A number of useful photosynthetic parameters are commonly derived from saturation pulse-induced fluorescence analysis. We show, that qP, an estimate of the fraction of open centers, is based on a pure 'puddle' antenna model, where each Photosystem (PS) II center possesses its own independent antenna system. This parameter is incompatible with more realistic models of the photosynthetic unit, where reaction centers are connected by shared antenna, that is, the so-called 'lake' or 'connected units' models. We thus introduce a new parameter, qL, based on a Stern-Volmer approach using a lake model, which estimates the fraction of open PS II centers. We suggest that qL should be a useful parameter for terrestrial plants consistent with a high connectivity of PS II units, whereas some marine species with distinct antenna architecture, may require the use of more complex parameters based on intermediate models of the photosynthetic unit. Another useful parameter calculated from fluorescence analysis is ΦII, the yield of PS II. In contrast to qL, we show that the ΦII parameter can be derived from either a pure 'lake' or pure 'puddle' model, and is thus likely to be a robust parameter. The energy absorbed by PS II is divided between the fraction used in photochemistry, ΦII, and that lost non-photochemically. We introduce two additional parameters that can be used to estimate the flux of excitation energy into competing non-photochemical pathways, the yield induced by downregulatory processes, ΦNPQ, and the yield for other energy losses, ΦNO.

Comparing photosynthetic and photovoltaic efficiencies is not a simple issue. Although both processes harvest the energy in sunlight, they operate in distinctly different ways and produce different types of products: biomass or chemical fuels in the case of natural photosynthesis and nonstored electrical current in the case of photovoltaics. In order to find common ground for evaluating energy-conversion efficiency, we compare natural photosynthesis with present technologies for photovoltaic-driven electrolysis of water to produce hydrogen. Photovoltaic-driven electrolysis is the more efficient process when measured on an annual basis, yet short-term yields for photosynthetic conversion under optimal conditions come within a factor of 2 or 3 of the photovoltaic benchmark. We consider opportunities in which the frontiers of synthetic biology might be used to enhance natural photosynthesis for improved solar energy conversion efficiency.

The biochemical, biophysical, and physiological properties of the PsbS protein were studied in relation to mutations of two symmetry-related, lumen-exposed glutamate residues, Glu-122 and Glu-226. These two glutamates are targets for protonation during lumen acidification in excess light. Mutation of PsbS did not affect xanthophyll cycle pigment conversion or pool size. In conditions of excess light, photosynthetic light harvesting is regulated by a feedback de-excitation mechanism termed energy-dependent quenching (qE), 1 which increases thermal dissipation of excess absorbed light energy in photosystem II (PSII). The qE mechanism is triggered by conditions that limit photosynthetic carbon fixation and result in increased acidification of the chloroplast thylakoid lumen (1-4). The thermal dissipation of excess excitation energy is most commonly measured and referred to as nonphotochemical quenching (NPQ) of PSII chlorophyll (Chl) a fluorescence. Although there are several components of NPQ, in higher plants qE can account for the major part of NPQ and is characterized by its relatively fast induction and relaxation kinetics, on a physiological time scale of seconds to minutes. The decrease in the intensity of Chl fluorescence is the result of the decrease in the electronic excited state lifetime of Chl caused by an increased thermal dissipation rate constant (5). The rapid response of the qE process is chemically associated with changes in the trans-thylakoid membrane pH gradient (⌬pH). The ⌬pH change has at least two functions in qE. First, it activates the violaxanthin de-epoxidase that converts violaxanthin (V) to antheraxanthin (A) and zeaxanthin (Z) (6). A and/or Z are essential elements of qE (7-9). Second, the lower pH in the lumen results in protonation of PSII proteins, including the 22-kDa PSII subunit, PsbS, which plays a key role in qE (10). When both pH-induced changes occur together it is believed that Chls in PSII can transfer their excess energy to Z, which can return to the ground state via thermal decay (7,11,12). Plants containing PsbS mutations of both glutamatesThe pH-sensing mechanism of the PsbS protein is influenced by two pairs of symmetrically arranged glutamate residues, each located within or close to the two lumen-exposed loops of the protein (13). Dicyclohexylcarbodiimide (DCCD), a well known inhibitor of qE (14 -16) is a carboxylate-modifying agent (17) that binds to PsbS (18). Although it was suggested that the DCCD binding site is in the lumenal loops of PsbS, the exact binding site has not been determined. Importantly, site-directed mutagenesis experiments indicated that two of the PsbS glutamates, Glu-122 and Glu-226, are necessary for the function of PsbS (13).In this article we used single and double mutations of PsbS (E122Q/E226Q) to make a detailed biochemical and biophysical analysis of the role of these two glutamates in pH sensing and DCCD binding. We probed the role of the Glu-122 and Glu-226 residues by monitoring the changes in the PSII Chl a fluores-

The light-dependent production of ATP and reductants by the photosynthetic apparatus in vivo involves a series of electron and proton transfers. Consideration is given as to how electron fluxes through photosystem I (PSI), using absorption spectroscopy, and through photosystem II (PSII), using chlorophyll fluorescence analyses, can be estimated in vivo. Measurements of light-induced electrochromic shifts using absorption spectroscopy provide a means of analyzing the proton fluxes across the thylakoid membranes in vivo. Regulation of these electron and proton fluxes is required for the thylakoids to meet the fluctuating metabolic demands of the cell. Chloroplasts exhibit a wide and flexible range of mechanisms to regulate electron and proton fluxes that enable chloroplasts to match light use for ATP and reductant production with the prevailing metabolic requirements. Non-invasive probing of electron fluxes through PSI and PSII, and proton fluxes across the thylakoid membranes can provide insights into the operation of such regulatory processes in vivo.

Plants resist infection and herbivory with innate immune responses that are often associated with reduced growth. Despite the importance of growth-defense tradeoffs in shaping plant productivity in natural and agricultural ecosystems, the molecular mechanisms that link growth and immunity are poorly understood. Here, we demonstrate that growth-defense tradeoffs mediated by the hormone jasmonate are uncoupled in an Arabidopsis mutant (jazQ phyB) lacking a quintet of Jasmonate ZIM-domain transcriptional repressors and the photoreceptor phyB. Analysis of epistatic interactions between jazQ and phyB reveal that growth inhibition associated with enhanced anti-insect resistance is likely not caused by diversion of photoassimilates from growth to defense but rather by a conserved transcriptional network that is hardwired to attenuate growth upon activation of jasmonate signalling. The ability to unlock growth-defense tradeoffs through relief of transcription repression provides an approach to assemble functional plant traits in new and potentially useful ways.