Niyogi Lab Publications


EA Arsenault, Y Yoneda, M Iwai, KK Niyogi, GR Fleming. (2020) The role of mixed vibronic Qy-Qx states in green light absorption of light-harvesting complex II. Nat Commun. 11:6011.

CJ Steen, JM Morris, AH Short, KK Niyogi, GR Fleming. (2020) Complex Roles of PsbS and Xanthophylls in the Regulation of Nonphotochemical Quenching in Arabidopsis thaliana under Fluctuating Light. J Phys Chem B.124:10311-10325. 

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. (2020 ) Chloroplast Sec14-like 1 (CPSFL1) is essential for normal chloroplast development and affects carotenoid accumulation in Chlamydomonas. Proc Natl Acad Sci USA 117:12452-12463.

AP Hertle, JG García-Cerdán, U Armbruster, R Shih, JJ Lee, W Wong, KK Niyogi. (2020) A Sec14 domain protein is required for photoautotrophic growth and chloroplast vesicle formation in Arabidopsis thaliana. Proc Natl Acad Sci USA 117:9101-9111.

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 118:1876-1886

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


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.


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.


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.


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.


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.


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.

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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


YZ Ma, NE Holt, XP Li, KK Niyogi, GR Fleming. (2003) Evidence for direct carotenoid involvement in the regulation of photosynthetic light harvesting. Proc Natl Acad Sci USA 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.


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.


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.


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. 3:455-60.


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.


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.


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.


KK Niyogi, O Björkman, AR Grossman. (1997) The roles of specific xanthophylls in photoprotection. Proc Natl Acad Sci USA 94:14162-14167

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.