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Cytosolic and mitochondrial extracts were prepared using a Mitochondrial/Cytosol Fractionation kit (BioVision).
Mitochondrial extracts were incubated with GST-hERK1 or GST-null recombinant proteins and extensively washed.
Mitochondrial extracts were prepared with lysis buffer containing 10 mM HEPES, 10 mM KCl, 1.5 mM MgCl2, 0.5 mM DTT, 1% NP40, 1 mM phenylmethylsulfonyl fluoride, 25% glycerol, and 0.2 mM EDTA.
Crude mitochondrial extracts were isolated by differential centrifugations as described previously (Hoppins et al., 2011).
Mitochondrial extracts were prepared from 1.0 × 108 cells following the procedure described earlier [ 20].
As control experiments, mitochondrial extracts were treated with equal volumes of phosphate buffer instead of KCl.
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Mitochondrial extracts are unable to support 5′-end processing of a tRNASer AGY) that is not flanked by an intact tRNAHis [86].
Under these conditions, Fcj1-GFP in both the wild type (sized at 0.6 to 1.5 MDa in published work) and in ∆MICOS mitochondrial extracts was quantitatively recovered in the supernatant fraction.
Cells or mitochondrial extract were lysed by the Laemmli sample buffer as previously described [ 19, 20].
The lysate was centrifuged at 12000 rpm for 15 min, and the supernatant containing the mitochondrial extract was collected.
To confirm that Mdj1 is associated with the mitochondrial nucleoid we performed a control experiment in which the mitochondrial extract was treated with DNaseI prior to centrifugation.
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