Figure 6.

Global responses of the wild-type (WT) transcriptome to a shift from HC to LC supply compared with the transcriptional differences of the ∆4 and ∆ndhR mutants. A, PCA scores plot of a nontargeted PCA based on all transcript changes from this study (ST1) compared with an independent previous study, ST2 (Klähn et al., 2015). Arrows mark the constitutive differences of the ∆4 mutant compared with both the wild type and the ∆ndhR mutant as well as the common transitions of the transcriptome from HC to LC supply. A transcriptional phenocopy of the ∆4 mutant under HC conditions is indicated (asterisks). B, Preformed transcriptional changes in the ∆4 mutant under HC conditions compared with the significant wild-type 24-h LC shift response of this study (ST1). Note the partial correlation of both increased and decreased transcripts, which is indicative of a transcriptome phenocopy. C, Preformed transcriptional changes in the ∆ndhR mutant under HC conditions compared with the significant wild-type 24-h LC shift response of study ST2. Note the absence of common down-regulated transcripts and the few correlated up-regulated transcripts that constitute part of the subtle preacclimation of this mutant to LC conditions (Klähn et al., 2015). All transcript data from these analyses were normalized to the paired average expression levels of the wild type under HC conditions from the respective studies. Transcript data were averaged from two independently repeated biological shift experiments per genotype (Supplemental Table S2). Fold changes were regarded significant if the log₂ value was −1 or less or +1 or more and the adjusted Benjamini-Hochberg-corrected P value was P < 0.05.