del- and swinger RNA and expanded codons. Accounting for natural proteolysis completes trypsin-biased mitopeptidome analyses, independently confirms non-canonical transcriptions and translations.

show abstract

Essential molecular functions associated with the circular code evolution

Cited by 40 publications

References 30 publications

Evolution of Nucleotide Punctuation Marks: From Structural to Linear Signals

Evolution of Nucleotide Punctuation Marks: From Structural to Linear Signals

Circular codes revisited: A statistical approach

Unbiased Mitoproteome Analyses Confirm Non-canonical RNA, Expanded Codon Translations

Contact Info

Product

Resources

About