Seligmann Hervé
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.
Biosystems. 2016 Sep;147:78-93. doi: 10.1016/j.biosystems.2016.07.010. Epub 2016 Jul 28.
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.
(a) 在三核苷酸后删除单/二核苷酸（delRNA），(b) 交换核苷酸（摆动RNA），按照三联体翻译，(c) 四联体和五联体密码子（由第4个（和第5个）沉默核苷酸扩展的密码子）。摆动转录是23种双射变换，9种对称变换（X<->Y，例如A<->C）和14种不对称交换（X->Y->Z->X，例如A->C->G->A）。在此，假设在W、Y、F之后切割（类胰凝乳蛋白酶，用于胰蛋白酶消化的样品）的蛋白质组分析检测到的经胰凝乳蛋白酶消化的肽段比经胰蛋白酶消化的肽段少。对于经胰凝乳蛋白酶消化的肽段，检测到的非经典肽段优先映射到检测到的非经典RNA上，正如之前在经胰蛋白酶消化的肽段中所发现的那样。这表明在实验性胰蛋白酶消化的肽段数据中可检测到残留的天然类胰凝乳蛋白酶消化。一些经胰蛋白酶消化的肽段通过假设胰蛋白酶和假设胰凝乳蛋白酶切割的分析被检测到两次。它们的光谱计数比仅被检测到一次的肽段更高，这意味着丰富的肽段更频繁地被检测到，但检测确定性与仅被检测到一次的肽段相似。假设“不正确”消化的分析对于生物样品中天然具有活性的消化酶来说是不充分的阴性对照。胰凝乳蛋白酶分析独立于假设胰蛋白酶消化所获得的结果证实了非经典转录/翻译，增加了非经典肽组覆盖范围，表明线粒体基因组编码了尚未检测到的蛋白质。
