Species radiation by DNA replication that systematically exchanges nucleotides?

Seligmann, Hervé

doi:10.1016/j.jtbi.2014.08.036

Cited by 29 publications

(12 citation statements)

References 45 publications

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“…Further little known mechanisms increase numbers of proteins potentially coded by single sequences. Polymerization occasionally exchanges systematically between nucleotides during DNA replication [44][45][46] or RNA transcription [47][48][49][50][51][52][53] for long sequence stretches (23 exchange rules are possible, nine symmetric, e.g., A<>C, and fourteen asymmetric, e.g., A > C > G > A), producing swinger sequences. Swinger replication, in particular the double symmetric exchange A<>T + C<>G, seems most frequent for mitochondrial ribosomal RNAs [46].…”

Section: Alternative Coding By Swinger Polymerizationmentioning

confidence: 99%

“…This analysis tentatively indicates that stop codon depletion and coding by frameshifting and translation of stop codons might associate with a phenomenon increasing tolerance to frameshifts during translation. Indeed, frequencies of off frame stop codons in mitochondrial genes are inversely correlated to predicted ribosomal RNA stability [86][87][88], suggesting that genes adapt to avoid negative effects of ribosomal frameshifts [44,89,90]. Stop codon-depletion may enable coding for more proteins, in addition to increasing redundancies between frames.…”

Section: Coding Redundancy Between Frames and Tolerating Ribosomal Frmentioning

confidence: 99%

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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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Section: Alternative Coding By Swinger Polymerizationmentioning

confidence: 99%

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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“…(Seligmann, 2016e). Swinger DNA also occurs (Seligmann, 2014a;Seligmann, 2014b). Molecular functions and associations of swinger polymerizations with healthy or unhealthy cells remain unknown.…”

Section: Introductionmentioning

confidence: 99%

Systematic Nucleotide Exchange Analysis of ESTs From the Human Cancer Genome Project Report: Origins of 347 Unknown ESTs Indicate Putative Transcription of Non-Coding Genomic Regions

2020

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Expressed sequence tags (ESTs) provide an imprint of cellular RNA diversity irrespectively of sequence homology with template genomes. NCBI databases include many unknown RNAs from various normal and cancer cells. These are usually ignored assuming sequencing artefacts or contamination due to their lack of sequence homology with template DNA. Here, we report genomic origins of 347 ESTs previously assumed artefacts/unknown, from the FAPESP/LICR Human Cancer Genome Project. EST template detection uses systematic nucleotide exchange analyses called swinger transformations. Systematic nucleotide exchanges replace systematically particular nucleotides with different nucleotides. Among 347 unknown ESTs, 51 ESTs match mitogenome transcription, 17 and 2 ESTs are from nuclear chromosome non-coding regions, and uncharacterized nuclear genes. Identified ESTs mapped on 205 proteincoding genes, 10 genes had swinger RNAs in several biosamples. Whole cell transcriptome searches for 17 ESTs mapping on non-coding regions confirmed their transcription. The 10 swinger-transcribed genes identified more than once associate with cancer induction and progression, suggesting swinger transformation occurs mainly in highly transcribed genes. Swinger transformation is a unique method to identify noncanonical RNAs obtained from NGS, which identifies putative ncRNA transcribed regions. Results suggest that swinger transcription occurs in highly active genes in normal and genetically unstable cancer cells.

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“…Note that swinger DNA has been detected (mainly corresponding to rRNA genes) for mitochondrial and nuclear sequences [36][37][38]. Hence, swinger RNAs result from canonical transcription of swinger-transformed DNA or swinger transcription of regular DNA [22].…”

Section: Introductionmentioning

confidence: 99%

Swinger RNAs in the Human Mitochondrial Transcriptome

Warthi¹,

Seligmann²

2018

Mitochondrial DNA - New Insights

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Transcriptomes include coding and non-coding RNAs and RNA fragments with no apparent homology to parent genomes. Non-canonical transcriptions systematically transforming template DNA sequences along precise rules explain some transcripts. Among these systematic transformations, 23 systematic exchanges between nucleotides, i.e. 9 symmetric (X ↔ Y, e.g. C ↔ T) and 14 asymmetric (X → Y → Z → X, e.g. A → T → G → A) exchanges. Here, comparisons between mitochondrial swinger RNAs previously detected in a complete human transcriptome dataset (including cytosolic RNAs) and swinger RNAs detected in purified mitochondrial transcriptomic data (not including cytosolic RNAs) show high reproducibility and exclude cytosolic contaminations. These results based on next-generation sequencing Illumina technology confirm detections of mitochondrial swinger RNAs in GenBank's EST database sequenced by the classical Sanger method, assessing the existence of swinger polymerizations.

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Species radiation by DNA replication that systematically exchanges nucleotides?

Cited by 29 publications

References 45 publications

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

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

Systematic Nucleotide Exchange Analysis of ESTs From the Human Cancer Genome Project Report: Origins of 347 Unknown ESTs Indicate Putative Transcription of Non-Coding Genomic Regions

Swinger RNAs in the Human Mitochondrial Transcriptome

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