After 16 h, when the respiratory rate had recovered and reached an equilibrium (Fig. 1A, phase II), whole cell respiration was further dissected using respiratory inhibitors (Supplemental Fig. S2A). Total oxygen consumption rate, after addition of carbonyl cyanide m-chlorophenylhydrazone to remove adenylate control, was unchanged by rotenone treatment when expressed on a cell dry weight basis. Addition of 1 mm  n-propyl gallate (nPG) to inhibit the AOX pathway showed that maximal respiration through the COX pathway was unchanged by rotenone treatment (Supplemental Fig. S2A). Blue-native PAGE (BN-PAGE) separation of respiratory complexes and detection of NADH dehydrogenase activity revealed that complex I was present and active in mitochondria isolated from rotenone-treated cells (Supplemental Fig. S2B), consistent with the evidence that rotenone is a reversible inhibitor and is lost during mitochondrial isolation (Singer, 1979). These gels also showed that the other classic mitochondrial OxPhos complexes were present and had similar total protein stain intensity in both control and rotenone-treated samples. This is consistent with the fact that there were scarcely any transcriptional responses to rotenone treatment by any of the mitochondrial (Supplemental Fig. S3) or nuclear genes encoding components of the OxPhos complexes (Table I