Supplementary Information 1) Comparison of spectra at t=0 obtained from different state-locked WT cells Figure S1. Comparison of estimated spectra at t=0 obtained from state-1-locked and state-2-locked cells. For explanation see main text (results). 2) Comparison of state transitions in WT and STT7 kinase mutant In order to confirm that the observed differences observed for cells with either an oxidized and an overreduced plastoquinone pool are indeed due to state transitions we repeated the measurement under identical conditions with STT7 mutant cells, which are lacking the kinase that is responsible for the phosphorylation required for state transitions. The results could only be fitted in a meaningful way using 4 decay components, in contrast to the results obtained for WT cells which required 5 components. In order to allow a direct comparison between mutant and WT cells, we also fitted the time-resolved fluorescence data on WT cells with 4 decay components and the results are shown in Figure S2. Figure S2. The decay associated spectra (DAS) for state-1- and state-2-locked cells using 4 exponentials for the fitting. The lifetimes are indicated in the figure. All spectra are normalized and for a detailed explanation of the normalization process, we refer to the Results section in the main text. As before one can observe clear differences for all DAS in state 1 and state 2 and in particular the 3rd (blue) DAS shows that the long-lived PSII contribution (around 685 nm) has largely decreased whereas the PSI contribution around 710 nm hardly has changed. In sharp contrast to what is observed for the WT cells, the STT7 cells show hardly any differences for the conditions that are responsible for state 1 and 2 in WT cells. Both the lifetimes and the shapes of the different components are very similar, although not entirely identical. However, all the major changes that are discussed for the WT cells are missing for these mutant cells.