Nonphotochemical quenching (NPQ) of excitation energy, which protects higher plant photosynthetic machinery from photodamage, is triggered by acidification of the thylakoid lumen as a result of light-induced proton pumping, which also drives the synthesis of ATP. It is clear that the sensitivity of NPQ is modulated in response to changing physiological conditions, but the mechanism for this modulation has remained unclear. Evidence is presented that, in intact tobacco or Arabidopsis leaves, NPQ modulation in response to changing CO 2 levels occurs predominantly by alterations in the conductivity of the CF O-CF1 ATP synthase to protons (g H ؉ ). At a given proton flux, decreasing g H ؉ will increase transthylakoid proton motive force (pmf ), thus lowering lumen pH and contributing to the activation of NPQ. violaxanthin deepoxidase ͉ photoinhibition ͉ xanthophyll cycle ͉ proton motive force ͉ chemiosmotic coupling L ight-driven transthylakoid proton motive force (pmf ) serves two essential roles in higher plant photosynthesis (1). First, it is the central intermediate in the chemiosmotic circuit for light-driven ATP synthesis. Light-driven electron transfer leads to the pumping of protons from the stroma to the thylakoid lumen, establishing pmf, which drives the endergonic synthesis of ATP from ADP and orthophosphate (P i ) at the CF O -CF 1 ATP synthase (ATP synthase).Second, the ⌬pH component of pmf is the key regulatory signal for initiation of nonphotochemical quenching (NPQ) of excitation energy, which is important for photoprotection. Light absorption by the light-harvesting complexes (LHCs) in excess of that which can be processed can lead to harmful side reactions, collectively termed photoinhibition, that can occur at several levels, including the antenna complexes, the oxidizing and reducing sides of photosystem II (PS II), and the reducing side of photosystem I (PS I) (see reviews in refs. 2 and 3).In higher plants, photoinhibition is avoided in part by activation of NPQ, which can dump a large fraction of excitation energy, preventing the accumulation of reactive intermediates (see reviews in refs. 4 and 5-7). It is now generally accepted that NPQ involves two processes activated by acidification of the lumen, the interconversion of xanthophyll cycle carotenoids by violaxanthin deepoxidase (VDE), and the protonation of residues on key LHC components, in particular the psbS subunit (reviewed in ref. 7). Arabidopsis mutants deficient in NPQ are light sensitive, confirming its role in photoprotection (e.g., refs. 8 and 9-12).In the most basic working model for NPQ function (e.g., figure 2 of reference 12), where the kinetic and thermodynamic properties of each step in the process are consistent, NPQ should be a continuous function of linear electron flow (LEF). On the other hand, it has become clear that the relationship between LEF and NPQ is strongly modulated in response to rapid changes in physiological state, and we provide a direct demonstration of this below. It has been suggested that such NPQ mod...