The minor light-harvesting complexes CP24, CP26, and CP29 have been proposed to play a key role in the zeaxanthin (Zx)-dependent high light-induced regulation (NPQ) of excitation energy in higher plants. To characterize the detailed roles of these minor complexes in NPQ and to determine their specific quenching effects we have studied the ultrafast fluorescence kinetics in knockout (ko) mutants koCP26, koCP29, and the double mutant koCP24/CP26. The data provide detailed insight into the quenching processes and the reorganization of the Photosystem (PS) II supercomplex under quenching conditions. All genotypes showed two NPQ quenching sites. Quenching site Q1 is formed by a light-induced functional detachment of parts of the PSII supercomplex and a pronounced quenching of the detached antenna parts. The antenna remaining bound to the PSII core was also quenched substantially in all genotypes under NPQ conditions (quenching site Q2) as compared with the darkadapted state. The latter quenching was about equally strong in koCP26 and the koCP24/CP26 mutants as in the WT. Q2 quenching was substantially reduced, however, in koCP29 mutants suggesting a key role for CP29 in the total NPQ. The observed quenching effects in the knockout mutants are complicated by the fact that other minor antenna complexes do compensate in part for the lack of the CP24 and/or CP29 complexes. Their lack also causes some LHCII dissociation already in the dark.Plants use light as the energy source for their metabolism. During the early steps of photosynthesis, solar energy is efficiently absorbed, and excitons are transferred to the photosynthetic reaction centers (RC) 3 by a complex array of pigmentbinding proteins, the light-harvesting antenna complexes (LHC), localized at the periphery of each photosystem (PS) (1, 2) (for recent reviews, see Refs. 3 and 4). However, Lhc proteins are not only involved in light harvesting. Rather, they are also acting in photoprotection by multiple mechanisms, including chlorophyll (Chl) singlet (Chl*) energy dissipation, Chl triplet quenching, and scavenging of reactive oxygen species. The antenna system, thus, has a dual function. On the one hand, it harvests photons and extends the cross-section for light absorption under light-limiting conditions. On the other hand, it prevents or limits damage to the photosynthetic apparatus when light is in excess (5, 6). Among the photoprotective mechanisms catalyzed in the PSII antenna system of higher plants, the high energy-dependent quenching of Chl singlet excited states (qE part of NPQ) is essential for protection under variable light conditions (7) by dissipating the excess energy as heat. Triggering of qE occurs upon decrease of the thylakoid lumen pH (7, 8) under conditions when ATPase cannot fully use the proton gradient created across the thylakoid membrane. Low lumenal pH induces the conversion of violaxanthin (Vx) to zeaxanthin (Zx) via the xanthophyll cycle (9 -11) and activates the PsbS protein (12, 13). Both events are essential for the full establis...