@article{hao_simple_2023,
	title = {A {Simple} {Sonication} {Method} to {Isolate} the {Chloroplast} {Lumen} in {Arabidopsis} thaliana},
	volume = {13},
	url = {https://bio-protocol.org/en/bpdetail?id=4756&type=0},
	doi = {10.21769/BioProtoc.4756},
	abstract = {The chloroplast lumen contains at least 80 proteins whose function and regulation are not yet fully understood. Isolating the chloroplast lumen enables the characterization of the lumenal proteins. The lumen can be isolated in several ways through thylakoid disruption using a Yeda press or sonication, or through thylakoid solubilization using a detergent. Here, we present a simple procedure to isolate thylakoid lumen by sonication using leaves of the plant Arabidopsis thaliana. The step-by-step procedure is as follows: thylakoids are isolated from chloroplasts, loosely associated thylakoid surface proteins from the stroma are removed, and the lumen fraction is collected in the supernatant following sonication and centrifugation. Compared to other procedures, this method is easy to implement and saves time, plant material, and cost. Lumenal proteins are obtained in high quantity and purity; however, some stromal membrane–associated proteins are released to the lumen fraction, so this method could be further adapted if needed by decreasing sonication power and/or time.},
	language = {en},
	number = {15},
	urldate = {2023-08-21},
	journal = {Bio-protocol},
	author = {Hao, Jingfang and Malnoë, Alizée},
	month = aug,
	year = {2023},
	pages = {4756},
}

The chloroplast lumen contains at least 80 proteins whose function and regulation are not yet fully understood. Isolating the chloroplast lumen enables the characterization of the lumenal proteins. The lumen can be isolated in several ways through thylakoid disruption using a Yeda press or sonication, or through thylakoid solubilization using a detergent. Here, we present a simple procedure to isolate thylakoid lumen by sonication using leaves of the plant Arabidopsis thaliana. The step-by-step procedure is as follows: thylakoids are isolated from chloroplasts, loosely associated thylakoid surface proteins from the stroma are removed, and the lumen fraction is collected in the supernatant following sonication and centrifugation. Compared to other procedures, this method is easy to implement and saves time, plant material, and cost. Lumenal proteins are obtained in high quantity and purity; however, some stromal membrane–associated proteins are released to the lumen fraction, so this method could be further adapted if needed by decreasing sonication power and/or time.

@article{yu_structure_2022,
	title = {Structure of {Arabidopsis} {SOQ1} lumenal region unveils {C}-terminal domain essential for negative regulation of photoprotective {qH}},
	volume = {8},
	copyright = {2022 The Author(s), under exclusive licence to Springer Nature Limited},
	issn = {2055-0278},
	url = {https://www.nature.com/articles/s41477-022-01177-z},
	doi = {10.1038/s41477-022-01177-z},
	abstract = {Non-photochemical quenching (NPQ) plays an important role for phototrophs in decreasing photo-oxidative damage. qH is a sustained form of NPQ and depends on the plastid lipocalin (LCNP). A thylakoid membrane-anchored protein SUPPRESSOR OF QUENCHING1 (SOQ1) prevents qH formation by inhibiting LCNP. SOQ1 suppresses qH with its lumen-located thioredoxin (Trx)-like and NHL domains. Here we report structural data, genetic modification and biochemical characterization of Arabidopsis SOQ1 lumenal domains. Our results show that the Trx-like and NHL domains are associated together, with the cysteine motif located at their interface. Residue E859, required for SOQ1 function, is pivotal for maintaining the Trx–NHL association. Importantly, the C-terminal region of SOQ1 forms an independent β-stranded domain that has structural homology to the N-terminal domain of bacterial disulfide bond protein D and is essential for negative regulation of qH. Furthermore, SOQ1 is susceptible to cleavage at the loops connecting the neighbouring lumenal domains both in vitro and in vivo, which could be a regulatory process for its suppression function of qH.},
	language = {en},
	number = {7},
	urldate = {2022-07-22},
	journal = {Nature Plants},
	author = {Yu, Guimei and Hao, Jingfang and Pan, Xiaowei and Shi, Lifang and Zhang, Yong and Wang, Jifeng and Fan, Hongcheng and Xiao, Yang and Yang, Fuquan and Lou, Jizhong and Chang, Wenrui and Malnoë, Alizée and Li, Mei},
	month = jul,
	year = {2022},
	note = {Number: 7
Publisher: Nature Publishing Group},
	keywords = {Photosynthesis, Plant sciences},
	pages = {840--855},
}

Non-photochemical quenching (NPQ) plays an important role for phototrophs in decreasing photo-oxidative damage. qH is a sustained form of NPQ and depends on the plastid lipocalin (LCNP). A thylakoid membrane-anchored protein SUPPRESSOR OF QUENCHING1 (SOQ1) prevents qH formation by inhibiting LCNP. SOQ1 suppresses qH with its lumen-located thioredoxin (Trx)-like and NHL domains. Here we report structural data, genetic modification and biochemical characterization of Arabidopsis SOQ1 lumenal domains. Our results show that the Trx-like and NHL domains are associated together, with the cysteine motif located at their interface. Residue E859, required for SOQ1 function, is pivotal for maintaining the Trx–NHL association. Importantly, the C-terminal region of SOQ1 forms an independent β-stranded domain that has structural homology to the N-terminal domain of bacterial disulfide bond protein D and is essential for negative regulation of qH. Furthermore, SOQ1 is susceptible to cleavage at the loops connecting the neighbouring lumenal domains both in vitro and in vivo, which could be a regulatory process for its suppression function of qH.

@article{bru_major_2022,
	title = {The major trimeric antenna complexes serve as a site for {qH}-energy dissipation in plants},
	volume = {298},
	issn = {0021-9258},
	url = {https://www.sciencedirect.com/science/article/pii/S0021925822009620},
	doi = {10.1016/j.jbc.2022.102519},
	abstract = {Plants and algae are faced with a conundrum: harvesting sufficient light to drive their metabolic needs while dissipating light in excess to prevent photodamage, a process known as nonphotochemical quenching. A slowly relaxing form of energy dissipation, termed qH, is critical for plants’ survival under abiotic stress; however, qH location in the photosynthetic membrane is unresolved. Here, we tested whether we could isolate subcomplexes from plants in which qH was induced that would remain in an energy-dissipative state. Interestingly, we found that chlorophyll (Chl) fluorescence lifetimes were decreased by qH in isolated major trimeric antenna complexes, indicating that they serve as a site for qH-energy dissipation and providing a natively quenched complex with physiological relevance to natural conditions. Next, we monitored the changes in thylakoid pigment, protein, and lipid contents of antenna with active or inactive qH but did not detect any evident differences. Finally, we investigated whether specific subunits of the major antenna complexes were required for qH but found that qH was insensitive to trimer composition. Because we previously observed that qH can occur in the absence of specific xanthophylls, and no evident changes in pigments, proteins, or lipids were detected, we tentatively propose that the energy-dissipative state reported here may stem from Chl–Chl excitonic interaction.},
	language = {en},
	number = {11},
	urldate = {2022-12-02},
	journal = {Journal of Biological Chemistry},
	author = {Bru, Pierrick and Steen, Collin J. and Park, Soomin and Amstutz, Cynthia L. and Sylak-Glassman, Emily J. and Lam, Lam and Fekete, Agnes and Mueller, Martin J. and Longoni, Fiamma and Fleming, Graham R. and Niyogi, Krishna K. and Malnoë, Alizée},
	month = nov,
	year = {2022},
	keywords = {CRISPR/Cas9, CRISPR–Cas9, abiotic stress, energy dissipation, light-harvesting complexes, non-photochemical quenching qH, nonphotochemical quenching qH, photosynthesis, time-resolved fluorescence},
	pages = {102519},
}

Plants and algae are faced with a conundrum: harvesting sufficient light to drive their metabolic needs while dissipating light in excess to prevent photodamage, a process known as nonphotochemical quenching. A slowly relaxing form of energy dissipation, termed qH, is critical for plants’ survival under abiotic stress; however, qH location in the photosynthetic membrane is unresolved. Here, we tested whether we could isolate subcomplexes from plants in which qH was induced that would remain in an energy-dissipative state. Interestingly, we found that chlorophyll (Chl) fluorescence lifetimes were decreased by qH in isolated major trimeric antenna complexes, indicating that they serve as a site for qH-energy dissipation and providing a natively quenched complex with physiological relevance to natural conditions. Next, we monitored the changes in thylakoid pigment, protein, and lipid contents of antenna with active or inactive qH but did not detect any evident differences. Finally, we investigated whether specific subunits of the major antenna complexes were required for qH but found that qH was insensitive to trimer composition. Because we previously observed that qH can occur in the absence of specific xanthophylls, and no evident changes in pigments, proteins, or lipids were detected, we tentatively propose that the energy-dissipative state reported here may stem from Chl–Chl excitonic interaction.

@article{bru_genetic_2020,
	title = {A {Genetic} {Screen} to {Identify} {New} {Molecular} {Players} {Involved} in {Photoprotection} {qH} in {Arabidopsis} thaliana},
	volume = {9},
	issn = {2223-7747},
	url = {https://www.mdpi.com/2223-7747/9/11/1565},
	doi = {10.3390/plants9111565},
	abstract = {Photosynthesis is a biological process which converts light energy into chemical energy that is used in the Calvin–Benson cycle to produce organic compounds. An excess of light can induce damage to the photosynthetic machinery. Therefore, plants have evolved photoprotective mechanisms such as non-photochemical quenching (NPQ). To focus molecular insights on slowly relaxing NPQ processes in Arabidopsis thaliana, previously, a qE-deficient line—the PsbS mutant—was mutagenized and a mutant with high and slowly relaxing NPQ was isolated. The mutated gene was named suppressor of quenching 1, or SOQ1, to describe its function. Indeed, when present, SOQ1 negatively regulates or suppresses a form of antenna NPQ that is slow to relax and is photoprotective. We have now termed this component qH and identified the plastid lipocalin, LCNP, as the effector for this energy dissipation mode to occur. Recently, we found that the relaxation of qH1, ROQH1, protein is required to turn off qH. The aim of this study is to identify new molecular players involved in photoprotection qH by a whole genome sequencing approach of chemically mutagenized Arabidopsis thaliana. We conducted an EMS-mutagenesis on the soq1 npq4 double mutant and used chlorophyll fluorescence imaging to screen for suppressors and enhancers of qH. Out of 22,000 mutagenized plants screened, the molecular players cited above were found using a mapping-by-sequencing approach. Here, we describe the phenotypic characterization of the other mutants isolated from this genetic screen and an additional 8000 plants screened. We have classified them in several classes based on their fluorescence parameters, NPQ kinetics, and pigment content. A high-throughput whole genome sequencing approach on 65 mutants will identify the causal mutations thanks to allelic mutations from having reached saturation of the genetic screen. The candidate genes could be involved in the formation or maintenance of quenching sites for qH, in the regulation of qH at the transcriptional level, or be part of the quenching site itself.},
	language = {en},
	number = {11},
	urldate = {2021-06-07},
	journal = {Plants},
	author = {Bru, Pierrick and Nanda, Sanchali and Malnoë, Alizée},
	month = nov,
	year = {2020},
	pages = {1565},
}

Photosynthesis is a biological process which converts light energy into chemical energy that is used in the Calvin–Benson cycle to produce organic compounds. An excess of light can induce damage to the photosynthetic machinery. Therefore, plants have evolved photoprotective mechanisms such as non-photochemical quenching (NPQ). To focus molecular insights on slowly relaxing NPQ processes in Arabidopsis thaliana, previously, a qE-deficient line—the PsbS mutant—was mutagenized and a mutant with high and slowly relaxing NPQ was isolated. The mutated gene was named suppressor of quenching 1, or SOQ1, to describe its function. Indeed, when present, SOQ1 negatively regulates or suppresses a form of antenna NPQ that is slow to relax and is photoprotective. We have now termed this component qH and identified the plastid lipocalin, LCNP, as the effector for this energy dissipation mode to occur. Recently, we found that the relaxation of qH1, ROQH1, protein is required to turn off qH. The aim of this study is to identify new molecular players involved in photoprotection qH by a whole genome sequencing approach of chemically mutagenized Arabidopsis thaliana. We conducted an EMS-mutagenesis on the soq1 npq4 double mutant and used chlorophyll fluorescence imaging to screen for suppressors and enhancers of qH. Out of 22,000 mutagenized plants screened, the molecular players cited above were found using a mapping-by-sequencing approach. Here, we describe the phenotypic characterization of the other mutants isolated from this genetic screen and an additional 8000 plants screened. We have classified them in several classes based on their fluorescence parameters, NPQ kinetics, and pigment content. A high-throughput whole genome sequencing approach on 65 mutants will identify the causal mutations thanks to allelic mutations from having reached saturation of the genetic screen. The candidate genes could be involved in the formation or maintenance of quenching sites for qH, in the regulation of qH at the transcriptional level, or be part of the quenching site itself.

@article{amstutz_atypical_2020,
	title = {An atypical short-chain dehydrogenase–reductase functions in the relaxation of photoprotective {qH} in {Arabidopsis}},
	volume = {6},
	issn = {2055-0278},
	url = {http://www.nature.com/articles/s41477-020-0591-9},
	doi = {10.1038/s41477-020-0591-9},
	abstract = {Photosynthetic organisms experience wide fluctuations in light intensity and regulate light harvesting accordingly to prevent damage from excess energy. The antenna quenching component qH is a sustained form of energy dissipation that protects the photosynthetic apparatus under stress conditions. This photoprotective mechanism requires the plastid lipocalin LCNP and is prevented by SUPPRESSOR OF QUENCHING1 (SOQ1) under non-stress conditions. However, the molecular mechanism of qH relaxation has yet to be resolved. Here, we isolated and characterized RELAXATION OF QH1 (ROQH1), an atypical short-chain dehydrogenase–reductase that functions as a qH-relaxation factor in Arabidopsis. The ROQH1 gene belongs to the GreenCut2 inventory specific to photosynthetic organisms, and the ROQH1 protein localizes to the chloroplast stroma lamellae membrane. After a cold and high-light treatment, qH does not relax in roqh1 mutants and qH does not occur in leaves overexpressing ROQH1. When the soq1 and roqh1 mutations are combined, qH can neither be prevented nor relaxed and soq1 roqh1 displays constitutive qH and light-limited growth. We propose that LCNP and ROQH1 perform dosage-dependent, antagonistic functions to protect the photosynthetic apparatus and maintain light-harvesting efficiency in plants.},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Nature Plants},
	author = {Amstutz, Cynthia L. and Fristedt, Rikard and Schultink, Alex and Merchant, Sabeeha S. and Niyogi, Krishna K. and Malnoë, Alizée},
	month = feb,
	year = {2020},
	pages = {154--166},
}

Photosynthetic organisms experience wide fluctuations in light intensity and regulate light harvesting accordingly to prevent damage from excess energy. The antenna quenching component qH is a sustained form of energy dissipation that protects the photosynthetic apparatus under stress conditions. This photoprotective mechanism requires the plastid lipocalin LCNP and is prevented by SUPPRESSOR OF QUENCHING1 (SOQ1) under non-stress conditions. However, the molecular mechanism of qH relaxation has yet to be resolved. Here, we isolated and characterized RELAXATION OF QH1 (ROQH1), an atypical short-chain dehydrogenase–reductase that functions as a qH-relaxation factor in Arabidopsis. The ROQH1 gene belongs to the GreenCut2 inventory specific to photosynthetic organisms, and the ROQH1 protein localizes to the chloroplast stroma lamellae membrane. After a cold and high-light treatment, qH does not relax in roqh1 mutants and qH does not occur in leaves overexpressing ROQH1. When the soq1 and roqh1 mutations are combined, qH can neither be prevented nor relaxed and soq1 roqh1 displays constitutive qH and light-limited growth. We propose that LCNP and ROQH1 perform dosage-dependent, antagonistic functions to protect the photosynthetic apparatus and maintain light-harvesting efficiency in plants.

@article{malnoe_photoinhibition_2018,
	title = {Photoinhibition or photoprotection of photosynthesis? {Update} on the (newly termed) sustained quenching component {qH}},
	volume = {154},
	issn = {00988472},
	shorttitle = {Photoinhibition or photoprotection of photosynthesis?},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0098847218301862},
	doi = {10.1016/j.envexpbot.2018.05.005},
	abstract = {Non-photochemical quenching (NPQ) of chlorophyll fluorescence is a valuable feature for the study of photosynthetic organisms’ light utilization and dissipation. However, all too often NPQ is simply equated with the harmless dissipation of excess absorbed light energy as heat. This is not always the case as some processes cause NPQ without thermal dissipation. Photoinhibitory quenching, qI, is sustained NPQ that continuously depresses the commonly used fluorescence parameter “quantum yield of photosystem II (PSII)”, or Fv/Fm, and is often viewed as a result of PSII core inactivation due to D1 damage. Inactivated PSII cores might have a photoprotective role but that is not the topic of the present review. Instead, this review focuses on a sustained photoprotective antenna quenching component, which we have termed qH, and summarizes the recently uncovered molecular players of this sustained form of NPQ.},
	language = {en},
	urldate = {2021-06-07},
	journal = {Environmental and Experimental Botany},
	author = {Malnoë, Alizée},
	month = oct,
	year = {2018},
	pages = {123--133},
}

Non-photochemical quenching (NPQ) of chlorophyll fluorescence is a valuable feature for the study of photosynthetic organisms’ light utilization and dissipation. However, all too often NPQ is simply equated with the harmless dissipation of excess absorbed light energy as heat. This is not always the case as some processes cause NPQ without thermal dissipation. Photoinhibitory quenching, qI, is sustained NPQ that continuously depresses the commonly used fluorescence parameter “quantum yield of photosystem II (PSII)”, or Fv/Fm, and is often viewed as a result of PSII core inactivation due to D1 damage. Inactivated PSII cores might have a photoprotective role but that is not the topic of the present review. Instead, this review focuses on a sustained photoprotective antenna quenching component, which we have termed qH, and summarizes the recently uncovered molecular players of this sustained form of NPQ.

@article{malnoe_plastid_2018,
	title = {The {Plastid} {Lipocalin} {LCNP} {Is} {Required} for {Sustained} {Photoprotective} {Energy} {Dissipation} in {Arabidopsis}},
	volume = {30},
	issn = {1040-4651, 1532-298X},
	url = {https://academic.oup.com/plcell/article/30/1/196-208/6100355},
	doi = {10/gc3tvv},
	abstract = {Light utilization is finely tuned in photosynthetic organisms to prevent cellular damage. The dissipation of excess absorbed light energy, a process termed nonphotochemical quenching (NPQ), plays an important role in photoprotection. Little is known about the sustained or slowly reversible form(s) of NPQ and whether they are photoprotective, in part due to the lack of mutants. The Arabidopsis thaliana suppressor of quenching1 (soq1) mutant exhibits enhanced sustained NPQ, which we term qH. To identify molecular players involved in qH, we screened for suppressors of soq1 and isolated mutants affecting either chlorophyllide a oxygenase or the chloroplastic lipocalin, now renamed plastid lipocalin (LCNP). Analysis of the mutants confirmed that qH is localized to the peripheral antenna (LHCII) of photosystem II and demonstrated that LCNP is required for qH, either directly (by forming NPQ sites) or indirectly (by modifying the LHCII membrane environment). qH operates under stress conditions such as cold and high light and is photoprotective, as it reduces lipid peroxidation levels. We propose that, under stress conditions, LCNP protects the thylakoid membrane by enabling sustained NPQ in LHCII, thereby preventing singlet oxygen stress.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {The Plant Cell},
	author = {Malnoë, Alizée and Schultink, Alex and Shahrasbi, Sanya and Rumeau, Dominique and Havaux, Michel and Niyogi, Krishna K.},
	month = jan,
	year = {2018},
	pages = {196--208},
}

Light utilization is finely tuned in photosynthetic organisms to prevent cellular damage. The dissipation of excess absorbed light energy, a process termed nonphotochemical quenching (NPQ), plays an important role in photoprotection. Little is known about the sustained or slowly reversible form(s) of NPQ and whether they are photoprotective, in part due to the lack of mutants. The Arabidopsis thaliana suppressor of quenching1 (soq1) mutant exhibits enhanced sustained NPQ, which we term qH. To identify molecular players involved in qH, we screened for suppressors of soq1 and isolated mutants affecting either chlorophyllide a oxygenase or the chloroplastic lipocalin, now renamed plastid lipocalin (LCNP). Analysis of the mutants confirmed that qH is localized to the peripheral antenna (LHCII) of photosystem II and demonstrated that LCNP is required for qH, either directly (by forming NPQ sites) or indirectly (by modifying the LHCII membrane environment). qH operates under stress conditions such as cold and high light and is photoprotective, as it reduces lipid peroxidation levels. We propose that, under stress conditions, LCNP protects the thylakoid membrane by enabling sustained NPQ in LHCII, thereby preventing singlet oxygen stress.

@article{wang_high_2017,
	title = {The {High} {Light} {Response} and {Redox} {Control} of {Thylakoid} {FtsH} {Protease} in {Chlamydomonas} reinhardtii},
	volume = {10},
	issn = {16742052},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1674205216302210},
	doi = {10.1016/j.molp.2016.09.012},
	abstract = {In Chlamydomonas reinhardtii, the major protease involved in the maintenance of photosynthetic machinery in thylakoid membranes, the FtsH protease, mostly forms large hetero-oligomers (∼1 MDa) comprising FtsH1 and FtsH2 subunits, whatever the light intensity for growth. Upon high light exposure, the FtsH subunits display a shorter half-life, which is counterbalanced by an increase in FTSH1/2 mRNA levels, resulting in the modest upregulation of FtsH1/2 proteins. Furthermore, we found that high light increases the protease activity through a hitherto unnoticed redox-controlled reduction of intermolecular disulfide bridges. We isolated a Chlamydomonas FTSH1 promoter-deficient mutant, ftsh1-3, resulting from the insertion of a TOC1 transposon, in which the high light-induced upregulation of FTSH1 gene expression is largely lost. In ftsh1-3, the abundance of FtsH1 and FtsH2 proteins are loosely coupled (decreased by 70\% and 30\%, respectively) with no formation of large and stable homo-oligomers. Using strains exhibiting different accumulation levels of the FtsH1 subunit after complementation of ftsh1-3, we demonstrate that high light tolerance is tightly correlated with the abundance of the FtsH protease. Thus, the response of Chlamydomonas to light stress involves higher levels of FtsH1/2 subunits associated into large complexes with increased proteolytic activity.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Molecular Plant},
	author = {Wang, Fei and Qi, Yafei and Malnoë, Alizée and Choquet, Yves and Wollman, Francis-André and de Vitry, Catherine},
	month = jan,
	year = {2017},
	pages = {99--114},
}

In Chlamydomonas reinhardtii, the major protease involved in the maintenance of photosynthetic machinery in thylakoid membranes, the FtsH protease, mostly forms large hetero-oligomers (∼1 MDa) comprising FtsH1 and FtsH2 subunits, whatever the light intensity for growth. Upon high light exposure, the FtsH subunits display a shorter half-life, which is counterbalanced by an increase in FTSH1/2 mRNA levels, resulting in the modest upregulation of FtsH1/2 proteins. Furthermore, we found that high light increases the protease activity through a hitherto unnoticed redox-controlled reduction of intermolecular disulfide bridges. We isolated a Chlamydomonas FTSH1 promoter-deficient mutant, ftsh1-3, resulting from the insertion of a TOC1 transposon, in which the high light-induced upregulation of FTSH1 gene expression is largely lost. In ftsh1-3, the abundance of FtsH1 and FtsH2 proteins are loosely coupled (decreased by 70% and 30%, respectively) with no formation of large and stable homo-oligomers. Using strains exhibiting different accumulation levels of the FtsH1 subunit after complementation of ftsh1-3, we demonstrate that high light tolerance is tightly correlated with the abundance of the FtsH protease. Thus, the response of Chlamydomonas to light stress involves higher levels of FtsH1/2 subunits associated into large complexes with increased proteolytic activity.

@article{rappaport_gordon_2015,
	title = {Gordon research conference on photosynthesis: from evolution of fundamental mechanisms to radical re-engineering},
	volume = {123},
	issn = {1573-5079 (Electronic) 0166-8595 (Linking)},
	shorttitle = {Gordon research conference on photosynthesis},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25425217},
	doi = {10/gj6zms},
	abstract = {We provide here a News Report on the 2014 Gordon Research Conference on Photosynthesis, with the subtitle "From Evolution of Fundamental Mechanisms to Radical Re-Engineering." It was held at Mount Snow Resort, West Dover, Vermont, during August 10-15, 2014. After the formal sessions ended, four young scientists (Ute Ambruster of USA; Han Bao of USA; Nicoletta Liguori of the Netherlands; and Anat Shperberg-Avni of Israel) were recognized for their research; they each received a book from one of us (G) in memory of Colin A. Wraight (1945-2014), a brilliant and admired scientist who had been very active in the bioenergetics field in general and in past Gordon Conferences in particular, having chaired the 1988 Gordon Conference on Photosynthesis. (See an article on Wraight by one of us (Govindjee) at http://www.life.illinois.edu/plantbio/Features/ColinWraight/ColinWraight.html .).},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Photosynth Res},
	author = {Rappaport, F. and Malnoe, A. and {Govindjee}},
	month = feb,
	year = {2015},
	note = {Edition: 2014/11/27},
	keywords = {*Biological Evolution, *Photosynthesis, Congresses as Topic, Vermont},
	pages = {213--23},
}

We provide here a News Report on the 2014 Gordon Research Conference on Photosynthesis, with the subtitle "From Evolution of Fundamental Mechanisms to Radical Re-Engineering." It was held at Mount Snow Resort, West Dover, Vermont, during August 10-15, 2014. After the formal sessions ended, four young scientists (Ute Ambruster of USA; Han Bao of USA; Nicoletta Liguori of the Netherlands; and Anat Shperberg-Avni of Israel) were recognized for their research; they each received a book from one of us (G) in memory of Colin A. Wraight (1945-2014), a brilliant and admired scientist who had been very active in the bioenergetics field in general and in past Gordon Conferences in particular, having chaired the 1988 Gordon Conference on Photosynthesis. (See an article on Wraight by one of us (Govindjee) at http://www.life.illinois.edu/plantbio/Features/ColinWraight/ColinWraight.html .).

@article{dent_large-scale_2015,
	title = {Large-scale insertional mutagenesis of {Chlamydomonas} supports phylogenomic functional prediction of photosynthetic genes and analysis of classical acetate-requiring mutants},
	volume = {82},
	issn = {1365-313X (Electronic) 0960-7412 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25711437},
	doi = {10/f67nvt},
	abstract = {Chlamydomonas reinhardtii is a unicellular green alga that is a key model organism in the study of photosynthesis and oxidative stress. Here we describe the large-scale generation of a population of insertional mutants that have been screened for phenotypes related to photosynthesis and the isolation of 459 flanking sequence tags from 439 mutants. Recent phylogenomic analysis has identified a core set of genes, named GreenCut2, that are conserved in green algae and plants. Many of these genes are likely to be central to the process of photosynthesis, and they are over-represented by sixfold among the screened insertional mutants, with insertion events isolated in or adjacent to 68 of 597 GreenCut2 genes. This enrichment thus provides experimental support for functional assignments based on previous bioinformatic analysis. To illustrate one of the uses of the population, a candidate gene approach based on genome position of the flanking sequence of the insertional mutant CAL027\_01\_20 was used to identify the molecular basis of the classical C. reinhardtii mutation ac17. These mutations were shown to affect the gene PDH2, which encodes a subunit of the plastid pyruvate dehydrogenase complex. The mutants and associated flanking sequence data described here are publicly available to the research community, and they represent one of the largest phenotyped collections of algal insertional mutants to date.},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Plant J},
	author = {Dent, R. M. and Sharifi, M. N. and Malnoe, A. and Haglund, C. and Calderon, R. H. and Wakao, S. and Niyogi, K. K.},
	month = apr,
	year = {2015},
	note = {Edition: 2015/02/26},
	keywords = {Acetates/metabolism, Chlamydomonas reinhardtii, Chlamydomonas reinhardtii/*genetics/*metabolism, GreenCut, Mutagenesis, Insertional, Mutation, Pdh2, Photosynthesis/*genetics, Plant Proteins/genetics/*metabolism, genomics, insertion mutant, oxidative stress, photosynthesis},
	pages = {337--51},
}

Chlamydomonas reinhardtii is a unicellular green alga that is a key model organism in the study of photosynthesis and oxidative stress. Here we describe the large-scale generation of a population of insertional mutants that have been screened for phenotypes related to photosynthesis and the isolation of 459 flanking sequence tags from 439 mutants. Recent phylogenomic analysis has identified a core set of genes, named GreenCut2, that are conserved in green algae and plants. Many of these genes are likely to be central to the process of photosynthesis, and they are over-represented by sixfold among the screened insertional mutants, with insertion events isolated in or adjacent to 68 of 597 GreenCut2 genes. This enrichment thus provides experimental support for functional assignments based on previous bioinformatic analysis. To illustrate one of the uses of the population, a candidate gene approach based on genome position of the flanking sequence of the insertional mutant CAL027_01_20 was used to identify the molecular basis of the classical C. reinhardtii mutation ac17. These mutations were shown to affect the gene PDH2, which encodes a subunit of the plastid pyruvate dehydrogenase complex. The mutants and associated flanking sequence data described here are publicly available to the research community, and they represent one of the largest phenotyped collections of algal insertional mutants to date.

@article{sylak-glassman_distinct_2014,
	title = {Distinct roles of the photosystem {II} protein {PsbS} and zeaxanthin in the regulation of light harvesting in plants revealed by fluorescence lifetime snapshots},
	volume = {111},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1418317111},
	doi = {10/f6sjhj},
	abstract = {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 excited-state 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.},
	language = {en},
	number = {49},
	urldate = {2021-06-08},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Sylak-Glassman, Emily J. and Malnoë, Alizée and De Re, Eleonora and Brooks, Matthew D. and Fischer, Alexandra Lee and Niyogi, Krishna K. and Fleming, Graham R.},
	month = dec,
	year = {2014},
	pages = {17498--17503},
}

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 excited-state 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.

@article{wei_nitric_2014,
	title = {Nitric {Oxide}–{Triggered} {Remodeling} of {Chloroplast} {Bioenergetics} and {Thylakoid} {Proteins} upon {Nitrogen} {Starvation} in \textit{{Chlamydomonas} reinhardtii}},
	volume = {26},
	issn = {1532-298X, 1040-4651},
	url = {https://academic.oup.com/plcell/article/26/1/353/6102308},
	doi = {10/gj6zmv},
	abstract = {Abstract
            Starving microalgae for nitrogen sources is commonly used as a biotechnological tool to boost storage of reduced carbon into starch granules or lipid droplets, but the accompanying changes in bioenergetics have been little studied so far. Here, we report that the selective depletion of Rubisco and cytochrome b  6  f complex that occurs when Chlamydomonas reinhardtii is starved for nitrogen in the presence of acetate and under normoxic conditions is accompanied by a marked increase in chlororespiratory enzymes, which converts the photosynthetic thylakoid membrane into an intracellular matrix for oxidative catabolism of reductants. Cytochrome b  6  f subunits and most proteins specifically involved in their biogenesis are selectively degraded, mainly by the FtsH and Clp chloroplast proteases. This regulated degradation pathway does not require light, active photosynthesis, or state transitions but is prevented when respiration is impaired or under phototrophic conditions. We provide genetic and pharmacological evidence that NO production from intracellular nitrite governs this degradation pathway: Addition of a NO scavenger and of two distinct NO producers decrease and increase, respectively, the rate of cytochrome b  6  f degradation; NO-sensitive fluorescence probes, visualized by confocal microscopy, demonstrate that nitrogen-starved cells produce NO only when the cytochrome b  6  f degradation pathway is activated.},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Wei, Lili and Derrien, Benoit and Gautier, Arnaud and Houille-Vernes, Laura and Boulouis, Alix and Saint-Marcoux, Denis and Malnoë, Alizée and Rappaport, Fabrice and de Vitry, Catherine and Vallon, Olivier and Choquet, Yves and Wollman, Francis-André},
	month = feb,
	year = {2014},
	pages = {353--372},
}

Abstract Starving microalgae for nitrogen sources is commonly used as a biotechnological tool to boost storage of reduced carbon into starch granules or lipid droplets, but the accompanying changes in bioenergetics have been little studied so far. Here, we report that the selective depletion of Rubisco and cytochrome b  6  f complex that occurs when Chlamydomonas reinhardtii is starved for nitrogen in the presence of acetate and under normoxic conditions is accompanied by a marked increase in chlororespiratory enzymes, which converts the photosynthetic thylakoid membrane into an intracellular matrix for oxidative catabolism of reductants. Cytochrome b  6  f subunits and most proteins specifically involved in their biogenesis are selectively degraded, mainly by the FtsH and Clp chloroplast proteases. This regulated degradation pathway does not require light, active photosynthesis, or state transitions but is prevented when respiration is impaired or under phototrophic conditions. We provide genetic and pharmacological evidence that NO production from intracellular nitrite governs this degradation pathway: Addition of a NO scavenger and of two distinct NO producers decrease and increase, respectively, the rate of cytochrome b  6  f degradation; NO-sensitive fluorescence probes, visualized by confocal microscopy, demonstrate that nitrogen-starved cells produce NO only when the cytochrome b  6  f degradation pathway is activated.

@article{malnoe_thylakoid_2014,
	title = {Thylakoid {FtsH} {Protease} {Contributes} to {Photosystem} {II} and {Cytochrome} \textit{b} 6 \textit{f} {Remodeling} in \textit{{Chlamydomonas} reinhardtii} under {Stress} {Conditions}},
	volume = {26},
	issn = {1532-298X, 1040-4651},
	url = {https://academic.oup.com/plcell/article/26/1/373/6102321},
	doi = {10/f5vk82},
	abstract = {Abstract
            FtsH is the major thylakoid membrane protease found in organisms performing oxygenic photosynthesis. Here, we show that FtsH from Chlamydomonas reinhardtii forms heterooligomers comprising two subunits, FtsH1 and FtsH2. We characterized this protease using FtsH mutants that we identified through a genetic suppressor approach that restored phototrophic growth of mutants originally defective for cytochrome b  6  f accumulation. We thus extended the spectrum of FtsH substrates in the thylakoid membranes beyond photosystem II, showing the susceptibility of cytochrome b  6  f complexes (and proteins involved in the c  i heme binding pathway to cytochrome b  6) to FtsH. We then show how FtsH is involved in the response of C. reinhardtii to macronutrient stress. Upon phosphorus starvation, photosynthesis inactivation results from an FtsH-sensitive photoinhibition process. In contrast, we identified an FtsH-dependent loss of photosystem II and cytochrome b  6  f complexes in darkness upon sulfur deprivation. The D1 fragmentation pattern observed in the latter condition was similar to that observed in photoinhibitory conditions, which points to a similar degradation pathway in these two widely different environmental conditions. Our experiments thus provide extensive evidence that FtsH plays a major role in the quality control of thylakoid membrane proteins and in the response of C. reinhardtii to light and macronutrient stress.},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Malnoë, Alizée and Wang, Fei and Girard-Bascou, Jacqueline and Wollman, Francis-André and de Vitry, Catherine},
	month = feb,
	year = {2014},
	pages = {373--390},
}

Abstract FtsH is the major thylakoid membrane protease found in organisms performing oxygenic photosynthesis. Here, we show that FtsH from Chlamydomonas reinhardtii forms heterooligomers comprising two subunits, FtsH1 and FtsH2. We characterized this protease using FtsH mutants that we identified through a genetic suppressor approach that restored phototrophic growth of mutants originally defective for cytochrome b  6  f accumulation. We thus extended the spectrum of FtsH substrates in the thylakoid membranes beyond photosystem II, showing the susceptibility of cytochrome b  6  f complexes (and proteins involved in the c  i heme binding pathway to cytochrome b  6) to FtsH. We then show how FtsH is involved in the response of C. reinhardtii to macronutrient stress. Upon phosphorus starvation, photosynthesis inactivation results from an FtsH-sensitive photoinhibition process. In contrast, we identified an FtsH-dependent loss of photosystem II and cytochrome b  6  f complexes in darkness upon sulfur deprivation. The D1 fragmentation pattern observed in the latter condition was similar to that observed in photoinhibitory conditions, which points to a similar degradation pathway in these two widely different environmental conditions. Our experiments thus provide extensive evidence that FtsH plays a major role in the quality control of thylakoid membrane proteins and in the response of C. reinhardtii to light and macronutrient stress.

@article{calderon_conserved_2013,
	title = {A {Conserved} {Rubredoxin} {Is} {Necessary} for {Photosystem} {II} {Accumulation} in {Diverse} {Oxygenic} {Photoautotrophs}},
	volume = {288},
	issn = {00219258},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0021925820490738},
	doi = {10/f5qnnj},
	abstract = {In oxygenic photosynthesis, two photosystems work in tandem to harvest light energy and generate NADPH and ATP. Photosystem II (PSII), the protein-pigment complex that uses light energy to catalyze the splitting of water, is assembled from its component parts in a tightly regulated process that requires a number of assembly factors. The 2pac mutant of the unicellular green alga Chlamydomonas reinhardtii was isolated and found to have no detectable PSII activity, whereas other components of the photosynthetic electron transport chain, including photosystem I, were still functional. PSII activity was fully restored by complementation with the RBD1 gene, which encodes a small iron-sulfur protein known as a rubredoxin. Phylogenetic evidence supports the hypothesis that this rubredoxin and its orthologs are unique to oxygenic phototrophs and distinct from rubredoxins in Archaea and bacteria (excluding cyanobacteria). Knockouts of the rubredoxin orthologs in the cyanobacterium Synechocystis sp. PCC 6803 and the plant Arabidopsis thaliana were also found to be specifically affected in PSII accumulation. Taken together, our data suggest that this rubredoxin is necessary for normal PSII activity in a diverse set of organisms that perform oxygenic photosynthesis},
	language = {en},
	number = {37},
	urldate = {2021-06-08},
	journal = {Journal of Biological Chemistry},
	author = {Calderon, Robert H. and García-Cerdán, José G. and Malnoë, Alizée and Cook, Ron and Russell, James J. and Gaw, Cynthia and Dent, Rachel M. and de Vitry, Catherine and Niyogi, Krishna K.},
	month = sep,
	year = {2013},
	pages = {26688--26696},
}

In oxygenic photosynthesis, two photosystems work in tandem to harvest light energy and generate NADPH and ATP. Photosystem II (PSII), the protein-pigment complex that uses light energy to catalyze the splitting of water, is assembled from its component parts in a tightly regulated process that requires a number of assembly factors. The 2pac mutant of the unicellular green alga Chlamydomonas reinhardtii was isolated and found to have no detectable PSII activity, whereas other components of the photosynthetic electron transport chain, including photosystem I, were still functional. PSII activity was fully restored by complementation with the RBD1 gene, which encodes a small iron-sulfur protein known as a rubredoxin. Phylogenetic evidence supports the hypothesis that this rubredoxin and its orthologs are unique to oxygenic phototrophs and distinct from rubredoxins in Archaea and bacteria (excluding cyanobacteria). Knockouts of the rubredoxin orthologs in the cyanobacterium Synechocystis sp. PCC 6803 and the plant Arabidopsis thaliana were also found to be specifically affected in PSII accumulation. Taken together, our data suggest that this rubredoxin is necessary for normal PSII activity in a diverse set of organisms that perform oxygenic photosynthesis

@article{malnoe_photosynthetic_2011,
	title = {Photosynthetic growth despite a broken {Q}-cycle},
	volume = {2},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/ncomms1299},
	doi = {10/fh7dj9},
	abstract = {Central in respiration or photosynthesis, the cytochrome bc1 and b6f complexes are regarded as functionally similar quinol oxidoreductases. They both catalyse a redox loop, the Q-cycle, which couples electron and proton transfer. This loop involves a bifurcated electron transfer step considered as being mechanistically mandatory, making the Q-cycle indispensable for growth. Attempts to falsify this paradigm in the case of cytochrome bc1 have failed. The rapid proteolytic degradation of b6f complexes bearing mutations aimed at hindering the Q-cycle has precluded so far the experimental assessment of this model in the photosynthetic chain. Here we combine mutations in Chlamydomonas that inactivate the redox loop but preserve high accumulation levels of b6f complexes. The oxidoreductase activity of these crippled complexes is sufficient to sustain photosynthetic growth, which demonstrates that the Q-cycle is dispensable for oxygenic photosynthesis.},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Nature Communications},
	author = {Malnoë, Alizée and Wollman, Francis-André and de Vitry, Catherine and Rappaport, Fabrice},
	month = sep,
	year = {2011},
	pages = {301},
}

Central in respiration or photosynthesis, the cytochrome bc1 and b6f complexes are regarded as functionally similar quinol oxidoreductases. They both catalyse a redox loop, the Q-cycle, which couples electron and proton transfer. This loop involves a bifurcated electron transfer step considered as being mechanistically mandatory, making the Q-cycle indispensable for growth. Attempts to falsify this paradigm in the case of cytochrome bc1 have failed. The rapid proteolytic degradation of b6f complexes bearing mutations aimed at hindering the Q-cycle has precluded so far the experimental assessment of this model in the photosynthetic chain. Here we combine mutations in Chlamydomonas that inactivate the redox loop but preserve high accumulation levels of b6f complexes. The oxidoreductase activity of these crippled complexes is sufficient to sustain photosynthetic growth, which demonstrates that the Q-cycle is dispensable for oxygenic photosynthesis.

@article{nguyen_transcriptome_2008,
	title = {Transcriptome for {Photobiological} {Hydrogen} {Production} {Induced} by {Sulfur} {Deprivation} in the {Green} {Alga} \textit{{Chlamydomonas} reinhardtii}},
	volume = {7},
	issn = {1535-9778, 1535-9786},
	url = {https://journals.asm.org/doi/10.1128/EC.00418-07},
	doi = {10/bv32ft},
	abstract = {ABSTRACT
            
              Photobiological hydrogen production using microalgae is being developed into a promising clean fuel stream for the future. In this study, microarray analyses were used to obtain global expression profiles of mRNA abundance in the green alga
              Chlamydomonas reinhardtii
              at different time points before the onset and during the course of sulfur-depleted hydrogen production. These studies were followed by real-time quantitative reverse transcription-PCR and protein analyses. The present work provides new insights into photosynthesis, sulfur acquisition strategies, and carbon metabolism-related gene expression during sulfur-induced hydrogen production. A general trend toward repression of transcripts encoding photosynthetic genes was observed. In contrast to all other
              LHCBM
              genes, the abundance of the
              LHCBM9
              transcript (encoding a major light-harvesting polypeptide) and its protein was strongly elevated throughout the experiment. This suggests a major remodeling of the photosystem II light-harvesting complex as well as an important function of
              LHCBM9
              under sulfur starvation and photobiological hydrogen production. This paper presents the first global transcriptional analysis of
              C. reinhardtii
              before, during, and after photobiological hydrogen production under sulfur deprivation.},
	language = {en},
	number = {11},
	urldate = {2021-06-10},
	journal = {Eukaryotic Cell},
	author = {Nguyen, Anh Vu and Thomas-Hall, Skye R. and Malnoë, Alizée and Timmins, Matthew and Mussgnug, Jan H. and Rupprecht, Jens and Kruse, Olaf and Hankamer, Ben and Schenk, Peer M.},
	month = nov,
	year = {2008},
	pages = {1965--1979},
}

ABSTRACT Photobiological hydrogen production using microalgae is being developed into a promising clean fuel stream for the future. In this study, microarray analyses were used to obtain global expression profiles of mRNA abundance in the green alga Chlamydomonas reinhardtii at different time points before the onset and during the course of sulfur-depleted hydrogen production. These studies were followed by real-time quantitative reverse transcription-PCR and protein analyses. The present work provides new insights into photosynthesis, sulfur acquisition strategies, and carbon metabolism-related gene expression during sulfur-induced hydrogen production. A general trend toward repression of transcripts encoding photosynthetic genes was observed. In contrast to all other LHCBM genes, the abundance of the LHCBM9 transcript (encoding a major light-harvesting polypeptide) and its protein was strongly elevated throughout the experiment. This suggests a major remodeling of the photosystem II light-harvesting complex as well as an important function of LHCBM9 under sulfur starvation and photobiological hydrogen production. This paper presents the first global transcriptional analysis of C. reinhardtii before, during, and after photobiological hydrogen production under sulfur deprivation.