@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},
	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},
}

@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},
	language = {en},
	urldate = {2021-06-07},
	journal = {Environmental and Experimental Botany},
	author = {Malnoë, Alizée},
	month = oct,
	year = {2018},
	pages = {123--133},
}

@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},
	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},
}

@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},
	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},
}

@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},
	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},
}

@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},
	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},
}

@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},
	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},
}

@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.