Seligmann Hervé
Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes, Faculté de Médecine, URMITE CNRS-IRD 198 UMER 6236, Université de la Méditerranée, Marseille, France.
Biosystems. 2016 Feb;140:38-48. doi: 10.1016/j.biosystems.2015.11.009. Epub 2015 Dec 23.
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 human mitochondrial transcriptome data (Illumina: RNA-seq) allowed to detect mitochondrial swinger RNAs for all 23 exchanges and (b) independent public human mitochondrial trypsinized proteomic mass spectrometry data allowed to detect peptides predicted from translation of parts of swinger-transformed mitogenomes covered by detected swinger reads. RNA-seq and previous EST swinger transcript data converge. Swinger RNA translation frequently inserts various amino acids at stop codons. Swinger RNA-peptide associations exist also for peptides matching systematically frameshifting translation, peptides entirely coded by tetra- and pentacodons (regular codons expanded by silent mononucleotides at 4th, and silent dinucleotides at 4th and 5th position(s), respectively). Swinger peptides differ from regular mitochondrial proteins: not membrane embedded, reflect warmer, anaerobic, low resource conditions, reminding a free-living ancestor. Tetra- and pentacoded peptides associate with low, high GC contents, respectively, suggesting expanded codon translations associate with thermic stresses. Results confirm experimentally predicted swinger, tetra- and pentacoded mitochondrial peptides, increasing mitogenomic coding density.
转录组和蛋白质组包含与常规转录/翻译不匹配的RNA和蛋白质片段。一些“非经典”线粒体转录本在经历23种核苷酸系统交换中的一种后与线粒体基因组匹配，在GenBank的EST数据库中产生摆动RNA（9种对称的，X↔Y，例如C↔T；14种不对称的，X→Y→Z→X，例如A→T→G→A）。在此，（a）对公开的人类线粒体转录组数据（Illumina：RNA测序）进行重新分析，得以检测到所有23种交换的线粒体摆动RNA，并且（b）对独立的公开人类线粒体胰蛋白酶消化蛋白质组质谱数据进行重新分析，得以检测到从由检测到的摆动读数覆盖的摆动转化线粒体基因组部分翻译预测的肽段。RNA测序和先前的EST摆动转录本数据趋于一致。摆动RNA翻译经常在终止密码子处插入各种氨基酸。对于与系统移码翻译匹配的肽段、完全由四联体密码子和五联体密码子编码的肽段（常规密码子分别在第4位由沉默单核苷酸扩展，以及在第4位和第5位由沉默二核苷酸扩展），也存在摆动RNA - 肽段关联。摆动肽段与常规线粒体蛋白质不同：不嵌入膜中，反映温暖、厌氧、低资源条件，让人联想到自由生活的祖先。四联体和五联体编码的肽段分别与低、高GC含量相关联，表明扩展密码子翻译与热应激相关。结果通过实验证实了预测的摆动、四联体和五联体编码的线粒体肽段，增加了线粒体基因组的编码密度。
