Niyogi Lab Publications

2020

JG García-Cerdán, EM Schmid, T Takeuchi, I McRae, KL McDonald, N Yordduangjun, AM Hassan, P Grob, CS Xu, HF Hess, DA Fletcher, E Nogales, KK Niyogi. Chloroplast Sec14-like 1 (CPSFL1) is essential for normal chloroplast development and affects carotenoid accumulation in Chlamydomonas. Proc Natl Acad Sci U S A. 2020 Jun 2;117(22):12452-12463. doi: 10.1073/pnas.1916948117. Epub 2020 May 13.

AP Hertle, JG García-Cerdán, U Armbruster, R Shih, JJ Lee, W Wong, KK Niyogi. A Sec14 domain protein is required for photoautotrophic growth and chloroplast vesicle formation in Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2020 Apr 3. pii: 201916946. doi: 10.1073/pnas.1916946117.
   
B Onoa, S Fukuda, M Iwai, C Bustamante, KK Niyogi. (2020) Atomic force microscopy visualizes mobility of photosynthetic proteins in grana thylakoid membranes. Biophysical Journal Mar 13. pii: S0006-3495(20)30232-0. doi: 10.1016/j.bpj.2020.02.029. [Epub ahead of print] PMID: 32224302

EA Arsenault, Y Yoneda, M Iwai, KK Niyogi. (2020) Vibronic mixing enables ultrafast energy flow in light-harvesting complex II. Nature Communications 11:1460.

O Dautermann, D Lyska, J Andersen-Ranberg, M Becker, J Fröhlich-Nowoisky, H Gartmann, LC Krämer, K Mayr, D Pieper, LM Rij, HM-L Wipf, KK Niyogi, M and Lohr. (2020) An algal enzyme required for biosynthesis of the most abundant marine carotenoids. Science Advances 6:eaaw9183.

CL Amstutz, R Fristedt, A Schultink, SS Merchant, KK Niyogi and A Malnoë. (2020) An atypical short-chain dehydrogenase–reductase functions in the relaxation of photoprotective qH in Arabidopsis. Nature Plants 6:154-166


2019

MS Roth, DJ Westcott, M Iwai, KK Niyogi. (2019) Hexokinase is necessary for glucose-mediated photosynthesis repression and lipid accumulation in a green alga. Communications Biology 2:347.

N Varoquaux, B Cole, C Gao, G Pierroz, CR Baker, D Patel, M Madera, T Jeffers, J Hollingsworth, J Sievert, Y Yoshinaga, JA Owiti, VR Singan, S DeGraaf, L Xu, MJ Blow, MJ Harrison, A Visel, C Jansson, KK Niyogi, R Hutmacher, D Coleman-Derr, RC O’Malley, JW Taylor, J Dahlberg, JP Vogel, PG Lemaux, and E Purdom. (2019) Transcriptomic analysis of field-droughted sorghum from seedling to maturity reveals biotic and metabolic responses. Proc Natl Acad Sci USA 116:27124-27132.

ST Gabilly, CR Baker, S Wakao, T Crisanto, K Guan, K Bi, E Guiet, CR Guadagno, KK Niyogi. (2019) Regulation of photoprotection gene expression in Chlamydomonas by a putative E3 ubiquitin ligase complex and a homolog of CONSTANS. Proc Natl Acad Sci USA 116:17556-17562.

JG García-Cerdán, AL Furst, KL McDonald, D Schünemann, MB Francis, KK Niyogi. (2019) A thylakoid membrane-bound and redox-active rubredoxin (RBD1) functions in de novo assembly and repair of photosystem II. Proc Natl Acad Sci USA 116:16631-16640.

MS Roth, SD Gallaher, DJ Westcott, M Iwai, KB Louie, M Mueller, A Walter, F Foflonker, BP Bowen, NN Ataii, J Song, J-H Chen, CE Blaby-Haas, C Larabell, M Auer, TR Northen, SS Merchant, KK Niyogi. (2019) Regulation of oxygenic photosynthesis during trophic transitions in the green alga Chromochloris zofingiensis. Plant Cell 31:579-601.

S Park, CJ Steen, D Lyska, AL Fischer, B Endelman, M Iwai, KK Niyogi, GR Fleming. (2019) Chlorophyll-carotenoid excitation energy transfer and charge transfer in Nannochloropsis oceanica for the regulation of photosynthesis. Proc Natl Acad Sci USA 116:3385-3390.

2018

M Iwai, P Grob, AT Iavarone, E Nogales, KK Niyogi. (2018) A unique supramolecular organization of photosystem I in the moss Physcomitrella patens. Nature Plants 4:904-909.

S Park, AL Fischer, C Steen, M Iwai, JM Morris, PJ Walla, KK Niyogi, GR Fleming. (2018) Chlorophyll-carotenoid excitation energy transfer in high-light-acclimating thylakoid membranes investigated by snapshot transient absorption spectroscopy. Journal of the American Chemical Society 140:11965-11973.

M Iwai, MS Roth, KK Niyogi. (2018) Subdiffraction-resolution live-cell imaging for visualizing thylakoid membranes. Plant Journal 96:233-243.

TM Wittkopp, S Saroussi, W Yang, X Johnson, RG Kim, ML Heinnickel, JJ Russell, W Phuthong, RM Dent, CD Broeckling, G Peers, M Lohr, F-A Wollman, KK Niyogi, AR Grossman. (2018) GreenCut protein CPLD49 of Chlamydomonas reinhardtii associates with thylakoid membranes and is required for cytochrome b6f complex accumulation. Plant Journal 94:1023-1037.

K Glowacka, J Kromdijk, K Kucera, J Xie, AP Cavanagh, L Leonelli, ADB Leakey, DR Ort, KK Niyogi, SP Long. (2018) PsbS overexpression increases the efficiency of water use in a field-grown crop. Nature Communications 9:868.

A Malnoë, A Schultink, S Shahrasbi, D Rumeau, M Havaux, KK Niyogi. (2018) The plastid lipocalin LCNP is required for sustained photoprotective energy dissipation in Arabidopsis. Plant Cell 30:196-208.

2017

S Park, AL Fischer, Z Li, R Bassi, KK Niyogi, GR Fleming. (2017) Snapshot transient absorption spectroscopy of carotenoid radical cations in high-light-acclimating thylakoid membranes. Journal of Physical Chemistry Letters 2:5548-5554.

L Leonelli, MD Brooks, KK Niyogi. (2017) Engineering the lutein epoxide cycle into Arabidopsis thaliana. Proc Natl Acad Sci USA 114:E7002-E7008

M Leuenberger, JM Morris, AM Chan, L Leonelli, KK Niyogi, GR Fleming. (2017) Dissecting and modeling zeaxanthin- and lutein-dependent nonphotochemical quenching in Arabidopsis thaliana. Proc Natl Acad Sci USA  114:E7009-E7017    

KK Niyogi. (2017)  Editorial overview:Physiology and metabolism:Light responses from photoreceptors to photosynthesis and photoprotection. Current Opinion in Plant Biology. 37:iv-vi.

CS Xu, KJ Hayworth, Z Lu, P Grob, AM Hassan, JG García-Cerdán, KK Niyogi, E Nogales, RJ Weinberg, HF Hess. (2017) Enhanced FIB-SEM systems for large-volume 3D imaging. eLife 6:e25916.

MS Roth, SJ Cokus, SD Gallaher, A Walter, D Lopez, E Erickson, B Endelman, D Westcott, CA Larabell, SS Merchant, M Pellegrini, KK Niyogi. (2017) Chromosome-level genome assembly and transcriptome of the green alga Chromochloris zofingiensis illuminates astaxanthin production.  Proc Natl Acad Sci USA 114:E4296-E4305.

CW Gee, KK Niyogi. (2017) The carbonic anhydrase CAH1 is an essential component of the carbon-concentrating mechanism in Nannochloropsis oceanica. Proc Natl Acad Sci USA 114:4537-4542.

H Kirst, ST Gabilly, KK Niyogi, PG Lemaux, A Melis. (2017) Photosynthetic antenna engineering to improve crop yields. Planta 245:1009-1020.

L Dall'Osto, S Cazzaniga, M Bressan, D Paleček, K Židek, KK Niyogi, GR Fleming, D Zigmantas, R Bassi. (2017) Two mechanisms for dissipation of excess light in monomeric and trimeric light-harvesting complexes. Nature Plants 3:17033.

2016

G Allorent, L Lefebvre-Legendre, R Chappuis, M Kuntz, TB Truong, KK Niyogi, R Ulm, M Goldschmidt-Clermont. (2016) UV-B photoreceptor-mediated protection of the photosynthetic machinery in Chlamydomonas reinhardtii. Proc Natl Acad Sci USA 113:14864-14869.

K Głowacka, J Kromdijk, L Leonelli, KK Niyogi, TE Clemente, SP Long. (2016) An evaluation of new and established methods to determine T-DNA copy number and homozygosity in transgenic plants. Plant, Cell & Environment 39:908-17.

J Kromdijk, K Głowacka, l Leonelli, ST Gabilly. M Iwai, KK Niyogi, SP Long. (2016) Improving photosynthesis and crop productivity by accelerating recovery from photoprotection. Science 18 Nov:Vol. 354, Issue 6314, pp. 857-861.

Z Li, G Peers, RM Dent, Y Bai, SY Yang, W Apel, L Leonelli, KKNiyogi. (2016) Evolution of an atypical de-epoxidase for photoprotection in the green lineage. Nature Plants 12:16140.

L Leonelli, E Erickson, D Lyska, KK Niyogi. (2016) Transient expression in Nicotiana benthamiana for rapid functional analysis of genes involved in non-photochemical quenching and carotenoid biosynthesis. Plant Journal 88:375–386

V Correa-Galvis, P Redekop, K Guan, A Griess, TB Truong, S Wakao, KK KK Niyogi, P Jahns. (2016) Photosystem II Subunit PsbS Is Involved in the Induction of LHCSR Protein-dependent Energy Dissipation in Chlamydomonas reinhardtii. Journal of Biological Chemistry 291:17478-87.

U Armbruster, L Leonelli, V Correa Galvis, D Strand, EH Quinn, MC Jonikas, KK Niyogi. (2016) Regulation and Levels of the Thylakoid K+/H+ Antiporter KEA3 Shape the Dynamic Response of Photosynthesis in Fluctuating Light. Plant and Cell Physiology 57:1557-1567.

M Ballottari, TB Truong, E De Re, E Erickson, GR Stella, GR Fleming, R Bassi, KK Niyogi. (2016) Identification of pH-sensing Sites in the Light Harvesting Complex Stress-related 3 Protein Essential for Triggering Non-photochemical Quenching in Chlamydomonas reinhardtii. Journal of Biological Chemistry 291:7334-46.

P Brzezowski, MN Sharifi, RM Dent, MK Morhard, KK Niyogi, B Grimm. (2016) Mg chelatase in chlorophyll synthesis and retrograde signaling in Chlamydomonas reinhardtii:CHLI2 cannot substitute for CHLI1. Journal of Experimental Botany 67:3925-38.

K Głowacka, J Kromdijk, L Leonelli, KK Niyogi, TE Clemente, SP Long. (2016) An evaluation of new and established methods to determine T-DNA copy number and homozygosity in transgenic plants. Plant, Cell & Environment 39:908-17.

T Tibiletti, MA Hernández-Prieto, HC Matthijs, KK Niyogi, C Funk. (2016) Deletion of the gene family of small chlorophyll-binding proteins (ScpABCDE) offsets C/N homeostasis in Synechocystis PCC 6803. Biochimica et Biophysica Acta 1857:396-407.

2015

DR Ort, SS Merchant, J Alric, A Barkan, RE Blankenship, R Bock, R Croce, MR Hanson, JM Hibberd, SP Long, TA Moore, J Moroney, KK Niyogi, MA Parry, PP Peralta-Yahya, RC Prince, KE Redding, MH Spalding, KJ van Wijk, WF Vermaas, S von Caemmerer, AP Weber, TO Yeates, JS Yuan, XG Zhu. Redesigning photosynthesis to sustainably meet global food and bioenergy demand. Proc Natl Acad Sci USA 112:8529-36.

S Tietz, S Puthiyaveetil, HM Enlow, R Yarbrough, M Wood, DA Semchonok, T Lowry, Z Li, P Jahns, EJ Boekema, S Lenhert, KK Niyogi, H Kirchhoff H. (2015) Functional Implications of Photosystem II Crystal Formation in Photosynthetic Membranes. Journal of Biological Chemistry 290:14091-106.

E Erickson, S Wakao, KK Niyogi. (2015) Light stress and photoprotection in Chlamydomonas reinhardtii. The Plant Journal 82:449-465.

RM Dent, MN Sharifi, A Malnoë, C Haglund, RH Calderon, S Wakao, KK Niyogi. (2015) Large-scale insertional mutagenesis of Chlamydomonas supports phylogenomic functional prediction of photosynthetic genes and analysis of classical acetate-requiring mutants. The Plant Journal 82:337-351.

CY Ngan, CH Wong, C Choi, Y Yoshinaga, K Louie, J Jia, C Chen, B Bowen, H Cheng, L Leonelli, R Kuo, R Baran, JG García-Cerdán, A Pratap, M Wang, J Lim, H Tice, C Daum, J Xu, T Northen, A Visel, J Bristow, KK Niyogi, CL Wei. (2015) Lineage-specific chromatin signatures reveal a regulator of lipid metabolism in microalgae. Nature Plants 1:15107.

2014

EJ Sylak-Glassman, A Malnoë, E De Re, MD Brooks, AL Fischer, KK Niyogi, GR Fleming. (2014) Distinct roles of the photosystem II protein PsbS and zeaxanthin in the regulation of light harvesting in plants revealed by fluorescence lifetime snapshots. Proc Natl Acad Sci USA 111:17498-17503.

B Onoa B, AR Schneider, MD Brooks, P Grob, E Nogales, PL Geissler, KK Niyogi, C Bustamante. (2014) Atomic force microscopy of photosystem II and its unit cell clustering quantitatively delineate the mesoscale variability in Arabidopsis thylakoids. PLoS One 9:e101470.

P Brzezowski, H Schlicke, A Richter, RM Dent, KK Niyogi, B Grimm. (2014) The GUN4 protein plays a regulatory role in tetrapyrrole biosynthesis and chloroplast-to-nucleus signalling in Chlamydomonas reinhardtii. The Plant Journal 79:285-298.

S Wakao, BL Chin, HK Ledford, RM Dent, D Casero, M Pellegrini, SS Merchant, KK Niyogi. (2014) Phosphoprotein SAK1 is a regulator of acclimation to singlet oxygen in Chlamydomonas reinhardtii. eLife 3:e02286.

CH Clausen, MD Brooks, T-D Li, P Grob, G Kemalyan, E Nogales, KK Niyogi, DA Fletcher. (2014) Dynamic mechanical responses of Arabidopsis thylakoid membranes during PSII-specific illumination. Biophysical Journal 106:1864-1870.

X Johnson, J Steinbeck, RM Dent, H Takahashi, P Richaud, S-I Ozawa, L Houille-Vernes, D Petroutsos, F Rappaport, AR Grossman, KK Niyogi, M Hippler, J Alric . (2014) Proton gradient regulation 5-mediated cyclic electron flow under ATP- or redox-limited conditions:a study of ΔATpase pgr5 and ΔrbcL pgr5 mutants in the green alga Chlamydomonas reinhardtii. Plant Physiology 165:438-452.

PM Shih, J Zarzycki, KK Niyogi, CA Kerfeld. (2014) Introduction of a synthetic CO₂-fixing photorespiratory bypass into a cyanobacterium. Journal of Biological Chemistry 289:9493-9500.
 
2013

RH Calderon, JG García-Cerdán, A Malnoë, R Cook, JJ Russell, C Gaw, RM Dent, C de Vitry, KK Niyogi. (2013) A conserved rubredoxin is necessary for photosystem II accumulation in diverse oxygenic photoautotrophs. Journal of Biological Chemistry 288:26688-26696.

K Kobayashi, D SasakI, K Noguchi, D Fujinuma, H Komatsu, M Kobayashi, M Sato, K Toyooka, K Sugimoto, KK Niyogi, H Wada, T Masuda. (2013) Photosynthesis of root chloroplasts developed in Arabidopsis lines overexpressing GOLDEN2-LIKE transcription factors. Plant Cell Physiology 54:1365-1377.
 
Brooks MD, Sylak-Glassman EJ, GR Fleming, KK Niyogi. 2013. A thioredoxin-like/β-propeller protein maintains the efficiency of light harvesting in Arabidopsis. Proc Natl Acad Sci USA 110:E2733-2740.

KK Niyogi, TB Truong. (2013) Evolution of flexible non-photochemical quenching mechanisms that regulate light harvesting in oxygenic photosynthesis. Current Opinion in Plant Biology 16:307-314.

G Allorent, R Tokutsu, T Roach, G Peers, P Cardol, J Girard-Bascou, D Seigneurin-Berny, D Petroutsos, M Kuntz, C Breyton, F Franck, F-A Wollman, KK Niyogi, A Krieger-Liszkay, J Minagawa, G Finazzi. (2013) A dual strategy to cope with high light in Chlamydomonas reinhardtii. The Plant Cell 25:545-557.

D Duanmu, D Casero, RM Dent, S Gallaher, W Yang, NC Rockwell, SS Martin, M Pellegrini, KK Niyogi, SS Merchant, AR Grossman, JC Lagarias. (2013) Retrograde bilin signaling enables Chlamydomonas greening and phototrophic survival. Proc Natl Acad Sci USA 110:3621-3626.

ML Heinnickel, J Alric, T Wittkopp, W Yang, C Catalanotti, RM Dent, KK Niyogi, F-A Wollman, AR Grossman. (2013) Novel thylakoid membrane GreenCut protein CPLD38 impacts accumulation of the cytochrome b6f complex and associated regulatory processes. Journal of Biological Chemistry 288:7024-7036.

R Caliandro, KA Nagel, B Kastenholz, R Bassi, Z Li, KK Niyogi, BJ Pogson, U Schurr, S Matsubara. (2013) Effects of altered α- and β-branch carotenoid biosynthesis on photoprotection and whole-plant acclimation of Arabidopsis to photo-oxidative stress. Plant, Cell & Environment 36:438-453.

2012

S Cazzaniga, Z Li, KK Niyogi, R Bassi, L Dall’Osto. (2012) The Arabidopsis szl1 mutant reveals a critical role of b-carotene in photosystem I photoprotection. Plant Physiology 159:1745-1758.

K Amarnath, J Zaks, SD Park, KK Niyogi, GR Fleming. (2012) Fluorescence lifetime snapshots reveal two rapidly reversible mechanisms of photoprotection in live cells of Chlamydomonas reinhardtii. Proc Natl Acad Sci USA 109:8405-8410.

A Vieler, G Wu, C-H Tsai, B Bullard, AJ Cornish, C Harvey, I-B Reca, C Thornburg, R Achawanantakun, CJ Buehl, MS Campbell, D Cavalier, KL Childs, TJ Clark, R Deshpande, E Erickson, AA Ferguson, W Handee, Q Kong, X Li, B Liu, S Lundback, C Peng, RL  Roston,  Sanjaya, JP Simpson, A TerBush, J Warakanont  S Zäuner, EM Farre, EL Hegg, N Jiang, M-H Kuo, Y Lu, KK Niyogi, J Ohlrogge, KW Osteryoung, Y Shachar-Hill, BB Sears, Y Sun, H Takahashi, M Yandell, S-H Shiu, C Benning C. (2012) Genome, functional gene annotation, and nuclear transformation of the heterokont oleaginous alga Nannochloropsis oceanica CCMP1779. PLoS Genetics 8:e1003064.

PT Tran, MN Sharifi, S Poddar, RM Dent, KK Niyogi. (2012) Intragenic Enhancers and Suppressors of Phytoene Desaturase Mutations in Chlamydomonas reinhardtii. PloS ONE 7:e42196.

J Zaks, K Amarnath, DM Kramer, KK Niyogi, GR Fleming. (2012) A kinetic model of rapidly reversible nonphotochemical quenching. Proc Natl Acad Sci USA 109:15757-62.

Z Li, JD Keasling, KK Niyogi. (2012) Overlapping photoprotective function of vitamin E and carotenoids in Chlamydomonas. Plant Physiology 158:313-23.

BB Fischer, HK Ledford, S Wakao, SG Huang, D Casero, M Pellegrini, SS Merchant, A Koller, RI Eggen, KK Niyogi. (2012) SINGLET OXYGEN RESISTANT 1 links reactive electrophile signaling to singlet oxygen acclimation in Chlamydomonas reinhardtii. Proc Natl Acad Sci USA 109:E1302-11.

2011

O Kilian, CSE Benemann, KK Niyogi, B Vick. (2011) High-efficiency homologous recombination in the oil-producing alga Nannochloropsis sp.. Proc Natl Acad Sci USA 108:21265-9.

Bonente G, Ballottari M, Truong TB, Morosinotto T, Ahn TK, GR Fleming, KK Niyogi, R Bassi. 2011. Analysis of LHCSR3, a protein essential for feedback de-excitation in the green alga Chlamydomonas reinhardtii. PLoS Biology 9:e1000577.

EH Murchie, KK Niyogi. (2011) Manipulation of photoprotection to improve plant photosynthesis. Plant Physiology 155:86-92.

MD Brooks, KK Niyogi. (2011) Use of a pulse-amplitude modulated chlorophyll fluorometer to study the efficiency of photosynthesis in: Arabidopsis plants. Methods in Molecular Biology (Clifton, NJ) 775:299-310.

2010

HS Jung, Y Okegawa, PM Shih, E Kellogg, SE Abdel-Ghany, M Pilon, K Sjölander, T Shikanai, KK Niyogi. (2010) Arabidopsis thaliana PGR7 encodes a conserved chloroplast protein that is necessary for efficient photosynthetic electron transport. PloS ONE 5:e11688.

BB Fischer, RIL Eggen, KK Niyogi. 2010. Characterization of singlet oxygen-accumulating mutants isolated in a screen for altered oxidative stress response in Chlamydomonas reinhardtii. BMC Plant Biology 10:279.

Meinecke L, Alawady A, Schroda M, Willows R, Kobayashi MC, KK Niyogi, B Grimm, CF Beck. (2010) Chlorophyll-deficient mutants of Chlamydomonas reinhardtii that accumulate magnesium protoporphyrin IX. Plant Molecular Biology 72:643-58.

HS Jung, KK Niyogi. (2010) Mutations in Arabidopsis YCF20-like genes affect thermal dissipation of excess absorbed light energy. Planta 231:923-37.

AR Grossman, SJ Karpowicz, M Heinnickel, D Dewez, B Hamel, RM Dent, KK Niyogi, X Johnson, J Alric, F-A Wollman, H Li, SS Merchant. (2010) Phylogenomic analysis of the Chlamydomonas genome unmasks proteins potentially involved in photosynthetic function and regulation. Photosynthesis Research 106:3-17.

AM Terauchi, G Peers, MC Kobayashi, KK Niyogi, SS Merchant. (2010) Trophic status of Chlamydomonas reinhardtii influences the impact of iron deficiency on photosynthesis. Photosynthesis Research 105:39-49.

A Sirikhachornkit, KK Niyogi. (2010) Antioxidants and photo-oxidative stress responses in plants and algae. In: The chloroplast:basics and applications, CA Rebeiz, C Benning, H Bohnert, H Daniell, K Hoober, H Lichtenthaler, A Portis, B Tripathy, eds (Dordrecht: Springer), pp. 379-396.

2009

G Peers, TB Truong, E Ostendorf, A Busch, D Elrad, AR Grossman, M Hippler, KK Niyogi. (2009) An ancient light-harvesting protein is critical for the regulation of algal photosynthesis. Nature 462:518-21.

CM Cohu, SE Abdel-Ghany, KA Gogolin Reynolds, AM Onofrio, JR Bodecker, JA Kimbrel, KK Niyogi, M Pilon. (2009) Copper delivery by the copper chaperone for chloroplast and cytosolic copper/zinc-superoxide dismutases:regulation and unexpected phenotypes in an Arabidopsis mutant. Molecular Plant 2:1336-50.

BL Gutman, KK Niyogi. (2009) Evidence for base excision repair of oxidative DNA damage in chloroplasts of Arabidopsis thaliana. The Journal of Biological Chemistry 284:17006-12.

Z Li, TK Ahn, TJ Avenson, M Ballottari, JA Cruz, DM Kramer, R Bassi, GR Fleming, JD Keasling, KK Niyogi. (2009) Lutein accumulation in the absence of zeaxanthin restores nonphotochemical quenching in the Arabidopsis thaliana npq1 mutant. The Plant Cell 21:1798-812.

TK Ahn, TJ Avenson, G Peers, Z Li, L Dall’Osto, R Bassi, KK Niyogi, GR Fleming. (2009) Investigating energy partitioning during photosynthesis using an expanded quantum yield convention. Chemical Physics 357:151-158.

TJ Avenson, TK Ahn, KK Niyogi, M Ballottari, R Bassi, GR Fleming. (2009) Lutein can act as a switchable charge transfer quencher in the CP26 light-harvesting complex. The Journal of Biological Chemistry 284:2830-5.

EH Kim, XP Li, R Razeghifard, JM Anderson, KK Niyogi, BJ Pogson, WS Chow. (2009) The multiple roles of light-harvesting chlorophyll a/b-protein complexes define structure and optimize function of Arabidopsis chloroplasts: A study using two chlorophyll b-less mutants. Biochimica et Biophysica Acta 1787:973-84.

HS Jung, KK Niyogi. (2009) Quantitative genetic analysis of thermal dissipation in Arabidopsis. Plant Physiology 150:977-86.

A Sirikhachornkit, JW Shin, I Baroli, KK Niyogi. (2009) Replacement of alpha-tocopherol by beta-tocopherol enhances resistance to photooxidative stress in a xanthophyll-deficient strain of Chlamydomonas reinhardtii. Eukaryotic Cell 8:1648-57.

Z Li, S Wakao, BB Fischer, KK Niyogi. (2009) Sensing and responding to excess light. Annual Review of Plant Biology 60:239-60.

2008

TK Ahn, Avenson TJ, Ballottari M, YC Cheng, KK Niyogi, R Bassi, GR Fleming. (2008) Architecture of a charge-transfer state regulating light harvesting in a plant antenna protein. Science 320:794-7.

YC Cheng, TK Ahn, TJ Avenson, D Zigmantas, KK Niyogi, M Ballottari, R Bassi, GR Fleming. (2008) Kinetic modeling of charge-transfer quenching in the CP29 minor complex. The Journal of Physical Chemistry B 112:13418-23.

BA Logan, SG Terry, KK Niyogi. (2008) Arabidopsis genotypes with differing levels of psbS expression differ in photosystem II quantum yield, xanthophyll cycle pool size, and above-ground growth. International Journal of Plant Sciences169:597-604.

G Peers, KK Niyogi. (2008) Pond scum genomics: The genomes of Chlamydomonas and Ostreococcus. The Plant Cell 20:502-7.

TJ Avenson, TK Ahn, D Zigmantas, KK Niyogi, Z Li, M Ballottari, R Bassi, GR Fleming. (2008) Zeaxanthin radical cation formation in minor light-harvesting complexes of higher plant antenna. The Journal of Biological Chemistry 283:3550-8.

2007

SS Merchant, SE Prochnik, O Vallon, EH Harris, SJ Karpowicz, GB Witman, A Terry, A Salamov, LK Fritz-Laylin, L Maréchal-Drouard, WF Marshall, LH Qu, DR Nelson, AA Sanderfoot, MH Spalding, VV Kapitonov, Q Ren, P Ferris, E Lindquist, H Shapiro, SM Lucas, J Grimwood, J Schmutz, P Cardol, H Cerutti, G Chanfreau, CL Chen, V Cognat, MT Croft, RM Dent, S Dutcher, E Fernández, H Fukuzawa, D González-Ballester, D González-Halphen, A Hallmann, M Hanikenne, M Hippler, W Inwood, K Jabbari, M Kalanon, R Kuras, PA Lefebvre, SD Lemaire, AV Lobanov, M Lohr, A Manuell, I Meier, L Mets, M Mittag, T Mittelmeier, JV Moroney, J Moseley, C Napoli, AM Nedelcu, KK Niyogi, SV Novoselov, IT Paulsen, IT Pazour IT, IT Purton IT, JP Ral, DM Riaño-Pachón, W Riekhof, L Rymarquis, M Schroda, D Stern, J Umen, R Willows, N Wilson, SL Zimmer, J Allmer, J Balk, K Bisova, CJ Chen, M Elias, K Gendler, C Hauser, MR Lamb, H Ledford, JC Long, Minagawa J, Page MD, Pan J, Pootakham W, Roje S, Rose A, Stahlberg E, Terauchi AM, P Yang, S Ball, C Bowler, CL Dieckmann, VN Gladyshev, P Green, R Jorgensen, S Mayfield, B Mueller-Roeber, S Rajamani, RT Sayre, P Brokstein, I Dubchak, D Goodstein, L Hornick, YW Huang, J Jhaveri, Y Luo, D Martínez, WC Ngau, B Otillar, A Poliakov, A Porter, Porter L Porter, G Werner, K Zhou, IV Grigoriev, DS Rokhsar, Grossman AR. (2007)  The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 318: 245-251.

HK Ledford, Chin BL, KK Niyogi. (2007) Acclimation to singlet oxygen stress in Chlamydomonas reinhardtii. Eukaryotic Cell 6:919-30.

2006

N Shao, O Vallon, RM Dent, KK Niyogi, CF Beck. (2006) Defects in the cytochrome b6/f complex prevent light-induced expression of nuclear genes involved in chlorophyll biosynthesis. Plant Physiology 141:1128-37.

E Pichersky, KK Niyogi. (2006) Physiology and metabolism: the second coming of plant biochemistry and physiology. Current Opinion in Plant Biology 9:217–219.

T Golan, P Müller-Moulé, KK Niyogi. (2006) Photoprotection mutants of Arabidopsis thaliana acclimate to high light by increasing photosynthesis and specific antioxidants. Plant, Cell & Environment 29:879-87.

2005

HK Ledford, KK Niyogi. (2005) Singlet oxygen and photo-oxidative stress management in plants and algae. Plant Cell & Environment 28:1037–1045.

NE Holt, D Zigmantas, L Valkunas, XP Li, KK Niyogi, GR Fleming. (2005) Carotenoid cation formation and the regulation of photosynthetic light harvesting. Science 307:433-6.

RM Dent, CM Haglund, BL Chin, Kobayashi MC, KK Niyogi. (2005) Functional genomics of eukaryotic photosynthesis using insertional mutagenesis of Chlamydomonas reinhardtii. Plant Physiology 137:545-56.

KK Niyogi, XP Li, V Rosenberg, HS Jung. (2005) Is PsbS the site of non-photochemical quenching in photosynthesis? Journal of Experimental Botany 56:375-82.

SE Abdel-Ghany, P Müller-Moulé, KK Niyogi, M Pilon, T Shikanai. (2005) Two P-type ATPases are required for copper delivery in Arabidopsis thaliana chloroplasts. The Plant Cell 17:1233-51.

2004

P Müller-Moulé, T Golan, KK Niyogi. (2004) Ascorbate-deficient mutants of Arabidopsis grow in high light despite chronic photooxidative stress. Plant Physiology 134:1163-72.

BL Gutman, KK Niyogi. (2004) Chlamydomonas and Arabidopsis. A dynamic duo. Plant Physiology 135:607-10.

HK Ledford, I Baroli, JW Shin, BB Fischer, RIL Eggen, KK Niyogi. (2004) Comparative profiling of lipid-soluble antioxidants and transcripts reveals two phases of photo-oxidative stress in a xanthophyll-deficient mutant of Chlamydomonas reinhardtii. Molecular Genetics and Genomics 272:470-9.

M Anwaruzzaman, BL Chin, XP Li, M Lohr, DA Martinez, KK Niyogi. (2004) Genomic analysis of mutants affecting xanthophyll biosynthesis and regulation of photosynthetic light harvesting in Chlamydomonas reinhardtii. Photosynthesis Research 82:265-76.

I Baroli, BL Gutman, HK Ledford, JW Shin, BL Chin, M Havaux, KK Niyogi. (2004) Photo-oxidative stress in a xanthophyll-deficient mutant of Chlamydomonas. The Journal of Biological Chemistry 279:6337-44.

XP Li, AM Gilmore, S Caffarri, R Bassi, T Golan, D Kramer, KK Niyogi. (2004) Regulation of photosynthetic light harvesting involves intrathylakoid lumen pH sensing by the PsbS protein. The Journal of Biological Chemistry 279:22866-74.

NE Holt, GR Fleming, KK Niyogi. (2004) Toward an understanding of the mechanism of nonphotochemical quenching in green plants. Biochemistry 43:8281-9.

SS McCarthy, MC Kobayashi, KK Niyogi. (2004) White mutants of Chlamydomonas reinhardtii are defective in phytoene synthase. Genetics 168:1249-57.

M Vink, H Zer, N Alumot, A Gaathon, KK Niyogi, RG Herrmann, B Andersson, I Ohad. (2004) Light-modulated exposure of the light-harvesting complex II (LHCII) to protein kinase(s) and state transition in Chlamydomonas reinhardtii xanthophyll mutants.  Biochemistry 43:7824–7833.

2003

YZ Ma, NE Holt, XP Li, KK Niyogi, GR Fleming. (2003)  Evidence for direct carotenoid involvement in the regulation of photosynthetic light harvesting. Proceedings of the National Academy of Sciences of the United States of America 100:4377-82.

T Shikanai, P Müller-Moulé, Y Munekage, KK Niyogi, M Pilon. (2003) PAA1, a P-type ATPase of Arabidopsis, functions in copper transport in chloroplasts. The Plant Cell 15:1333-46.

I Baroli, AD Do, T Yamane, KK Niyogi.  (2003) Zeaxanthin accumulation in the absence of a functional xanthophyll cycle protects Chlamydomonas reinhardtii from photooxidative stress. The Plant Cell 15:992-1008.

P Müller-Moulé, M Havaux, KK Niyogi. (2003) Zeaxanthin deficiency enhances the high light sensitivity of an ascorbate-deficient mutant of Arabidopsis. Plant physiology 133:748-60.

2002

P Müller-Moulé, PL Conklin, KK Niyogi. (2002) Ascorbate deficiency can limit violaxanthin de-epoxidase activity in vivo. Plant Physiology 128:970-7.

D Elrad, KK Niyogi, AR Grossman. (2002) A major light-harvesting polypeptide of photosystem II functions in thermal dissipation. The Plant Cell 14:1801-16.

XP Li, A Phippard, J Pasari, KK Niyogi. (2002) Structure-function analysis of Photosystem II subunit S (PsbS) in vivo. Functional Plant Biology 29:1131–1139.

XP Li, AM Gilmore, KK Niyogi. (2002) Molecular and global time-resolved analysis of a psbS gene dosage effect on pH- and xanthophyll cycle-dependent nonphotochemical quenching in photosystem II. The Journal of Biological Chemistry 277:33590-7.

XP Li, P Muller-Moule, AM Gilmore, KK Niyogi.  (2002) PsbS-dependent enhancement of feedback de-excitation protects photosystem II from photoinhibition. Proc Natl Acad Sci USA  99:15222-7.

E Soupene, N King, E Feild, P Liu, KK Niyogi, CH Huang, S Kustu. (2002) Rhesus expression in a green alga is regulated by CO2. Proc Natl Acad Sci USA  99:7769-73.

2001

RM Dent, MC Kobayashi, KK Niyogi. (2001) Functional genomics of photosynthesis using Chlamydomonas reinhardtii. In: PS2001 Proceedings:12th International Congress on Photosynthesis (Collingwood, Australia: CSIRO Publishing), S41-006, pp. 1–6.

JE Polle, KK Niyogi, A Melis. (2001) Absence of lutein, violaxanthin and neoxanthin affects the functional chlorophyll antenna size of photosystem-II but not that of photosystem-I in the green alga Chlamydomonas reinhardtii. Plant & cell physiology. 42(5):482-91.

RM Dent, M Han, KK Niyogi. (2001) Functional genomics of plant photosynthesis in the fast lane using Chlamydomonas reinhardtii. Trends in plant science. 6:364-71.

P Müller-Moulé, KK Niyogi. (2001) Vitamin C deficiency enhances the light sensitivity of a xanthophyll cycle mutant of Arabidopsis thaliana. In: PS2001 Proceedings:12th International Congress on Photosynthesis (Collingwood, Australia: CSIRO Publishing), S3-021, pp. 1–4.

P Müller, XP Li, KK Niyogi. (2001) Non-photochemical quenching. A response to excess light energy. Plant physiology 125:1558-66.

KK Niyogi, C Shih, WS Chow, BJ Pogson, D Dellapenna, O Björkman. (2001) Photoprotection in a zeaxanthin- and lutein-deficient double mutant of Arabidopsis. Photosynthesis research. 67:139-45.

AE Yakushevska, AV Ruban, PE Jensen, H van Roon, KK Niyogi, P Horton, JP Dekker, EJ Boekema. (2001) Supermolecular organization of photosystem II and its associated light-harvesting antenna in the wild-type and npq4 mutant of Arabidopsis thaliana. In: PS2001 Proceedings:12th International Congress on Photosynthesis (Collingwood, Australia: CSIRO Publishing), S5-006, pp. 1–4.

I Baroli, AD Do, KK Niyogi. (2001) Suppression of the light sensitivity of a zeaxanthin- and lutein-deficient mutant of Chlamydomonas reinhardtii: Zeaxanthin is sufficient for protection from high light stress. In: PS2001 Proceedings:12th International Congress on Photosynthesis (Collingwood, Australia: CSIRO Publishing), S2-028, pp. 1–5.

2000

I Baroli, KK Niyogi. (2000) Molecular genetics of xanthophyll-dependent photoprotection in green algae and plants. Philosophical transactions of the Royal Society of London. Series B, Biological sciences. 355(1402):1385-94.

M Havaux, JP Bonfils, C Lütz, KK Niyogi. (2000) Photodamage of the photosynthetic apparatus and its dependence on the leaf developmental stage in the npq1 Arabidopsis mutant deficient in the xanthophyll cycle enzyme violaxanthin de-epoxidase. Plant physiology. 124:273-84.

R Malkin, KK Niyogi. (2000) Photosynthesis.  In: Biochemistry and Molecular Biology of Plants, B Buchanan, W Gruissem, R Jones, eds (Rockville, MD: American Society of Plant Physiologists) pp. 568–628.

XP Li, O Björkman, C Shih, AR Grossman, M Rosenquist, S Jansson, KK Niyogi. (2000) A pigment-binding protein essential for regulation of photosynthetic light harvesting. Nature 403:391-5.

KK Niyogi. (2000) Safety valves for photosynthesis. Current opinion in plant biology. 3(6):455-60.

1999

KK Niyogi. (1999) PHOTOPROTECTION REVISITED: Genetic and Molecular Approaches. Annual review of plant physiology and plant molecular biology 50:333-359.

KK Niyogi, C Casper-Lindley (1999) Book review: The molecular biology of chloroplasts and mitochondria in Chlamydomonas.  Photosynthesis Research 61: 97–98.

M Havaux, KK Niyogi. (1999) The violaxanthin cycle protects plants from photooxidative damage by more than one mechanism. Proc Natl Acad Sci USA  96(15):8762-7.

1998

BJ Pogson, KK Niyogi, O Björkman, D Dellapenna. (1998) Altered xanthophyll compositions adversely affect chlorophyll accumulation and nonphotochemical quenching in Arabidopsis mutants. Proc Natl Acad Sci USA  95:13324-9.

KK Niyogi, AR Grossman, O Björkman. (1998) Arabidopsis mutants define a central role for the xanthophyll cycle in the regulation of photosynthetic energy conversion. The Plant Cell 10:1121-34.

1997

KK Niyogi, O Björkman, AR Grossman. (1997)  Chlamydomonas Xanthophyll Cycle Mutants Identified by Video Imaging of Chlorophyll Fluorescence Quenching. The Plant Cell 9:1369-1380.

L Zhang, KK Niyogi, I Baroli, AR Grossman, A Melis. (1997) Mutagenesis for the elucidation of a photosystem II repair process in the green alga Chlamydomonas reinhardtii.  Photosynthesis Research 53: 173–184.