title: Natural chymotrypsin-like-cleaved human mitochondrial peptides confirm tetra-, pentacodon, non-canonical RNA translations.
abstract: 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.g. A<->C) and fourteen asymmetric exchanges (X->Y->Z->X, e.g. A->C->G->A). Here, proteomic analyses assuming cleavage after W,Y, F (chymotrypsin-like, for trypsinized samples) detect fewer chymotrypsinized than trypsinized peptides. Detected non-canonical peptides map preferentially on detected non-canonical RNAs for chymotrypsinized peptides, as previously found for trypsinized peptides. This suggests residual natural chymotrypsin-like digestion detectable within experimentally trypsinized peptide data. Some trypsinized peptides are detected twice, by analyses assuming trypsin, and those assuming chymotrypsin cleavages. They have higher spectra counts than peptides detected only once, meaning that abundant peptides are more frequently detected, but detection certainties resemble those for peptides detected only once. Analyses assuming 'incorrect' digestions are inadequate negative controls for digestion enzymes naturally active in biological samples. Chymotrypsin-analyses confirm non-canonical transcriptions/translations independently of results obtained assuming trypsinization, increase non-canonical peptidome coverage, indicating mitogenome-encoding of yet undetected proteins.
authors.affiliation: Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes, Faculté de Médecine, Université d'Aix-Marseille, URMITE CNRS-IRD 198 UMER 6236, Marseille, France. Electronic address: timonuslepidus@gmail.com.
authors.forename: Hervé
authors.initials: H
authors.lastname: Seligmann
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D002918:Chymotrypsin / Q000378:metabolism; D003062:Codon / Q000235:genetics*; D054629:Genome, Mitochondrial / Q000235:genetics; D006801:Humans; D013058:Mass Spectrometry; D024101:Mitochondrial Proteins / Q000235:genetics* / Q000378:metabolism; D009841:Oligonucleotides / Q000235:genetics; D010455:Peptides / Q000235:genetics* / Q000378:metabolism; D014176:Protein Biosynthesis; D020543:Proteome / Q000235:genetics / Q000378:metabolism; D040901:Proteomics / Q000379:methods; D012313:RNA / Q000235:genetics*; D000077278:RNA, Mitochondrial; D014158:Transcription, Genetic
chemical_list: D003062:Codon; D024101:Mitochondrial Proteins; D009841:Oligonucleotides; D010455:Peptides; D020543:Proteome; D000077278:RNA, Mitochondrial; D012313:RNA; D002918:Chymotrypsin
keywords: Bijective transformation; Digestion enzymes; Frameshifting transcription; Proteome; Systematic deletions; Translational frameshift; delRNA