Search results for: Hervé Seligmann

Items from 1 to 20 out of 53 results

article

Negative CG dinucleotide bias: An explanation based on feedback loops between Arginine codon assignments and theoretical minimal RNA rings

Jacques Demongeot, Andrés Moreira, Hervé Seligmann

BioEssays > 43 > 3 > n/a - n/a

Theoretical minimal RNA rings are candidate primordial genes evolved for non‐redundant coding of the genetic code's 22 coding signals (one codon per biogenic amino acid, a start and a stop codon) over the shortest possible length: 29520 22‐nucleotide‐long RNA rings solve this min‐max constraint. Numerous RNA ring properties are reminiscent of natural genes. Here we present analyses showing that all...

article

Why Is AUG the Start Codon?

Jacques Demongeot, Hervé Seligmann

BioEssays > 42 > 6 > n/a - n/a

The rational design of theoretical minimal RNA rings predetermines AUG as the universal start codon. This design maximizes coded amino acid diversity over minimal sequence length, defining in silico theoretical minimal RNA rings, candidate ancestral genes. RNA rings code for 21 amino acids and a stop codon after three consecutive translation rounds, and form a degradation‐delaying stem‐loop hairpin...

article

The Uroboros Theory of Life’s Origin: 22-Nucleotide Theoretical Minimal RNA Rings Reflect Evolution of Genetic Code and tRNA-rRNA Translation Machineries

Jacques Demongeot, Hervé Seligmann

Acta Biotheoretica > 2019 > 67 > 4 > 273-297

Theoretical minimal RNA rings attempt to mimick life’s primitive RNAs. At most 25 22-nucleotide-long RNA rings code once for each biotic amino acid, a start and a stop codon and form a stem-loop hairpin, resembling consensus tRNAs. We calculated, for each RNA ring’s 22 potential splicing positions, similarities of predicted secondary structures with tRNA vs. rRNA secondary structures. Assuming rRNAs...

article

Giant viruses: spore‐like missing links between Rickettsia and mitochondria?

Hervé Seligmann

Annals of the New York Academy of Sciences > 1447 > 1 > 69 - 79

Phyloproteomics indicate common viral origin from ancient cells before archaea, bacteria, and eukaryota split and subsequent size and complexity reductions occurred. Further independent evidence for the cellular origin of viruses is reviewed for the virus order Megavirales, focusing on the family Poxviridae. Megavirales comprises giant viruses, double‐stranded DNA viruses whose genomes exceed some...

article

Theoretical minimal RNA rings designed according to coding constraints mimic deamination gradients

Jacques Demongeot, Hervé Seligmann

The Science of Nature > 2019 > 106 > 7-8 > 1-15

Deaminations (A->G, C->T) increase with DNA singlestrandedness during replication, presumably creating spontaneous genomic mutational and nucleotide frequency gradients. Alternatively, genes are positioned to avoid deaminations. Deamination gradients affect directly mitogene third codon positions; conserved vertebrate mitochondrial tRNA and protein coding gene arrangements minimize deaminations...

article

More Pieces of Ancient than Recent Theoretical Minimal Proto-tRNA-Like RNA Rings in Genes Coding for tRNA Synthetases

Jacques Demongeot, Hervé Seligmann

Journal of Molecular Evolution > 2019 > 87 > 4-6 > 152-174

Theoretical minimal RNA rings were designed to mimick life’s primordial RNAs by forming stem-loop hairpins and coding once for each of the 20 amino acids, a start and a stop codon. At most 25 22-nucleotide long RNA rings follow these criteria. These align well with a consensus tRNA sequence, predicting for each RNA ring an anticodon and an associated cognate amino acid. Hypotheses on cognate amino...

article

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

Hervé Seligmann

Theory in Biosciences > 2018 > 137 > 1 > 17-31

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...

article

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

Hervé Seligmann

Biosystems > 2017 > 160 > C > 10-24

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,...

article

Natural mitochondrial proteolysis confirms transcription systematically exchanging/deleting nucleotides, peptides coded by expanded codons

Hervé Seligmann

Journal of Theoretical Biology > 2017 > 414 > C > 76-90

Protein sequences have higher linguistic complexities than human languages. This indicates undeciphered multilayered, overprinted information/genetic codes. Some superimposed genetic information is revealed by detections of transcripts systematically (a) exchanging nucleotides (nine symmetric, e.g. A<->C, fourteen asymmetric, e.g. A->C->G->A, swinger RNAs) translated according to tri-,...

article

Genetic Code Optimization for Cotranslational Protein Folding: Codon Directional Asymmetry Correlates with Antiparallel Betasheets, tRNA Synthetase Classes

Hervé Seligmann, Ganesh Warthi

Computational and Structural Biotechnology Journal > 2017 > 15 > C > 412-424

A new codon property, codon directional asymmetry in nucleotide content (CDA), reveals a biologically meaningful genetic code dimension: palindromic codons (first and last nucleotides identical, codon structure XZX) are symmetric (CDA=0), codons with structures ZXX/XXZ are 5′/3′ asymmetric (CDA=−1/1; CDA=−0.5/0.5 if Z and X are both purines or both pyrimidines, assigning negative/positive (−/+) signs...

article

Natural chymotrypsin-like-cleaved human mitochondrial peptides confirm tetra-, pentacodon, non-canonical RNA translations

Hervé Seligmann

Biosystems > 2016 > 147 > C > 78-93

Mass spectra of human mitochondrial peptides match non-canonical transcripts systematically (a) deleting mono/dinucleotides after trinucleotides (delRNA), (b) exchanging nucleotides (swinger RNA), translated according to tri, (c) tetra- and pentacodons (codons expanded by a 4th (and 5th) silent nucleotide(s)). Swinger transcriptions are 23 bijective transformations, nine symmetric (X<->Y, e...

article

Swinger RNA self-hybridization and mitochondrial non-canonical swinger transcription, transcription systematically exchanging nucleotides

Hervé Seligmann

Journal of Theoretical Biology > 2016 > 399 > C > 84-91

Stem-loop hairpins punctuate mitochondrial post-transcriptional processing. Regulation of mitochondrial swinger transcription, transcription producing RNAs matching the mitogenome only assuming systematic exchanges between nucleotides (23 bijective transformations along 9 symmetric exchanges X<>Y, e.g. A<>G, and 14 asymmetric exchanges X>Y>Z>X, e.g. A>G>C>A) remains unknown...

article

Cryptic tRNAs in chaetognath mitochondrial genomes

Roxane-Marie Barthélémy, Hervé Seligmann

Computational Biology and Chemistry > 2016 > 62 > C > 119-132

The chaetognaths constitute a small and enigmatic phylum of little marine invertebrates. Both nuclear and mitochondrial genomes have numerous originalities, some phylum-specific. Until recently, their mitogenomes seemed containing only one tRNA gene (trnMet), but a recent study found in two chaetognath mitogenomes two and four tRNA genes. Moreover, apparently two conspecific mitogenomes have different...

article

Unifying view of stem–loop hairpin RNA as origin of current and ancient parasitic and non-parasitic RNAs, including in giant viruses

Hervé Seligmann, Didier Raoult

Current Opinion in Microbiology > 2016 > 31 > C > 1-8

Putatively, stem–loop RNA hairpins explain networks of selfish elements and RNA world remnants. Their genomic density increases with intracellular lifestyle, especially when comparing giant viruses and their virophages. RNA protogenomes presumably templated for mRNAs and self-replicating stem–loops, ancestors of modern genes and parasitic sequences, including tRNAs and rRNAs. Primary and secondary...

article

Systematically frameshifting by deletion of every 4th or 4th and 5th nucleotides during mitochondrial transcription: RNA self-hybridization regulates delRNA expression

Hervé Seligmann

Biosystems > 2016 > 142-143 > C > 43-51

In mitochondria, secondary structures punctuate post-transcriptional RNA processing. Recently described transcripts match the human mitogenome after systematic deletions of every 4th, respectively every 4th and 5th nucleotides, called delRNAs. Here I explore predicted stem-loop hairpin formation by delRNAs, and their associations with delRNA transcription and detected peptides matching their translation...

article

Translation of mitochondrial swinger RNAs according to tri-, tetra- and pentacodons

Hervé Seligmann

Biosystems > 2016 > 140 > C > 38-48

Transcriptomes and proteomes include RNA and protein fragments not matching regular transcription/translation. Some ‘non-canonical’ mitochondrial transcripts match mitogenomes after assuming one among 23 systematic exchanges between nucleotides, producing swinger RNAs (nine symmetric, X↔Y, example C↔T; 14 asymmetric, X→Y→Z→X, example A→T→G→A) in GenBank's EST database. Here, reanalyzes of (a) public...

article

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

Hervé Seligmann

Computational and Structural Biotechnology Journal > 2016 > 14 > C > 391-403

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...

article

Chimeric mitochondrial peptides from contiguous regular and swinger RNA

Hervé Seligmann

Computational and Structural Biotechnology Journal > 2016 > 14 > C > 283-297

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...

article

Codon expansion and systematic transcriptional deletions produce tetra-, pentacoded mitochondrial peptides

Hervé Seligmann

Journal of Theoretical Biology > 2015 > 387 > C > 154-165

Genes include occasionally isolated codons with a fourth (and fifth) silent nucleotide(s). Assuming tetracodons, translated hypothetical peptides align with regular GenBank proteins; predicted tetracodons coevolve with predicted tRNAs with expanded anticodons in each mammal, Drosophila and Lepidosauria mitogenomes, GC contents and with lepidosaurian body temperatures, suggesting that expanded codons...

article

Systematic exchanges between nucleotides: Genomic swinger repeats and swinger transcription in human mitochondria

Hervé Seligmann

Journal of Theoretical Biology > 2015 > 384 > Complete > 70-77

Chargaff׳s second parity rule, quasi-equal single strand frequencies for complementary nucleotides, presumably results from insertion of repeats and inverted repeats during sequence genesis. Vertebrate mitogenomes escape this rule because repeats are counterselected: their hybridization produces loop bulges whose deletion is deleterious. Some DNA/RNA sequences match mitogenomes only after assuming...

Publication date

Set your own date range

INFONA - science communication portal

Search results for: Hervé Seligmann

Negative CG dinucleotide bias: An explanation based on feedback loops between Arginine codon assignments and theoretical minimal RNA rings

Why Is AUG the Start Codon?

The Uroboros Theory of Life’s Origin: 22-Nucleotide Theoretical Minimal RNA Rings Reflect Evolution of Genetic Code and tRNA-rRNA Translation Machineries

Giant viruses: spore‐like missing links between Rickettsia and mitochondria?

Theoretical minimal RNA rings designed according to coding constraints mimic deamination gradients

More Pieces of Ancient than Recent Theoretical Minimal Proto-tRNA-Like RNA Rings in Genes Coding for tRNA Synthetases

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

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

Natural mitochondrial proteolysis confirms transcription systematically exchanging/deleting nucleotides, peptides coded by expanded codons

Genetic Code Optimization for Cotranslational Protein Folding: Codon Directional Asymmetry Correlates with Antiparallel Betasheets, tRNA Synthetase Classes

Natural chymotrypsin-like-cleaved human mitochondrial peptides confirm tetra-, pentacodon, non-canonical RNA translations

Swinger RNA self-hybridization and mitochondrial non-canonical swinger transcription, transcription systematically exchanging nucleotides

Cryptic tRNAs in chaetognath mitochondrial genomes

Unifying view of stem–loop hairpin RNA as origin of current and ancient parasitic and non-parasitic RNAs, including in giant viruses

Systematically frameshifting by deletion of every 4th or 4th and 5th nucleotides during mitochondrial transcription: RNA self-hybridization regulates delRNA expression

Translation of mitochondrial swinger RNAs according to tri-, tetra- and pentacodons

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

Chimeric mitochondrial peptides from contiguous regular and swinger RNA

Codon expansion and systematic transcriptional deletions produce tetra-, pentacoded mitochondrial peptides

Systematic exchanges between nucleotides: Genomic swinger repeats and swinger transcription in human mitochondria

Filter options

Publication date

Content availability

Keywords

Data set

Journal

INFONA - science communication portal

Search results for: Hervé Seligmann

Add recipient

Sending message cancelled

Are you sure you want to cancel sending this message?

Send message

Filter options

Publication date

Date range setting

Set the date range to filter the displayed results. You can set a starting date, ending date or both. You can enter the dates manually or choose them from the calendar.

Content availability

Keywords

Data set

Journal

Reporting an error / abuse

Sending the report failed

Accessibility options