Fig. 1: Mitochondrial proteome changes after ablation of ATOM complex subunits. | Nature Communications

Fig. 1: Mitochondrial proteome changes after ablation of ATOM complex subunits.

From: Mistargeting of aggregation prone mitochondrial proteins activates a nucleus-mediated posttranscriptional quality control pathway in trypanosomes

Fig. 1

a General workflow of the quantitative proteomic analysis. The box on the left indicates a schematic model of the atypical translocase of the outer membrane (ATOM) complex with its seven subunits. Receptor subunits and the protein-conducting pore are indicated. ATOM69 is highlighted in orange. Using the stable isotope labelling by amino acids in cell culture (SILAC) method, six inducible RNAi cell lines and a conditional knock out cell line (ATOM11) were differentially labelled with stable-isotope coded heavy arginine (Arg10) and lysine (Lys8) or their light counterparts (Arg0/Lys0). Subsequently, induced (+Tet) and uninduced (−Tet) cells were mixed and crude mitochondrial fractions were purified by digitonin extractions (n = 3). For the ATOM69 RNAi cell line, whole cell samples were also analysed (see Fig. 2). All samples were subjected to liquid chromatography-mass spectrometry (LC-MS) followed by computational data analysis. b, c Volcano plots visualising SILAC-based quantitative MS data of crude mitochondrial extracts (Mito) for the ATOM core subunits ATOM40, ATOM19, ATOM14, ATOM12 and ATOM11 (b) and the ATOM receptor subunits ATOM46 and ATOM69 (c). Induction times for the indicated cell lines grown in SILAC medium were ATOM40 (3 d), ATOM19 (3.17 d), ATOM14 (3 d), ATOM12 (3 d), ATOM11 (4 d), ATOM46 (6 d) and ATOM69 (5 d).

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