The light-harvesting complexes of plants have evolved the ability to switch between efficient light harvesting and quenching forms to optimize photosynthesis in response to the environment. Several distinct mechanisms, collectively termed "nonphotochemical quenching" (NPQ), provide flexibility in this response. Here we report the isolation and characterization of a mutant, suppressor of quenching 1 (soq1), that has high NPQ even in the absence of photosystem II subunit S (PsbS), a protein that is necessary for the rapidly reversible component of NPQ. The formation of NPQ in soq1 was light intensity-dependent, and it exhibited slow relaxation kinetics and other characteristics that distinguish it from known NPQ components. Treatment with chemical inhibitors or an uncoupler, as well as crosses to mutants known to affect other NPQ components, showed that the NPQ in soq1 does not require a transthylakoid pH gradient, zeaxanthin formation, or the phosphorylation of light-harvesting complexes, and it appears to be unrelated to the photosystem II damage-and-repair cycle. Measurements of pigments and chlorophyll fluorescence lifetimes indicated that the additional NPQ in soq1 is the result of a decrease in chlorophyll excited-state lifetime and not pigment bleaching. The SOQ1 gene was isolated by mapbased cloning, and it encodes a previously uncharacterized thylakoid membrane protein with thioredoxin-like and β-propeller domains located in the lumen and a haloacid-dehalogenase domain exposed to the chloroplast stroma. We propose that the role of SOQ1 is to prevent formation of a slowly reversible form of antenna quenching, thereby maintaining the efficiency of light harvesting. P hotoautotrophic organisms harvest energy from the sun, sustaining themselves and nearly all life on Earth. In many habitats, fluctuations between limiting and excess light conditions occur on a wide range of timescales, as predictable diurnal and seasonal changes are integrated with more random events such as cloud cover and shading. Plants form large light-harvesting antenna complexes with hundreds of pigment molecules that maximize their ability to harvest energy in low light conditions. As light intensities increase, the rate of photosynthesis becomes saturated, and the excess energy that is absorbed can form damaging reactive oxygen species (1, 2). Therefore, plants have evolved many mechanisms, collectively termed "nonphotochemical quenching" (NPQ), to harmlessly dissipate excess energy absorbed in high light (3,4).The different components of NPQ, termed "qE," "qZ," "qT," and "qI," are separated based on their induction and relaxation kinetics as well as by their dependence on known factors. Feedback de-excitation, or qE, is the fastest component, turning on and relaxing within minutes. When the rate of light absorption exceeds that which can be used by the plant, a high pH gradient builds up across the thylakoid membrane, activating qE, which dissipates the excess energy as heat. The low pH in the thylakoid lumen protonates the photosyste...

Energy-dependent quenching (qE) in photosystem II (PSII) is a pH-dependent response that enables plants to regulate light harvesting in response to rapid fluctuations in light intensity. In this review, we aim to provide a physical picture for understanding the interplay between the triggering of qE by a pH gradient across the thylakoid membrane and subsequent changes in PSII. We discuss how these changes alter the energy transfer network of chlorophyll in the grana membrane and allow it to switch between an unquenched and quenched state. Within this conceptual framework, we describe the biochemical and spectroscopic measurements and models that have been used to understand the mechanism of qE in plants with a focus on measurements of samples that perform qE in response to light. In addition, we address the outstanding questions and challenges in the field. One of the current challenges in gaining a full understanding of qE is the difficulty in simultaneously measuring both the photophysical mechanism of quenching and the physiological state of the thylakoid membrane. We suggest that new experimental and modeling efforts that can monitor the many processes that occur on multiple timescales and length scales will be important for elucidating the quantitative details of the mechanism of qE.

The photosystem II (PSII) protein PsbS and the enzyme violaxanthin deepoxidase (VDE) are known to influence the dynamics of energy-dependent quenching (qE), the component of nonphotochemical quenching (NPQ) that allows plants to respond to fast fluctuations in light intensity. Although the absence of PsbS and VDE has been shown to change the amount of quenching, there have not been any measurements that can detect whether the presence of these proteins alters the type of quenching that occurs. The chlorophyll fluorescence lifetime probes the excitedstate chlorophyll relaxation dynamics and can be used to determine the amount of quenching as well as whether two different genotypes with the same amount of NPQ have similar dynamics of excited-state chlorophyll relaxation. We measured the fluorescence lifetimes on whole leaves of Arabidopsis thaliana throughout the induction and relaxation of NPQ for wild type and the qE mutants, npq4, which lacks PsbS; npq1, which lacks VDE and cannot convert violaxanthin to zeaxanthin; and npq1 npq4, which lacks both VDE and PsbS. These measurements show that although PsbS changes the amount of quenching and the rate at which quenching turns on, it does not affect the relaxation dynamics of excited chlorophyll during quenching. In addition, the data suggest that PsbS responds not only to ΔpH but also to the Δψ across the thylakoid membrane. In contrast, the presence of VDE, which is necessary for the accumulation of zeaxanthin, affects the excited-state chlorophyll relaxation dynamics.PsbS | nonphotochemical quenching | fluorescence lifetime | carotenoids | photosystem II P lants regulate light harvesting by photosystem II (PSII) in response to changes in light intensity. One way that plants are able to regulate light harvesting is through turning on and off mechanisms that dissipate excess energy. This energy dissipation is assessed via nonphotochemical quenching (NPQ) measurements of chlorophyll fluorescence. Energy-dependent quenching (qE) is the NPQ process with the fastest kinetics. It turns on and off in seconds to minutes, allowing plants to respond to rapid fluctuations in light intensity, which is thought to reduce photodamage (1, 2).Illumination causes the formation of gradients of electrical potential (Δψ) and of proton concentration (ΔpH) across the thylakoid membrane. Although it has been suggested that Δψ may play a role in qE (3), only ΔpH is thought to trigger different proteins and enzymes to induce qE (4). The major known factors involved in induction of qE are the enzyme violaxanthin deepoxidase (VDE) (5) and the PSII protein PsbS (6). The mutant npq1, which lacks VDE and cannot convert violaxanthin to zeaxanthin, has a phenotype with lower qE compared with the wild type (7). Transient absorption measurements suggest that zeaxanthin may quench excited chlorophyll (8). The npq4 mutant, which lacks PsbS, shows no rapidly reversible quenching of chlorophyll fluorescence, suggesting that PsbS is required for qE in vivo (6). PsbS is pH sensitive (9) but is not though...

We describe a technique to measure the fluorescence decay profiles of intact leaves during adaptation to high light and subsequent relaxation to dark conditions. We show how to ensure that photosystem II reaction centers are closed and compare data for wild type Arabidopsis thaliana with conventional pulse-amplitude modulated (PAM) fluorescence measurements. Unlike PAM measurements, the lifetime measurements are not sensitive to photobleaching or chloroplast shielding, and the form of the fluorescence decay provides additional information to test quantitative models of excitation dynamics in intact leaves.

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Excess light can induce photodamage to the photosynthetic machinery, therefore plants have evolved photoprotective mechanisms such as non-photochemical quenching (NPQ). Different NPQ components have been identified and classified based on their relaxation kinetics and molecular players. The NPQ component qE is induced and relaxed rapidly (seconds to minutes), whereas the NPQ component qH is induced and relaxed slowly (hours or longer). Molecular players regulating qH have recently been uncovered, but the photophysical mechanism of qH and its location in the photosynthetic membrane have not been determined. Using time-correlated single-photon counting analysis of the Arabidopsis thaliana suppressor of quenching 1 mutant (soq1), which displays higher qH than the wild type, we observed shorter average lifetime of chlorophyll fluorescence in leaves and thylakoids relative to wild type. Comparison of isolated photosynthetic complexes from plants in which qH was turned ON or OFF revealed a chlorophyll fluorescence decrease specifically in the trimeric light-harvesting complex II (LHCII) fraction when qH was ON. LHCII trimers are composed of Lhcb1, 2 and 3 proteins, so CRISPR-Cas9 edited and T-DNA insertion lhcb1, lhcb2 and lhcb3 mutants were crossed with soq1. In soq1 lhcb1, soq1 lhcb2, and soq1 lhcb3, qH was not abolished, indicating that no single major Lhcb isoform is necessary for qH. Using transient absorption spectroscopy of isolated thylakoids, no spectral signatures for chlorophyll-carotenoid excitation energy quenching or charge transfer quenching were observed, suggesting that qH may occur through chlorophyll-chlorophyll excitonic interaction.

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