Western blot analyses. To determine the protein level of HCV core protein, CuZn superoxide dismutase (CuZnSOD), Mn superoxide dismutase (MnSOD), Peroxiredoxin 1 and 3 (PRDX1 and 3), sulfonylated peroxiredoxin (PRDX-SO3), and cytosolic and mitochondrial aconitase (ACO1 and ACO2), cell pellets were incubated on ice with Tissue Protein Extraction reagent (T-PER, Fisher Scientific) supplemented with a protease inhibitor cocktail (Roche, Indianapolis, IN, USA), passed through 26 gauge needles several times, and centrifuged at 13,000 g, 4uC, for 2 min to remove cell debris. Total protein concentration was determined with a NanoVue Spectrophotometer (GE Healthcare, Piscataway, NJ, USA), and 50 ìg total proteins per lane were used for western blot analyses. Proteins were separated by 4-20% Mini-PROTEANH TGX gels (Bio-Rad, Hercules, CA, USA) (core, CuZnSOD, MnSOD, ACO1, and ACO2) or 16% Novex Tris-Glycine gels (Invitrogen) (PRDX1, PRDX3, and PRDX-SO3) and transferred to 0.2 mm nitrocellulose membranes (Bio-Rad). PRDX-SO3 antibody only detects sulfonylated PRDX and is not specific to PRDX1-SO3 or PRDX3-SO3. Consequently, sulfonylated PRDX1 and PRDX3 were distinguished based on their size difference ( Figure S5C ). To determine LC3 protein levels, cells cultured in 60 mm dishes were washed once with PBS and then scraped directly in the cell lysis buffer (50 mM Tris-Cl, pH 7.6, 150 mM NaCl, 2% SDS, 1 mM EDTA, 1x protease inhibitor cocktail) on ice. To break open the membranes, cell lysates were freeze-thawed two times and passed through a 26 gauge needle five times. Fifty mg of each cell lysate was separated with Any KD Mini-PROTEANH TGX gels (Bio-Rad) and transferred to 0.2 mm nitrocellulose membranes. The same membranes were used for thioredoxin 1 (TRX1) and thioredoxin 2 (TRX2) analyses. Alternatively, LC3-I and II were separated by 12% NuPAGE Bis-Tris gels (Invitrogen) in a subset of the studies. All membranes were incubated with primary antibodies overnight at 4uC followed by IR-labeled secondary antibodies for 1 hr at RT on a shaker. Membranes were washed three times each between primary and secondary antibody incubation and after secondary antibodies with PBST (PBS with 0.1% Tween 20). Membranes were then analyzed with the Odyssey Infrared Imaging System (Licor Biosciences, Lincoln, NE, USA). Signal intensity of each protein was normalized to that of âactin. Three to four independent experiments were carried out for each protein; all results are plotted as mean 6 SEM.