Figure 1. Light reactions of photosynthesis and associated alternative electron transfer pathways.

Linear electron flow from water to NADP⁺ results in protons being pumped into the lumen of the thylakoid membrane, which is then used to drive the formation of ATP at the ATP synthase. Alternative electron transfer pathways, such as PGR5/PGRL1- and NDH-mediated cyclic electron flow or PTOX- and APX-mediated water-to-water cycles, confer dynamic protection and prevent the formation of reactive oxygen species (ROS). In addition, ion channels and transporters respond to light fluctuations to regulate the proton motive force (pmf). All these are potential targets to optimize photosynthetic efficiency. The dashed box indicates a possible non-native route involving Flv1/Flv3 transferred from cyanobacteria to higher plants. Components lacking a high resolution structure are indicated as boxes. Reactions are not balanced. Empty arrows indicate ion movement via channels. Abbreviations: APX, ascorbate peroxidase; Fd, ferredoxin; Flv, flavodiiron protein; FNR, ferredoxin:NADP⁺ reductase; KEA3, potassium efflux antiporter 3; LHC, light-harvesting chlorophyll-a/b-binding complex; NDH, NADH dehydrogenase-like complex; PC, plastocyanin; PQ, plastoquinone; PQH₂, plastoquinol; PGR5, proton gradient regulation 5; PGRL1, PGR5-like protein 1; PSI, Photosystem I; PSII, Photosystem II; PTOX, plastid terminal oxidase; SOD, superoxide dismutase; TPK3, two-pore potassium channel 3. The following protein structures were used: PSII-LHCII from Pisum sativum (PDB ID: 5XNL); cytochrome b₆f from Chlamydomonas reinhardtii (PDB ID: 1Q90); PC from Spinacia oleracea (PDB ID: 1YLB); Fd-FNR from Zea mays (PDB ID: 1GAQ); PSI-LHCI from Pisum sativum (PDB ID: 4XK8). The CF_oF₁-ATPase is a speculated model based on the yeast F_oF₁-ATP synthase (PDB ID: 4B2Q), the chloroplast F₁-ATPase from Spinacia oleracea (PDB ID: 1FX0) and the homo 14-mer c ring of the ATP synthase from Triticum aestivum (PDB ID: 4MJN).