Krishna K. Niyogi

Professor
Ph.D.  Biology    Massachusetts Institute of Technology, 1993
B.A.   Biology    The Johns Hopkins University, 1986

441A Koshland Hall
Berkeley, California 94720-3102
niyogi@berkeley.edu
office: 510-643-6602   lab: 510-643-6604   fax:  510-642-4995

Web site         Recent publications     

Photosynthetic organisms are extremely responsive to changes in their environment, especially differences in incident light. My laboratory is studying how light and other environmental parameters influence photosynthesis, which comprises some of the most fundamentally important reactions in biology. In nature, photosynthetic organisms experience large variations in incident sunlight on a daily basis. Especially in unfavorable environments, algae and plants often absorb more light energy than they are capable of using for photosynthesis, and this excessive light can cause photo-oxidative damage (bleaching) and loss of photosynthetic efficiency. Photosynthetic organisms have evolved multiple mechanisms to cope with excessive light, and we are trying to identify and dissect these processes by isolating algal and plant mutants. Characterization of the mutants involves a diverse set of techniques, including genetics, physiology, biochemistry, and molecular biology.

The current work on algae is focused on one particular species, Chlamydomonas reinhardtii, a unicellular green alga with many advantages as a model photosynthetic organism. We are studying the cellular processes involved in coping with reactive oxygen species (ROS) produced in excessive light. In all photosynthetic organisms, xanthophyll pigments have an essential role in protection from oxidative damage. The phenotypes of Chlamydomonas xanthophyll mutants are being exploited to analyze photoprotective processes related to singlet oxygen production in the photosystem II light-harvesting antenna.

A major process involved in controlling photosynthesis in excessive light is the downregulation of photosystem II activity by pH- and xanthophyll-dependent dissipation of excess absorbed light energy as heat, measured as nonphotochemical quenching of chlorophyll fluorescence (NPQ). We are providing insights into the molecular mechanism of NPQ by isolating npq mutants of the model plant, Arabidopsis thaliana. Characterization of a subset of these mutants has contributed to our knowledge of the role of xanthophyll pigments in NPQ. Other npq mutants identify components besides the xanthophylls that are critical for NPQ, and the resources of the Arabidopsis genome project are being used to facilitate the isolation of the genes affected in these mutants.

The innovative use of genetics to dissect complex problems in the biochemistry and ecophysiology of photosynthesis will enable us to assess the relative importance of different processes for photoprotection. Future studies may allow us to manipulate plant productivity and the ability of plants to grow in different, often adverse, environments.

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

Sirikhachornkit A, Shin JW, Baroli I, Niyogi KK (2009). Replacement of α-tocopherol by β-tocopherol enhances resistance to photooxidative stress in a xanthophyll-deficient strain of Chlamydomonas reinhardtii. Eukaryot Cell 8: 1648-1657.

Li Z, Ahn TK, Avenson TJ, Ballottari M, Cruz JA, Kramer DM, Bassi R, Fleming GR, Keasling JD, Niyogi KK (2009). Lutein accumulation in the absence of zeaxanthin restores nonphotochemical quenching in the Arabidopsis thaliana npq1 mutant. Plant Cell 21: 1798-1812.

Kim E-H, Li X-P, Razeghifard R, Anderson JM, Niyogi KK, Pogson BJ, Chow WS (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. Biochim Biophys Acta 1787: 973-984.

Gutman BL, Niyogi KK (2009). Evidence for base excision repair of oxidative DNA damage in chloroplasts of Arabidopsis thaliana. J Biol Chem 284: 17006-17012.

Jung H-S, Niyogi KK (2009). Quantitative genetic analysis of thermal dissipation in Arabidopsis. Plant Physiol 150: 977-986.

Li Z, Wakao S, Fischer BB, Niyogi KK (2009). Sensing and responding to excess light. Annu Rev Plant Biol 60: 239-260.

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

Avenson TJ, Ahn TK, Niyogi KK, Ballottari M, Bassi R, Fleming GR (2009). Lutein can act as a switchable charge-transfer quencher in the CP26 light-harvesting complex. J Biol Chem 284: 2830-2835.

Niyogi KK (2008). Photoprotection and high light responses. In: The Chlamydomonas Sourcebook, Vol 2: Organellar and Metabolic Processes, Stern D, ed (San Diego: Elsevier), pp. 847-870.

Cheng Y-C, Ahn TK, Avenson TJ, Zigmantas D, Niyogi KK, Ballottari M, Bassi R, Fleming GR (2008). Kinetic modeling of charge-transfer quenching in the CP29 minor complex. J Phys Chem B 112: 13418-13423.

Logan BA, Terry SG, Niyogi KK (2008). Arabidopsis genotypes with differing levels of psbS expression differ in photosystem II quantum yield, xanthophyll cycle pool size, and above-ground growth. Int J Plant Sci 169: 597-604.

Ahn TK, Avenson TJ, Ballottari M, Cheng, Y-C, Niyogi KK, Bassi R, Fleming GR (2008). Architecture of a charge-transfer state regulating light harvesting in a plant antenna protein. Science 320: 794-797.

Peers G, Niyogi KK (2008). Pond scum genomics: the genomes of Chlamydomonas and Ostreococcus. Plant Cell 20: 502-507.

Avenson TJ, Ahn TK, Zigmantas D, Niyogi KK, Li Z, Ballottari M, Bassi R, Fleming GR (2008). Zeaxanthin radical cation formation in minor light-harvesting complexes of higher plant antenna. J Biol Chem 283: 3550-3558.

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

Ledford HK, Chin BL, Niyogi KK (2007). Acclimation to singlet oxygen stress in Chlamydomonas reinhardtii. Eukaryot Cell 6: 919–930.

Shao N, Vallon O, Dent R, Niyogi KK, Beck CF (2006). Defects in the cytochrome b6/f complex prevent light-induced expression of nuclear genes involved in chlorophyll biosynthesis. Plant Physiol 141: 1128–1137.

Pichersky E, Niyogi K (2006). Physiology and metabolism: the second coming of plant biochemistry and physiology. Curr Op Plant Biol 9: 217–219.

Jung H-S, Niyogi KK (2006). Molecular analysis of photoprotection of photosynthesis. In: Photoprotection, photoinhibition, gene regulation and environment, Demmig-Adams B, Adams WW III, and Mattoo AK, eds (Dordrecht: Springer), pp. 127–143.

Golan T, Müller-Moulé P, Niyogi KK (2006). Photoprotection mutants of Arabidopsis thaliana acclimate to high light by increasing photosynthesis and specific antioxidants. Plant Cell Environ 29: 879–887.

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

Abdel-Ghany SE, Müller-Moulé P, Niyogi KK, Pilon M, Shikanai T (2005). Two evolutionarily conserved Cu-transporting P-type ATPases regulate Cu delivery to chloroplasts in Arabidopsis. Plant Cell 17: 1233–1251.

Dent RM, Haglund CM, Chin BL, Kobayashi MC, Niyogi KK (2005). Functional genomics of eukaryotic photosynthesis using insertional mutagenesis of Chlamydomonas reinhardtii. Plant Physiol 137: 545–556. PDF 251k

Niyogi KK, Li X-P, Rosenberg V, Jung H-S (2005). Is PsbS the site of nonphotochemical quenching in photosynthesis? J Exp Bot 56: 375–382.

Holt NE, Zigmantas D, Valkunas L, Li X-P, Niyogi KK, Fleming GR (2005). Carotenoid cation formation and the regulation of photosynthetic light harvesting. Science 307: 433–436. PDF 321k

Ledford HK, Dent RM, Niyogi KK (2005). Chlamydomonas genomics: new approaches for a classical model system. In: Plant Functional Genomics, Leister D, ed (Binghamton, NY: Food Products Press), pp. 153–202.

Golan T, Li X-P, Müller-Moulé P, Niyogi KK (2004). Using mutants to understand light stress acclimation in plants. In: Chlorophyll a fluorescence: A signature of photosynthesis, Papageorgiou GC and Govindjee, eds (Dordrecht: Springer), pp. 525–554.

Anwaruzzaman M, Chin BL, Li X-P, Lohr M, Martinez DA, Niyogi KK (2004). Genomic analysis of mutants affecting xanthophyll biosynthesis and regulation of photosynthetic light harvesting in Chlamydomonas reinhardtii. Photosynth Res 82: 265–276.

McCarthy SS, Kobayashi MC, Niyogi KK (2004). White mutants of Chlamydomonas reinhardtii are defective in phytoene synthase. Genetics 168: 1249–1257.

Ledford HK, Baroli I, Shin JW, Fischer BB, Eggen RIL, Niyogi KK (2004). Comparative profiling of lipid-soluble antioxidants and transcripts reveals two phases of photo-oxidative stress in a xanthophyll-deficient mutant of Chlamydomonas reinhardtii. Mol Genet Genomics 272: 470-479.

Holt NE, Fleming GR, Niyogi KK (2004). Toward an understanding of the mechanism of nonphotochemical quenching in green plants. Biochemistry 43: 8281-8289.

Gutman BL, Niyogi KK (2004). Chlamydomonas and Arabidopsis: a dynamic duo. Plant Physiol 135: 607–610.

Vink M, Zer H, Alumot N, Gaathon A, Niyogi K, Herrmann RG, Andersson B, Ohad I (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.

Li X-P, Gilmore AM, Caffarri S, Bassi R, Golan T, Kramer D, Niyogi KK (2004). Regulation of photosynthetic light harvesting involves intrathylakoid lumen pH sensing by the PsbS protein. J Biol Chem 279: 22866–22874. PDF 448k

Müller-Moulé P, Golan T, and Niyogi KK (2004). Ascorbate-deficient mutants of Arabidopsis thaliana grow in high light despite chronic photo-oxidative stress. Plant Physiol 134: 1163–1172.

Baroli I, Gutman BL, Ledford HK, Shin JW, Chin BL, Havaux M, Niyogi KK (2004). Photo-oxidative stress in a xanthophyll-deficient mutant of Chlamydomonas. J Biol Chem 279: 6337–6344.

Müller-Moulé P, Havaux M, Niyogi KK (2003). Zeaxanthin deficiency enhances the high light sensitivity of an ascorbate-deficient mutant of Arabidopsis thaliana. Plant Physiol 133: 748–760.

Shikanai T, Müller-Moulé P, Munekage Y, Niyogi KK, Pilon M (2003). PAA1, a P-type ATPase of Arabidopsis, functions in copper transport in chloroplasts. Plant Cell 15: 1333–1346.

Ma Y-Z, Holt NE, Li X-P, Niyogi KK, Fleming GR (2003). Evidence for direct carotenoid involvement in the regulation of photosynthetic light harvesting. Proc Natl Acad Sci USA 100: 4377–4382.

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

Li X-P, Müller-Moulé P, Gilmore AM, Niyogi KK (2002). PsbS-dependent enhancement of feedback de-excitation protects photosystem II from photoinhibition. Proc Natl Acad Sci USA 99: 15222–15227.

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

Li X-P, Gilmore AM, Niyogi KK (2002). Molecular and global time-resolved analysis of a psbS gene dosage effect on pH- and xanthophyll cycle-dependent nonphotochemical quenching in photosystem II. J Biol Chem 277: 33590–33597.

Elrad D, Niyogi KK, Grossman AR (2002). A major light-harvesting polypeptide of photosystem II functions in thermal dissipation. Plant Cell 14: 1801–1816.

Soupene E, King, N, Feild E, Liu P, Niyogi, KK, Huang C-H, Kustu S (2002). Rhesus expression in a green alga is regulated by CO2. Proc Natl Acad Sci USA 99: 7769–7773.

Müller-Moulé P, Conklin, PL, Niyogi KK (2002). Ascorbate deficiency can limit violaxanthin de-epoxidase activity in vivo. Plant Physiol 128: 970–977.

Dent RM, Han M, Niyogi KK (2001). Functional genomics of plant photosynthesis in the fast lane using Chlamydomonas reinhardtii. Trends Plant Sci 6: 364–371.

Polle JEW, Niyogi KK, Melis A (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 Physiol 42: 482–491.

Niyogi KK, Shih C, Chow WS, Pogson BJ, DellaPenna D, Björkman O (2001). Photoprotection in a zeaxanthin- and lutein-deficient double mutant of Arabidopsis. Photosynth Res 67: 139–145.

Müller P, Li X-P, Niyogi KK (2001). Non-photochemical quenching. A response to excess light energy. Plant Physiol 125: 1558–1566.

Niyogi KK (2000). Safety valves for photosynthesis. Curr Op Plant Biol 3: 455–460.

Baroli I, Niyogi KK (2000). Molecular genetics of xanthophyll-dependent photoprotection in green algae and plants. Phil Trans R Soc Lond B 355: 1385–1393.

Havaux M, Bonfils J-P, Lütz C, Niyogi KK (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 Physiol 124: 273–284.

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

Li X-P, Björkman O, Shih C, Grossman AR, Rosenquist M, Jansson S, Niyogi KK (2000). A pigment-binding protein essential for regulation of photosynthetic light harvesting. Nature 403: 391–395.