Photosynthetic light harvesting in plants is regulated by a pH-and xanthophyll-dependent nonphotochemical quenching process (qE) that dissipates excess absorbed light energy and requires the psbS gene product. An Arabidopsis thaliana mutant, npq4-1, lacks qE because of a deletion of the psbS gene, yet it exhibits a semidominant phenotype. Here it is shown that the semidominance is due to a psbS gene dosage effect. Diploid Arabidopsis plants containing two psbS gene copies (wild-type), one psbS gene (npq4-1/NPQ4 heterozygote), and no psbS gene (npq4-1/npq4-1 homozygote) were compared. Heterozygous plants had 56% of the wild-type psbS mRNA level, 58% of the wild-type PsbS protein level, and 60% of the wild-type level of qE. Global analysis of the chlorophyll a fluorescence lifetime distributions revealed three components in wild-type and heterozygous plants, but only a single long lifetime component in npq4-1. The short lifetime distribution associated with qE was inhibited by more than 40% in heterozygous plants compared with the wild type. Thus, the extent of qE measured as either the fractional intensities of the PSII chlorophyll a fluorescence lifetime distributions or steady state intensities was stoichiometrically related to the amount of PsbS protein.Absorption of light in excess of photosynthetic capacity necessitates mechanisms to protect plants from photo-oxidative damage (1). Overexcitation of chlorophyll (Chl) 1 and overreduction of the electron transport chain can result in increased generation of reactive intermediates and harmful byproducts of photosynthesis. For example, when excitation energy in singlet-excited Chl ( 1 Chl*) cannot be used to drive electron transport, the lifetime of 1 Chl* increases, resulting in an increased yield of triplet-excited Chl ( 3 Chl*) via intersystem crossing. 3 Chl* can generate singlet O 2 ( 1 O 2 *), which can directly damage pigments, proteins, and lipids in the photosynthetic apparatus. To maintain a short lifetime of 1 Chl* and minimize photo-oxidative damage, a nonphotochemical quenching process, called qE, is induced in excessive light, resulting in deexcitation of 1 Chl* molecules and thermal dissipation of excess absorbed light energy in the light-harvesting antenna of photosystem (PS) II (2, 3). Because it decreases the lifetime of 1 Chl*, qE can be measured easily as a decrease in the maximum yield of Chl fluorescence in isolated chloroplast membranes, algal cells, or intact leaves.qE is induced by a low pH in the thylakoid lumen of chloroplasts during illumination with excessive light (reviewed in Refs. 2-5). Low pH activates the violaxanthin de-epoxidase, which converts violaxanthin, V, into antheraxanthin, A, and then zeaxanthin, Z, as part of a xanthophyll cycle (6 -9). Binding of de-epoxidized xanthophylls (A and Z) and protons (H ϩ ) to undefined PSII proteins is hypothesized to result in a conformational change that effectively switches a PSII unit into a quenched state in which nonphotochemical de-excitation of 1 Chl* is favored (reviewed in Refs....