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

Seligmann, Hervé

doi:10.1016/j.jtbi.2015.09.030

Cited by 39 publications

(54 citation statements)

References 75 publications

(32 reference statements)

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“…1). These results seem overall robust as detected non-canonical peptides mapped on the human mitogenome with corresponding non-canonical RNAs [22], [23]. Hence existences of non-canonical RNAs and peptides are validated by independent detections of non-canonical RNAs and peptides, and by convergences (associations) between detected non-canonical RNAs and peptides.…”

Section: Introductionmentioning

confidence: 62%

“…Below I review the different types of non-canonical transcriptions and translations, and relevant previous results. Previous conclusions about non-canonical peptides are then re-evaluated according to analyses that account for overfitting that could have affected the previously used proteomic search algorithm [22], [23]. These new analyses strengthen previous conclusions on non-canonical mitochondrial transcriptions and translations.…”

Section: Introductionmentioning

confidence: 67%

“…Two types of systematic transformations occur: (a) systematic deletions of mono- and dinucleotides after each trinucleotide, producing delRNAs in human mitochondria [22]; and 23 types of systematic exchanges between nucleotides (nine symmetric exchanges, type X ↔ Y, e.g. A ↔ C; and fourteen asymmetric exchanges, type X → Y → Z → X, e.g.…”

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…(a) Contiguous short RNA reads in the human transcriptome match the mitogenome transformed by systematic (mono- and dinucleotide) deletions after each trinucleotide [22]. (b) Peptides corresponding to these delRNAs were detected in proteomic data [22]. (c) The human mitogenome, after del-transformations, has more inverted palindromes potentially forming stem-loop hairpins than comparable randomly shuffled sequences [23].…”

Section: Introductionmentioning

confidence: 99%

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

Seligmann

2016

Computational and Structural Biotechnology Journal

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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.

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Section: Introductionmentioning

confidence: 62%

Section: Introductionmentioning

confidence: 67%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Seligmann

2016

Computational and Structural Biotechnology Journal

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

2020

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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 RNA rings lack dinucleotide CG (a mutable, chemically instable dinucleotide coding for Arginine), bearing a resemblance to known CG‐depleted genomes. CG in “incomplete” RNA rings (not coding for all coding signals, with only 3–12 nucleotides) gradually decreases towards CG absence in complete, 22‐nucleotide‐long RNA rings. Presumably, feedback loops during RNA ring growth during evolution (when amino acid assignment fixed the genetic code) assigned Arg to codons lacking CG (AGR) to avoid CG. Hence, as a chemical property of base pairs, CG mutability restructured the genetic code, thereby establishing itself as genetically encoded biological information.

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Origins, Technological Advancement, and Applications of Peptidomics

Schrader

2024

Methods in Molecular Biology

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

Cited by 39 publications

References 75 publications

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

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

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

Origins, Technological Advancement, and Applications of Peptidomics

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