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Summary One of the major factors limiting biomass productivity in algae is the low thermodynamic efficiency of photosynthesis. The greatest thermodynamic inefficiencies in photosynthesis occur during the conversion of light into chemical energy. At full sunlight the light‐harvesting antenna captures photons at a rate nearly 10 times faster than the rate‐limiting step in photosynthetic electron transport. Excess captured energy is dissipated by non‐productive pathways including the production of reactive oxygen species. Substantial improvements in photosynthetic efficiency have been achieved by reducing the optical cross‐section of the light‐harvesting antenna by selectively reducing chlorophyll b levels and peripheral light‐harvesting complex subunits. Smaller light‐harvesting antenna, however, may not exhibit optimal photosynthetic performance in low or fluctuating light environments. We describe a translational control system to dynamically adjust light‐harvesting antenna sizes for enhanced photosynthetic performance. By expressing a chlorophyllide a oxygenase (CAO) gene having a 5′ mRNA extension encoding a Nab1 translational repressor binding site in a CAO knockout line it was possible to continuously alter chlorophyll b levels and correspondingly light‐harvesting antenna sizes by light‐activated Nab1 repression of CAO expression as a function of growth light intensity. Significantly, algae having light‐regulated antenna sizes had substantially higher photosynthetic rates and two‐fold greater biomass productivity than the parental wild‐type strains as well as near wild‐type ability to carry out state transitions and non‐photochemical quenching. These results have broad implications for enhanced algae and plant biomass productivity.

Target of rapamycin (TOR) kinase is a conserved regulator of cell growth whose activity is modulated in response to nutrients, energy and stress. Key proteins involved in the pathway are conserved in the model photosynthetic microalga Chlamydomonas reinhardtii, but the substrates of TOR kinase and downstream signaling network have not been elucidated. Our study provides a new resource for investigating the phosphorylation networks governed by the TOR kinase pathway in Chlamydomonas. We used quantitative phosphoproteomics to investigate the effects of inhibiting Chlamydomonas TOR kinase on dynamic protein phosphorylation. Wild-type and AZD-insensitive Chlamydomonas strains were treated with TOR-specific chemical inhibitors (rapamycin, AZD8055 and Torin1), after which differentially affected phosphosites were identified. Our quantitative phosphoproteomic dataset comprised 2547 unique phosphosites from 1432 different proteins. Inhibition of TOR kinase caused significant quantitative changes in phosphorylation at 258 phosphosites, from 219 unique phosphopeptides. Our results include Chlamydomonas homologs of TOR signaling-related proteins, including a site on RPS6 with a decrease in phosphorylation. Additionally, phosphosites on proteins involved in translation and carotenoid biosynthesis were identified. Follow-up experiments guided by these phosphoproteomic findings in lycopene beta/epsilon cyclase showed that carotenoid levels are affected by TORC1 inhibition and carotenoid production is under TOR control in algae.

One of the unique features of electron transfer processes in photosystem II (PSII) reaction centers (RC) is the exclusive transfer of electrons down only one of the two parallel cofactor branches. In contrast to the RC core polypeptides (psaA and psaB) of photosystem I (PSI), where electron transfer occurs down both parallel redox-active cofactor branches, there is greater protein-cofactor asymmetry between the PSII RC core polypeptides (D1 and D2). We have focused on the identification of protein-cofactor relationships that determine the branch along which primary charge separation occurs (P(680)(+)/pheophytin(-)(Pheo)). We have previously shown that mutagenesis of the strong hydrogen-bonding residue, D1-E130, to less polar residues (D1-E130Q,H,L) shifted the midpoint potential of the Pheo(D1)/Pheo(D1)(-) couple to more negative values, reducing the quantum yield of primary charge separation. We did not observe, however, electron transfer down the inactive branch in D1-E130 mutants. The protein residue corresponding to D1-E130 on the inactive branch is D2-Q129 which presumably has a reduced hydrogen-bonding interaction with Pheo(D2) relative to the D1-E130 residue with Pheo(D1). Analysis of the recent 2.9 Å cyanobacterial PSII crystal structure indicated, however, that the D2-Q129 residue was too distant from the Pheo(D2) headgroup to serve as a possible hydrogen bond donor and directly impact its midpoint potential as well as potentially determine the directionality of electron transfer. Our objective was to characterize the function of this highly conserved inactive branch residue by replacing it with a nonconservative leucine or a conservative histidine residue. Measurements of Chl fluorescence decay kinetics and thermoluminescence studies indicate that the mutagenesis of D2-Q129 decreases the redox gap between Q(A) and Q(B) due to a lowering of the redox potential of Q(B). The resulting increased yield of S(2)Q(B)(-) charge recombination in the D2-Q129 mutants leads to an increased susceptibility to photoinhibitory light presumably due to (3)P(680)-mediated oxidative damage. The results indicate that the D2-Q129 residue plays a critical role in stabilizing the charge-separated state in PSII and further documents the structural and functional asymmetry between the two cofactor branches in PSII.

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1• Target of Rapamycin (TOR) kinase is a conserved regulator of cell growth whose activity is 2 modulated in response to nutrients, energy and stress. Key proteins involved in the pathway 3 are conserved in the model photosynthetic microalga Chlamydomonas reinhardtii, but the 4 substrates of TOR kinase and downstream signaling network have not been elucidated. Our 5 study provides a new resource for investigating the phosphorylation networks governed by the 6 TOR kinase pathway in Chlamydomonas. 7• We used quantitative phosphoproteomics to investigate the effects of inhibiting 8 Chlamydomonas TOR kinase on dynamic protein phosphorylation. Wild-type and AZD-9 insensitive Chlamydomonas strains were treated with TOR-specific chemical inhibitors 10 (rapamycin, AZD8055 and Torin1), after which differentially affected phosphosites were 11 identified. 12 • Our quantitative phosphoproteomic dataset comprised 2,547 unique phosphosites from 1,432 13 different proteins. Inhibition of TOR kinase caused significant quantitative changes in 14 phosphorylation at 258 phosphosites, from 219 unique phosphopeptides. 15 • Our results include Chlamydomonas homologs of TOR signaling-related proteins, including a 16 site on RPS6 with a decrease in phosphorylation. Additionally, phosphosites on proteins 17 involved in translation and carotenoid biosynthesis were identified. Follow-up experiments 18guided by these phosphoproteomic findings in lycopene beta/epsilon cyclase showed that 19 carotenoid levels are affected by TORC1 inhibition and carotenoid production is under TOR 20 control in algae. 21